1.Adaptive multi-view learning method for enhanced drug repurposing using chemical-induced transcriptional profiles,knowledge graphs,and large language models
Yudong YAN ; Yinqi YANG ; Zhuohao TONG ; Yu WANG ; Fan YANG ; Zupeng PAN ; Chuan LIU ; Mingze BAI ; Yongfang XIE ; Yuefei LI ; Kunxian SHU ; Yinghong LI
Journal of Pharmaceutical Analysis 2025;15(6):1354-1369
Drug repurposing offers a promising alternative to traditional drug development and significantly re-duces costs and timelines by identifying new therapeutic uses for existing drugs.However,the current approaches often rely on limited data sources and simplistic hypotheses,which restrict their ability to capture the multi-faceted nature of biological systems.This study introduces adaptive multi-view learning(AMVL),a novel methodology that integrates chemical-induced transcriptional profiles(CTPs),knowledge graph(KG)embeddings,and large language model(LLM)representations,to enhance drug repurposing predictions.AMVL incorporates an innovative similarity matrix expansion strategy and leverages multi-view learning(MVL),matrix factorization,and ensemble optimization techniques to integrate heterogeneous multi-source data.Comprehensive evaluations on benchmark datasets(Fdata-set,Cdataset,and Ydataset)and the large-scale iDrug dataset demonstrate that AMVL outperforms state-of-the-art(SOTA)methods,achieving superior accuracy in predicting drug-disease associations across multiple metrics.Literature-based validation further confirmed the model's predictive capabilities,with seven out of the top ten predictions corroborated by post-2011 evidence.To promote transparency and reproducibility,all data and codes used in this study were open-sourced,providing resources for pro-cessing CTPs,KG,and LLM-based similarity calculations,along with the complete AMVL algorithm and benchmarking procedures.By unifying diverse data modalities,AMVL offers a robust and scalable so-lution for accelerating drug discovery,fostering advancements in translational medicine and integrating multi-omics data.We aim to inspire further innovations in multi-source data integration and support the development of more precise and efficient strategies for advancing drug discovery and translational medicine.
2.Effect of dysbindin-1 deletion on exosomes derived from mouse testicular tissue
Shu ZHANG ; Pan-Pan ZHANG ; Xin SUN ; Hai-Yan LI ; Hui YAN ; Ya-Qin FENG
Acta Anatomica Sinica 2025;56(5):585-593
Objective To compare the differences in exosomes derived from testicular tissue between WT(wild type)mice and sdy mice with dysbindin-1(dystrobrevin binding protein 1)deletion mutations,and identify their protein components to explore the possible role of dysbindin-1 in the formation of exosomes derived from mouse testicular tissue.Methods The exosomes derived from mouse testicular tissue of WT and sdy mice were isolated by sucrose ultracentrifugation method.The expression of exosomes proteins was analyzed by Western blotting,the morphology of exosomes was observed by negative staining under transmission electron microscope(TEM),the particle size and distribution were analyzed by dynamic light scattering particle size analyzer,and the protein contents of exosomes were detected by mass spectrometry analysis.CD63+exosomes were obtained by immunoprecipitation with magnetic beads.Krt5(keratin5)protein was selected for validation.Results Dysbindin-1 deletion did not affect the morphology and quantity of exosomes,but decreased the expression of CD63,a marker of exosomes.Compared with the WT mice,there were 159 proteins that were highly expressed,209 proteins that were lowly expressed,and 184 proteins that were specifically expressed in the exosomes derived from sdy mice testicular tissue.In this experiment,CD63+exosomes from testicular tissue were obtained and 12 proteins were screened.There was indeed an interaction between krt5 protein and dysbindin-1.Interestingly,it was found that the expression of krt5 in the exosomes derived from sdy mice testicular tissue decreased after dysbindin-1 deletion.Conclusion After dysbindin-1 deletion,the morphology and quantity of exosomes derived from mouse testicular tissue are not affected,but dysbindin-1 may affect the types and content of exosomal proteins,by affecting the transport of exosome proteins through protein interactions.
3.A case report of premature ovarian insufficiency caused by a novel FANCL mutation(c.1033G>A)and in vitro functional validation
Yi-qing LIU ; Shu-ting REN ; Yun-cheng PAN ; Feng ZHANG ; Xiao-jin ZHANG ; Yan-hua WU
Fudan University Journal of Medical Sciences 2025;52(2):270-276,291
Objective To investigate the characteristics of a novel FANCL mutation identified in a patient with premature ovarian insufficiency(POI)and to explore its potential functional impacts in vitro.Methods A novel FANCL heterozygous mutation c.1033G>A(p.Glu345Lys)was screened in a patient with POI using whole exome sequencing(WES),which was found to be inherited from a mother who had undergone early menopause.The authenticity of the mutation was identified by Sanger sequencing and the conserved nature of the mutation site was predicted by software.Overexpressing FANCL mutant and wildtype plasmids were constructed and transiently transfected into HEK293T cell lines,and the effect of the mutation was detected by qPCR,immunofluorescence and Western blot.Results The mutation site of FANCL was located within the Ring domain of FANCL,which was highly conserved across multiple species.The mutant showed no significant change in mRNA expression level,while the protein expression level was significantly down-regulated.In vitro cellular experiments further revealed that the mutation leads to decreased expression levels by reducing protein stability.Conclusion A FANCL c.1033G>A mutation was found and it may cause disease in the POI patient due to decreased protein stability.
4.Clinicopathological features and prognosis of 117 cases of fumarate hydratase-deficient uterine leiomyomas
Wennian YU ; Siyi PAN ; Cong WANG ; Zhendong HUANG ; Xianglian WANG ; Shu ZHU ; Yan DING ; Xiuli WANG
Chinese Journal of Obstetrics and Gynecology 2025;60(6):450-460
Objective:To explore the clinicopathological characteristics and prognosis of fumarate hydratase-deficient uterine leiomyoma (FH-dUL).Methods:Clinical data and follow-up information for 117 patients with FH-dUL diagnosed through surgical pathology and immunohistochemistry in the First Affiliated Hospital of Nanjing Medical University from January 2020 to December 2024, were collected. A control group of 130 patients with common uterine leiomyomas was also included. The differences between the two groups in clinical, imaging, and pathological characteristics were compared. Additionally, recurrence rates, fertility outcomes for FH-dUL patients, and the incidence of renal cancer in FH germline mutation carriers were monitored.Results:(1) Comparison of clinicopathological characteristics: the median age of 117 FH-dUL patients was 35 years, and the median age at first diagnosis of uterine leiomyomas was 29 years, both significantly younger than the control group (41 and 36 years; both P<0.01). The FH-dUL group showed significantly higher incidences of uterine myomectomy, multiple leiomyomas, diffusion restriction on pelvic magnetic resonance imaging diffusion weighted imaging, and typical pathological features (candelabra-like vessels, bizarre nuclei, cytoplasmic eosinophilic globules, perinuclear halo, cellular atypia) and higher ultrasound blood flow score (all P<0.05). Of the 30 FH-dUL patients who underwent genetic testing, 9 had germline mutations, 3 had somatic mutations, and 6 had mutations of unclear origin. Among the 9 FH gene germline mutation patients, 2 had already developed renal cell carcinoma. (2) Recurrence analysis: among the 56 patients who underwent uterine myomectomy, 22 (39.3%, 22/56) experienced recurrence during follow-up, compared to 12 (21.8%, 12/55) of the 55 patients in the control group, the difference between the two groups was statistically significant ( P=0.046). Multivariate binary logistic regression analysis showed that cellular leiomyomas ( OR=9.489, 95% CI: 1.740-51.755; P=0.009) and multiple uterine leiomyomas ( OR=10.709, 95% CI: 1.354-84.683; P=0.025) were significant risk factors for recurrence in FH-dUL. (3) Fertility analysis: among the 66 FH-dUL patients who underwent fertility-preserving surgery, 16 had the intention to have fertility desire, only 2 (2/16) completed their fertility plans during follow-up. Conclusions:Clinicopathological features and imaging features help to differentiate FH-dUL from common type uterine fibroids, but lack specificity, and the diagnosis of FH-dUL is based on immunohistochemistry. The recurrence rate after resection of FH-dUL is high, and cellular and multiple leiomyomas are important predictors of recurrence. It is crucial to perform genetic testing, genetic counseling, drug treatment to prevent recurrence, fertility guidance, and long-term comprehensive management after surgery for FH-dUL management.
5.Adaptive multi-view learning method for enhanced drug repurposing using chemical-induced transcriptional profiles, knowledge graphs, and large language models.
Yudong YAN ; Yinqi YANG ; Zhuohao TONG ; Yu WANG ; Fan YANG ; Zupeng PAN ; Chuan LIU ; Mingze BAI ; Yongfang XIE ; Yuefei LI ; Kunxian SHU ; Yinghong LI
Journal of Pharmaceutical Analysis 2025;15(6):101275-101275
Drug repurposing offers a promising alternative to traditional drug development and significantly reduces costs and timelines by identifying new therapeutic uses for existing drugs. However, the current approaches often rely on limited data sources and simplistic hypotheses, which restrict their ability to capture the multi-faceted nature of biological systems. This study introduces adaptive multi-view learning (AMVL), a novel methodology that integrates chemical-induced transcriptional profiles (CTPs), knowledge graph (KG) embeddings, and large language model (LLM) representations, to enhance drug repurposing predictions. AMVL incorporates an innovative similarity matrix expansion strategy and leverages multi-view learning (MVL), matrix factorization, and ensemble optimization techniques to integrate heterogeneous multi-source data. Comprehensive evaluations on benchmark datasets (Fdataset, Cdataset, and Ydataset) and the large-scale iDrug dataset demonstrate that AMVL outperforms state-of-the-art (SOTA) methods, achieving superior accuracy in predicting drug-disease associations across multiple metrics. Literature-based validation further confirmed the model's predictive capabilities, with seven out of the top ten predictions corroborated by post-2011 evidence. To promote transparency and reproducibility, all data and codes used in this study were open-sourced, providing resources for processing CTPs, KG, and LLM-based similarity calculations, along with the complete AMVL algorithm and benchmarking procedures. By unifying diverse data modalities, AMVL offers a robust and scalable solution for accelerating drug discovery, fostering advancements in translational medicine and integrating multi-omics data. We aim to inspire further innovations in multi-source data integration and support the development of more precise and efficient strategies for advancing drug discovery and translational medicine.
6.Additional role of low-density lipoprotein cholesterol on the risk of osteoporosis in men with or without coronary heart disease: a real-world longitudinal study.
Jing ZENG ; Zi-Mo PAN ; Ting LI ; Ze-Yu CHEN ; Xiao-Yan CAI ; Mei-Liang GONG ; Xin-Li DENG ; Sheng-Shu WANG ; Nan LI ; Miao LIU ; Chun-Lin LI
Journal of Geriatric Cardiology 2025;22(2):219-228
BACKGROUND:
Early control of low-density lipoprotein cholesterol (LDL-C) is crucial for reducing the progress of cardiovascular disease. However, its additional role to the risk of primary osteoporosis in men with coronary heart disease was inconclusive. Our study aims to determine the association of LDL-C and its trajectories for osteoporosis risk in the middle-aged and aged men of China.
METHODS:
The retrospective cohort study of 1546 men aged 69.74 ± 11.30 years conducted in Beijing, China from 2015 to 2022. And the incidence of primary osteoporosis was annually recorded. LDL-C trajectories were further identified by latent class growth model using repeated measurements of LDL-C. The association of baseline LDL-C for osteoporosis was estimated using hazard ratio (HR) with 95% CI in Cox proportional hazard model, while mean level and trajectories of LDL-C for osteoporosis were evaluated using odds ratio (OR) with 95% CI in logistic regression model.
RESULTS:
During the median 6.2-year follow-up period, 70 men developed primary osteoporosis. The higher level of baseline LDL-C (HR = 1.539, 95% CI: 1.012-2.342) and mean LDL-C (OR = 2.190, 95% CI: 1.443-3.324) were associated with higher risk of osteoporosis in men with coronary heart disease after adjusted for covariates. Compared with those in the LDL-C trajectory of low-stable decrease, participants with medium-fluctuant trajectory, whose longitudinal LDL-C started with a medium LDL-C level and appeared an increase and then decrease, were negatively associated with osteoporosis risk (OR = 2.451, 95% CI: 1.152-5.216). And participants with initially high LDL-C level and then a rapid decrease demonstrated a tendency towards reduced risk (OR = 0.718, 95% CI: 0.212-2.437).
CONCLUSIONS
Elevated LDL-C level and its long-term fluctuation may increase the risk of primary osteoporosis in men. Early controlling a stable level of LDL-C is also essential for bone health.
7.Advances in Microfluidic Chip Based on Loop-mediated Isothermal Amplification Technology for Rapid Detection of Foodborne Pathogens
Yan-Zhu PAN ; Jia-Hua TANG ; Yue-Xiang CHAI ; Lu-Xi SHU ; Jia-Xin XIE ; Yan ZHANG
Chinese Journal of Analytical Chemistry 2025;53(9):1447-1456
Loop-mediated isothermal amplification(LAMP)is a newin vitronucleic acid amplification technique,which has been widely used in rapid detection of pathogenic bacteria,with advantages of high efficiency,simple operation and low cost.Microfluidic chip technique is a kind of miniaturized and integrated analytical technology,which integrates automation and high throughput,and can effectively avoid sample cross-contamination and has the advantages of high sample utilization rate and high cost-effectivenes.LAMP combined with microfluidic chip can detect multiple samples of the same pathogen at the same time or single samples of different pathogens at the same time,providing a new method for the rapid,field detection of pathogens.In this paper,the research progresses of LAMP microfluidic chip and its application in rapid detection of pathogenic bacteria in recent years were reviewed,and the future prospect was discussed.
8.Clinicopathological features and prognosis of 117 cases of fumarate hydratase-deficient uterine leiomyomas
Wennian YU ; Siyi PAN ; Cong WANG ; Zhendong HUANG ; Xianglian WANG ; Shu ZHU ; Yan DING ; Xiuli WANG
Chinese Journal of Obstetrics and Gynecology 2025;60(6):450-460
Objective:To explore the clinicopathological characteristics and prognosis of fumarate hydratase-deficient uterine leiomyoma (FH-dUL).Methods:Clinical data and follow-up information for 117 patients with FH-dUL diagnosed through surgical pathology and immunohistochemistry in the First Affiliated Hospital of Nanjing Medical University from January 2020 to December 2024, were collected. A control group of 130 patients with common uterine leiomyomas was also included. The differences between the two groups in clinical, imaging, and pathological characteristics were compared. Additionally, recurrence rates, fertility outcomes for FH-dUL patients, and the incidence of renal cancer in FH germline mutation carriers were monitored.Results:(1) Comparison of clinicopathological characteristics: the median age of 117 FH-dUL patients was 35 years, and the median age at first diagnosis of uterine leiomyomas was 29 years, both significantly younger than the control group (41 and 36 years; both P<0.01). The FH-dUL group showed significantly higher incidences of uterine myomectomy, multiple leiomyomas, diffusion restriction on pelvic magnetic resonance imaging diffusion weighted imaging, and typical pathological features (candelabra-like vessels, bizarre nuclei, cytoplasmic eosinophilic globules, perinuclear halo, cellular atypia) and higher ultrasound blood flow score (all P<0.05). Of the 30 FH-dUL patients who underwent genetic testing, 9 had germline mutations, 3 had somatic mutations, and 6 had mutations of unclear origin. Among the 9 FH gene germline mutation patients, 2 had already developed renal cell carcinoma. (2) Recurrence analysis: among the 56 patients who underwent uterine myomectomy, 22 (39.3%, 22/56) experienced recurrence during follow-up, compared to 12 (21.8%, 12/55) of the 55 patients in the control group, the difference between the two groups was statistically significant ( P=0.046). Multivariate binary logistic regression analysis showed that cellular leiomyomas ( OR=9.489, 95% CI: 1.740-51.755; P=0.009) and multiple uterine leiomyomas ( OR=10.709, 95% CI: 1.354-84.683; P=0.025) were significant risk factors for recurrence in FH-dUL. (3) Fertility analysis: among the 66 FH-dUL patients who underwent fertility-preserving surgery, 16 had the intention to have fertility desire, only 2 (2/16) completed their fertility plans during follow-up. Conclusions:Clinicopathological features and imaging features help to differentiate FH-dUL from common type uterine fibroids, but lack specificity, and the diagnosis of FH-dUL is based on immunohistochemistry. The recurrence rate after resection of FH-dUL is high, and cellular and multiple leiomyomas are important predictors of recurrence. It is crucial to perform genetic testing, genetic counseling, drug treatment to prevent recurrence, fertility guidance, and long-term comprehensive management after surgery for FH-dUL management.
9.A case report of premature ovarian insufficiency caused by a novel FANCL mutation(c.1033G>A)and in vitro functional validation
Yi-qing LIU ; Shu-ting REN ; Yun-cheng PAN ; Feng ZHANG ; Xiao-jin ZHANG ; Yan-hua WU
Fudan University Journal of Medical Sciences 2025;52(2):270-276,291
Objective To investigate the characteristics of a novel FANCL mutation identified in a patient with premature ovarian insufficiency(POI)and to explore its potential functional impacts in vitro.Methods A novel FANCL heterozygous mutation c.1033G>A(p.Glu345Lys)was screened in a patient with POI using whole exome sequencing(WES),which was found to be inherited from a mother who had undergone early menopause.The authenticity of the mutation was identified by Sanger sequencing and the conserved nature of the mutation site was predicted by software.Overexpressing FANCL mutant and wildtype plasmids were constructed and transiently transfected into HEK293T cell lines,and the effect of the mutation was detected by qPCR,immunofluorescence and Western blot.Results The mutation site of FANCL was located within the Ring domain of FANCL,which was highly conserved across multiple species.The mutant showed no significant change in mRNA expression level,while the protein expression level was significantly down-regulated.In vitro cellular experiments further revealed that the mutation leads to decreased expression levels by reducing protein stability.Conclusion A FANCL c.1033G>A mutation was found and it may cause disease in the POI patient due to decreased protein stability.
10.Study on Association of Preconception Dietary Patterns with Neonate Birth Weight
Acta Medicinae Universitatis Scientiae et Technologiae Huazhong 2024;53(1):52-58
Objective To investigate the associations between preconception dietary patterns(DPs)among Chinese women of childbearing age and neonatal birth weight.Methods The subjects selected for the questionnaire survey and follow-up were women of childbearing age who underwent prenatal eugenic examination at Jiang'an Maternal and Child Health Hospi-tal.Dietary intake information was collected using a semi-quantitative food frequency questionnaire,dietary patterns were extrac-ted by principal component analysis,and the relationship between DPs and birth weight was analyzed by modified Poisson re-gression or linear regression models.Results The final analysis of 221 maternal and infant pairs showed that women who fol-lowed the"nuts-poultry"pattern,one of the four dietary patterns,had a lower risk of delivering large for gestational age(LGA)infants(RR:0.25;95%CI:0.08-0.79),which was more pronounced in those who delivered male infants(RR:0.14;95%CI:0.03-0.72).Conclusion The risk of having LGA newborn is decreased in woman who takes a preconception dietary pattern characterized by nuts and poultry,which is more pronounced in those delivering male infants.Females of childbearing age should maintain good dietary habits before conception to ensure proper growth and development of the fetus and reduce the risk of ad-verse birth outcomes.

Result Analysis
Print
Save
E-mail