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Singh P, Srivastava A, Guin D, Thakran S, Yadav J, Chandna P, Sood M, Chadda RK, Kukreti R. Genetic Landscape of Major Depressive Disorder: Assessment of Potential Diagnostic and Antidepressant Response Markers. Int J Neuropsychopharmacol 2023; 26:692-738. [PMID: 36655406 PMCID: PMC10586057 DOI: 10.1093/ijnp/pyad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 01/18/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The clinical heterogeneity in major depressive disorder (MDD), variable treatment response, and conflicting findings limit the ability of genomics toward the discovery of evidence-based diagnosis and treatment regimen. This study attempts to curate all genetic association findings to evaluate potential variants for clinical translation. METHODS We systematically reviewed all candidates and genome-wide association studies for both MDD susceptibility and antidepressant response, independently, using MEDLINE, particularly to identify replicated findings. These variants were evaluated for functional consequences using different in silico tools and further estimated their diagnostic predictability by calculating positive predictive values. RESULTS A total of 217 significantly associated studies comprising 1200 variants across 545 genes and 128 studies including 921 variants across 412 genes were included with MDD susceptibility and antidepressant response, respectively. Although the majority of associations were confirmed by a single study, we identified 31 and 18 replicated variants (in at least 2 studies) for MDD and antidepressant response. Functional annotation of these 31 variants predicted 20% coding variants as deleterious/damaging and 80.6% variants with regulatory effect. Similarly, the response-related 18 variants revealed 25% coding variant as damaging and 88.2% with substantial regulatory potential. Finally, we could calculate the diagnostic predictability of 19 and 5 variants whose positive predictive values ranges from 0.49 to 0.66 for MDD and 0.36 to 0.66 for response. CONCLUSIONS The replicated variants presented in our data are promising for disease diagnosis and improved response outcomes. Although these quantitative assessment measures are solely directive of available observational evidence, robust homogenous validation studies are required to strengthen these variants for molecular diagnostic application.
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Affiliation(s)
- Priyanka Singh
- Genomics and Molecular Medicine Unit, Council of Scientific and Industrial Research (CSIR) - Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ankit Srivastava
- Genomics and Molecular Medicine Unit, Council of Scientific and Industrial Research (CSIR) - Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Debleena Guin
- Genomics and Molecular Medicine Unit, Council of Scientific and Industrial Research (CSIR) - Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Delhi, India
| | - Sarita Thakran
- Genomics and Molecular Medicine Unit, Council of Scientific and Industrial Research (CSIR) - Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Jyoti Yadav
- Genomics and Molecular Medicine Unit, Council of Scientific and Industrial Research (CSIR) - Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Puneet Chandna
- Indian Society of Colposcopy and Cervical Pathology (ISCCP), Safdarjung Hospital, New Delhi, India
| | - Mamta Sood
- Department of Psychiatry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Rakesh Kumar Chadda
- Department of Psychiatry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Ritushree Kukreti
- Genomics and Molecular Medicine Unit, Council of Scientific and Industrial Research (CSIR) - Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Lyu X, Qiang Y, Zhang B, Xu W, Cui Y, Ma L. Identification of immuno-infiltrating MAP1A as a prognosis-related biomarker for bladder cancer and its ceRNA network construction. Front Oncol 2022; 12:1016542. [PMID: 36408130 PMCID: PMC9667867 DOI: 10.3389/fonc.2022.1016542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/22/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUNDS Approximately 75% of bladder cancer occurrences are of the non-muscle-invasive type. The estimated five-year survival rate is 26%-55%. Currently, there is no reliable biomarker available for early diagnosis and prognosis of bladder cancer. The present study aims to identify a biomarker using bioinformatic approaches to provide a new insight in clinical research for early diagnosis and prognosis of bladder cancer. METHODS Clinical data and a transcriptome of bladder cancer were obtained from TCGA, GEO, GETx, and UCSC Xena. The differential expressed gene (DEG) analysis, weighted gene co-expression network analysis (WGCNA), and survival analysis using the Kaplan-Meier and Cox proportional-hazards models were used to identify the Microtubule-associated Proteins 1A (MAP1A). on overall survival (OS) and disease-free survival (DFS) was analyzed using GEPIA and GETx databases. The TIMER 2.0 database predicted the correlation between MAP1A and immunocytes and immune checkpoints. Target prediction of the regulated competing endogenous RNAs (ceRNAs) network of MAP1A was performed using starBase and TargetScan. Cystoscope v3.7.2 software was used to visualize the ceRNA coexpression network. The R programming language v4.0.2 was applied as an analytic tool. Gene expression of MAP1A verified by RT-qPCR. RESULTS The low expression of MAP1A was verified in bladder cancer tissues and bladder cancer cell lines SW780 and 5637. P < 0.001 were obtained by Kaplan-Meier survival analysis and Cox proportional hazards model, with a hazard ratio (HR) of 1.4. Significant correlations between MAP1A and OS (P < 0.001, HR = 1.9) as well as DFS (P < 0.05, HR = 1.7) in bladder cancer were identified through gene expression profiling interactive analysis (GEPIA), indicating MAP1A may be a high-risk factor. Significant correlation in single copy-number variation of MAP1A gene with CD8+ T cells, and myeloid dendritic cells (MDCs) (P < 0.05) was noted. MAP1A expression was shown to be significantly correlated with the amount of CD4+ T cells and CD8+ T cells, MDCs, macrophages, and neutrophils in a statistically significant positive manner (P < 0.001). However, the MAP1A expression demonstrated a strong negative connection with B cells (P < 0.001). Except for macrophage M1 genes IRF5 and PTGS2, MAP1A expression was significantly correlated with the gene levels in immunocytes such as CD4+ T cells, CD8+ T cells, B cells, dendritic cells (DCs), macrophages, and neutrophils (Cor > 0.2, P < 0.001), as well as immune checkpoint related genes including cytotoxic t-lymphocyte-associated protein 4 (CTLA-4), programmed death 1 (PD-1), programmed death ligand 1 (PD-L1) (P < 0.001). Finally, we predicted that the MAP1A-interacting miRNA was miR-34a-5p, and the MAP1A endogenous competing RNAs were LNC00667, circ_MAP1B, and circ_MYLK, respectively. These findings support the need for further studies on the mechanism underlying the pathogenesis of this disease. CONCLUSION MAP1A is considered as a prospective biomarker for early diagnosis, therapeutic observation, and prognosis analysis in bladder cancer.
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Affiliation(s)
- Xiaoyue Lyu
- College of Life Sciences, Northwest University, Xi’an, China
| | - Yujie Qiang
- College of Life Sciences, Northwest University, Xi’an, China
| | - Bo Zhang
- Ankang Hospital of Traditional Chinese Medicine, Ankang, Shaanxi, China
| | - Wei Xu
- College of Life Sciences, Northwest University, Xi’an, China
| | - Yali Cui
- College of Life Sciences, Northwest University, Xi’an, China,*Correspondence: Yali Cui, ; Le Ma,
| | - Le Ma
- College of Life Sciences, Northwest University, Xi’an, China,*Correspondence: Yali Cui, ; Le Ma,
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Yoo TK, Lee WS, Kim J, Kim MK, Park IA, Kim JH, Han W. Mutational Analysis of Triple-Negative Breast Cancer Using Targeted Kinome Sequencing. J Breast Cancer 2022; 25:164-177. [PMID: 35657000 PMCID: PMC9250872 DOI: 10.4048/jbc.2022.25.e15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/07/2022] [Accepted: 04/17/2022] [Indexed: 11/30/2022] Open
Abstract
Purpose Triple-negative breast cancer (TNBC) does not have defined therapeutic targets and is currently treated with chemotherapy only. Kinase dysregulation triggers cancer cell proliferation and metastasis and is a crucial therapeutic target for cancer. In this study, targeted kinome sequencing of TNBC tumors was performed to assess the association between kinome gene alterations and disease outcomes in TNBC. Methods A kinome gene panel consisting of 612 genes was used for the targeted sequencing of 166 TNBC samples and matched normal tissues. Analyses of the significantly mutated genes were performed. Genomic differences between Asian and non-Asian patients with TNBC were evaluated using two Asian TNBC datasets (from Seoul National University Hospital [SNUH] and Fudan University Shanghai Cancer Center [FUSCC]) and three non-Asian TNBC datasets (The Cancer Genome Atlas [TCGA], METABRIC, and Gustave Roussy). The prognostic value of kinome gene mutations was evaluated using tumor mutational burden (TMB) and oncogenic pathway analyses. Mutational profiles from the TCGA were used for validation. Results The significantly mutated genes included TP53 (60% of patients), PIK3CA (21%), BRCA2 (8%), and ATM (8%). Compared with data from non-Asian public databases, the mutation rates of PIK3CA p.H1047R/Q were significantly higher in the SNUH cohort (p = 0.003, 0.048, and 0.032, respectively). This was verified using the FUSCC dataset (p = 0.003, 0.078, and 0.05, respectively). The TMB-high group showed a trend toward longer progression-free survival in our cohort and the TCGA TNBC cohort (p = 0.041 and 0.195, respectively). Kinome gene alterations in the Wnt pathway in patients with TNBC were associated with poor survival in both datasets (p = 0.002 and 0.003, respectively). Conclusion Comprehensive analyses of kinome gene alterations in TNBC revealed genomic alterations that offer therapeutic targets and should help identify high-risk patients more precisely in future studies.
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Affiliation(s)
- Tae-Kyung Yoo
- Department of Surgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Woo Seung Lee
- Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul, Korea
| | - Jisun Kim
- Division of Breast Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Min Kyoon Kim
- Department of Surgery, Chung-Ang University Hospital, Seoul, Korea
| | - In-Ae Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Ju Han Kim
- Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul, Korea
| | - Wonshik Han
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
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Lee WS, Lee J, Choi JJ, Kang HG, Lee SC, Kim JH. Paired comparisons of mutational profiles before and after brachytherapy in asian uveal melanoma patients. Sci Rep 2021; 11:18594. [PMID: 34545149 PMCID: PMC8452742 DOI: 10.1038/s41598-021-98084-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/31/2021] [Indexed: 01/22/2023] Open
Abstract
Uveal melanoma(UM) is the most common primary intraocular malignancy in adults. However, the incidence of UM in Asia is 10 to 20 times less than in Western populations. Therefore, for the first time, we report our whole exome sequencing (WES) data analysis to discover differences in the molecular features of Asian and Western UM, and to determine the disparities between the primary tumor before brachytherapy and enucleated samples after brachytherapy. WES of 19 samples (13 primary tumors, 5 enucleation samples after brachytherapy, and 1 liver metastasis) from 13 patients diagnosed with UM and treated between 2007 and 2019 at the Yonsei University Health System (YUHS) were analyzed using bioinformatics pipelines. We identified significantly altered genes in Asian UM and changes in mutational profiles before and after brachytherapy using various algorithms. GNAQ, BAP1, GNA11, SF3B1 and CYSLTR2 were significantly mutated in Asian UM, which is similar that reported frequently in previous Western-based UM studies. There were also similar copy number alterations (M3, 1p loss, 6p gain, 8q gain) in both groups. In paired comparisons of the same patients, DICER1 and LRP1B were distinctly mutated only in tumor samples obtained after brachytherapy using rare-variant association tests (P = 0.01, 0.01, respectively). The mutational profiles of Asian UM were generally similar to the data from previous Western-based studies. DICER1 and LRP1B were newly mutated genes with statistical significance in the regrowth samples after brachytherapy compared to the primary tumors, which may be related to resistance to brachytherapy.
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Affiliation(s)
- Woo Seung Lee
- Division of Biomedical Informatics, Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Junwon Lee
- Department of Ophthalmology, Institute of Human Barrier Research, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea.
| | - Jun Jeong Choi
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, 06273, South Korea
| | - Hyun Goo Kang
- Department of Ophthalmology, Institute of Human Barrier Research, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung Chul Lee
- Department of Ophthalmology, Konyang University College of Medicine, Daejeon, South Korea
| | - Ju Han Kim
- Division of Biomedical Informatics, Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul, 03080, South Korea.
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Pisanu C, Congiu D, Severino G, Ardau R, Chillotti C, Del Zompo M, Baune BT, Squassina A. Investigation of genetic loci shared between bipolar disorder and risk-taking propensity: potential implications for pharmacological interventions. Neuropsychopharmacology 2021; 46:1680-1692. [PMID: 34035470 PMCID: PMC8280111 DOI: 10.1038/s41386-021-01045-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 11/09/2022]
Abstract
Patients with bipolar disorder (BD) often show increased risk-taking propensity, which may contribute to poor clinical outcome. While these two phenotypes are genetically correlated, there is scarce knowledge on the shared genetic determinants. Using GWAS datasets on BD (41,917 BD cases and 371,549 controls) and risk-taking (n = 466,571), we dissected shared genetic determinants using conjunctional false discovery rate (conjFDR) and local genetic covariance analysis. We investigated specificity of identified targets using GWAS datasets on schizophrenia (SCZ) and attention-deficit hyperactivity disorder (ADHD). The putative functional role of identified targets was evaluated using different tools and GTEx v. 8. Target druggability was evaluated using DGIdb and enrichment for drug targets with genome for REPositioning drugs (GREP). Among 102 loci shared between BD and risk-taking, 87% showed the same direction of effect. Sixty-two were specifically shared between risk-taking propensity and BD, while the others were also shared between risk-taking propensity and either SCZ or ADHD. By leveraging pleiotropic enrichment, we reported 15 novel and specific loci associated with BD and 22 with risk-taking. Among cross-disorder genes, CACNA1C (a known target of calcium channel blockers) was significantly associated with risk-taking propensity and both BD and SCZ using conjFDR (p = 0.001 for both) as well as local genetic covariance analysis, and predicted to be differentially expressed in the cerebellar hemisphere in an eQTL-informed gene-based analysis (BD, Z = 7.48, p = 3.8E-14; risk-taking: Z = 4.66, p = 1.6E-06). We reported for the first time shared genetic determinants between BD and risk-taking propensity. Further investigation into calcium channel blockers or development of innovative ligands of calcium channels might form the basis for innovative pharmacotherapy in patients with BD with increased risk-taking propensity.
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Affiliation(s)
- Claudia Pisanu
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Donatella Congiu
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Giovanni Severino
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Raffaella Ardau
- Unit of Clinical Pharmacology of the University Hospital of Cagliari, Cagliari, Italy
| | - Caterina Chillotti
- Unit of Clinical Pharmacology of the University Hospital of Cagliari, Cagliari, Italy
| | - Maria Del Zompo
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
- Unit of Clinical Pharmacology of the University Hospital of Cagliari, Cagliari, Italy
| | - Bernhard T Baune
- Department of Psychiatry, University of Münster, Münster, Germany
- Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy.
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Park JH, Lim SW, Myung W, Park I, Jang HJ, Kim S, Lee MS, Chang HS, Yum D, Suh YL, Kim JW, Kim DK. Whole-genome sequencing reveals KRTAP1-1 as a novel genetic variant associated with antidepressant treatment outcomes. Sci Rep 2021; 11:4552. [PMID: 33633223 PMCID: PMC7907209 DOI: 10.1038/s41598-021-83887-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/08/2021] [Indexed: 12/30/2022] Open
Abstract
Achieving remission following initial antidepressant therapy in patients with major depressive disorder (MDD) is an important clinical result. Making predictions based on genetic markers holds promise for improving the remission rate. However, genetic variants found in previous genetic studies do not provide robust evidence to aid pharmacogenetic decision-making in clinical settings. Thus, the objective of this study was to perform whole-genome sequencing (WGS) using genomic DNA to identify genetic variants associated with the treatment outcomes of selective serotonin reuptake inhibitors (SSRIs). We performed WGS on 100 patients with MDD who were treated with escitalopram (discovery set: 36 remitted and 64 non-remitted). The findings were applied to an additional 553 patients with MDD who were treated with SSRIs (replication set: 185 remitted and 368 non-remitted). A novel loss-of-function variant (rs3213755) in keratin-associated protein 1-1 (KRTAP1-1) was identified in this study. This rs3213755 variant was significantly associated with remission following antidepressant treatment (p = 0.0184, OR 3.09, 95% confidence interval [CI] 1.22-7.80 in the discovery set; p = 0.00269, OR 1.75, 95% CI 1.22-2.53 in the replication set). Moreover, the expression level of KRTAP1-1 in surgically resected human temporal lobe samples was significantly associated with the rs3213755 genotype. WGS studies on a larger sample size in various ethnic groups are needed to investigate genetic markers useful in the pharmacogenetic prediction of remission following antidepressant treatment.
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Affiliation(s)
- Jong-Ho Park
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea.,Clinical Genomics Center, Samsung Medical Center, Seoul, Korea
| | - Shinn-Won Lim
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea
| | - Woojae Myung
- Department of Neuropsychiatry, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Inho Park
- Precision Medicine Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Hyeok-Jae Jang
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea
| | - Seonwoo Kim
- Statistics and Data Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | - Min-Soo Lee
- Department of Psychiatry, College of Medicine, Korea University, Seoul, Korea
| | - Hun Soo Chang
- Soonchunhyang Medical Institute, College of Medicine, Soonchunhyang University, Asan, Korea
| | - DongHo Yum
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yeon-Lim Suh
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Won Kim
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea. .,Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Korea.
| | - Doh Kwan Kim
- Department of Psychiatry, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 135-710, Korea.
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