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Xie T, Danieli-Mackay A, Buccarelli M, Barbieri M, Papadionysiou I, D'Alessandris QG, Robens C, Übelmesser N, Vinchure OS, Lauretti L, Fotia G, Schwarz RF, Wang X, Ricci-Vitiani L, Gopalakrishnan J, Pallini R, Papantonis A. Pervasive structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs. Nat Commun 2024; 15:3905. [PMID: 38724522 PMCID: PMC11082206 DOI: 10.1038/s41467-024-48053-2] [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: 11/24/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Glioblastoma multiforme (GBM) encompasses brain malignancies marked by phenotypic and transcriptional heterogeneity thought to render these tumors aggressive, resistant to therapy, and inevitably recurrent. However, little is known about how the spatial organization of GBM genomes underlies this heterogeneity and its effects. Here, we compile a cohort of 28 patient-derived glioblastoma stem cell-like lines (GSCs) known to reflect the properties of their tumor-of-origin; six of these were primary-relapse tumor pairs from the same patient. We generate and analyze 5 kbp-resolution chromosome conformation capture (Hi-C) data from all GSCs to systematically map thousands of standalone and complex structural variants (SVs) and the multitude of neoloops arising as a result. By combining Hi-C, histone modification, and gene expression data with chromatin folding simulations, we explain how the pervasive, uneven, and idiosyncratic occurrence of neoloops sustains tumor-specific transcriptional programs via the formation of new enhancer-promoter contacts. We also show how even moderately recurrent neoloops can relate to patient-specific vulnerabilities. Together, our data provide a resource for dissecting GBM biology and heterogeneity, as well as for informing therapeutic approaches.
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Affiliation(s)
- Ting Xie
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Adi Danieli-Mackay
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Mariachiara Buccarelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Mariano Barbieri
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Q Giorgio D'Alessandris
- Department of Neuroscience, Catholic University School of Medicine, Rome, Italy
- Department of Neuroscience, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Claudia Robens
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), University of Cologne, Cologne, Germany
| | - Nadine Übelmesser
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Omkar Suhas Vinchure
- Institute of Human Genetics, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Liverana Lauretti
- Department of Neuroscience, Catholic University School of Medicine, Rome, Italy
| | - Giorgio Fotia
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy
| | - Roland F Schwarz
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), University of Cologne, Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data (BIFOLD), Berlin, Germany
| | - Xiaotao Wang
- Institute of Reproduction and Development, Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Lucia Ricci-Vitiani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Jay Gopalakrishnan
- Institute of Human Genetics, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Institute of Human Genetics, Jena University Hospital and Friedrich Schiller University of Jena, Jena, Germany
| | - Roberto Pallini
- Department of Neuroscience, Catholic University School of Medicine, Rome, Italy.
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany.
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2
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Yao J, Zhou Y, Yao Z, Meng Y, Yu W, Yang X, Zhou D, Yang X, Zhou Y. A novel machine learning-derived four-gene signature predicts STEMI and post-STEMI heart failure. BIOMOLECULES & BIOMEDICINE 2024; 24:423-433. [PMID: 37715537 PMCID: PMC10950350 DOI: 10.17305/bb.2023.9629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/05/2023] [Accepted: 09/15/2023] [Indexed: 09/17/2023]
Abstract
High mortality and morbidity rates associated with ST-elevation myocardial infarction (STEMI) and post-STEMI heart failure (HF) necessitate proper risk stratification for coronary artery disease (CAD). A prediction model that combines specificity and convenience is highly required. This study aimed to design a monocyte-based gene assay for predicting STEMI and post-STEMI HF. A total of 1,956 monocyte expression profiles and corresponding clinical data were integrated from multiple sources. Meta-results were obtained through the weighted gene co-expression network analysis (WGCNA) and differential analysis to identify characteristic genes for STEMI. Machine learning models based on the decision tree (DT), support vector machine (SVM), and random forest (RF) algorithms were trained and validated. Five genes overlapped and were subjected to the model proposal. The discriminative performance of the DT model outperformed the other two methods. The established four-gene panel (HLA-J, CFP, STX11, and NFYC) could discriminate STEMI and HF with an area under the curve (AUC) of 0.86 or above. In the gene set enrichment analysis (GSEA), several cardiac pathogenesis pathways and cardiovascular disorder signatures showed statistically significant, concordant differences between subjects with high and low expression levels of the four-gene panel, affirming the validity of the established model. In conclusion, we have developed and validated a model that offers the hope for accurately predicting the risk of STEMI and HF, leading to optimal risk stratification and personalized management of CAD, thereby improving individual outcomes.
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Affiliation(s)
- Jialu Yao
- Department of Cardiology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Cardiology, Dushu Lake Hospital Affiliated to Soochow University, Medical Center of Soochow University, Institute for Hypertension of Soochow University, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials of Soochow University, Suzhou, Jiangsu Province, China
| | - Yujia Zhou
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
- Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Zhichao Yao
- Department of Vascular Surgery, Gusu School of Nanjing Medical University, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital (HQ), Suzhou, Jiangsu Province, China
| | - Ye Meng
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
- Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Wangjianfei Yu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
- Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Xinyu Yang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
- Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Dayong Zhou
- Department of Vascular Surgery, Gusu School of Nanjing Medical University, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital (HQ), Suzhou, Jiangsu Province, China
| | - Xiaoqin Yang
- Department of Cardiology, Dushu Lake Hospital Affiliated to Soochow University, Medical Center of Soochow University, Institute for Hypertension of Soochow University, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials of Soochow University, Suzhou, Jiangsu Province, China
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
- Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Yafeng Zhou
- Department of Cardiology, Dushu Lake Hospital Affiliated to Soochow University, Medical Center of Soochow University, Institute for Hypertension of Soochow University, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials of Soochow University, Suzhou, Jiangsu Province, China
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3
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Patel B, Eskander MA, Fang-Mei Chang P, Chapa B, Ruparel SB, Lai Z, Chen Y, Akopian A, Ruparel NB. Understanding painful versus non-painful dental pain in female and male patients: A transcriptomic analysis of human biopsies. PLoS One 2023; 18:e0291724. [PMID: 37733728 PMCID: PMC10513205 DOI: 10.1371/journal.pone.0291724] [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: 04/28/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Abstract
Dental pain from apical periodontitis is an infection induced-orofacial pain condition that presents with diversity in pain phenotypes among patients. While 60% of patients with a full-blown disease present with the hallmark symptom of mechanical allodynia, nearly 40% of patients experience no pain. Furthermore, a sexual dichotomy exists, with females exhibiting lower mechanical thresholds under basal and diseased states. Finally, the prevalence of post-treatment pain refractory to commonly used analgesics ranges from 7-19% (∼2 million patients), which warrants a thorough investigation of the cellular changes occurring in different patient cohorts. We, therefore, conducted a transcriptomic assessment of periapical biopsies (peripheral diseased tissue) from patients with persistent apical periodontitis. Surgical biopsies from symptomatic male (SM), asymptomatic male (AM), symptomatic female (SF), and asymptomatic female (AF) patients were collected and processed for bulk RNA sequencing. Using strict selection criteria, our study found several unique differentially regulated genes (DEGs) between symptomatic and asymptomatic patients, as well as novel candidate genes between sexes within the same pain group. Specifically, we found the role of cells of the innate and adaptive immune system in mediating nociception in symptomatic patients and the role of genes involved in tissue homeostasis in potentially inhibiting nociception in asymptomatic patients. Furthermore, sex-related differences appear to be tightly regulated by macrophage activity, its secretome, and/or migration. Collectively, we present, for the first time, a comprehensive assessment of peripherally diseased human tissue after a microbial insult and shed important insights into the regulation of the trigeminal system in female and male patients.
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Affiliation(s)
- Biraj Patel
- Department of Endodontics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Michael A. Eskander
- Department of Endodontics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Phoebe Fang-Mei Chang
- Department of Endodontics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Brett Chapa
- Department of Endodontics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Shivani B. Ruparel
- Department of Endodontics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Zhao Lai
- Greehey Children’s Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Yidong Chen
- Greehey Children’s Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
- Department of Population Health Sciences, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Armen Akopian
- Department of Endodontics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Nikita B. Ruparel
- Department of Endodontics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
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4
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Jeong YJ, Knutsdottir H, Shojaeian F, Lerner MG, Wissler MF, Henriet E, Ng T, Datta S, Navarro-Serer B, Chianchiano P, Kinny-Köster B, Zimmerman JW, Stein-O’Brien G, Gaida MM, Eshleman JR, Lin MT, Fertig EJ, Ewald AJ, Bader JS, Wood LD. Morphology-guided transcriptomic analysis of human pancreatic cancer organoids reveals microenvironmental signals that enhance invasion. J Clin Invest 2023; 133:e162054. [PMID: 36881486 PMCID: PMC10104894 DOI: 10.1172/jci162054] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) frequently presents with metastasis, but the molecular programs in human PDAC cells that drive invasion are not well understood. Using an experimental pipeline enabling PDAC organoid isolation and collection based on invasive phenotype, we assessed the transcriptomic programs associated with invasion in our organoid model. We identified differentially expressed genes in invasive organoids compared with matched noninvasive organoids from the same patients, and we confirmed that the encoded proteins were enhanced in organoid invasive protrusions. We identified 3 distinct transcriptomic groups in invasive organoids, 2 of which correlated directly with the morphological invasion patterns and were characterized by distinct upregulated pathways. Leveraging publicly available single-cell RNA-sequencing data, we mapped our transcriptomic groups onto human PDAC tissue samples, highlighting differences in the tumor microenvironment between transcriptomic groups and suggesting that non-neoplastic cells in the tumor microenvironment can modulate tumor cell invasion. To further address this possibility, we performed computational ligand-receptor analysis and validated the impact of multiple ligands (TGF-β1, IL-6, CXCL12, MMP9) on invasion and gene expression in an independent cohort of fresh human PDAC organoids. Our results identify molecular programs driving morphologically defined invasion patterns and highlight the tumor microenvironment as a potential modulator of these programs.
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Affiliation(s)
- Yea Ji Jeong
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hildur Knutsdottir
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland, USA
| | - Fatemeh Shojaeian
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael G. Lerner
- Department of Physics and Astronomy, Earlham College, Richmond, Indiana, USA
| | - Maria F. Wissler
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Tammy Ng
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shalini Datta
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Bernat Navarro-Serer
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Peter Chianchiano
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Jacquelyn W. Zimmerman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
- Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Genevieve Stein-O’Brien
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
- Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthias M. Gaida
- Department of Pathology, University of Mainz, Mainz, Germany
- TRON, Translational Oncology at the University Medical Center, Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
| | - James R. Eshleman
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
| | - Ming-Tseh Lin
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elana J. Fertig
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
- Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew J. Ewald
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland, USA
- Department of Cell Biology
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
| | - Joel S. Bader
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
| | - Laura D. Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
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5
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Zhang W, Xu K, Li Z, Wang L, Chen H. Tumor immune microenvironment components and the other markers can predict the efficacy of neoadjuvant chemotherapy for breast cancer. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2023; 25:1579-1593. [PMID: 36652115 DOI: 10.1007/s12094-023-03075-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023]
Abstract
Breast cancer is an epithelial malignant tumor that occurs in the terminal ducts of the breast. Neoadjuvant chemotherapy (NACT) is an important part of breast cancer treatment. Its purpose is to use systemic treatment for some locally advanced breast cancer patients, to decrease the tumor size and clinical stage so that non-operable breast cancer patients can have a chance to access surgical treatment, or patients who are not suitable for breast-conserving surgery can get the opportunity of breast-conserving. However, some patients who do not respond to NACT will lead deterioration in their condition. Therefore, prediction of NACT efficacy in breast cancer is vital for precision therapy. The tumor microenvironment (TME) has a crucial role in the carcinogenesis and therapeutic response of breast cancer. In this review, we summarized the immune cells, immune checkpoints, and other biomarkers in the TME that can evaluate the efficacy of NACT in treating breast cancer. We believe that the detection and evaluation of the TME components in breast cancer are helpful to predict the efficacy of NACT, and the prediction methods are in the prospect. In addition, we also summarized other predictive factors of NACT, such as imaging examination, biochemical markers, and multigene/multiprotein profiling.
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Affiliation(s)
- Weiqian Zhang
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, People's Republic of China.,Department of Pathology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, People's Republic of China
| | - Ke Xu
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, People's Republic of China.,Department of Pathology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, People's Republic of China
| | - Zhengfa Li
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, People's Republic of China.,Department of Pathology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, People's Republic of China
| | - Linwei Wang
- Department of Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, People's Republic of China
| | - Honglei Chen
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, People's Republic of China. .,Department of Pathology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, People's Republic of China.
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6
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Zhou S, Sun W, Zhang P, Li L. Predicting Pseudogene-miRNA Associations Based on Feature Fusion and Graph Auto-Encoder. Front Genet 2021; 12:781277. [PMID: 34966413 PMCID: PMC8710693 DOI: 10.3389/fgene.2021.781277] [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: 09/22/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudogenes were originally regarded as non-functional components scattered in the genome during evolution. Recent studies have shown that pseudogenes can be transcribed into long non-coding RNA and play a key role at multiple functional levels in different physiological and pathological processes. microRNAs (miRNAs) are a type of non-coding RNA, which plays important regulatory roles in cells. Numerous studies have shown that pseudogenes and miRNAs have interactions and form a ceRNA network with mRNA to regulate biological processes and involve diseases. Exploring the associations of pseudogenes and miRNAs will facilitate the clinical diagnosis of some diseases. Here, we propose a prediction model PMGAE (Pseudogene–MiRNA association prediction based on the Graph Auto-Encoder), which incorporates feature fusion, graph auto-encoder (GAE), and eXtreme Gradient Boosting (XGBoost). First, we calculated three types of similarities including Jaccard similarity, cosine similarity, and Pearson similarity between nodes based on the biological characteristics of pseudogenes and miRNAs. Subsequently, we fused the above similarities to construct a similarity profile as the initial representation features for nodes. Then, we aggregated the similarity profiles and associations of nodes to obtain the low-dimensional representation vector of nodes through a GAE. In the last step, we fed these representation vectors into an XGBoost classifier to predict new pseudogene–miRNA associations (PMAs). The results of five-fold cross validation show that PMGAE achieves a mean AUC of 0.8634 and mean AUPR of 0.8966. Case studies further substantiated the reliability of PMGAE for mining PMAs and the study of endogenous RNA networks in relation to diseases.
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Affiliation(s)
- Shijia Zhou
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Weicheng Sun
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Ping Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Li Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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Association of Polygenetic Risk Scores Related to Immunity and Inflammation with Hyperthyroidism Risk and Interactions between the Polygenetic Scores and Dietary Factors in a Large Cohort. J Thyroid Res 2021; 2021:7664641. [PMID: 34567510 PMCID: PMC8457978 DOI: 10.1155/2021/7664641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/14/2021] [Indexed: 12/13/2022] Open
Abstract
Graves's disease and thyroiditis induce hyperthyroidism, the causes of which remain unclear, although they are involved with genetic and environmental factors. We aimed to evaluate polygenetic variants for hyperthyroidism risk and their interaction with metabolic parameters and nutritional intakes in an urban hospital-based cohort. A genome-wide association study (GWAS) of participants with (cases; n = 842) and without (controls, n = 38,799) hyperthyroidism was used to identify and select genetic variants. In clinical and lifestyle interaction with PRS, 312 participants cured of hyperthyroidism were excluded. Single nucleotide polymorphisms (SNPs) associated with gene-gene interactions were selected by hyperthyroidism generalized multifactor dimensionality reduction. Polygenic risk scores (PRSs) were generated by summing the numbers of selected SNP risk alleles. The best gene-gene interaction model included tumor-necrosis factor (TNF)_rs1800610, mucin 22 (MUC22)_rs1304322089, tribbles pseudokinase 2 (TRIB2)_rs1881145, cytotoxic T-lymphocyte-associated antigen 4 (CTLA4)_rs231775, lipoma-preferred partner (LPP)_rs6780858, and human leukocyte antigen (HLA)-J_ rs767861647. The PRS of the best model was positively associated with hyperthyroidism risk by 1.939-fold (1.317-2.854) after adjusting for covariates. PRSs interacted with age, metabolic syndrome, and dietary inflammatory index (DII), while hyperthyroidism risk interacted with energy, calcium, seaweed, milk, and coffee intake (P < 0.05). The PRS impact on hyperthyroidism risk was observed in younger (<55 years) participants and adults without metabolic syndrome. PRSs were positively associated with hyperthyroidism risk in participants with low dietary intakes of energy (OR = 2.74), calcium (OR = 2.84), seaweed (OR = 3.43), milk (OR = 2.91), coffee (OR = 2.44), and DII (OR = 3.45). In conclusion, adults with high PRS involved in inflammation and immunity had a high hyperthyroidism risk exacerbated under low intakes of energy, calcium, seaweed, milk, or coffee. These results can be applied to personalized nutrition in a clinical setting.
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8
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Paganini J, Picard C, Gouret P, Chiaroni J, Di Cristofaro J. Validation of new HLA-J alleles assigned by next generation sequencing. HLA 2021; 98:173-175. [PMID: 33914413 DOI: 10.1111/tan.14288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/30/2022]
Abstract
We describe nine novel HLA-J alleles validated by in silico and experimental data.
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Affiliation(s)
| | - Christophe Picard
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France.,Aix Marseille University, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
| | | | - Jacques Chiaroni
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France.,Aix Marseille University, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
| | - Julie Di Cristofaro
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France.,Aix Marseille University, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
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