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Wang D, Liu Y, Zhang Y, Chen Q, Han Y, Hou W, Liu C, Yu Y, Li Z, Li Z, Zhao J, Shi L, Zheng Y, Li J, Zhang R. A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials. Nat Commun 2024; 15:6167. [PMID: 39039053 PMCID: PMC11263697 DOI: 10.1038/s41467-024-50420-y] [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: 12/12/2023] [Accepted: 07/02/2024] [Indexed: 07/24/2024] Open
Abstract
Translating RNA-seq into clinical diagnostics requires ensuring the reliability and cross-laboratory consistency of detecting clinically relevant subtle differential expressions, such as those between different disease subtypes or stages. As part of the Quartet project, we present an RNA-seq benchmarking study across 45 laboratories using the Quartet and MAQC reference samples spiked with ERCC controls. Based on multiple types of 'ground truth', we systematically assess the real-world RNA-seq performance and investigate the influencing factors involved in 26 experimental processes and 140 bioinformatics pipelines. Here we show greater inter-laboratory variations in detecting subtle differential expressions among the Quartet samples. Experimental factors including mRNA enrichment and strandedness, and each bioinformatics step, emerge as primary sources of variations in gene expression. We underscore the profound influence of experimental execution, and provide best practice recommendations for experimental designs, strategies for filtering low-expression genes, and the optimal gene annotation and analysis pipelines. In summary, this study lays the foundation for developing and quality control of RNA-seq for clinical diagnostic purposes.
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Affiliation(s)
- Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yuanfeng Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Cong Liu
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ziyang Li
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Ziqiang Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Jiaxin Zhao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai, China.
- International Human Phenome Institutes, Shanghai, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai, China.
- International Human Phenome Institutes, Shanghai, China.
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China.
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China.
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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Kumar V, Bauer C, Stewart JH. Targeting cGAS/STING signaling-mediated myeloid immune cell dysfunction in TIME. J Biomed Sci 2023; 30:48. [PMID: 37380989 PMCID: PMC10304357 DOI: 10.1186/s12929-023-00942-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023] Open
Abstract
Myeloid immune cells (MICs) are potent innate immune cells serving as first responders to invading pathogens and internal changes to cellular homeostasis. Cancer is a stage of altered cellular homeostasis that can originate in response to different pathogens, chemical carcinogens, and internal genetic/epigenetic changes. MICs express several pattern recognition receptors (PRRs) on their membranes, cytosol, and organelles, recognizing systemic, tissue, and organ-specific altered homeostasis. cGAS/STING signaling is a cytosolic PRR system for identifying cytosolic double-stranded DNA (dsDNA) in a sequence-independent but size-dependent manner. The longer the cytosolic dsDNA size, the stronger the cGAS/STING signaling activation with increased type 1 interferon (IFN) and NF-κB-dependent cytokines and chemokines' generation. The present article discusses tumor-supportive changes occurring in the tumor microenvironment (TME) or tumor immune microenvironment (TIME) MICs, specifically emphasizing cGAS/STING signaling-dependent alteration. The article further discusses utilizing MIC-specific cGAS/STING signaling modulation as critical tumor immunotherapy to alter TIME.
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Affiliation(s)
- Vijay Kumar
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Science Center (LSUHSC), 1700 Tulane Avenue, New Orleans, LA, 70012, USA.
| | - Caitlin Bauer
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Science Center (LSUHSC), 1700 Tulane Avenue, New Orleans, LA, 70012, USA
| | - John H Stewart
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Science Center (LSUHSC), 1700 Tulane Avenue, New Orleans, LA, 70012, USA.
- Louisiana Children's Medical Center Cancer Center, Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Science Center (LSUHSC), 1700 Tulane Avenue, New Orleans, LA, 70012, USA.
- Surgery, Section of Surgical Oncology, Louisiana State University New Orleans-Louisiana Children's Medical Center Cancer Center, Louisiana State University Health Science Center (LSUHSC), 1700 Tulane Avenue, New Orleans, LA, 70012, USA.
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Cheng B, Yu Q, Wang W. Intimate communications within the tumor microenvironment: stromal factors function as an orchestra. J Biomed Sci 2023; 30:1. [PMID: 36600243 DOI: 10.1186/s12929-022-00894-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/18/2022] [Indexed: 01/06/2023] Open
Abstract
Extensive studies of the tumor microenvironment (TME) in the last decade have reformed the view of cancer as a tumor cell-centric disease. The tumor microenvironment, especially termed the "seed and soil" theory, has emerged as the key determinant in cancer development and therapeutic resistance. The TME mainly consists of tumor cells, stromal cells such as fibroblasts, immune cells, and other noncellular components. Within the TME, intimate communications among these components largely determine the fate of the tumor. The pivotal roles of the stroma, especially cancer-associated fibroblasts (CAFs), the most common component within the TME, have been revealed in tumorigenesis, tumor progression, therapeutic response, and tumor immunity. A better understanding of the function of the TME sheds light on tumor therapy. In this review, we summarize the emerging understanding of stromal factors, especially CAFs, in cancer progression, drug resistance, and tumor immunity with an emphasis on their functions in epigenetic regulation. Moreover, the importance of epigenetic regulation in reshaping the TME and the basic biological principles underpinning the synergy between epigenetic therapy and immunotherapy will be further discussed.
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Affiliation(s)
- Bing Cheng
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Guangdong Research Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Qiang Yu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
- Guangdong Research Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
- Cancer Precision Medicine, Genome Institute of Singapore, Agency for Science, Technology, and Research, Biopolis, Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Cancer and Stem Cell Biology, DUKE-NUS Graduate Medical School of Singapore, Singapore, Singapore.
| | - Wenyu Wang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
- Guangdong Research Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
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Ren C, Gao A, Fu C, Teng X, Wang J, Lu S, Gao J, Huang J, Liu D, Xu J. The biomarkers related to immune infiltration to predict distant metastasis in breast cancer patients. Front Genet 2023; 14:1105689. [PMID: 36911401 PMCID: PMC9992813 DOI: 10.3389/fgene.2023.1105689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
Background: The development of distant metastasis (DM) results in poor prognosis of breast cancer (BC) patients, however, it is difficult to predict the risk of distant metastasis. Methods: Differentially expressed genes (DEGs) were screened out using GSE184717 and GSE183947. GSE20685 were randomly assigned to the training and the internal validation cohort. A signature was developed according to the results of univariate and multivariate Cox regression analysis, which was validated by using internal and external (GSE6532) validation cohort. Gene set enrichment analysis (GSEA) was used for functional analysis. Finally, a nomogram was constructed and calibration curves and concordance index (C-index) were compiled to determine predictive and discriminatory capacity. The clinical benefit of this nomogram was revealed by decision curve analysis (DCA). Finally, we explored the relationships between candidate genes and immune cell infiltration, and the possible mechanism. Results: A signature containing CD74 and TSPAN7 was developed according to the results of univariate and multivariate Cox regression analysis, which was validated by using internal and external (GSE6532) validation cohort. Mechanistically, the signature reflect the overall level of immune infiltration in tissues, especially myeloid immune cells. The expression of CD74 and TSPAN7 is heterogeneous, and the overexpression is positively correlated with the infiltration of myeloid immune cells. CD74 is mainly derived from myeloid immune cells and do not affect the proportion of CD8+T cells. Low expression levels of TSPAN7 is mainly caused by methylation modification in BC cells. This signature could act as an independent predictive factor in patients with BC (p = 0.01, HR = 0.63), and it has been validated in internal (p = 0.023, HR = 0.58) and external (p = 0.0065, HR = 0.67) cohort. Finally, we constructed an individualized prediction nomogram based on our signature. The model showed good discrimination in training, internal and external cohort, with a C-index of 0.742, 0.801, 0.695 respectively, and good calibration. DCA demonstrated that the prediction nomogram was clinically useful. Conclusion: A new immune infiltration related signature developed for predicting metastatic risk will improve the treatment and management of BC patients.
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Affiliation(s)
- Chengsi Ren
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Anran Gao
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Chengshi Fu
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Xiangyun Teng
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Jianzhang Wang
- Department of Pathology, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Shaofang Lu
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Jiahui Gao
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Jinfeng Huang
- Department of Pathology, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Dongdong Liu
- Department of Laboratory Science, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianhua Xu
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
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Liu X, Qin J, Nie J, Sun H, Pan Y, Wang S. Reclassifying TNM stage I/II colorectal cancer into two subgroups with different overall survival, tumor microenvironment, and response to immune checkpoint blockade treatment. Front Genet 2022; 13:948920. [PMID: 36212126 PMCID: PMC9532767 DOI: 10.3389/fgene.2022.948920] [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: 05/20/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The traditional TNM staging system is often insufficient to differentiate the survival discrepancies of colorectal cancer (CRC) patients at TNM stage I/II. Our study aimed to reclassify stage I/II CRC patients into several subgroups with different prognoses and explore their suitable therapeutic methods. Methods: Single-cell RNA (scRNA) sequencing data, bulk RNA sequencing data, and clinicopathological information of CRC patients were enrolled from the TCGA and GEO databases. The tumor microenvironment of CRC tissues was accessed by the ESTIMATE algorithm. The prognostic genes were identified by Cox regression analysis. GO and KEGG analyses were conducted in the DAVID database. GSEA analysis was performed for annotation of the correlated gene sets. Results: We successfully reclassified stage I/II CRC patients into two subgroups and discovered that patients in cluster-2 underwent worse overall survival than those in cluster-1. GSEA analysis showed that immune-associated gene sets were positively enriched in cluster-2. Besides, the differentially expressed genes (DEGs) between cluster-1 and cluster-2 patients also participated in immune-related biological processes and signaling pathways. Moreover, we found that more immune cells infiltrated the microenvironment of cluster-2 patients compared to that of cluster-1 patients, such as Tregs and tumor-associated macrophages. ScRNA sequencing analysis uncovered that most of the enriched immune-associated signaling in cluster-2 patients was mainly attributed to these upregulated immune cells whose infiltration levels were also high in CRC tissues rather than in normal tissues. In addition, we demonstrated that the expression of immune checkpoint genes was significantly higher in cluster-2 patients compared to cluster-1 patients. ScRNA sequencing analysis revealed that the infiltrated CD8+T cells in CRC were naïve T cells and can be activated into effector T cells after immune checkpoint blockade (ICB) treatment. Conclusion: TNM stage I/II CRC patients can be divided into two subgroups, which have different overall survival rates, tumor microenvironment, and response to ICB therapy.
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Affiliation(s)
- Xiangxiang Liu
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jian Qin
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Junjie Nie
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Huiling Sun
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuqin Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- *Correspondence: Yuqin Pan, ; Shukui Wang,
| | - Shukui Wang
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- *Correspondence: Yuqin Pan, ; Shukui Wang,
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Liang R, Zhu X, Lan T, Ding D, Zheng Z, Chen T, Huang Y, Liu J, Yang X, Shao J, Wei H, Wei B. TIGIT promotes CD8 +T cells exhaustion and predicts poor prognosis of colorectal cancer. Cancer Immunol Immunother 2021; 70:2781-2793. [PMID: 33634371 DOI: 10.1007/s00262-021-02886-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/08/2021] [Indexed: 12/12/2022]
Abstract
TIGIT is a lymphocyte surface receptor, which is mainly expressed on the surface of CD8+T cells. The role of TIGIT in colorectal cancer and its expression pattern in colorectal cancer infiltrating lymphocytes are still controversial. This study aimed at identifying the function of TIGIT in colorectal cancer. Patients with colorectal cancer showed significantly higher TIGIT+CD8+T cell infiltration in tumor tissues, metastases compared with paired PBMC and normal tissues through flow cytometry. TIGIT+CD8+T cells showed an exhausted phenotype and expressed low levels of killer cytokines IFN-γ, IL-2, TNF-α. In addition, more inhibitory receptors such as PD-1, LAG-3, and TIM-3 were expressed on the surface of TIGIT+CD8+T cells. TGF-β1 could promote the expression of TIGIT and inhibit CD8+T cell function in vitro. Moreover, the accumulation of TIGIT+T cells in tumors was associated with advanced disease, predicted early recurrence, and reduced survival rates in colorectal cancer patients. Our results indicate that TIGIT can be a biological marker for the prognosis of colorectal cancer, and TIGIT can be used as a potential target for treatment.
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Affiliation(s)
- Rongpu Liang
- Department of Gastrointestinal Surgery, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510630, People's Republic of China
| | - Xudong Zhu
- Department of Gastrointestinal Surgery, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510630, People's Republic of China
| | - Tianyun Lan
- Central Laboratory, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, Guangdong, People's Republic of China
| | - Dongbing Ding
- Department of Gastrointestinal Surgery, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510630, People's Republic of China
| | - Zongheng Zheng
- Department of Gastrointestinal Surgery, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510630, People's Republic of China
| | - Tufeng Chen
- Department of Gastrointestinal Surgery, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510630, People's Republic of China
| | - Yong Huang
- Department of Gastrointestinal Surgery, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510630, People's Republic of China
| | - Jianpei Liu
- Department of Gastrointestinal Surgery, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510630, People's Republic of China
| | - Xiaofeng Yang
- Department of Gastrointestinal Surgery, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510630, People's Republic of China
| | - Jun Shao
- Department of Gastrointestinal Surgery, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510630, People's Republic of China
| | - Hongbo Wei
- Department of Gastrointestinal Surgery, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510630, People's Republic of China.
| | - Bo Wei
- Department of Gastrointestinal Surgery, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510630, People's Republic of China.
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Saleh R, Sasidharan Nair V, Al-Dhaheri M, Khawar M, Abu Nada M, Alajez NM, Elkord E. RNA-Seq Analysis of Colorectal Tumor-Infiltrating Myeloid-Derived Suppressor Cell Subsets Revealed Gene Signatures of Poor Prognosis. Front Oncol 2020; 10:604906. [PMID: 33312958 PMCID: PMC7703275 DOI: 10.3389/fonc.2020.604906] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
Elevated levels of myeloid-derived suppressor cells (MDSCs), including polymorphonuclear MDSCs (PMN-MDSCs) and immature MDSCs (I-MDSCs), are usually associated with disease progression in cancer patients, including colorectal cancer (CRC). However, biological mechanisms and molecular pathways regulated by MDSC subpopulations in the CRC tumor microenvironment (TME) have not been fully investigated. In this study, we performed transcriptomic analysis of tumor-infiltrating I-MDSCs and PMN-MDSCs isolated from tumor tissues of six CRC patients, compared to antigen-presenting cells (APCs). We also compared the transcriptomic profiles of tumor-infiltrating PMN-MDSCs to I-MDSCs. Our results showed different molecular pathways regulated by each MDSC subset, potentially reflecting their phenotypical/molecular/functional characteristics in the CRC TME. Moreover, we identified gene signatures in PMN-MDSC and I-MDSC of poor overall survival (OS) and disease-free survival (DFS) using the Cancer Genome Atlas (TCGA) dataset from patients with colon adenocarcinoma (COAD). However, functional studies are required to validate these findings.
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Affiliation(s)
- Reem Saleh
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Varun Sasidharan Nair
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | | | - Mahwish Khawar
- Department of Surgery, Hamad Medical Corporation, Doha, Qatar
| | | | - Nehad M Alajez
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Eyad Elkord
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.,Biomedical Research Center, School of Science, Engineering and Environment, University of Salford, Manchester, United Kingdom
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