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#41 : The Effectiveness of GnRH Agonist Administration Prior to Frozen-Thawed Embryo Transfer with Artificial Cycle: A Systematic Review and Meta-Analysis of different Protocols and Infertile Populations

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Fertility & Reproduction 2023年第4期5卷 337-337页

作者： Nguyen Tuong Ho dang Khanh Ngan Ho Xuan Hong Tomai Yu-Ming Hu Yen-Ping Ho Shyr-Yeu Lin Ruey-Sheng Wang Yi-Xuan Lee Shun-Jen Tan Shu-Huei Kao Chii-Ruey Tzeng International Ph.D. Program in Medicine College of Medicine Taipei Medical University Taipei Taiwan Taipei Fertility Center Taipei Taiwan School of Nutrition and Health Sciences College of Nutrition Taipei Medical University Taipei Taiwan Office of International Relations Ho Chi Minh City University of Medicine and Pharmacy Ho Chi Minh City Vietnam School of Medical Laboratory Science and Biotechnology College of Medical Science and Technology Taipei Medical University Taipei Taiwan Ph.D. Program in Medical Biotechnology College of Medical Science and Technology Taipei Medical University Taipei Taiwan

Background and Aims: We investigated the use of GnRHa pretreatment with different protocols and durations of treatment on pregnancy outcomes in women undergoing FET with artificial cycles (AC-FET). Method: A systematic search of PubMed, EMBASE, Google Scholar, and Cochrane library was performed to include only eligible peer-reviewed studies in English published before September 01, 2022. This review was registered on PROSPERO (CRd42022299259) Results: A total of 41 studies (43021 individuals) were included with low to moderate risk of bias. Overall, GnRHa pretreatment improved clinical pregnancy rate (CPR) (OR=1.27, 95%CI:1.12-1.44), implantation rate (IR) (OR=1.24, 95%CI:1.07-1.45), live birth rate (LBR) (OR=1.31, 95%CI:1.07-1.60) and endometrial thickness (Md=0.16, 95%CI:0.03-0.30). Subgroup analyses of randomized and non-randomized studies both demonstrated the benefits of GnRHa pretreatment in CPR, IR, and LBR. Protocols using depot GnRHa (OR=1.19, 95%CI:1.04-1.36) showed a better LBR than daily GnRHa (OR=1.04, 95%CI:0.93-1.16). Women administered GnRHa for more than one cycle had better CPR (OR=2.01, 95%CI:1.29-3.13) and IR (OR=2.14, 95%CI:0.98-4.67) than those treated with GnRHa within one cycle before FET ([OR=1.18, 95%CI:1.04-1.33] and [OR=1.16, 95%CI:1.01-1.32], respectively). In women with PCOS, pituitary suppression with GnRHa significantly improved CPR (OR=1.24, 95%CI:0.98-4.67), LBR (OR=1.22, 95%CI:1.05-1.42) and reduced the miscarriage rate (OR=0.75, 95%CI:0.59-0.95). In contrast, women with regular menstruation had a higher endometrial thickness (Md=0.16, 95%CI: 0.04-0.28) but no significant improvements in pregnancy outcomes. GnRHa pretreatment considerably improved IR (OR=2.21, 95%CI:1.60-3.07) in women with adenomyosis and CPR (OR=1.74, 95%CI:1.12-2.71), and LBR (OR=1.67, 95%CI:1.06-2.63) in women with endometriosis. Conclusion: GnRHa pretreatment, especially with longer suppression duration and the use of depot GnRHa, demonstrates a beneficial rol

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Effects of Citrus depressa Hayata juice on high-fat diet-induced obesity in HBV transgenic mice

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Heliyon 2024年第2期10卷

作者： Chu, Pei-Yi Hsu, Chang-Lu Lin, Yen-An Pan, Yi-Cheng dai, Yun-Hao Yu, Ying-Chun Yang, Juan-Cheng Ma, Wen-Lung Chen, Yi-Jinn Lillian Lee, Chia-Lin Wu, Yang-Chang Chinese Medicine Research and Development Center China Medical University Hospital Taichung Taiwan Department of Business Administration National Chiayi University Chiayi Taiwan Graduate Institute of Biomedical Sciences China Medical University Taichung Taiwan .Ph.D. Program for Cancer Biology and Drug Discovery China Medical University and Academia Sinica Taichung Taiwan School of Pharmacy China Medical University Taichung Taiwan Department of Medical Research and Organ Transplantation Center China Medical University Hospital Taichung Taiwan School of Chinese Medicine College of Chinese Medicine China Medical University Taichung Taiwan Department of Physics National Kaohsiung Normal University Kaohsiung Taiwan Department of Cosmeceutics China Medical University Taichung 40604 Taiwan Graduate Institute of Integrated Medicine College of Chinese Medicine China Medical University Taichung Taiwan Department of Medical Laboratory Science and Biotechnology College of Medical and Health Science Asia University Taichung Taiwan

The present study investigated the potential anti-obesity properties of Citrus depressa Hayata (CdH) juice in HBV transgenic mice, as well as the impact of fermentation on the effectiveness of the juice. The results revealed that fermentation increased the levels of polyph.nols and hesperidin in CdH juice. The animal study demonstrated that both juices were effective in mitigating the weight gain induced by a high-fat diet by correcting metabolic parameter imbalances, reducing hepatic lipid accumulation, and reversing hepatic immune suppression. Furthermore, fermented juice exhibited superior efficacy in managing body weight and inhibiting the expansion of white adipose tissue (WAT). Fermented juice significantly enhanced adiponectin production and PPARγ expression in WAT, while also reducing hypertroph.. This study offers valuable insights into the potential role of CdH juices in combating obesity associated with high fat consumption and underscores the promise of CdH juice as a functional beverage. © 2024 The Authors

关键词： Citrus depressa hayata fermentation HBV Hesperidin High-fat diet-induced obesity Juice Mice Polyph.nol

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Peptide-Coated Bacteriorhodopsin-Based ph.toelectric Biosensor for detecting Rheumatoid Arthritis

Biosensors

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Biosensors 2023年第10期13卷 929-929页

作者： Chen, Hsiu-Mei Tsai, Yi-Hsuan Hsu, Chien-Yi Wang, Yong-Yi Hsieh, Cheng-En Chen, Jin-Hua Chang, Yu-Sheng Lin, Ching-Yu Department of Chemical Engineering National Taiwan University of Science and Technology Taipei10607 Taiwan Department of Family Medicine Wan Fang Hospital Taipei Medical University Taipei11696 Taiwan Division of Cardiology and Cardiovascular Research Center Department of Internal Medicine Taipei Medical University Hospital Taipei11031 Taiwan Division of Cardiology Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei11031 Taiwan Taipei Heart Institute Taipei Medical University Taipei11031 Taiwan Graduate Institute of Data Science College of Management Taipei Medical University Taipei11031 Taiwan Office of Data Science Taipei Medical University Taipei11031 Taiwan Division of Allergy Immunology and Rheumatology Department of Internal Medicine Shuang Ho Hospital Taipei Medical University New Taipei City23561 Taiwan Division of Allergy Immunology and Rheumatology Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei11031 Taiwan School of Medical Laboratory Science and Biotechnology College of Medical Science and Technology Taipei Medical University Taipei11031 Taiwan Ph.D. Program in Medical Biotechnology College of Medical Science and Technology Taipei Medical University Taipei11031 Taiwan

An effective early diagnosis is important for rheumatoid arthritis (RA) management. This study reveals a novel RA detection method using bacteriorhodopsin as a ph.toelectric transducer, a light-driven proton pump in purple membranes (PMs). It was devised by covalently conjugating a PM monolayer-coated electrode with a citrullinated-inter-alph.-trypsin inhibitor heavy chain 3 (ITIH3)542–556 peptide that recognizes the serum RA-associated autoantibodies. The direct serum coating decreased the ph.tocurrents in the biosensor, with the reduction in the ph.tocurrent caused by coating with an RA-patient serum that is significantly larger than that with a healthy-control serum (38.1% vs. 20.2%). The difference in the reduction in the ph.tocurrent between those two serum groups widened after the serum-coated biosensor was further labeled with gold nanoparticle (AuNP)-conjugated anti-IgA (anti-IgA-AuNP) (53.6% vs. 30.6%). Both atomic force microscopic (AFM) and Raman analyses confirmed the sequential peptide, serum, and anti-IgA-AuNP coatings on the PM-coated substrates. The reductions in the ph.tocurrent measured in both the serum and anti-IgA-AuNPs coating steps correlated well with the results using commercial enzyme-linked immunosorbent assay kits (Spearman rho = 0.805 and 0.787, respectively), with both a sensitivity and specificity close to 100% in both steps. It was shown that an RA diagnosis can be performed in either a single- or two-step mode using the developed biosensor. © 2023 by the authors.

关键词： Peptides

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development and Application of the Electrospun Microtube Array Membrane (MTAM) Substrate as a Potential drug Encapsulation Platform for Continuous drug Release Platform for Treatment of Elevated Intraocular Pressure (IOP) in Glaucoma disease.

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Polymer 2025年

作者： Jou-Chen Huang Ching-Yu Lee Chee Ho Chew Wan-Ting Huang Shun-Chieh Chang Chien-Chung Chen Department of Ophthalmology Taipei Medical University Hospital Taipei Medical University Department of Ophthalmology School of Medicine College of Medicine Taipei Medical University Department of Orthopedics Taipei Medical University Hospital Taipei Medical University Department of Orthopedics School of Medicine College of Medicine Taipei Medical University Graduate Institute of Biomedical Materials and Tissue Engineering Taipei Medical University Taipei 11052 Taiwan International PhD Program for Cell Therapy and Regeneration Medicine College of Medicine Taipei Medical University Taipei 110 Taiwan The PhD Program for Translational Medicine Taipei Medical University Taipei 11052 Taiwan International Ph.D. Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei 110 Taiwan Ph.D Program in Biotechnology Research and Development College of Pharmacy Taipei Medical University Taipei 110 Taiwan

Glaucoma is the leading cause of blindness which is characterized by the elevation of intraocular pressure (IOP) which results in optic nerve damage. Clinically, the current mainstay of treatment which involves the use of anti-glaucoma agents delivered in the form of topical eye drops have limitations such as short drug retention times, pulsatile delivery and localized adverse effects. In this work, we strive to demonstrate the development of a novel drug encapsulation device, known as Microtube Array Membrane (MTAM) as a potential substrate for encapsulation of clinically available anti-glaucoma agent that is based on the materials Polysulfone (PSF) and poly(lactic acid) (PLA) and poly(glycolic acid) (PLA-PLGA) copolymer. The resulting MTAM variants demonstrated tunable microstructures, mechanical properties and drug release; where pore sizes ranging from from 0.24 ± 0.02 μm to 17.62 ± 4.62 μm was successfully fabricated, and with loading efficiency of Brimonidine Tartrate up to 90%. Sustained drug release was observed over 3 days under simulated tear ph.siological conditions, with the PLA-PLGA MTAM variants released the greatest amount of drug encapsulated within and sustained even in the presence of simulated tears turnover. Critically, the encapsulation of the drug within the respective MTAMs seemed to mitigate any toxicity effects that was largely reported in direct use of Brimonidine Tartrate. Potentially, with more research and development, the MTAM based drug encapsulation could effective be deployed as a novel drug release system in future localized and sustained drug delivery.

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Enhancing healthcare AI stability with edge computing and machine learning for extubation prediction

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Scientific Reports 2025年第1期15卷 1-11页

作者： Huang, Kuo-Yang Hsu, Ying-Lin Chung, Che-Liang Chen, Huang-Chi Horng, Ming-Hwarng Lin, Ching-Hsiung Liu, Ching-Sen Xu, Jia-Lang Division of Chest Medicine Department of Internal Medicine Changhua Christian Hospital Changhua Taiwan Institute of Genomics and Bioinformatics National Chung Hsing University Taichung Taiwan Ph.D. Program in Medical Biotechnology National Chung Hsing University Taichung Taiwan Institute of Statistics National Chung Hsing University Taichung Taiwan Division of Chest Medicine Department of Internal Medicine Yuanlin Christian Hospital Changhua Taiwan Department of Applied Mathematics National Chung Hsing University Taichung Taiwan Department of Computer Science and Information Engineering Chaoyang University of Technology Taichung Taiwan

The advancement of the Internet of medical Things (IoMT) has revolutionized data acquisition and processing in critical care settings. Given the pivotal role of ventilators, accurately predicting extubation outcomes is essential to optimize patient care. This study presents an edge computing-based framework that incorporates machine learning algorithms to predict ventilator extubation success using real-time data collected directly from ventilators. The system was deployed on edge devices to enable on-site inference with minimal latency. Among the evaluated models, Random Forest and XGBoost, the latter demonstrated superior predictive performance under both holdout and tenfold cross-validation schemes. Notably, the edge-based architecture reduced server data transmissions by 83.33%, while improving system stability, resilience, and sustainability. This paper details the model evaluation and demonstrates the feasibility and efficiency of edge intelligence in ventilator weaning decision support. © The Author(s) 2025.

关键词： Clinical decision support system Edge-computing Extubation Internet of medical things Machine learning

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Improvement of extracellular polysaccharides production from Cordyceps militaris immobilized alginate beads in repeated-batch fermentation

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LWT 2024年 193卷

作者： Hou, Shi-Jing Cheng, Kuan-Chen Lin, Shyh-Hsiang Hsiao, I-Lun Santoso, Shella Permatasari Singajaya, Steph.nie Chou, Yu-Chieh Lin, Shin-Ping Master Program in Food Safety Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan Institute of Biotechnology National Taiwan University 1 Roosevelt Rd. Sec. 4 Taipei10617 Taiwan Graduate Institute of Food Science and Technology National Taiwan University 1 Roosevelt Rd. Sec. 4 Taipei10617 Taiwan Department of Medical Research China Medical University Hospital China Medical University 91 Hsueh-Shih Rd. Taichung40402 Taiwan Department of Optometry Asia University 500 Lioufeng Rd. Wufeng Taichung41354 Taiwan School of Nutrition and Health Sciences Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan School of Food Safety Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan Department of Chemical Engineering Widya Mandala Surabaya Catholic University Kalijudan 37 East Java Surabaya60114 Indonesia Collaborative Research Center for Sustainable and Zero Waste Industries Kalijudan 37 East Java Surabaya60114 Indonesia Ph.D. Program in Drug Discovery and Development Industry Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan Research Center of Biomedical Device Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan TMU Research Center for Digestive Medicine Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan

Cordyceps militaris (C. militaris) is a unique medicinal fungus of the genus Cordyceps. It has high economic value due to various biological functions from the extracellular polysaccharides (EPSs) it produces. The aim of this study was to establish a mycelium-immobilization system for EPS production in a bubble column system. First, EPS production was optimized by 90.2% (from 0.72 to 1.37 g/L) using response surface methodology under an alginate-immobilized mycelium system with 6 days of cultivation. The highest EPS production was obtained (5.3 g/L) in a flask system through elongation to 15 days of cultivation. EPS production subsequently further increased to 10.42 g/L utilizing a bubble column reactor. Furthermore, the system can be reused for at least three rounds. In the EPS characteristics analysis, the produced EPSs were mainly composed of glucose and galactose. They presented strong antibacterial activity against Staph.lococcus aureus. In terms of antioxidant activity, respective the EPS concentration that caused 50% scavenging of dPph.and ABTS free radicals values (IC50) were 4.65 and 7.92 mg/mL. In summary, these findings should be helpful for establishing a suitable industrial fermentation system for C. militaris and can be studied in the food and medical industries in future work. © 2024 The Authors

关键词： Mycelium

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Asymptomatic hemoglobin SE compound heterozygous hemoglobinopathy in an Aryan male from Northeast India

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medical journal, Armed Forces India 2023年第SUPPL 1期79卷 S394-S396页

作者： Noymi Basumatary dipankar Baruah Paresh Kumar Sarma Jatin Sarmah Senior Scholar Lady Tata Memorial Trust Mumbai India & Ph. D Scholar (Biotechnology) Bodoland University Kokrajhar Assam India. Associate Professor (Pathology) Gauhati Medical College & Hospital Guwahati Assam India. Associate Professor (Medicine) Fakhruddin Ali Ahmed Medical College & Hospital Barpeta Assam India. Professor (Biotechnology) Bodoland University Kokrajhar Assam India.

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Anethole mitigates H2O2-induced inflammation in HIG-82 synoviocytes by suppressing the aquaporin 1 expression and activating the protein kinase A pathway

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Environmental Toxicology 2024年第2期39卷 965-978页

作者： Huang, Tai-Lung Chang, Yu-Chun Tsai, Bruce Chi-Kang Chen, Tung-Sheng Kao, Shih-Wen Tsai, Yung-Yun Lin, Shinn-Zong Yao, Chun-Hsu Lin, Kuan-Ho Kuo, Wei-Wen Huang, Chih-Yang Department of Biological Science and Technology College of Life Sciences China Medical University Taichung Taiwan Department of Orthopedics Chung-Kang Branch Cheng Ching General Hospital Taichung Taiwan Cardiovascular and Mitochondrial Related Disease Research Center Hualien Tzu Chi Hospital Buddhist Tzu Chi Medical Foundation Hualien Taiwan School of Life Science National Taiwan Normal University Taipei Taiwan Department of Orthopaedic Surgery Chung-Shan Medical University Hospital Taichung Taiwan Department of Physical Therapy Asia University Taichung Taiwan Department of Neurosurgery Hualien Tzu Chi Hospital Buddhist Tzu Chi Medical Foundation Hualien Taiwan Bioinnovation Center Buddhist Tzu Chi Medical Foundation Hualien Taiwan Department of Biomedical Imaging and Radiological Science China Medical University Taichung Taiwan School of Chinese Medicine China Medical University Taichung Taiwan Biomaterials Translational Research Center China Medical University Hospital Taichung Taiwan Department of Bioinformatics and Medical Engineering Asia University Taichung Taiwan Division of Cardiovascular Medicine Department of Internal Medicine China Medical University Hospital Taichung Taiwan Department of Emergency Medicine China Medical University Hospital Taichung Taiwan College of Medicine China Medical University Taichung Taiwan Ph.D. Program for Biotechnology Industry China Medical University Taichung Taiwan Department of Medical Research China Medical University Hospital China Medical University Taichung Taiwan Graduate Institute of Biomedical Sciences China Medical University Taichung Taiwan Department of Medical Laboratory Science and Biotechnology Asia University Taichung Taiwan Center of General Education Buddhist Tzu Chi Medical Foundation Tzu Chi University of Science and Technology Hualien Taiwan

Rheumatoid arthritis (RA) is an autoimmune inflammatory disease affecting approximately 1% of the global population, with a higher prevalence in women than in men. Chronic inflammation and oxidative stress play pivotal roles in the pathogenesis of RA. Anethole, a prominent compound derived from fennel (Foeniculum vulgare), possesses a spectrum of therapeutic properties, including anti-arthritic, anti-inflammatory, antioxidant, and tumor-suppressive effects. However, its specific impact on RA remains underexplored. This study sought to uncover the potential therapeutic value of anethole in treating RA by employing an H2O2-induced inflammation model with HIG-82 synovial cells. Our results demonstrated that exposure to H2O2 induced the inflammation and apoptosis in these cells. Remarkably, anethole treatment effectively countered these inflammatory and apoptotic processes triggered by H2O2. Moreover, we identified the aquaporin 1 (AQP1) and protein kinase A (PKA) pathway as critical regulators of inflammation and apoptosis. H2O2 stimulation led to an increase in the AQP1 expression and a decrease in p-PKA-C, contributing to cartilage degradation. Conversely, anethole not only downregulated the AQP1 expression but also activated the PKA pathway, effectively suppressing cell inflammation and apoptosis. Furthermore, anethole also inhibited the enzymes responsible for cartilage degradation. In summary, our findings highlight the potential of anethole as a therapeutic agent for mitigating H2O2-induced inflammation and apoptosis in synovial cells, offering promising prospects for future RA treatments. © 2023 Wiley Periodicals LLC.

关键词： Cell death

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Calycosin Enhances Heat Shock Related-Proteins in H9c2 Cells to Modulate Survival and Apoptosis against Heat Shock

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The American journal of Chinese medicine 2024年第4期52卷 1173-1193页

作者： Pei-Fang Lai Ramasamy Mahendran Bruce Chi-Kang Tsai Cheng-You Lu Chia-Hua Kuo Kuan-Ho Lin Shang-Yeh Lu Yu-Ling Wu Yung-Ming Chang Wei-Wen Kuo Chih-Yang Huang Department of Emergency Medicine Hualien Tzu Chi Hospital Buddhist Tzu Chi Medical Foundation Hualien 970 Taiwan. Department of Medicine Tzu Chi University Hualien 970 Taiwan. Cardiovascular and Mitochondrial Related Disease Research Center Hualien Tzu Chi Hospital Buddhist Tzu Chi Medical Foundation Hualien 970 Taiwan. Department of Post-Baccalaureate Medicine College of Medicine National Chung Hsing University Taichung 402 Taiwan. Laboratory of Exercise Biochemistry University of Taipei Taipei 111 Taiwan. Institute of Sports Sciences University of Taipei Taipei 111 Taiwan. School of Physical Education and Sports Science Soochow University Suzhou 215021 China. Department of Kinesiology and Health College of William and Mary Williamsburg VA 23185 USA. Department of Emergency Medicine China Medical University Hospital Taichung 404 Taiwan. College of Medicine China Medical University Taichung 406 Taiwan. Division of Cardiovascular Medicine Department of Internal Medicine China Medical University Hospital Taichung 404 Taiwan. The School of Chinese Medicine for Post-Baccalaureate I-Shou University 840 Kaohsiung Taiwan. Chinese Medicine Department E-DA Hospital Kaohsiung 824 Taiwan. 1PT Biotechnology Co. Ltd. Taichung 433 Taiwan. Department of Biological Science and Technology College of Life Sciences China Medical University Taichung 406 Taiwan. Ph.D. Program for Biotechnology Industry China Medical University Taichung 406 Taiwan. School of Pharmacy China Medical University Taichung 406 Taiwan. Graduate Institute of Biomedical Sciences China Medical University Taichung 406 Taiwan. Department of Medical Laboratory Science and Biotechnology Asia University Taichung 413 Taiwan. Center of General Education Buddhist Tzu Chi Medical Foundation Tzu Chi University of Science and Technology Hualien 970 Taiwan. Department of Medical Research China Medical University Hospital China Medical University Taichung 404 Taiwan.

Heat shock proteins (HSPs), which function as chaperones, are activated in response to various environmental stressors. In addition to their role in diverse aspects of protein production, HSPs protect against harmful protein-related stressors. Calycosin exhibits numerous beneficial properties. This study aims to explore the protective effects of calycosin in the heart under heat shock and determine its underlying mechanism. H9c2 cells, western blot, TUNEL staining, flow cytometry, and immunofluorescence staining were used. The time-dependent effects of heat shock analyzed using western blot revealed increased HSP expression for up to 2[Formula: see text]h, followed by protein degradation after 4[Formula: see text]h. Hence, a heat shock damage duration of 4[Formula: see text]h was chosen for subsequent investigations. Calycosin administered post-heat shock demonstrated dose-dependent recovery of cell viability. Under heat shock conditions, calycosin prevented the apoptosis of H9c2 cells by upregulating HSPs, suppressing p-JNK, enhancing Bcl-2 activation, and inhibiting cleaved caspase 3. Calycosin also inhibited Fas/FasL expression and activated cell survival markers (p-PI3K, p-ERK, p-Akt), indicating their cytoprotective properties through PI3K/Akt activation and JNK inhibition. TUNEL staining and flow cytometry confirmed that calycosin reduced apoptosis. Moreover, calycosin reversed the inhibitory effects of quercetin on HSF1 and Hsp70 expression, illustrating its role in enhancing Hsp70 expression through HSF1 activation during heat shock. Immunofluorescence staining demonstrated HSF1 translocation to the nucleus following calycosin treatment, emph.sizing its cytoprotective effects. In conclusion, calycosin exhibits pronounced protective effects against heat shock-induced damages by modulating HSP expression and regulating key signaling pathways to promote cell survival in H9c2 cells.

关键词： Astragalus Membranaceus Calycosin Cardiomyocyte Heart Protection Heat Shock Heat Shock-Related Protein

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Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles

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Nucleic Acids Research 2024年第3期52卷 E17页

作者： Chang, Lan-Yun Lee, Meng-Zhan Wu, Yujia Lee, Wen-Kai Ma, Chia-Liang Chang, Jun-Mao Chen, Ciao-Wen Huang, Tzu-Chun Lee, Chia-Hwa Lee, Jih-Chin Tseng, Yu-Yao Lin, Chun-Yu Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu 300 Taiwan School of Medical Laboratory Science and Biotechnology College of Medical Science and Technology Taipei Medical University New Taipei City 235 Taiwan Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B) National Yang Ming Chiao Tung University Hsinchu 300 Taiwan TMU Research Center of Cancer Translational Medicine Taipei Medical University Taipei 110 Taiwan Ph.D. Program in Medical Biotechnology College of Medical Science and Technology Taipei Medical University New Taipei City 235 Taiwan Department of Otolaryngology-Head and Neck Surgery Tri-Service General Hospital National Defense Medical Center Taipei 110 Taiwan Department of Food Science Nutrition and Nutraceutical Biotechnology Shih Chien University Taipei 104 Taiwan Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu 300 Taiwan Cancer and Immunology Research Center National Yang Ming Chiao Tung University Taipei 112 Taiwan Institute of Data Science and Engineering National Yang Ming Chiao Tung University Hsinchu 300 Taiwan School of Dentistry Kaohsiung Medical University Kaohsiung 807 Taiwan

Pathway analysis, including nontopology-based (non-TB) and topology-based (TB) methods, is widely used to interpret the biological ph.nomena underlying differences in expression data between two ph.notypes. By considering dependencies and interactions between genes, TB methods usually perform better than non-TB methods in identifying pathways that include closely relevant or directly causative genes for a given ph.notype. However, most TB methods may be limited by incomplete pathway data used as the reference network or by difficulties in selecting appropriate reference networks for different research topics. Here, we propose a gene set correlation enrichment analysis method, Gscore, based on an expression dataset-derived coexpression network to examine whether a differentially expressed gene (dEG) list (or each of its dEGs) is associated with a known gene set. Gscore is better able to identify target pathways in 89 human disease expression datasets than eight other state-of-the-art methods and offers insight into how disease-wide and pathway-wide associations reflect clinical outcomes. When applied to RNA-seq data from COVId-19-related cells and patient samples, Gscore provided a means for studying how dEGs are implicated in COVId-19-related pathways. In summary, Gscore offers a powerful analytical approach for annotating individual dEGs, dEG lists, and genome-wide expression profiles based on existing biological knowledge. © 2024 Oxford University Press. All rights reserved.

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