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Andersen L, Kisistók J, Henriksen TV, Bramsen JB, Reinert T, Øgaard N, Mattesen TB, Birkbak NJ, Andersen CL. Exploring the biology of ctDNA release in colorectal cancer. Eur J Cancer 2024; 207:114186. [PMID: 38943900 DOI: 10.1016/j.ejca.2024.114186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/16/2024] [Indexed: 07/01/2024]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has emerged as a promising tool for early cancer detection and minimal residual disease monitoring. However, the biology underlying ctDNA release and its variation across cancer types and histologies remains poorly understood. This study investigated the biology behind ctDNA shedding in colorectal cancer. METHODS The study included a local cohort of 747 stage I-III colorectal cancer patients. All patients had ctDNA measurement prior to treatment and extensive clinical data. Primary tumor RNA sequencing and whole exome sequencing was performed in 95 and 652 patients respectively. Additionally, the study evaluated 89 non-small cell lung cancer patients from the TRACERx cohort, comprising primary tumor RNA sequencing and ctDNA measurement. RESULTS We found tumor size and proliferative capacity to be key factors associated with ctDNA shedding in colorectal cancer. Furthermore, we found that the secretory and CMS3 colorectal cancer subtypes exhibited lower ctDNA shedding, while microsatellite instability (MSI) tumors had higher levels of ctDNA. Mutational analysis did not reveal any genes or pathways associated with ctDNA shedding in colorectal cancer. A comparison of transcriptomic profiles across multiple cancer types demonstrated that colorectal cancer and lung squamous cell carcinoma tumors shared a high-proliferative ctDNA shedding phenotype, while lung adenocarcinoma tumors displayed a distinct low-proliferative subgroup. Additionally, proliferation levels correlated with ctDNA detection sensitivity across multiple cancer types. CONCLUSION These findings suggest that tumor size and proliferative capacity are drivers of ctDNA release in colorectal cancer and provide insights into the biology of ctDNA shedding on a pan-cancer level.
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Affiliation(s)
- Laura Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark; Bioinformatics Research Centre, Aarhus University, Denmark
| | - Judit Kisistók
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark; Bioinformatics Research Centre, Aarhus University, Denmark
| | - Tenna V Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Jesper B Bramsen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Nadia Øgaard
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Trine B Mattesen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Nicolai J Birkbak
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark; Bioinformatics Research Centre, Aarhus University, Denmark.
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark.
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2
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Fu D, Zhang T, Liu J, Chang B, Zhang Q, Tan Y, Chen X, Tan L. Identification of adipocyte infiltration-related gene subtypes for predicting colorectal cancer prognosis and responses of immunotherapy/chemotherapy. Heliyon 2024; 10:e33616. [PMID: 39050460 PMCID: PMC11266998 DOI: 10.1016/j.heliyon.2024.e33616] [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: 01/02/2024] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024] Open
Abstract
Colorectal cancer (CRC) is a prevalent and aggressive malignancy characterized by a complex tumor microenvironment (TME). Given the variations in the level of adipocyte infiltration in TME, the prognosis may differ among CRC patients. Thus, there is an urgent need to establish a reliable method for identifying adipocyte subtypes in CRC in order to elucidate the impact of adipocyte infiltration on CRC treatment and prognosis. Herein, 144 adipocyte-infiltration-related genes (AIRGs) were identified as predictive markers for the immune-associated features and prognosis of CRC patients. Based on the 144 genes, the unsupervised clustering algorithm identified two distinct clusters of CRC patients with variations in molecular and signaling pathways, clinicopathological characteristics and responses to CRC chemotherapy and immunotherapy. Furthermore, an AIRG prognostic signature was constructed and validated in independent datasets. Overall, this study developed a prognostic signature based on AIRGs in CRC, which may contribute to the development of personalized treatment strategies and enhance prognostic prediction for CRC patients.
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Affiliation(s)
- Daan Fu
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Key Laboratory of Anesthesiology and Resuscitation (Huazhong University of Science and Technology), Ministry of Education, China
- Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Tianhao Zhang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jia Liu
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bingcheng Chang
- The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, 550003, China
| | - Qingqing Zhang
- Haiyan County Hospital of Traditional Chinese Medicine, JiaXing, 314399, China
| | - Yuyan Tan
- Department of Breast and Thyroid Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang, 443000, China
| | - Xiangdong Chen
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Key Laboratory of Anesthesiology and Resuscitation (Huazhong University of Science and Technology), Ministry of Education, China
- Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Lulu Tan
- Department of Breast and Thyroid Surgery, The First College of Clinical Medical Science, China Three Gorges University, Yichang, 443000, China
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Suwatthanarak T, Tanjak P, Chaiboonchoe A, Acharayothin O, Thanormjit K, Chanthercrob J, Suwatthanarak T, Niyomchan A, Tanaka M, Okochi M, Pongpaibul A, Chalermwai WV, Trakarnsanga A, Methasate A, Pithukpakorn M, Chinswangwatanakul V. Overexpression of TSPAN8 in consensus molecular subtype 3 colorectal cancer. Exp Mol Pathol 2024; 137:104911. [PMID: 38861838 DOI: 10.1016/j.yexmp.2024.104911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/21/2024] [Accepted: 06/05/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND Recently, consensus molecular subtypes (CMSs) have been proposed as a robust transcriptome-based classification system for colorectal cancer (CRC). Tetraspanins (TSPANs) are transmembrane proteins. They have been associated with the development of numerous malignancies, including CRC, through their role as "master organizers" for multi-molecular membrane complexes. No previous study has investigated the correlation between TSPANs and CMS classification. Herein, we investigated the expression of TSPANs in patient-derived primary CRC tissues and their CMS classifications. METHODS RNA samples were derived from primary CRC tissues (n = 100 patients diagnosed with colorectal adenocarcinoma) and subjected to RNA sequencing for transcriptome-based CMS classification and TSPAN-relevant analyses. Immunohistochemistry (IHC) and immunofluorescence (IF) stains were conducted to observe the protein expression level. To evaluate the relative biological pathways, gene-set enrichment analysis was performed. RESULTS Of the highly expressed TSPAN genes in CRC tissues (TSPAN8, TSPAN29, and TSPAN30), TSPAN8 was notably overexpressed in CMS3-classified primary tissues. The overexpression of TSPAN8 protein in CMS3 CRC was also observed by IHC and IF staining. As a result of gene-set enrichment analysis, TSPAN8 may potentially play a role in organizing signaling complexes for kinase-based metabolic deregulation in CMS3 CRC. CONCLUSIONS The present study reports the overexpression of TSPAN8 in CMS3 CRC. This study proposes TSPAN8 as a subtype-specific biomarker for CMS3 CRC. This finding provides a foundation for future CMS-based studies of CRC, a complex disease and the second leading cause of cancer mortality worldwide.
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Affiliation(s)
- Thanawat Suwatthanarak
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pariyada Tanjak
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Amphun Chaiboonchoe
- Siriraj Center of Systems Pharmacy, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Siriraj Center of Research Excellence in Precision Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Onchira Acharayothin
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kullanist Thanormjit
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jantappapa Chanthercrob
- Siriraj Center of Systems Pharmacy, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Siriraj Center of Research Excellence in Precision Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tharathorn Suwatthanarak
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Apichaya Niyomchan
- Department of Anatomy, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Masayoshi Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Kanagawa, Japan
| | - Mina Okochi
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Tokyo, Japan
| | - Ananya Pongpaibul
- Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wipapat Vicki Chalermwai
- Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Atthaphorn Trakarnsanga
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Asada Methasate
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Manop Pithukpakorn
- Siriraj Center of Research Excellence in Precision Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Vitoon Chinswangwatanakul
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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4
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Langerud J, Eilertsen IA, Moosavi SH, Klokkerud SMK, Reims HM, Backe IF, Hektoen M, Sjo OH, Jeanmougin M, Tejpar S, Nesbakken A, Lothe RA, Sveen A. Multiregional transcriptomics identifies congruent consensus subtypes with prognostic value beyond tumor heterogeneity of colorectal cancer. Nat Commun 2024; 15:4342. [PMID: 38773143 PMCID: PMC11109119 DOI: 10.1038/s41467-024-48706-2] [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: 08/23/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Intra-tumor heterogeneity compromises the clinical value of transcriptomic classifications of colorectal cancer. We investigated the prognostic effect of transcriptomic heterogeneity and the potential for classifications less vulnerable to heterogeneity in a single-hospital series of 1093 tumor samples from 692 patients, including multiregional samples from 98 primary tumors and 35 primary-metastasis sets. We show that intra-tumor heterogeneity of the consensus molecular subtypes (CMS) is frequent and has poor-prognostic associations independently of tumor microenvironment markers. Multiregional transcriptomics uncover cancer cell-intrinsic and low-heterogeneity signals that recapitulate the intrinsic CMSs proposed by single-cell sequencing. Further subclassification identifies congruent CMSs that explain a larger proportion of variation in patient survival than intra-tumor heterogeneity. Plasticity is indicated by discordant intrinsic phenotypes of matched primary and metastatic tumors. We conclude that multiregional sampling reconciles the prognostic power of tumor classifications from single-cell and bulk transcriptomics in the context of intra-tumor heterogeneity, and phenotypic plasticity challenges the reconciliation of primary and metastatic subtypes.
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Affiliation(s)
- Jonas Langerud
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Seyed H Moosavi
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Solveig M K Klokkerud
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Henrik M Reims
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Ingeborg F Backe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Merete Hektoen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ole H Sjo
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Sabine Tejpar
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Arild Nesbakken
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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5
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Merz N, Hartel JC, Grösch S. How ceramides affect the development of colon cancer: from normal colon to carcinoma. Pflugers Arch 2024:10.1007/s00424-024-02960-x. [PMID: 38635059 DOI: 10.1007/s00424-024-02960-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/16/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024]
Abstract
The integrity of the colon and the development of colon cancer depend on the sphingolipid balance in colon epithelial cells. In this review, we summarize the current knowledge on how ceramides and their complex derivatives influence normal colon development and colon cancer development. Ceramides, glucosylceramides and sphingomyelin are essential membrane components and, due to their biophysical properties, can influence the activation of membrane proteins, affecting protein-protein interactions and downstream signalling pathways. Here, we review the cellular mechanisms known to be affected by ceramides and their effects on colon development. We also describe which ceramides are deregulated during colorectal carcinogenesis, the molecular mechanisms involved in ceramide deregulation and how this affects carcinogenesis. Finally, we review new methods that are now state of the art for studying lipid-protein interactions in the physiological environment.
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Affiliation(s)
- Nadine Merz
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Jennifer Christina Hartel
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Sabine Grösch
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Theodor Stern Kai 7, 60590, Frankfurt, Germany.
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt Am Main, Germany.
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6
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Dunne PD, Arends MJ. Molecular pathological classification of colorectal cancer-an update. Virchows Arch 2024; 484:273-285. [PMID: 38319359 PMCID: PMC10948573 DOI: 10.1007/s00428-024-03746-3] [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: 12/06/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/07/2024]
Abstract
Colorectal cancer (CRC) has a broad range of molecular alterations with two major mechanisms of genomic instability (chromosomal instability and microsatellite instability) and has been subclassified into 4 consensus molecular subtypes (CMS) based on bulk RNA sequence data. Here, we update the molecular pathological classification of CRC with an overview of more recent bulk and single-cell RNA data analysis for development of transcriptional classifiers and risk stratification methods, taking into account the marked inter-tumoural and intra-tumoural heterogeneity of CRC. The importance of the stromal and immune components or tumour microenvironment (TME) to prognosis has emerged from these analyses. Attempts to remove the contribution of the tumour microenvironment and reveal neoplastic-specific transcriptional traits involved identification of the CRC intrinsic subtypes (CRIS). The use of immunohistochemistry and digital pathology to implement classification systems are evolving fields. Conventional adenoma versus serrated polyp pathway transcriptomic analysis and characterisation of canonical LGR5+ crypt base columnar stem cell versus ANXA1+ regenerative stem cell phenotypes emerged as key properties for improved understanding of transcriptional signals involved in molecular subclassification of colorectal cancers. Recently, classification by three pathway-derived subtypes (PDS1-3) has been developed, revealing a continuum of intrinsic biology associated with biological, stem cell, histopathological, and clinical attributes.
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Affiliation(s)
- Philip D Dunne
- Patrick G. Johnston Centre for Cancer Research, Queens University Belfast, Belfast, Northern Ireland, BT8 7AE, UK
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, G61 1QH, UK
| | - Mark J Arends
- Edinburgh Pathology & Cancer Research UK Scotland Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XR, UK.
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7
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El Hindi K, Brachtendorf S, Hartel JC, Renné C, Birod K, Schilling K, Labocha S, Thomas D, Ferreirós N, Hahnefeld L, Dorochow E, Del Turco D, Deller T, Scholich K, Fuhrmann DC, Weigert A, Brüne B, Geisslinger G, Wittig I, Link KH, Grösch S. Hypoxia induced deregulation of sphingolipids in colon cancer is a prognostic marker for patient outcome. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166906. [PMID: 37802156 DOI: 10.1016/j.bbadis.2023.166906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/08/2023]
Abstract
Sphingolipids are important for the physicochemical properties of cellular membranes and deregulated in tumors. In human colon cancer tissue ceramide synthase (CerS) 4 and CerS5 are reduced which correlates with a reduced survival probability of late-stage colon cancer patients. Both enzymes are reduced after hypoxia in advanced colorectal cancer (CRC) cells (HCT-116, SW620) but not in non-metastatic CRC cells (SW480, Caco-2). Downregulation of CerS4 or CerS5 in advanced CRC cells enhanced tumor formation in nude mice and organoid growth in vitro. This was accompanied by an enhanced proliferation rate and metabolic changes leading to a shift towards the Warburg effect. In contrast, CerS4 or CerS5 depletion in Caco-2 cells reduced tumor growth in vivo. Lipidomic and proteomic analysis of membrane fractions revealed significant changes in tumor-promoting cellular pathways and cellular transporters. This study identifies CerS4 and CerS5 as prognostic markers for advanced colon cancer patients and provides a comprehensive overview about the associated cellular metabolic changes. We propose that the expression level of CerS4 and CerS5 in colon tumors could serve as a basis for decision-making for personalized treatment of advanced colon cancer patients. Trial registration: The study was accredited by the study board of the Deutsche Krebsgesellschaft (Registration No: St-D203, 2017/06/30, retrospectively registered).
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Affiliation(s)
- Khadija El Hindi
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Sebastian Brachtendorf
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Jennifer C Hartel
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Goethe-University Frankfurt, Department of Life Sciences, 60590 Frankfurt, Germany
| | - Christoph Renné
- Institute of Pathology and Cytology, Group Practice Wiesbaden, Germany
| | - Kerstin Birod
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Karin Schilling
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Sandra Labocha
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Dominique Thomas
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Nerea Ferreirós
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Lisa Hahnefeld
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Erika Dorochow
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Domenico Del Turco
- Goethe-University Frankfurt, Institute of Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Faculty of Medicine, Theodor Stern Kai 7, 60596 Frankfurt am Main, Germany
| | - Thomas Deller
- Goethe-University Frankfurt, Institute of Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Faculty of Medicine, Theodor Stern Kai 7, 60596 Frankfurt am Main, Germany
| | - Klaus Scholich
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Dominik C Fuhrmann
- Goethe-University Frankfurt, Institute of Biochemistry I, Faculty of Medicine, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany
| | - Andreas Weigert
- Goethe-University Frankfurt, Institute of Biochemistry I, Faculty of Medicine, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany
| | - Bernhard Brüne
- Goethe-University Frankfurt, Institute of Biochemistry I, Faculty of Medicine, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany
| | - Gerd Geisslinger
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Ilka Wittig
- Goethe-University Frankfurt, Functional Proteomics, Institute of Cardiovascular Physiology, Faculty of Medicine, Frankfurt am Main, Germany
| | - Karl-Heinrich Link
- Asklepios Tumor Center (ATC) and Surgical Center, Asklepios Paulinen Klinik, Wiesbaden 65197, Germany
| | - Sabine Grösch
- Goethe-University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany.
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8
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Qiu X, Quan G, Ou W, Wang P, Huang X, Li X, Shen Y, Yang W, Wang J, Wu X. Unraveling TIMP1: a multifaceted biomarker in colorectal cancer. Front Genet 2023; 14:1265137. [PMID: 37842645 PMCID: PMC10570617 DOI: 10.3389/fgene.2023.1265137] [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: 07/22/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023] Open
Abstract
Background: The pathogenic genes of colorectal cancer (CRC) have not yet been fully elucidated, and there is currently a lack of effective therapeutic targets. This study used bioinformatics methods to explore and experimentally validate the most valuable biomarkers for colorectal cancer and further investigate their potential as targets. Methods: We analyzed differentially expressed genes (DEGs) based on the Gene Expression Omnibus (GEO) dataset and screened out hub genes. ROC curve and univariate Cox analysis of The Cancer Genome Atlas (TCGA) dataset revealed the most diagnostically and prognostically valuable genes. Immunohistochemistry (IHC) experiments were then conducted to validate the expression level of these selected genes in colorectal cancer. Gene set enrichment analysis (GSEA) was performed to evaluate the enriched signaling pathways associated with the gene. Using the CIBERSORT algorithm in R software, we analyzed the immune infiltrating cell abundance in both high and low gene expression groups and examined the gene's correlation with immune cells and immune checkpoints. Additionally, we performed drug sensitivity analysis utilizing the DepMap database, and explored the correlation between gene expression levels and ferroptosis based on the The Cancer Genome Atlas dataset. Results: The study identified a total of 159 DEGs, including 7 hub genes: SPP1, MMP1, CXCL8, CXCL1, TIMP1, MMP3, and CXCL10. Further analysis revealed TIMP1 as the most valuable diagnostic and prognostic biomarker for colorectal cancer, with IHC experiments verifying its high expression. Additionally, GSEA results showed that the high TIMP1 expression group was involved in many cancer signaling pathways. Analysis of the TCGA database revealed a positive correlation between TIMP1 expression and infiltration of macrophages (M0, M1, M2) and neutrophils, as well as the expression of immune checkpoint genes, including CTLA-4 and HAVCR2. Drug sensitivity analysis, conducted using the DepMap database, revealed that colorectal cancer cell lines exhibiting elevated levels of TIMP1 expression were more responsive to certain drugs, such as CC-90003, Pitavastatin, Atuveciclib, and CT7001, compared to those with low levels of TIMP1. Furthermore, TIMP1 expression was positively correlated with that of ferroptosis-related genes, such as GPX4 and HSPA5. Conclusion: TIMP1 can be used as a biomarker for colorectal cancer and is associated with the immunological microenvironment, drug sensitivity, and ferroptosis inhibition in this disease.
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Affiliation(s)
- Xiaode Qiu
- Department of Clinical Medicine, Fujian Medical University, Fuzhou, China
- Department of General Surgery, Affiliated Nanping First Hospital, Fujian Medical University, Nanping, China
| | - Guangqian Quan
- Department of General Surgery, Affiliated Nanping First Hospital, Fujian Medical University, Nanping, China
| | - Wenquan Ou
- Department of General Surgery, Affiliated Nanping First Hospital, Fujian Medical University, Nanping, China
| | - Pengfei Wang
- Department of Gastroenterology, Affiliated Nanping First Hospital, Fujian Medical University, Nanping, China
| | - Xing Huang
- Department of General Surgery, Affiliated Nanping First Hospital, Fujian Medical University, Nanping, China
| | - Xinhua Li
- Department of Pathology, Affiliated Nanping First Hospital, Fujian Medical University, Nanping, China
| | - Yufan Shen
- Department of Clinical Medicine, Fujian Medical University, Fuzhou, China
- Department of General Surgery, Affiliated Nanping First Hospital, Fujian Medical University, Nanping, China
| | - Weifeng Yang
- Department of General Surgery, Affiliated Nanping First Hospital, Fujian Medical University, Nanping, China
| | - Jian Wang
- Department of General Surgery, Affiliated Nanping First Hospital, Fujian Medical University, Nanping, China
| | - Xiaohua Wu
- Department of General Surgery, Affiliated Nanping First Hospital, Fujian Medical University, Nanping, China
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9
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Wang L, Zhu Y, Ren Z, Sun W, Wang Z, Zi T, Li H, Zhao Y, Qin X, Gao D, Zhang L, He Z, Le W, Wu Q, Wu G. An immunogenic cell death-related classification predicts prognosis and response to immunotherapy in kidney renal clear cell carcinoma. Front Oncol 2023; 13:1147805. [PMID: 37681027 PMCID: PMC10482408 DOI: 10.3389/fonc.2023.1147805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/03/2023] [Indexed: 09/09/2023] Open
Abstract
Introduction Immunogenic cell death (ICD) is a form of regulated cell death that activates an adaptive immune response in an immunocompetent host and is particularly sensitive to antigens from tumor cells. Kidney clear cell carcinoma (KIRC) is an immunogenic tumor with extensive tumor heterogeneity. However, no reliable predictive biomarkers have been identified to reflect the immune microenvironment and therapeutic response of KIRC. Methods Therefore, we used the CIBERSORT and ESTIMATE algorithms to define three ICD clusters based on the expression of ICD-related genes in 661 KIRC patients. Subsequently, we identified three different ICD gene clusters based on the overlap of differentially expressed genes (DEGs) within the ICD clusters. In addition, principal component analysis (PCA) was performed to calculate the ICD scores. Results The results showed that patients with reduced ICD scores had a poorer prognosis and reduced transcript levels of immune checkpoint genes regulated with T cell differentiation. Furthermore, the ICD score was negatively correlated with the tumor mutation burden (TMB) value of KICD. patients with higher ICD scores showed clinical benefits and advantages of immunotherapy, indicating that the ICD score is an accurate and valid predictor to assess the effect of immunotherapy. Discussion Overall, our study presents a comprehensive KICD immune-related ICD landscape that can provide guidance for current immunotherapy and predict patient prognosis to help physicians make judgments about the patient's disease and treatment modalities, and can guide current research on immunotherapy strategies for KICD.
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Affiliation(s)
- Licheng Wang
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yaru Zhu
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhen Ren
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wenhuizi Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhijing Wang
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Tong Zi
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Haopeng Li
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yan Zhao
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xin Qin
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Dacheng Gao
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Libo Zhang
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ziyang He
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Le
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qiang Wu
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Gang Wu
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
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10
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Duda D, Dima S, Sorop A, Kitahara S, Setia N, Chivu-Economescu M, Matei L, Herlea V, Pechianu N, Inomata T, Matsui A, Khachatryan A, Aoki S, Lauwers G, Popescu I. A tumor microenvironment-based classification of gastric cancer for more effective diagnosis and treatment. RESEARCH SQUARE 2023:rs.3.rs-3089359. [PMID: 37577519 PMCID: PMC10418549 DOI: 10.21203/rs.3.rs-3089359/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
With approximately one million diagnosed cases and over 700,000 deaths recorded annually, gastric cancer (GC) is the third most common cause of cancer-related deaths worldwide. GC is a heterogeneous tumor. Thus, optimal management requires biomarkers of prognosis, treatment selection, and treatment response. The Cancer Genome Atlas program sub-classified GC into molecular subtypes, providing a framework for treatment personalization using traditional chemotherapies or biologics. Here, we report a comprehensive study of GC vascular and immune tumor microenvironment (TME)-based on stage and molecular subtypes of the disease and their correlation with outcomes. Using tissues and blood circulating biomarkers and a molecular classification, we identified cancer cell and tumor archetypes, which show that the TME evolves with the disease stage and is a major determinant of prognosis. Moreover, our TME-based subtyping strategy allowed the identification of archetype-specific prognostic biomarkers such as CDH1-mutant GC and circulating IL-6 that provided information beyond and independent of TMN staging, MSI status, and consensus molecular subtyping. The results show that integrating molecular subtyping with TME-specific biomarkers could contribute to improved patient prognostication and may provide a basis for treatment stratification, including for contemporary anti-angiogenesis and immunotherapy approaches.
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Affiliation(s)
| | | | | | | | | | | | - Lilia Matei
- Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | | | | | | | - Aya Matsui
- Graduate School of Medical Science, Kanazawa University
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11
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Kan CM, Pei XM, Yeung MHY, Jin N, Ng SSM, Tsang HF, Cho WCS, Yim AKY, Yu ACS, Wong SCC. Exploring the Role of Circulating Cell-Free RNA in the Development of Colorectal Cancer. Int J Mol Sci 2023; 24:11026. [PMID: 37446204 DOI: 10.3390/ijms241311026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/25/2023] [Accepted: 07/02/2023] [Indexed: 07/15/2023] Open
Abstract
Circulating tumor RNA (ctRNA) has recently emerged as a novel and attractive liquid biomarker. CtRNA is capable of providing important information about the expression of a variety of target genes noninvasively, without the need for biopsies, through the use of circulating RNA sequencing. The overexpression of cancer-specific transcripts increases the tumor-derived RNA signal, which overcomes limitations due to low quantities of circulating tumor DNA (ctDNA). The purpose of this work is to present an up-to-date review of current knowledge regarding ctRNAs and their status as biomarkers to address the diagnosis, prognosis, prediction, and drug resistance of colorectal cancer. The final section of the article discusses the practical aspects involved in analyzing plasma ctRNA, including storage and isolation, detection technologies, and their limitations in clinical applications.
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Affiliation(s)
- Chau-Ming Kan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Martin Ho Yin Yeung
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Nana Jin
- Codex Genetics Limited, Shatin, Hong Kong SAR, China
| | - Simon Siu Man Ng
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong SAR, China
| | | | | | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
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12
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Yu L, Wang L, Sun J, Zhou X, Hu Y, Hu L, He Y, Lin C, Chen J, Xu X, Dunlop MG, Theodoratou E, Ding K, Li X. N6-methyladenosine related gene expression signatures for predicting the overall survival and immune responses of patients with colorectal cancer. Front Genet 2023; 14:885930. [PMID: 36936424 PMCID: PMC10020527 DOI: 10.3389/fgene.2023.885930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
N6-methyladenosine (m6A) modification has been demonstrated to exhibit a crucial prognostic effect on colorectal cancer (CRC). Nonetheless, potential mechanism of m6A in survival rate and immunotherapeutic response remains unknown. Here we investigated the genes associated with m6A regulators and developed a risk score for predicting the overall survival (OS) of CRC patients. RNA-seq transcriptomic profiling data of COAD/READ samples were obtained from The Cancer Genome Atlas (TCGA) database. Absolute Shrinkage and Selection Operator (LASSO)- Cox regression analysis was conducted to identify the m6A-related gene expression signatures and the selected genes were inputted into stepwise regression to develop a prognostic risk score in TCGA, and its predictive performance of CRC survival was further validated in Gene Expression Omnibus (GEO) datasets. According to our results, the risk score comprising 18 m6A-related mRNAs was significantly associated with CRC survival in both TCGA and GEO datasets. And the stratified analysis also confirmed that high-risk score acted as a poor factor in different age, sex, T stage, and tumour, node, metastasis (TNM) stages. The m6A-related prognostic score in combination with clinical characteristics yielded time-dependent area under the receiver operating characteristic curve (AUCs) of 0.85 (95%CI: 0.79-0.91), 0.84 (95%CI: 0.79-0.90) and 0.80 (95%CI: 0.71-0.88) for the prediction of the 1-, 3-, 5-year OS of CRC in TCGA cohort. Furthermore, mutation of oncogenes occurred more frequently in the high-risk group and the composition of immune cells in tumour microenvironment (TME) was significantly distinct between the low- and high-risk groups. The low-risk group had a lower microsatellite instability (MSI) score, T-cell exclusion score and dysfunction score, implying that low-risk patients may have a better immunotherapy response than high-risk patients. In summary, a prognostic risk score derived from m6A-related gene expression signatures could serve as a potential prognostic predictor for CRC survival and indicator for predicting immunotherapy response in CRC patients.
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Affiliation(s)
- Lili Yu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Analytics of The Second Affiliated Hospital and Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data, Zhejiang University School of Medicine, Hangzhou, China
| | - Lijuan Wang
- Analytics of The Second Affiliated Hospital and Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Sun
- Analytics of The Second Affiliated Hospital and Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuan Zhou
- Analytics of The Second Affiliated Hospital and Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data, Zhejiang University School of Medicine, Hangzhou, China
| | - Yeting Hu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lidan Hu
- The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yazhou He
- Department of Oncology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chunqing Lin
- National Cancer Center, National Clinical Research Center for Cancer, and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Chen
- Center for Global Health, Zhejiang University, Hangzhou, China
| | - Xiaolin Xu
- Analytics of The Second Affiliated Hospital and Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data, Zhejiang University School of Medicine, Hangzhou, China
| | - Malcolm G. Dunlop
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Evropi Theodoratou
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Kefeng Ding
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Xue Li
- Analytics of The Second Affiliated Hospital and Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data, Zhejiang University School of Medicine, Hangzhou, China
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13
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A Novel Molecular Analysis Approach in Colorectal Cancer Suggests New Treatment Opportunities. Cancers (Basel) 2023; 15:cancers15041104. [PMID: 36831448 PMCID: PMC9953902 DOI: 10.3390/cancers15041104] [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: 01/13/2023] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Colorectal cancer (CRC) is a molecular and clinically heterogeneous disease. In 2015, the Colorectal Cancer Subtyping Consortium classified CRC into four consensus molecular subtypes (CMS), but these CMS have had little impact on clinical practice. The purpose of this study is to deepen the molecular characterization of CRC. A novel approach, based on probabilistic graphical models (PGM) and sparse k-means-consensus cluster layer analyses, was applied in order to functionally characterize CRC tumors. First, PGM was used to functionally characterize CRC, and then sparse k-means-consensus cluster was used to explore layers of biological information and establish classifications. To this aim, gene expression and clinical data of 805 CRC samples from three databases were analyzed. Three different layers based on biological features were identified: adhesion, immune, and molecular. The adhesion layer divided patients into high and low adhesion groups, with prognostic value. The immune layer divided patients into immune-high and immune-low groups, according to the expression of immune-related genes. The molecular layer established four molecular groups related to stem cells, metabolism, the Wnt signaling pathway, and extracellular functions. Immune-high patients, with higher expression of immune-related genes and genes involved in the viral mimicry response, may benefit from immunotherapy and viral mimicry-related therapies. Additionally, several possible therapeutic targets have been identified in each molecular group. Therefore, this improved CRC classification could be useful in searching for new therapeutic targets and specific therapeutic strategies in CRC disease.
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14
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Identification of Aging and Young Subtypes for Predicting Colorectal Cancer Prognosis and Immunotherapy Responses. Int J Mol Sci 2023; 24:ijms24021516. [PMID: 36675039 PMCID: PMC9862647 DOI: 10.3390/ijms24021516] [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: 12/16/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Colorectal cancer (CRC) is critically related to aging and severely threatens human lives. To better explore the effects of aging on CRC progression and therapy outcome, a reliable aging subtypes identification of CRC is urgently desired. Here, 28 aging-related genes associated with the CRC prognosis were selected by univariate Cox analyses. Based on these 28 genes, CRC patients were divided into the aging subtype and young subtype by non-negative matrix factorization clustering. Aging subtype and young subtype of CRC were identified with distinct molecular features and clinical prognosis. The aging subtype was characterized by upregulation of senescence-associated secretory phenotype, higher frequencies of TP53 and immune checkpoint molecules, and high sensitivity to protein kinase and angiogenesis inhibitors. Furthermore, 14 genes were selected by LASSO penalized Cox regression analyses for aging-related risk signature construction. The constructed aging risk signature exhibited good prediction and the nomogram showed robust discrimination power over the traditional CRC staging system. In conclusion, this study successfully established aging subtype and young subtype of CRC, which is helpful to identify patients with aging characteristics to evaluate prognosis and treatment outcomes. Introducing aging-based subtypes into clinical concern and patient prognostication provides new opportunities for personalized CRC treatment.
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15
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Simó-Riudalbas L, Offner S, Planet E, Duc J, Abrami L, Dind S, Coudray A, Coto-Llerena M, Ercan C, Piscuoglio S, Andersen CL, Bramsen JB, Trono D. Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis. Nat Commun 2022; 13:4913. [PMID: 35987910 PMCID: PMC9392749 DOI: 10.1038/s41467-022-32649-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractThe treatment of colorectal cancer (CRC) is an unmet medical need in absence of early diagnosis. Here, upon characterizing cancer-specific transposable element-driven transpochimeric gene transcripts (TcGTs) produced by this tumor in the SYSCOL cohort, we find that expression of the hominid-restricted retrogene POU5F1B through aberrant activation of a primate-specific endogenous retroviral promoter is a strong negative prognostic biomarker. Correlating this observation, we demonstrate that POU5F1B fosters the proliferation and metastatic potential of CRC cells. We further determine that POU5F1B, in spite of its phylogenetic relationship with the POU5F1/OCT4 transcription factor, is a membrane-enriched protein that associates with protein kinases and known targets or interactors as well as with cytoskeleton-related molecules, and induces intracellular signaling events and the release of trans-acting factors involved in cell growth and cell adhesion. As POU5F1B is an apparently non-essential gene only lowly expressed in normal tissues, and as POU5F1B-containing TcGTs are detected in other tumors besides CRC, our data provide interesting leads for the development of cancer therapies.
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16
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Identification of two intrinsic epithelial subtypes of colorectal cancer. Nat Genet 2022; 54:924-925. [PMID: 35798900 DOI: 10.1038/s41588-022-01101-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Joanito I, Wirapati P, Zhao N, Nawaz Z, Yeo G, Lee F, Eng CLP, Macalinao DC, Kahraman M, Srinivasan H, Lakshmanan V, Verbandt S, Tsantoulis P, Gunn N, Venkatesh PN, Poh ZW, Nahar R, Oh HLJ, Loo JM, Chia S, Cheow LF, Cheruba E, Wong MT, Kua L, Chua C, Nguyen A, Golovan J, Gan A, Lim WJ, Guo YA, Yap CK, Tay B, Hong Y, Chong DQ, Chok AY, Park WY, Han S, Chang MH, Seow-En I, Fu C, Mathew R, Toh EL, Hong LZ, Skanderup AJ, DasGupta R, Ong CAJ, Lim KH, Tan EKW, Koo SL, Leow WQ, Tejpar S, Prabhakar S, Tan IB. Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer. Nat Genet 2022; 54:963-975. [PMID: 35773407 PMCID: PMC9279158 DOI: 10.1038/s41588-022-01100-4] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 05/16/2022] [Indexed: 12/12/2022]
Abstract
The consensus molecular subtype (CMS) classification of colorectal cancer is based on bulk transcriptomics. The underlying epithelial cell diversity remains unclear. We analyzed 373,058 single-cell transcriptomes from 63 patients, focusing on 49,155 epithelial cells. We identified a pervasive genetic and transcriptomic dichotomy of malignant cells, based on distinct gene expression, DNA copy number and gene regulatory network. We recapitulated these subtypes in bulk transcriptomes from 3,614 patients. The two intrinsic subtypes, iCMS2 and iCMS3, refine CMS. iCMS3 comprises microsatellite unstable (MSI-H) cancers and one-third of microsatellite-stable (MSS) tumors. iCMS3 MSS cancers are transcriptomically more similar to MSI-H cancers than to other MSS cancers. CMS4 cancers had either iCMS2 or iCMS3 epithelium; the latter had the worst prognosis. We defined the intrinsic epithelial axis of colorectal cancer and propose a refined ‘IMF’ classification with five subtypes, combining intrinsic epithelial subtype (I), microsatellite instability status (M) and fibrosis (F). A single-cell transcriptomic analysis of 63 patients with colorectal cancer classifies tumor cells into two epithelial subtypes. An improved tumor classification based on epithelial subtype, microsatellite stability and fibrosis reveals differences in pathway activation and metastasis.
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Affiliation(s)
- Ignasius Joanito
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Pratyaksha Wirapati
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nancy Zhao
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zahid Nawaz
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Grace Yeo
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Fiona Lee
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National Cancer Centre, Singapore, Singapore
| | - Christine L P Eng
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National Cancer Centre, Singapore, Singapore
| | | | - Merve Kahraman
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Harini Srinivasan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National Cancer Centre, Singapore, Singapore
| | | | - Sara Verbandt
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Petros Tsantoulis
- Hôpitaux Universitaires de Genève, Geneva, Switzerland.,University of Geneva, Geneva, Switzerland
| | - Nicole Gunn
- National Cancer Centre, Singapore, Singapore
| | - Prasanna Nori Venkatesh
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zhong Wee Poh
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Rahul Nahar
- MSD International GmbH (Singapore Branch), Singapore, Singapore
| | | | - Jia Min Loo
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shumei Chia
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Elsie Cheruba
- National University of Singapore, Singapore, Singapore
| | | | - Lindsay Kua
- National Cancer Centre, Singapore, Singapore
| | | | | | | | - Anna Gan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wan-Jun Lim
- National Cancer Centre, Singapore, Singapore
| | - Yu Amanda Guo
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Choon Kong Yap
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Brenda Tay
- National Cancer Centre, Singapore, Singapore
| | - Yourae Hong
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Dawn Qingqing Chong
- National Cancer Centre, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Aik-Yong Chok
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Shuting Han
- National Cancer Centre, Singapore, Singapore
| | - Mei Huan Chang
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Isaac Seow-En
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Cherylin Fu
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Ronnie Mathew
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Ee-Lin Toh
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore.,EL Toh Colorectal & Minimally Invasive Surgery, Singapore, Singapore
| | - Lewis Z Hong
- MSD International GmbH (Singapore Branch), Singapore, Singapore
| | - Anders Jacobsen Skanderup
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ramanuj DasGupta
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chin-Ann Johnny Ong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.,SingHealth Duke-NUS Surgery Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.,Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore
| | - Kiat Hon Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Emile K W Tan
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Si-Lin Koo
- National Cancer Centre, Singapore, Singapore
| | - Wei Qiang Leow
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Sabine Tejpar
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium.
| | - Shyam Prabhakar
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Iain Beehuat Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,National Cancer Centre, Singapore, Singapore. .,Duke-National University of Singapore Medical School, Singapore, Singapore.
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18
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Zhang Y, Wang Y, Wang J, Zhang K. The Immune Cell Infiltration Patterns and Characterization Score in Bladder Cancer to Identify Prognosis. Front Genet 2022; 13:852708. [PMID: 35801082 PMCID: PMC9255635 DOI: 10.3389/fgene.2022.852708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/16/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Bladder cancer (BLCA) is among the most frequent types of cancer. Patients with BLCA have a significant recurrence rate and a poor post-surgery survival rate. Recent research has found a link between tumor immune cell infiltration (ICI) and the prognosis of BLCA patients. However, the ICI’s picture of BLCA remains unclear. Methods: Common gene expression data were obtained by combining the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) expression databases. Two computational algorithms were proposed to unravel the ICI landscape of BLCA patients. The R package “limma” was applied to find differentially expressed genes (DEGs). ICI patterns were defined by the unsupervised clustering method. Principal-component analysis (PCA) was used to calculate the ICI score. In addition, the combined ICI score and tumor burden mutation (TMB) were utilized to assess BLCA patients’ prognosis. The predictive value of ICI scores was verified by different clinical characteristics. Results: A total of 569 common gene expression data were retrieved from TCGA and GEO cohorts. CD8+ T cells were found to have a substantial positive connection with activated memory CD4+ T cells and immune score. On the contrary, CD8+ T cells were found to have a substantial negative connection with macrophages M0. Thirty-eight DEGs were selected. Two ICI patterns were defined by the unsupervised clustering method. Patients of BLCA were separated into two groups. The high ICI score group exhibited a better outcome than the low ICI score one (p < 0.001). Finally, the group with a high tumor mutation burden (TMB) as well as a high ICI score had the best outcome. (p < 0.001). Conclusions: Combining TMB and ICI scores resulted in a more accurate survival prediction, suggesting that ICI scores could be used as a prognostic marker for BLCA patients.
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Affiliation(s)
- Yongsheng Zhang
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Yunlong Wang
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Bioengineering Research Center, Zhengzhou, China
- *Correspondence: Yunlong Wang,
| | - Jichuang Wang
- Henan Bioengineering Research Center, Zhengzhou, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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19
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Liu F, Wang P, Sun W, Jiang Y, Gong Q. Identification of Ligand-Receptor Pairs Associated With Tumour Characteristics in Clear Cell Renal Cell Carcinoma. Front Immunol 2022; 13:874056. [PMID: 35734169 PMCID: PMC9207243 DOI: 10.3389/fimmu.2022.874056] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
The tumour microenvironment (TME) of clear cell renal cell carcinoma (ccRCC) comprises multiple cell types, which promote tumour progression and modulate drug resistance and immune cell infiltrations via ligand-receptor (LR) interactions. However, the interactions, expression patterns, and clinical relevance of LR in the TME in ccRCC are insufficiently characterised. This study characterises the complex composition of the TME in ccRCC by analysing the single-cell sequencing (scRNA-seq) data of patients with ccRCC from the Gene expression omnibus database. On analysing the scRNA-seq data combined with the cancer genome atlas kidney renal clear cell carcinoma (TCGA-KIRC) dataset, 46 LR-pairs were identified that were significantly correlated and had prognostic values. Furthermore, a new molecular subtyping model was proposed based on these 46 LR-pairs. Molecular subtyping was performed in two ccRCC cohorts, revealing significant differences in prognosis between the subtypes of the two ccRCC cohorts. Different molecular subtypes exhibited different clinicopathological features, mutational, pathway, and immune signatures. Finally, the LR.score model that was constructed using ten essential LR-pairs that were identified based on LASSO Cox regression analysis revealed that the model could accurately predict the prognosis of patients with ccRCC. In addition, the differential expression of ten LR-pairs in tumour and normal cell lines was identified. Further functional experiments showed that CX3CL1 can exert anti-tumorigenic role in ccRCC cell line. Altogether, the effects of immunotherapy were connected to LR.scores, indicating that potential medications targeting these LR-pairs could contribute to the clinical benefit of immunotherapy. Therefore, this study identifies LR-pairs that could be effective biomarkers and predictors for molecular subtyping and immunotherapy effects in ccRCC. Targeting LR-pairs provides a new direction for immunotherapy regimens and prognostic evaluations in ccRCC.
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Affiliation(s)
- Fahui Liu
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Ping Wang
- Department of Dermatology, Fujian Provincial Geriatric Hospital, Fuzhou, China
| | - Wenjuan Sun
- Department of Internal Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Yan Jiang
- Guixi Key Laboratory for High Incidence Diseases, Youjiang Medical University for Nationalities, Baise, China
- *Correspondence: Qiming Gong, ; Yan Jiang,
| | - Qiming Gong
- Department of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- *Correspondence: Qiming Gong, ; Yan Jiang,
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20
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Qian B, Sun J, Zuo P, Da M, Mo X, Fang Y. Verification of genetic differences and immune cell infiltration subtypes in the neuroblastoma tumour microenvironment during immunotherapy. World J Surg Oncol 2022; 20:169. [PMID: 35643506 PMCID: PMC9145414 DOI: 10.1186/s12957-022-02641-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 05/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background Improved understanding of the tumour microenvironment (TME) has enabled remarkable advancements in research on cancer progression in the past few years. It is crucial to understand the nature and function of the TME because precise treatment strategies, including immunotherapy, for managing specific cancers have received widespread attention. The immune infiltrative profiles of neuroblastoma (NB) have not yet been completely illustrated. The purpose of this research was to analyse tumour immune cell infiltration (ICI) in the microenvironment of NB. Methods We applied the CIBERSORT and ESTIMATE algorithms to evaluate the ICI status of 438 NB samples. Three ICI models were selected, and ICI scores were acquired. Subgroups with high ICI scores determined based on the presence of immune activation signalling pathways had better overall survival. Results Genes involved in the immunosuppressive heparan sulphate glycosaminoglycan biosynthesis signalling pathway were markedly enriched in the low ICI score subgroup. It was inferred that patients with high ICI NB subtypes were more likely to respond to immunotherapy and have a better prognosis than those of patients with low ICI NB subtypes. Conclusion Notably, our ICI data not only provide a new clinical and theoretical basis for mining NB prognostic markers related to the microenvironment but also offer new ideas for the development of NB precision immunotherapy methods.
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21
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He R, Zhang M, He L, Huang J, Man C, Wang X, Lang Y, Fan Y. Integrated Analysis of Necroptosis-Related Genes for Prognosis, Immune Microenvironment Infiltration, and Drug Sensitivity in Colon Cancer. Front Med (Lausanne) 2022; 9:845271. [PMID: 35479956 PMCID: PMC9036446 DOI: 10.3389/fmed.2022.845271] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/16/2022] [Indexed: 12/12/2022] Open
Abstract
Background Necroptosis, is intimately linked to tumor development and prognosis and has been considered as a target for anticancer therapy. However, the role of necroptosis-related genes (NRGs) in colon cancer is unclear. Methods In the present study, we screened 76 NRGs from previous studies and described the landscape of transcriptomic and genetic variation of NRGs in colon cancer (CC) patient samples. Molecular subtypes of necroptosis in colon cancer were identified by clustering analysis, and these molecular subtypes were linked to patient prognosis and TME cell infiltration characteristics. Then, the NRS-score for predicting overall survival (OS) was built based on the TCGA database and validated in the GSE39582 cohort for its predictive power in CC patients. Besides, the ESTIMATE and CIBERSORT algorithms were applied to explore the relationship between NRS-score and tumor immune microenvironment. Results We identified two molecular subtypes associated with necroptosis in CC, which have diverse prognosis and immune microenvironment characteristics. Based on the differentially expressed genes between the two molecular subtypes, we further developed a necroptosis risk score signature, referred to as NRS-score. High NRS-score was associated with poor prognosis in CC through immunosuppressive microenvironment and immune escape mechanisms. The nomogram based on NRS-score showed excellent ability to predict prognosis. In addition, NRS-score presented a positive correlation with tumor mutational burden (TMB) and immune checkpoint blockade (ICB) expression and was closely correlated with multiple anticancer agent susceptibility. Conclusion This work revealed a close relationship between necroptosis and the prognosis and immune microenvironment of colon cancer. The NRS-score based on the 8-gene signature may be used to predict the sensitivity of immunotherapy and chemotherapy in colon cancer patients, and provides a foundation for future studies targeting necroptosis and its immune microenvironment.
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Affiliation(s)
- Rong He
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Meiling Zhang
- Department of Gastroenterology, The Affiliated Suqian First People's Hospital of Nanjing Medical University, Suqian, China
| | - Lian He
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Jiabin Huang
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Changfeng Man
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Xiaoyan Wang
- Department of Gastroenterology, The Affiliated Suqian First People's Hospital of Nanjing Medical University, Suqian, China
| | - Yakun Lang
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
- Yakun Lang
| | - Yu Fan
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
- *Correspondence: Yu Fan
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22
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Liu Z, Huang C, Tian H, Liu Y, Huang Y, Zhu Z. Establishment of a Dynamic Nomogram for Predicting the Risk of Lymph Node Metastasis in T1 Stage Colorectal Cancer. Front Surg 2022; 9:845666. [PMID: 35388361 PMCID: PMC8977409 DOI: 10.3389/fsurg.2022.845666] [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: 12/30/2021] [Accepted: 02/16/2022] [Indexed: 12/03/2022] Open
Abstract
Background Accurate prediction of the risk of lymph node metastasis in patients with stage T1 colorectal cancer is crucial for the formulation of treatment plans for additional surgery and lymph node dissection after endoscopic resection. The purpose of this study was to establish a predictive model for evaluating the risk of LNM in patients with stage T1 colorectal cancer. Methods The clinicopathological and imaging data of 179 patients with T1 stage colorectal cancer who underwent radical resection of colorectal cancer were collected. LASSO regression and a random forest algorithm were used to screen the important risk factors for LNM, and a multivariate logistic regression equation and dynamic nomogram were constructed. The C index, Calibration curve, and area under the ROC curve were used to evaluate the discriminant and prediction ability of the nomogram. The net reclassification index (NRI), comprehensive discriminant improvement index (IDI), and clinical decision curve (DCA) were compared with traditional ESMO criteria to evaluate the accuracy, net benefit, and clinical practicability of the model. Results The probability of lymph node metastasis in patients with T1 colorectal cancer was 11.17% (20/179). Multivariate analysis showed that the independent risk factors for LNM in T1 colorectal cancer were submucosal invasion depth, histological grade, CEA, lymphovascular invasion, and imaging results. The dynamic nomogram model constructed with independent risk factors has good discrimination and prediction capabilities. The C index was 0.914, the corrected C index was 0.890, the area under the ROC curve was 0.914, and the accuracy, sensitivity, and specificity were 93.3, 80.0, and 91.8%, respectively. The NRI, IDI, and DCA show that this model is superior to the ESMO standard. Conclusion This study establishes a dynamic nomogram that can effectively predict the risk of lymph node metastasis in patients with stage T1 colorectal cancer, which will provide certain help for the formulation of subsequent treatment plans for patients with stage T1 CRC after endoscopic resection.
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Li C, Pan J, Jiang Y, Yu Y, Jin Z, Chen X. Characteristics of the Immune Cell Infiltration Landscape in Gastric Cancer to Assistant Immunotherapy. Front Genet 2022; 12:793628. [PMID: 35069691 PMCID: PMC8770548 DOI: 10.3389/fgene.2021.793628] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Gastric cancer (GC) was usually associated with poor prognosis and invalid therapeutical response to immunotherapy due to biological heterogeneity. It is urgent to screen reliable indices especially immunotherapy-associated parameters that can predict the therapeutic responses to immunotherapy of GC patients. Methods: Gene expression profile of 854 GC patients were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets (GSE84433) with their corresponding clinical and somatic mutation data. Based on immune cell infiltration (ICI) levels, molecular clustering classification was performed to identify subtypes and ICI scores in GC patients. After functional enrichment analysis of subtypes, we further explored the correlation between ICI scores and Tumor Mutation Burden (TMB) and the significance in clinical immunotherapy response. Results: Three subtypes were identified based on ICI scores with distinct immunological and prognostic characteristics. The ICI-cluster C, associated with better outcomes, was characterized by significantly higher stromal and immune scores, T lymphocytes infiltration and up-regulation of PD-L1. ICI scores were identified through using principal component analysis (PCA) and the low ICI scores were consistent with the increased TMB and the immune-activating signaling pathways. Contrarily, the high-ICI score cluster was involved in the immunosuppressive pathways, such as TGF-beta, MAPK and WNT signaling pathways, which might be responsible for poor prognosis of GC. External immunotherapy and chemotherapy cohorts validated the patients with lower ICI scores exhibited significant therapeutic responses and clinical benefits. Conclusion: This study elucidated that ICI score could sever as an effective prognostic and predictive indicator for immunotherapy in GC. These findings indicated that the systematic assessment of tumor ICI landscapes and identification of ICI scores have crucial clinical implications and facilitate tailoring optimal immunotherapeutic strategies.
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Affiliation(s)
- Chenlu Li
- Department of Gastroenterology, Affiliated Yueqing Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jingjing Pan
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yinyan Jiang
- Department of Hematopathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yan Yu
- Wenzhou Medical University, Wenzhou, China
| | - Zhenlin Jin
- Department of Hematopathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xupeng Chen
- Department of Gastroenterology, Affiliated Yueqing Hospital, Wenzhou Medical University, Wenzhou, China
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Qin Y, Li M, Lin Q, Pan X, Liang Y, Huang Z, Liu Z, Huang L, Fang M. Colorectal Cancer Cell Differentiation Trajectory Predicts Patient Immunotherapy Response and Prognosis. Cancer Control 2022; 29:10732748221121382. [PMID: 36036380 PMCID: PMC9421035 DOI: 10.1177/10732748221121382] [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] [Indexed: 12/03/2022] Open
Abstract
Objectives This study aimed to investigate the differentiation state and clinical significance of colorectal cancer cells, as well as to predict the immune response and prognosis of patients based on differentiation-related genes of colorectal cancer. Introduction Colorectal cancer cells exhibit different differentiation states under the influence of the tumor microenvironment, which determines the cell fates. Methods We combined single-cell sequencing (scRNA-seq) data from The Cancer Genome Atlas source with extensive transcriptome data from the Gene Expression Omnibus database. We obtained colorectal cancer differentiation-related genes using cell trajectory analysis and developed a colorectal cancer differentiation-related gene based molecular typing and prognostic model to predict the immune response and prognosis of patients with colorectal cancer. Results We identified 5 distinct cell differentiation subsets and 620 colorectal cancer differentiation-related genes. Colorectal cancer differentiation-related genes were significantly associated with metabolism, angiogenesis, and immunity. We separated patients into 3 subtypes based on colorectal cancer differentiation-related gene expression in the tumor and found differences among the different subtypes in immune infiltration status, immune checkpoint gene expression, clinicopathological features, and overall survival. Immunotherapeutic interventions involving a highly expressed immune checkpoint blockade may be selectively effective in the corresponding cancer subtypes. We built a risk score prediction model (5-year AUC: .729) consisting of the 4 most important predictors of survival (TIMP1, MMP1, LGALS4, and ITLN1). Finally, we generated and validated a nomogram consisting of the risk score and clinicopathological variables. Conclusion This study highlights the significance of genes involved in cell differentiation for clinical prognosis and immunotherapy in patients and provides prospective therapeutic targets for colorectal cancer.
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Affiliation(s)
- Yuling Qin
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, China.,Guangxi Clinical Research Center for Anesthesiology, China.,Guangxi Engineering Research Center for Tissue & Organ Injury and Repair Medicine, China.,Guangxi Key Laboratory for Basic Science and Prevention of Perioperative Organ Disfunction, China
| | - Meiqin Li
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, China
| | - Qiumei Lin
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, China
| | - Xiaolan Pan
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, China
| | - Yihua Liang
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, China
| | - Zhaodong Huang
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, China
| | - Zhimin Liu
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, China
| | - Lingsha Huang
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, China
| | - Min Fang
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, China.,Guangxi Clinical Research Center for Anesthesiology, China.,Guangxi Engineering Research Center for Tissue & Organ Injury and Repair Medicine, China.,Guangxi Key Laboratory for Basic Science and Prevention of Perioperative Organ Disfunction, China
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25
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Mohammed M, Mboya IB, Mwambi H, Elbashir MK, Omolo B. Predictors of colorectal cancer survival using cox regression and random survival forests models based on gene expression data. PLoS One 2021; 16:e0261625. [PMID: 34965262 PMCID: PMC8716055 DOI: 10.1371/journal.pone.0261625] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/06/2021] [Indexed: 12/30/2022] Open
Abstract
Understanding and identifying the markers and clinical information that are associated with colorectal cancer (CRC) patient survival is needed for early detection and diagnosis. In this work, we aimed to build a simple model using Cox proportional hazards (PH) and random survival forest (RSF) and find a robust signature for predicting CRC overall survival. We used stepwise regression to develop Cox PH model to analyse 54 common differentially expressed genes from three mutations. RSF is applied using log-rank and log-rank-score based on 5000 survival trees, and therefore, variables important obtained to find the genes that are most influential for CRC survival. We compared the predictive performance of the Cox PH model and RSF for early CRC detection and diagnosis. The results indicate that SLC9A8, IER5, ARSJ, ANKRD27, and PIPOX genes were significantly associated with the CRC overall survival. In addition, age, sex, and stages are also affecting the CRC overall survival. The RSF model using log-rank is better than log-rank-score, while log-rank-score needed more trees to stabilize. Overall, the imputation of missing values enhanced the model’s predictive performance. In addition, Cox PH predictive performance was better than RSF.
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Affiliation(s)
- Mohanad Mohammed
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, Scottsville, South Africa
- Faculty of Mathematical and Computer Sciences, University of Gezira, Wad Madani, Sudan
- * E-mail:
| | - Innocent B. Mboya
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, Scottsville, South Africa
- Department of Epidemiology and Biostatistics, Kilimanjaro Christian Medical University College (KCMUCo), Moshi, Tanzania
| | - Henry Mwambi
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, Scottsville, South Africa
| | - Murtada K. Elbashir
- College of Computer and Information Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Bernard Omolo
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, Scottsville, South Africa
- Division of Mathematics & Computer Science, University of South Carolina-Upstate, Spartanburg, United States of America
- School of Public Health, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
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26
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Guo S, Ye Y, Liu X, Gong Y, Xu M, Song L, Liu H. Intra-Tumor Heterogeneity of Colorectal Cancer Necessitates the Multi-Regional Sequencing for Comprehensive Mutational Profiling. Cancer Manag Res 2021; 13:9209-9223. [PMID: 34949941 PMCID: PMC8689048 DOI: 10.2147/cmar.s327596] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 12/01/2021] [Indexed: 11/23/2022] Open
Abstract
Background The panorama and details of quantitative intratumor heterogeneity have not been fully investigated in colorectal cancer (CRC) patients with solitary lesion without distal metastasis, and its influences on sequencing interpretation and therapeutic strategies have not been explored. Methods Cancer tissues and matched blood from 70 sporadic CRC patients were collected and were divided into two cohorts. Four individual tissue biopsies were obtained from each of the 47 patients (multi-sample cohort). One random cancer tissue biopsy was obtained from each of the rest 23 patients (single-sample cohort). A 10 mL of blood was collected from all patients and the circulating cell-free DNA (cfDNA) was extracted. A 605-gene panel was used for targeted sequencing with tissue and paired blood. Results Mutational landscape revealed significantly higher mutational frequency in APC, CARD11 and CSMD3 in multi-sample cohort than single-sample cohort (P<0.05). The number of mutations and the ratio of trunk, shared and branch mutations showed extensive heterogeneity in multi-sample cohort, and the percentage of trunk mutations in major driver genes, including APC, TP53 and KRAS, was higher than 70%. A total of 929 mutations were detected in tissue/blood in multi-sample group, with 921(99.1%) from tissue and 472(50.8%) from blood (464 common mutations,49.9%). In contrast, 394 mutations were detected in tissue/blood in single-sample group, with 231 (58.6%) from tissue and 219 (55.6%) from blood (56 common mutations, 11.9%). The number of mutations of major driver genes detected in tissue was higher than that in blood in the multi-sample cohort, while it was similar in the single-sample group. Quantification analysis revealed differential correlation between tissue and blood VAF in trunk, shared and branch mutations. Meanwhile, VAF of trunk mutations was significantly higher than shared mutations and branch mutations. VAF exhibited significant differences among distinct stages, locations, differentiation and sex status. Conclusion Characteristic extensive heterogeneity was revealed for solitary CRC without distal metastasis. Multi-regional biopsy was necessary for comprehensive mutation detection in CRC.
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Affiliation(s)
- Shaohua Guo
- Department of General Surgery, The First Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
- Department of General Surgery, The Eighth Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Yumeng Ye
- Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Xinyi Liu
- Department of Medical Division, HaploX Biotechnology, Shenzhen, People’s Republic of China
| | - Yuan Gong
- Department of Gastroenterology, The Second Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Mingyan Xu
- Department of Medical Division, HaploX Biotechnology, Shenzhen, People’s Republic of China
| | - Lele Song
- Department of Medical Division, HaploX Biotechnology, Shenzhen, People’s Republic of China
- Department of Radiotherapy, The Eighth Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
- Lele Song Department of Radiotherapy, The Eighth Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of ChinaTel +86-13240149188 Email
| | - Hongyi Liu
- Department of General Surgery, The First Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
- Correspondence: Hongyi Liu Department of General Surgery, The First Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of ChinaTel +86-10-66937533 Email
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Hu LF, Lan HR, Huang D, Li XM, Jin KT. Personalized Immunotherapy in Colorectal Cancers: Where Do We Stand? Front Oncol 2021; 11:769305. [PMID: 34888246 PMCID: PMC8649954 DOI: 10.3389/fonc.2021.769305] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/26/2021] [Indexed: 12/17/2022] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer death in the world. Immunotherapy using monoclonal antibodies, immune-checkpoint inhibitors, adoptive cell therapy, and cancer vaccines has raised great hopes for treating poor prognosis metastatic CRCs that are resistant to the conventional therapies. However, high inter-tumor and intra-tumor heterogeneity hinder the success of immunotherapy in CRC. Patients with a similar tumor phenotype respond differently to the same immunotherapy regimen. Mutation-based classification, molecular subtyping, and immunoscoring of CRCs facilitated the multi-aspect grouping of CRC patients and improved immunotherapy. Personalized immunotherapy using tumor-specific neoantigens provides the opportunity to consider each patient as an independent group deserving of individualized immunotherapy. In the recent decade, the development of sequencing and multi-omics techniques has helped us classify patients more precisely. The expansion of such advanced techniques along with the neoantigen-based immunotherapy could herald a new era in treating heterogeneous tumors such as CRC. In this review article, we provided the latest findings in immunotherapy of CRC. We elaborated on the heterogeneity of CRC patients as a bottleneck of CRC immunotherapy and reviewed the latest advances in personalized immunotherapy to overcome CRC heterogeneity.
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Affiliation(s)
- Li-Feng Hu
- Department of Colorectal Surgery, Shaoxing People’s Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, China
| | - Huan-Rong Lan
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Dong Huang
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xue-Min Li
- Department of Hepatobiliary Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Ke-Tao Jin
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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Meng J, Huang X, Qiu Y, Zheng X, Huang J, Wen Z, Yao J. Pyroptosis-related gene mediated modification patterns and immune cell infiltration landscapes in cutaneous melanoma to aid immunotherapy. Aging (Albany NY) 2021; 13:24379-24401. [PMID: 34753832 PMCID: PMC8610130 DOI: 10.18632/aging.203687] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/27/2021] [Indexed: 01/05/2023]
Abstract
Tumor occurrence, infiltration, and metastasis are significantly affected by the tumor microenvironment (TME). Increasing evidence has elucidated TME's clinical significance in prognostic assessment and immunotherapy efficacy. Nonetheless, no studies have reported the potential pyroptosis-related genes (PRGs) function in TME immune cell infiltration. In this study, we systematically analyzed different PRG modification patterns in 685 cutaneous melanoma (CM) cases. We comprehensively explored the relationship between these PRG modification patterns and TME cell infiltration characteristics. Then, we used principal component analysis to construct a pyroptosis scoring system to quantify the PRG modification patterns in each CM patient. Three different PRG modification patterns were identified. Pyroptosis score was confirmed as an independent prognostic factor for CM patients. High pyroptosis score was characterized by high immunophenscore and more lymphocytes infiltration, such as T, B, and NK cells - indicating a strong ability to monitor and clear tumors, which may be responsible for the advantageous survival. Three independent cohorts that received immunotherapy confirmed the significant therapeutic efficacy and clinical benefit in high pyroptosis scores patients. This study revealed that the PRG modification patterns have a crucial effect on the CM complex and diverse microenvironment. Pyroptosis scores might serve as credible predictors of immunotherapy response and prognostic assessment. This provides a new direction for personalized immunotherapy strategies and appropriate immunotherapy candidates screening.
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Affiliation(s)
- Jinzhi Meng
- Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Xing Huang
- Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Yue Qiu
- Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Xifan Zheng
- Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Junpu Huang
- Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Zhenpei Wen
- Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
| | - Jun Yao
- Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People’s Republic of China
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Shi K, Lin W, Zhao XM. Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2514-2525. [PMID: 32305934 DOI: 10.1109/tcbb.2020.2986387] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Molecular biomarkers are certain molecules or set of molecules that can be of help for diagnosis or prognosis of diseases or disorders. In the past decades, thanks to the advances in high-throughput technologies, a huge amount of molecular 'omics' data, e.g., transcriptomics and proteomics, have been accumulated. The availability of these omics data makes it possible to screen biomarkers for diseases or disorders. Accordingly, a number of computational approaches have been developed to identify biomarkers by exploring the omics data. In this review, we present a comprehensive survey on the recent progress of identification of molecular biomarkers with machine learning approaches. Specifically, we categorize the machine learning approaches into supervised, un-supervised and recommendation approaches, where the biomarkers including single genes, gene sets and small gene networks. In addition, we further discuss potential problems underlying bio-medical data that may pose challenges for machine learning, and provide possible directions for future biomarker identification.
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Deng J, Tian AL, Pan H, Sauvat A, Leduc M, Liu P, Zhao L, Zhang S, Chen H, Taly V, Laurent-Puig P, Senovilla L, Li Y, Kroemer G, Kepp O. Everolimus and plicamycin specifically target chemoresistant colorectal cancer cells of the CMS4 subtype. Cell Death Dis 2021; 12:978. [PMID: 34675191 PMCID: PMC8531384 DOI: 10.1038/s41419-021-04270-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/19/2021] [Accepted: 10/05/2021] [Indexed: 12/24/2022]
Abstract
Colorectal cancers (CRC) can be classified into four consensus molecular subtypes (CMS), among which CMS1 has the best prognosis, contrasting with CMS4 that has the worst outcome. CMS4 CRC is notoriously resistant against therapeutic interventions, as demonstrated by preclinical studies and retrospective clinical observations. Here, we report the finding that two clinically employed agents, everolimus (EVE) and plicamycin (PLI), efficiently target the prototypic CMS4 cell line MDST8. As compared to the prototypic CMS1 cell line LoVo, MDST8 cells treated with EVE or PLI demonstrated stronger cytostatic and cytotoxic effects, increased signs of apoptosis and autophagy, as well as a more pronounced inhibition of DNA-to-RNA transcription and RNA-to-protein translation. Moreover, nontoxic doses of EVE and PLI induced the shrinkage of MDST8 tumors in mice, yet had only minor tumor growth-reducing effects on LoVo tumors. Altogether, these results suggest that EVE and PLI should be evaluated for their clinical activity against CMS4 CRC.
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Affiliation(s)
- Jiayin Deng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Université Paris Sud, Paris Saclay, Faculty of Medicine, Kremlin Bicêtre, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France
| | - Ai-Ling Tian
- Université Paris Sud, Paris Saclay, Faculty of Medicine, Kremlin Bicêtre, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France
| | - Hui Pan
- Université Paris Sud, Paris Saclay, Faculty of Medicine, Kremlin Bicêtre, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France
| | - Allan Sauvat
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France
| | - Marion Leduc
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France
| | - Peng Liu
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France
| | - Liwei Zhao
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France
| | - Shuai Zhang
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France
| | - Hui Chen
- Université Paris Sud, Paris Saclay, Faculty of Medicine, Kremlin Bicêtre, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France
| | - Valérie Taly
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France
- Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), Universidad de Valladolid - CSIC, Valladolid, Spain
| | - Laura Senovilla
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France
- Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), Universidad de Valladolid - CSIC, Valladolid, Spain
| | - Yingqiu Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France.
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France.
- Pôle de Biologie, Institut du Cancer Paris Carpem, APHP, Hôpital Européen Georges Pompidou, Paris, France.
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, Jiangsu, China.
- Karolinska Institutet, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.
| | - Oliver Kepp
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France.
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138 and CNRS SNC 5096, Institut Universitaire de France, Paris, France.
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Xie P, An R, Yu S, He J, Zhang H. A novel immune subtype classification of ER-positive, PR-negative and HER2-negative breast cancer based on the genomic and transcriptomic landscape. J Transl Med 2021; 19:398. [PMID: 34544424 PMCID: PMC8454077 DOI: 10.1186/s12967-021-03076-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/10/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The diversity and plasticity behind ER+/PR-/HER2- breast cancer have not been widely explored. It is essential to identify heterogeneous microenvironment phenotypes and investigate specific genomic events driving the formation of these phenotypes. METHODS Based on the immune-related gene expression profiles of 411 ER+/PR-/HER2- breast cancers in the METABRIC cohort, we used consensus clustering to identify heterogeneous immune subtypes and assessed their reproducibility in an independent meta-cohort including 135 patients collected from GEO database. We further analyzed the differences of cellular and molecular characteristics, and potential immune escape mechanism among immune subtypes. In addition, we constructed a transcriptional trajectory to visualize the distribution of individual patient. RESULTS Our analysis identified and validated five reproducible immune subtypes with distinct cellular and molecular characteristics, potential immune escape mechanisms, genomic drivers, as well as clinical outcomes. An immune-cold subtype, with the least amount of lymphocyte infiltration, had a poorer prognosis. By contrast, an immune-hot subtype, which demonstrated the highest infiltration of CD8+ T cells, DCs and NK cells, and elevated IFN-γ response, had a comparatively favorable prognosis. Other subtypes showed more diverse gene expression and immune infiltration patterns with distinct clinical outcomes. Finally, our analysis revealed a complex immune landscape consisting of both discrete cluster and continuous spectrum. CONCLUSION Overall, this study revealed five heterogeneous immune subtypes among ER+/PR-/HER2- breast cancer, also provided important implications for clinical translations.
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Affiliation(s)
- Peiling Xie
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, People's Republic of China
| | - Rui An
- Department of Hepatological Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, People's Republic of China
| | - Shibo Yu
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, People's Republic of China
| | - Jianjun He
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, People's Republic of China.
| | - Huimin Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, People's Republic of China.
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Shi S, Ma T, Xi Y. Characterization of the immune cell infiltration landscape in bladder cancer to aid immunotherapy. Arch Biochem Biophys 2021; 708:108950. [PMID: 34118215 DOI: 10.1016/j.abb.2021.108950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/08/2021] [Accepted: 05/29/2021] [Indexed: 12/15/2022]
Abstract
The tumor microenvironment (TME) is composed mainly of tumor cells, tumorinfiltrating immune cells, and matrix components. Recent clinical studies have indicated that tumor immune cell infiltration (ICI) is related to the sensitivity of immunotherapy and the prognosis of patients with bladder cancer (BC). Nevertheless, up to now, the landscape of immune infiltration in BC has not been clearly defined. Here we present two algorithms to reveal the landscape of ICI in 277 cases of BC. Two kinds of ICI patterns were established, and ICI scores were based on the analysis of the main components. In sub-types with high ICI scores, we found highly expressed immunecheckpoint and activated transforming growth factor b and WNT signal pathways. These might be the cause of poor prognosis. A low ICI score indicated a better prognosis. Our study showed that ICI scores in immunotherapy could be a valid biomarker for the prognosis of patients and a predictive indicator. The evaluation of ICI patterns of a larger cohort of samples would expand our cognition of TME, and the present study might guide the strategies of immunotherapy for patients with BC.
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Affiliation(s)
- Shanping Shi
- Diabetes Center, Zhejiang Provincial Key Laboratory of Pathophysiology, Institute of Biochemistry and Molecular Biology, School of Medicine, Ningbo University, Ningbo, China
| | - Ting Ma
- Diabetes Center, Zhejiang Provincial Key Laboratory of Pathophysiology, Institute of Biochemistry and Molecular Biology, School of Medicine, Ningbo University, Ningbo, China
| | - Yang Xi
- Diabetes Center, Zhejiang Provincial Key Laboratory of Pathophysiology, Institute of Biochemistry and Molecular Biology, School of Medicine, Ningbo University, Ningbo, China.
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Dong Y, Shang T, Ji H, Zhou X, Chen Z. Identification of Distinct Molecular Patterns and a Four-Gene Signature in Colon Cancer Based on Invasion-Related Genes. Front Genet 2021; 12:685371. [PMID: 34421995 PMCID: PMC8378182 DOI: 10.3389/fgene.2021.685371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/16/2021] [Indexed: 12/28/2022] Open
Abstract
Background The pathological stage of colon cancer cannot accurately predict recurrence, and to date, no gene expression characteristics have been demonstrated to be reliable for prognostic stratification in clinical practice, perhaps because colon cancer is a heterogeneous disease. The purpose was to establish a comprehensive molecular classification and prognostic marker for colon cancer based on invasion-related expression profiling. Methods From the Gene Expression Omnibus (GEO) database, we collected two microarray datasets of colon cancer samples, and another dataset was obtained from The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) further underwent univariate analysis, least absolute shrinkage, selection operator (LASSO) regression analysis, and multivariate Cox survival analysis to screen prognosis-associated feature genes, which were further verified with test datasets. Results Two molecular subtypes (C1 and C2) were identified based on invasion-related genes in the colon cancer samples in TCGA training dataset, and C2 had a good prognosis. Moreover, C1 was more sensitive to immunotherapy. A total of 1,514 invasion-related genes, specifically 124 downregulated genes and 1,390 upregulated genes in C1 and C2, were identified as DEGs. A four-gene prognostic signature was identified and validated, and colon cancer patients were stratified into a high-risk group and a low-risk group. Multivariate regression analyses and a nomogram indicated that the four-gene signature developed in this study was an independent predictive factor and had a relatively good predictive capability when adjusting for other clinical factors. Conclusion This research provided novel insights into the mechanisms underlying invasion and offered a novel biomarker of a poor prognosis in colon cancer patients.
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Affiliation(s)
- Yunfei Dong
- Department of Proctology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
| | - Tao Shang
- Department of Proctology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
| | - HaiXin Ji
- Department of Proctology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
| | - Xiukou Zhou
- Department of Proctology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
| | - Zhi Chen
- Department of Proctology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
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34
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Deng D, Luo X, Zhang S, Xu Z. Immune cell infiltration-associated signature in colon cancer and its prognostic implications. Aging (Albany NY) 2021; 13:19696-19709. [PMID: 34349038 PMCID: PMC8386549 DOI: 10.18632/aging.203380] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/15/2021] [Indexed: 02/05/2023]
Abstract
Tumor immune cell infiltration (ICI) has been reported in various studies to be correlated with tumor diagnosis, clinical treatment sensitivity and prognosis. It is an important direction to study the characteristics of immune cell infiltration and develop new prognostic markers to improve the treatment of colon cancer. In this paper, we systematically analyzed the ICI characteristics and obtained three ICI clusters. Then, the ICI scores were constructed and its prognostic implications were discussed. From the results, the ICI score patterns were linked to a great survival difference (p<0.001). A high ICI score was characterized by a higher fraction of plasma cells, CD8+ T cells, memory resting CD4+ T cells, monocytes, eosinophils and dendritic cells, which had better prognosis. Macrophages and neutrophils were increased in low ICI score patients with decreased overall survival. Immune checkpoint molecules (PDCD1, CD274, LAG3, IDO1, CTLA-4, TIGHT and HAVCR2) were found to be significantly overexpressed in the low ICI score subgroup. In addition, we also studied the correlation between the tumor mutation burden (TMB) and ICI score. This study indicated the ICI score could serve as a potential prognostic biomarker for colon cancer patients’ immunotherapy.
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Affiliation(s)
- Dan Deng
- Department of Cardiology, Zhuzhou Central Hospital, Zhuzhou 412007, China.,Department of Integrated Traditional Chinese and Western Internal Medicine, The Second Xiangya Hospital of Central South University, Changsha 410012, China
| | - Xin Luo
- Department of Cardiology, Zhuzhou Central Hospital, Zhuzhou 412007, China
| | - Sifang Zhang
- Department of Integrated Traditional Chinese and Western Internal Medicine, The Second Xiangya Hospital of Central South University, Changsha 410012, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital of Central South University, Changsha 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
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Analyzing the characteristics of immune cell infiltration in lung adenocarcinoma via bioinformatics to predict the effect of immunotherapy. Immunogenetics 2021; 73:369-380. [PMID: 34302518 DOI: 10.1007/s00251-021-01223-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/14/2021] [Indexed: 02/05/2023]
Abstract
Recent studies have shown that tumor immune cell infiltration (ICI) is associated with immunotherapy sensitivity and the prognosis of lung adenocarcinoma (LUAD). However, the immunoinfiltrative landscape of LUAD has not been elucidated. We propose two computational algorithms to unravel the ICI landscape to evaluate the efficacy of immunotherapy in LUAD patients. The raw data of LUAD patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were analyzed. After merging these datasets and removing the batch differences, we used the Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) algorithm to obtain the immune cell content of all the samples. The unsupervised consistency clustering algorithm was used to analyze the ICI subtypes, and three subgroups were obtained. In addition, the unsupervised consistency clustering algorithm was used to analyze the differentially expressed genes (DEGs) of the ICI subtypes and obtain three ICI gene clusters. Finally, the ICI score was determined by using principal component analysis (PCA) for the gene signature. The ICI score of LUAD patients ranged from - 32.26 to 12.89 and represents the prognosis and the response to immunotherapy. High ICI scores were characterized by the T cell receptor signaling pathway, B cell receptor signaling pathway, and natural killer cell-mediated cytotoxicity, suggesting that some immune cells were activated and had increased activity, which may be the cause of the better prognosis for patients with high ICI scores. Additionally, patients with higher ICI scores showed a significant immune therapeutic advantage and clinical benefit. This study shows that the ICI score may be a potent prognostic biomarker and predictor of therapy with immune checkpoint inhibitors.
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Xu H, Xu Q, Yin L. Prognostic value of tumor immune cell infiltration patterns in colon adenocarcinoma based on systematic bioinformatics analysis. Cancer Cell Int 2021; 21:344. [PMID: 34217290 PMCID: PMC8254898 DOI: 10.1186/s12935-021-02048-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
Background Although immunotherapy for colon cancer has made promising progress, only a few patients currently benefit from it. A recent study revealed that infiltrating immune cells are highly relevant to tumor prognosis and influence the expression of immune-related genes. However, the characterization of immune cell infiltration (ICI) has not yet been comprehensively analyzed and quantified in colon adenocarcinoma (COAD). Methods The multiomic data of COAD samples were downloaded from TCGA. ESTIMATE algorithm, ssGSEA method and CIBERSORT analysis were conducted to estimate the subpopulations of infiltrating immune cells. COAD subtypes based on ICI pattern were identified by consensus clustering then principal-component analysis was performed to obtain ICI scores to quantify the ICI patterns in individual tumors. Kaplan–Meier analysis was employed to validate prognostic value. Gene set enrichment analysis (GSEA) was applied for functional annotation. Finally, the mutation data was analyzed by employing “maftools” package. Results Three bioinformatics algorithms were used to evaluate the ICI patterns from 538 patients with COAD. Two ICI subtypes were determined using consensus clustering, and the ICI score was constructed by performing principal component analysis. Our findings showed that a higher ICI score often indicated a more advanced tumor and worse prognosis. The high-ICI score subgroup had a higher stromal score and more M0 macrophages but fewer plasma cells and decreased CD8 T cell infiltration. In addition, patients with high ICI scores had significantly higher expression levels of HAVCR2 and PCDC1LG2. Real-time polymerase chain reaction (PCR) was conducted to determine the prognostic significances of ICI-related genes. Conclusions In conclusion, ICI score may be considered as an original and useful indicator for independent prognostic prediction and individual immune-related therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02048-x.
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Affiliation(s)
- Hao Xu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qianhui Xu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lu Yin
- Department of Pathology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Chen ZG, Wang Y, Fong WP, Hu MT, Liang JY, Wang L, Li YH. A quantitative score of immune cell infiltration predicts the prognosis in pancreatic ductal adenocarcinoma. Int Immunopharmacol 2021; 98:107890. [PMID: 34174701 DOI: 10.1016/j.intimp.2021.107890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/06/2021] [Accepted: 06/11/2021] [Indexed: 12/20/2022]
Abstract
Pancreatic Ductal Adenocarcinoma (PDAC) is characterized by an extensive and dense fibrous stroma, which plays an active role in tumor growth and metastasis. Despite the growing importance of the tumor microenvironment in PDAC prognosis, the immune cell infiltration landscape of PDAC has not been elucidated. In this study, we applied a credible computational algorithm to comprehensively estimate the immune cell infiltration (ICI) patterns of 876 PDAC patients. Two ICI phenotypes were identified, and a ICIscore was constructed using ssGSEA algorithm. The ICIscore could significantly predict the prognosis and chemotherapy benefit of PDAC patients in both the discovery and the five validation cohorts. Multivariate cox analysis also identified the independent predictive role of the ICIscore in PDAC prognosis. A high ICIscore subtype was characterized by immune-active signaling pathways and anti-tumor immunity while a low ICIscore subtype was associated with tumor progressive signaling pathways. Four immunotherapy cohorts further supported the use of the ICIscore as a prognostic biomarker for patients receiving immune checkpoint inhibitors in other cancer types. The ICIscore reveals a close relationship between the ICI environment and prognosis and may provide new treatment strategies for PDAC patients.
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Affiliation(s)
- Zhi-Gang Chen
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Yun Wang
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - William Pat Fong
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ming-Tao Hu
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Jie-Ying Liang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Lingyun Wang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China.
| | - Yu-Hong Li
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
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Ten Hoorn S, de Back TR, Sommeijer DW, Vermeulen L. Clinical Value of Consensus Molecular Subtypes in Colorectal Cancer: A Systematic Review and Meta-Analysis. J Natl Cancer Inst 2021; 114:503-516. [PMID: 34077519 PMCID: PMC9002278 DOI: 10.1093/jnci/djab106] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/23/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
Background The consensus molecular subtypes (CMSs) of colorectal cancer (CRC) capture tumor heterogeneity at the gene-expression level. Currently, a restricted number of molecular features are used to guide treatment for CRC. We summarize the evidence on the clinical value of the CMSs. Methods We systematically identified studies in Medline and Embase that evaluated the prognostic and predictive value of CMSs in CRC patients. A random-effect meta-analysis was performed on prognostic data. Predictive data were summarized. Results In local disease, CMS4 tumors were associated with worse overall survival (OS) compared with CMS1 (hazard ratio [HR] = 3.28, 95% confidence interval = 1.27 to 8.47) and CMS2 cancers (HR = 2.60, 95% confidence interval = 1.93 to 3.50). In metastatic disease, CMS1 consistently had worse survival than CMS2-4 (OS HR range = 0.33-0.55; progression-free survival HR range = 0.53-0.89). Adjuvant chemotherapy in stage II and III CRC was most beneficial for OS in CMS2 and CMS3 (HR range = 0.16-0.45) and not effective in CMS4 tumors. In metastatic CMS4 cancers, an irinotecan-based regimen improved outcome compared with oxaliplatin (HR range = 0.31-0.72). The addition of bevacizumab seemed beneficial in CMS1, and anti-epidermal growth factor receptor therapy improved outcome for KRAS wild-type CMS2 patients. Conclusions The CMS classification holds clear potential for clinical use in predicting both prognosis and response to systemic therapy, which seems to be independent of the classifier used. Prospective studies are warranted to support implementation of the CMS taxonomy in clinical practice.
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Affiliation(s)
- Sanne Ten Hoorn
- Amsterdam UMC, University of Amsterdam, LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, Amsterdam, The Netherlands
| | - Tim R de Back
- Amsterdam UMC, University of Amsterdam, LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, Amsterdam, The Netherlands
| | - Dirkje W Sommeijer
- Amsterdam UMC, University of Amsterdam, LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Flevohospital, Department of Internal Medicine, Hospitaalweg 1, 1315 RA, Almere, The Netherlands
| | - Louis Vermeulen
- Amsterdam UMC, University of Amsterdam, LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
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Luo D, Kuang F, Du J, Zhou M, Peng F, Gan Y, Fang C, Yang X, Li B, Su S. Characterization of the Immune Cell Infiltration Profile in Pancreatic Carcinoma to Aid in Immunotherapy. Front Oncol 2021; 11:677609. [PMID: 34055645 PMCID: PMC8155731 DOI: 10.3389/fonc.2021.677609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/19/2021] [Indexed: 12/14/2022] Open
Abstract
The tumor microenvironment (TME) is comprised of tumor cells, infiltrating immune cells, and stroma. Multiple reports suggest that the immune cell infiltration (ICI) in TME is strongly associated with responsiveness to immunotherapy and prognosis of certain cancers. Thus far, the ICI profile of pancreatic carcinoma (PC) remains unclear. Here, we employed two algorithms to characterize the ICI profile of PC patients. Based on our results, we identified 2 ICI patterns and calculated the ICI score by using principal component analysis. Furthermore, we revealed that patients with low ICI scores had a better prognosis, compared to high ICI scores. Moreover, we discovered that a low tumor mutation burden (TMB) offered better overall survival (OS), relative to high TMB. In this study, a high ICI score referred to elevated PD-L1/TGF-β levels, increased activation of cell cycle pathway and DNA repair pathway, as well as reduced expression of immune-activation-related genes. We also demonstrated that three metabolic pathways were suppressed in the low ICI score group. These data may explain why a high ICI score equates to a poor prognosis. Based on our analysis, the ICI score can be used as an effective predictor of PC prognosis. Hence, establishing an ICI profile, based on a large patient population, will not only enhance our knowledge of TME but also aid in the development of immunotherapies specific to PC.
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Affiliation(s)
- De Luo
- Department of Hepatobiliary Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Fei Kuang
- Department of General Surgery, Changhai Hospital of The Second Military Medical University, Shanghai, China
| | - Juan Du
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Mengjia Zhou
- Department of Ultrasound, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fangyi Peng
- Department of Hepatobiliary Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yu Gan
- Department of Hepatobiliary Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Cheng Fang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiaoli Yang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Bo Li
- Department of Hepatobiliary Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Song Su
- Department of Hepatobiliary Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, China
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Li WX, Dai SX, An SQ, Sun T, Liu J, Wang J, Liu LG, Xun Y, Yang H, Fan LX, Zhang XL, Liao WQ, You H, Tamagnone L, Liu F, Huang JF, Liu D. Transcriptome integration analysis and specific diagnosis model construction for Hodgkin's lymphoma, diffuse large B-cell lymphoma, and mantle cell lymphoma. Aging (Albany NY) 2021; 13:11833-11859. [PMID: 33885377 PMCID: PMC8109084 DOI: 10.18632/aging.202882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 03/02/2021] [Indexed: 01/20/2023]
Abstract
Transcriptome differences between Hodgkin's lymphoma (HL), diffuse large B-cell lymphoma (DLBCL), and mantle cell lymphoma (MCL), which are all derived from B cell, remained unclear. This study aimed to construct lymphoma-specific diagnostic models by screening lymphoma marker genes. Transcriptome data of HL, DLBCL, and MCL were obtained from public databases. Lymphoma marker genes were screened by comparing cases and controls as well as the intergroup differences among lymphomas. A total of 9 HL marker genes, 7 DLBCL marker genes, and 4 MCL marker genes were screened in this study. Most HL marker genes were upregulated, whereas DLBCL and MCL marker genes were downregulated compared to controls. The optimal HL-specific diagnostic model contains one marker gene (MYH2) with an AUC of 0.901. The optimal DLBCL-specific diagnostic model contains 7 marker genes (LIPF, CCDC144B, PRO2964, PHF1, SFTPA2, NTS, and HP) with an AUC of 0.951. The optimal MCL-specific diagnostic model contains 3 marker genes (IGLV3-19, IGKV4-1, and PRB3) with an AUC of 0.843. The present study reveals the transcriptome data-based differences between HL, DLBCL, and MCL, when combined with other clinical markers, may help the clinical diagnosis and prognosis.
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Affiliation(s)
- Wen-Xing Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, Guangdong, China
| | - Shao-Xing Dai
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - San-Qi An
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Tingting Sun
- National School of Development, Peking University, Beijing 100871, China
| | - Justin Liu
- Department of Statistics, University of California, Riverside, CA 92521, USA
| | - Jun Wang
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | | | - Yang Xun
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | - Hua Yang
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | - Li-Xia Fan
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | - Xiao-Li Zhang
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | - Wan-Qin Liao
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | - Hua You
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Luca Tamagnone
- Istituto di Istologia ed Embriologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Fang Liu
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | - Jing-Fei Huang
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Dahai Liu
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
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Li X, Kulkarni AS, Liu X, Gao WQ, Huang L, Hu Z, Qian K. Metal-Organic Framework Hybrids Aid Metabolic Profiling for Colorectal Cancer. SMALL METHODS 2021; 5:e2001001. [PMID: 34927854 DOI: 10.1002/smtd.202001001] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/05/2020] [Indexed: 06/14/2023]
Abstract
Colorectal cancer (CRC) is the third most common fatal cancer worldwide, accounting for ≈10% of cancer-related mortality. Metabolic shift occurs from the very early stage during the development of CRC, which is of significant etiological and diagnostic importance toward precision medicine. Here, an advanced molecular tool to characterize the metabolic alterations in CRC, based on metal-organic framework (MOF) hybrids is reported. Consuming only 500 nL of plasma without any sample pretreatment, MOF hybrids yield direct metabolic fingerprints by laser desorption/ionization mass spectrometry in seconds. A diagnostic prediction model by a machine learning algorithm is constructed, to discriminate CRC patients from normal controls with an average area under the curve of 0.947 for the discovery cohort and 0.912 for the independent validation cohort. In addition, CRC-specific metabolic signature consisting of 34 potential biomarkers, based on the aforementioned diagnostic model is identified. The results advance the design of nanomaterial-based platforms for metabolic analysis and establish a new liquid biopsy tool for CRC screening compatible with the current clinical workflow in practice.
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Affiliation(s)
- Xinxing Li
- Department of Gastrointestinal Surgery, Tongji Hospital, Medical College of Tongji University, Shanghai, 200065, P. R. China
- Department of General Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, P. R. China
| | - Anuja Shreeram Kulkarni
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Xun Liu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Wei-Qiang Gao
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Lin Huang
- Stem Cell Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Zhiqian Hu
- Department of Gastrointestinal Surgery, Tongji Hospital, Medical College of Tongji University, Shanghai, 200065, P. R. China
- Department of General Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
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Su H, Li X, Huang L, Cao J, Zhang M, Vedarethinam V, Di W, Hu Z, Qian K. Plasmonic Alloys Reveal a Distinct Metabolic Phenotype of Early Gastric Cancer. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007978. [PMID: 33742513 DOI: 10.1002/adma.202007978] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/09/2021] [Indexed: 05/20/2023]
Abstract
Gastric cancer (GC) is a multifactorial process, accompanied by alterations in metabolic pathways. Non-invasive metabolic profiling facilitates GC diagnosis at early stage leading to an improved prognostic outcome. Herein, mesoporous PdPtAu alloys are designed to characterize the metabolic profiles in human blood. The elemental composition is optimized with heterogeneous surface plasmonic resonance, offering preferred charge transfer for photoinduced desorption/ionization and enhanced photothermal conversion for thermally driven desorption. The surface structure of PdPtAu is further tuned with controlled mesopores, accommodating metabolites only, rather than large interfering compounds. Consequently, the optimized PdPtAu alloy yields direct metabolic fingerprints by laser desorption/ionization mass spectrometry in seconds, consuming 500 nL of native plasma. A distinct metabolic phenotype is revealed for early GC by sparse learning, resulting in precise GC diagnosis with an area under the curve of 0.942. It is envisioned that the plasmonic alloy will open up a new era of minimally invasive blood analysis to improve the surveillance of cancer patients in the clinical setting.
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Affiliation(s)
- Haiyang Su
- State Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Xinxing Li
- Department of Gastrointestinal Surgery, Tongji Hospital, Medical College of Tongji University, Shanghai, 200065, P. R. China
- Department of General Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, P. R. China
| | - Lin Huang
- Stem Cell Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Jing Cao
- State Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Mengji Zhang
- State Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Vadanasundari Vedarethinam
- State Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Wen Di
- State Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Zhiqian Hu
- Department of Gastrointestinal Surgery, Tongji Hospital, Medical College of Tongji University, Shanghai, 200065, P. R. China
- Department of General Surgery, Changzheng Hospital, Naval Medical University, Shanghai, 200003, P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes, Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
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Proteomic Analyses of Fibroblast- and Serum-Derived Exosomes Identify QSOX1 as a Marker for Non-invasive Detection of Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13061351. [PMID: 33802764 PMCID: PMC8002505 DOI: 10.3390/cancers13061351] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Early diagnosis of colorectal cancer (CRC) is crucial to improve patient outcomes. The tumour microenvironment immediately adapts to malignant transformations, including the activation of fibroblasts in the connective tissue nearby. In this study, we investigated fibroblast activity-related protein secretion via extracellular vesicles (EVs). QSOX1, a protein identified to be significantly reduced in activated fibroblasts and derived EVs, was also found to be significantly reduced in circulating blood plasma EVs of CRC patients as compared to control patients. Hence, blood plasma EV-associated QSOX1 represents a promising platform for diagnostic CRC screening. Abstract The treatment of colorectal cancer (CRC) has improved during the last decades, but methods for crucial early diagnosis are yet to be developed. The influence of the tumour microenvironment on liquid biopsies for early cancer diagnostics are gaining growing interest, especially with emphasis on exosomes (EXO), a subgroup of extracellular vesicles (EVs). In this study, we established paired cancer-associated (CAFs) and normal fibroblasts (NF) from 13 CRC patients and investigated activation status-related protein abundance in derived EXOs. Immunohistochemical staining of matched patient tissue was performed and an independent test cohort of CRC patient plasma-derived EXOs was assessed by ELISA. A total of 11 differentially abundant EV proteins were identified between NFs and CAFs. In plasma EXOs, the CAF-EXO enriched protein EDIL3 was elevated, while the NF-EXO enriched protein QSOX1 was diminished compared to whole plasma. Both markers were significantly reduced in patient-matched CRC tissue compared to healthy colon tissue. In an independent test cohort, a significantly reduced protein abundance of QSOX1 was observed in plasma EXOs from CRC patients compared to controls and diagnostic ROC curve analysis revealed an AUC of 0.904. In conclusion, EXO-associated QSOX1 is a promising novel marker for early diagnosis and non-invasive risk stratification in CRC.
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Ganig N, Baenke F, Thepkaysone ML, Lin K, Rao VS, Wong FC, Polster H, Schneider M, Helm D, Pecqueux M, Seifert AM, Seifert L, Weitz J, Rahbari NN, Kahlert C. Proteomic Analyses of Fibroblast- and Serum-Derived Exosomes Identify QSOX1 as a Marker for Non-invasive Detection of Colorectal Cancer. Cancers (Basel) 2021. [PMID: 33802764 DOI: 10.3390/cancers130613510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The treatment of colorectal cancer (CRC) has improved during the last decades, but methods for crucial early diagnosis are yet to be developed. The influence of the tumour microenvironment on liquid biopsies for early cancer diagnostics are gaining growing interest, especially with emphasis on exosomes (EXO), a subgroup of extracellular vesicles (EVs). In this study, we established paired cancer-associated (CAFs) and normal fibroblasts (NF) from 13 CRC patients and investigated activation status-related protein abundance in derived EXOs. Immunohistochemical staining of matched patient tissue was performed and an independent test cohort of CRC patient plasma-derived EXOs was assessed by ELISA. A total of 11 differentially abundant EV proteins were identified between NFs and CAFs. In plasma EXOs, the CAF-EXO enriched protein EDIL3 was elevated, while the NF-EXO enriched protein QSOX1 was diminished compared to whole plasma. Both markers were significantly reduced in patient-matched CRC tissue compared to healthy colon tissue. In an independent test cohort, a significantly reduced protein abundance of QSOX1 was observed in plasma EXOs from CRC patients compared to controls and diagnostic ROC curve analysis revealed an AUC of 0.904. In conclusion, EXO-associated QSOX1 is a promising novel marker for early diagnosis and non-invasive risk stratification in CRC.
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Affiliation(s)
- Nicole Ganig
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Franziska Baenke
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - May-Linn Thepkaysone
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Kuailu Lin
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Venkatesh S Rao
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Fang Cheng Wong
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Heike Polster
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Martin Schneider
- MS-based Protein Analysis Unit, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Dominic Helm
- MS-based Protein Analysis Unit, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Mathieu Pecqueux
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Adrian M Seifert
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, D-69120 Heidelberg, Germany
| | - Lena Seifert
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, D-69120 Heidelberg, Germany
| | - Jürgen Weitz
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Nuh N Rahbari
- Department of Surgery, University Medicine Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, D-68167 Mannheim, Germany
| | - Christoph Kahlert
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, D-69120 Heidelberg, Germany
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Mattesen TB, Andersen CL, Bramsen JB. MethCORR infers gene expression from DNA methylation and allows molecular analysis of ten common cancer types using fresh-frozen and formalin-fixed paraffin-embedded tumor samples. Clin Epigenetics 2021; 13:20. [PMID: 33509261 PMCID: PMC7842045 DOI: 10.1186/s13148-021-01000-0] [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: 09/18/2020] [Accepted: 01/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background Transcriptional analysis is widely used to study the molecular biology of cancer and hold great biomarker potential for clinical patient stratification. Yet, accurate transcriptional profiling requires RNA of a high quality, which often cannot be retrieved from formalin-fixed, paraffin-embedded (FFPE) tumor tissue that is routinely collected and archived in clinical departments. To overcome this roadblock to clinical testing, we previously developed MethCORR, a method that infers gene expression from DNA methylation data, which is robustly retrieved from FFPE tissue. MethCORR was originally developed for colorectal cancer and with this study, we aim to: (1) extend the MethCORR method to 10 additional cancer types and (2) to illustrate that the inferred gene expression is accurate and clinically informative. Results Regression models to infer gene expression information from DNA methylation were developed for ten common cancer types using matched RNA sequencing and DNA methylation profiles (HumanMethylation450 BeadChip) from The Cancer Genome Atlas Project. Robust and accurate gene expression profiles were inferred for all cancer types: on average, the expression of 11,000 genes was modeled with good accuracy and an intra-sample correlation of R2 = 0.90 between inferred and measured gene expression was observed. Molecular pathway analysis and transcriptional subtyping were performed for breast, prostate, and lung cancer samples to illustrate the general usability of the inferred gene expression profiles: overall, a high correlation of r = 0.96 (Pearson) in pathway enrichment scores and a 76% correspondence in molecular subtype calls were observed when using measured and inferred gene expression as input. Finally, inferred expression from FFPE tissue correlated better with RNA sequencing data from matched fresh-frozen tissue than did RNA sequencing data from FFPE tissue (P < 0.0001; Wilcoxon rank-sum test). Conclusions In all cancers investigated, MethCORR enabled DNA methylation-based transcriptional analysis, thus enabling future analysis of cancer in situations where high-quality DNA, but not RNA, is available. Here, we provide the framework and resources for MethCORR modeling of ten common cancer types, thereby widely expanding the possibilities for transcriptional studies of archival FFPE material.
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Affiliation(s)
- Trine B Mattesen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
| | - Jesper B Bramsen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
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Árnadóttir SS, Mattesen TB, Vang S, Madsen MR, Madsen AH, Birkbak NJ, Bramsen JB, Andersen CL. Transcriptomic and proteomic intra-tumor heterogeneity of colorectal cancer varies depending on tumor location within the colorectum. PLoS One 2020; 15:e0241148. [PMID: 33332369 PMCID: PMC7746197 DOI: 10.1371/journal.pone.0241148] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023] Open
Abstract
Background Intra-tumor heterogeneity (ITH) of colorectal cancer (CRC) complicates molecular tumor classification, such as transcriptional subtyping. Differences in cellular states, biopsy cell composition, and tumor microenvironment may all lead to ITH. Here we analyze ITH at the transcriptomic and proteomic levels to ascertain whether subtype discordance between multiregional biopsies reflects relevant biological ITH or lack of classifier robustness. Further, we study the impact of tumor location on ITH. Methods Multiregional biopsies from stage II and III CRC tumors were analyzed by RNA sequencing (41 biopsies, 14 tumors) and multiplex immune protein analysis (89 biopsies, 29 tumors). CRC subtyping was performed using consensus molecular subtypes (CMS), CRC intrinsic subtypes (CRIS), and TUMOR types. ITH-scores and network maps were defined to determine the origin of heterogeneity. A validation cohort was used with one biopsy per tumor (162 tumors). Results Overall, inter-tumor transcriptional variation exceeded ITH, and subtyping calls were frequently concordant between multiregional biopsies. Still, some tumors had high transcriptional ITH and were classified discordantly. Subtyping of proximal MSS tumors were discordant for 50% of the tumors, this ITH was related to differences in the microenvironment. Subtyping of distal MSS tumors were less discordant, here the ITH was more cancer-cell related. The subtype discordancy reflected actual molecular ITH within the tumors. The relevance of the subtypes was reflected at protein level where several inflammation markers were significantly increased in immune related transcriptional subtypes, which was verified in an independent cohort (Wilcoxon rank sum test; p<0.05). Unsupervised hierarchical clustering of the protein data identified large ITH at protein level; as the multiregional biopsies clustered together for only 9 out of 29 tumors. Conclusion Our transcriptomic and proteomic analyses show that the tumor location along the colorectum influence the ITH of CRC, which again influence the concordance of subtyping.
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Affiliation(s)
- Sigrid Salling Árnadóttir
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Trine Block Mattesen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mogens Rørbæk Madsen
- Surgical Research Unit, Department of Surgery, Herning Regional Hospital, Herning, Denmark
| | - Anders Husted Madsen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Surgical Research Unit, Department of Surgery, Herning Regional Hospital, Herning, Denmark
| | - Nicolai Juul Birkbak
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jesper Bertram Bramsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- * E-mail:
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Identification of NEO1 as a prognostic biomarker and its effects on the progression of colorectal cancer. Cancer Cell Int 2020; 20:510. [PMID: 33088218 PMCID: PMC7568410 DOI: 10.1186/s12935-020-01604-1] [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: 10/17/2019] [Accepted: 10/12/2020] [Indexed: 11/20/2022] Open
Abstract
Background Due to the high morbidity and poor clinical outcomes, early predictive and prognostic biomarker identification is desiderated in colorectal cancer (CRC). As a homologue of the Deleted in Colorectal Cancer (DCC) gene, the role of Neogenin-1 (NEO1) in CRC remained unveiled. This study was designed to probe into the effects and potential function of NEO1 in CRC. Methods Online databases, Gene Set Enrichment Analysis (GSEA), quantitative real-time PCR and western blotting were used to evaluate NEO1 expression in colorectal cancer tissues. Survival analysis was performed to predict the prognosis of CRC patients based on NEO1 expression level. Then, cell proliferation was detected by colony formation and Cell Counting Kit 8 (CCK-8) assays. CRC cell migration and invasion were examined by transwell assays. Finally, we utilized the Gene Set Variation Analysis (GSVA) and GSEA to dig the potential mechanisms of NEO1 in CRC. Results Oncomine database and The Cancer Genome Atlas (TCGA) database showed that NEO1 was down-regulated in CRC. Further results validated that NEO1 mRNA and protein expression were both significantly lower in CRC tumor tissues than in the adjacent tissues in our clinical samples. NEO1 expression was decreased with the progression of CRC. Survival and other clinical characteristic analyses exhibited that low NEO1 expression was related with poor prognosis. A gain-of-function study showed that overexpression of NEO1 restrained proliferation, migration and invasion of CRC cells while a loss-of-function showed the opposite effects. Finally, functional pathway enrichment analysis revealed that NEO1 low expression samples were enriched in inflammation-related signaling pathways, EMT and angiogenesis. Conclusion A tumor suppressor gene NEO1 was identified and verified to be correlated with the prognosis and progression of CRC, which could serve as a prognostic biomarker for CRC patients.
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Bhudia J, Glynne-Jones R, Smith T, Hall M. Neoadjuvant Chemotherapy without Radiation in Colorectal Cancer. Clin Colon Rectal Surg 2020; 33:287-297. [PMID: 32968364 PMCID: PMC7500967 DOI: 10.1055/s-0040-1713746] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In colon cancer, primary surgery followed by postoperative chemotherapy represents the standard of care. In rectal cancer, the standard of care is preoperative radiotherapy or chemoradiation, which significantly reduces local recurrence but has no impact on subsequent metastatic disease or overall survival. The administration of neoadjuvant chemotherapy (NACT) before surgery can increase the chance of a curative resection and improves long-term outcomes in patients with liver metastases. Hence, NACT is being explored in both primary rectal and colon cancers as an alternative strategy to shrink the tumor, facilitate a curative resection, and simultaneously counter the risk of metastases. Yet, this lack of clarity regarding the precise aims of NACT (downstaging, maximizing response, or improving survival) is hindering progress. The appropriate cytotoxic agents, the optimal regimen, the number of cycles, or duration of NACT prior to surgery or in the postoperative setting remains undefined. Several potential strategies for integrating NACT are discussed with their advantages and disadvantages.
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Affiliation(s)
- Jyotsna Bhudia
- Department of Radiotherapy, Mount Vernon Centre for Cancer Treatment, Mount Vernon Hospital, Northwood, United Kingdom
| | - Rob Glynne-Jones
- Department of Radiotherapy, Mount Vernon Centre for Cancer Treatment, Mount Vernon Hospital, Northwood, United Kingdom
| | - Thomas Smith
- Department of Radiotherapy, Mount Vernon Centre for Cancer Treatment, Mount Vernon Hospital, Northwood, United Kingdom
| | - Marcia Hall
- Department of Medical Oncology, Mount Vernon Centre for Cancer Treatment, Mount Vernon Hospital, Northwood, United Kingdom
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Zhang X, Shi M, Chen T, Zhang B. Characterization of the Immune Cell Infiltration Landscape in Head and Neck Squamous Cell Carcinoma to Aid Immunotherapy. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 22:298-309. [PMID: 33230435 PMCID: PMC7522342 DOI: 10.1016/j.omtn.2020.08.030] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/25/2020] [Indexed: 01/16/2023]
Abstract
The tumor microenvironment (TME) chiefly consists of tumor cells and tumor-infiltrating immune cells admixed with the stromal component. A recent clinical trial has shown that the tumor immune cell infiltration (ICI) is correlated with the sensitivity to immunotherapy and the head and neck squamous cell carcinoma (HNSC) prognosis. However, to date, the immune infiltrative landscape of HNSC has not yet been elucidated. Herein, we proposed two computational algorithms to unravel the ICI landscape of 1,029 HNSC patients. Three ICI patterns were defined, and the ICI scores were determined by using principal-component analysis. A high ICI score was characterized by an increased tumor mutation burden (TMB) and the immune-activating signaling pathways. Activation of transforming growth factor-β (TGF-β) and WNT signaling pathways were observed in low ICI score subtypes, indicating T cell suppression, and may be responsible for poor prognosis. Two immunotherapy cohorts confirmed patients with higher ICI scores demonstrated significant therapeutic advantages and clinical benefits. This study demonstrated that the ICI scores serve as an effective prognostic biomarker and predictive indicator for immunotherapy. Evaluating the ICI patterns of a larger cohort of samples will extend our understanding of TME, and it may provide directions to the current research investigations on immunotherapeutic strategies for HNSC.
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Affiliation(s)
- Xinhai Zhang
- Oral Research Center of CPLA, Changhai Hospital, Second Military Medical University, 15 Dongjiangwan Road, Shanghai 200081, China
| | - Mengqi Shi
- Department of Stomatology, Navy Speciality Medical Center of Peoples’ Liberation Army Navy, Shanghai 200052, China
| | - Tielou Chen
- Oral Research Center of CPLA, Changhai Hospital, Second Military Medical University, 15 Dongjiangwan Road, Shanghai 200081, China
| | - Boxin Zhang
- Department of Stomatology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
- Corresponding author: Boxin Zhang, Department of Stomatology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
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Kasi A, Handa S, Bhatti S, Umar S, Bansal A, Sun W. Molecular Pathogenesis and Classification of Colorectal Carcinoma. CURRENT COLORECTAL CANCER REPORTS 2020; 16:97-106. [PMID: 32905465 DOI: 10.1007/s11888-020-00458-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Purpose of review Molecular pathways in colorectal carcinogenesis involve several complex genetic and epigenetic modulations that cause normal colonic mucosa to metamorphose into a benign polyp and subsequently into a malignant tumor. Our purpose is to recapitulate historical and recent genomic research in order to augment the understanding of colorectal cancer pathogenesis. Recent Findings In 2015, the molecular classification for colorectal cancers was unified into one system with four distinct groups, also called as consensus molecular subtypes. This led to an enhanced understanding of molecular and immune signatures which has implications on predicting the clinical behavior as well as response to different therapeutic agents. Summary In this review, we expound on the current literature as well as draw on our own experience to present the important molecular pathogenesis pathways, key genetic mutations, differences in pathogenesis of left versus right sided tumors as well as the molecular classification of colorectal cancers.
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Affiliation(s)
- Anup Kasi
- Department of Medicine, Division of Medical Oncology, Kansas University Medical Center, Kansas City, KS, U.S.A
| | - Shivani Handa
- Department of Internal Medicine, Icahn School of Medicine at Mount Sinai West & Morningside, NY, NY
| | - Sajjad Bhatti
- Department of Medicine, Division of Medical Oncology, Kansas University Medical Center, Kansas City, KS, U.S.A
| | - Shahid Umar
- Department of Medicine, Division of Surgery, Kansas University Medical Center, Kansas City, KS, U.S.A
| | - Ajay Bansal
- Department of Medicine, Division of Gastroenterology, Kansas University Medical Center, Kansas City, KS, U.S.A
| | - Weijing Sun
- Department of Medicine, Division of Medical Oncology, Kansas University Medical Center, Kansas City, KS, U.S.A
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