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Sun C, Zhang H, Li Y, Yu Y, Liu J, Liu R, Sun C. Elucidation of clinical implications Arising from circadian rhythm and insights into the tumor immune landscape in breast cancer. Heliyon 2024; 10:e27356. [PMID: 38500978 PMCID: PMC10945177 DOI: 10.1016/j.heliyon.2024.e27356] [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: 10/07/2023] [Revised: 02/03/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Background Circadian rhythm is an internal timing system generated by circadian-related genes (CRGs). Disruption in this rhythm has been associated with a heightened risk of breast cancer (BC) and regulation of the immune microenvironment of tumors. This study aimed to investigate the clinical significance of CRGs in BC and the immune microenvironment. Methods CRGs were identified using the GeneCards and MSigDB databases. Through unsupervised clustering, we identified two circadian-related subtypes in patients with BC. We constructed a prognostic model and nomogram for circadian-related risk scores using LASSO and Cox regression analyses. Using multi-omics analysis, the mutation profile and immunological microenvironment of tumors were investigated, and the immunotherapy response in different groups of patients was predicted based on their risk strata. Results The two circadian-related subtypes of BC that were identified differed significantly in their prognoses, clinical characteristics, and tumor immune microenvironments. Subsequently, we constructed a circadian-related risk score (CRRS) model containing eight signatures (SIAH2, EZR, GSN, TAGLN2, PRDX1, MCM4, EIF4EBP1, and CD248) and a nomogram. High-risk individuals had a greater burden of tumor mutations, richer immune cell infiltration, and higher expression of immune checkpoint genes, than low-risk individuals, indicating a "hot tumor" immune phenotype and a more favorable treatment outcome. Conclusions Two circadian-related subtypes of BC were identified and used to establish a CRRS prognostic model and nomogram. These will be valuable in providing guidance for forecasting prognosis and developing personalized treatment plans for BC.
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Affiliation(s)
- Chunjie Sun
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250355 Shandong, China
| | - Hanyun Zhang
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250355 Shandong, China
| | - Ye Li
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, Taipa, 999078, China
| | - Yang Yu
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, Taipa, 999078, China
| | - Jingyang Liu
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, Taipa, 999078, China
| | - Ruijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, 261041 Shandong, China
| | - Changgang Sun
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, 261041 Shandong, China
- College of Traditional Chinese Medicine, Shandong Second Medical University, Weifang, 261053 Shandong, China
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2
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Zhou Y, Gao M, Jing Y, Wang X. Pan-cancer analyses reveal IGSF10 as an immunological and prognostic biomarker. Front Genet 2023; 13:1032382. [PMID: 36685968 PMCID: PMC9845414 DOI: 10.3389/fgene.2022.1032382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Background: IGSF10 is a member of the immunoglobulin superfamily. Over the previous decade, growing proof has validated definitive correlations between individuals of the immunoglobulin superfamily and human diseases. However, the function of IGSF10 in pan-cancer stays unclear. We aimed to analyze the immunological and prognostic value of IGSF10 in pan-cancer. Methods: We utilized a vary of bioinformatic ways to inspect the function of IGSF10 in pan-cancer, including its correlation with prognosis, immune cell infiltration, tumor mutational burden (TMB), microsatellite instability (MSI), mismatch repair (MMR), DNA methyltransferases, genetic alteration, drug sensitivity, etc. Results: We noticed low expression of IGSF10 in most cancer types. IGSF10 expression in tumor samples correlates with prognosis in most cancers. In most cancer types, IGSF10 expression was strongly related to immune cells infiltration, immune checkpoints, immune modulators, TMB, MSI, MMR, and DNA methyltransferases, among others. Functional enrichment analyses indicated that IGSF10 expression was involved in lymphocyte differentiation, cell molecules adhesion, etc. Furthermore, low IGSF10 expression could increase the drug sensitivity of many drugs. Conclusion: IGSF10 could serve as a novel prognostic marker and attainable immunotherapy target for several malignancies.
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Affiliation(s)
- Yongxia Zhou
- Department of Hematology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China,Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China,Tianjin’s Clinical Research Center for Cancer, Tianjin, China,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Manzhi Gao
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China,Tianjin’s Clinical Research Center for Cancer, Tianjin, China,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Yaoyao Jing
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China,Tianjin’s Clinical Research Center for Cancer, Tianjin, China,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China,Day Ward of Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
| | - Xiaofang Wang
- Department of Hematology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China,Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, China,Tianjin’s Clinical Research Center for Cancer, Tianjin, China,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China,*Correspondence: Xiaofang Wang,
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3
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Medeiros JJF, Capo-Chichi JM, Shlush LI, Dick JE, Arruda A, Minden MD, Abelson S. SmMIP-tools: a computational toolset for processing and analysis of single-molecule molecular inversion probes-derived data. Bioinformatics 2022; 38:2088-2095. [PMID: 35150236 PMCID: PMC9004652 DOI: 10.1093/bioinformatics/btac081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/13/2022] [Accepted: 02/07/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Single-molecule molecular inversion probes (smMIPs) provide an exceptionally cost-effective and modular approach for routine or large-cohort next-generation sequencing. However, processing the derived raw data to generate highly accurate variants calls remains challenging. RESULTS We introduce SmMIP-tools, a comprehensive computational method that promotes the detection of single nucleotide variants and short insertions and deletions from smMIP-based sequencing. Our approach delivered near-perfect performance when benchmarked against a set of known mutations in controlled experiments involving DNA dilutions and outperformed other commonly used computational methods for mutation detection. Comparison against clinically approved diagnostic testing of leukaemia patients demonstrated the ability to detect both previously reported variants and a set of pathogenic mutations that did not pass detection by clinical testing. Collectively, our results indicate that increased performance can be achieved when tailoring data processing and analysis to its related technology. The feasibility of using our method in research and clinical settings to benefit from low-cost smMIP technology is demonstrated. AVAILABILITY AND IMPLEMENTATION The source code for SmMIP-tools, its manual and additional scripts aimed to foster large-scale data processing and analysis are all available on github (https://github.com/abelson-lab/smMIP-tools). Raw sequencing data generated in this study have been submitted to the European Genome-Phenome Archive (EGA; https://ega-archive.org) and can be accessed under accession number EGAS00001005359. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jessie J F Medeiros
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada,Ontario Institute for Cancer Research, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jose-Mario Capo-Chichi
- Genome Diagnostics, Department of Clinical Laboratory Genetics, University Health Network, Toronto, ON, Canada
| | - Liran I Shlush
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Andrea Arruda
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada,Department of Hematology and Medical Oncology, University Health Network, Toronto, ON, Canada
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Willey JC, Morrison TB, Austermiller B, Crawford EL, Craig DJ, Blomquist TM, Jones WD, Wali A, Lococo JS, Haseley N, Richmond TA, Novoradovskaya N, Kusko R, Chen G, Li QZ, Johann DJ, Deveson IW, Mercer TR, Wu L, Xu J. Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA. CELL REPORTS METHODS 2021; 1:100106. [PMID: 35475002 PMCID: PMC9017191 DOI: 10.1016/j.crmeth.2021.100106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/31/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022]
Abstract
The primary objective of the FDA-led Sequencing and Quality Control Phase 2 (SEQC2) project is to develop standard analysis protocols and quality control metrics for use in DNA testing to enhance scientific research and precision medicine. This study reports a targeted next-generation sequencing (NGS) method that will enable more accurate detection of actionable mutations in circulating tumor DNA (ctDNA) clinical specimens. To accomplish this, a synthetic internal standard spike-in was designed for each actionable mutation target, suitable for use in NGS following hybrid capture enrichment and unique molecular index (UMI) or non-UMI library preparation. When mixed with contrived ctDNA reference samples, internal standards enabled calculation of technical error rate, limit of blank, and limit of detection for each variant at each nucleotide position in each sample. True-positive mutations with variant allele fraction too low for detection by current practice were detected with this method, thereby increasing sensitivity.
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Affiliation(s)
- James C. Willey
- College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | - Tom B. Morrison
- AccuGenomics Inc., The Atrium, Suite 105, 1410 Commonwealth Drive, Wilmington, NC 28403, USA
| | - Bradley Austermiller
- AccuGenomics Inc., The Atrium, Suite 105, 1410 Commonwealth Drive, Wilmington, NC 28403, USA
| | - Erin L. Crawford
- College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | - Daniel J. Craig
- College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | - Thomas M. Blomquist
- College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | | | - Aminah Wali
- Q Solutions, EA Genomics, Morrisville, NC 27560, USA
| | | | - Nathan Haseley
- Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | | | | | | | - Guangchun Chen
- University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Quan-Zhen Li
- University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Donald J. Johann
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham Street, Little Rock, AR 72205, USA
| | - Ira W. Deveson
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Timothy R. Mercer
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Leihong Wu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
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Technical and biological constraints on ctDNA-based genotyping. Trends Cancer 2021; 7:995-1009. [PMID: 34219051 DOI: 10.1016/j.trecan.2021.06.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/18/2022]
Abstract
Circulating tumor DNA (ctDNA) enables real-time genomic profiling of cancer without the need for tissue biopsy. ctDNA-based technology is seeing rapid uptake in clinical practice due to the potential to inform patient management from diagnosis to advanced disease. In metastatic disease, ctDNA can identify somatic mutations, copy-number variants (CNVs), and structural rearrangements that are predictive of therapy response. However, the ctDNA fraction (ctDNA%) is unpredictable and confounds variant detection strategies, undermining confidence in liquid biopsy results. Assay design also influences which types of genomic alterations are identifiable. Here, we describe the relationships between ctDNA%, methodology, and sensitivity-specificity for major classes of genomic alterations in prostate cancer. We provide recommendations to navigate the technical complexities that constrain the detection of clinically relevant genomic alterations in ctDNA.
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