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de Back TR, van Hooff SR, Sommeijer DW, Vermeulen L. Transcriptomic subtyping of gastrointestinal malignancies. Trends Cancer 2024:S2405-8033(24)00120-1. [PMID: 39019673 DOI: 10.1016/j.trecan.2024.06.007] [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: 04/25/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/19/2024]
Abstract
Gastrointestinal (GI) cancers are highly heterogeneous at multiple levels. Tumor heterogeneity can be captured by molecular profiling, such as genetic, epigenetic, proteomic, and transcriptomic classification. Transcriptomic subtyping has the advantage of combining genetic and epigenetic information, cancer cell-intrinsic properties, and the tumor microenvironment (TME). Unsupervised transcriptomic subtyping systems of different GI malignancies have gained interest because they reveal shared biological features across cancers and bear prognostic and predictive value. Importantly, transcriptomic subtypes accurately reflect complex phenotypic states varying not only per tumor region, but also throughout disease progression, with consequences for clinical management. Here, we discuss methodologies of transcriptomic subtyping, proposed taxonomies for GI malignancies, and the challenges posed to clinical implementation, highlighting opportunities for future transcriptomic profiling efforts to optimize clinical impact.
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Affiliation(s)
- Tim R de Back
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Sander R van Hooff
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Dirkje W Sommeijer
- Flevohospital, Department of Internal Medicine, Hospitaalweg 1, 1315 RA, Almere, The Netherlands
| | - Louis Vermeulen
- Cancer Center Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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2
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Harvey BJ, Harvey HM. Sex Differences in Colon Cancer: Genomic and Nongenomic Signalling of Oestrogen. Genes (Basel) 2023; 14:2225. [PMID: 38137047 PMCID: PMC10742859 DOI: 10.3390/genes14122225] [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: 11/22/2023] [Revised: 12/10/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Colon cancer (CRC) is a prevalent malignancy that exhibits distinct differences in incidence, prognosis, and treatment responses between males and females. These disparities have long been attributed to hormonal differences, particularly the influence of oestrogen signalling. This review aims to provide a comprehensive analysis of recent advances in our understanding of the molecular mechanisms underlying sex differences in colon cancer and the protective role of membrane and nuclear oestrogen signalling in CRC development, progression, and therapeutic interventions. We discuss the epidemiological and molecular evidence supporting sex differences in colon cancer, followed by an exploration of the impact of oestrogen in CRC through various genomic and nongenomic signalling pathways involving membrane and nuclear oestrogen receptors. Furthermore, we examine the interplay between oestrogen receptors and other signalling pathways, in particular the Wnt/β-catenin proliferative pathway and hypoxia in shaping biological sex differences and oestrogen protective actions in colon cancer. Lastly, we highlight the potential therapeutic implications of targeting oestrogen signalling in the management of colon cancer and propose future research directions to address the current gaps in our understanding of this complex phenomenon.
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Affiliation(s)
- Brian J. Harvey
- Faculty of Medicine, Royal College of Surgeons in Ireland, RCSI University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland
| | - Harry M. Harvey
- Princess Margaret Cancer Centre, Toronto, ON M5G 1Z5, Canada;
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3
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McGowan KP, Delgado E, Keeley TM, Hibdon ES, Turgeon DK, Stoffel EM, Samuelson LC. Region-specific Wnt signaling responses promote gastric polyp formation in patients with familial adenomatous polyposis. JCI Insight 2023; 8:e174546. [PMID: 37943618 PMCID: PMC10896006 DOI: 10.1172/jci.insight.174546] [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: 08/03/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023] Open
Abstract
Germline adenomatous polyposis coli (APC) mutation in patients with familial adenomatous polyposis (FAP) promotes gastrointestinal polyposis, including the formation of frequent gastric fundic gland polyps (FGPs). In this study, we investigated how dysregulated Wnt signaling promotes FGPs and why they localize to the corpus region of the stomach. We developed a biobank of FGP and surrounding nonpolyp corpus biopsies and organoids from patients with FAP for comparative studies. Polyp biopsies and polyp-derived organoids exhibited enhanced Wnt target gene expression. Polyp-derived organoids with intrinsically upregulated Wnt signaling showed poor tolerance to further induction, suggesting that high Wnt restricts growth. Targeted genomic sequencing revealed that most gastric polyps did not arise via APC loss of heterozygosity. Studies in genetic mouse models demonstrated that heterozygous Apc loss increased epithelial cell proliferation in the corpus but not the antrum, while homozygous Apc loss was not maintained in the corpus yet induced hyperproliferation in the antrum. Our findings suggest that heterozygous APC mutation in patients with FAP may be sufficient to drive polyp formation in the corpus region while subsequent loss of heterozygosity to further enhance Wnt signaling is not tolerated. This finding contextualizes the abundant yet benign nature of gastric polyps in FAP patient corpus compared with the rare, yet adenomatous polyps in the antrum.
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Affiliation(s)
| | | | | | | | - D Kim Turgeon
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Elena M Stoffel
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Linda C Samuelson
- Department of Molecular & Integrative Physiology and
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Sanson R, Lazzara SL, Cune D, Pitasi CL, Trentesaux C, Fraudeau M, Letourneur F, Saintpierre B, Le Gall M, Bossard P, Terris B, Finetti P, Bertucci F, Mamessier E, Romagnolo B, Perret C. Axin1 Protects Colon Carcinogenesis by an Immune-Mediated Effect. Cell Mol Gastroenterol Hepatol 2023; 15:689-715. [PMID: 36356835 PMCID: PMC9874083 DOI: 10.1016/j.jcmgh.2022.10.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND & AIMS Axin1 is a negative regulator of wingless-type MMTV integration site family, member 1 (Wnt)/β-catenin signaling with tumor-suppressor function. The Wnt pathway has a critical role in the intestine, both during homeostasis and cancer, but the role of Axin1 remains elusive. METHODS We assessed the role of Axin1 in normal intestinal homeostasis, with control, epithelial-specific, Axin1-knockout mice (Axin1ΔIEC) and Axin2-knockout mice. We evaluated the tumor-suppressor function of Axin1 during chemically induced colorectal tumorigenesis and dextran sulfate sodium-induced colitis, and performed comparative gene expression profiling by whole-genome RNA sequencing. The clinical relevance of the Axin1-dependent gene expression signature then was tested in a database of 2239 clinical colorectal cancer (CRC) samples. RESULTS We found that Axin1 was dispensable for normal intestinal homeostasis and redundant with Axin2 for Wnt pathway down-regulation. Axin1 deficiency in intestinal epithelial cells rendered mice more susceptible to chemically induced colon carcinogenesis, but reduced dextran sulfate sodium-induced colitis by attenuating the induction of a proinflammatory program. RNA-seq analyses identified an interferon γ/T-helper1 immune program controlled by Axin1 that enhances the inflammatory response and protects against CRC. The Axin1-dependent gene expression signature was applied to human CRC samples and identified a group of patients with potential vulnerability to immune checkpoint blockade therapies. CONCLUSIONS Our study establishes, in vivo, that Axin1 has redundant function with Axin2 for Wnt down-regulation and infers a new role for Axin1. Physiologically, Axin1 stimulates gut inflammation via an interferon γ/Th1 program that prevents tumor growth. Linked to its T-cell-mediated effect, the colonic Axin1 signature offers therapeutic perspectives for CRC.
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Affiliation(s)
- Romain Sanson
- Université de Paris, Institut Cochin, INSERM, Centre National Recherche Scientifique, Paris, France; Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Silvia Luna Lazzara
- Université de Paris, Institut Cochin, INSERM, Centre National Recherche Scientifique, Paris, France; Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - David Cune
- Université de Paris, Institut Cochin, INSERM, Centre National Recherche Scientifique, Paris, France; Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Caterina Luana Pitasi
- Université de Paris, Institut Cochin, INSERM, Centre National Recherche Scientifique, Paris, France; Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Coralie Trentesaux
- Université de Paris, Institut Cochin, INSERM, Centre National Recherche Scientifique, Paris, France; Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Marie Fraudeau
- Université de Paris, Institut Cochin, INSERM, Centre National Recherche Scientifique, Paris, France; Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Franck Letourneur
- Genomic Facility, Université de Paris, Institut Cochin, INSERM, Centre National Recherche Scientifique, Paris, France
| | - Benjamin Saintpierre
- Genomic Facility, Université de Paris, Institut Cochin, INSERM, Centre National Recherche Scientifique, Paris, France
| | - Morgane Le Gall
- Proteomic Facility, Université de Paris, Institut Cochin, INSERM, Centre National Recherche Scientifique, Paris, France
| | - Pascale Bossard
- Université de Paris, Institut Cochin, INSERM, Centre National Recherche Scientifique, Paris, France; Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Benoit Terris
- Université de Paris, Institut Cochin, INSERM, Centre National Recherche Scientifique, Paris, France; Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France; Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Pathology Department, Hôpital Cochin, Paris, France
| | - Pascal Finetti
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, INSERM Unité Mixte de Recherche 1068, Centre National Recherche Scientifique Unité Mixte de Recherche 725, Marseille, France
| | - François Bertucci
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, INSERM Unité Mixte de Recherche 1068, Centre National Recherche Scientifique Unité Mixte de Recherche 725, Marseille, France
| | - Emilie Mamessier
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, INSERM Unité Mixte de Recherche 1068, Centre National Recherche Scientifique Unité Mixte de Recherche 725, Marseille, France
| | - Béatrice Romagnolo
- Université de Paris, Institut Cochin, INSERM, Centre National Recherche Scientifique, Paris, France; Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France.
| | - Christine Perret
- Université de Paris, Institut Cochin, INSERM, Centre National Recherche Scientifique, Paris, France; Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France.
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Swoboda J, Mittelsdorf P, Chen Y, Weiskirchen R, Stallhofer J, Schüle S, Gassler N. Intestinal Wnt in the transition from physiology to oncology. World J Clin Oncol 2022; 13:168-185. [PMID: 35433295 PMCID: PMC8966512 DOI: 10.5306/wjco.v13.i3.168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/07/2021] [Accepted: 02/20/2022] [Indexed: 02/06/2023] Open
Abstract
Adult stem cells are necessary for self-renewal tissues and regeneration after damage. Especially in the intestine, which self-renews every few days, they play a key role in tissue homeostasis. Therefore, complex regulatory mechanisms are needed to prevent hyperproliferation, which can lead in the worst case to carcinogenesis or under-activation of stem cells, which can result in dysfunctional epithelial. One main regulatory signaling pathway is the Wnt/β-catenin signaling pathway. It is a highly conserved pathway, with β-catenin, a transcription factor, as target protein. Translocation of β-catenin from cytoplasm to nucleus activates the transcription of numerous genes involved in regulating stem cell pluripo-tency, proliferation, cell differentiation and regulation of cell death. This review presents a brief overview of the Wnt/β-catenin signaling pathway, the regulatory mechanism of this pathway and its role in intestinal homeostasis. Additionally, this review highlights the molecular mechanisms and the histomorphological features of Wnt hyperactivation. Furthermore, the central role of the Wnt signaling pathway in intestinal carcinogenesis as well as its clinical relevance in colorectal carcinoma are discussed.
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Affiliation(s)
- Julia Swoboda
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07747, Germany
| | - Patrick Mittelsdorf
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07747, Germany
| | - Yuan Chen
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07747, Germany
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry, RWTH University Hospital Aachen, Aachen 52074, Germany
| | - Johannes Stallhofer
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena 07747, Germany
| | - Silke Schüle
- Department of General, Visceral and Vascular Surgery, Jena University Hospital, Jena 07747, Germany
| | - Nikolaus Gassler
- Section Pathology, Institute of Forensic Medicine, Jena University Hospital, Jena 07747, Germany
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Wang B, Wang X, Tseng Y, Huang M, Luo F, Zhang J, Liu J. Distinguishing colorectal adenoma from hyperplastic polyp by WNT2 expression. J Clin Lab Anal 2021; 35:e23961. [PMID: 34477243 PMCID: PMC8529141 DOI: 10.1002/jcla.23961] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Colorectal adenoma (CRA) is a classical premalignant lesion, with high incidence and mainly coexisting with hyperplastic polyp (HPP). Hence, this study aimed to distinguish CRA from HPP by molecular expression profiling and advance the prevention of CRA and its malignance. METHODS CRA and paired HPP biopsies were collected by endoscopy. Through RNA-sequencing (RNA-seq), the differentially expressed genes (DEGs) were obtained. Functional enrichment analysis was performed based on the DEGs. The STRING database and Cytoscape were used to construct the protein-protein interaction (PPI) network and perform module analysis. Hub genes were validated by real-time quantitative PCR (RT-qPCR) and immunohistochemistry. The ROC curve was drawn to establish the specificity of the hub genes. RESULTS 485 significant DEGs were identified including 133 up-regulated and 352 down-regulated. The top 10 up-regulated genes were DLX5, MMP10, TAC1, ACAN, TAS2R38, WNT2, PHYHIPL, DKK4, DUSP27, and ABCA12. The top 10 down-regulated genes were SFRP2, CHRDL1, KBTBD12, RERGL, DPP10, CLCA4, GREM2, TMIGD1, FEV, and OTOP3. Wnt signaling pathway and extracellular matrix (ECM) were up-regulated in CRA. Three hub genes including WNT2, WNT5A, and SFRP1 were filtered out via Cytoscape. Further RT-qPCR and immunohistochemistry confirmed that WNT2 was highly expressed in CRA. The area under the ROC curve (AUC) at 0.98 indicated the expression level of WNT2 as a candidate to differ CRA from HPP. CONCLUSION Our study suggests Wnt signaling pathway and ECM are enriched in CRA, and WNT2 may be used as a novel biomarker for distinguishing CRA from HPP and preventing the malignance of CRA.
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Affiliation(s)
- Bangting Wang
- Department of Digestive Diseases, Huashan HospitalFudan UniversityShanghaiChina
| | - Xin Wang
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesFudan UniversityShanghaiChina
| | - Yujen Tseng
- Department of Digestive Diseases, Huashan HospitalFudan UniversityShanghaiChina
| | - Meina Huang
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesFudan UniversityShanghaiChina
| | - Feifei Luo
- Department of Digestive Diseases, Huashan HospitalFudan UniversityShanghaiChina
| | - Jun Zhang
- Department of Digestive Diseases, Huashan HospitalFudan UniversityShanghaiChina
| | - Jie Liu
- Department of Digestive Diseases, Huashan HospitalFudan UniversityShanghaiChina
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Apc-mutant cells act as supercompetitors in intestinal tumour initiation. Nature 2021; 594:436-441. [PMID: 34079128 DOI: 10.1038/s41586-021-03558-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/15/2021] [Indexed: 02/05/2023]
Abstract
A delicate equilibrium of WNT agonists and antagonists in the intestinal stem cell (ISC) niche is critical to maintaining the ISC compartment, as it accommodates the rapid renewal of the gut lining. Disruption of this balance by mutations in the tumour suppressor gene APC, which are found in approximately 80% of all human colon cancers, leads to unrestrained activation of the WNT pathway1,2. It has previously been established that Apc-mutant cells have a competitive advantage over wild-type ISCs3. Consequently, Apc-mutant ISCs frequently outcompete all wild-type stem cells within a crypt, thereby reaching clonal fixation in the tissue and initiating cancer formation. However, whether the increased relative fitness of Apc-mutant ISCs involves only cell-intrinsic features or whether Apc mutants are actively involved in the elimination of their wild-type neighbours remains unresolved. Here we show that Apc-mutant ISCs function as bona fide supercompetitors by secreting WNT antagonists, thereby inducing differentiation of neighbouring wild-type ISCs. Lithium chloride prevented the expansion of Apc-mutant clones and the formation of adenomas by rendering wild-type ISCs insensitive to WNT antagonists through downstream activation of WNT by inhibition of GSK3β. Our work suggests that boosting the fitness of healthy cells to limit the expansion of pre-malignant clones may be a powerful strategy to limit the formation of cancers in high-risk individuals.
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Organoids and Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13112657. [PMID: 34071313 PMCID: PMC8197877 DOI: 10.3390/cancers13112657] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
Organoids were first established as a three-dimensional cell culture system from mouse small intestine. Subsequent development has made organoids a key system to study many human physiological and pathological processes that affect a variety of tissues and organs. In particular, organoids are becoming very useful tools to dissect colorectal cancer (CRC) by allowing the circumvention of classical problems and limitations, such as the impossibility of long-term culture of normal intestinal epithelial cells and the lack of good animal models for CRC. In this review, we describe the features and current knowledge of intestinal organoids and how they are largely contributing to our better understanding of intestinal cell biology and CRC genetics. Moreover, recent data show that organoids are appropriate systems for antitumoral drug testing and for the personalized treatment of CRC patients.
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