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39057526_p6
|
39057526
|
sec[1]/sec[2]/p[0]
|
2.3. Ethics Statement
| 1.381836 |
biomedical
|
Other
|
[
0.96240234375,
0.004482269287109375,
0.03326416015625
] |
[
0.37548828125,
0.6201171875,
0.002056121826171875,
0.002330780029296875
] |
This study was approved by the Institutional Review Board (IRB) of Chang Gung Medical Foundation . The sample size of the study was not determined based on any criteria. We included patients based on IRB-approved enrollment time. Data were collected retrospectively and anonymized before the analysis. The IRB waived the requirement for informed consent from patients.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
39057526_p7
|
39057526
|
sec[1]/sec[3]/p[0]
|
2.4. Statistical Analysis
| 3.925781 |
biomedical
|
Study
|
[
0.99951171875,
0.0002636909484863281,
0.0002532005310058594
] |
[
0.9990234375,
0.0005950927734375,
0.00021898746490478516,
0.00006461143493652344
] |
The Kolmogorov–Smirnov test showed that the data were not normally distributed. Therefore, the chi-square test and Mann–Whitney U test were used to compare categorical and continuous variables, respectively. We performed univariate and multivariate analyses via logistic regression. We employed forward stepwise selection followed by multiple logistic regression; all variables included in the univariate analysis were entered into the final multivariable analysis. Data were analyzed using MedCalc software (version 18.6; MedCalc, Ostend, Belgium). p < 0.05 was considered to indicate statistical significance.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
39057526_p8
|
39057526
|
sec[2]/p[0]
|
3. Results
| 2.910156 |
biomedical
|
Study
|
[
0.97265625,
0.026519775390625,
0.0006723403930664062
] |
[
0.98388671875,
0.0101776123046875,
0.0006551742553710938,
0.00531768798828125
] |
Table 1 presents the clinical characteristics of the 383 patients with DNIs (254 [66.31%] males and 129 [33.69%] females; mean age: 52.01 ± 18.92 years). The mean chief complaint duration was 5.06 ± 4.34 days.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999999 |
39057526_p9
|
39057526
|
sec[2]/p[1]
|
3. Results
| 3.521484 |
biomedical
|
Study
|
[
0.994140625,
0.0057220458984375,
0.0003380775451660156
] |
[
0.99462890625,
0.004108428955078125,
0.0002589225769042969,
0.0009899139404296875
] |
The mean WBC count was 15,360.65 ± 6041.59 µL and the mean CRP level was 134.67 ± 105.78 mg/L. There were 111 (28.98%) patients with involvement of multiple deep neck spaces (≥3).
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
39057526_p10
|
39057526
|
sec[2]/p[2]
|
3. Results
| 3.712891 |
biomedical
|
Study
|
[
0.99365234375,
0.00620269775390625,
0.00036025047302246094
] |
[
0.994140625,
0.00469207763671875,
0.00039124488830566406,
0.0009918212890625
] |
The parapharyngeal, submandibular, retropharyngeal, parotid, masticator, anterior cervical, visceral, perivertebral, carotid, and posterior cervical spaces were involved in 230 (60.05%), 161 (42.03%), 109 (28.45%), 84 (21.93%), 74 (19.32%), 31 (8.09%), 22 (5.74%), 17 (4.43%), 12 (3.13%), and 8 (2.08%) patients, respectively.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
39057526_p11
|
39057526
|
sec[2]/p[3]
|
3. Results
| 4.121094 |
biomedical
|
Study
|
[
0.99609375,
0.0037174224853515625,
0.0002551078796386719
] |
[
0.99853515625,
0.0004901885986328125,
0.0005888938903808594,
0.0002903938293457031
] |
Table 2 compares differences in the clinical characteristics of patients with and without DM. Among the individuals studied, there were 147 patients with DM and 236 patients without DM. In terms of age, there was a notable disparity between the two groups ( p < 0.001); those with DM were considerably older, with a mean age of 56.28 ± 16.65 compared to 49.36 ± 19.77 for those without DM. When it comes to WBC and CRP, both levels were significantly higher in patients with DM ( p = 0.029 and p < 0.001). The mean duration of DM was 3.93 ± 4.27 years, and mean HbA1c was 6.74 ± 0.51%. Regarding anti-diabetic drugs, 35 patients (23.81%) received insulin control, 85 patients (57.83%) used one anti-diabetic drug, and 27 patients (18.36%) used more than two anti-diabetic drugs. The proportion of more than three deep neck spaces involved in patients with DM is significantly higher than those without DM (38.09% vs. 23.31%, p = 0.002).
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999998 |
39057526_p12
|
39057526
|
sec[2]/p[4]
|
3. Results
| 4.085938 |
biomedical
|
Study
|
[
0.970703125,
0.028839111328125,
0.0006499290466308594
] |
[
0.99609375,
0.0016870498657226562,
0.0011548995971679688,
0.0010576248168945312
] |
Table 3 illustrates the comparison of management strategies and morbidity outcomes between patients with and without DM. The mean length of hospital stay was 9.97 ± 8.38 days. The analysis indicated that the length of hospital stay in patients with DM was longer than those without DM ( p < 0.001). Tracheostomy was performed in 47 (12.27%) patients, and 172 (44.91%) patients underwent open I&D for DNIs. Retinopathy, nephropathy, and neuropathy were noted in 17 (11.56%), 11 (7.48%), and 31 (21.08%) patients. Mediastinitis, pneumonia, necrotizing fasciitis, and septic shock were present in 25 (6.52%), 23 (6.01%), 19 (4.96%), and 17 (4.43%) patients, respectively. Nevertheless, there were no marked differences in the length of hospital days, number of tracheostomies, surgical I&D, morbidities, and mortality between patients with and without DM.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
39057526_p13
|
39057526
|
sec[2]/p[5]
|
3. Results
| 4.058594 |
biomedical
|
Study
|
[
0.9990234375,
0.000659942626953125,
0.00020444393157958984
] |
[
0.99951171875,
0.0002715587615966797,
0.00028228759765625,
0.00008118152618408203
] |
Table 4 shows the comparison of pathogens between patients with and without DM. The prevalence of Klebsiella pneumoniae between the two groups was significantly different ( p = 0.002), and was higher in those with DM. Klebsiella pneumoniae (21.08%) was the most common pathogen in patients with DM, followed by Streptococcus constellatus (20.41%), Parvimonas micra (10.88%), and Streptococcus anginosus (10.88%). Meanwhile, Parvimonas micra (16.94%) , Prevotella buccae (15.67%), and Streptococcus constellatus (14.41%) were the top three most prevalent pathogens in patients without DM.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
39057526_p14
|
39057526
|
sec[2]/p[6]
|
3. Results
| 4.117188 |
biomedical
|
Study
|
[
0.99853515625,
0.001438140869140625,
0.00025272369384765625
] |
[
0.9990234375,
0.0004162788391113281,
0.00038051605224609375,
0.0001399517059326172
] |
Table 5 shows univariate and multivariate analyses of 147 DM patients for prolonged hospitalization. For univariate analysis, the higher WBC level (odds ratio (OR) = 1.0001, 95% confidence interval (CI): 1.0000–1.0002, p = 0.001), the higher CRP , the involvement of at least three spaces , and mediastinitis were significant risk factors for prolonged hospitalization in DM patients. All factors were subjected to forward stepwise selection, which was followed by multivariate logistic regression. A higher CRP level was a significant independent risk factor for prolonged hospitalization.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999998 |
39057526_p15
|
39057526
|
sec[2]/p[7]
|
3. Results
| 3.363281 |
biomedical
|
Study
|
[
0.99462890625,
0.004642486572265625,
0.000759124755859375
] |
[
0.998046875,
0.0012035369873046875,
0.0003495216369628906,
0.0002796649932861328
] |
Table 6 displays the comparison between DNI patients with poorly controlled (HbA1c ≥ 6.5) and well-controlled (HbA1c < 6.5) DM. The analysis indicated that the lengths of hospital stays in patients with poorly controlled DM were longer than those without DM ( p = 0.027).
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999998 |
39057526_p16
|
39057526
|
sec[3]/p[0]
|
4. Discussion
| 2.244141 |
biomedical
|
Other
|
[
0.9853515625,
0.0125885009765625,
0.0021800994873046875
] |
[
0.01053619384765625,
0.9736328125,
0.01107025146484375,
0.004779815673828125
] |
Although DNIs are an emergent condition because of their severe sequelae, the mortality rate has significantly declined because of improved diagnostic techniques, greater availability of antibiotics, and the development of advanced surgical interventions . Nevertheless, DNIs are still associated with severe complications and even death . Thus, the treatment of DNIs remains challenging.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
39057526_p17
|
39057526
|
sec[3]/p[1]
|
4. Discussion
| 4.226563 |
biomedical
|
Study
|
[
0.99951171875,
0.00028896331787109375,
0.00022995471954345703
] |
[
0.9619140625,
0.0007939338684082031,
0.03729248046875,
0.00021159648895263672
] |
DM has a significant impact on the course of infections. In Taiwan, disease control using appropriate medications is achieved in 60% of DM patients; the remaining patients have uncontrolled disease . DM represents a group of physiological dysfunctions characterized by hyperglycemia due to insufficient insulin production, glucagon hypersecretion (type 1 DM), or directly from insulin resistance (type 2 DM) . Type 1 DM is a chronic autoimmune disease that affects about 1% of the population in developed countries . This immune response is induced and promoted by the interaction of environmental as well as genetic factors . In contrast, in type 2 diabetes, insulin resistance appears to be the primary cause of hyperglycemia (affecting around 8.5% of the adult population) . Patients with systemic diseases such as DM may experience the opportunistic advancement of seemingly minor infections due to compromised immune systems and vascular function . Huang et al. found that the prevalence of DM was higher in DNI patients than in the general population of Taiwan. DM patients have a higher risk of infection and impaired cutaneous wound and soft tissue healing . Thus, DNI patients with DM have more severe and extensive inflammation .
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999998 |
39057526_p18
|
39057526
|
sec[3]/p[2]
|
4. Discussion
| 3.939453 |
biomedical
|
Study
|
[
0.99853515625,
0.0011968612670898438,
0.00021886825561523438
] |
[
0.9990234375,
0.0005931854248046875,
0.000316619873046875,
0.0001704692840576172
] |
In the present study, DNI patients with DM were older and had longer hospital stays, a higher WBC count and CRP level, and a greater number of involved deep neck spaces compared to DNI patients without DM. Patients with DNI and DM have more serious infections, a worse prognosis, and a higher rate of Klebsiella pneumoniae infection compared to patients with DNI alone.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
39057526_p19
|
39057526
|
sec[3]/p[3]
|
4. Discussion
| 4.078125 |
biomedical
|
Study
|
[
0.9990234375,
0.0008778572082519531,
0.00018286705017089844
] |
[
0.99853515625,
0.0003840923309326172,
0.0011281967163085938,
0.00012683868408203125
] |
In our research, patients with DM were older and had a longer hospital stay than patients without DM. Older patients with systemic diseases have impaired defense against pathogenic infections and a worse recovery rate, leading to prolonged hospital stays . DM is an expected risk depending on the age of the patients. It is a risk factor that must be controlled in every surgery. In addition, DM patients also had a higher WBC counts and CRP levels, as well as greater numbers of involved deep neck spaces compared to patients without DM, suggesting that the DM patients had more severe inflammation and worse outcomes . Sideris et al. found that CRP level correlated with blood glucose level. Furthermore, the involvement of multiple deep neck spaces was a risk factor for the need for tracheostomy . Cheng et al. also found that DM patients were at an increased risk of necrotizing fasciitis. Based on the findings that DM patients have more severe DNIs and poor outcomes, blood glucose levels should be monitored and appropriately controlled.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
39057526_p20
|
39057526
|
sec[3]/p[4]
|
4. Discussion
| 3.310547 |
biomedical
|
Other
|
[
0.87939453125,
0.11810302734375,
0.00262451171875
] |
[
0.00445556640625,
0.9853515625,
0.003276824951171875,
0.0070343017578125
] |
Timely open surgery is essential for the treatment of DNIs, and repeated surgical I&D is necessary in some patients . Therapeutic needle aspiration has also been performed in select cases . Although pus cultures obtained via needle aspiration or surgical drainage can aid the selection of appropriate antibiotics, empirical antibiotics should be administered before the culture results become available .
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
39057526_p21
|
39057526
|
sec[3]/p[5]
|
4. Discussion
| 2.53125 |
biomedical
|
Other
|
[
0.998046875,
0.0010890960693359375,
0.0006885528564453125
] |
[
0.1436767578125,
0.833984375,
0.01885986328125,
0.003509521484375
] |
A DNI is typically caused by polymicrobial aerobic and anaerobic organisms . Studies from different countries and areas have reported different pathogenic causes of DNIs . Furthermore, the causative organisms of DNIs may change over time and might be influenced by the choice of antibiotics .
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
39057526_p22
|
39057526
|
sec[3]/p[6]
|
4. Discussion
| 4.125 |
biomedical
|
Study
|
[
0.99951171875,
0.00039124488830566406,
0.0001373291015625
] |
[
0.99853515625,
0.0003490447998046875,
0.0007739067077636719,
0.00009959936141967773
] |
We found that DM patients had a higher rate of Klebsiella pneumoniae infection than patients without DM, in line with previous studies . One study found that Klebsiella pneumoniae is responsible for more than half of all DNI cases among DM patients . Klebsiella pneumoniae is a Gram-negative aerobe . The higher rate of identification of Klebsiella pneumoniae in DNI patients with DM may be because of oropharyngeal colonization by Gram-negative bacilli and a defective host defense, particularly phagocytosis . Although odontogenic infection is the most common etiology of DNIs , Huang et al. found that DM patients had a high culture rate of Klebsiella pneumoniae , irrespective of the odontogenic or nonodontogenic origin of their DNI. Klebsiella pneumoniae is susceptible to cefazolin, gentamicin, and trimethoprim/sulfamethoxazole . However, clindamycin should not be administered alone because of its weak effect against Klebsiella pneumoniae .
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999994 |
39057526_p23
|
39057526
|
sec[3]/p[7]
|
4. Discussion
| 4.007813 |
biomedical
|
Other
|
[
0.953125,
0.045257568359375,
0.0015926361083984375
] |
[
0.0157318115234375,
0.912109375,
0.0638427734375,
0.0084381103515625
] |
Uncontrolled hyperglycemia correlates with a fatal outcome in DM patients with infectious diseases . Appropriate blood glucose control reduces the microangiopathic and macroangiopathic complications of DM . To achieve a favorable prognosis, the blood glucose level should be maintained below 200 mg/dL . For optimal empiric coverage, it is recommended to use either penicillin in combination with a β -lactamase inhibitor or a β -lactamase–resistant antibiotic combined with a drug highly effective against most anaerobes . Moreover, the addition of gentamicin is for effective Gram-negative coverage against Klebsiella pneumoniae , especially in DM patients, when it is resistant to clindamycin .
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
39057526_p24
|
39057526
|
sec[4]/p[0]
|
5. Study Limitations
| 2.230469 |
biomedical
|
Study
|
[
0.99658203125,
0.001861572265625,
0.00138092041015625
] |
[
0.990234375,
0.00852203369140625,
0.0006604194641113281,
0.0005693435668945312
] |
This was a retrospective study performed at a single tertiary hospital. The treatments and management for patients with DNIs may have been relatively similar. When performing research in the future, patients could be enrolled from multiple hospitals to reduce such biases. Additionally, our study included only 383 cases. An increased number of samples can provide more comprehensive results.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
39057526_p25
|
39057526
|
sec[4]/p[1]
|
5. Study Limitations
| 2.248047 |
biomedical
|
Other
|
[
0.51513671875,
0.4755859375,
0.00904083251953125
] |
[
0.003574371337890625,
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0.0156402587890625
] |
Ideally, patients with infections should be switched from oral hypoglycemic agents to insulin. However, some patients still want to maintain their original oral hypoglycemic agents for treatment during hospitalization. As long as the patient’s condition did not worsen, we kept the patient’s original oral hypoglycemic agents.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
39057526_p26
|
39057526
|
sec[4]/p[2]
|
5. Study Limitations
| 2.373047 |
biomedical
|
Study
|
[
0.9970703125,
0.0010156631469726562,
0.0021305084228515625
] |
[
0.40478515625,
0.3583984375,
0.2327880859375,
0.004100799560546875
] |
Diabetes complications, such as diabetic retinopathy and peripheral neuropathy, can lead to balance impairment . However, this retrospective article mainly discusses the impact of DM on DNI patients with potential risk of mortality and does not document whether the patients suffered from diabetic balance or vertigo. The effect of DM on balance is an important topic worthy of future research.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
39057526_p27
|
39057526
|
sec[5]/p[0]
|
6. Conclusions
| 4.039063 |
biomedical
|
Study
|
[
0.994140625,
0.005558013916015625,
0.00016129016876220703
] |
[
0.98583984375,
0.008880615234375,
0.003849029541015625,
0.0013599395751953125
] |
Our data showed several characteristic features among DM patients with DNIs, including an older age, elevated levels of WBC and CRP, the involvement of multiple spaces, and extended hospital stays. Therefore, we recommend a more rigorous approach when dealing with DNIs in DM patients, emphasizing the importance of good glycemic control to prevent the occurrence of more severe complications. In addition, since the prevalence of Klebsiella pneumoniae is increased in patients with DM, the selection of empiric antibiotics should also take this into consideration.
|
[
"Ting-I Liao",
"Chia-Ying Ho",
"Shy-Chyi Chin",
"Yu-Chien Wang",
"Kai-Chieh Chan",
"Shih-Lung Chen"
] |
https://doi.org/10.3390/healthcare12141383
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p0
|
PMC11276569
|
sec[0]/p[0]
|
1. Introduction
| 3.861328 |
biomedical
|
Study
|
[
0.99169921875,
0.0002868175506591797,
0.00787353515625
] |
[
0.8046875,
0.12841796875,
0.06634521484375,
0.0003719329833984375
] |
Drought stress seriously affects the productivity of crops worldwide . Due to climate fluctuations and irregular rainfall, crops are increasingly exposed to drought and high temperatures . Drought stress affects ionic and osmotic homeostasis signaling pathways, detoxification response pathways, and pathways for growth regulation . Drought stress first causes cellular water loss and then induces reactive oxygen species accumulation, followed by damage to cellular components such as membrane lipids, proteins, and nucleic acids, and metabolic dysfunction .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999995 |
PMC11276569_p1
|
PMC11276569
|
sec[0]/p[1]
|
1. Introduction
| 1.462891 |
other
|
Other
|
[
0.184814453125,
0.0015106201171875,
0.8134765625
] |
[
0.008758544921875,
0.98974609375,
0.001068115234375,
0.0003712177276611328
] |
Sweet potato ( I. batatas (L.) Lam.) is one of the most important root crops cultivated worldwide . Because of its adaptability, high yield potential, and nutritional value, sweet potato has become an important food crop, particularly in developing countries . This crop is often grown on ridges and is easily subjected to drought stress after long-term dry weather .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p2
|
PMC11276569
|
sec[0]/p[2]
|
1. Introduction
| 4.15625 |
biomedical
|
Study
|
[
0.9990234375,
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] |
[
0.986328125,
0.0003495216369628906,
0.01331329345703125,
0.0000947713851928711
] |
Transcriptomic and proteomic analyses have provided a new approach to understanding drought tolerance mechanisms. Proteomic analysis of four tomato species and transcriptomic analysis of Sulla coronaria (L.) have uncovered many pathways involved in drought stress response . Lau et al. discovered 122 drought-responsive genes using RNA-Seq analysis . Arisha et al. studied the purple-fleshed sweet potato “Xuzi-8” and identified many drought-responsive unigenes, many of which encode osmolyte biosynthesis enzymes, water channels, sugar and proline transporters, detoxification enzymes, chaperones, and late embryogenesis abundant (LEA) proteins . Transcriptome analysis of seven sweet potato cultivars found that pathways involved in plant signal transduction, flavonoid biosynthesis, phenypropanoid biosynthesis, and isoquinoline alkaloid biosynthesis play important roles in regulating drought stress tolerance .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999995 |
PMC11276569_p3
|
PMC11276569
|
sec[0]/p[3]
|
1. Introduction
| 4.121094 |
biomedical
|
Study
|
[
0.99267578125,
0.00037789344787597656,
0.00714111328125
] |
[
0.99951171875,
0.0002505779266357422,
0.00017702579498291016,
0.00003534555435180664
] |
Previous studies have demonstrated that drought stress can reduce the root yield of sweet potato to varying degrees, and water scarcity in the early stages has a more significant impact on sweet potato yield than in the later stage . To elucidate the drought tolerance mechanism in the early stages of sweet potato, in this study, transcriptomic analysis of roots and leaves from the drought-tolerant sweet potato cultivar “WanSu 63” was conducted on the Illumina NovoSeq6000 platform at 15 and 45 days after transplanting. These transcriptome sequencing data from hexaploid sweet potato under drought stress can provide a useful resource for sweet potato breeding and offer new candidate genes that constitute a valuable reference for the furtherance of research on the functional genomics of sweet potato.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999995 |
PMC11276569_p4
|
PMC11276569
|
sec[1]/sec[0]/p[0]
|
2.1. Plant Growth Conditions
| 3.576172 |
biomedical
|
Study
|
[
0.88037109375,
0.0009737014770507812,
0.1187744140625
] |
[
0.99853515625,
0.0010318756103515625,
0.0001996755599975586,
0.00005710124969482422
] |
The yellow-fleshed sweet potato cultivar “WanSu 63” was used as the experimental material. Uniform healthy shoots of the top 25 cm were planted in each pot; the pots were 30 cm in diameter and 60 cm in height. One plant was planted per pot, and there were 30 pots for each treatment, with a total of 60 pots. Drip irrigation was used to precisely control the soil moisture throughout the entire growth stage. The soil moisture was measured using a TDR150 soil moisture meter (Spectrum technologies, Inc., Aurora, IL, USA), with 60 ± 5% soil water content as the normal treatment, and 30 ± 5% soil water content set as drought stress treatment. Samples were taken 15 and 45 days after drought stress (i.e., seedling stage and root expansion stage, respectively).
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p5
|
PMC11276569
|
sec[1]/sec[0]/p[1]
|
2.1. Plant Growth Conditions
| 3.464844 |
biomedical
|
Study
|
[
0.99169921875,
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] |
[
0.9990234375,
0.0008969306945800781,
0.00018978118896484375,
0.00006198883056640625
] |
On days 15 and 45 after drought stress, the third, fourth, and fifth unfolded leaves from the main vine of representative individual plants were collected and then mixed as leaf samples. Fibrous roots (tubers) were also collected as root samples for RNA extraction, followed by transcriptome sequencing (8 samples with 3 biological replicates each).
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p6
|
PMC11276569
|
sec[1]/sec[0]/p[2]
|
2.1. Plant Growth Conditions
| 2.574219 |
biomedical
|
Study
|
[
0.9365234375,
0.0015497207641601562,
0.061981201171875
] |
[
0.9853515625,
0.0140380859375,
0.0005621910095214844,
0.0002321004867553711
] |
At harvest, 10 representative individual plants from each treatment were selected. The number of tubers per plant, the fresh weight of tubers, the fresh weight of stems and vines, the length of vines, and the number of branches were measured.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p7
|
PMC11276569
|
sec[1]/sec[1]/p[0]
|
2.2. Drought-Related Physiological Chemical Contents and Yield-Related Indexes
| 3.990234 |
biomedical
|
Study
|
[
0.99951171875,
0.0001837015151977539,
0.000507354736328125
] |
[
0.99951171875,
0.00039076805114746094,
0.000209808349609375,
0.00004380941390991211
] |
Samples were taken 15 and 45 days after transplanting. The proline content was quantified using a colorimetric assay kit (Catalog No. A107) sourced from Nanjing Jiancheng Bioengineering Institute. Furthermore, the enzymatic activities of superoxide dismutase, as well as total antioxidant capacity (T-AOC), were assessed using respective kits from the same institute (Catalog No. A001-1 and A015, respectively). The concentration of ABA we measured using a competitive enzyme-linked immunosorbent assay .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p8
|
PMC11276569
|
sec[1]/sec[1]/p[1]
|
2.2. Drought-Related Physiological Chemical Contents and Yield-Related Indexes
| 2.486328 |
biomedical
|
Study
|
[
0.50244140625,
0.0008711814880371094,
0.49658203125
] |
[
0.9208984375,
0.078125,
0.0005340576171875,
0.00029659271240234375
] |
Sweet potato was grown on 12 June and harvested on 23 October, with a life span of 132 days. The yield-related traits of sweet potato including length of vine, tuberous root number, branching number, tuberous root weight, aboveground biomass, and total biomass were measured at harvest. The fresh tuberous roots were shaved into shreds and baked in an oven at 85 degrees Celsius for 48 h until a constant weight was reached, and the dry rate was calculated subsequently.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999998 |
PMC11276569_p9
|
PMC11276569
|
sec[1]/sec[2]/p[0]
|
2.3. Total RNA Isolation and Library Construction
| 4.007813 |
biomedical
|
Study
|
[
0.99951171875,
0.00013554096221923828,
0.00021278858184814453
] |
[
0.98828125,
0.01081085205078125,
0.0008029937744140625,
0.0001838207244873047
] |
Total RNA was isolated using Trizol reagent (Invitrogen, Waltham, MA, USA) according to the manufacturer’s protocol. RNA concentration was measured using Qubit ® RNA Assay Kit in Qubit ® 2.0 Flurometer (Life Technologies, Carlsbad, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA).
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p10
|
PMC11276569
|
sec[1]/sec[2]/p[1]
|
2.3. Total RNA Isolation and Library Construction
| 4.097656 |
biomedical
|
Study
|
[
0.99951171875,
0.00018990039825439453,
0.00020301342010498047
] |
[
0.9970703125,
0.0025310516357421875,
0.0003464221954345703,
0.00011008977890014648
] |
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using the NEBNext ® Ultra TM RNA Library Prep Kit for Illumina ® (NEB, Ipswich, MA, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. The concentration of the libraries was initially measured using Qubit ® 2.0 (Life Technologies, Carlsbad, CA, USA). The libraries were diluted to 1 ng/μL and an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) was used to test the insert size of the libraries.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999998 |
PMC11276569_p11
|
PMC11276569
|
sec[1]/sec[2]/p[2]
|
2.3. Total RNA Isolation and Library Construction
| 3.59375 |
biomedical
|
Study
|
[
0.998046875,
0.0002582073211669922,
0.0015497207641601562
] |
[
0.998046875,
0.0015106201171875,
0.00016415119171142578,
0.00007921457290649414
] |
Next, we used the Illumina NovoSeq 6000 (Illumina, San Diego, CA, USA) sequencing platform to explore the transcriptome in leaf tissues (3rd, 4th, and 5th unfolded leaves collected as leaf samples) and root tissues 15 days and 45 days after transplanting, respectively.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999995 |
PMC11276569_p12
|
PMC11276569
|
sec[1]/sec[3]/p[0]
|
2.4. Analysis of Differentially Expressed Genes
| 4.113281 |
biomedical
|
Study
|
[
0.99951171875,
0.0001773834228515625,
0.0003821849822998047
] |
[
0.9990234375,
0.000782012939453125,
0.00023031234741210938,
0.00006395578384399414
] |
Raw reads were filtered using SOAPnuke software (v2.1.0) to obtain clean reads; the main parameters were as follows: -lowQual = 20, -nRate = 0.005, -qualRate = 0.5, other parameters default. The clean reads were mapped to the I. batatas genome using HISAT2 (V2.1.0) software . We mapped the reads to the merged transcriptome set using bowtie2 (V2.3.5) and quantified the normalized expression level (FPKM) of each gene and transcript using RSEM (V1.3.1) .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p13
|
PMC11276569
|
sec[1]/sec[3]/p[1]
|
2.4. Analysis of Differentially Expressed Genes
| 4.070313 |
biomedical
|
Study
|
[
0.99951171875,
0.00019252300262451172,
0.0001952648162841797
] |
[
0.9990234375,
0.0003941059112548828,
0.00031113624572753906,
0.000056684017181396484
] |
Differentially expressed genes between sample groups were evaluated using DESeq2 (V1.22.2) . The false discovery rate (FDR) was used to identify the threshold p values in multiple tests to compute the significance of the differences. Here, only genes with |log2(FoldChange)| ≥ 1 and FDR significance score (padj) < 0.01 were selected for subsequent analysis.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p14
|
PMC11276569
|
sec[1]/sec[4]/p[0]
|
2.5. Gene Ontology Term Enrichment Analysis and KEGG Enrichment Analysis
| 4.082031 |
biomedical
|
Study
|
[
0.9990234375,
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] |
[
0.99951171875,
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0.000044345855712890625
] |
Differentially expressed genes were compared against various databases for their functional annotations. We compared plant-specific sequences from the NCBI NR database and the SwissProt database using BLASTX (V2.6.0) with an e-value cut-off of 10 −5 . The best blast-hit based on bit-score was used for subsequent functional annotation. Gene Ontology annotation was performed based on the corresponding genes in NCBI and their GO annotations . The database of this correspondence was obtained from https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz . KEGG pathway annotation was performed using BLASTx against the plant-specific sequences from the KEGG database . GO and KEGG enrichment was performed using the hypergeometric test as implemented in the R phyper function.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999998 |
PMC11276569_p15
|
PMC11276569
|
sec[2]/sec[0]/p[0]
|
3.1. Physiological Responses of Tuberous Roots and Leaves under Drought Stress
| 4.144531 |
biomedical
|
Study
|
[
0.994140625,
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0.005153656005859375
] |
[
0.99951171875,
0.00015866756439208984,
0.000274658203125,
0.00003647804260253906
] |
Drought stress severely disturbs plant growth. To investigate the physiological response of sweet potato to drought, we measured the content of water, proline, ABA, and total protein. The results showed that under stress, water content slightly decreased in leaves from sweet potato 15 days after transplanting (L15), roots 15 days after transplanting (R15), and leaves from sweet potato 45 days after transplanting (L45) but was not affected in roots from sweet potato 45 days after transplanting (R45) between drought versus each control, respectively . Total protein content increased after drought stress in sweet potato in all comparisons . The ABA concentration significantly increased in all comparisons as expected, and was more pronounced in leaf tissue. (L15 and L45) . We also measured some enzyme activities. After drought, the T-AOC (total antioxidant capacity) increased in all comparisons . The content of proline also increased in all comparisons as expected. SOD enzyme activity increased in all tissues and was notably higher in leaf tissues (L15 and L45) compared to root tissues (R15 and R45) in drought stress versus control, respectively .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p16
|
PMC11276569
|
sec[2]/sec[0]/p[1]
|
3.1. Physiological Responses of Tuberous Roots and Leaves under Drought Stress
| 2.339844 |
biomedical
|
Study
|
[
0.66748046875,
0.0010995864868164062,
0.33154296875
] |
[
0.96630859375,
0.033050537109375,
0.0004761219024658203,
0.00026702880859375
] |
The growth of sweet potato is severely inhibited under drought stress. The harvest-related traits were measured at 132 days after transplanting. Except that the tuberous root numbers slightly increased, the other traits including length of the main vein, branch number, total biomass, aboveground biomass, and tuberous root weight significantly decreased after drought stress .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p17
|
PMC11276569
|
sec[2]/sec[1]/p[0]
|
3.2. Transcriptome Sequencing, Quality Filtering, and Assembly
| 4.109375 |
biomedical
|
Study
|
[
0.99951171875,
0.00028395652770996094,
0.00028061866760253906
] |
[
0.99951171875,
0.0001819133758544922,
0.00020372867584228516,
0.00005894899368286133
] |
Twenty-four cDNA libraries were constructed, and 198.9 Gb of clean data was generated after adaptor sequences and low-quality reads were removed. The correlation heatmap showed that three biological replicates within each sample have the highest correlation . In all libraries, the Q30 ratio ranges from 91.89 to 94.77% and guanine–cytosine (GC) content ranges from 46% to 49% ( Table 1 ). The ratio of genomic reads to clean reads was greater than 65% in R45 tissue and 70% in the other tissues, and total mapped reads ranged from 82% to 87%, which was sufficient for the next step of the analysis ( Table S1 ).
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999999 |
PMC11276569_p18
|
PMC11276569
|
sec[2]/sec[2]/p[0]
|
3.3. Comparison of Differentially Expressed Genes among All Four Libraries between Drought Versus Corresponding Control Samples
| 3.46875 |
biomedical
|
Study
|
[
0.9931640625,
0.00023174285888671875,
0.0064239501953125
] |
[
0.982421875,
0.0169830322265625,
0.00034546852111816406,
0.00015211105346679688
] |
The carotenoid-rich cultivar ‘Taizhong 6’ genome sequence was used as the reference genome . This version was re-sequenced using nanopore sequencing (Oxford Nanopore Technologies, Oxford, UK) to improve sweet potato genome assembly quality and is now the latest version . Sweet potato cultivars with different drought tolerance performances showed distinct mechanisms for their response to drought stress .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p19
|
PMC11276569
|
sec[2]/sec[2]/p[1]
|
3.3. Comparison of Differentially Expressed Genes among All Four Libraries between Drought Versus Corresponding Control Samples
| 4.113281 |
biomedical
|
Study
|
[
0.9990234375,
0.0003247261047363281,
0.0007638931274414062
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[
0.99951171875,
0.00011932849884033203,
0.00020301342010498047,
0.000042378902435302734
] |
As mentioned above, the level of gene expression in individual samples was calculated by FPKM, using the criteria of FDR < 0.05 and |log2 of fold change (FC)| >1. DEGs were generated in pairwise comparisons in different tissues at two developmental stages to observe the drought stress response, i.e., CK_L15-vs-DR_L15 , CK_L45-vs-DR_L45 , CK_R15-vs-DR_R15 , and CK_R45-vs-DR_R45 (930 DEGs in total, with 445 up-regulated and 485 down-regulated) ( Table S2 ). The results showed that as the sweet potato grew, the number of differentially expressed genes declined sharply, especially in root tissues. Compared with L15 tissues, DEGs in L45 tissues declined by 23%, whereas in R15 tissue, with 8811 DEGs, the number declined to 930 DEGs in R45 tissue, a decline of 89%. This indicates that drought tolerance increased as the sweet potato grew, and roots were more tolerant to drought stress than leaf tissues ( Table 1 ).
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999995 |
PMC11276569_p20
|
PMC11276569
|
sec[2]/sec[2]/p[2]
|
3.3. Comparison of Differentially Expressed Genes among All Four Libraries between Drought Versus Corresponding Control Samples
| 3.439453 |
biomedical
|
Study
|
[
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0.00698089599609375
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[
0.9970703125,
0.00270843505859375,
0.00025844573974609375,
0.00008928775787353516
] |
The DEGs from root tissues differ from those of leaf tissues . There are only 15 commonly up-regulated and 14 commonly down-regulated DEGs in all four comparisons . There are 2349 common DEGs between CK_L15-vs-DR_L15 and CK_L45-vs-DR_L45, of which 569 are up-regulated and 1470 are down-regulated . There are also 256 common DEGs between CK_R15-vs-DR_R15 and CK_R45-vs-DR_R45, of which 342 are up-regulated and 86 down-regulated .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p21
|
PMC11276569
|
sec[2]/sec[2]/p[3]
|
3.3. Comparison of Differentially Expressed Genes among All Four Libraries between Drought Versus Corresponding Control Samples
| 4.035156 |
biomedical
|
Study
|
[
0.99951171875,
0.00018298625946044922,
0.0004954338073730469
] |
[
0.99951171875,
0.0004398822784423828,
0.00019633769989013672,
0.00005525350570678711
] |
A group of genes encoding heat shock protein, sporamin, LEA protein, and genes involved in ABA Biosynthesis and Signaling Pathway were significantly enriched in DEGs . Genes involved in osmotic homeostasis, damage control and repair. In L15 stage, HSP encoding genes accounted for 35%(14 in 40) in top 40 up-regulated DEGs. The same trends occurred in R15 stage as well . Several inositol oxygenase family gene members extremely enriched in R45 .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999995 |
PMC11276569_p22
|
PMC11276569
|
sec[2]/sec[3]/p[0]
|
3.4. Functional Annotation and Classification of DEGs
| 4.136719 |
biomedical
|
Study
|
[
0.99951171875,
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[
0.9990234375,
0.00046443939208984375,
0.000347137451171875,
0.000044286251068115234
] |
The GO (Gene Ontology) database is suitable for various species and can define and describe genes and proteins. Genes can be categorized into three main GO categories: BP (biological process), CC (cellular component), and MF (molecular function). The most enriched GO categories in CK_L15 vs. DR_L15 up-regulated DEGs were “RNA modification”, “Cytoplasm”, “Response to heat”, “intracellular anatomical structure”, and “Response to temperature stimulus”. The most enriched GO categories in CK_R15 vs. DR_R15 up-regulated DEGs were “Response to heat”, “Response to abiotic stimulus”, “nucleolus”, “Response to temperature stimulus”, and “preribosome” . In 45 days after transplanting, the most enriched GO categories in CK_L45 vs. DR_L45 up-regulated DEGs were “ribosome”, “structural constituent of ribosome”, “structural molecular activity”, “peptide metabolic process”, and “translation”. The most enriched GO categories in CK_R45 vs. DR_R45 up-regulated DEGs were “structural constituent of ribosome”, “ribosome”, “structural molecular activity”, “translation”, and “peptide biosynthetic process” .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p23
|
PMC11276569
|
sec[2]/sec[3]/p[1]
|
3.4. Functional Annotation and Classification of DEGs
| 3.953125 |
biomedical
|
Study
|
[
0.99951171875,
0.0001659393310546875,
0.0004811286926269531
] |
[
0.99853515625,
0.0008106231689453125,
0.00042939186096191406,
0.000060558319091796875
] |
The most enriched GO categories in CK_L15 vs. DR_L15 down-regulated DEGs were “membrane”, “intrinsic component of membrane”, “integral component of membrane”, “cell periphery”, and “carbohydrate metabolic process”. The most enriched GO categories in CK_R15 vs. DR_R15 down-regulated DEGs were “cell periphery”, “extracellular region”, “intrinsic component of membrane”, “integral component of membrane”, and “plasma membrane”. The most enriched GO categories in CK_L45 vs. DR_L45 down-regulated DEGs were “carbohydrate metabolic process”, “cell periphery”, “membrane”, “intrinsic component of membrane”, and “integral component of membrane” . The most enriched GO categories in CK_R45 vs. DR_R45 down-regulated DEGs were “peptidase regulator activity”, “peptidase inhibitor activity”, “endopeptidase regulator activity”, “endopeptidase inhibitor activity”, and “response to stress” .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p24
|
PMC11276569
|
sec[2]/sec[3]/p[2]
|
3.4. Functional Annotation and Classification of DEGs
| 4.125 |
biomedical
|
Study
|
[
0.99951171875,
0.00016987323760986328,
0.0003666877746582031
] |
[
0.9990234375,
0.00041961669921875,
0.00038123130798339844,
0.000054717063903808594
] |
In both L15 and R15 tissues, up-regulated genes were specially enriched in the GO terms “GO:0009628 response to abiotic stimulus”, “GO:0009451 RNA modification”, “GO:0009408 response to heat”, “GO:0009622 response to temperature stimulus”, “GO:0006457 protein folding”, and “GO:0005622 intracellular anatomical structure”. In both L45 and R45 tissues, “GO:0003735 structural constituent of ribosome”, “GO:0005198 structural molecular activity”, and other protein biosynthesis-related GO terms are enriched.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999998 |
PMC11276569_p25
|
PMC11276569
|
sec[2]/sec[3]/p[3]
|
3.4. Functional Annotation and Classification of DEGs
| 4.078125 |
biomedical
|
Study
|
[
0.9990234375,
0.00021386146545410156,
0.0007610321044921875
] |
[
0.9990234375,
0.00045108795166015625,
0.0002551078796386719,
0.00005042552947998047
] |
The GO terms “GO:0016020 membrane”, “GO:0031224 intrinsic component of membrane”, and “GO:0005618 cell wall” were commonly enriched in L15, R15, and L45 stages and tissues. A total of 485 down-regulated DEGs in DR_R45 vs. CK_R45 showed distinct expression profiles in pathways such as “Ko:04141 Protein processing in endoplasmic reticulum”, “Ko:00196 Photosynthesis—antenna proteins”, and “Ko:04626 Plant-pathogen interaction”.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999995 |
PMC11276569_p26
|
PMC11276569
|
sec[2]/sec[3]/p[4]
|
3.4. Functional Annotation and Classification of DEGs
| 3.896484 |
biomedical
|
Study
|
[
0.99951171875,
0.00018548965454101562,
0.0005388259887695312
] |
[
0.984375,
0.01444244384765625,
0.0011501312255859375,
0.0002434253692626953
] |
KEGG pathway enrichment analysis showed that “KO:03010 Ribosome”, “KO:03008 Ribosome biogenesis in eukaryotes”, “KO:04141 protein processing in endoplasmic reticulum”, “KO:02010 ABC transporter”, “KO:04120 Ubiquitin mediated proteolysis”, and “KO:04146 Peroxisome” are enriched.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p27
|
PMC11276569
|
sec[2]/sec[3]/p[5]
|
3.4. Functional Annotation and Classification of DEGs
| 4.132813 |
biomedical
|
Study
|
[
0.9990234375,
0.00020170211791992188,
0.0006732940673828125
] |
[
0.9990234375,
0.00038504600524902344,
0.00038433074951171875,
0.00004500150680541992
] |
As for KEGG pathway enrichment analysis of down-regulated DEGs, “KO:04626 plant-pathogen interaction”, “KO:00500 starch and sucrose metabolism”, “KO:00520 Amino sugar and nucleotide sugar metabolism”, “KO:00940 phenylpropanoid biosynthesis”, and “KO:00460 cyanoamino acid metabolism” are enriched . These KEGG pathways are expected as drought inhibits sweet potato growth by suppressing starch and sucrose metabolism. The common down-regulated DEGs in all stages and tissues enriched in the KEGG pathway include “KO:00940 phenylpropanoid biosynthesis”, “KO:00520 Amino sugar and nucleotide sugar metabolism”, and “KO:00500 Starch and sucrose metabolism”. The commonly up-regulated DEGs include “KO:04120 Ubiquitin mediated proteolysis” and “Ko:03008 Ribosome biogenesis in eukaryotes” .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p28
|
PMC11276569
|
sec[2]/sec[4]/p[0]
|
3.5. Differentially Expressed Transcriptional Factors
| 4.121094 |
biomedical
|
Study
|
[
0.9990234375,
0.0002741813659667969,
0.0004782676696777344
] |
[
0.99951171875,
0.0001773834228515625,
0.0002086162567138672,
0.00004589557647705078
] |
Based on the Hammscan function , 301, 233, 473, and 40 DEGs were annotated as transcription factors in L15, L45, R15, and R45 in drought versus control, respectively ( Table S4 ), with 389 up-regulated DEGs and 658 down-regulated DEGs in total. Among them, AP2-EREBP transcriptional factors (150 genes, 14.3%), MYB transcriptional factors (142 genes, 13.6%), bHLH transcriptional factors (104 genes, 9.9%), and WRKY transcriptional factors (56 genes, 5.3%) were the top four enriched TF families ( Table S4 ).
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p29
|
PMC11276569
|
sec[2]/sec[4]/p[1]
|
3.5. Differentially Expressed Transcriptional Factors
| 4.144531 |
biomedical
|
Study
|
[
0.998046875,
0.00019919872283935547,
0.0017337799072265625
] |
[
0.9990234375,
0.00067901611328125,
0.0003223419189453125,
0.00004392862319946289
] |
It is reasonable that most of the ABI3VP1 transcriptional factors (with 22 members up-regulated and 10 down-regulated) and HSF transcriptional factors (with 16 members up-regulated and 8 down-regulated) are up-regulated, because the ABI3VP1 family members are involved in the ABA signaling pathway, and HSF family members have the function to activate the HSP proteins. A large proportion of TFs are down regulated, indicating that most gene expressions are repressed under drought stress. Some transcription factors are disproportionately down-regulated, such as the WRKY transcriptional factor (9 up-regulated and 47 down-regulated) and GRAS transcription factor members (6 up-regulated and 44 down-regulated), which may play a vital role in sweet potato root and stem growth and development.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p30
|
PMC11276569
|
sec[2]/sec[5]/p[0]
|
3.6. Receptor-like Kinases Differentially Expressed in Response to Drought
| 4.167969 |
biomedical
|
Study
|
[
0.9990234375,
0.0002589225769042969,
0.0004754066467285156
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[
0.99951171875,
0.00020420551300048828,
0.0002796649932861328,
0.000046253204345703125
] |
On the basis of signature motifs in their extracellular domains, receptor-like kinases (RLKs) are categorized into 14 classes . All transcription factors are listed in Supplemental Table S4 . Using the term “kinase” as a keyword to search the DEGs list, a total of 316 (42 up-regulated and 274 down-regulated), 333 (54 up-regulated and 279 down-regulated), 290 (126 up-regulated and 164 down-regulated), and 16 (1 up-regulated and 15 down-regulated) receptor-like kinases are differentially expressed in the L15, R15, L45, and R45 stages in drought stress versus control, respectively . Among them, leucine-rich repeat (LRR) receptor kinases account for the largest proportion, followed by lectin (G-lectin and L-lectin) RLK, wall-associated kinase (WAK), cysteine-rich RLK, and leaf rust kinase-like RLKs .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999998 |
PMC11276569_p31
|
PMC11276569
|
sec[3]/p[0]
|
4. Discussion
| 1.543945 |
other
|
Other
|
[
0.261962890625,
0.001850128173828125,
0.736328125
] |
[
0.005001068115234375,
0.994140625,
0.0007920265197753906,
0.0002841949462890625
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Sweet potato is one of the most important root crops cultivated worldwide . It is a versatile crop that can be used as a nutritious food to alleviate vitamin A deficiency, and it can also be used as a raw material to produce starch and alcohol . Due to the fluctuation of rainfall, especially rainfall shortage in the seedling stage, drought is an increasingly limiting factor for sweet potato yield.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999998 |
PMC11276569_p32
|
PMC11276569
|
sec[3]/p[1]
|
4. Discussion
| 2.462891 |
other
|
Study
|
[
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0.0008764266967773438,
0.58642578125
] |
[
0.87255859375,
0.125732421875,
0.0011529922485351562,
0.00041365623474121094
] |
Drought stress can greatly reduce the growth of sweet potato seedling leaves and roots, thus decreasing the seedling survival rate during the very early stage of transplanting. In the early stages of growth (0–60 d after transplanting), the number of leaves, leaf area, and stem length, as well as the formation and expansion of tuberous root, are also seriously affected . The effect of drought on the fresh potato yield was more serious in the early stages than in the later stages .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p33
|
PMC11276569
|
sec[3]/p[2]
|
4. Discussion
| 3.880859 |
biomedical
|
Study
|
[
0.9951171875,
0.00034165382385253906,
0.00463104248046875
] |
[
0.99951171875,
0.0004723072052001953,
0.0001499652862548828,
0.000048100948333740234
] |
The release of the sweet potato genome in 2017 greatly accelerated functional genome research . However, the highly heterozygous hexaploid genome of I. batatas remains an obstacle. Transcriptome analysis makes it easy to uncover the defense mechanism against drought stress, which may further facilitate breeding for drought-tolerant sweet potato cultivars . This study is the first to evaluate the drought-responsive genes and pathways in roots and leaves in both the seedling stage and tuberous expansion stage.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p34
|
PMC11276569
|
sec[3]/sec[0]/p[0]
|
4.1. Pathways of Drought Tolerance in Different Tissues and Developmental Stages
| 4.113281 |
biomedical
|
Study
|
[
0.9970703125,
0.0003352165222167969,
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[
0.99951171875,
0.00016117095947265625,
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0.00003141164779663086
] |
Drought stress signal transduction consists of the ionic and osmotic homeostasis signaling pathway, detoxification (i.e., damage control and repair) response pathway, and pathways for growth regulation . The number of DEGs is related to the drought tolerance degree. Previous studies showed that the extremely drought-tolerant sweet potato cultivar “xuzi-8” was almost unaffected by drought stress . We can conclude that as sweet potatoes grow, their drought resistance increases, as evidenced by the significant decrease in the number of DEGs from 7119 in L15 to 5463 in L45.In roots, the number of DEGs decreased from 8811 in R15 to 930 in R45 ( Table 2 ). As the sweet potato plant grows, root tissue becomes more tolerant to drought than leaf tissue, as indicated by the reduced number of DEGs from 8811 in R15 to 930 in R45, compared to 7119 in L15 to 5463 in L45 ( Table 2 ).
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p35
|
PMC11276569
|
sec[3]/sec[0]/p[1]
|
4.1. Pathways of Drought Tolerance in Different Tissues and Developmental Stages
| 4.097656 |
biomedical
|
Study
|
[
0.9990234375,
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[
0.9990234375,
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From the perspective of the transplanting day, we can conclude that up-regulated DEGs in both L15 and R15 are assigned to “GO:0005622 intracellular anatomical structure”, “GO:0006457 protein folding”, “GO:0009628 response to abiotic stimulus”, “GO:0009451 RNA modification”, “GO:0009408 response to heat”, and “GO:0009266 response to temperature stimulus”. However, the situation in both L45 and R45 is different. Up-regulated DEGs are commonly assigned to “GO:0005840 ribosome”, “GO:0006421 translation”, “GO:0006518 peptide metabolic process”, “GO:0043228 non-membrane-bounded organelle”, and so on. All these GO terms are involved in protein biosynthesis processes .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p36
|
PMC11276569
|
sec[3]/sec[0]/p[2]
|
4.1. Pathways of Drought Tolerance in Different Tissues and Developmental Stages
| 4.171875 |
biomedical
|
Study
|
[
0.9990234375,
0.0002980232238769531,
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[
0.99951171875,
0.00015616416931152344,
0.0003962516784667969,
0.00005042552947998047
] |
The down-regulated DEGs in L15, L45, and R15 between drought and CK commonly were strongly enriched for membrane-related GO terms, including “GO:0031224 intrinsic component of membrane”, “GO:0016021 integral component of membrane”, “GO:0016020 membrane”, and “GO:0005886 plasma membrane” . Under the GO term “GO:0016020 term membrane”, genes encoding ABC transporter, water channel protein aquaporin family members, ion transporters such as Na + and K + ion transporters and H + -ATPase, Ca 2+ channel protein, and receptor-like kinases are all included. However, in the R45 stage, most enriched GO terms are assigned to “GO:0004866 endopeptidase inhibitor activity”, “GO:0016679 oxidoreductase activity, acting on diphenols and related substances as donors”, “GO:0006950, response to stress”, “GO:0030554 adenyl nucleotide”, “GO:0050896 response to stimulus”, and so on . The most important gene families involved in drought stress in this study are discussed below.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p37
|
PMC11276569
|
sec[3]/sec[1]/p[0]
|
4.2. ABA Biosynthesis and Signaling Pathway
| 4.105469 |
biomedical
|
Study
|
[
0.9970703125,
0.00044035911560058594,
0.0026798248291015625
] |
[
0.72412109375,
0.266357421875,
0.00901031494140625,
0.0004982948303222656
] |
The ABA signaling pathway is critical in regulating plant water balance and osmotic stress tolerance . In this pathway, ABA binds to the soluble PYR/PYL/RCAR receptors, allowing the receptors to physically interact with and inhibit the activity of PP2C-A phosphatases, which in turn release SnRK2 kinases from their association with and inhibition by the PP2Cs .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p38
|
PMC11276569
|
sec[3]/sec[1]/p[1]
|
4.2. ABA Biosynthesis and Signaling Pathway
| 3.964844 |
biomedical
|
Study
|
[
0.9990234375,
0.00017976760864257812,
0.0009326934814453125
] |
[
0.98583984375,
0.01342010498046875,
0.0007510185241699219,
0.000152587890625
] |
DEGs related to ABA biosynthesis and signaling pathway in all four groups are assigned to “GO:0009737 response to abscisic acid”, “GO:0010427 abscisic acid binding”, “GO:0009738 abscisic acid-activated signaling pathway”, “GO:0071215 cellular response to abscisic acid stimulus”, “GO:0009787 regulation of abscisic acid-activated signaling pathway”, “GO:0009687 abscisic acid metabolic process”, and “GO:0009688 abscisic acid biosynthetic process”.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p39
|
PMC11276569
|
sec[3]/sec[1]/p[2]
|
4.2. ABA Biosynthesis and Signaling Pathway
| 4.226563 |
biomedical
|
Study
|
[
0.9990234375,
0.0003192424774169922,
0.0005159378051757812
] |
[
0.99951171875,
0.0001659393310546875,
0.00023317337036132812,
0.0000622868537902832
] |
The ABA content expectedly increased in all four groups between drought treatment versus control . The NCED encodes 9-cis-epoxycarotenoid dioxygenase, a key ABA biosynthesis enzyme. Our results showed that NCED members are expectedly upregulated in the L15 stage compared to control ( Supplemental Table S1 ), consistent with the increase in ABA content. The above-mentioned genes can be assigned to the KEGG pathway “KO:00906 Carotenoid biosynthesis”. The abscisic acid receptor PYL8 was up-regulated as well, both in the L15 stage and L45 stage ( Supplemental Table S1 ). The role of ABA in drought is diverse, encompassing at least two key aspects: water balance and cellular dehydration tolerance. The role in water balance is predominantly executed through the regulation of guard cells, whereas the latter facet pertains to triggering the expression of genes encoding dehydration-resistant proteins across virtually all cell types . An important part of the transport of ABA to stomatal guard cells is ABA transporter proteins, such as NITRATE TRANSPORTER 1 ( NRT1 ). In the L45 stage, g57285, which was annotated as NRT1, was expectedly up-regulated ( Table S2 ).
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p40
|
PMC11276569
|
sec[3]/sec[2]/p[0]
|
4.3. Plant–Pathogen Interaction
| 4.027344 |
biomedical
|
Study
|
[
0.99609375,
0.00028014183044433594,
0.003833770751953125
] |
[
0.998046875,
0.0015659332275390625,
0.0004775524139404297,
0.000058650970458984375
] |
Drought stress affects plant pathogen defense as DEGs are enriched in “KO:04626 Plant-pathogen interaction”. In this pathway, the expression of a group of protein genes involved in signaling sensing like calcium-dependent protein kinases, LRR receptor-like kinases, and calmodulin are affected. “Disease resistance protein RPM1-like” takes the largest proportion. It is noticeable that most plant–pathogen interaction genes mentioned above are downregulated, and this indicates that drought stress may weaken the plant pathogen defense responses.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p41
|
PMC11276569
|
sec[3]/sec[3]/p[0]
|
4.4. Osmotic Homeostasis
| 3.878906 |
biomedical
|
Study
|
[
0.99853515625,
0.00021588802337646484,
0.0010404586791992188
] |
[
0.84765625,
0.1485595703125,
0.003124237060546875,
0.0004875659942626953
] |
The genes related to osmotic homeostasis are mainly assigned to “GO:0022857 transmembrane transporter activity”. This GO term includes water channel protein aquaporins, osmotin-like protein TPM1, ion channels, ion transporters, NRT1 family members, sugar transporters, and sucrose transporters, among others.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999995 |
PMC11276569_p42
|
PMC11276569
|
sec[3]/sec[4]/p[0]
|
4.5. Osmotin-like Protein TPM1
| 4.03125 |
biomedical
|
Study
|
[
0.99853515625,
0.00016391277313232422,
0.00142669677734375
] |
[
0.99951171875,
0.0004303455352783203,
0.0001773834228515625,
0.00004082918167114258
] |
Osmotin is a cationic, secretory protein that targets the vacuole. It exerts antifungal activity and plays an important role in cold, salinity, and water deficiency tolerance . Studies on tobacco cell cultures acclimated to 428 mM NaCl showed that osmotin accumulation represents 12% of the total cellular proteins . Previous research on sweet potato drought tolerance showed that TPM-1 is sharply up-regulated after drought, heat, or combined stresses . In our studies, TPM-1 genes were differentially expressed. Some members, like g16028 in the L45 stage and g16031 and g15950 in the R15 stage, were up-regulated. There are still other members that were down regulated after drought.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999999 |
PMC11276569_p43
|
PMC11276569
|
sec[3]/sec[5]/p[0]
|
4.6. Aquaporin
| 4.1875 |
biomedical
|
Study
|
[
0.99951171875,
0.0001596212387084961,
0.00036907196044921875
] |
[
0.9990234375,
0.0003829002380371094,
0.0003981590270996094,
0.00005161762237548828
] |
Aquaporin is a family of small proteins located in the membrane that mediate water, urea, glycerol, NH 3 /NH 4 + , and CO 2 transmembrane transport . Higher plant aquaporin members include TIP, NIP, SIP, and PIP subfamilies. TIP is localized in vacuolar membranes of seed, leaf, and root tissue. NIP is localized in root nodules. PIP is localized in the plasma membrane of roots, shoots, leaves, and florescence . In our research, aquaporin PIP1-2 was consistently down-regulated in all four groups, aquaporin TIP2-1 was down-regulated in L15, and aquaporin NIP1-1 was down-regulated in R45. Fourteen aquaporin family members in “GO:0016020 membrane”, “GO:0005372 water transmembrane transporter activity”, and “GO:0015250 water channel activity” were downregulated. Of course, the downregulation of these proteins might be beneficial for water balance, but it also reduces the intake of small solutes and CO₂, thus reducing photosynthesis rate.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p44
|
PMC11276569
|
sec[3]/sec[6]/sec[0]/p[0]
|
Heat Shock Proteins
| 4.15625 |
biomedical
|
Study
|
[
0.9990234375,
0.00019788742065429688,
0.0005369186401367188
] |
[
0.99951171875,
0.00017571449279785156,
0.00022912025451660156,
0.00003534555435180664
] |
In this research, heat shock proteins are significantly enriched throughout the seedling stage to tuberous expansion stage, especially in CK_L15-vs-DR_L15. These genes belonged to “GO:0009408 response to heat”, “GO:0005737 cytoplasm”. “GO:0009266 response to temperature stimulus”, and “GO:0006457 protein folding”. There are 12 genes annotated as HSP members in the top 40 up-regulated genes screened by p value . In CK_R15-vs-DR_R15, there are also seven genes annotated as HSP in the up-regulated genes. Many of the morphological and phenotypic effects of heat stress can be explained by the aggregation of proteins and an imbalance of protein homeostasis in general . Heat shock proteins are a group of small proteins that respond to heat and drought. The most conserved HSPs are molecular chaperones that prevent the formation of nonspecific protein aggregates and assist proteins in the acquisition of their native structures .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999995 |
PMC11276569_p45
|
PMC11276569
|
sec[3]/sec[7]/p[0]
|
4.8. Sporamin
| 4.1875 |
biomedical
|
Study
|
[
0.9990234375,
0.0001537799835205078,
0.0006260871887207031
] |
[
0.99951171875,
0.00032806396484375,
0.00031185150146484375,
0.00004416704177856445
] |
Sporamins are characterized as trypsin inhibitors and have been shown to have various antioxidant functions related to stress tolerance, such as DHA and MDA reductase activities . This kind of protein is constitutively expressed in the tuberous root but not normally expressed in the stem or leaves . We observed many sporamin genes including g46653 , g46661 , g46666 , g46667 , and g46651 that were highly enriched in leaf tissues, both in L15 and L45 . It has been stated that those proteins are expressed systemically in response to wounding and other abiotic stresses, Sporamin also possesses scavenging activity against 1,1-diphenyl-2-picrylhydrazyl (DPPH) and hydroxyl radicals as well as glutathione peroxidase-like activity , which may elucidate why those proteins are greatly up-regulated in non-root tissues during drought stress.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p46
|
PMC11276569
|
sec[3]/sec[8]/p[0]
|
4.9. LEA Proteins
| 4.101563 |
biomedical
|
Study
|
[
0.998046875,
0.0002014636993408203,
0.0016069412231445312
] |
[
0.99951171875,
0.0002970695495605469,
0.0001672506332397461,
0.00003546476364135742
] |
Late embryogenesis abundant (LEA) proteins are extremely hydrophilic proteins that can stabilize and protect other proteins and membranes during drying . In both L15 and R15, the LEA protein dehydrin DHN2 is prominently upregulated between drought stress and the control. Another LEA protein gene, g20722, is constantly upregulated in all four stages and tissues. A previous study showed that LEA4-group genes from the resurrection plant Boea hygrometrica, BhLEA1 and BhLEA2 , confer dehydration tolerance in transgenic tobacco . There are 14 LEA proteins/dehydrin genes enriched in L15 and R15 samples and only 3 LEA proteins/dehydrin genes in L45 samples ( Supplemental Tables S2 and S3 ). This suggests that these genes play a more important role in the earlier stages of sweet potato.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p47
|
PMC11276569
|
sec[3]/sec[9]/p[0]
|
4.10. Proteins Required for Detoxification
| 3.511719 |
biomedical
|
Other
|
[
0.99267578125,
0.0004317760467529297,
0.006954193115234375
] |
[
0.45947265625,
0.529296875,
0.0105743408203125,
0.0005578994750976562
] |
Drought stress causes reactive oxygen species generation and alters the cellular redox balance. On one hand, ROS acts as a signal to trigger drought response-related signaling pathways. The over-accumulation of ROS in cellular compartments results in increased plasma membrane permeability, decreased chlorophyll, and metabolic disorders.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p48
|
PMC11276569
|
sec[3]/sec[9]/p[1]
|
4.10. Proteins Required for Detoxification
| 4.089844 |
biomedical
|
Study
|
[
0.99951171875,
0.0001285076141357422,
0.0002753734588623047
] |
[
0.9990234375,
0.0007500648498535156,
0.0002193450927734375,
0.000054717063903808594
] |
Proteins in the ROS-scavenging system are necessary for cellular redox balance . In this research, DEGs encoding proteins for detoxification, including glutathione S-transferase, ABC transporter, glutathione peroxidase, and superoxide dismutase (SOD), are assigned to the KEGG pathway “KO:04146 peroxisome”, “KO:00480 Glutathione metabolism”, and “KO:02010 ABC transporters”.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p49
|
PMC11276569
|
sec[3]/sec[10]/sec[0]/p[0]
|
GDSL Esterase/Lipase
| 4.152344 |
biomedical
|
Study
|
[
0.9990234375,
0.0001811981201171875,
0.0005712509155273438
] |
[
0.99951171875,
0.0002467632293701172,
0.0003688335418701172,
0.00004112720489501953
] |
GDSL esterase/lipase proteins (GELPs) compose a family of enzymes identified by a unique “GDSL” amino acid sequence motif. GELPs can accept a broad range of substrates and are functionally diverse. Plant GELPs play roles mainly in modulating development, metabolism, response against pathogens and abiotic stresses, or cuticle biogenesis and degradation. In our study, a group of GDSL esterase/lipases were constantly downregulated in leaf tissues, for example, g37717 in L15, g54917 , g57399 , g11768 , g57611 , and g60792 in L45. It has been reported that overexpression of GmGELP28 and ZmAchE increased drought and heat tolerance, and GELP mutants with cutinase or transferase activity caused rapid water loss .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p50
|
PMC11276569
|
sec[3]/sec[11]/p[0]
|
4.12. Growth Inhibition
| 3.662109 |
biomedical
|
Study
|
[
0.98583984375,
0.00028514862060546875,
0.013702392578125
] |
[
0.96826171875,
0.0304718017578125,
0.0010366439819335938,
0.0001665353775024414
] |
The growth of sweet potato is severely inhibited under drought stress. The biomass of both sweet potato roots and shoots declined sharply under drought conditions . Many genes and pathways are involved in growth inhibition under drought stress. The affected genes are mainly assigned to the following pathways: “KO:04075 Plant hormone signal transduction”, “KO:00908 Zeatin biosynthesis”, “KO:00905 Brassinosteroid biosynthesis”, “KO:00500 Starch and sucrose metabolism”, “KO:00710 Carbon fixation in photosynthetic organisms”, and “Ko:00195 Photosynthesis”.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276569_p51
|
PMC11276569
|
sec[3]/sec[11]/p[1]
|
4.12. Growth Inhibition
| 4.085938 |
biomedical
|
Study
|
[
0.998046875,
0.00028514862060546875,
0.0018453598022460938
] |
[
0.99951171875,
0.0003452301025390625,
0.0002391338348388672,
0.00004297494888305664
] |
As we can see in our research, almost all kinds of plant hormone-related genes are affected in plant hormone signal transduction pathways. Among them, the auxin-induced genes IAAs and small auxin up RNA SAUR account for more than half ( Supplemental Tables S2 and S3 ). A group of zeatin O-xylosyltransferase-like protein genes which play a key role in cytokinin biosynthesis are downregulated( Supplemental Table S3 ). The GA20 oxidase GA20OX1-encoding gene and others involved in GA and auxin biosynthesis and their signaling pathways, which play important roles in stem elongation, are also down-regulated .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999995 |
PMC11276569_p52
|
PMC11276569
|
sec[3]/sec[11]/p[2]
|
4.12. Growth Inhibition
| 4.054688 |
biomedical
|
Study
|
[
0.9990234375,
0.00013756752014160156,
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] |
[
0.99853515625,
0.00106048583984375,
0.00023806095123291016,
0.0000591278076171875
] |
Drought stress will rebalance normal growth and drought-induced response metabolism. Both in L45 and R45, between drought treatment and control, the ribonucleoprotein complex, including a group of 30S, 40S, and 60S ribosome proteins, was enriched in the pathway “KO:03010 Ribosome”. It has been reported that ribosomal components increased in Arabidopsis thaliana and Gossypium hirsutum under salt stress. Like salt stress, drought stress appears to cause a similar effect. And total protein contents increased after drought in all stages and tissues, as expected .
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276569_p53
|
PMC11276569
|
sec[4]/p[0]
|
5. Conclusions
| 4.128906 |
biomedical
|
Study
|
[
0.99658203125,
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0.0028820037841796875
] |
[
0.99951171875,
0.0001379251480102539,
0.00031828880310058594,
0.0000374913215637207
] |
In conclusion, this research found that drought stress can seriously inhibit the growth of sweet potato. The concentration of ABA increased significantly after drought stress. In addition, drought-responsive genes in the roots and leaves of sweet potato at different transplanting stages have distinct expression profiles. Compared with leaf tissue, the number of differentially expressed genes in root tissue was smaller, indicating that roots were less sensitive to drought stress.More differentially expressed genes at the seedling stage indicated that seedlings were more sensitive to drought stress. Drought-response genes were mainly involved in ABA signaling pathways, osmotic homeostasis, damage control and repair, detoxification, lipid metabolism, and growth regulation signaling pathways. These results provide new insights and candidate genes for further study of drought tolerance mechanisms of sweet potato.
|
[
"Peng Cheng",
"Fanna Kong",
"Yang Han",
"Xiaoping Liu",
"Jiaping Xia"
] |
https://doi.org/10.3390/genes15070948
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276581_p0
|
PMC11276581
|
sec[0]/p[0]
|
1. Introduction
| 4.300781 |
biomedical
|
Review
|
[
0.9990234375,
0.0006690025329589844,
0.00046515464782714844
] |
[
0.309814453125,
0.0049285888671875,
0.6845703125,
0.0009407997131347656
] |
Inherited retinal diseases (IRDs) encompass a broad spectrum of retinal phenotypes characterized by extensive clinical variability and profound genetic heterogeneity . Among IRDs, retinitis pigmentosa (RP) stands out as one of the most prevalent and heterogeneous conditions in humans, caused by disease-causing mutations in over 60 genes contributing to its etiology. The inheritance patterns of RP include autosomal recessive (AR) in 50–60%, autosomal dominant (AD) in 30–40% of cases, and X-linked (XL) in 5–15%, along with rare digenic and mitochondrial modes .
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276581_p1
|
PMC11276581
|
sec[0]/p[1]
|
1. Introduction
| 3.962891 |
biomedical
|
Review
|
[
0.99853515625,
0.0011415481567382812,
0.0005383491516113281
] |
[
0.06298828125,
0.14013671875,
0.7939453125,
0.0028476715087890625
] |
RP is a progressive inherited retinal degenerative disease primarily affecting rod photoreceptors cells, followed by cone photoreceptors. Most patients initially experience night blindness, which progresses to a gradual loss of visual acuity and narrowing of the visual field . The condition can be classified into syndromic RP, which involves multiple organ systems leading to significant dysfunction, and non-syndromic RP, accounting for 70–80% of cases, in which only the retina is affected .
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276581_p2
|
PMC11276581
|
sec[0]/p[2]
|
1. Introduction
| 3.988281 |
biomedical
|
Review
|
[
0.998046875,
0.0010271072387695312,
0.00091552734375
] |
[
0.029022216796875,
0.00981903076171875,
0.96044921875,
0.0005450248718261719
] |
Currently, there is no effective treatment for the vast majority of IRDs, although this field has led to breakthroughs in developing therapeutic modalities for inherited diseases. Over the last two decades, gene augmentation therapy has been proved efficient in numerous animal models for IRDs and the first-in-man gene augmentation therapy was approved by the Food and Drug Administration (FDA) in 2017 for biallelic RPE65 pathogenic variants . The success of this treatment led to the development of other therapeutic modalities for IRDs, such as CRISPR and antisense oligonucleotide treatment .
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276581_p3
|
PMC11276581
|
sec[0]/p[3]
|
1. Introduction
| 4.210938 |
biomedical
|
Review
|
[
0.99267578125,
0.0033512115478515625,
0.003925323486328125
] |
[
0.00850677490234375,
0.0185089111328125,
0.97216796875,
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The advent of substantial sequencing breakthroughs over the past few decades as well as improved bioinformatics and functional analyses has heralded a remarkable advancement in mutation detection methods as well as mutation characterization . These include next-generation sequencing (NGS), whole exome sequencing (WES), whole genome sequencing (WGS), functional genomic techniques (such as CRISPR-Cas9 gene editing, RNA sequencing, and functional assays), bioinformatics analysis, single-cell genomics, epigenomic profiling techniques (including ChIP-seq and DNA methylation profiling), and multi-omics integration. Each of these modern methodologies offers unique advantages in elucidating the genetic underpinnings of various diseases.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999999 |
PMC11276581_p4
|
PMC11276581
|
sec[0]/p[4]
|
1. Introduction
| 3.568359 |
biomedical
|
Other
|
[
0.9951171875,
0.00331878662109375,
0.0016918182373046875
] |
[
0.006542205810546875,
0.8662109375,
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0.002544403076171875
] |
From providing a comprehensive view of disease mechanisms to facilitating the identification of novel mutations and understanding complex diseases with heterogeneous genetic backgrounds, these techniques are often employed synergistically to enhance diagnostics, tailor personalized treatments, and refine disease management strategies.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276581_p5
|
PMC11276581
|
sec[0]/p[5]
|
1. Introduction
| 3.818359 |
biomedical
|
Review
|
[
0.9990234375,
0.0003833770751953125,
0.0007123947143554688
] |
[
0.35400390625,
0.129638671875,
0.515625,
0.0006833076477050781
] |
However, the selection of an appropriate method is fraught with challenges due to several inherent limitations. These include cost considerations, the complexity of data analysis, the potential for false positives and false negatives, limitations in functional validation, incomplete genomic coverage, ethnic diversity, ethical and privacy concerns surrounding genomic data, and the intricacies of clinical utility and interpretation.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276581_p6
|
PMC11276581
|
sec[0]/p[6]
|
1. Introduction
| 2.753906 |
biomedical
|
Other
|
[
0.99560546875,
0.0011053085327148438,
0.0033664703369140625
] |
[
0.054779052734375,
0.94091796875,
0.003208160400390625,
0.0009083747863769531
] |
In light of these challenges, we endeavor to navigate the landscape of available methodologies, striving to identify the most suitable approach that aligns with our goal of providing comprehensive genetic insights to many patients. Our aim is to unveil all pertinent mutations contributing to the heterogeneity of IRDs.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276581_p7
|
PMC11276581
|
sec[0]/p[7]
|
1. Introduction
| 3.560547 |
biomedical
|
Study
|
[
0.9990234375,
0.0004279613494873047,
0.0003459453582763672
] |
[
0.99853515625,
0.0008854866027832031,
0.0002321004867553711,
0.00013697147369384766
] |
Here, we used a single gene panel to screen the DNA of 252 unsolved cases with IRDs. The analysis revealed the identification of the cause of disease in 55% of cases, with variability in detection rates between sub-groups.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276581_p8
|
PMC11276581
|
sec[1]/sec[0]/p[0]
|
2.1. Patient Recruitment and Clinical Analyses
| 4.0625 |
biomedical
|
Study
|
[
0.99951171875,
0.0005102157592773438,
0.0002155303955078125
] |
[
0.99951171875,
0.0002880096435546875,
0.00017702579498291016,
0.00007873773574829102
] |
Our cohort of patients with IRD at the Hadassah Medical Center includes over 2300 Israeli and Palestinian families that were recruited in the last 25 years. For the current study, participating patients were recruited between 2006 and 2022, some of whom were genetically evaluated prior to the current study using various techniques as detailed below and in Table S1 . Blood and/or saliva samples were collected from 252 patients with IRDs, representing diverse ethnic backgrounds, genders, ages, and retinal conditions ( Table S1 ). This sub-cohort included newly recruited patients that did not undergo previous genetic analysis ( n = 98) and those who remained unsolved following previous screening tests ( n = 154). From the newly recruited group, saliva samples or DNA that was extracted from blood (see below) were shipped to Blueprint Genetics, and from the previously screened group, DNA that was extracted from blood was shipped.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276581_p9
|
PMC11276581
|
sec[1]/sec[0]/p[1]
|
2.1. Patient Recruitment and Clinical Analyses
| 1.332031 |
biomedical
|
Other
|
[
0.947265625,
0.00502777099609375,
0.047943115234375
] |
[
0.0628662109375,
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0.0009489059448242188,
0.0014781951904296875
] |
The sample collection process adhered to ethical standards, receiving explicit approval from the Hadassah Hospital Institutional Review Board. Informed consent, obtained in writing, ensured compliance with all relevant ethical regulations and safeguarded the rights and privacy of participants.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999995 |
PMC11276581_p10
|
PMC11276581
|
sec[1]/sec[0]/p[2]
|
2.1. Patient Recruitment and Clinical Analyses
| 3.992188 |
biomedical
|
Study
|
[
0.99951171875,
0.0002987384796142578,
0.000232696533203125
] |
[
0.99951171875,
0.00024008750915527344,
0.00021147727966308594,
0.00006091594696044922
] |
The following parameters were calculated in this study: diagnostic success rates (% of solved cases), modes of inheritance (% of each inheritance pattern following gene identification), the presence of structural variants (SVs; % of SV alleles out of the total number of mutated alleles), and the distribution of affected genes (% of cases solved by a specific gene out of all solved cases).
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276581_p11
|
PMC11276581
|
sec[1]/sec[0]/p[3]
|
2.1. Patient Recruitment and Clinical Analyses
| 4.039063 |
biomedical
|
Study
|
[
0.9931640625,
0.006549835205078125,
0.00014781951904296875
] |
[
0.9814453125,
0.01293182373046875,
0.002254486083984375,
0.00360870361328125
] |
A few cases, representing either rare conditions or elusive sequence variants, were selected for detailed clinical description. Ophthalmic evaluation included a full ophthalmological examination, Goldmann perimetry (using Humphrey or Octopus systems), full-field electroretinography (FFERG) according to the ISCEV standard (using LKC or Diagnosys systems), color vision testing using the Ishihara 38-panel and Farnsworth–Munsell D-15 tests, and color, autofluorescence and OCT imaging using Optos, (Marlborough, MA, USA), TOPCON (Capelle aan den Ijssel, The Netherlands), Eidon (Vantaa, Finland), and Heidelberg Spectralis systems (Franklin, MA, USA).
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276581_p12
|
PMC11276581
|
sec[1]/sec[1]/p[0]
|
2.2. DNA Extraction
| 4.039063 |
biomedical
|
Study
|
[
0.99951171875,
0.0001888275146484375,
0.00015437602996826172
] |
[
0.99560546875,
0.003681182861328125,
0.0004858970642089844,
0.00013387203216552734
] |
Genomic DNA was extracted from blood samples using the Promega kit and a Promega Maxwell DNA extraction device (Promega, Madison, WI, USA). For DNA extraction from saliva, buccal swab samples were collected from patients using the OracolectDNA OCR-100 Saliva Kit (DNA Genotek, Ottawa, ON, Canada). DNA concentration was examined using a Nanodrop microvolume spectrophotometer (ThermoFisher; Waltham, MA, USA) and 1% agarose gel staining.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276581_p13
|
PMC11276581
|
sec[1]/sec[2]/p[0]
|
2.3. Next-Generation Sequencing (NGS)
| 4.238281 |
biomedical
|
Study
|
[
0.99951171875,
0.0004239082336425781,
0.0001436471939086914
] |
[
0.9990234375,
0.0003504753112792969,
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0.00014030933380126953
] |
The retinal dystrophy panel , including 351 IRD genes ( Table S2 ), was used to analyze the DNA of 252 IRD cases. Clinical-grade NGS on the Illumina NovaSeq system was employed using the NovaSeq 6000 kit, allowing comprehensive coverage across various genomic IRD genes covering 99.86% of the target region, with a minimal depth of >20×. Raw sequencing data were transformed into FASTQ format using Illumina’s software bcl2fastq v.2.20 and mapped to the human reference genome (GRCh37/hg19). Burrows-Wheeler Aligner (BWA-MEM v1.1.5) software was used for read alignment. Duplicate read marking, local realignment around indels, base quality score recalibration and variant calling were performed using the GATK algorithm. Variant data were annotated using a collection of tools (VcfAnno and VEP) with a variety of public variant databases including gnomAD, ClinVar and HGMD. The analysis included the detection of single-nucleotide variations (SNVs), SVs (defined as a single exon or larger deletions or duplications), insertions, deletions, and indels. Median sequencing depth was 80× at the nucleotide level, ensuring unparalleled sensitivity and accuracy in variant detection. Each interpretation obtained by the Blueprint pipeline was re-evaluated using population-specific information using prior available information on allele frequency in the Israeli and Palestinian IRD cohorts.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276581_p14
|
PMC11276581
|
sec[1]/sec[2]/p[1]
|
2.3. Next-Generation Sequencing (NGS)
| 4.164063 |
biomedical
|
Study
|
[
0.99951171875,
0.0002779960632324219,
0.00015592575073242188
] |
[
0.9990234375,
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0.0005021095275878906,
0.00008845329284667969
] |
The detection performance of the panel yielded high results. The following sensitivity values were obtained: for nuclear DNA: 99.89%, for SNVs detection—99.2% for indels of 1–50 bps, 100% for a single exon deletion, and 98.7%, for 5 exons SVs, with high specificity value of >99.9% for most variant types; for mtDNA: 100.0%, 94.7%, and 87.3% for SVs and indels (10–100% heteroplasmy level, 5–10% heteroplasmy level, and <5% heteroplasmy level; respectively), and 100.0% for gross deletions, with specificity of >99.9% for all.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999998 |
PMC11276581_p15
|
PMC11276581
|
sec[2]/sec[0]/p[0]
|
3.1. Patient Demographics
| 3.951172 |
biomedical
|
Study
|
[
0.9990234375,
0.0004925727844238281,
0.0004229545593261719
] |
[
0.99951171875,
0.000255584716796875,
0.00012123584747314453,
0.00006085634231567383
] |
A total of 252 index cases, selected from a cohort of over 2300 families, were enrolled in this study. Of these, 230 DNA samples were extracted from blood, with 98 having undergone testing with a negative output. Additionally, 22 fresh saliva samples from newly recruited patients were shipped for analysis. Our cohort exhibited ethnic diversity, with 66% Jews (including 26% Ashkenazi Jews and 12% North African Jews), 31% Arab Muslims (including 3% Bedouins), and other ethnicities with less than 1% each. Gender and age distribution show uniform recruitment from an early age through the age of 80 years, including both males and females at relatively similar ratios, with a higher percentage of females (54% vs. 46% for males).
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276581_p16
|
PMC11276581
|
sec[2]/sec[1]/p[0]
|
3.2. Efficiency of the Gene Panel
| 4.140625 |
biomedical
|
Study
|
[
0.99951171875,
0.0004100799560546875,
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] |
[
0.99951171875,
0.00021517276763916016,
0.0003514289855957031,
0.00008445978164672852
] |
The genetic cause of disease (pathogenic or likely pathogenic mutation/s) was identified in 138 out of the 252 analyzed samples, with a yield rate of 55% . Consequently, 114 cases remained unsolved . Further analysis revealed varying rates of gene identification between two distinct groups: newly recruited samples exhibited a 74% success rate, while previously analyzed samples with negative results (the analysis included genotyping of founder mutations, IRD gene panels, and WES) showed a 24% success rate . Out of the 138 solved cases, 50 (36%) carry a heterozygous AR mutation in another IRD gene, and out of the 114 unsolved cases, 52 (46%) are carriers.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999995 |
PMC11276581_p17
|
PMC11276581
|
sec[2]/sec[1]/p[1]
|
3.2. Efficiency of the Gene Panel
| 4.261719 |
biomedical
|
Study
|
[
0.9990234375,
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] |
[
0.9990234375,
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0.00023674964904785156
] |
In 11 cases ( Table S3 ), variant interpretation by the Blueprint pipeline was revised, mainly due to data that were not available in the literature. This includes five cases in which the initial interpretation concluded that these cases were solved but additional information contradicted it and six cases in which the revised analysis concluded that the variant was pathogenic. For example, case MOL1839-1 carried three heterozygous variants in the AR gene ABCA4 , two were interpreted as likely pathogenic and one as a variant of unknown significance (VUS). However, the patient phenotype (congenital stationary night blindness—CSNB) did not fit this causative gene and the variants did not cosegregate with the phenotype in the family, leading to the conclusion that the ABCA4 was not the cause of disease in this case. On the other hand, case MOL1970-1 of Ashkenazi Jewish origin was diagnosed with RP and a VUS in the CFAP410 gene was identified. In gnomAD, this variant was found mainly in Ashkenazi Jewish cases, none of them were homozygous, with an MAF of 0.51%. However, in our cohort, patients from three different families who shared the same phenotype were homozygous for this variant, and therefore, we concluded that it was likely to be a photogenic variant.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999999 |
PMC11276581_p18
|
PMC11276581
|
sec[2]/sec[2]/p[0]
|
3.3. Charecarization of Solved Cases by Inheritance Pattern, Gene, and Phenotype
| 4.128906 |
biomedical
|
Study
|
[
0.99951171875,
0.00036263465881347656,
0.0001596212387084961
] |
[
0.9990234375,
0.0004227161407470703,
0.0006685256958007812,
0.0001251697540283203
] |
The majority of solved cases were attributed to an autosomal recessive (AR) inheritance pattern (75%), followed by X-linked (10%), autosomal dominant (AD) (8%), and mitochondrial (7%) . The most frequently implicated genes were ABCA4 accounting for 8%, EYS with 7%, and USH2A with 6% . Five phenotypes (with at least five cases each) showed a relatively high proportion of solved cases , with more than 50% solved. No difference was evident between the mean age of solved and unsolved cases .
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276581_p19
|
PMC11276581
|
sec[2]/sec[3]/p[0]
|
3.4. Frequency of the Most Common Mutations
| 4.1875 |
biomedical
|
Study
|
[
0.99951171875,
0.0002830028533935547,
0.00015687942504882812
] |
[
0.9990234375,
0.0004379749298095703,
0.000362396240234375,
0.00011295080184936523
] |
Missense mutations constituted the most common variant type (38%), followed by frameshift (17%), nonsense (16%), structural variants (SVs) (12%), splice-site (10%), intronic (4%), and in-frame mutations (3%) . Notably, the most recurrent mutations identified were c.1297_1298ins353 in MAK and c.1355_1356del in FAM161A .
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999998 |
PMC11276581_p20
|
PMC11276581
|
sec[2]/sec[4]/p[0]
|
3.5. Case Details of Rare Phenotypes and Elusive Mutations
| 2.191406 |
biomedical
|
Study
|
[
0.99658203125,
0.0015583038330078125,
0.0016460418701171875
] |
[
0.88720703125,
0.1072998046875,
0.002857208251953125,
0.0025272369384765625
] |
We selected a few cases aiming to present the variability of the studied cohort, rare cases with regard to both phenotype and genotype, and elusive mutations that might be missed without the proper knowledge.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999996 |
PMC11276581_p21
|
PMC11276581
|
sec[2]/sec[4]/sec[0]/p[0]
|
3.5.1. KIF11 and Non-Syndromic Chorioretinopathy
| 4.007813 |
biomedical
|
Study
|
[
0.99951171875,
0.00026726722717285156,
0.00024580955505371094
] |
[
0.99755859375,
0.00203704833984375,
0.00028061866760253906,
0.00025200843811035156
] |
The KIF11 gene encodes a homo-tetrameric motor protein crucial for spindle polarity during mitosis. Variants in this ubiquitously expressed protein are typically de novo and associated with various developmental syndromes, including impacts on retinal vasculature development. Considered rare, only one family in Israel is documented with a KIF11 mutation . Surprisingly, among the 142 cases solved in our study, KIF11 emerged as the causal gene in two unrelated Ashkenazi Jewish patients.
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999998 |
PMC11276581_p22
|
PMC11276581
|
sec[2]/sec[4]/sec[0]/p[1]
|
3.5.1. KIF11 and Non-Syndromic Chorioretinopathy
| 4 |
clinical
|
Clinical case
|
[
0.446533203125,
0.55078125,
0.0028781890869140625
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[
0.0211029052734375,
0.0087738037109375,
0.003246307373046875,
0.966796875
] |
Case MOL1984-1 was diagnosed at the age of 10 years with reduced visual acuity, mild myopia (−3 D), and photophobia. His best corrected visual acuity (BCVA) at the age of 16 was 0.6/0.5 in the right and left eye, respectively, and OCT showed a retinoschisis pattern. He has no family history of visual deficiencies. An ERG test at the age of 18 years revealed sub-normal responses, including cone flicker, mixed cone-rod b-wave, and rod responses. Color vision was within the normal range. An ophthalmic evaluation at the age of 19 years revealed atrophic chorioretinal patches next to the optic disk and the inferior arcade. Following a clinical evaluation at the age of 19, no other clinical features were identified in this case, as reported in a few other KIF11 cases . The patient was therefore diagnosed with non-syndromic chorioretinopathy. Interestingly, gene panel analysis revealed a heterozygous frameshift mutation in KIF11 ( Table S1 ).
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999997 |
PMC11276581_p23
|
PMC11276581
|
sec[2]/sec[4]/sec[0]/p[2]
|
3.5.1. KIF11 and Non-Syndromic Chorioretinopathy
| 4.011719 |
biomedical
|
Clinical case
|
[
0.6435546875,
0.354248046875,
0.0022945404052734375
] |
[
0.038330078125,
0.01291656494140625,
0.00360107421875,
0.9453125
] |
Case MOL2101-1 was diagnosed with a congenital retinal disease, including chorioretinal scars and retinoschisis. Visual acuity deteriorated and at the age of 11 reached 0.4 in the right eye and hand motion in the left eye with mild myopia (−3.5 diopters). Multiple electroretinography (ERG) examinations revealed non-progressive sub-normal ERG responses, including cone flicker, mixed cone-rod a and b-wave and rod responses. Following multiple clinical evaluations between ages 1 and 19 years, no other clinical features were identified in this case. The patient was therefore diagnosed with non-syndromic chorioretinopathy. Interestingly, gene panel analysis revealed a heterozygous de novo nonsense mutation in KIF11 ( Table S1 ).
|
[
"Maria Abu Elasal",
"Samira Mousa",
"Manar Salameh",
"Anat Blumenfeld",
"Samer Khateb",
"Eyal Banin",
"Dror Sharon"
] |
https://doi.org/10.3390/genes15070926
|
N/A
|
https://creativecommons.org/licenses/by/4.0/
|
en
| 0.999995 |
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