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Dennis CL, Singla DR, Brown HK, Savel K, Clark CT, Grigoriadis S, Vigod SN. Postpartum Depression: A Clinical Review of Impact and Current Treatment Solutions. Drugs 2024; 84:645-659. [PMID: 38811474 DOI: 10.1007/s40265-024-02038-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2024] [Indexed: 05/31/2024]
Abstract
Depression during the first year postpartum (postpartum depression) impacts millions of women and their families worldwide. In this narrative review, we provide a summary of postpartum depression, examining the etiology and consequences, pharmacological and psychological treatments, and potential mechanisms of change and current barriers to care. Psychological treatments are effective and preferred by many perinatal patients over medications, but they often remain inaccessible. Key potential mechanisms underlying their effectiveness include treatment variables (e.g., dosage and therapeutic alliance) and patient behaviors (e.g., activation and avoidance and emotional regulation). Among pharmacological treatments, the selective serotonin reuptake inhibitor (SSRI) sertraline is generally the first-line antidepressant medication recommended to women in the postpartum period due to its minimal passage into breastmilk and the corresponding decades of safety data. Importantly, most antidepressant drugs are considered compatible with breastfeeding. Neurosteroids are emerging as an effective treatment for postpartum depression, although currently this treatment is not widely available. Barriers to widespread access to treatment include those that are systematic (e.g., lack of specialist providers), provider-driven (e.g., lack of flexibility in treatment delivery), and patient-driven (e.g., stigma and lack of time for treatment engagement). We propose virtual care, task-sharing to non-specialist treatment providers, and collaborative care models as potential solutions to enhance the reach and scalability of effective treatments to address the growing burden of postpartum depression worldwide and its negative impact on families and society.
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Affiliation(s)
- Cindy-Lee Dennis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Canada.
- Lawrence S. Bloomberg Faculty of Nursing, University of Toronto, 155 College Street, Rm 280, Toronto, ON, M6J 1H4, Canada.
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada.
| | - Daisy R Singla
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada
| | - Hilary K Brown
- Department of Health and Society, University of Toronto, Toronto, Canada
- Women's College Hospital, Toronto, Canada
- Women's College Research Institute, Toronto, Canada
| | - Katarina Savel
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Canada
| | - Crystal T Clark
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
- Women's College Hospital, Toronto, Canada
- Women's College Research Institute, Toronto, Canada
| | - Sophie Grigoriadis
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Simone N Vigod
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
- Women's College Hospital, Toronto, Canada
- Women's College Research Institute, Toronto, Canada
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Hajiaghabozorgi M, Fischbach M, Albrecht M, Wang W, Myers CL. BridGE: a pathway-based analysis tool for detecting genetic interactions from GWAS. Nat Protoc 2024; 19:1400-1435. [PMID: 38514837 DOI: 10.1038/s41596-024-00954-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/22/2023] [Indexed: 03/23/2024]
Abstract
Genetic interactions have the potential to modulate phenotypes, including human disease. In principle, genome-wide association studies (GWAS) provide a platform for detecting genetic interactions; however, traditional methods for identifying them, which tend to focus on testing individual variant pairs, lack statistical power. In this protocol, we describe a novel computational approach, called Bridging Gene sets with Epistasis (BridGE), for discovering genetic interactions between biological pathways from GWAS data. We present a Python-based implementation of BridGE along with instructions for its application to a typical human GWAS cohort. The major stages include initial data processing and quality control, construction of a variant-level genetic interaction network, measurement of pathway-level genetic interactions, evaluation of statistical significance using sample permutations and generation of results in a standardized output format. The BridGE software pipeline includes options for running the analysis on multiple cores and multiple nodes for users who have access to computing clusters or a cloud computing environment. In a cluster computing environment with 10 nodes and 100 GB of memory per node, the method can be run in less than 24 h for typical human GWAS cohorts. Using BridGE requires knowledge of running Python programs and basic shell script programming experience.
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Affiliation(s)
- Mehrad Hajiaghabozorgi
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Mathew Fischbach
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
- Graduate Program in Bioinformatics and Computational Biology (BICB), University of Minnesota, Minneapolis, MN, USA
| | - Michael Albrecht
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.
- Graduate Program in Bioinformatics and Computational Biology (BICB), University of Minnesota, Minneapolis, MN, USA.
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Dong J, Chen Q, Xie T, Wang M, Wang M, Zha L. Polymorphism of IL-12/IL-23 axis is associated with coronary heart disease. J Cell Mol Med 2024; 28:e18100. [PMID: 38189641 PMCID: PMC10844691 DOI: 10.1111/jcmm.18100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/05/2023] [Accepted: 12/10/2023] [Indexed: 01/09/2024] Open
Abstract
IL12B encodes the shared p40 subunit (IL-12p40) of IL-12 and IL-23, which have diverse immune functions and are closely related to the occurrence and development of atherosclerosis (AS). However, the exact role of IL12B in coronary heart disease (CHD) was still unknown. A case-control association analysis was performed between five single nucleotide polymorphisms (SNPs) of IL12B (rs1003199, rs3212219, rs2569254, rs2853694 and rs3212227) and CHD in Chinese Han population (1824 patients with CHD vs. 2784 controls). Logistic regression analyses were used to study the relationships between SNPs and CHD, while multiple linear regression analyses were used to test the association between the SNP and the severity of CHD. In addition, the plasma IL12B concentration of CHD patients were detected by ELISA. We detected a significant association between one of the SNPs, rs2853694-G and CHD (padj = 2.075 × 10-5 , OR, 0.773 [95% CI, 0.686-0.870]). Stratified analysis showed that rs2853694 was associated with CHD in both male and female populations and was significantly associated with both early- and late-onset CHD. In addition, rs2853694 is also related to the different types of CHD including clinical-CHD and anatomical-CHD. Moreover, there are significant differences in serum IL12B concentrations between rs2853694-TT carriers and rs2853694-GT carriers in CHD patients (p = 0.010). A common variant of IL12B was found significantly associated with CHD and its subgroups. As a shared subunit of IL-12 and IL-23, IL-12p40 may play a key role in IL-12/IL-23 axis mediated AS, which is expected to be an effective therapeutic target for CHD.
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Affiliation(s)
- Jiangtao Dong
- Department of Cardiology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of Cardiovascular SurgeryUnion Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Qianwen Chen
- Department of Cardiology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Tian Xie
- Department of Cardiology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Mengru Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome ResearchCardio‐X Institute, Huazhong University of Science and TechnologyWuhanChina
| | - Mengqi Wang
- Department of Cardiology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Lingfeng Zha
- Department of Cardiology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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Peng H, Liu Y, Song Z. SPP2 plays a role in the tumorigenesis of hepatocellular carcinoma: A bioinformatic based analysis. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2023; 48:1779-1792. [PMID: 38448371 PMCID: PMC10930748 DOI: 10.11817/j.issn.1672-7347.2023.230077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Indexed: 03/08/2024]
Abstract
OBJECTIVES Hepatocellular carcinoma (HCC) patients at the same stage exhibit different prognosis, and the underlying molecular mechanism remains unclear. This study aims to identify the key genes impacting the prognosis of HCC patients. METHODS Differentially expressed gene analyses were performed between HCC samples and normal ones, and between patients with long overall survival (OS) and those with short OS, in TCGA-LIHC and GSE14520 datasets. The Kaplan-Meier method with log-rank test was used to evaluate the role of secreted phosphoprotein 2 (SPP2) in the prognosis of HCC patients. Gene set enrichment analysis (GSEA) was used to understand the difference of enriched signaling pathways between SPP2-stratified HCC subgroups. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the potential functional pathways in which SPP2 might participate. RESULTS SPP2 was significantly down-regulated in tumors when compared with normal tissues, or in tumor samples with short OS when compared with those with long OS [fold change (FC)>2 and false discovery rate (FDR)<0.05]. Low expression of SPP2 was associated with worse clinicopathological features like vascular invasion (P=1.6e-05), poor cancer status (with tumor, P=0.021), advanced T stage (T3 or T4, P=4.5e-04), advanced TNM stage (stage III or IV, P=3.1e-04), and with unfavorable prognosis (shorter OS, P=0.002). Gene enrichment analyses revealed that SPP2 might involve in the metabolic homeostasis of HCC and in the development of liver fibrosis and cirrhosis. CONCLUSIONS SPP2 might inhibit the development of liver fibrosis and cirrhosis and the tumorigenesis of HCC, and analogs of SPP2 might be potential drugs in the prevention of these diseases.
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Affiliation(s)
- Honghua Peng
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha 410013.
| | - Yang Liu
- Department of Pathology, Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Zewen Song
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha 410013.
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Changalidis AI, Alexeev DA, Nasykhova YA, Glotov AS, Barbitoff YA. bioGWAS: A Simple and Flexible Tool for Simulating GWAS Datasets. BIOLOGY 2023; 13:10. [PMID: 38248441 PMCID: PMC11154295 DOI: 10.3390/biology13010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/03/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
Genome-wide association studies (GWAS) have proven to be a powerful tool for the identification of genetic susceptibility loci affecting human complex traits. In addition to pinpointing individual genes involved in a particular trait, GWAS results can be used to discover relevant biological processes for these traits. The development of new tools for extracting such information from GWAS results requires large-scale datasets with known biological ground truth. Simulation of GWAS results is a powerful method that may provide such datasets and facilitate the development of new methods. In this work, we developed bioGWAS, a simple and flexible pipeline for the simulation of genotypes, phenotypes, and GWAS summary statistics. Unlike existing methods, bioGWAS can be used to generate GWAS results for simulated quantitative and binary traits with a predefined set of causal genetic variants and/or molecular pathways. We demonstrate that the proposed method can recapitulate complete GWAS datasets using a set of reported genome-wide associations. We also used our method to benchmark several tools for gene set enrichment analysis for GWAS data. Taken together, our results suggest that bioGWAS provides an important set of functionalities that would aid the development of new methods for downstream processing of GWAS results.
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Affiliation(s)
- Anton I. Changalidis
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia; (A.I.C.); (Y.A.N.)
- Bioinformatics Institute, 197342 St. Petersburg, Russia;
- Faculty of Software Engineering and Computer Systems, ITMO University, 197101 St. Petersburg, Russia
| | | | - Yulia A. Nasykhova
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia; (A.I.C.); (Y.A.N.)
| | - Andrey S. Glotov
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia; (A.I.C.); (Y.A.N.)
| | - Yury A. Barbitoff
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia; (A.I.C.); (Y.A.N.)
- Bioinformatics Institute, 197342 St. Petersburg, Russia;
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Priyam J, Saxena U. Stage-specific coexpression network analysis of Myc in cohorts of renal cancer. Sci Rep 2023; 13:11848. [PMID: 37481674 PMCID: PMC10363146 DOI: 10.1038/s41598-023-38681-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023] Open
Abstract
The present study investigates the molecular dynamics of Myc in normal precursors and in different stages (I/II/III/IV) of cohorts of renal cancer using two distinct yet complementary approaches: gene expression and gene coexpression. We also analysed the variation of coexpression networks of Myc through the stage-wise progression of renal cancer cohorts. Myc expression is significantly higher in stage I compared to normal tissue but changed inconsistently across stages of renal cancer. We identified that Myc consistently coexpressed with fourteen genes in the KIPAN [Pan-kidney cohort (KICH + KIRC + KIRP)] and eight in the KIRC (Kidney renal clear cell carcinoma) across all stages, providing potential prognostic and diagnostic biomarkers. Coexpression network complexity decreased from normal precursor tissues to associated tumour stage I in KIPAN and KIRC but was inconsistent after that. In the process of cancer development, there is generally lower cross-tissue cancer network homology observed among coexpressed genes with Myc during the normal to the stage I compared to the stage-wise progression of cancer. Overall, this research provides novel perceptions of the molecular causes of kidney cancer. It also highlights potential genes and pathways crucial for diagnosing and treating this disease.
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Affiliation(s)
- Jyotsna Priyam
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, 506004, Telangana, India
| | - Urmila Saxena
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, 506004, Telangana, India.
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Doering TM, Thompson JLM, Budiono BP, MacKenzie-Shalders KL, Zaw T, Ashton KJ, Coffey VG. The muscle proteome reflects changes in mitochondrial function, cellular stress and proteolysis after 14 days of unilateral lower limb immobilization in active young men. PLoS One 2022; 17:e0273925. [PMID: 36048851 PMCID: PMC9436066 DOI: 10.1371/journal.pone.0273925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/17/2022] [Indexed: 12/05/2022] Open
Abstract
Skeletal muscle unloading due to joint immobilization induces muscle atrophy, which has primarily been attributed to reductions in protein synthesis in humans. However, no study has evaluated the skeletal muscle proteome response to limb immobilization using SWATH proteomic methods. This study characterized the shifts in individual muscle protein abundance and corresponding gene sets after 3 and 14 d of unilateral lower limb immobilization in otherwise healthy young men. Eighteen male participants (25.4 ±5.5 y, 81.2 ±11.6 kg) underwent 14 d of unilateral knee-brace immobilization with dietary provision and following four-weeks of training to standardise acute training history. Participant phenotype was characterized before and after 14 days of immobilization, and muscle biopsies were obtained from the vastus lateralis at baseline (pre-immobilization) and at 3 and 14 d of immobilization for analysis by SWATH-MS and subsequent gene-set enrichment analysis (GSEA). Immobilization reduced vastus group cross sectional area (-9.6 ±4.6%, P <0.0001), immobilized leg lean mass (-3.3 ±3.9%, P = 0.002), unilateral 3-repetition maximum leg press (-15.6 ±9.2%, P <0.0001), and maximal oxygen uptake (-2.9 ±5.2%, P = 0.044). SWATH analyses consistently identified 2281 proteins. Compared to baseline, two and 99 proteins were differentially expressed (FDR <0.05) after 3 and 14 d of immobilization, respectively. After 14 d of immobilization, 322 biological processes were different to baseline (FDR <0.05, P <0.001). Most (77%) biological processes were positively enriched and characterized by cellular stress, targeted proteolysis, and protein-DNA complex modifications. In contrast, mitochondrial organization and energy metabolism were negatively enriched processes. This study is the first to use data independent proteomics and GSEA to show that unilateral lower limb immobilization evokes mitochondrial dysfunction, cellular stress, and proteolysis. Through GSEA and network mapping, we identify 27 hub proteins as potential protein/gene candidates for further exploration.
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Affiliation(s)
- Thomas M. Doering
- School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, Queensland, Australia
- Bond Institute of Health and Sport, Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Queensland, Australia
- * E-mail: (TMD); (VGC)
| | - Jamie-Lee M. Thompson
- Bond Institute of Health and Sport, Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Queensland, Australia
| | - Boris P. Budiono
- School of Dentistry and Medical Sciences, Charles Sturt University, Port Macquarie, New South Wales, Australia
| | - Kristen L. MacKenzie-Shalders
- Bond Institute of Health and Sport, Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Queensland, Australia
| | - Thiri Zaw
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Kevin J. Ashton
- Bond Institute of Health and Sport, Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Queensland, Australia
| | - Vernon G. Coffey
- Bond Institute of Health and Sport, Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Queensland, Australia
- * E-mail: (TMD); (VGC)
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