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Mouillet-Richard S, Cazelles A, Sroussi M, Gallois C, Taieb J, Laurent-Puig P. Clinical Challenges of Consensus Molecular Subtype CMS4 Colon Cancer in the Era of Precision Medicine. Clin Cancer Res 2024; 30:2351-2358. [PMID: 38564259 PMCID: PMC11145159 DOI: 10.1158/1078-0432.ccr-23-3964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/31/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
Over the past decade, our understanding of the diversity of colorectal cancer has expanded significantly, raising hopes of tailoring treatments more precisely for individual patients. A key achievement in this direction was the establishment of the consensus molecular classification, particularly identifying the challenging consensus molecular subtype (CMS) CMS4 associated with poor prognosis. Because of its aggressive nature, extensive research is dedicated to the CMS4 subgroup. Recent years have unveiled molecular and microenvironmental features at the tissue level specific to CMS4 colorectal cancer. This has paved the way for mechanistic studies and the development of preclinical models. Simultaneously, efforts have been made to easily identify patients with CMS4 colorectal cancer. Reassessing clinical trial results through the CMS classification lens has improved our understanding of the therapeutic challenges linked to this subtype. Exploration of the biology of CMS4 colorectal cancer is yielding potential biomarkers and novel treatment approaches. This overview aims to provide insights into the clinico-biological characteristics of the CMS4 subgroup, the molecular pathways driving this subtype, and available diagnostic options. We also emphasize the therapeutic challenges associated with this subtype, offering potential explanations. Finally, we summarize the current tailored treatments for CMS4 colorectal cancer emerging from fundamental and preclinical studies.
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Affiliation(s)
- Sophie Mouillet-Richard
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Antoine Cazelles
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Marine Sroussi
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
| | - Claire Gallois
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Gastroenterology and Gastrointestinal Oncology Department, APHP.Centre - Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Julien Taieb
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Gastroenterology and Gastrointestinal Oncology Department, APHP.Centre - Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Pierre Laurent-Puig
- Team “Personalized medicine, pharmacogenomics, therapeutic optimization”, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Department of Biology, APHP.Centre - Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
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Abedizadeh R, Majidi F, Khorasani HR, Abedi H, Sabour D. Colorectal cancer: a comprehensive review of carcinogenesis, diagnosis, and novel strategies for classified treatments. Cancer Metastasis Rev 2024; 43:729-753. [PMID: 38112903 DOI: 10.1007/s10555-023-10158-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
Colorectal cancer is the third most common and the second deadliest cancer worldwide. To date, colorectal cancer becomes one of the most important challenges of the health system in many countries. Since the clinical symptoms of this cancer appear in the final stages of the disease and there is a significant golden time between the formation of polyps and the onset of cancer, early diagnosis can play a significant role in reducing mortality. Today, in addition to colonoscopy, minimally invasive methods such as liquid biopsy have received much attention. The treatment of this complex disease has been mostly based on traditional treatments including surgery, radiotherapy, and chemotherapy; the high mortality rate indicates a lack of success for current treatment methods. Moreover, disease recurrence is another problem of traditional treatments. Recently, new approaches such as targeted therapy, immunotherapy, and nanomedicine have opened new doors for cancer treatment, some of which have already entered the market, and many methods have shown promising results in clinical trials. The success of immunotherapy in the treatment of refractory disease, the introduction of these methods into neoadjuvant therapy, and the successful results in tumor shrinkage without surgery have made immunotherapy a tough competitor for conventional treatments. It seems that the combination of those methods with such targeted therapies will go through promising changes in the future of colorectal cancer treatment.
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Affiliation(s)
- Roya Abedizadeh
- Department of Cancer Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Isar 11, Babol, 47138-18983, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Bani-Hashem Square, Tehran, 16635-148, Iran
| | - Fateme Majidi
- Department of Cancer Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Isar 11, Babol, 47138-18983, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Bani-Hashem Square, Tehran, 16635-148, Iran
| | - Hamid Reza Khorasani
- Department of Cancer Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Isar 11, Babol, 47138-18983, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Bani-Hashem Square, Tehran, 16635-148, Iran
| | - Hassan Abedi
- Department of Internal Medicine, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
| | - Davood Sabour
- Department of Cancer Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Isar 11, Babol, 47138-18983, Iran.
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Bani-Hashem Square, Tehran, 16635-148, Iran.
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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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4
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Bahrambeigi V, Lee JJ, Branchi V, Rajapakshe KI, Xu Z, Kui N, Henry JT, Kun W, Stephens BM, Dhebat S, Hurd MW, Sun R, Yang P, Ruppin E, Wang W, Kopetz S, Maitra A, Guerrero PA. Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-Specific Transcriptome and Molecular Subtype. Cancer Res 2024; 84:1719-1732. [PMID: 38451249 PMCID: PMC11096054 DOI: 10.1158/0008-5472.can-23-4070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
Longitudinal monitoring of patients with advanced cancers is crucial to evaluate both disease burden and treatment response. Current liquid biopsy approaches mostly rely on the detection of DNA-based biomarkers. However, plasma RNA analysis can unleash tremendous opportunities for tumor state interrogation and molecular subtyping. Through the application of deep learning algorithms to the deconvolved transcriptomes of RNA within plasma extracellular vesicles (evRNA), we successfully predicted consensus molecular subtypes in patients with metastatic colorectal cancer. Analysis of plasma evRNA also enabled monitoring of changes in transcriptomic subtype under treatment selection pressure and identification of molecular pathways associated with recurrence. This approach also revealed expressed gene fusions and neoepitopes from evRNA. These results demonstrate the feasibility of using transcriptomic-based liquid biopsy platforms for precision oncology approaches, spanning from the longitudinal monitoring of tumor subtype changes to the identification of expressed fusions and neoantigens as cancer-specific therapeutic targets, sans the need for tissue-based sampling. SIGNIFICANCE The development of an approach to interrogate molecular subtypes, cancer-associated pathways, and differentially expressed genes through RNA sequencing of plasma extracellular vesicles lays the foundation for liquid biopsy-based longitudinal monitoring of patient tumor transcriptomes.
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Affiliation(s)
- Vahid Bahrambeigi
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaewon J. Lee
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Vittorio Branchi
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kimal I. Rajapakshe
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhichao Xu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Naishu Kui
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason T. Henry
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wang Kun
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Bret M. Stephens
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah Dhebat
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark W. Hurd
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Yang
- Department Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Statistics Rice University, Houston, TX, USA
| | - Eytan Ruppin
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Wenyi Wang
- Department Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paola A. Guerrero
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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5
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Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A. Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis. Nat Commun 2024; 15:3909. [PMID: 38724493 PMCID: PMC11082183 DOI: 10.1038/s41467-024-47957-3] [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: 03/18/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Aberrant signaling pathway activity is a hallmark of tumorigenesis and progression, which has guided targeted inhibitor design for over 30 years. Yet, adaptive resistance mechanisms, induced by rapid, context-specific signaling network rewiring, continue to challenge therapeutic efficacy. Leveraging progress in proteomic technologies and network-based methodologies, we introduce Virtual Enrichment-based Signaling Protein-activity Analysis (VESPA)-an algorithm designed to elucidate mechanisms of cell response and adaptation to drug perturbations-and use it to analyze 7-point phosphoproteomic time series from colorectal cancer cells treated with clinically-relevant inhibitors and control media. Interrogating tumor-specific enzyme/substrate interactions accurately infers kinase and phosphatase activity, based on their substrate phosphorylation state, effectively accounting for signal crosstalk and sparse phosphoproteome coverage. The analysis elucidates time-dependent signaling pathway response to each drug perturbation and, more importantly, cell adaptive response and rewiring, experimentally confirmed by CRISPR knock-out assays, suggesting broad applicability to cancer and other diseases.
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Affiliation(s)
- George Rosenberger
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Mikko Turunen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jing He
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Prem S Subramaniam
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sergey Pampou
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Aaron T Griffin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles Karan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Patrick Kerwin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Diana Murray
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Barry Honig
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
- Chan Zuckerberg Biohub New York, New York, NY, USA.
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Pengnam S, Jitkaroon W, Srisuphan R, Wongprayoon P, Rayanil KO, Charoensuksai P. Furanocoumarin compounds isolated from Dorstenia foetida potentiate irinotecan anticancer activity against colorectal cancer cells. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2024; 74:67-79. [PMID: 38554381 DOI: 10.2478/acph-2024-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 04/01/2024]
Abstract
Although the anticancer activity of Dorstenia foetida was already observed, the chemical entity responsible for this activity remained unidentified. In this study, the cytotoxic activity of two furanocoumarin compounds, i.e., 5-methoxy--3-(3-methyl-2,3-dihydroxybutyl)-psoralen (1) and 5-methoxy-3-(3-methyl-2,3-dihydroxybutyl)-psoralen diacetate (2) isolated from ethyl acetate fraction of D. foetida (whole plant) was investigated in several cancer cell lines including HN22, MDA-MB-231, HCT116, and HT29. The results revealed that compound 2 exhibited cytotoxic activity, particularly against colorectal cancer cell lines HCT116 and HT29. The interplay between compound 2 and irinotecan (Iri) showed synergism against HCT116, which was analyzed by CompuSyn software. The simulation revealed that, at the molar ratio of Iri:2 of 1:40, the concentration predicted to achieve a 90 % inhibitory effect when used in the combination would be ~28- and ~4-fold lower than the concentration of compound 2 and Iri, resp., when used individually. Finally, the percentage of apoptotic cells in the HCT116 line treated with the combination was markedly higher than in the cells treated with the individual agent (60 % apoptotic cells for the combination compared to 17 and 45 % for Iri and compound 2 monotherapy, resp). In conclusion, our results identified compound 2 as a plant-derived compound exhibiting anticancer properties that can act synergistically with Iri and warranted further research to assess the potential of this synergism for colorectal cancer treatment.
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Affiliation(s)
- Supusson Pengnam
- Department of Biomedicine and Health Informatics, Green Innovations Group (PDGIG), Faculty of Pharmacy Silpakorn University, Nakhon Pathom 73000, Thailand
| | - Watcharapa Jitkaroon
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom, 73000, Thailand
| | - Roongtiwa Srisuphan
- Bioactives from Natural Resources Research Collaboration for Excellence in Pharmaceutical Sciences (BNEP) Faculty of Pharmacy, Silpakorn University, Nakhon Pathom 73000 Thailand
| | - Pawaris Wongprayoon
- Department of Biomedicine and Health Informatics and Bioactives from Natural Resources Research Collaboration for Excellence in Pharmaceutical Sciences (BNEP), Faculty of Pharmacy, Silpakorn University, Nakhon Pathom 73000 Thailand
| | - Kanok-On Rayanil
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom, 73000, Thailand
| | - Purin Charoensuksai
- Department of Biomedicine and Health Informatics and Bioactives from Natural Resources Research Collaboration for Excellence in Pharmaceutical Sciences (BNEP), Faculty of Pharmacy, Silpakorn University, Nakhon Pathom 73000 Thailand
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Li X, Wu D, Li Q, Gu J, Gao W, Zhu X, Yin W, Zhu R, Zhu L, Jiao N. Host-microbiota interactions contributing to the heterogeneous tumor microenvironment in colorectal cancer. Physiol Genomics 2024; 56:221-234. [PMID: 38073489 DOI: 10.1152/physiolgenomics.00103.2023] [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: 09/01/2023] [Revised: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024] Open
Abstract
Colorectal cancer (CRC) exhibits pronounced heterogeneity and is categorized into four widely accepted consensus molecular subtypes (CMSs) with unique tumor microenvironments (TMEs). However, the intricate landscape of the microbiota and host-microbiota interactions within these TMEs remains elusive. Using RNA-sequencing data from The Cancer Genome Atlas, we analyzed the host transcriptomes and intratumoral microbiome profiles of CRC samples. Distinct host genes and microbial genera were identified among the CMSs. Immune microenvironments were evaluated using CIBERSORTx and ESTIMATE, and microbial coabundance patterns were assessed with FastSpar. Through LASSO penalized regression, we explored host-microbiota associations for each CMS. Our analysis revealed distinct host gene signatures within the CMSs, which encompassed ferroptosis-related genes and specific immune microenvironments. Moreover, we identified 293, 153, 66, and 109 intratumoral microbial genera with differential abundance, and host-microbiota associations contributed to distinct TMEs, characterized by 829, 1,270, 634, and 1,882 robust gene-microbe associations for each CMS in CMS1-CMS4, respectively. CMS1 featured inflammation-related HSF1 activation and gene interactions within the endothelin pathway and Flammeovirga. Integrin-related genes displayed positive correlations with Sutterella in CMS2, whereas CMS3 spotlighted microbial associations with biosynthetic and metabolic pathways. In CMS4, genes involved in collagen biosynthesis showed positive associations with Sutterella, contributing to disruptions in homeostasis. Notably, immune-rich subtypes exhibited pronounced ferroptosis dysregulation, potentially linked to tissue microbial colonization. This comprehensive investigation delineates the diverse landscapes of the TME within each CMS, incorporating host genes, intratumoral microbiota, and their complex interactions. These findings shed light on previously uncharted mechanisms underpinning CRC heterogeneity and suggest potential therapeutic targets.NEW & NOTEWORTHY This study determined the following: 1) providing a comprehensive landscape of consensus molecular subtype (CMS)-specific tumor microenvironments (TMEs); 2) constructing CMS-specific networks, including host genes, intratumoral microbiota, and enriched pathways, analyzing their associations to uncover unique patterns that demonstrate the intricate interplay within the TME; and 3) revealing a connection between immune-rich subtypes and ferroptosis activation, suggesting a potential regulatory role of the microbiota in ferroptosis dysregulation of the colorectal cancer TME.
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Affiliation(s)
- Xiaoyi Li
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Dingfeng Wu
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Qiuyu Li
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Jinglan Gu
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Wenxing Gao
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Xinyue Zhu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Wenjing Yin
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Ruixin Zhu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Lixin Zhu
- Department of Colorectal Surgery, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Na Jiao
- Department of Nephrology, Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
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8
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Alipourgivi F, Motolani A, Qiu AY, Qiang W, Yang GY, Chen S, Lu T. Genetic Alterations of NF-κB and Its Regulators: A Rich Platform to Advance Colorectal Cancer Diagnosis and Treatment. Int J Mol Sci 2023; 25:154. [PMID: 38203325 PMCID: PMC10779007 DOI: 10.3390/ijms25010154] [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: 10/04/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
Colorectal cancer (CRC) is the third leading cause of cancer mortality in the United States, with an estimated 52,000 deaths in 2023. Though significant progress has been made in both diagnosis and treatment of CRC in recent years, genetic heterogeneity of CRC-the culprit for possible CRC relapse and drug resistance, is still an insurmountable challenge. Thus, developing more effective therapeutics to overcome this challenge in new CRC treatment strategies is imperative. Genetic and epigenetic changes are well recognized to be responsible for the stepwise development of CRC malignancy. In this review, we focus on detailed genetic alteration information about the nuclear factor (NF)-κB signaling, including both NF-κB family members, and their regulators, such as protein arginine methyltransferase 5 (PRMT5), and outer dynein arm docking complex subunit 2 (ODAD2, also named armadillo repeat-containing 4, ARMC4), etc., in CRC patients. Moreover, we provide deep insight into different CRC research models, with a particular focus on patient-derived xenografts (PDX) and organoid models, and their potential applications in CRC research. Genetic alterations on NF-κB signaling components are estimated to be more than 50% of the overall genetic changes identified in CRC patients collected by cBioportal for Cancer Genomics; thus, emphasizing its paramount importance in CRC progression. Consequently, various genetic alterations on NF-κB signaling may hold great promise for novel therapeutic development in CRC. Future endeavors may focus on utilizing CRC models (e.g., PDX or organoids, or isogenic human embryonic stem cell (hESC)-derived colonic cells, or human pluripotent stem cells (hPSC)-derived colonic organoids, etc.) to further uncover the underpinning mechanism of these genetic alterations in NF-κB signaling in CRC progression. Moreover, establishing platforms for drug discovery in dishes, and developing Biobanks, etc., may further pave the way for the development of innovative personalized medicine to treat CRC in the future.
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Affiliation(s)
- Faranak Alipourgivi
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (F.A.); (A.M.)
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
| | - Aishat Motolani
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (F.A.); (A.M.)
| | - Alice Y. Qiu
- Center for Developmental Therapeutics, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; (A.Y.Q.); (W.Q.)
| | - Wenan Qiang
- Center for Developmental Therapeutics, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; (A.Y.Q.); (W.Q.)
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611, USA;
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Guang-Yu Yang
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611, USA;
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA;
| | - Tao Lu
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (F.A.); (A.M.)
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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9
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Gambaro K, Marques M, McNamara S, Couetoux du Tertre M, Hoffert C, Srivastava A, Schab A, Alcindor T, Langleben A, Sideris L, Abdelsalam M, Tehfe M, Couture F, Batist G, Kavan P. A Phase II Exploratory Study to Identify Biomarkers Predictive of Clinical Response to Regorafenib in Patients with Metastatic Colorectal Cancer Who Have Failed First-Line Therapy. Int J Mol Sci 2023; 25:43. [PMID: 38203214 PMCID: PMC10778949 DOI: 10.3390/ijms25010043] [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: 10/27/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
Single-agent regorafenib is approved in Canada for metastatic colorectal cancer (mCRC) patients who have failed previous lines of therapy. Identifying prognostic biomarkers is key to optimizing therapeutic strategies for these patients. In this clinical study (NCT01949194), we evaluated the safety and efficacy of single-agent regorafenib as a second-line therapy for mCRC patients who received it after failing first-line therapy with an oxaliplatin or irinotecan regimen with or without bevacizumab. Using various omics approaches, we also investigated putative biomarkers of response and resistance to regorafenib in metastatic lesions and blood samples in the same cohort. Overall, the safety profile of regorafenib seemed similar to the CORRECT trial, where regorafenib was administered as ≥ 2 lines of therapy. While the mutational landscape showed typical mutation rates for the top five driver genes (APC, KRAS, BRAF, PIK3CA, and TP53), KRAS mutations were enriched in intrinsically resistant lesions. Additional exploration of genomic-phenotype associations revealed several biomarker candidates linked to unfavorable prognoses in patients with mCRC using various approaches, including pathway analysis, cfDNA profiling, and copy number analysis. However, further research endeavors are necessary to validate the potential utility of these promising genes in understanding patients' responses to regorafenib treatment.
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Affiliation(s)
- Karen Gambaro
- Canadian National Centres of Excellence-Exactis Innovations, Montreal, QC H3T 1Y6, Canada; (K.G.); (M.M.); (S.M.)
- Consortium de Recherche en Oncologie Clinique du Québec (Q-CROC), Quebec, QC G1V 3X8, Canada
- Segal Cancer Centre-Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Maud Marques
- Canadian National Centres of Excellence-Exactis Innovations, Montreal, QC H3T 1Y6, Canada; (K.G.); (M.M.); (S.M.)
- Segal Cancer Centre-Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Suzan McNamara
- Canadian National Centres of Excellence-Exactis Innovations, Montreal, QC H3T 1Y6, Canada; (K.G.); (M.M.); (S.M.)
- Consortium de Recherche en Oncologie Clinique du Québec (Q-CROC), Quebec, QC G1V 3X8, Canada
| | - Mathilde Couetoux du Tertre
- Canadian National Centres of Excellence-Exactis Innovations, Montreal, QC H3T 1Y6, Canada; (K.G.); (M.M.); (S.M.)
- Consortium de Recherche en Oncologie Clinique du Québec (Q-CROC), Quebec, QC G1V 3X8, Canada
| | - Cyrla Hoffert
- Canadian National Centres of Excellence-Exactis Innovations, Montreal, QC H3T 1Y6, Canada; (K.G.); (M.M.); (S.M.)
- Consortium de Recherche en Oncologie Clinique du Québec (Q-CROC), Quebec, QC G1V 3X8, Canada
- Segal Cancer Centre-Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Archana Srivastava
- Canadian National Centres of Excellence-Exactis Innovations, Montreal, QC H3T 1Y6, Canada; (K.G.); (M.M.); (S.M.)
- Consortium de Recherche en Oncologie Clinique du Québec (Q-CROC), Quebec, QC G1V 3X8, Canada
- Segal Cancer Centre-Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Anna Schab
- Canadian National Centres of Excellence-Exactis Innovations, Montreal, QC H3T 1Y6, Canada; (K.G.); (M.M.); (S.M.)
- Consortium de Recherche en Oncologie Clinique du Québec (Q-CROC), Quebec, QC G1V 3X8, Canada
| | | | | | - Lucas Sideris
- Hôpital Maisonneuve Rosemont, Montreal, QC H1T 2M4, Canada
| | | | - Mustapha Tehfe
- Hematology-Oncology, Oncology Center-Centre Hospitalier de l’Université de Montreal, Montreal, QC H2X 0C1, Canada
| | | | - Gerald Batist
- Segal Cancer Centre-Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Petr Kavan
- Segal Cancer Centre-Jewish General Hospital, Montreal, QC H3T 1E2, Canada
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10
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Zhu Q, Zhao X, Zhang Y, Li Y, Liu S, Han J, Sun Z, Wang C, Deng D, Wang S, Tang Y, Huang Y, Jiang S, Tian C, Chen X, Yuan Y, Li Z, Yang T, Lai T, Liu Y, Yang W, Zou X, Zhang M, Cui H, Liu C, Jin X, Hu Y, Chen A, Xu X, Li G, Hou Y, Liu L, Liu S, Fang L, Chen W, Wu L. Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines. Nat Commun 2023; 14:8170. [PMID: 38071219 PMCID: PMC10710513 DOI: 10.1038/s41467-023-43991-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Human cancer cell lines have long served as tools for cancer research and drug discovery, but the presence and the source of intra-cell-line heterogeneity remain elusive. Here, we perform single-cell RNA-sequencing and ATAC-sequencing on 42 and 39 human cell lines, respectively, to illustrate both transcriptomic and epigenetic heterogeneity within individual cell lines. Our data reveal that transcriptomic heterogeneity is frequently observed in cancer cell lines of different tissue origins, often driven by multiple common transcriptional programs. Copy number variation, as well as epigenetic variation and extrachromosomal DNA distribution all contribute to the detected intra-cell-line heterogeneity. Using hypoxia treatment as an example, we demonstrate that transcriptomic heterogeneity could be reshaped by environmental stress. Overall, our study performs single-cell multi-omics of commonly used human cancer cell lines and offers mechanistic insights into the intra-cell-line heterogeneity and its dynamics, which would serve as an important resource for future cancer cell line-based studies.
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Affiliation(s)
- Qionghua Zhu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Xin Zhao
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuanhang Zhang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yanping Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Shang Liu
- BGI Research, 518083, Shenzhen, China
| | - Jingxuan Han
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Zhiyuan Sun
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Chunqing Wang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Daqi Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Yisen Tang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Siyuan Jiang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Chi Tian
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xi Chen
- BGI Research, 518083, Shenzhen, China
| | - Yue Yuan
- BGI Research, 518083, Shenzhen, China
| | - Zeyu Li
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Tao Yang
- China National GeneBank, 518120, Shenzhen, China
| | - Tingting Lai
- China National GeneBank, 518120, Shenzhen, China
| | - Yiqun Liu
- China National GeneBank, 518120, Shenzhen, China
| | - Wenzhen Yang
- China National GeneBank, 518120, Shenzhen, China
| | - Xuanxuan Zou
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | | | - Huanhuan Cui
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Xin Jin
- BGI Research, 518083, Shenzhen, China
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Ao Chen
- BGI Research, 518083, Shenzhen, China
- JFL-BGI STOmics Center, Jinfeng Laboratory, 401329, Chongqing, China
- The Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong, China
| | - Xun Xu
- BGI Research, 518083, Shenzhen, China
| | - Guipeng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Yong Hou
- BGI Research, 518083, Shenzhen, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, 518100, Shenzhen, China
| | - Longqi Liu
- BGI Research, 518083, Shenzhen, China.
- BGI Research, 310012, Hangzhou, China.
- Shenzhen Bay Laboratory, 518000, Shenzhen, China.
| | - Shiping Liu
- BGI Research, 518083, Shenzhen, China.
- The Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong, China.
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, 518100, Shenzhen, China.
- BGI Research, 310012, Hangzhou, China.
- Shenzhen Bay Laboratory, 518000, Shenzhen, China.
| | - Liang Fang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Wei Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Liang Wu
- BGI Research, 518083, Shenzhen, China.
- JFL-BGI STOmics Center, Jinfeng Laboratory, 401329, Chongqing, China.
- BGI Research, 401329, Chongqing, China.
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11
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Xiang Y, Liu X, Sun Q, Liao K, Liu X, Zhao Z, Feng L, Liu Y, Wang B. The development of cancers research based on mitochondrial heat shock protein 90. Front Oncol 2023; 13:1296456. [PMID: 38098505 PMCID: PMC10720920 DOI: 10.3389/fonc.2023.1296456] [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: 09/18/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
Mitochondrial heat shock protein 90 (mtHsp90), including Tumor necrosis factor receptor-associated protein 1 (TRAP1) and Hsp90 translocated from cytoplasm, modulating cellular metabolism and signaling pathways by altering the conformation, activity, and stability of numerous client proteins, and is highly expressed in tumors. mtHsp90 inhibition results in the destabilization and eventual degradation of its client proteins, leading to interference with various tumor-related pathways and efficient control of cancer cell development. Among these compounds, gamitrinib, a specific mtHsp90 inhibitor, has demonstrated its safety and efficacy in several preclinical investigations and is currently undergoing evaluation in clinical trials. This review aims to provide a comprehensive overview of the present knowledge pertaining to mtHsp90, encompassing its structure and function. Moreover, our main emphasis is on the development of mtHsp90 inhibitors for various cancer therapies, to present a thorough overview of the recent pre-clinical and clinical advancements in this field.
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Affiliation(s)
- Yuchu Xiang
- West China Hospital of Sichuan University, Sichuan University, Chengdu, China
| | - Xudong Liu
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Qi Sun
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, Centre for Safe Medication Practice and Research, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Kuo Liao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaohan Liu
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China
| | - Zihui Zhao
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lishuang Feng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yan Liu
- Department of Organ Transplantation, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Bo Wang
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
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12
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Brisset M, Mehlen P, Meurette O, Hollande F. Notch receptor/ligand diversity: contribution to colorectal cancer stem cell heterogeneity. Front Cell Dev Biol 2023; 11:1231416. [PMID: 37860822 PMCID: PMC10582728 DOI: 10.3389/fcell.2023.1231416] [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: 05/30/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Cancer cell heterogeneity is a key contributor to therapeutic failure and post-treatment recurrence. Targeting cell subpopulations responsible for chemoresistance and recurrence seems to be an attractive approach to improve treatment outcome in cancer patients. However, this remains challenging due to the complexity and incomplete characterization of tumor cell subpopulations. The heterogeneity of cells exhibiting stemness-related features, such as self-renewal and chemoresistance, fuels this complexity. Notch signaling is a known regulator of cancer stem cell (CSC) features in colorectal cancer (CRC), though the effects of its heterogenous signaling on CRC cell stemness are only just emerging. In this review, we discuss how Notch ligand-receptor specificity contributes to regulating stemness, self-renewal, chemoresistance and cancer stem cells heterogeneity in CRC.
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Affiliation(s)
- Morgan Brisset
- Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Melbourne, VIC, Australia
- Centre for Cancer Research, The University of Melbourne, Melbourne, VIC, Australia
- Cancer Cell Death Laboratory, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Patrick Mehlen
- Cancer Cell Death Laboratory, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Olivier Meurette
- Cancer Cell Death Laboratory, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Frédéric Hollande
- Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Melbourne, VIC, Australia
- Centre for Cancer Research, The University of Melbourne, Melbourne, VIC, Australia
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13
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Ramsay RG, Whitehall V, Flood MP. Technological advances define shifting pathway signaling from normal to primary and metastatic colorectal cancer. Growth Factors 2023; 41:179-191. [PMID: 37351905 DOI: 10.1080/08977194.2023.2227274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/08/2023] [Indexed: 06/24/2023]
Abstract
Adoption of organoid/tumoroid propagation of normal and malignant intestinal epithelia has provided unparalleled opportunities to compare cell growth factor and signaling dependencies. These 3D structures recapitulate tumours in terms of gene expression regarding the tumor cells but also allow deeper insights into the contribution of the tumour microenvironment (TME). Elements of the TME can be manipulated or added back in the form of infiltrating cytotoxic lymphocytes and/or cancer associated fibroblasts. The effectiveness of chemo-, radio- and immunotherapies can be explored within weeks of deriving these patient-derived tumour avatars informing treatment of these exact patients in a timely manner. Entrenched paths to colorectal cancer (CRC) from the earliest steps of conventional adenoma or serrated lesion formation, and the recognition of further sub-categorisations embodied by consensus-molecular-subtypes (CMS), provide genetic maps allowing a molecular form of pathologic taxonomy. Recent advances in organoid propagation and scRNAseq are reshaping our understanding of CMS and CRC.
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Affiliation(s)
- Robert G Ramsay
- Sir Peter MacCallum Department of Oncology and Peter MacCallum Cancer Centre, The University of Melbourne, Parkville, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Australia
| | - Vicki Whitehall
- QIMR Berghofer Medical Research Institute, Queensland, Australia
- Conjoint Internal Medicine Laboratory, Pathology Queensland, Queensland, Australia
| | - Michael P Flood
- Sir Peter MacCallum Department of Oncology and Peter MacCallum Cancer Centre, The University of Melbourne, Parkville, Australia
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14
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Jamialahmadi H, Nazari SE, TanzadehPanah H, Saburi E, Asgharzadeh F, Khojasteh-Leylakoohi F, Alaei M, Mirahmadi M, Babaei F, Asghari SZ, Mansouri S, Khalili-Tanha G, Maftooh M, Fiuji H, Hassanian SM, Ferns GA, Khazaei M, Avan A. Targeting transforming growth factor beta (TGF-β) using Pirfenidone, a potential repurposing therapeutic strategy in colorectal cancer. Sci Rep 2023; 13:14357. [PMID: 37658230 PMCID: PMC10474052 DOI: 10.1038/s41598-023-41550-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023] Open
Abstract
The modulating factors within the tumor microenvironment, for example, transforming growth factor beta (TGF-β), may limit the response to chemo and immunotherapy protocols in colorectal cancer (CRC). In the current study, the therapeutic potential of targeting the TGF-β pathway using Pirfenidone (PFD), a TGF-β inhibitor, either alone or in combination with five fluorouracil (5-FU) has been explored in preclinical models of CRC. The anti-proliferative and migratory effects of PFD were assessed by MTT and wound-healing assays respectively. Xenograft models were used to study the anti-tumor activity, histopathological, and side effects analysis. Targeting of TGF-β resulted in suppression of cell proliferation and migration, associated with modulation of survivin and MMP9/E-cadherin. Moreover, the PFD inhibited TGF-β induced tumor progression, fibrosis, and inflammatory response through perturbation of collagen and E-cadherin. Targeting the TGF-β pathway using PFD may increase the anti-tumor effects of 5-FU and reduce tumor development, providing a new therapeutic approach to CRC treatment.
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Affiliation(s)
- Hamid Jamialahmadi
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyedeh Elnaz Nazari
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid TanzadehPanah
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Saburi
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fereshteh Asgharzadeh
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Khojasteh-Leylakoohi
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Alaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdi Mirahmadi
- Department of Pharmacology, Faculty of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Babaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyedeh Zahra Asghari
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeide Mansouri
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ghazaleh Khalili-Tanha
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mina Maftooh
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Fiuji
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Division of Medical Education, Brighton and Sussex Medical School, Falmer, Brighton, BN1 9PH, Sussex, UK
| | - Majid Khazaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- College of Medicine, University of Warith Al-Anbiyaa, Karbala, Iraq.
- School of Mechanical, Medical and Process Engineering, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia.
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.
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15
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Rotermund A, Staege MS, Brandt S, Luetzkendorf J, Lucas H, Mueller LP, Mueller T. Luciferase Expressing Preclinical Model Systems Representing the Different Molecular Subtypes of Colorectal Cancer. Cancers (Basel) 2023; 15:4122. [PMID: 37627150 PMCID: PMC10452405 DOI: 10.3390/cancers15164122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease. More insight into the biological diversity of CRC is needed to improve therapeutic outcomes. Established CRC cell lines are frequently used and were shown to be representative models of the main subtypes of CRC at the genomic and transcriptomic level. In the present work, we established stable, luciferase expressing derivatives from 10 well-established CRC cell lines, generated spheroids and subcutaneous xenograft tumors in nude mice, and performed comparative characterization of these model systems. Transcriptomic analyses revealed the close relation of cell lines with their derived spheroids and xenograft tumors. The preclinical model systems clustered with patient tumor samples when compared to normal tissue thereby confirming that cell-line-based tumor models retain specific characteristics of primary tumors. Xenografts showed different differentiation patterns and bioluminescence imaging revealed metastatic spread to the lungs. In addition, the models were classified according to the CMS classification system, with further sub-classification according to the recently identified two intrinsic epithelial tumor cell states of CRC, iCMS2 and iCMS3. The combined data showed that regarding primary tumor characteristics, 3D-spheroid cultures resemble xenografts more closely than 2D-cultured cells do. Furthermore, we set up a bioluminescence-based spheroid cytotoxicity assay in order to be able to perform dose-response relationship studies in analogy to typical monolayer assays. Applying the established assay, we studied the efficacy of oxaliplatin. Seven of the ten used cell lines showed a significant reduction in the response to oxaliplatin in the 3D-spheroid model compared to the 2D-monolayer model. Therapy studies in selected xenograft models confirmed the response or lack of response to oxaliplatin treatment. Analyses of differentially expressed genes in these models identified CAV1 as a possible marker of oxaliplatin resistance. In conclusion, we established a combined 2D/3D, in vitro/in vivo model system representing the heterogeneity of CRC, which can be used in preclinical research applications.
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Affiliation(s)
- Arne Rotermund
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
| | - Martin S. Staege
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany;
| | - Sarah Brandt
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
| | - Jana Luetzkendorf
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
| | - Henrike Lucas
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany;
| | - Lutz P. Mueller
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
| | - Thomas Mueller
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
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16
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Bastin J, Sroussi M, Nemazanyy I, Laurent-Puig P, Mouillet-Richard S, Djouadi F. Downregulation of mitochondrial complex I induces ROS production in colorectal cancer subtypes that differently controls migration. J Transl Med 2023; 21:522. [PMID: 37533102 PMCID: PMC10398918 DOI: 10.1186/s12967-023-04341-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/10/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) can be classified into four molecular subtypes (CMS) among which CMS1 is associated with the best prognosis, while CMS4, the mesenchymal subtype, has the worst outcome. Although mitochondria are considered to be hubs of numerous signaling pathways, the study of mitochondrial metabolism has been neglected for many years. Mitochondrial Complex I (CI) plays a dual role, both in energy and reactive oxygen species (ROS) production. However, the possible contribution of CI to tumorigenesis in cancer remains unclear. The purpose of this study was to investigate the CI under the prism of the CMS classification of CRC in ex vivo models. METHODS Biochemical dosages, bioenergetics analysis and western-blot were used to characterize CI expression, function and redox balance in LoVo and MDST8 cell lines, belonging to CMS1 and CMS4 subgroups, respectively. Cell proliferation and migration were assessed by xCELLigence technology. Overproduction or scavenging of mitochondrial ROS (mtROS) were performed to analyze the effect of mtROS on proliferation, migration, and mesenchymal markers. Focal adhesion kinase (FAK) and its activation were analyzed by immunofluorescence. We assessed the distribution of two CI scores in CRC cohorts according to CMS classification and their relevance for patient survival. RESULTS We found that CI is downregulated in CMS4 cells and is associated with elevated mtROS. We establish for the first time that in these migrating cells, mtROS production is maintained at optimal levels not only through changes in CI activity but also by inactivation/acetylation of superoxide dismutase 2 (SOD2), a major mitochondrial antioxidant enzyme. We show that promoting or scavenging mtROS both mitigate CMS4 cells' migration. Our results also point to a mtROS-mediated focal adhesion kinase (FAK) activation, which likely sustains their migratory phenotype. Using cohorts of CRC patients, we document that the expression of CI is downregulated in the CMS4 subgroup, and that low CI expression is associated with poor prognosis. Patients' datasets reveal an inverse correlation between CI and the epithelial-mesenchymal transition (EMT) pathway. CONCLUSION We showed that inhibition of CI contributes to heighten mtROS, which likely foster MDST8 migration and might account for the specific EMT signature of CMS4 tumors. These data reveal a novel role of mitochondrial CI in CRC, with biological consequences that may be targeted with anti- or pro-oxidant drugs in clinical practice.
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Affiliation(s)
- Jean Bastin
- Centre de Recherche des Cordeliers, INSERM U1138, Sorbonne Université, Université Paris-Cité, 15, Rue de l'Ecole de Médecine, 75006, Paris, France
| | - Marine Sroussi
- Centre de Recherche des Cordeliers, INSERM U1138, Sorbonne Université, Université Paris-Cité, 15, Rue de l'Ecole de Médecine, 75006, Paris, France
- Laboratoire de Biochimie, Ecole Supérieure de Physique et de Chimie Industrielle de la Ville de Paris, 75005, Paris, France
| | - Ivan Nemazanyy
- Plate Plateforme d'étude du Métabolisme, SFR Necker, INSERM US24/CNRS UAR3633, 75015, Paris, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM U1138, Sorbonne Université, Université Paris-Cité, 15, Rue de l'Ecole de Médecine, 75006, Paris, France
- Institut du Cancer Paris CARPEM, Department of Biology Hôpital Georges Pompidou, 75015, Paris, France
| | - Sophie Mouillet-Richard
- Centre de Recherche des Cordeliers, INSERM U1138, Sorbonne Université, Université Paris-Cité, 15, Rue de l'Ecole de Médecine, 75006, Paris, France
| | - Fatima Djouadi
- Centre de Recherche des Cordeliers, INSERM U1138, Sorbonne Université, Université Paris-Cité, 15, Rue de l'Ecole de Médecine, 75006, Paris, France.
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Xu H, Wu A, Ren H, Yu C, Liu G, Liu L. Classification of colorectal cancer consensus molecular subtypes using attention-based multi-instance learning network on whole-slide images. Acta Histochem 2023; 125:152057. [PMID: 37300984 DOI: 10.1016/j.acthis.2023.152057] [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: 04/13/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Colorectal cancer (CRC) is the third most common and second most lethal cancer globally. It is highly heterogeneous with different clinical-pathological characteristics, prognostic status, and therapy responses. Thus, the precise diagnosis of CRC subtypes is of great significance for improving the prognosis and survival of CRC patients. Nowadays, the most commonly used molecular-level CRC classification system is the Consensus Molecular Subtypes (CMSs). In this study, we applied a weakly supervised deep learning method, named attention-based multi-instance learning (MIL), on formalin-fixed paraffin-embedded (FFPE) whole-slide images (WSIs) to distinguish CMS1 subtype from CMS2, CMS3, and CMS4 subtypes, as well as distinguish CMS4 from CMS1, CMS2, and CMS3 subtypes. The advantage of MIL is training a bag of the tiled instance with bag-level labels only. Our experiment was performed on 1218 WSIs obtained from The Cancer Genome Atlas (TCGA). We constructed three convolutional neural network-based structures for model training and evaluated the ability of the max-pooling operator and mean-pooling operator on aggregating bag-level scores. The results showed that the 3-layer model achieved the best performance in both comparison groups. When compared CMS1 with CMS234, max-pooling reached the ACC of 83.86 % and the mean-pooling operator reached the AUC of 0.731. While comparing CMS4 with CMS123, mean-pooling reached the ACC of 74.26 % and max-pooling reached the AUC of 0.609. Our results implied that WSIs could be utilized to classify CMSs, and manual pixel-level annotation is not a necessity for computational pathology imaging analysis.
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Affiliation(s)
- Huilin Xu
- Institutes of Biomedical Sciences and Intelligent Medicine Institute, Fudan University, Shanghai 200032, China
| | - Aoshen Wu
- Institutes of Biomedical Sciences and Intelligent Medicine Institute, Fudan University, Shanghai 200032, China
| | - He Ren
- Faculty of Medical Instrumentation, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
| | - Chenghang Yu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China, WHO Collaborating Center for Tropical Diseases, Shanghai 200025, China
| | - Gang Liu
- Institutes of Biomedical Sciences and Intelligent Medicine Institute, Fudan University, Shanghai 200032, China.
| | - Lei Liu
- Institutes of Biomedical Sciences and Intelligent Medicine Institute, Fudan University, Shanghai 200032, China.
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18
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Pickles OJ, Wanigasooriya K, Ptasinska A, Patel AJ, Robbins HL, Bryer C, Whalley CM, Tee L, Lal N, Pinna CM, Elzefzafy N, Taniere P, Beggs AD, Middleton GM. MHC Class II is Induced by IFNγ and Follows Three Distinct Patterns of Expression in Colorectal Cancer Organoids. CANCER RESEARCH COMMUNICATIONS 2023; 3:1501-1513. [PMID: 37565053 PMCID: PMC10411481 DOI: 10.1158/2767-9764.crc-23-0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/17/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023]
Abstract
Tumor-specific MHC class II (tsMHC-II) expression impacts tumor microenvironmental immunity. tsMHC-II positive cancer cells may act as surrogate antigen-presenting cells and targets for CD4+ T cell-mediated lysis. In colorectal cancer, tsMHC-II negativity is common, in cell lines due to CIITA promoter methylation. To clarify mechanisms of tsMHC-II repression in colorectal cancer, we analyzed colorectal cancer organoids which are epigenetically faithful to tissue of origin. 15 primary colorectal cancer organoids were treated with IFNγ ± epigenetic modifiers: flow cytometry was used for tsMHC-II expression. qRT-PCR, total RNA sequencing, nanopore sequencing, bisulfite conversion/pyrosequencing, and Western blotting was used to quantitate CIITA, STAT1, IRF1, and JAK1 expression, mutations and promoter methylation and chromatin immunoprecipitation to quantitate H3K9ac, H3K9Me2, and EZH2 occupancy at CIITA. We define three types of response to IFNγ in colorectal cancer: strong, weak, and noninducibility. Delayed and restricted expression even with prolonged IFNγ exposure was due to IFNγ-mediated EZH2 occupancy at CIITA. tsMHC-II expression was enhanced by EZH2 and histone deacetylase inhibition in the weakly inducible organoids. Noninducibility is seen in three consensus molecular subtype 1 (CMS1) organoids due to JAK1 mutation. No organoid demonstrates CIITA promoter methylation. Providing IFNγ signaling is intact, most colorectal cancer organoids are class II inducible. Upregulation of tsMHC-II through targeted epigenetic therapy is seen in one of fifteen organoids. Our approach can serve as a blueprint for investigating the heterogeneity of specific epigenetic mechanisms of immune suppression across individual patients in other cancers and how these might be targeted to inform the conduct of future trials of epigenetic therapies as immune adjuvants more strategically in cancer. Significance Cancer cell expression of MHC class II significantly impacts tumor microenvironmental immunity. Previous studies investigating mechanisms of repression of IFNγ-inducible class II expression using cell lines demonstrate epigenetic silencing of IFN pathway genes as a frequent immune evasion strategy. Unlike cell lines, patient-derived organoids maintain epigenetic fidelity to tissue of origin. In the first such study, we analyze patterns, dynamics, and epigenetic control of IFNγ-induced class II expression in a series of colorectal cancer organoids.
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Affiliation(s)
- Oliver J. Pickles
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Kasun Wanigasooriya
- Institute of Cancer and Genomic Science, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Science, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Akshay J. Patel
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Helen L. Robbins
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Claire Bryer
- Institute of Cancer and Genomic Science, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Celina M. Whalley
- Institute of Cancer and Genomic Science, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Louise Tee
- Institute of Cancer and Genomic Science, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Neeraj Lal
- Institute of Cancer and Genomic Science, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Claudia M.A. Pinna
- Institute of Cancer and Genomic Science, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Nahla Elzefzafy
- Institute of Cancer and Genomic Science, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- Cancer Biology Department, NCI, Cairo University, Cairo, Egypt
| | - Philippe Taniere
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Andrew D. Beggs
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Cancer and Genomic Science, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Gary M. Middleton
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
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19
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Chowdhury S, Gupta R, Millstein J, Lin K, Haridas V, Zeineddine MA, Parseghian C, Lenz HJ, Kopetz S, Shen JP. Transcriptional Profiling and Consensus Molecular Subtype Assignment to Understand Response and Resistance to Anti-Epidermal Growth Factor Receptor Therapy in Colorectal Cancer. JCO Precis Oncol 2023; 7:e2200422. [PMID: 37487150 PMCID: PMC10581628 DOI: 10.1200/po.22.00422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 04/10/2023] [Accepted: 05/08/2023] [Indexed: 07/26/2023] Open
Abstract
PURPOSE Activating mutations in KRAS, NRAS, and BRAF are known to cause resistance to anti-epidermal growth factor receptor (EGFR) therapy; however, only approximately 40% of patients with colorectal cancer (CRC) with RASWT tumors respond to anti-EGFR treatment. We sought to discover novel biomarkers to predict response to anti-EGFR antibody treatment in CRC and to understand mechanisms of resistance to anti-EGFR therapy. MATERIALS AND METHODS Transcriptomic profiles from three clinical and two preclinical cohorts treated with cetuximab were used to assign consensus molecular subtypes (CMS) to each sample and correlated with outcomes. RESULTS Restricting to RASWT patients, we observed that CMS2 tumors (canonical subtype) had significantly higher response rates relative to other CMS when treated with cetuximab combination with doublet chemotherapy (Okita et al cohort: 92% disease control rate (DCR) for CMS2, chi-square P = .04; CALGB/SWOG 80405 cohort: 90% objective response rate (ORR) for CMS2, chi-square P < .001) and with single-agent cetuximab (68%, chi-square P = .01). CMS2 tumors showed best response among right-sided (ORR = 80%) and left-sided (ORR = 92%) tumors in the CALGB/SWOG 80405 cohort. CMS2 cells lines were most likely to be sensitive to cetuximab (60%) and CMS2 patient-derived xenograft had the highest DCR (84%). We found Myc, E2F, and mammalian target of rapamycin pathways were consistently upregulated in resistant samples (enrichment score >1, false discovery rate <0.25). Inhibitors of these pathways in resistant cell lines exhibited additive effects with cetuximab. CONCLUSION These data suggest that CRC transcriptional profiles, when used to assign CMS, provide additional ability to predict response to anti-EGFR therapy relative to using tumor sidedness alone. Notably both right-sided and left-sided CMS2 tumors had excellent response, suggesting that anti-EGFR therapy be included as a treatment option for right-sided CMS2 tumors.
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Affiliation(s)
- Saikat Chowdhury
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ria Gupta
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Joshua Millstein
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA
| | - Kangyu Lin
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Valsala Haridas
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Mohammad A. Zeineddine
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Christine Parseghian
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Heinz-Josef Lenz
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
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20
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Wu X, Yan H, Qiu M, Qu X, Wang J, Xu S, Zheng Y, Ge M, Yan L, Liang L. Comprehensive characterization of tumor microenvironment in colorectal cancer via molecular analysis. eLife 2023; 12:e86032. [PMID: 37267125 PMCID: PMC10238095 DOI: 10.7554/elife.86032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 05/10/2023] [Indexed: 06/04/2023] Open
Abstract
Colorectal cancer (CRC) remains a challenging and deadly disease with high tumor microenvironment (TME) heterogeneity. Using an integrative multi-omics analysis and artificial intelligence-enabled spatial analysis of whole-slide images, we performed a comprehensive characterization of TME in colorectal cancer (CCCRC). CRC samples were classified into four CCCRC subtypes with distinct TME features, namely, C1 as the proliferative subtype with low immunogenicity; C2 as the immunosuppressed subtype with the terminally exhausted immune characteristics; C3 as the immune-excluded subtype with the distinct upregulation of stromal components and a lack of T cell infiltration in the tumor core; and C4 as the immunomodulatory subtype with the remarkable upregulation of anti-tumor immune components. The four CCCRC subtypes had distinct histopathologic and molecular characteristics, therapeutic efficacy, and prognosis. We found that the C1 subtype may be suitable for chemotherapy and cetuximab, the C2 subtype may benefit from a combination of chemotherapy and bevacizumab, the C3 subtype has increased sensitivity to the WNT pathway inhibitor WIKI4, and the C4 subtype is a potential candidate for immune checkpoint blockade treatment. Importantly, we established a simple gene classifier for accurate identification of each CCCRC subtype. Collectively our integrative analysis ultimately established a holistic framework to thoroughly dissect the TME of CRC, and the CCCRC classification system with high biological interpretability may contribute to biomarker discovery and future clinical trial design.
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Affiliation(s)
- Xiangkun Wu
- Department of Pathology, Nanfang Hospital/School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Hong Yan
- Department of Pathology, Nanfang Hospital/School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of ChinaHefeiChina
| | - Mingxing Qiu
- Department of Pathology, Nanfang Hospital/School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Xiaoping Qu
- Nanjing Simcere Medical Laboratory Science Co., LtdNanjingChina
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Jing Wang
- Department of Pathology, Nanfang Hospital/School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Shaowan Xu
- Department of Pathology, Nanfang Hospital/School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Yiran Zheng
- Nanjing Simcere Medical Laboratory Science Co., LtdNanjingChina
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Minghui Ge
- Nanjing Simcere Medical Laboratory Science Co., LtdNanjingChina
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Linlin Yan
- Nanjing Simcere Medical Laboratory Science Co., LtdNanjingChina
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Li Liang
- Department of Pathology, Nanfang Hospital/School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Jinfeng LaboratoryChongqingChina
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21
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Luo H, Zhang Q, Liu X, Luo Y, Jiang X, Wang C, Chen B, He Q, Zhang Y, Shu O, Dai P, He C. Molecular subtypes and tumor microenvironment infiltration signatures based on cuproptosis-related genes in colon cancer. Front Oncol 2023; 13:999193. [PMID: 37274263 PMCID: PMC10234596 DOI: 10.3389/fonc.2023.999193] [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: 07/20/2022] [Accepted: 04/24/2023] [Indexed: 06/06/2023] Open
Abstract
Background Colon cancer is one of the common cancers, and its prognosis remains to be improved. The role of cuproptosis as a newly discovered form of cell death in the development of colon cancer has not been determined. Methods Based on 983 colon cancer samples in the TCGA database and the GEO database, we performed a comprehensive genomic analysis to explore the molecular subtypes mediated by cuproptosis-related genes. Single-sample gene set enrichment analysis (ssGSEA) was utilized to quantify the relative abundance of each cell infiltrate in the TME. A risk score was established using least absolute shrinkage and selection operator regression (LASSO), and its predictive ability for colon cancer patients was verified to explore its guiding value for treatment. Results We identified two distinct cuproptosis-related molecular subtypes in colon cancer. These two distinct molecular subtypes can predict clinicopathological features, prognosis, TME activity, and immune-infiltrating cells. A risk model was developed and its predictive ability was verified. Compared with patients in the high-risk score group, patients in the low-risk score group were characterized by lower tumor microenvironment score, higher stem cell activity, lower tumor mutational burden, lower microsatellite instability, higher sensitivity to chemotherapeutics, and better immunotherapy efficacy. Conclusion This study contributes to understanding the molecular characteristics of cuproptosis-related subtypes. We demonstrate a critical role for cuproptosis genes in colon cancer s in the TME. Our study contributes to the development of individualized treatment regimens for colon cancer.
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Affiliation(s)
- Hongwei Luo
- People’s Hospital of Mianzhu, Deyang, Sichuan, China
| | - Que Zhang
- People’s Hospital of Mianzhu, Deyang, Sichuan, China
| | - Xiangchu Liu
- People’s Hospital of Mianzhu, Deyang, Sichuan, China
| | - Yue Luo
- People’s Hospital of Mianzhu, Deyang, Sichuan, China
| | - Xing Jiang
- People’s Hospital of Mianzhu, Deyang, Sichuan, China
| | - Chao Wang
- People’s Hospital of Mianzhu, Deyang, Sichuan, China
| | - Bin Chen
- People’s Hospital of Mianzhu, Deyang, Sichuan, China
| | - Qiming He
- People’s Hospital of Mianzhu, Deyang, Sichuan, China
| | | | - Ou Shu
- People’s Hospital of Zhongjiang, Deyang, Sichuan, China
| | - Penggao Dai
- Fujian Medical University, Fuzhou, Fujian, China
| | - Chengcheng He
- People’s Hospital of Zhongjiang, Deyang, Sichuan, China
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22
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Wen R, Zhou L, Peng Z, Fan H, Zhang T, Jia H, Gao X, Hao L, Lou Z, Cao F, Yu G, Zhang W. Single-cell sequencing technology in colorectal cancer: a new technology to disclose the tumor heterogeneity and target precise treatment. Front Immunol 2023; 14:1175343. [PMID: 37256123 PMCID: PMC10225552 DOI: 10.3389/fimmu.2023.1175343] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/24/2023] [Indexed: 06/01/2023] Open
Abstract
Colorectal Cancer (CRC) is one of the most common gastrointestinal tumors, and its high tumor heterogeneity makes traditional sequencing methods incapable of obtaining information about the heterogeneity of individual cancer cells in CRC. Therefore, single-cell sequencing technology can be applied to better analyze the differences in genetic and protein information between cells, to obtain genomic sequence information of single cells, and to more thoroughly analyze the cellular characteristics and interactions in the CRC microenvironment. This will provide a more comprehensive understanding of colorectal cancer development and metastasis and indicate the treatment plan and prognosis. In this study, we review the application of single-cell sequencing to analyze the tumor microenvironment of CRC, explore the mechanisms involved in CRC metastasis and progression, and provide a reference for potential treatment options.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Fuao Cao
- *Correspondence: Wei Zhang, ; Guanyu Yu, ; Fuao Cao,
| | - Guanyu Yu
- *Correspondence: Wei Zhang, ; Guanyu Yu, ; Fuao Cao,
| | - Wei Zhang
- *Correspondence: Wei Zhang, ; Guanyu Yu, ; Fuao Cao,
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23
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Rejali L, Seifollahi Asl R, Sanjabi F, Fatemi N, Asadzadeh Aghdaei H, Saeedi Niasar M, Ketabi Moghadam P, Nazemalhosseini Mojarad E, Mini E, Nobili S. Principles of Molecular Utility for CMS Classification in Colorectal Cancer Management. Cancers (Basel) 2023; 15:2746. [PMID: 37345083 DOI: 10.3390/cancers15102746] [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: 03/21/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
Colorectal cancer (CRC) is the second cause of cancer-related deaths in both sexes globally and presents different clinical outcomes that are described by a range of genomic and epigenomic alterations. Despite the advancements in CRC screening plans and treatment strategies, the prognosis of CRC is dismal. In the last two decades, molecular biomarkers predictive of prognosis have been identified in CRC, although biomarkers predictive of treatment response are only available for specific biological drugs used in stage IV CRC. Translational clinical trials mainly based on "omic" strategies allowed a better understanding of the biological heterogeneity of CRCs. These studies were able to classify CRCs into subtypes mainly related to prognosis, recurrence risk, and, to some extent, also to treatment response. Accordingly, the comprehensive molecular characterizations of CRCs, including The Cancer Genome Atlas (TCGA) and consensus molecular subtype (CMS) classifications, were presented to improve the comprehension of the genomic and epigenomic landscapes of CRCs for a better patient management. The CMS classification obtained by the CRC subtyping consortium categorizes CRC into four consensus molecular subtypes (CMS1-4) characterized by different prognoses. In this review, we discussed the CMS classification in different settings with a focus on its relationships with precursor lesions, tumor immunophenotype, and gut microbiota, as well as on its role in predicting prognosis and/or response to pharmacological treatments, as a crucial step towards precision medicine.
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Affiliation(s)
- Leili Rejali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Romina Seifollahi Asl
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Fatemeh Sanjabi
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran P.O. Box 14496-14535, Iran
| | - Nayeralsadat Fatemi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Mahsa Saeedi Niasar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Pardis Ketabi Moghadam
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yaman Street, Chamran Expressway, Tehran P.O. Box 19857-17411, Iran
| | - Enrico Mini
- Department of Health Sciences, University of Florence, Viale Pieraccini, 6, 50139 Firenze, Italy
| | - Stefania Nobili
- Department of Neuroscience, Psychology, Drug Research and Child Health-NEUROFARBA-Pharmacology and Toxicology Section, University of Florence, Viale Pieraccini, 6, 50139 Firenze, Italy
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24
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Källberg J, Harrison A, March V, Bērziņa S, Nemazanyy I, Kepp O, Kroemer G, Mouillet-Richard S, Laurent-Puig P, Taly V, Xiao W. Intratumor heterogeneity and cell secretome promote chemotherapy resistance and progression of colorectal cancer. Cell Death Dis 2023; 14:306. [PMID: 37142595 PMCID: PMC10160076 DOI: 10.1038/s41419-023-05806-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/03/2023] [Accepted: 04/11/2023] [Indexed: 05/06/2023]
Abstract
The major underlying cause for the high mortality rate in colorectal cancer (CRC) relies on its drug resistance, to which intratumor heterogeneity (ITH) contributes substantially. CRC tumors have been reported to comprise heterogeneous populations of cancer cells that can be grouped into 4 consensus molecular subtypes (CMS). However, the impact of inter-cellular interaction between these cellular states on the emergence of drug resistance and CRC progression remains elusive. Here, we explored the interaction between cell lines belonging to the CMS1 (HCT116 and LoVo) and the CMS4 (SW620 and MDST8) in a 3D coculture model, mimicking the ITH of CRC. The spatial distribution of each cell population showed that CMS1 cells had a preference to grow in the center of cocultured spheroids, while CMS4 cells localized at the periphery, in line with observations in tumors from CRC patients. Cocultures of CMS1 and CMS4 cells did not alter cell growth, but significantly sustained the survival of both CMS1 and CMS4 cells in response to the front-line chemotherapeutic agent 5-fluorouracil (5-FU). Mechanistically, the secretome of CMS1 cells exhibited a remarkable protective effect for CMS4 cells against 5-FU treatment, while promoting cellular invasion. Secreted metabolites may be responsible for these effects, as demonstrated by the existence of 5-FU induced metabolomic shifts, as well as by the experimental transfer of the metabolome between CMS1 and CMS4 cells. Overall, our results suggest that the interplay between CMS1 and CMS4 cells stimulates CRC progression and reduces the efficacy of chemotherapy.
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Affiliation(s)
- Julia Källberg
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Alexandra Harrison
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Valerie March
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Santa Bērziņa
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Ivan Nemazanyy
- Platform for Metabolic Analyses, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS 3633, Paris, France
| | - Oliver Kepp
- Equipe labellisée par La Ligue contre le cancer, Université Paris Cité, Sorbonne Université, INSERM UMR1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Villejuif, France
| | - Guido Kroemer
- Equipe labellisée par La Ligue contre le cancer, Université Paris Cité, Sorbonne Université, INSERM UMR1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Villejuif, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Sophie Mouillet-Richard
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
- Institut du Cancer Paris CARPEM, Department of Oncology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Valérie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France.
| | - Wenjin Xiao
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France.
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25
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Liu Y, Wu W, Cai C, Zhang H, Shen H, Han Y. Patient-derived xenograft models in cancer therapy: technologies and applications. Signal Transduct Target Ther 2023; 8:160. [PMID: 37045827 PMCID: PMC10097874 DOI: 10.1038/s41392-023-01419-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Patient-derived xenograft (PDX) models, in which tumor tissues from patients are implanted into immunocompromised or humanized mice, have shown superiority in recapitulating the characteristics of cancer, such as the spatial structure of cancer and the intratumor heterogeneity of cancer. Moreover, PDX models retain the genomic features of patients across different stages, subtypes, and diversified treatment backgrounds. Optimized PDX engraftment procedures and modern technologies such as multi-omics and deep learning have enabled a more comprehensive depiction of the PDX molecular landscape and boosted the utilization of PDX models. These irreplaceable advantages make PDX models an ideal choice in cancer treatment studies, such as preclinical trials of novel drugs, validating novel drug combinations, screening drug-sensitive patients, and exploring drug resistance mechanisms. In this review, we gave an overview of the history of PDX models and the process of PDX model establishment. Subsequently, the review presents the strengths and weaknesses of PDX models and highlights the integration of novel technologies in PDX model research. Finally, we delineated the broad application of PDX models in chemotherapy, targeted therapy, immunotherapy, and other novel therapies.
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Affiliation(s)
- Yihan Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Wantao Wu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China.
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China.
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26
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Rotermund A, Brandt S, Staege MS, Luetzkendorf J, Mueller LP, Mueller T. Differential CMS-Related Expression of Cell Surface Carbonic Anhydrases IX and XII in Colorectal Cancer Models-Implications for Therapy. Int J Mol Sci 2023; 24:ijms24065797. [PMID: 36982873 PMCID: PMC10056265 DOI: 10.3390/ijms24065797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Tumor-associated carbonic anhydrases IX (CAIX) and XII (CAXII) have long been in the spotlight as potential new targets for anti-cancer therapy. Recently, CAIX/CAXII specific inhibitor SLC-0111 has passed clinical phase I study and showed differential response among patients with colorectal cancer (CRC). CRC can be classified into four different consensus molecular subgroups (CMS) showing unique expression patterns and molecular traits. We questioned whether there is a CMS-related CAIX/CAXII expression pattern in CRC predicting response. As such, we analyzed transcriptomic data of tumor samples for CA9/CA12 expression using Cancertool. Protein expression pattern was examined in preclinical models comprising cell lines, spheroids and xenograft tumors representing the CMS groups. Impact of CAIX/CAXII knockdown and SLC-0111 treatment was investigated in 2D and 3D cell culture. The transcriptomic data revealed a characteristic CMS-related CA9/CA12 expression pattern with pronounced co-expression of both CAs as a typical feature of CMS3 tumors. Protein expression in spheroid- and xenograft tumor tissue clearly differed, ranging from close to none (CMS1) to strong CAIX/CAXII co-expression in CMS3 models (HT29, LS174T). Accordingly, response to SLC-0111 analyzed in the spheroid model ranged from no (CMS1) to clear (CMS3), with moderate in CMS2 and mixed in CMS4. Furthermore, SLC-0111 positively affected impact of single and combined chemotherapeutic treatment of CMS3 spheroids. In addition, combined CAIX/CAXII knockdown and more effective treatment with SLC-0111 reduced clonogenic survival of CMS3 modelling single cells. In conclusion, the preclinical data support the clinical approach of targeted CAIX/CAXII inhibition by showing linkage of expression with response and suggest that patients with CMS3-classified tumors would most benefit from such treatment.
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Affiliation(s)
- Arne Rotermund
- Department of Internal Medicine IV (Hematology/Oncology), Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Sarah Brandt
- Department of Internal Medicine IV (Hematology/Oncology), Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Martin S Staege
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Jana Luetzkendorf
- Department of Internal Medicine IV (Hematology/Oncology), Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Lutz P Mueller
- Department of Internal Medicine IV (Hematology/Oncology), Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Thomas Mueller
- Department of Internal Medicine IV (Hematology/Oncology), Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
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27
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Bootsma S, Bijlsma MF, Vermeulen L. The molecular biology of peritoneal metastatic disease. EMBO Mol Med 2023; 15:e15914. [PMID: 36700339 PMCID: PMC9994485 DOI: 10.15252/emmm.202215914] [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: 10/14/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 01/27/2023] Open
Abstract
Peritoneal metastases are a common form of tumor cell dissemination in gastrointestinal malignancies. Peritoneal metastatic disease (PMD) is associated with severe morbidity and resistance to currently employed therapies. Given the distinct route of dissemination compared with distant organ metastases, and the unique microenvironment of the peritoneal cavity, specific tumor cell characteristics are needed for the development of PMD. In this review, we provide an overview of the known histopathological, genomic, and transcriptomic features of PMD. We find that cancers representing the mesenchymal subtype are strongly associated with PMD in various malignancies. Furthermore, we discuss the peritoneal niche in which the metastatic cancer cells reside, including the critical role of the peritoneal immune system. Altogether, we show that PMD should be regarded as a distinct disease entity, that requires tailored treatment strategies.
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Affiliation(s)
- Sanne Bootsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular MedicineAmsterdam UMC, Location University of AmsterdamAmsterdamThe Netherlands
- Cancer Center Amsterdam, Cancer BiologyAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology MetabolismAmsterdamThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular MedicineAmsterdam UMC, Location University of AmsterdamAmsterdamThe Netherlands
- Cancer Center Amsterdam, Cancer BiologyAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology MetabolismAmsterdamThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular MedicineAmsterdam UMC, Location University of AmsterdamAmsterdamThe Netherlands
- Cancer Center Amsterdam, Cancer BiologyAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology MetabolismAmsterdamThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
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28
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Buikhuisen JY, Gomez Barila PM, Cameron K, Suijkerbuijk SJE, Lieftink C, di Franco S, Krotenberg Garcia A, Uceda Castro R, Lenos KJ, Nijman LE, Torang A, Longobardi C, de Jong JH, Dekker D, Stassi G, Vermeulen L, Beijersbergen RL, van Rheenen J, Huveneers S, Medema JP. Subtype-specific kinase dependency regulates growth and metastasis of poor-prognosis mesenchymal colorectal cancer. J Exp Clin Cancer Res 2023; 42:56. [PMID: 36869386 PMCID: PMC9983221 DOI: 10.1186/s13046-023-02600-9] [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: 09/21/2022] [Accepted: 01/15/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) can be divided into four consensus molecular subtypes (CMS), each with distinct biological features. CMS4 is associated with epithelial-mesenchymal transition and stromal infiltration (Guinney et al., Nat Med 21:1350-6, 2015; Linnekamp et al., Cell Death Differ 25:616-33, 2018), whereas clinically it is characterized by lower responses to adjuvant therapy, higher incidence of metastatic spreading and hence dismal prognosis (Buikhuisen et al., Oncogenesis 9:66, 2020). METHODS To understand the biology of the mesenchymal subtype and unveil specific vulnerabilities, a large CRISPR-Cas9 drop-out screen was performed on 14 subtyped CRC cell lines to uncover essential kinases in all CMSs. Dependency of CMS4 cells on p21-activated kinase 2 (PAK2) was validated in independent 2D and 3D in vitro cultures and in vivo models assessing primary and metastatic outgrowth in liver and peritoneum. TIRF microscopy was used to uncover actin cytoskeleton dynamics and focal adhesion localization upon PAK2 loss. Subsequent functional assays were performed to determine altered growth and invasion patterns. RESULTS PAK2 was identified as a key kinase uniquely required for growth of the mesenchymal subtype CMS4, both in vitro and in vivo. PAK2 plays an important role in cellular attachment and cytoskeletal rearrangements (Coniglio et al., Mol Cell Biol 28:4162-72, 2008; Grebenova et al., Sci Rep 9:17171, 2019). In agreement, deletion or inhibition of PAK2 impaired actin cytoskeleton dynamics in CMS4 cells and, as a consequence, significantly reduced invasive capacity, while it was dispensable for CMS2 cells. Clinical relevance of these findings was supported by the observation that deletion of PAK2 from CMS4 cells prevented metastatic spreading in vivo. Moreover, growth in a model for peritoneal metastasis was hampered when CMS4 tumor cells were deficient for PAK2. CONCLUSION Our data reveal a unique dependency of mesenchymal CRC and provide a rationale for PAK2 inhibition to target this aggressive subgroup of colorectal cancer.
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Affiliation(s)
- Joyce Y Buikhuisen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Patricia M Gomez Barila
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Kate Cameron
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Saskia J E Suijkerbuijk
- Oncode Institute, Amsterdam, The Netherlands.,Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Oncode Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Simone di Franco
- Department of Surgical Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Ana Krotenberg Garcia
- Oncode Institute, Amsterdam, The Netherlands.,Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rebeca Uceda Castro
- Oncode Institute, Amsterdam, The Netherlands.,Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kristiaan J Lenos
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Lisanne E Nijman
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Arezo Torang
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Ciro Longobardi
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Joan H de Jong
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Daniëlle Dekker
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Giorgio Stassi
- Department of Surgical Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Oncode Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jacco van Rheenen
- Oncode Institute, Amsterdam, The Netherlands.,Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Stephan Huveneers
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. .,Oncode Institute, Amsterdam, The Netherlands.
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29
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[Targeting HER2 in colorectal cancer]. Bull Cancer 2023; 110:402-411. [PMID: 36870811 DOI: 10.1016/j.bulcan.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 03/06/2023]
Abstract
Among the molecular subgroups of interest in metastatic colorectal cancer (mCRC), innovations are underway for tumors with overexpression of HER2 (Human Epidermal Growth Factor Receptor 2). Overexpression of the HER2 protein concerns 2 to 5% of CRC at any stage mainly located in the distal colon and rectum. Diagnosis is based on immunohistochemistry, in situ hybridization with appropriate criteria for colorectal localization, and molecular biology (NGS: next-generation sequencing). Overexpression of HER2 is a predictive factor for resistance to treatments targeting EGFR which are indicated in the case where the tumor is wild-type RAS. It seems to be associated with a poor prognosis of mCRC with a higher risk of brain metastasis. Regarding treatments targeting HER2, no randomized controlled phase III has been published to date. However, several combinations have been evaluated in phase II with clinically meaningful objective response rates: trastuzumab-deruxtecan (45%), trastuzumab-tucatinib (46%), trastuzumab-pyrotinib (45%), trastuzumab-pertuzumab (30%) ou trastuzumab-lapatinib (30%). In this literature review, we present here the current state of knowledge on the diagnostic methods of HER2 overexpression in CRC, the main clinical, molecular and prognostic characteristics, and the efficacy results of the different therapeutic combinations for the patients with HER2 overexpressed mCRC. This justifies, despite the lack of marketing authorization in France and in Europe for agents targeting HER2 in CRC, the systematic evaluation of the HER2 status, as recommended in particular by the NCCN (National Comprehensive Cancer Network).
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30
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Yamamoto Y, Shimada S, Akiyama Y, Tsukihara S, Sugimoto R, Kabashima A, Tokunaga M, Kinugasa Y, Kawakami Y, Tanaka S. RTP4 silencing provokes tumor-intrinsic resistance to immune checkpoint blockade in colorectal cancer. J Gastroenterol 2023; 58:540-553. [PMID: 36859628 DOI: 10.1007/s00535-023-01969-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 02/06/2023] [Indexed: 03/03/2023]
Abstract
BACKGROUND Recent advances in immune checkpoint blockade (ICB) have improved patient prognosis in mismatch repair-deficient and microsatellite instability-high colorectal cancer (dMMR/MSI-H CRC); however, PD-1 blockade has faced a challenge in early progressive disease. We aimed to understand the early event in ICB resistance using an in vivo model. METHODS We subcutaneously transplanted the MC38 colon cancer cells into C57BL/6 mice, intraperitoneally injected anti-PD-1 antibody and then isolated ICB-resistant subclones from the recurrent tumors. RESULTS Comparative gene expression analysis discovered seven genes significantly downregulated in the ICB-resistant cells. Tumorigenicity assay of the MC38 cells knocked out each of the seven candidate genes into C57BL/6 mice treated with anti-PD-1 antibody and bioinformatics analysis of the relationship between the expression of the seven candidate genes and the outcome of cancer patients receiving immunotherapy identified Rtp4, an interferon-stimulated gene and a chaperon protein of G protein-coupled receptors, as a gene involved in ICB resistance. Immunohistochemical analysis of transplanted tumor tissues demonstrated that anti-PD-1 antibody failed to recruit T lymphocytes in the Rtp4-KO MC38 cells. Mouse and human RTP4 expression could be silenced via histone H3 lysine 9 (H3K9) trimethylation, and public transcriptome data indicated the high expression level of RTP4 in most but not all of dMMR/MSI-H CRC. CONCLUSIONS We clarified that RTP4 could be silenced by histone H3K9 methylation as the early event of ICB resistance. RTP4 expression could be a promising biomarker for predicting ICB response, and the combination of epigenetic drugs and immune checkpoint inhibitors might exhibit synergistic effects on dMMR/MSI-H CRC.
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Affiliation(s)
- Yudai Yamamoto
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Department of Gastrointestinal Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shu Shimada
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.
| | - Yoshimitsu Akiyama
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Shu Tsukihara
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Department of Surgery, The Jikei University School of Medicine, Tokyo, Japan
| | - Raizo Sugimoto
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Ayano Kabashima
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Masanori Tokunaga
- Department of Gastrointestinal Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yusuke Kinugasa
- Department of Gastrointestinal Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yutaka Kawakami
- Institute for Advanced Medical Research, Division of Cellular Signaling, Keio University School of Medicine, Tokyo, Japan.,Department of Immunology, School of Medicine, International University of Health and Welfare, Chiba, Japan
| | - Shinji Tanaka
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.
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31
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Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A. Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528736. [PMID: 36824919 PMCID: PMC9949144 DOI: 10.1101/2023.02.15.528736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Aberrant signaling pathway activity is a hallmark of tumorigenesis and progression, which has guided targeted inhibitor design for over 30 years. Yet, adaptive resistance mechanisms, induced by rapid, context-specific signaling network rewiring, continue to challenge therapeutic efficacy. By leveraging progress in proteomic technologies and network-based methodologies, over the past decade, we developed VESPA-an algorithm designed to elucidate mechanisms of cell response and adaptation to drug perturbations-and used it to analyze 7-point phosphoproteomic time series from colorectal cancer cells treated with clinically-relevant inhibitors and control media. Interrogation of tumor-specific enzyme/substrate interactions accurately inferred kinase and phosphatase activity, based on their inferred substrate phosphorylation state, effectively accounting for signal cross-talk and sparse phosphoproteome coverage. The analysis elucidated time-dependent signaling pathway response to each drug perturbation and, more importantly, cell adaptive response and rewiring that was experimentally confirmed by CRISPRko assays, suggesting broad applicability to cancer and other diseases.
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Affiliation(s)
- George Rosenberger
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Mikko Turunen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jing He
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Present address: Regeneron Genetics Center, Tarrytown, NY, USA
| | - Prem S Subramaniam
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sergey Pampou
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Aaron T Griffin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles Karan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Patrick Kerwin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Diana Murray
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Barry Honig
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
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32
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Kin R, Hoshi D, Fujita H, Kosaka T, Takamura H, Kiyokawa E. Prognostic significance of p16, p21, and Ki67 expression at the invasive front of colorectal cancers. Pathol Int 2023; 73:81-90. [PMID: 36484761 DOI: 10.1111/pin.13295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
Cancer cells at the invasive front are believed to be responsible for invasion/metastasis. This has led to examining various morphological features and protein expressions at the invasive front. However, accurate assessment of the pathological section requires long-time training, and inter-observer disagreement is problematic. Immunohistochemistry and digital imaging analysis may mitigate these problems; however, the choice of which proteins to stain and the best analysis method remains controversial. We used the "go-or-grow" hypothesis to select markers with the greatest prognostic relevance. Importantly, nonproliferating cells can migrate. We used Ki67 as a proliferation marker, with p16 and p21 designating nonproliferating cells. We established a semi-automated quantification workflow to study protein expression in serial pathological sections. A total of 51 patients with completely resected colorectal cancer (stages I-IV) were analyzed, and 44 patients were followed up. Patients with cancer cells with p16-high/p21-low or p21-low/Ki67-low at the deepest invasive front demonstrated a significantly worse prognosis than those who did not display these characteristics. These results suggest that the nonproliferating cancer cells at the invasion front possess invasion/metastatic property with heterogeneity of senescence.
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Affiliation(s)
- Ryosuke Kin
- Department of Surgery, Kanazawa Medical University, Ishikawa, Japan
| | - Daisuke Hoshi
- Department of Oncologic Pathology, Kanazawa Medical University, Ishikawa, Japan
| | - Hideto Fujita
- Department of Surgery, Kanazawa Medical University, Ishikawa, Japan
| | - Takeo Kosaka
- Department of Surgery, Kanazawa Medical University, Ishikawa, Japan.,Department of Surgery, Houju Memorial Hospital, Ishikawa, Japan
| | | | - Etsuko Kiyokawa
- Department of Oncologic Pathology, Kanazawa Medical University, Ishikawa, Japan
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Lu DY, Lu TR. Drug Sensitivity Testing for Cancer Therapy, Technique Analysis and Trends. Curr Rev Clin Exp Pharmacol 2023; 18:3-11. [PMID: 34515020 DOI: 10.2174/2772432816666210910104649] [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: 03/07/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 02/08/2023]
Abstract
The techniques and qualities of drug sensitivity testing (DST) for anticancer treatment have grown rapidly in the past two decades worldwide. Much of DST progress came from advanced systems of technical versatility (faster, highly-throughput, highly-sensitive, and smaller in tumor quantity). As the earliest drug selective system, biomedical knowledge and technical advances for DST are mutually supported. More importantly, many pharmacological controversies are resolved by these technical advances. With this technical stride, the clinical landscape of DST entered into a new phase (>500 samples per testing and extremely low quantity of tumor cells). As a forerunner of the drug selection system, DST awaits a new version that can adapt to complicated therapeutic situations and diverse tumor categories in the clinic. By upholding this goal of pathogenic and therapeutic diversity, DST could eventually cure more cancer patients by establishing high-quality drug selection systems. To smoothen DST development, there is a need to increase the understanding of cancer biology, pathology and pharmacology (cancer heterogeneity, plasticity, metastasis and drug resistance) with well-informative parameters before chemotherapy. In this article, medicinal and technical insights into DST are especially highlighted.
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Affiliation(s)
- Da-Yong Lu
- School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China
| | - Ting-Ren Lu
- College of Science, Shanghai University, Shanghai 200444, P.R. China
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34
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Lu DY, Lu TR, Yarla NS, Xu B. Drug Sensitivity Testing for Cancer Therapy, Key Areas. Rev Recent Clin Trials 2022; 17:291-299. [PMID: 35986532 DOI: 10.2174/1574887117666220819094528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 01/15/2023]
Abstract
AIMS Cancer is a high-mortality disease (9.6 million deaths in 2018 worldwide). Given various anticancer drugs, drug selection plays a key role in patient survival in clinical trials. METHODS Drug Sensitivity Testing (DST), one of the leading drug selective systems, was widely practiced for therapeutic promotion in the clinic. Notably, DSTs assist in drug selection that benefits drug responses against cancer from 20-22% to 30-35% over the past two decades. The relationship between drug resistance in vitro and drug treatment benefits was associated with different tumor origins and subtypes. Medical theory and underlying DST mechanisms remain poorly understood until now. The study of the clinical scenario, sustainability and financial support for mechanism and technical promotions is indispensable. RESULTS Despite the great technical advance, therapeutic prediction and drug selection by DST needs to be miniature, versatility and cost-effective in the clinic. Multi-parameters and automation of DST should be a future trend. Advanced biomedical knowledge and clinical approaches to translating oncologic profiles into drug selection were the main focuses of DST developments. With a great technical stride, the clinical architecture of the DST platform was entering higher levels (drug response testing at any stage of cancer patients and miniaturization of tumor samples). DISCUSSION The cancer biology and pharmacology for drug selection mutually benefit the clinic. New proposals to reveal more therapeutic information and drug response prediction at genetic, molecular and omics levels should be estimated overall. CONCLUSION By upholding this goal of non-invasive, versatility and automation, DST could save the life of several thousand annually worldwide. In this article, new insights into DST novelty and development are highlighted.
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Affiliation(s)
- Da-Yong Lu
- School of Life Sciences, Shanghai University, Shanghai 200444, PRC, China
| | - Ting-Ren Lu
- College of Science, Shanghai University, Shanghai 200444, PRC, China
| | | | - Bin Xu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China
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35
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Mochizuki K, Kudo SE, Kato K, Kudo K, Ogawa Y, Kouyama Y, Takashina Y, Ichimasa K, Tobo T, Toshima T, Hisamatsu Y, Yonemura Y, Masuda T, Miyachi H, Ishida F, Nemoto T, Mimori K. Molecular and clinicopathological differences between depressed and protruded T2 colorectal cancer. PLoS One 2022; 17:e0273566. [PMID: 36264865 PMCID: PMC9584453 DOI: 10.1371/journal.pone.0273566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/11/2022] [Indexed: 11/05/2022] Open
Abstract
Background Colorectal cancer (CRC) can be classified into four consensus molecular subtypes (CMS) according to genomic aberrations and gene expression profiles. CMS is expected to be useful in predicting prognosis and selecting chemotherapy regimens. However, there are still no reports on the relationship between the morphology and CMS. Methods This retrospective study included 55 subjects with T2 CRC undergoing surgical resection, of whom 30 had the depressed type and 25 the protruded type. In the classification of the CMS, we first defined cases with deficient mismatch repair as CMS1. And then, CMS2/3 and CMS4 were classified using an online classifier developed by Trinh et al. The staining intensity of CDX2, HTR2B, FRMD6, ZEB1, and KER and the percentage contents of CDX2, FRMD6, and KER are input into the classifier to obtain automatic output classifying the specimen as CMS2/3 or CMS4. Results According to the results yielded by the online classifier, of the 30 depressed-type cases, 15 (50%) were classified as CMS2/3 and 15 (50%) as CMS4. Of the 25 protruded-type cases, 3 (12%) were classified as CMS1 and 22 (88%) as CMS2/3. All of the T2 CRCs classified as CMS4 were depressed CRCs. More malignant pathological findings such as lymphatic invasion were associated with the depressed rather than protruded T2 CRC cases. Conclusions Depressed-type T2 CRC had a significant association with CMS4, showing more malignant pathological findings such as lymphatic invasion than the protruded-type, which could explain the reported association between CMS4 CRC and poor prognosis.
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Affiliation(s)
- Kenichi Mochizuki
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Shin-ei Kudo
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Kazuki Kato
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Koki Kudo
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Yushi Ogawa
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Yuta Kouyama
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Yuki Takashina
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Katsuro Ichimasa
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
- Department of Gastroenterology and Hepatology, National University Hospital, Singapore, Singapore
| | - Taro Tobo
- Department of Clinical Laboratory, Kyushu University Beppu Hospital, Beppu, Japan
| | - Takeo Toshima
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Yuichi Hisamatsu
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Yusuke Yonemura
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Hideyuki Miyachi
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Fumio Ishida
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Tetsuo Nemoto
- Department of Diagnostic Pathology, School of Medicine, Showa University, Yokohama Northern Hospital, Kanagawa, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
- * E-mail:
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36
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Liu F, Bouznad N, Kaller M, Shi X, König J, Jaeckel S, Hermeking H. Csf1r mediates enhancement of intestinal tumorigenesis caused by inactivation of Mir34a. Int J Biol Sci 2022; 18:5415-5437. [PMID: 36147476 PMCID: PMC9461672 DOI: 10.7150/ijbs.75503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/04/2022] [Indexed: 12/03/2022] Open
Abstract
The CSF1 receptor (CSF1R) encoding mRNA represents a direct target of miR-34a. However, the in vivo relevance of the suppression of CSF1R by miR-34a for intestinal tumor suppression mediated by the p53/miR-34a pathway has remained unknown. Here, ApcMin/+ mice with intestinal-epithelial cell (IEC)-specific deletions of Mir34a showed increased formation of adenomas and decreased survival, whereas deletion of Csf1r decreased adenoma formation and increased survival. In adenomas deletion of Mir34a enhanced proliferation, STAT3 signaling, infiltration with fibroblasts, immune cells and microbes, and tumor stem cell abundance and decreased apoptosis. Deletion of Csf1r had the opposite effects. In addition, homeostasis of intestinal secretory and stem cells, and tumoroid formation were affected in opposite directions by deletion of Mir34a and CSF1R. Concomitant deletion of Csf1r and Mir34a neutralized the effects of the single deletions. mRNAs containing Mir34a seed-matching sites, which encode proteins related to EMT (epithelial-mesenchymal transition), stemness and Wnt signaling, were enriched after Mir34a inactivation in adenomas and derived tumoroids. Netrin-1/Ntn1 and Transgelin/Tagln were characterized as direct targets of Mir34a and Csf1r signaling. Mir34a-inactivation related expression signatures were associated with CMS4/CRISB+D, stage 4 CRCs and poor patient survival. In tumoroids the loss of Mir34a conferred resistance to 5-FU which was mediated by Csf1r. This study provides genetic evidence for a requirement of Mir34a-mediated Csf1r suppression for intestinal stem/secretory cell homeostasis and tumor suppression, and suggests that therapeutic targeting of CSF1R may be effective for the treatment of CRCs with defects in the p53/miR-34a pathway.
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Affiliation(s)
- Fangteng Liu
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University München, Germany
| | - Nassim Bouznad
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University München, Germany
| | - Markus Kaller
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University München, Germany
| | - Xiaolong Shi
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University München, Germany
| | - Janine König
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University München, Germany
| | - Stephanie Jaeckel
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University München, Germany
| | - Heiko Hermeking
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University München, Germany.,German Cancer Consortium (DKTK), D-69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
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37
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Wang S, Cheng L, Wu H, Li G. Mechanisms and prospects of circular RNAs and their interacting signaling pathways in colorectal cancer. Front Oncol 2022; 12:949656. [PMID: 35992800 PMCID: PMC9382640 DOI: 10.3389/fonc.2022.949656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Colorectal cancer (CRC) is the leading malignant tumor in terms of morbidity and mortality worldwide, and its pathogenesis involves multiple factors, including environment, lifestyle, and genetics. Continuing evidence suggests that circular RNAs (circRNAs), as a novel non-coding RNA, constitute an important genetic variable in the pathogenesis of CRC. These circRNAs with covalently closed-loop structures exist objectively in organisms. They not only have the biological functions of regulating the expression of target genes, changing the activity of proteins, and translating proteins, but also play a key role in the proliferation, invasion, migration, and apoptosis of tumor cells. CRC is one of the most common cancers in which circRNAs are involved in tumorigenesis, metastasis, and drug resistance, and circRNAs have been demonstrated to function through crosstalk with multiple signaling pathways. Therefore, this review summarizes the biological and carcinogenic functions of circRNAs and their related PI3K/AKT, MAPK, Notch, JAK/STAT, Hippo/YAP, WNT/β-catenin, and VEGF signaling pathways in CRC. We further explore the clinical value of circRNAs and important signaling proteins in the diagnosis, prognosis, and treatment of CRC.
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38
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Precision Medicine in Metastatic Colorectal Cancer: Targeting ERBB2 (HER-2) Oncogene. Cancers (Basel) 2022; 14:cancers14153718. [PMID: 35954382 PMCID: PMC9367374 DOI: 10.3390/cancers14153718] [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: 06/29/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Colorectal cancer (CRC) is the third most common cancer in terms of incidence rate in adults and the second most common cause of cancer-related death in Europe. The treatment of metastatic CRC (mCRC) is based on the use of chemotherapy, anti-vascular endothelial growth factor (VEGF), and anti-epidermal growth factor receptor (EGFR) for RAS wild-type tumors. Precision medicine tries to identify molecular alterations that could be treated with targeted therapies. Although ERBB2 (also known as HER-2) has an important therapeutic role in breast and esophagogastric cancer, there are no approved ERBB2-targeted therapies for mCRC. The purpose of this review is to describe the landscape of ERBB2-positive mCRC. Abstract Colorectal cancer (CRC) is the third most common cancer in terms of incidence rate in adults and the second most common cause of cancer-related death in Europe. The treatment of metastatic CRC (mCRC) is based on the use of chemotherapy, anti-vascular endothelial growth factor (VEGF), and anti-epidermal growth factor receptor (EGFR) for RAS wild-type tumors. Precision medicine tries to identify molecular alterations that could be treated with targeted therapies. ERBB2 amplification (also known as HER-2) has been identified in 2–3% of patients with mCRC, but there are currently no approved ERBB2-targeted therapies for mCRC. The purpose of this review is to describe the molecular structure of ERBB2, clinical features of these patients, diagnosis of ERBB2 alterations, and the most relevant clinical trials with ERBB2-targeted therapies in mCRC.
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Dias Carvalho P, Martins F, Mendonça S, Ribeiro A, Machado AL, Carvalho J, Oliveira MJ, Velho S. Mutant KRAS modulates colorectal cancer cells invasive response to fibroblast‐secreted factors through the HGF/C‐MET axis. Int J Cancer 2022; 151:1810-1823. [DOI: 10.1002/ijc.34225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Patrícia Dias Carvalho
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
- ICBAS ‐ Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto Porto Portugal
| | - Flávia Martins
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
- Department of Pathology FMUP – Faculty of Medicine of the University of Porto Porto Portugal
| | - Susana Mendonça
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
- Department of Pathology FMUP – Faculty of Medicine of the University of Porto Porto Portugal
| | - Andreia Ribeiro
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
| | - Ana Luísa Machado
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
- Department of Pathology FMUP – Faculty of Medicine of the University of Porto Porto Portugal
- Ciências Químicas e das Biomoléculas, Centro de Investigação em Saúde e Ambiente, Escola Superior de Saúde do Porto, Instituto Politécnico do Porto Porto Portugal
| | - Joana Carvalho
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
| | - Maria José Oliveira
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- INEB – Institute of Biomedical Engineering, University of Porto Porto Portugal
| | - Sérgia Velho
- i3S ‐ Instituto de Investigação e Inovação em Saúde, Universidade do Porto Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal
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Multifocal organoids reveal clonal associations between synchronous intestinal tumors with pervasive heterogeneous drug responses. NPJ Genom Med 2022; 7:42. [PMID: 35853873 PMCID: PMC9296490 DOI: 10.1038/s41525-022-00313-0] [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: 01/18/2022] [Accepted: 06/29/2022] [Indexed: 11/23/2022] Open
Abstract
Multifocal colorectal cancer (CRC) comprises both clonally independent primary tumors caused by inherited predisposition and clonally related tumors mainly due to intraluminal spreading along an intact basement membrane. The distinction between these multifocal CRCs is essential because therapeutic strategies vary according to the clonal association of multiple tumor masses. Here, we report one unique case of synchronous intestinal cancer (SIC) with tumors occurring along the entire bowel tract, including the small intestine. We established six patient-derived organoids (PDOs), and patient-derived cell lines (PDCs) from each site of the SIC, which were subjected to extensive genomic, transcriptomic, and epigenomic sequencing. We also estimated the drug responses of each multifocal SIC to 25 clinically relevant therapeutic compounds to validate how the clinically actionable alternations between SICs were associated with drug sensitivity. Our data demonstrated distinct clonal associations across different organs, which were consistently supported by multi-omics analysis, as well as the accordant responses to various therapeutic compounds. Our results indicated the imminent drawback of a single tumor-based diagnosis of multifocal CRC and suggested the necessity of an in-depth molecular analysis of all tumor regions to avoid unexpected resistance to the currently available targeted therapies.
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41
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Aulas A, Liberatoscioli ML, Finetti P, Cabaud O, Birnbaum DJ, Usclade L, Birnbaum D, Bertucci F, Mamessier E. Low cholesterol biosynthesis favors epithelial-to-mesenchymal transition maintenance and influences tumor molecular subtyping and disease-free survival in colon cancer patients. Cancer Commun (Lond) 2022; 42:793-797. [PMID: 35771388 PMCID: PMC9395314 DOI: 10.1002/cac2.12329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/16/2022] [Accepted: 06/21/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Anaïs Aulas
- Predictive Oncology Laboratory, Cancer Research Center of Marseille, Institut Paoli-Calmettes, "Ligue contre le cancer" label, Aix-Marseille University, Marseille, 13009, France
| | - Maria Lucia Liberatoscioli
- Predictive Oncology Laboratory, Cancer Research Center of Marseille, Institut Paoli-Calmettes, "Ligue contre le cancer" label, Aix-Marseille University, Marseille, 13009, France
| | - Pascal Finetti
- Predictive Oncology Laboratory, Cancer Research Center of Marseille, Institut Paoli-Calmettes, "Ligue contre le cancer" label, Aix-Marseille University, Marseille, 13009, France
| | - Olivier Cabaud
- Predictive Oncology Laboratory, Cancer Research Center of Marseille, Institut Paoli-Calmettes, "Ligue contre le cancer" label, Aix-Marseille University, Marseille, 13009, France
| | - David J Birnbaum
- Predictive Oncology Laboratory, Cancer Research Center of Marseille, Institut Paoli-Calmettes, "Ligue contre le cancer" label, Aix-Marseille University, Marseille, 13009, France.,Department of Digestive Surgery, Hospital Nord, Chemin des Bourrely, Aix-Marseille University, Marseille, 13015, France
| | - Lucas Usclade
- Predictive Oncology Laboratory, Cancer Research Center of Marseille, Institut Paoli-Calmettes, "Ligue contre le cancer" label, Aix-Marseille University, Marseille, 13009, France
| | - Daniel Birnbaum
- Predictive Oncology Laboratory, Cancer Research Center of Marseille, Institut Paoli-Calmettes, "Ligue contre le cancer" label, Aix-Marseille University, Marseille, 13009, France
| | - François Bertucci
- Predictive Oncology Laboratory, Cancer Research Center of Marseille, Institut Paoli-Calmettes, "Ligue contre le cancer" label, Aix-Marseille University, Marseille, 13009, France.,Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, 13009, France
| | - Emilie Mamessier
- Predictive Oncology Laboratory, Cancer Research Center of Marseille, Institut Paoli-Calmettes, "Ligue contre le cancer" label, Aix-Marseille University, Marseille, 13009, France
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Elsayed I, Geraghty R, Mekki SO, Mohamedani AA, Ahern S, Salim OEH, Khalil BBM, Abdelrahim S, Suliman SH, Elhassan MMA, Salah SO, Salih ME, Widatalla AH, Abdelhamed OS, Wang X, Ryan ÉJ, Winter D, Bakhiet S, Sheahan K. Evaluating utility and feasibility of mismatch repair testing of colorectal cancer patients in a low-middle-income country. Sci Rep 2022; 12:10998. [PMID: 35768447 PMCID: PMC9243080 DOI: 10.1038/s41598-022-14644-6] [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: 12/29/2021] [Accepted: 06/09/2022] [Indexed: 12/24/2022] Open
Abstract
Molecular pathology services for colorectal cancer (CRC) in Sudan represent a significant unmet clinical need. In a retrospective cohort study involving 50 patients diagnosed with CRC at three major medical settings in Sudan, we aimed to outline the introduction of a molecular genetic service for CRC in Sudan, and to explore the CRC molecular features and their relationship to patient survival and clinicopathological characteristics. Mismatch repair (MMR) and BRAF (V600E) mutation status were determined by immunohistochemistry. A mismatch repair deficient (dMMR) subtype was demonstrated in 16% of cases, and a presumptive Lynch Syndrome (LS) diagnosis was made in up to 14% of patients. dMMR CRC in Sudan is characterized by younger age at diagnosis and a higher incidence of right-sided tumours. We report a high mortality in Sudanese CRC patients, which correlates with advanced disease stage, and MMR status. Routine MMR immunohistochemistry (with sequential BRAF mutation analysis) is a feasible CRC prognostic and predictive molecular biomarker, as well as a screening tool for LS in low-middle-income countries (LMICs).
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Affiliation(s)
- Inas Elsayed
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China.,Department of Pharmacology, Faculty of Pharmacy, University of Gezira, P.O. Box: 20, Wad Madani, Sudan
| | - Robert Geraghty
- Department of Pathology, Centre for Colorectal Disease, St. Vincent's University Hospital, Dublin 4, Ireland
| | - Salwa O Mekki
- Department of Histopathology, Soba University Hospital, Khartoum, Sudan
| | - Ahmed A Mohamedani
- Department of Pathology, Faculty of Medicine, University of Gezira, P.O. Box: 20, Wad Madani, Sudan
| | - Susan Ahern
- Department of Pathology, Centre for Colorectal Disease, St. Vincent's University Hospital, Dublin 4, Ireland
| | - Omer E H Salim
- Department of Surgery, Soba University Hospital, Khartoum, Sudan
| | - Balgis B M Khalil
- Department of Histopathology, Ibn Sina Specialized Hospital, Khartoum, Sudan
| | - Sawsan Abdelrahim
- Department of Histopathology, Soba University Hospital, Khartoum, Sudan
| | | | - Moawia M A Elhassan
- Department of Oncology, National Cancer Institute, University of Gezira, P.O. Box: 20, Wad Madani, Sudan
| | - Salah O Salah
- Department of Oncology, Khartoum Oncology Hospital, Khartoum, Sudan
| | - Mohamed E Salih
- Department of Surgery, Faculty of Medicine, University of Gezira, P.O. Box: 20, Wad Madani, Sudan
| | | | | | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
| | - Éanna J Ryan
- Department of Surgery, Centre for Colorectal Disease, St. Vincent's University Hospital, Dublin, Ireland
| | - Des Winter
- Department of Surgery, Centre for Colorectal Disease, St. Vincent's University Hospital, Dublin, Ireland.,School of Medicine and Medical Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - Salih Bakhiet
- Hull Royal Infirmary, Hull University Hospital NHS Trust, Hull, East Yorkshire, UK
| | - Kieran Sheahan
- Department of Pathology, Centre for Colorectal Disease, St. Vincent's University Hospital, Dublin 4, Ireland. .,School of Medicine and Medical Sciences, University College Dublin, Belfield, Dublin 4, Ireland.
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43
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Chen R, Wang X, Deng X, Chen L, Liu Z, Li D. CPDR: An R Package of Recommending Personalized Drugs for Cancer Patients by Reversing the Individual’s Disease-Related Signature. Front Pharmacol 2022; 13:904909. [PMID: 35795573 PMCID: PMC9252520 DOI: 10.3389/fphar.2022.904909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Due to cancer heterogeneity, only some patients can benefit from drug therapy. The personalized drug usage is important for improving the treatment response rate of cancer patients. The value of the transcriptome of patients has been recently demonstrated in guiding personalized drug use, and the Connectivity Map (CMAP) is a reliable computational approach for drug recommendation. However, there is still no personalized drug recommendation tool based on transcriptomic profiles of patients and CMAP. To fill this gap, here, we proposed such a feasible workflow and a user-friendly R package—Cancer-Personalized Drug Recommendation (CPDR). CPDR has three features. 1) It identifies the individual disease signature by using the patient subgroup with transcriptomic profiles similar to those of the input patient. 2) Transcriptomic profile purification is supported for the subgroup with high infiltration of non-cancerous cells. 3) It supports in silico drug efficacy assessment using drug sensitivity data on cancer cell lines. We demonstrated the workflow of CPDR with the aid of a colorectal cancer dataset from GEO and performed the in silico validation of drug efficacy. We further assessed the performance of CPDR by a pancreatic cancer dataset with clinical response to gemcitabine. The results showed that CPDR can recommend promising therapeutic agents for the individual patient. The CPDR R package is available at https://github.com/AllenSpike/CPDR.
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Affiliation(s)
| | | | | | | | | | - Dong Li
- *Correspondence: Zhongyang Liu, ; Dong Li,
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44
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Wang D, Madunić K, Zhang T, Mayboroda OA, Lageveen-Kammeijer GSM, Wuhrer M. High Diversity of Glycosphingolipid Glycans of Colorectal Cancer Cell Lines Reflects the Cellular Differentiation Phenotype. Mol Cell Proteomics 2022; 21:100239. [PMID: 35489554 PMCID: PMC9157004 DOI: 10.1016/j.mcpro.2022.100239] [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: 02/21/2022] [Revised: 04/04/2022] [Accepted: 04/26/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC)–associated changes of protein glycosylation have been widely studied. In contrast, the expression of glycosphingolipid (GSL) patterns in CRC has, hitherto, remained largely unexplored. Even though GSLs are major carriers of cell surface carbohydrates, they are understudied due to their complexity and analytical challenges. In this study, we provide an in-depth analysis of GSL glycans of 22 CRC cell lines using porous graphitized carbon nano–liquid chromatography coupled with electrospray ionization–mass spectrometry. Our data revealed that the GSL expression varies among different cell line classifications, with undifferentiated cell lines showing high expression of blood group A, B, and H antigens while for colon-like cell lines the most prominent GSL glycans contained (sialyl)-LewisA/X and LewisB/Y antigens. Moreover, the GSL expression correlated with relevant glycosyltransferases that are involved in their biosynthesis as well as with transcription factors (TFs) implicated in colon differentiation. Additionally, correlations between certain glycosyltransferases and TFs at mRNA expression level were found, such as FUT3, which correlated with CDX1, ETS2, HNF1A, HNF4A, MECOM, and MYB. These TFs are upregulated in colon-like cell lines pointing to their potential role in regulating fucosylation during colon differentiation. In conclusion, our study reveals novel layers of potential GSL glycans regulation relevant for future research in colon differentiation and CRC. Undifferentiated cell lines showed high expression of blood group A, B, and H antigens. Colon-like cell lines are high in GSLs carrying (sialyl)-LewisA/X and LewisB/Y antigens. (Sialyl)-LewisA/X and LewisB/Y antigens associated with expression of FUT3 and CDX1. I-branching was elevated in undifferentiated cells.
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Affiliation(s)
- Di Wang
- Leiden University Medical Center, Center for Proteomics and Metabolomics, RC Leiden, The Netherlands
| | - Katarina Madunić
- Leiden University Medical Center, Center for Proteomics and Metabolomics, RC Leiden, The Netherlands
| | - Tao Zhang
- Leiden University Medical Center, Center for Proteomics and Metabolomics, RC Leiden, The Netherlands
| | - Oleg A Mayboroda
- Leiden University Medical Center, Center for Proteomics and Metabolomics, RC Leiden, The Netherlands
| | | | - Manfred Wuhrer
- Leiden University Medical Center, Center for Proteomics and Metabolomics, RC Leiden, The Netherlands.
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45
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Hassin O, Nataraj NB, Shreberk-Shaked M, Aylon Y, Yaeger R, Fontemaggi G, Mukherjee S, Maddalena M, Avioz A, Iancu O, Mallel G, Gershoni A, Grosheva I, Feldmesser E, Ben-Dor S, Golani O, Hendel A, Blandino G, Kelsen D, Yarden Y, Oren M. Different hotspot p53 mutants exert distinct phenotypes and predict outcome of colorectal cancer patients. Nat Commun 2022; 13:2800. [PMID: 35589715 PMCID: PMC9120190 DOI: 10.1038/s41467-022-30481-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 04/28/2022] [Indexed: 01/27/2023] Open
Abstract
The TP53 gene is mutated in approximately 60% of all colorectal cancer (CRC) cases. Over 20% of all TP53-mutated CRC tumors carry missense mutations at position R175 or R273. Here we report that CRC tumors harboring R273 mutations are more prone to progress to metastatic disease, with decreased survival, than those with R175 mutations. We identify a distinct transcriptional signature orchestrated by p53R273H, implicating activation of oncogenic signaling pathways and predicting worse outcome. These features are shared also with the hotspot mutants p53R248Q and p53R248W. p53R273H selectively promotes rapid CRC cell spreading, migration, invasion and metastasis. The transcriptional output of p53R273H is associated with preferential binding to regulatory elements of R273 signature genes. Thus, different TP53 missense mutations contribute differently to cancer progression. Elucidation of the differential impact of distinct TP53 mutations on disease features may make TP53 mutational information more actionable, holding potential for better precision-based medicine.
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Affiliation(s)
- Ori Hassin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Yael Aylon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Saptaparna Mukherjee
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Martino Maddalena
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Avioz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ortal Iancu
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | | | - Anat Gershoni
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Grosheva
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Ester Feldmesser
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ayal Hendel
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - David Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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46
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Althenayyan S, AlGhamdi A, AlMuhanna MH, Hawsa E, Aldeghaither D, Iqbal J, Mohammad S, Aziz MA. Modulation of ATP8B1 gene expression in colorectal cancer cells suggest its role as a tumor suppressor. Curr Cancer Drug Targets 2022; 22:577-590. [PMID: 35585825 DOI: 10.2174/1568009622666220517092340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/04/2021] [Accepted: 05/24/2021] [Indexed: 11/22/2022]
Abstract
AIM The study aims to understand the role of tumor suppressor genes in colorectal cancer initiation and progression. BACKGROUND Sporadic colorectal cancer (CRC) develops through distinct molecular events. Loss of the 18q chromosome is a conspicuous event in the progression of adenoma to carcinoma. There is limited information regarding the molecular effectors of this event. Earlier, we had reported ATP8B1 as a novel gene associated with CRC. ATP8B1 belongs to the family of P-type ATPases (P4 ATPase) that primarily function to facilitate the translocation of phospholipids. OBJECTIVE In this study, we attempt to implicate the ATP8B1 gene located on chromosome 18q as a tumor suppressor gene. METHODS Cells culture, Patient data analysis, Generation of stable ATP8B1 overexpressing SW480 cell line, Preparation of viral particles, Cell Transduction, Generation of stable ATP8B1 knockdown HT29 cell line with CRISPR/Cas9, Generation of stable ATP8B1 knockdown HT29 cell line with shRNA, Quantification of ATP8B1 gene expression, Real-time cell proliferation and migration assays, Cell proliferation assay, Cell migration assay, Protein isolation and western blotting, Endpoint cell viability assay, Uptake and efflux of sphingolipid, Statistical and computational analyses. RESULTS We studied indigenous patient data and confirmed the reduced expression of ATP8B1 in tumor samples. CRC cell lines were engineered with reduced and enhanced levels of ATP8B1, which provided a tool to study its role in cancer progression. Forced reduction of ATP8B1 expression either by CRISPR/Cas9 or shRNA was associated with increased growth and proliferation of CRC cell line - HT29. In contrast, overexpression of ATP8B1 resulted in reduced growth and proliferation of SW480 cell lines. We generated a network of genes that are downstream of ATP8B1. Further, we provide the predicted effect of modulation of ATP8B1 levels on this network and the possible effect on fatty acid metabolism-related genes. CONCLUSION Tumor suppressor gene (ATP8B1) located on chromosome 18q could be responsible in the progression of colorectal cancer. Knocking down of this gene causes an increased rate of cell proliferation and reduced cell death, suggesting its role as a tumor suppressor. Increasing the expression of this gene in colorectal cancer cells slowed down their growth and increased cell death. These evidences suggest the role of ATP8B1 as a tumor suppressor gene.
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Affiliation(s)
- Saleh Althenayyan
- Department of Cellular King Abdullah International Medical Research Center, Colorectal Cancer Research Program, Therapy and Cancer Research, Riyadh, 11481, Saudi Arabia.,Department King Saud Bin Abdulaziz University for Health Sciences, Riyadh, 11481, Saudi Arabia
| | - Amal AlGhamdi
- Department of Cellular King Abdullah International Medical Research Center, Colorectal Cancer Research Program, Therapy and Cancer Research, Riyadh, 11481, Saudi Arabia.,Department King Saud Bin Abdulaziz University for Health Sciences, Riyadh, 11481, Saudi Arabia
| | - Mohammed H AlMuhanna
- Department of Cellular King Abdullah International Medical Research Center, Colorectal Cancer Research Program, Therapy and Cancer Research, Riyadh, 11481, Saudi Arabia.,Department King Saud Bin Abdulaziz University for Health Sciences, Riyadh, 11481, Saudi Arabia
| | - Esra Hawsa
- Department of Cellular King Abdullah International Medical Research Center, Colorectal Cancer Research Program, Therapy and Cancer Research, Riyadh, 11481, Saudi Arabia.,Department King Saud Bin Abdulaziz University for Health Sciences, Riyadh, 11481, Saudi Arabia
| | - Dalal Aldeghaither
- Department of Cellular King Abdullah International Medical Research Center, Colorectal Cancer Research Program, Therapy and Cancer Research, Riyadh, 11481, Saudi Arabia.,Department of King Saud Bin Abdulaziz University for Health Sciences, College of Science and Health Professions, Basic Science. Riyadh, 11481, Saudi Arabia
| | - Jahangir Iqbal
- King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City Hospital, Ministry of National Guard Health Affairs, Al Hasa, 31982, Saudi Arabia
| | - Sameer Mohammad
- Department of King Abdullah International Medical Research Center, Experimental Medicine, Riyadh, 11481, Saudi Arabia
| | - Mohammad Azhar Aziz
- King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City Hospital, Ministry of National Guard Health Affairs, Al Hasa, 31982, Saudi Arabia
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Orouji E, Raman AT, Singh AK, Sorokin A, Arslan E, Ghosh AK, Schulz J, Terranova CJ, Jiang S, Tang M, Maitituoheti M, Barrodia P, Jiang Y, Callahan SC, Tomczak KJ, Jiang Z, Davis JS, Ghosh S, Lee HM, Reyes-Uribe L, Chang K, Liu Y, Chen H, Azhdarnia A, Morris JS, Vilar E, Carmon KS, Kopetz S, Rai K. Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer. Gut 2022; 71:938-949. [PMID: 34059508 PMCID: PMC8745382 DOI: 10.1136/gutjnl-2020-322835] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 05/14/2021] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Enhancer aberrations are beginning to emerge as a key epigenetic feature of colorectal cancers (CRC), however, a comprehensive knowledge of chromatin state patterns in tumour progression, heterogeneity of these patterns and imparted therapeutic opportunities remain poorly described. DESIGN We performed comprehensive epigenomic characterisation by mapping 222 chromatin profiles from 69 samples (33 colorectal adenocarcinomas, 4 adenomas, 21 matched normal tissues and 11 colon cancer cell lines) for six histone modification marks: H3K4me3 for Pol II-bound and CpG-rich promoters, H3K4me1 for poised enhancers, H3K27ac for enhancers and transcriptionally active promoters, H3K79me2 for transcribed regions, H3K27me3 for polycomb repressed regions and H3K9me3 for heterochromatin. RESULTS We demonstrate that H3K27ac-marked active enhancer state could distinguish between different stages of CRC progression. By epigenomic editing, we present evidence that gains of tumour-specific enhancers for crucial oncogenes, such as ASCL2 and FZD10, was required for excessive proliferation. Consistently, combination of MEK plus bromodomain inhibition was found to have synergistic effects in CRC patient-derived xenograft models. Probing intertumour heterogeneity, we identified four distinct enhancer subtypes (EPIgenome-based Classification, EpiC), three of which correlate well with previously defined transcriptomic subtypes (consensus molecular subtypes, CMSs). Importantly, CMS2 can be divided into two EpiC subgroups with significant survival differences. Leveraging such correlation, we devised a combinatorial therapeutic strategy of enhancer-blocking bromodomain inhibitors with pathway-specific inhibitors (PARPi, EGFRi, TGFβi, mTORi and SRCi) for EpiC groups. CONCLUSION Our data suggest that the dynamics of active enhancer underlies CRC progression and the patient-specific enhancer patterns can be leveraged for precision combination therapy.
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Affiliation(s)
- Elias Orouji
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA,Present address: Epigenetics Initiative, Princess Margaret Genomics Centre, Toronto, ON, Canada
| | - Ayush T. Raman
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA,Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA,Present address: Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anand K. Singh
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexey Sorokin
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer center, Houston, TX, USA
| | - Emre Arslan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Archit K. Ghosh
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan Schulz
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher J. Terranova
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shan Jiang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ming Tang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mayinuer Maitituoheti
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Praveen Barrodia
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yingda Jiang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - S. Carson Callahan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katarzyna J. Tomczak
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhiqin Jiang
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer center, Houston, TX, USA
| | - Jennifer S. Davis
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sukhen Ghosh
- Center for Translational Cancer Research, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hey Min Lee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer center, Houston, TX, USA
| | - Laura Reyes-Uribe
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kyle Chang
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yusha Liu
- Department of Bioinformatics and Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huiqin Chen
- Department of Bioinformatics and Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ali Azhdarnia
- Center for Translational Cancer Research, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jeffrey S. Morris
- Department of Bioinformatics and Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA,Present address: Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kendra S. Carmon
- Center for Translational Cancer Research, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer center, Houston, TX, USA
| | - Kunal Rai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA .,Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Strickler JH, Yoshino T, Graham RP, Siena S, Bekaii-Saab T. Diagnosis and Treatment of ERBB2-Positive Metastatic Colorectal Cancer: A Review. JAMA Oncol 2022; 8:760-769. [PMID: 35238866 DOI: 10.1001/jamaoncol.2021.8196] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Importance Amplification of ERBB2 (formerly referred to as HER2) is present in nearly 3% of patients with metastatic colorectal cancer overall and 5% of patients with KRAS and NRAS wild-type tumors. Despite the availability of several ERBB2-targeted therapeutic options for patients with ERBB2-positive breast and gastric/gastroesophageal tumors, to date, there are currently no approved therapies for patients with ERBB2-positive metastatic colorectal cancer, although ERBB2-targeted therapies are recommended in National Comprehensive Cancer Network guidelines. Recent evidence indicates that anti-ERBB2 therapeutic strategies are active in patients with ERBB2-positive metastatic colorectal cancer and could potentially represent a new standard-of-care. Observations The protein ERBB2 is a member of a family of epidermal growth factor receptors that also includes epidermal growth factor receptor (ERBB1), ERBB3, and ERBB4. Amplification of ERBB2 leads to overexpression of the ERBB2 tyrosine kinase receptor, resulting in aberrant signaling and cell migration, growth, adhesion, and differentiation. Colorectal tumors that harbor ERBB2 amplification are more likely to originate on the left side of the colon, are associated with primary and acquired resistance to anti-epidermal growth factor receptor therapies, and have increased incidence of central nervous system metastases. Using immunohistochemistry, fluorescence in situ hybridization, next-generation sequencing, and liquid biopsy techniques, several randomized clinical trials have evaluated the efficacy of ERBB2-targeted therapies in patients with ERBB2-positive metastatic colorectal cancer. These therapies include monoclonal antibodies, antibody-drug conjugates, and tyrosine kinase inhibitors, many of which were associated with favorable efficacy and safety profiles when treating patients with ERBB2-positive metastatic colorectal cancer. Conclusions and Relevance The results of this review suggest the ERBB2 receptor is a promising target for patients with metastatic colorectal cancer; however, to date, no therapies are approved for use in this patient population. Therefore, it is imperative to continue to work to address this unmet need so that patients with ERBB2-positive metastatic colorectal cancer have therapeutic options should they become refractory to treatment with standard therapies.
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Affiliation(s)
| | - Takayuki Yoshino
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Rondell P Graham
- Division of Laboratory Genetics and Genomics, Division of Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda and Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
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49
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Li S, Yang Y, Wang X, Li J, Yu J, Li X, Wong KC. Colorectal cancer subtype identification from differential gene expression levels using minimalist deep learning. BioData Min 2022; 15:12. [PMID: 35461302 PMCID: PMC9034628 DOI: 10.1186/s13040-022-00295-w] [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: 10/05/2021] [Accepted: 03/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Cancer molecular subtyping plays a critical role in individualized patient treatment. In previous studies, high-throughput gene expression signature-based methods have been proposed to identify cancer subtypes. Unfortunately, the existing ones suffer from the curse of dimensionality, data sparsity, and computational deficiency. Methods To address those problems, we propose a computational framework for colorectal cancer subtyping without any exploitation in model complexity and generality. A supervised learning framework based on deep learning (DeepCSD) is proposed to identify cancer subtypes. Specifically, based on the differentially expressed genes under cancer consensus molecular subtyping, we design a minimalist feed-forward neural network to capture the distinct molecular features in different cancer subtypes. To mitigate the overfitting phenomenon of deep learning as much as possible, L1 and L2 regularization and dropout layers are added. Results For demonstrating the effectiveness of DeepCSD, we compared it with other methods including Random Forest (RF), Deep forest (gcForest), support vector machine (SVM), XGBoost, and DeepCC on eight independent colorectal cancer datasets. The results reflect that DeepCSD can achieve superior performance over other algorithms. In addition, gene ontology enrichment and pathology analysis are conducted to reveal novel insights into the cancer subtype identification and characterization mechanisms. Conclusions DeepCSD considers all subtype-specific genes as input, which is pathologically necessary for its completeness. At the same time, DeepCSD shows remarkable robustness in handling cross-platform gene expression data, achieving similar performance on both training and test data without significant model overfitting or exploitation of model complexity. Supplementary Information The online version contains supplementary material available at (10.1186/s13040-022-00295-w).
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Affiliation(s)
- Shaochuan Li
- Department of Information Science and Technology, Northeast Normal University, Changchun, Jilin, China
| | - Yuning Yang
- Department of Information Science and Technology, Northeast Normal University, Changchun, Jilin, China
| | - Xin Wang
- Department of Surgery, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, and School of Data Science, City University of Hong Kong, Hong Kong SAR, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun, Jilin, China. .,Department of Computer Science, City University of Hong Kong, Hong Kong SAR, China.
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR, China.
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50
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Seo MK, Kang H, Kim S. Tumor microenvironment-aware, single-transcriptome prediction of microsatellite instability in colorectal cancer using meta-analysis. Sci Rep 2022; 12:6283. [PMID: 35428835 PMCID: PMC9012745 DOI: 10.1038/s41598-022-10182-3] [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: 10/26/2021] [Accepted: 03/28/2022] [Indexed: 01/27/2023] Open
Abstract
Detecting microsatellite instability (MSI) in colorectal cancers (CRCs) is essential because it is the determinant of treatment strategies, including immunotherapy and chemotherapy. Yet, no attempt has been made to exploit transcriptomic profile and tumor microenvironment (TME) of it to unveil MSI status in CRC. Hence, we developed a novel TME-aware, single-transcriptome predictor of MSI for CRC, called MAP (Microsatellite instability Absolute single sample Predictor). MAP was developed utilizing recursive feature elimination-random forest with 466 CRC samples from The Cancer Genome Atlas, and its performance was validated in independent cohorts, including 1118 samples. MAP showed robustness and predictive power in predicting MSI status in CRC. Additional advantages for MAP were demonstrated through comparative analysis with existing MSI classifier and other cancer types. Our novel approach will provide access to untouched vast amounts of publicly available transcriptomic data and widen the door for MSI CRC research and be useful for gaining insights to help with translational medicine.
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Affiliation(s)
- Mi-Kyoung Seo
- Department of Biomedical Systems Informatics, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Hyundeok Kang
- Department of Biomedical Systems Informatics, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, South Korea.
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