1.LocPro: A deep learning-based prediction of protein subcellular localization for promoting multi-directional pharmaceutical research.
Yintao ZHANG ; Lingyan ZHENG ; Nanxin YOU ; Wei HU ; Wanghao JIANG ; Mingkun LU ; Hangwei XU ; Haibin DAI ; Tingting FU ; Ying ZHOU
Journal of Pharmaceutical Analysis 2025;15(8):101255-101255
Drug development encompasses multiple processes, wherein protein subcellular localization is essential. It promotes target identification, treatment development, and the design of drug delivery systems. In this research, a deep learning framework called LocPro is presented for predicting protein subcellular localization. Specifically, LocPro is unique in (a) combining protein representations from the pre-trained large language model (LLM) ESM2 and the expert-driven tool PROFEAT, (b) implementing a hybrid deep neural network architecture that integrates convolutional neural network (CNN), fully connected (FC) layer, and bidirectional long short-term memory (BiLSTM) blocks, and (c) developing a multi-label framework for predicting protein subcellular localization at multiple granularity levels. Additionally, a dataset was curated and divided using a homology-based strategy for training and validation. Comparative analyses show that LocPro outperforms existing methods in sequence-based multi-label protein subcellular localization prediction. The practical utility of this framework is further demonstrated through case studies on drug target subcellular localization. All in all, LocPro serves as a valuable complement to existing protein localization prediction tools. The web server is freely accessible at https://idrblab.org/LocPro/.
2.Effects of evodiamine on inflammation and apoptosis of airway epithelial cells in asthma model rats and its mechanism
Jun LEI ; Lijun LU ; Lingyan LUO ; Song QIAO ; Yanan TONG ; Yang ZHENG ; Lei YAO
China Pharmacy 2024;35(11):1351-1356
OBJECTIVE To explore the effects and potential mechanism of evodiamine on inflammatory response and apoptosis of epithelial cells in asthma model rats. METHODS SD rats were separated into control group, model group, evodiamine low-dose group (10 mg/kg), evodiamine high-dose group (20 mg/kg), dexamethasone group (positive control, 0.5 mg/kg), epidermal growth factor (EGF) group [mitogen-activated protein kinase (MAPK) activator, 10 μg], evodiamine high-dose+EGF group (20 mg/kg evodiamine+10 μg EGF), with 10 rats in each group. Except for the control group, the other groups were sensitized by 3-point injection of 10% ovalbumin(OVA)-aluminium hydroxide mixture and stimulated by inhalation of 2%OVA nebulized liquid to establish an asthma model. The count of inflammatory cells (macrophages and lymphocytes) in bronchoalveolar lavage fluid (BALF) was detected in each group; pathological changes of lung tissue in rats were observed; the apoptosis of airway epithelial cells, the levels of serum inflammatory factors [tumor necrosis factor-α, interleukin-6 (IL-6) and IL-4], the expressions of pathway-related proteins p38 MAPK, phosphorylated p38 MAPK (p-p38 MAPK), signal transduction and transcription activating factor 1 (STAT1)] and apoptosis-related proteins [B cell lymphoma-2 (Bcl-2) and Bcl-2 associated X protein (Bax)] were all detected in lung tissue. RESULTS Compared with the control group, bronchial mucosal edema, thickening of alveolar septa and extensive infiltration of inflammatory cells were observed in the lung tissue of rats in the model group; the number of inflammatory cells, apoptosis rate of airway epithelial cells, the levels of inflammatory factors, p-38 MAPK/p-38 MAPK, and the protein expressions of Bax and STAT1 were increased significantly; the expressions of Bcl-2 protein and Bcl-2/Bax were reduced significantly (P<0.05). Compared with the model group, the pathological changes in lung tissues were alleviated to varying degrees in evodiamine low-dose and high-dose groups, and dexamethasone groups, and the above indicators were significantly reversed. However, the change trends of corresponding indicators in the EGF group were opposite to the above (P<0.05). EGF could significantly attenuate the effect of high-dose evodiamine on inflammatory response in asthmatic rats (P<0.05). CONCLUSIONS Evodiamine can relieve inflammatory reactions and inhibit the apoptosis of airway epithelial cells in asthmatic rats, the mechanism of which may be associated with inhibiting p38 MAPK/STAT1 signaling pathway.
3.Effects of evodiamine on inflammation and apoptosis of airway epithelial cells in asthma model rats and its mechanism
Jun LEI ; Lijun LU ; Lingyan LUO ; Song QIAO ; Yanan TONG ; Yang ZHENG ; Lei YAO
China Pharmacy 2024;35(11):1351-1356
OBJECTIVE To explore the effects and potential mechanism of evodiamine on inflammatory response and apoptosis of epithelial cells in asthma model rats. METHODS SD rats were separated into control group, model group, evodiamine low-dose group (10 mg/kg), evodiamine high-dose group (20 mg/kg), dexamethasone group (positive control, 0.5 mg/kg), epidermal growth factor (EGF) group [mitogen-activated protein kinase (MAPK) activator, 10 μg], evodiamine high-dose+EGF group (20 mg/kg evodiamine+10 μg EGF), with 10 rats in each group. Except for the control group, the other groups were sensitized by 3-point injection of 10% ovalbumin(OVA)-aluminium hydroxide mixture and stimulated by inhalation of 2%OVA nebulized liquid to establish an asthma model. The count of inflammatory cells (macrophages and lymphocytes) in bronchoalveolar lavage fluid (BALF) was detected in each group; pathological changes of lung tissue in rats were observed; the apoptosis of airway epithelial cells, the levels of serum inflammatory factors [tumor necrosis factor-α, interleukin-6 (IL-6) and IL-4], the expressions of pathway-related proteins p38 MAPK, phosphorylated p38 MAPK (p-p38 MAPK), signal transduction and transcription activating factor 1 (STAT1)] and apoptosis-related proteins [B cell lymphoma-2 (Bcl-2) and Bcl-2 associated X protein (Bax)] were all detected in lung tissue. RESULTS Compared with the control group, bronchial mucosal edema, thickening of alveolar septa and extensive infiltration of inflammatory cells were observed in the lung tissue of rats in the model group; the number of inflammatory cells, apoptosis rate of airway epithelial cells, the levels of inflammatory factors, p-38 MAPK/p-38 MAPK, and the protein expressions of Bax and STAT1 were increased significantly; the expressions of Bcl-2 protein and Bcl-2/Bax were reduced significantly (P<0.05). Compared with the model group, the pathological changes in lung tissues were alleviated to varying degrees in evodiamine low-dose and high-dose groups, and dexamethasone groups, and the above indicators were significantly reversed. However, the change trends of corresponding indicators in the EGF group were opposite to the above (P<0.05). EGF could significantly attenuate the effect of high-dose evodiamine on inflammatory response in asthmatic rats (P<0.05). CONCLUSIONS Evodiamine can relieve inflammatory reactions and inhibit the apoptosis of airway epithelial cells in asthmatic rats, the mechanism of which may be associated with inhibiting p38 MAPK/STAT1 signaling pathway.
4.Clinical features of critically ill pregnant and parturient women infected with chronic hepatitis B virus: An analysis of 41 cases
Yuhao JU ; Wen LI ; Yu WANG ; Lingyan XIAO ; Yishan ZHENG ; Guorong HAN
Journal of Clinical Hepatology 2024;40(2):258-263
ObjectiveTo investigate the clinical features and outcomes of critically ill pregnant and parturient women with chronic hepatitis B virus (HBV) infection, and to provide clinical experience for the rescue of critically ill pregnant and parturient women and the prevention and treatment of the severe exacerbation of liver disease. MethodsA total of 41 pregnant and parturient women with chronic HBV infection who were admitted to Department of Critical Care Medicine, Nanjing Second Hospital, from March 2013 to March 2023 were enrolled in this study, and their clinical data were collected through the electronic medical record system of hospital to summarize the main causes of transfer to the intensive care unit (ICU), the causes of death, and treatment. The independent-samples t test was used for comparison of normally distributed continuous data between two groups, and the Mann-Whitney U test was used for comparison of non-normally distributed continuous data between two groups. The chi-square test was used for comparison of categorical data between two groups. ResultsAmong the 41 patients, 13 (31.71%) did not receive regular antenatal examination and 8 (19.51%) with a high viral load (HBV DNA ≥2×105 IU/mL) did not receive antiviral therapy. Cesarean section was the main mode of delivery in 32 patients (78.05%); 23 patients (56.10%) had premature delivery, and 5 patients died (12.20%). The top three causes of transfer to the ICU were liver failure, postpartum hemorrhage, and hypertensive disorders of pregnancy. Liver failure mainly occurred in late pregnancy, with hepatic encephalopathy as the most common complication (28.57%) and intrahepatic cholestasis of pregnancy as the most common comorbidity (21.43%); among the 14 patients with liver failure, 6 (42.86%) received regular antenatal examination, and 13 (92.86%) did not receive antiviral therapy before admission. The mean length of ICU stay was 3.31±1.65 days for the patients with postpartum hemorrhage, among whom the patients with severe liver disease had coagulation disorders before delivery, which were difficult to correct after 48 hours of treatment. ConclusionPregnant and parturient women with chronic HBV infection tend to have complex conditions and a relatively high mortality rate. For pregnant and parturient women with chronic HBV infection, assessment of liver status, regular antenatal examination, and timely antiviral therapy are of vital importance to reduce severe exacerbation and mortality rate.
5.QL1604 plus paclitaxel-cisplatin/ carboplatin in patients with recurrent or metastatic cervical cancer:an open-label, single-arm, phase II trial
Cheng FANG ; Yun ZHOU ; Yanling FENG ; Liping HE ; Jinjin YU ; Yuzhi LI ; Mei FENG ; Mei PAN ; Lina ZHAO ; Dihong TANG ; Xiumin LI ; Buzhen TAN ; Ruifang AN ; Xiaohui ZHENG ; Meimei SI ; Baihui ZHANG ; Lingyan LI ; Xiaoyan KANG ; Qi ZHOU ; Jihong LIU
Journal of Gynecologic Oncology 2024;35(6):e77-
Objective:
QL1604 is a highly selective, humanized monoclonal antibody against programmed death protein 1. We assessed the efficacy and safety of QL1604 plus chemotherapy as first-line treatment in patients with advanced cervical cancer.
Methods:
This was a multicenter, open-label, single-arm, phase II study. Patients with advanced cervical cancer and not previously treated with systemic chemotherapy were enrolled to receive QL1604 plus paclitaxel and cisplatin/carboplatin on day 1 of each 21-day cycle for up to 6 cycles, followed by QL1604 maintenance treatment.
Results:
Forty-six patients were enrolled and the median follow-up duration was 16.5 months. An 84.8% of patients had recurrent disease and 13.0% had stage IVB disease. The objective response rate (ORR) per Response Evaluation Criteria in Advanced Solid Tumors (RECIST) v1.1 was 58.7% (27/46). The immune ORR per immune RECIST was 60.9% (28/46).The median duration of response was 9.6 months (95% confidence interval [CI]=5.5–not estimable). The median progression-free survival was 8.1 months (95% CI=5.7–14.0). Fortyfive (97.8%) patients experienced treatment-related adverse events (TRAEs). The most common grade≥3 TRAEs (>30%) were neutrophil count decrease (50.0%), anemia (32.6%), and white blood cell count decrease (30.4%).
Conclusion
QL1604 plus paclitaxel-cisplatin/carboplatin showed promising antitumor activity and manageable safety profile as first-line treatment in patients with advanced cervical cancer. Programmed cell death protein 1 inhibitor plus chemotherapy may be a potential treatment option for the patient population who have contraindications or can’t tolerate bevacizumab, which needs to be further verified in phase III confirmatory study.
6.QL1604 plus paclitaxel-cisplatin/ carboplatin in patients with recurrent or metastatic cervical cancer:an open-label, single-arm, phase II trial
Cheng FANG ; Yun ZHOU ; Yanling FENG ; Liping HE ; Jinjin YU ; Yuzhi LI ; Mei FENG ; Mei PAN ; Lina ZHAO ; Dihong TANG ; Xiumin LI ; Buzhen TAN ; Ruifang AN ; Xiaohui ZHENG ; Meimei SI ; Baihui ZHANG ; Lingyan LI ; Xiaoyan KANG ; Qi ZHOU ; Jihong LIU
Journal of Gynecologic Oncology 2024;35(6):e77-
Objective:
QL1604 is a highly selective, humanized monoclonal antibody against programmed death protein 1. We assessed the efficacy and safety of QL1604 plus chemotherapy as first-line treatment in patients with advanced cervical cancer.
Methods:
This was a multicenter, open-label, single-arm, phase II study. Patients with advanced cervical cancer and not previously treated with systemic chemotherapy were enrolled to receive QL1604 plus paclitaxel and cisplatin/carboplatin on day 1 of each 21-day cycle for up to 6 cycles, followed by QL1604 maintenance treatment.
Results:
Forty-six patients were enrolled and the median follow-up duration was 16.5 months. An 84.8% of patients had recurrent disease and 13.0% had stage IVB disease. The objective response rate (ORR) per Response Evaluation Criteria in Advanced Solid Tumors (RECIST) v1.1 was 58.7% (27/46). The immune ORR per immune RECIST was 60.9% (28/46).The median duration of response was 9.6 months (95% confidence interval [CI]=5.5–not estimable). The median progression-free survival was 8.1 months (95% CI=5.7–14.0). Fortyfive (97.8%) patients experienced treatment-related adverse events (TRAEs). The most common grade≥3 TRAEs (>30%) were neutrophil count decrease (50.0%), anemia (32.6%), and white blood cell count decrease (30.4%).
Conclusion
QL1604 plus paclitaxel-cisplatin/carboplatin showed promising antitumor activity and manageable safety profile as first-line treatment in patients with advanced cervical cancer. Programmed cell death protein 1 inhibitor plus chemotherapy may be a potential treatment option for the patient population who have contraindications or can’t tolerate bevacizumab, which needs to be further verified in phase III confirmatory study.
7.QL1604 plus paclitaxel-cisplatin/ carboplatin in patients with recurrent or metastatic cervical cancer:an open-label, single-arm, phase II trial
Cheng FANG ; Yun ZHOU ; Yanling FENG ; Liping HE ; Jinjin YU ; Yuzhi LI ; Mei FENG ; Mei PAN ; Lina ZHAO ; Dihong TANG ; Xiumin LI ; Buzhen TAN ; Ruifang AN ; Xiaohui ZHENG ; Meimei SI ; Baihui ZHANG ; Lingyan LI ; Xiaoyan KANG ; Qi ZHOU ; Jihong LIU
Journal of Gynecologic Oncology 2024;35(6):e77-
Objective:
QL1604 is a highly selective, humanized monoclonal antibody against programmed death protein 1. We assessed the efficacy and safety of QL1604 plus chemotherapy as first-line treatment in patients with advanced cervical cancer.
Methods:
This was a multicenter, open-label, single-arm, phase II study. Patients with advanced cervical cancer and not previously treated with systemic chemotherapy were enrolled to receive QL1604 plus paclitaxel and cisplatin/carboplatin on day 1 of each 21-day cycle for up to 6 cycles, followed by QL1604 maintenance treatment.
Results:
Forty-six patients were enrolled and the median follow-up duration was 16.5 months. An 84.8% of patients had recurrent disease and 13.0% had stage IVB disease. The objective response rate (ORR) per Response Evaluation Criteria in Advanced Solid Tumors (RECIST) v1.1 was 58.7% (27/46). The immune ORR per immune RECIST was 60.9% (28/46).The median duration of response was 9.6 months (95% confidence interval [CI]=5.5–not estimable). The median progression-free survival was 8.1 months (95% CI=5.7–14.0). Fortyfive (97.8%) patients experienced treatment-related adverse events (TRAEs). The most common grade≥3 TRAEs (>30%) were neutrophil count decrease (50.0%), anemia (32.6%), and white blood cell count decrease (30.4%).
Conclusion
QL1604 plus paclitaxel-cisplatin/carboplatin showed promising antitumor activity and manageable safety profile as first-line treatment in patients with advanced cervical cancer. Programmed cell death protein 1 inhibitor plus chemotherapy may be a potential treatment option for the patient population who have contraindications or can’t tolerate bevacizumab, which needs to be further verified in phase III confirmatory study.
8.Management of helicopter medical transport in 36 patients with critical cardiac disease
Gaigai ZHENG ; Qiaofang YANG ; Man YU ; Lingyan MA ; Na WU ; Huan TIAN ; Yue YIN
Chinese Critical Care Medicine 2023;35(2):201-205
Objective:To summarize the management experience of helicopter medical transport in patients with critical heart disease, so as to provide reference for transport of patients with critical heart disease under the background of major natural disasters.Methods:The clinical and transport data of 36 critically ill cardiac patients in Fuwai Central China Cardiovascular Hospital from 16:30 on July 21 to 19:30 on July 22, 2021 due to historically rare heavy rainstorms were collected. All 36 critically ill cardiac patients were transported by helicopter. The safe transportation was implemented under the measures of quickly forming a transport leadership and coordination group, clarifying responsibilities and division of labor, doing a good job in the pretreatment of the patient's condition, pipeline assessment and mechanical circulation support (MCS) equipment, simulating and practicing the transfer process, improving the safety of the transfer implementation process, and effectively handing over with the target hospital. The gender, age, disease type, MCS, transport and outcome of patients were collected.Results:Thirty-six patients with cardiac critical illness were from adult extracardiac intensive care unit (ICU), adult cardiac care unit (CCU), children's CCU, comprehensive ICU and department of neurology. There were 24 males and 12 females; age (50.93±20.86) years old. There were 12 patients using respirator, 7 patients needing MCS, 2 of whom needed both extracorporeal membrane oxygenation (ECMO) and intra-aortic balloon pump (IABP), and 7 patients with post-cardiac surgery. The total distance of transportation of 36 patients was 1 638.4 km, the transit time was 10.5 hours, one way flight time of helicopter was about 8 minutes, and the average transport time per patient was about 17.5 minutes. The vital signs of 36 patients during transport were basically stable, without complications, and all of them reached the target hospital safely.Conclusion:Under the seamless connection of the rapid establishment of the transfer leadership coordination group, assessment of the patient's condition and pretreatment, the simulation of the transfer process, and the effective handover with the receiving hospital, the use of helicopter for medical transport for critically ill heart patients is feasible and safe, which can buy valuable time for saving patients' lives and further treatment.
9.Clinical implications of the concentration of alveolar nitric oxide in non-small cell lung cancer.
Xiaodan CHANG ; Hua LIAO ; Lingyan XIE ; Yuehua CHEN ; Liying ZHENG ; Jianpeng LIANG ; Weiwei YU ; Yuexian WU ; Yanmei YE ; Shuyu HUANG ; Haijin ZHAO ; Shaoxi CAI ; Hangming DONG
Chinese Medical Journal 2023;136(18):2246-2248
10.Clinical features and outcomes of newly diagnosed follicular lymphoma concurrent with diffuse large B-cell lymphoma component
Zhijuan LIN ; Jie ZHA ; Shuhua YI ; Zhifeng LI ; Lingyan PING ; Xiaohua HE ; Haifeng YU ; Zhong ZHENG ; Wei XU ; Feili CHEN ; Ying XIE ; Biyun CHEN ; Huilai ZHANG ; Li WANG ; Kaiyang DING ; Wenyu LI ; Haiyan YANG ; Weili ZHAO ; Lugui QIU ; Zhiming LI ; Yuqin SONG ; Bing XU
Chinese Journal of Hematology 2022;43(6):456-462
Objective:To explore the clinical features and survival of newly diagnosed follicular lymphoma (FL) patients with diffuse large B-cell lymphoma (DLBCL) component.Methods:1845 newly diagnosed FL patients aged ≥ 18 years with grades 1-3a in 11 medical centers in China from 2000 to 2020 were included, and patients with DLBCL component were screened. The clinical data and survival data of the patients were retrospectively analyzed, and the prognostic factors were screened by univariate and multivariate analysis.Results:146 patients (7.9% ) with newly diagnosed FL had DLBCL component. The median age was 56 (25-83) years, 79 males (54.1% ) . The pathology of 127 patients showed the proportion of DLBCL component. Patients were divided into two groups according to whether the proportion of DLBCL component was ≥ 50% . The study found that patients with DLBCL component ≥ 50% had higher grade 3 ratio (94.3% vs 91.9% , P=0.010) , Ki-67 index ≥ 70% ratio (58.5% vs 32.9% , P=0.013) and PET-CT SUVmax ≥ 13 ratio (72.4% vs 46.3% , P=0.030) than patients with DLBCL component<50% . All patients received CHOP or CHOP like ± rituximab chemotherapy. The overall response rate (ORR) was 88.2% , and the complete response (CR) rate was 76.4% . In the groups with different proportions of DLBCL component, there was no significant difference in the remission rate after induction treatment and the incidence of disease progression within 2 years after initiation of treatment (POD24) ( P<0.05) . The overall estimated 5-year progression free survival (PFS) rate was 58.9% , and the 5-year overall survival (OS) rate was 90.4% . The 5-year OS rate of POD24 patients was lower than that of non POD24 patients (70.3% vs 98.5% , P<0.001) . Compared with non maintenance treatment of rituximab, maintenance treatment of rituximab could not benefit the 5-year PFS rate (57.7% vs 58.8% , P=0.543) , and the 5-year OS rate had a benefit trend, but the difference was not statistically significant (100% vs 87.8% , P=0.082) . Multivariate analysis showed that failure to reach CR after induction treatment was an independent risk factor for PFS ( P=0.006) , while LDH higher than normal was an independent risk factor for OS ( P=0.031) . Conclusion:FL patients with DLBCL component ≥50% have more invasive clinical and pathological features. CHOP/CHOP like ± rituximab regimen can improve the clinical efficacy of patients. Rituximab maintenance therapy can not benefit the PFS and OS of patients. Failure to reach CR after induction therapy was the independent unfavorable factor for PFS.

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