3
|
Long Y, Huang F, Zhang J, Zhang J, Cheng R, Zhu L, Chen Q, Yang D, Pan X, Yang W, Qin M, Huang J. Identification of SUMOylation-related signature genes associated with immune infiltration in ulcerative colitis through bioinformatics analysis and experimental validation. Gene 2025; 935:148996. [PMID: 39395728 DOI: 10.1016/j.gene.2024.148996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2024] [Revised: 09/13/2024] [Accepted: 10/09/2024] [Indexed: 10/14/2024]
Abstract
OBJECTIVE Ulcerative colitis (UC) is a chronic inflammatory disorder challenging to diagnose clinically. We focused on identifying and validating SUMOylation-related signature genes in UC and their association with immune infiltration. METHODS Five eligible gene expression profiles were selected from the Gene Expression Omnibus (GEO) database and merged into a single dataset comprising 260 UC patients and 76 healthy controls (HC). Differentially expressed genes (DEGs) were identified, and these were intersected with SUMOylation-related genes to obtain differentially expressed SUMOylation-related genes (DESRGs). Next, we identify the signature genes and validate them through comprehensive analyses employing GO, KEGG, GSVA, Lasso-cox regression, ROC curves, and clustering analysis. The infiltrating immune cells were analyzed using the CIBERSORT algorithm and Pearson correlation analysis. Finally, in vitro and in vivo experiments validated the identified signature genes. RESULTS PALMD, THRB, MAGED1, PARP1, and SLC16A1 were identified. Next, an excellent predictive model for UC was established and distinct subgroups of patients associated with SUMOylation were identified. Moreover, the NF-κB signaling pathway likely plays a pivotal role in the regulation of SUMOylation in UC. Additionally, we validated that the alterations in PALMD, THRB, and MAGED1 expression in LPS-induced Caco-2 cells concurred with our bioinformatics findings, particularly demonstrating statistically significant differences in PALMD and THRB expression. Finally, in a DSS-induced mouse colitis model, we observed a significant upregulation of PALMD expression. Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation. CONCLUSION This study comprehensively elucidates the biological roles of SUMOylation-related genes in UC, identifying PALMD, MAGED1, THRB, PARP1, and SLC16A1 as signature genes that represent promising biomarkers for UC diagnosis and prognosis.
Collapse
Affiliation(s)
- Ying Long
- Department of Gastroenterology, the Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China; Department of Gastroenterology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou 545006, People's Republic of China
| | - Feihong Huang
- Spine and Osteopathy Ward, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, People's Republic of China
| | - Juan Zhang
- Department of Pediatrics, Zhuzhou Central Hospital, Zhuzhou 412000, People's Republic of China
| | - Jinxiu Zhang
- Department of Gastroenterology, the Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Ruoxi Cheng
- Department of Gastroenterology, the Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Liye Zhu
- Department of Gastroenterology, the Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Qiuling Chen
- Department of Gastroenterology, the Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Dan Yang
- Department of Gastroenterology, the Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Xiaoping Pan
- Department of Gastroenterology, the Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Wenfang Yang
- Department of Gastroenterology, the Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Mengbin Qin
- Department of Gastroenterology, the Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China.
| | - Jiean Huang
- Department of Gastroenterology, the Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China.
| |
Collapse
|
5
|
Ma XR, Conley SD, Kosicki M, Bredikhin D, Cui R, Tran S, Sheth MU, Qiu WL, Chen S, Kundu S, Kang HY, Amgalan D, Munger CJ, Duan L, Dang K, Rubio OM, Kany S, Zamirpour S, DePaolo J, Padmanabhan A, Olgin J, Damrauer S, Andersson R, Gu M, Priest JR, Quertermous T, Qiu X, Rabinovitch M, Visel A, Pennacchio L, Kundaje A, Glass IA, Gifford CA, Pirruccello JP, Goodyer WR, Engreitz JM. Molecular convergence of risk variants for congenital heart defects leveraging a regulatory map of the human fetal heart. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.11.20.24317557. [PMID: 39606363 PMCID: PMC11601760 DOI: 10.1101/2024.11.20.24317557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Congenital heart defects (CHD) arise in part due to inherited genetic variants that alter genes and noncoding regulatory elements in the human genome. These variants are thought to act during fetal development to influence the formation of different heart structures. However, identifying the genes, pathways, and cell types that mediate these effects has been challenging due to the immense diversity of cell types involved in heart development as well as the superimposed complexities of interpreting noncoding sequences. As such, understanding the molecular functions of both noncoding and coding variants remains paramount to our fundamental understanding of cardiac development and CHD. Here, we created a gene regulation map of the healthy human fetal heart across developmental time, and applied it to interpret the functions of variants associated with CHD and quantitative cardiac traits. We collected single-cell multiomic data from 734,000 single cells sampled from 41 fetal hearts spanning post-conception weeks 6 to 22, enabling the construction of gene regulation maps in 90 cardiac cell types and states, including rare populations of cardiac conduction cells. Through an unbiased analysis of all 90 cell types, we find that both rare coding variants associated with CHD and common noncoding variants associated with valve traits converge to affect valvular interstitial cells (VICs). VICs are enriched for high expression of known CHD genes previously identified through mapping of rare coding variants. Eight CHD genes, as well as other genes in similar molecular pathways, are linked to common noncoding variants associated with other valve diseases or traits via enhancers in VICs. In addition, certain common noncoding variants impact enhancers with activities highly specific to particular subanatomic structures in the heart, illuminating how such variants can impact specific aspects of heart structure and function. Together, these results implicate new enhancers, genes, and cell types in the genetic etiology of CHD, identify molecular convergence of common noncoding and rare coding variants on VICs, and suggest a more expansive view of the cell types instrumental in genetic risk for CHD, beyond the working cardiomyocyte. This regulatory map of the human fetal heart will provide a foundational resource for understanding cardiac development, interpreting genetic variants associated with heart disease, and discovering targets for cell-type specific therapies.
Collapse
Affiliation(s)
- X Rosa Ma
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Stephanie D Conley
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Danila Bredikhin
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ran Cui
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven Tran
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Maya U Sheth
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Wei-Lin Qiu
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sijie Chen
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Soumya Kundu
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Helen Y Kang
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Current address: PhD Program in Computational and Systems Biology, MIT, Cambridge, MA, USA
| | - Dulguun Amgalan
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Maternal and Child Health Research Institute, Stanford University, Stanford, CA, USA
| | - Chad J Munger
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Lauren Duan
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Katherine Dang
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Oriane Matthys Rubio
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Shinwan Kany
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Cardiology, University Heart and Vascular Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Siavash Zamirpour
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - John DePaolo
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arun Padmanabhan
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco School of Medicine, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jeffrey Olgin
- Division of Cardiology, Department of Medicine and Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Scott Damrauer
- Division of Vascular Surgery and Endovascular Therapy, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robin Andersson
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mingxia Gu
- Center for Stem Cell and Organoid Medicine, Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- University of Cincinnati School of Medicine, Cincinnati, OH, USA
| | - James R Priest
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Tenaya Therapeutics, South San Francisco, CA, USA
| | - Thomas Quertermous
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Xiaojie Qiu
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Maternal and Child Health Research Institute, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Bio-X, Stanford University, Stanford, CA, USA
| | - Marlene Rabinovitch
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University, Stanford, CA, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, USA
| | - Len Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ian A Glass
- Maternal and Child Health Research Institute, Stanford University, Stanford, CA, USA
- Department of Pediatrics and Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Casey A Gifford
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Maternal and Child Health Research Institute, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - James P Pirruccello
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Cardiology, Department of Medicine and Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Bakar Computation Health Sciences Institute, University of California, San Francisco, CA, USA
| | - William R Goodyer
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Maternal and Child Health Research Institute, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Jesse M Engreitz
- Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Maternal and Child Health Research Institute, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| |
Collapse
|