1
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Tourigny DS, Altieri B, Secener KA, Sbiera S, Schauer MP, Arampatzi P, Herterich S, Sauer S, Fassnacht M, Ronchi CL. Cellular landscape of adrenocortical carcinoma at single-nuclei resolution. Mol Cell Endocrinol 2024; 590:112272. [PMID: 38759836 DOI: 10.1016/j.mce.2024.112272] [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: 03/11/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Adrenocortical carcinoma (ACC) is a rare yet devastating tumour of the adrenal gland with a molecular pathology that remains incompletely understood. To gain novel insights into the cellular landscape of ACC, we generated single-nuclei RNA sequencing (snRNA-seq) data sets from twelve ACC tumour samples and analysed these alongside snRNA-seq data sets from normal adrenal glands (NAGs). We find the ACC tumour microenvironment to be relatively devoid of immune cells compared to NAG tissues, consistent with known high tumour purity values for ACC as an immunologically "cold" tumour. Our analysis identifies three separate groups of ACC samples that are characterised by different relative compositions of adrenocortical cell types. These include cell populations that are specifically enriched in the most clinically aggressive and hormonally active tumours, displaying hallmarks of reorganised cell mechanobiology and dysregulated steroidogenesis, respectively. We also identified and validated a population of mitotically active adrenocortical cells that strongly overexpress genes POLQ, DIAPH3 and EZH2 to support tumour expansion alongside an LGR4+ progenitor-like or cell-of-origin candidate for adrenocortical carcinogenesis. Trajectory inference suggests the fate adopted by malignant adrenocortical cells upon differentiation is associated with the copy number or allelic balance state of the imprinted DLK1/MEG3 genomic locus, which we verified by assessing bulk tumour DNA methylation status. In conclusion, our results therefore provide new insights into the clinical and cellular heterogeneity of ACC, revealing how genetic perturbations to healthy adrenocortical renewal and zonation provide a molecular basis for disease pathogenesis.
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Affiliation(s)
- David S Tourigny
- School of Mathematics, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Barbara Altieri
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Kerim A Secener
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany; Institute of Biochemistry, Department of Biology, Chemistry and Pharmacy, Free University Berlin, Berlin, 14195, Germany
| | - Silviu Sbiera
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Marc P Schauer
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany; Center for Cellular Immunotherapy, Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, 97080, Germany
| | | | - Sabine Herterich
- Central Laboratory, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Sascha Sauer
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany
| | - Martin Fassnacht
- Division of Endocrinology and Diabetes, University Hospital of Würzburg, Würzburg, 97080, Germany
| | - Cristina L Ronchi
- Institute of Metabolism and System Research, University of Birmingham, Birmingham, B15 2TT, UK; Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham, B15 2GW, UK.
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2
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Li J, Simmons AJ, Hawkins CV, Chiron S, Ramirez-Solano MA, Tasneem N, Kaur H, Xu Y, Revetta F, Vega PN, Bao S, Cui C, Tyree RN, Raber LW, Conner AN, Pilat JM, Jacobse J, McNamara KM, Allaman MM, Raffa GA, Gobert AP, Asim M, Goettel JA, Choksi YA, Beaulieu DB, Dalal RL, Horst SN, Pabla BS, Huo Y, Landman BA, Roland JT, Scoville EA, Schwartz DA, Washington MK, Shyr Y, Wilson KT, Coburn LA, Lau KS, Liu Q. Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn's disease. Nat Commun 2024; 15:7204. [PMID: 39169060 PMCID: PMC11339313 DOI: 10.1038/s41467-024-51580-7] [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: 08/28/2023] [Accepted: 08/13/2024] [Indexed: 08/23/2024] Open
Abstract
Crohn's disease (CD) is a complex chronic inflammatory disorder with both gastrointestinal and extra-intestinal manifestations associated immune dysregulation. Analyzing 202,359 cells from 170 specimens across 83 patients, we identify a distinct epithelial cell type in both terminal ileum and ascending colon (hereon as 'LND') with high expression of LCN2, NOS2, and DUOX2 and genes related to antimicrobial response and immunoregulation. LND cells, confirmed by in-situ RNA and protein imaging, are rare in non-IBD controls but expand in active CD, and actively interact with immune cells and specifically express IBD/CD susceptibility genes, suggesting a possible function in CD immunopathogenesis. Furthermore, we discover early and late LND subpopulations with different origins and developmental potential. A higher ratio of late-to-early LND cells correlates with better response to anti-TNF treatment. Our findings thus suggest a potential pathogenic role for LND cells in both Crohn's ileitis and colitis.
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Affiliation(s)
- Jia Li
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alan J Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Caroline V Hawkins
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sophie Chiron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marisol A Ramirez-Solano
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Naila Tasneem
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Harsimran Kaur
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yanwen Xu
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Frank Revetta
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paige N Vega
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shunxing Bao
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Can Cui
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Regina N Tyree
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Larry W Raber
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anna N Conner
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer M Pilat
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Justin Jacobse
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kara M McNamara
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Margaret M Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gabriella A Raffa
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alain P Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mohammad Asim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeremy A Goettel
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yash A Choksi
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Dawn B Beaulieu
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robin L Dalal
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara N Horst
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Baldeep S Pabla
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuankai Huo
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elizabeth A Scoville
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David A Schwartz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Kay Washington
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA.
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA.
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA.
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA.
| | - Ken S Lau
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA.
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3
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Spelier S, Derksen S, Hofland R, Beekman JM, Yetkin-Arik B. CFTR and colorectal cancer susceptibility: an urgent need for further studies. Trends Cancer 2024:S2405-8033(24)00146-8. [PMID: 39147661 DOI: 10.1016/j.trecan.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/05/2024] [Accepted: 07/18/2024] [Indexed: 08/17/2024]
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene result in cystic fibrosis, a multiorgan disease characterized by aberrant epithelial cell fluid secretion. Recent studies describe a connection between CFTR malfunctioning and a heightened susceptibility to colorectal cancer (CRC). Here, we outline these links and suggest directions for further studies.
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Affiliation(s)
- S Spelier
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, The Netherlands.
| | - S Derksen
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - R Hofland
- Department of Respiratory Medicine, University Medical Center, Cystic Fibrosis Center, Utrecht University, 3584 EA Utrecht, The Netherlands
| | - J M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, The Netherlands; Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Princetonlaan 6, 3584 CB Utrecht, The Netherlands
| | - B Yetkin-Arik
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, The Netherlands; Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Princetonlaan 6, 3584 CB Utrecht, The Netherlands
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4
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Baas FS, Brusselaers N, Nagtegaal ID, Engstrand L, Boleij A. Navigating beyond associations: Opportunities to establish causal relationships between the gut microbiome and colorectal carcinogenesis. Cell Host Microbe 2024; 32:1235-1247. [PMID: 39146796 DOI: 10.1016/j.chom.2024.07.008] [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: 05/15/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 08/17/2024]
Abstract
The gut microbiota has been recognized as an important determinant in the initiation and progression of colorectal cancer (CRC), with recent studies shining light on the molecular mechanisms that may contribute to the interactions between microbes and the CRC microenvironment. Despite the increasing wealth of associations being established in the field, proving causality remains challenging. Obstacles include the high variability of the microbiome and its context, both across individuals and across time. Additionally, there is a lack of large and representative cohort studies with long-term follow-up and/or appropriate sampling methods for studying the mucosal microbiome. Finally, most studies focus on CRC, whereas interactions between host and bacteria in early events in carcinogenesis remain elusive, reinforced by the heterogeneity of CRC development. Here, we discuss these current most prominent obstacles, the recent developments, and research needs.
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Affiliation(s)
- Floor S Baas
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nele Brusselaers
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Karolinska Hospital, Stockholm, Sweden; Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Karolinska Hospital, Stockholm, Sweden
| | - Annemarie Boleij
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.
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5
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Kinoshita H, Martinez-Ordoñez A, Cid-Diaz T, Han Q, Duran A, Muta Y, Zhang X, Linares JF, Nakanishi Y, Kasashima H, Yashiro M, Maeda K, Albaladejo-Gonzalez A, Torres-Moreno D, García-Solano J, Conesa-Zamora P, Inghirami G, Diaz-Meco MT, Moscat J. Epithelial aPKC deficiency leads to stem cell loss preceding metaplasia in colorectal cancer initiation. Dev Cell 2024; 59:1972-1987.e8. [PMID: 38815584 PMCID: PMC11303105 DOI: 10.1016/j.devcel.2024.05.001] [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: 08/01/2023] [Revised: 12/19/2023] [Accepted: 05/03/2024] [Indexed: 06/01/2024]
Abstract
The early mechanisms of spontaneous tumor initiation that precede malignancy are largely unknown. We show that reduced aPKC levels correlate with stem cell loss and the induction of revival and metaplastic programs in serrated- and conventional-initiated premalignant lesions, which is perpetuated in colorectal cancers (CRCs). Acute inactivation of PKCλ/ι in vivo and in mouse organoids is sufficient to stimulate JNK in non-transformed intestinal epithelial cells (IECs), which promotes cell death and the rapid loss of the intestinal stem cells (ISCs), including those that are LGR5+. This is followed by the accumulation of revival stem cells (RSCs) at the bottom of the crypt and fetal-metaplastic cells (FMCs) at the top, creating two spatiotemporally distinct cell populations that depend on JNK-induced AP-1 and YAP. These cell lineage changes are maintained during cancer initiation and progression and determine the aggressive phenotype of human CRC, irrespective of their serrated or conventional origin.
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Affiliation(s)
- Hiroto Kinoshita
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Anxo Martinez-Ordoñez
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Tania Cid-Diaz
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Qixiu Han
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Angeles Duran
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yu Muta
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Xiao Zhang
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Juan F Linares
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yuki Nakanishi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiroaki Kasashima
- Department of Gastroenterological Surgery, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka city 545-8585, Japan
| | - Masakazu Yashiro
- Department of Gastroenterological Surgery, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka city 545-8585, Japan
| | - Kiyoshi Maeda
- Department of Gastroenterological Surgery, Osaka Metropolitan University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka city 545-8585, Japan
| | - Ana Albaladejo-Gonzalez
- Department of Histology and Pathology, Faculty of Life Sciences, Universidad Católica de Murcia (UCAM), 30107 Murcia, Spain; Department of Pathology, Santa Lucía General University Hospital (HGUSL), Calle Mezquita sn, 30202 Cartagena, Spain
| | - Daniel Torres-Moreno
- Department of Histology and Pathology, Faculty of Life Sciences, Universidad Católica de Murcia (UCAM), 30107 Murcia, Spain; Department of Clinical Analysis, Santa Lucía General University Hospital (HGUSL), Calle Mezquita sn, 30202 Cartagena, Spain
| | - José García-Solano
- Department of Histology and Pathology, Faculty of Life Sciences, Universidad Católica de Murcia (UCAM), 30107 Murcia, Spain; Department of Pathology, Santa Lucía General University Hospital (HGUSL), Calle Mezquita sn, 30202 Cartagena, Spain
| | - Pablo Conesa-Zamora
- Department of Histology and Pathology, Faculty of Life Sciences, Universidad Católica de Murcia (UCAM), 30107 Murcia, Spain; Department of Clinical Analysis, Santa Lucía General University Hospital (HGUSL), Calle Mezquita sn, 30202 Cartagena, Spain
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Maria T Diaz-Meco
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Jorge Moscat
- Department of Pathology and Laboratory Medicine and Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA.
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6
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Trinks A, Milek M, Beule D, Kluge J, Florian S, Sers C, Horst D, Morkel M, Bischoff P. Robust detection of clinically relevant features in single-cell RNA profiles of patient-matched fresh and formalin-fixed paraffin-embedded (FFPE) lung cancer tissue. Cell Oncol (Dordr) 2024; 47:1221-1231. [PMID: 38300468 PMCID: PMC11322409 DOI: 10.1007/s13402-024-00922-0] [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] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
PURPOSE Single-cell transcriptional profiling reveals cell heterogeneity and clinically relevant traits in intra-operatively collected patient-derived tissue. So far, single-cell studies have been constrained by the requirement for prospectively collected fresh or cryopreserved tissue. This limitation might be overcome by recent technical developments enabling single-cell analysis of FFPE tissue. METHODS We benchmark single-cell profiles from patient-matched fresh, cryopreserved and archival FFPE cancer tissue. RESULTS We find that fresh tissue and FFPE routine blocks can be employed for the robust detection of clinically relevant traits on the single-cell level. Specifically, single-cell maps of fresh patient tissues and corresponding FFPE tissue blocks could be integrated into common low-dimensional representations, and cell subtype clusters showed highly correlated transcriptional strengths of signaling pathway, hallmark, and clinically useful signatures, although expression of single genes varied due to technological differences. FFPE tissue blocks revealed higher cell diversity compared to fresh tissue. In contrast, single-cell profiling of cryopreserved tissue was prone to artifacts in the clinical setting. CONCLUSION Our analysis highlights the potential of single-cell profiling in the analysis of retrospectively and prospectively collected archival pathology cohorts and increases the applicability in translational research.
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Affiliation(s)
- Alexandra Trinks
- Bioportal Single Cells, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Miha Milek
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Julie Kluge
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Stefan Florian
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
- BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christine Sers
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK) Partner Site Berlin, Heidelberg, Germany
| | - David Horst
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK) Partner Site Berlin, Heidelberg, Germany
| | - Markus Morkel
- Bioportal Single Cells, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany.
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK) Partner Site Berlin, Heidelberg, Germany.
| | - Philip Bischoff
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany.
- BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK) Partner Site Berlin, Heidelberg, Germany.
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7
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Verhagen MP, Schmitt M, Fodde R. Western lifestyle, metaflammation and the cell of origin of colon cancer. Nat Rev Gastroenterol Hepatol 2024:10.1038/s41575-024-00964-7. [PMID: 39048736 DOI: 10.1038/s41575-024-00964-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Affiliation(s)
- Mathijs P Verhagen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mark Schmitt
- Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - Riccardo Fodde
- Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands.
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8
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Yang W, Li Z, Li Y, He W, Yan J. Transforming Albumin into a Trojan Horse of Immunotherapy-Resistant Colorectal Cancer with a High Microsatellite Instability. ACS NANO 2024; 18:19332-19344. [PMID: 38990329 PMCID: PMC11271175 DOI: 10.1021/acsnano.4c05893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
The therapeutic response of microsatellite instability-high (MSI-H) colorectal cancer (CRC) to immune checkpoint inhibitors (ICI) is indeed surprising; however, the emergence of acquired resistance poses an even greater threat to the survival of these patients. Herein, bioinformatics analysis of MSI-H CRC samples revealed that Wnt signaling pathway represents a promising target for acquired immune reactivation, while subsequent analysis and biochemical testing substantiated the inclination of Wnt-hyperactive CRC cells to engage in macropinocytosis with human serum albumin (HSA). These findings have inspired us to develop an engineered HSA that not only possesses the ability to specifically target cancer cells but also effectively suppresses the Wnt/β-catenin cascade within these malignant cells. In pursuit of this objective, a comprehensive screening of reported Wnt small-molecule inhibitors was conducted to evaluate their affinity with HSA, and it was discovered that Carnosic acid (CA) exhibited the highest affinity while simultaneously revealing multiple binding sites. Further investigation revealed that CA HSA the capability to engineer HSA into spherical and size-tunable nanostructures known as eHSA (Engineering HSA particle), which demonstrated optimized macropinocytosis-dependent cellular internalization. As anticipated, eHSA effectively suppressed the Wnt signaling pathway and reactivated the acquired immune response in vivo. Furthermore, eHSA successfully restored sensitivity to Anti-PD1's anticancer effects in both subcutaneous and orthotopic mouse homograft models of MSI-H CRC, as well as a humanized hu-PBMC patient-derived orthotopic xenograft (PDOX) mouse model of MSI-H CRC, all while maintaining a favorable safety profile. The collective implementation of this clinically viable immune reactivation strategy not only enables the delivery of Wnt inhibitors for CRC therapy, but also serves as an exemplary demonstration of precision-medicine-guided nanopharmaceutical development that effectively harnesses specific cellular indications in pathological states.
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Affiliation(s)
- Wenguang Yang
- Department
of Medical Oncology and Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong
University, Xi'an 710061, PR. China
| | - Zhanfeng Li
- Department
of Medical Oncology and Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong
University, Xi'an 710061, PR. China
| | - Yong Li
- National
& Local Joint Engineering Research Center of Biodiagnosis and
Biotherapy, The Second Affiliated Hospital
of Xi'an Jiaotong University, Xi'an 710004, PR. China
| | - Wangxiao He
- Department
of Medical Oncology and Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong
University, Xi'an 710061, PR. China
| | - Jin Yan
- Department
of Medical Oncology and Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong
University, Xi'an 710061, PR. China
- National
& Local Joint Engineering Research Center of Biodiagnosis and
Biotherapy, The Second Affiliated Hospital
of Xi'an Jiaotong University, Xi'an 710004, PR. China
- Department
of Infectious Diseases, The Second Affiliated
Hospital of Xi'an Jiaotong University, Xi'an 710004, China
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9
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Xiao Y, Gao L, Zhao X, Zhao W, Mai L, Ma C, Han Y, Li X. Novel prognostic alternative splicing events in colorectal Cancer: Impact on immune infiltration and therapy response. Int Immunopharmacol 2024; 139:112603. [PMID: 39043103 DOI: 10.1016/j.intimp.2024.112603] [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: 01/15/2024] [Revised: 06/06/2024] [Accepted: 06/29/2024] [Indexed: 07/25/2024]
Abstract
OBJECTIVE This study aims to comprehensively analyze alternative splicing (AS) features in colorectal cancer (CRC) using integrative multi-omics and to elucidate their relationship with the CRC immune microenvironment. METHODS Transcriptomic data, clinical information, and Percent Spliced In (PSI) values of AS events for CRC patients were obtained from The Cancer Genome Atlas (TCGA) and TCGA SpliceSeq databases. Differentially expressed AS events were identified. Univariate Cox analysis was used to pinpoint prognosis-related AS events. A prognostic risk model was developed and validated using multivariate Cox analysis, patient survival analysis, and the area under the receiver operating characteristic (ROC) curve (AUC). Gene Set Enrichment Analysis (GSEA), immune infiltration, immunotherapy, chemotherapy sensitivity analyses, and regulatory relationships between AS events and splicing factors (SFs) were conducted. Single-cell sequencing was used to study the distribution of key factors. siRNA and overexpression vectors were utilized to silence/overexpress BCAS1 in CRC cells and evaluate their effects on cell growth, migration, and invasion. Furthermore, the interaction between BCAS1 and ANO7 pre-mRNA was investigated using RIP-PCR. RESULTS 82 prognosis-related AS events were identified in CRC patients. A 15-AS prognostic model was constructed, which correlated with immune cell infiltration and showed differences in immunotherapy and chemotherapy sensitivity. BCAS1 was identified as a potential regulator of the ANO7|58341|AT splicing event in CRC. Single-cell sequencing analysis revealed the distribution of BCAS1 and ANO7 in cancer stem cells. In vitro experiments demonstrated that overexpression of BCAS1 and silencing of ANO7 inhibit the proliferation, migration, and invasion of CRC cells. Moreover, BCAS1 suppresses the progression of CRC by modulating ANO7 alternative splicing. CONCLUSION This study provides new insights into the role of alternative splicing in colorectal cancer, particularly the potential regulatory action of BCAS1 on the ANO7|58341|AT splicing event. It also identifies the impact of alternative splicing on the tumor microenvironment and potential implications for immunotherapy, highlighting its relevance for the in-depth study and treatment of CRC.
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Affiliation(s)
- Yizhi Xiao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Liangqing Gao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Xiaojuan Zhao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Wang Zhao
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Lei Mai
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Chengmin Ma
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China
| | - Yanzhi Han
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China.
| | - Xiaofeng Li
- Department of Gastroenterology, Fifth Affiliated Hospital of Sun Yat-sen University, No. 52, Meihua East Road, Xiangzhou District, Zhuhai 519000, Guangdong Province, China.
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10
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Li K, Wang R, Liu GW, Peng ZY, Wang JC, Xiao GD, Tang SC, Du N, Zhang J, Zhang J, Ren H, Sun X, Yang YP, Liu DP. Refining the optimal CAF cluster marker for predicting TME-dependent survival expectancy and treatment benefits in NSCLC patients. Sci Rep 2024; 14:16766. [PMID: 39034310 PMCID: PMC11271481 DOI: 10.1038/s41598-024-55375-0] [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: 07/11/2023] [Accepted: 02/22/2024] [Indexed: 07/23/2024] Open
Abstract
The tumor microenvironment (TME) plays a pivotal role in the onset, progression, and treatment response of cancer. Among the various components of the TME, cancer-associated fibroblasts (CAFs) are key regulators of both immune and non-immune cellular functions. Leveraging single-cell RNA sequencing (scRNA) data, we have uncovered previously hidden and promising roles within this specific CAF subgroup, paving the way for its clinical application. However, several critical questions persist, primarily stemming from the heterogeneous nature of CAFs and the use of different fibroblast markers in various sample analyses, causing confusion and hindrance in their clinical implementation. In this groundbreaking study, we have systematically screened multiple databases to identify the most robust marker for distinguishing CAFs in lung cancer, with a particular focus on their potential use in early diagnosis, staging, and treatment response evaluation. Our investigation revealed that COL1A1, COL1A2, FAP, and PDGFRA are effective markers for characterizing CAF subgroups in most lung adenocarcinoma datasets. Through comprehensive analysis of treatment responses, we determined that COL1A1 stands out as the most effective indicator among all CAF markers. COL1A1 not only deciphers the TME signatures related to CAFs but also demonstrates a highly sensitive and specific correlation with treatment responses and multiple survival outcomes. For the first time, we have unveiled the distinct roles played by clusters of CAF markers in differentiating various TME groups. Our findings confirm the sensitive and unique contributions of CAFs to the responses of multiple lung cancer therapies. These insights significantly enhance our understanding of TME functions and drive the translational application of extensive scRNA sequence results. COL1A1 emerges as the most sensitive and specific marker for defining CAF subgroups in scRNA analysis. The CAF ratios represented by COL1A1 can potentially serve as a reliable predictor of treatment responses in clinical practice, thus providing valuable insights into the influential roles of TME components. This research marks a crucial step forward in revolutionizing our approach to cancer diagnosis and treatment.
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Affiliation(s)
- Kai Li
- Department of Otorhinolaryngology‑Head and Neck Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Rui Wang
- Department of Thoracic Surgery and Oncology, Cancer Centre, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Guo-Wei Liu
- Department of Thoracic Surgery, Qinghai Provincial People's Hospital, Gonghe Road No. 2, Chengdong District, Xining, 810007, Qinghai, China
| | - Zi-Yang Peng
- School of Future Technology, National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Ji-Chang Wang
- Department of Vascular Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Guo-Dong Xiao
- Oncology Department, The First Affiliated Hospital of Zhengzhou University, Zheng Zhou, 450052, Henan, China
| | - Shou-Ching Tang
- Section of Hematology Oncology, Department of Internal Medicine, LSUHSC Cancer Center, School of Medicine, 1700 Tulane Avenue, New Orleans, LA, 70112, USA
| | - Ning Du
- Department of Thoracic Surgery and Oncology, Cancer Centre, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Jia Zhang
- Department of Thoracic Surgery and Oncology, Cancer Centre, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Jing Zhang
- Department of Thoracic Surgery and Oncology, Cancer Centre, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Hong Ren
- Department of Thoracic Surgery and Oncology, Cancer Centre, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Xin Sun
- Department of Thoracic Surgery and Oncology, Cancer Centre, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, Shaanxi, China
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Yi-Ping Yang
- Department of Radiotherapy, Shaanxi Provincial Tumor Hospital, 309 Yanta W Rd, Yanta District, Xi'an, 710063, Shaanxi, China.
| | - Da-Peng Liu
- Department of Thoracic Surgery and Oncology, Cancer Centre, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, Shaanxi, China.
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11
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Nafisi S, Støer NC, Veierød MB, Randel KR, Hoff G, Löfling L, Bosetti C, Botteri E. Low-Dose Aspirin and Prevention of Colorectal Cancer: Evidence From a Nationwide Registry-Based Cohort in Norway. Am J Gastroenterol 2024; 119:1402-1411. [PMID: 38300127 PMCID: PMC11208058 DOI: 10.14309/ajg.0000000000002695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/24/2024] [Indexed: 02/02/2024]
Abstract
INTRODUCTION To examine the association between low-dose aspirin use and risk of colorectal cancer (CRC). METHODS In this nationwide cohort study, we identified individuals aged 50 years or older residing for 6 months or more in Norway in 2004-2018 and obtained data from national registers on drug prescriptions, cancer occurrence, and sociodemographic factors. Multivariable Cox regression models were used to estimate the association between low-dose aspirin use and CRC risk. In addition, we calculated the number of CRC potentially averted by low-dose aspirin use. RESULTS We included 2,186,390 individuals. During the median follow-up of 10.9 years, 579,196 (26.5%) used low-dose aspirin, and 38,577 (1.8%) were diagnosed with CRC. Current use of aspirin vs never use was associated with lower CRC risk (hazard ratio [HR] 0.87, 95% confidence interval [CI] 0.84-0.90). The association was more pronounced for metastatic CRC (HR 0.79; 95% CI 0.74-0.84) than regionally advanced (HR 0.89; 95% CI 0.85-0.92) and localized CRC (HR 0.93; 95% CI 0.87-1.00; P heterogeneity = 0.001). A significant trend was found between duration of current use and CRC risk: HR 0.91 (95% CI 0.86-0.95) for <3 years, HR 0.85 (0.80-0.91) for ≥3 and <5 years, and HR 0.84 (0.80-0.88) for ≥5 years of use vs never use ( P trend < 0.001). For past use, HR were 0.89 (95% CI 0.84-0.94) for <3 years, 0.90 (0.83-0.99) for ≥3 and <5 years, and 0.98 (0.91-1.06) for ≥5 years since last use vs never use ( P -trend < 0.001). We estimated that aspirin use averted 1,073 cases of CRC (95% CI 818-1,338) in the study period. DISCUSSION In this nationwide cohort, use of low-dose aspirin was associated with a lower risk of CRC.
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Affiliation(s)
- Sara Nafisi
- Department of Research, Cancer Registry of Norway, National Institute of Public Health, Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Nathalie C. Støer
- Department of Research, Cancer Registry of Norway, National Institute of Public Health, Oslo, Norway
| | - Marit B. Veierød
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Kristin R. Randel
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, National Institute of Public Health, Oslo, Norway
| | - Geir Hoff
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, National Institute of Public Health, Oslo, Norway
- Department of Research and Development, Telemark Hospital Trust, Skien, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lukas Löfling
- Department of Research, Cancer Registry of Norway, National Institute of Public Health, Oslo, Norway
| | - Cristina Bosetti
- Department of Medical Epidemiology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Edoardo Botteri
- Department of Research, Cancer Registry of Norway, National Institute of Public Health, Oslo, Norway
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, National Institute of Public Health, Oslo, Norway
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12
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Cho CJ, Brown JW, Mills JC. Origins of cancer: ain't it just mature cells misbehaving? EMBO J 2024; 43:2530-2551. [PMID: 38773319 PMCID: PMC11217308 DOI: 10.1038/s44318-024-00099-0] [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: 08/26/2023] [Revised: 03/15/2024] [Accepted: 03/22/2024] [Indexed: 05/23/2024] Open
Abstract
A pervasive view is that undifferentiated stem cells are alone responsible for generating all other cells and are the origins of cancer. However, emerging evidence demonstrates fully differentiated cells are plastic, can be coaxed to proliferate, and also play essential roles in tissue maintenance, regeneration, and tumorigenesis. Here, we review the mechanisms governing how differentiated cells become cancer cells. First, we examine the unique characteristics of differentiated cell division, focusing on why differentiated cells are more susceptible than stem cells to accumulating mutations. Next, we investigate why the evolution of multicellularity in animals likely required plastic differentiated cells that maintain the capacity to return to the cell cycle and required the tumor suppressor p53. Finally, we examine an example of an evolutionarily conserved program for the plasticity of differentiated cells, paligenosis, which helps explain the origins of cancers that arise in adults. Altogether, we highlight new perspectives for understanding the development of cancer and new strategies for preventing carcinogenic cellular transformations from occurring.
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Affiliation(s)
- Charles J Cho
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey W Brown
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Jason C Mills
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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13
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Tardito S, Matis S, Zocchi MR, Benelli R, Poggi A. Epidermal Growth Factor Receptor Targeting in Colorectal Carcinoma: Antibodies and Patient-Derived Organoids as a Smart Model to Study Therapy Resistance. Int J Mol Sci 2024; 25:7131. [PMID: 39000238 PMCID: PMC11241078 DOI: 10.3390/ijms25137131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer-related death worldwide. Therefore, the need for new therapeutic strategies is still a challenge. Surgery and chemotherapy represent the first-line interventions; nevertheless, the prognosis for metastatic CRC (mCRC) patients remains unacceptable. An important step towards targeted therapy came from the inhibition of the epidermal growth factor receptor (EGFR) pathway, by the anti-EGFR antibody, Cetuximab, or by specific tyrosine kinase inhibitors (TKI). Cetuximab, a mouse-human chimeric monoclonal antibody (mAb), binds to the extracellular domain of EGFR thus impairing EGFR-mediated signaling and reducing cell proliferation. TKI can affect the EGFR biochemical pathway at different steps along the signaling cascade. Apart from Cetuximab, other anti-EGFR mAbs have been developed, such as Panitumumab. Both antibodies have been approved for the treatment of KRAS-NRAS wild type mCRC, alone or in combination with chemotherapy. These antibodies display strong differences in activating the host immune system against CRC, due to their different immunoglobulin isotypes. Although anti-EGFR antibodies are efficient, drug resistance occurs with high frequency. Resistant tumor cell populations can either already be present before therapy or develop later by biochemical adaptations or new genomic mutations in the EGFR pathway. Numerous efforts have been made to improve the efficacy of the anti-EGFR mAbs or to find new agents that are able to block downstream EGFR signaling cascade molecules. Indeed, we examined the importance of analyzing the anti-EGFR antibody-drug conjugates (ADC) developed to overcome resistance and/or stimulate the tumor host's immunity against CRC growth. Also, patient-derived CRC organoid cultures represent a useful and feasible in vitro model to study tumor behavior and therapy response. Organoids can reflect tumor genetic heterogeneity found in the tissue of origin, representing a unique tool for personalized medicine. Thus, CRC-derived organoid cultures are a smart model for studying the tumor microenvironment and for the preclinical assay of anti-EGFR drugs.
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Affiliation(s)
- Samuele Tardito
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC 20010, USA;
| | - Serena Matis
- Molecular Oncology and Angiogenesis Unit, IRRCS Ospedale Policlinico San Martino, 16132 Genoa, Italy;
| | - Maria Raffaella Zocchi
- Department of Immunology, Transplant and Infectious Diseases, IRCCS Scientific Institute San Raffaele, 20132 Milan, Italy;
| | - Roberto Benelli
- Molecular Oncology and Angiogenesis Unit, IRRCS Ospedale Policlinico San Martino, 16132 Genoa, Italy;
| | - Alessandro Poggi
- Molecular Oncology and Angiogenesis Unit, IRRCS Ospedale Policlinico San Martino, 16132 Genoa, Italy;
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14
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Fey SK, Vaquero-Siguero N, Jackstadt R. Dark force rising: Reawakening and targeting of fetal-like stem cells in colorectal cancer. Cell Rep 2024; 43:114270. [PMID: 38787726 DOI: 10.1016/j.celrep.2024.114270] [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: 02/20/2024] [Revised: 04/14/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Stem cells play pivotal roles in maintaining intestinal homeostasis, orchestrating regeneration, and in key steps of colorectal cancer (CRC) initiation and progression. Intriguingly, adult stem cells are reduced during many of these processes. On the contrary, primitive fetal programs, commonly detected in development, emerge during tissue repair, CRC metastasis, and therapy resistance. Recent findings indicate a dynamic continuum between adult and fetal stem cell programs. We discuss critical mechanisms facilitating the plasticity between stem cell states and highlight the heterogeneity observed upon the appearance of fetal-like states. We focus on therapeutic opportunities that arise by targeting fetal-like CRC cells and how those concepts can be translated into the clinic.
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Affiliation(s)
- Sigrid K Fey
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Nuria Vaquero-Siguero
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Rene Jackstadt
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), DKFZ, Core Center Heidelberg, 69120 Heidelberg, Germany.
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15
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Zhang S, Xiao X, Yi Y, Wang X, Zhu L, Shen Y, Lin D, Wu C. Tumor initiation and early tumorigenesis: molecular mechanisms and interventional targets. Signal Transduct Target Ther 2024; 9:149. [PMID: 38890350 PMCID: PMC11189549 DOI: 10.1038/s41392-024-01848-7] [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: 01/01/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 06/20/2024] Open
Abstract
Tumorigenesis is a multistep process, with oncogenic mutations in a normal cell conferring clonal advantage as the initial event. However, despite pervasive somatic mutations and clonal expansion in normal tissues, their transformation into cancer remains a rare event, indicating the presence of additional driver events for progression to an irreversible, highly heterogeneous, and invasive lesion. Recently, researchers are emphasizing the mechanisms of environmental tumor risk factors and epigenetic alterations that are profoundly influencing early clonal expansion and malignant evolution, independently of inducing mutations. Additionally, clonal evolution in tumorigenesis reflects a multifaceted interplay between cell-intrinsic identities and various cell-extrinsic factors that exert selective pressures to either restrain uncontrolled proliferation or allow specific clones to progress into tumors. However, the mechanisms by which driver events induce both intrinsic cellular competency and remodel environmental stress to facilitate malignant transformation are not fully understood. In this review, we summarize the genetic, epigenetic, and external driver events, and their effects on the co-evolution of the transformed cells and their ecosystem during tumor initiation and early malignant evolution. A deeper understanding of the earliest molecular events holds promise for translational applications, predicting individuals at high-risk of tumor and developing strategies to intercept malignant transformation.
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Affiliation(s)
- Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyi Xiao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yonglin Yi
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyu Wang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Lingxuan Zhu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Changping Laboratory, 100021, Beijing, China
| | - Yanrong Shen
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, 510060, China.
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- CAMS Oxford Institute, Chinese Academy of Medical Sciences, 100006, Beijing, China.
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16
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Xiong J, Kaur H, Heiser CN, McKinley ET, Roland JT, Coffey RJ, Shrubsole MJ, Wrobel J, Ma S, Lau KS, Vandekar S. GammaGateR: semi-automated marker gating for single-cell multiplexed imaging. Bioinformatics 2024; 40:btae356. [PMID: 38833684 PMCID: PMC11193056 DOI: 10.1093/bioinformatics/btae356] [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: 09/07/2023] [Revised: 04/20/2024] [Accepted: 06/03/2024] [Indexed: 06/06/2024] Open
Abstract
MOTIVATION Multiplexed immunofluorescence (mIF) is an emerging assay for multichannel protein imaging that can decipher cell-level spatial features in tissues. However, existing automated cell phenotyping methods, such as clustering, face challenges in achieving consistency across experiments and often require subjective evaluation. As a result, mIF analyses often revert to marker gating based on manual thresholding of raw imaging data. RESULTS To address the need for an evaluable semi-automated algorithm, we developed GammaGateR, an R package for interactive marker gating designed specifically for segmented cell-level data from mIF images. Based on a novel closed-form gamma mixture model, GammaGateR provides estimates of marker-positive cell proportions and soft clustering of marker-positive cells. The model incorporates user-specified constraints that provide a consistent but slide-specific model fit. We compared GammaGateR against the newest unsupervised approach for annotating mIF data, employing two colon datasets and one ovarian cancer dataset for the evaluation. We showed that GammaGateR produces highly similar results to a silver standard established through manual annotation. Furthermore, we demonstrated its effectiveness in identifying biological signals, achieved by mapping known spatial interactions between CD68 and MUC5AC cells in the colon and by accurately predicting survival in ovarian cancer patients using the phenotype probabilities as input for machine learning methods. GammaGateR is a highly efficient tool that can improve the replicability of marker gating results, while reducing the time of manual segmentation. AVAILABILITY AND IMPLEMENTATION The R package is available at https://github.com/JiangmeiRubyXiong/GammaGateR.
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Affiliation(s)
- Jiangmei Xiong
- Department of Biostatistics, Vanderbilt University, 2525 West End Avenue, Suite 1100, Nashville, TN 37203-1741, United States
| | - Harsimran Kaur
- Program of Chemical and Physical Biology, Vanderbilt University School of Medicine, 340 Light Hall, 2215 Garland Ave, Nashville, TN 37232, United States
- Epithelial Biology Center, Vanderbilt University Medical Center, MRBIV 10415-E, 2213 Garland Avenue, Nashville, TN 37232, United States
| | - Cody N Heiser
- Program of Chemical and Physical Biology, Vanderbilt University School of Medicine, 340 Light Hall, 2215 Garland Ave, Nashville, TN 37232, United States
- Epithelial Biology Center, Vanderbilt University Medical Center, MRBIV 10415-E, 2213 Garland Avenue, Nashville, TN 37232, United States
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Road, Tarrytown, NY 10591, United States
| | - Eliot T McKinley
- Epithelial Biology Center, Vanderbilt University Medical Center, MRBIV 10415-E, 2213 Garland Avenue, Nashville, TN 37232, United States
- GlaxoSmithKline, 410 Blackwell St, Durham, NC 27701, United States
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, MRBIV 10415-E, 2213 Garland Avenue, Nashville, TN 37232, United States
- Department of Surgery, Vanderbilt University Medical Center, 2215 Garland Ave Medical Research Building IV, Nashville, TN 37232, United States
| | - Robert J Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, MRBIV 10415-E, 2213 Garland Avenue, Nashville, TN 37232, United States
- Department of Medicine, Vanderbilt University Medical Center, 1161 21st Ave S, Nashville, TN 37232, United States
| | - Martha J Shrubsole
- Department of Medicine, Vanderbilt University Medical Center, 1161 21st Ave S, Nashville, TN 37232, United States
| | - Julia Wrobel
- Department of Biostatistics and Bioinformatics, Emory University, 1518 Clifton Rd, Atlanta, GA 30322, United States
| | - Siyuan Ma
- Department of Biostatistics, Vanderbilt University, 2525 West End Avenue, Suite 1100, Nashville, TN 37203-1741, United States
| | - Ken S Lau
- Program of Chemical and Physical Biology, Vanderbilt University School of Medicine, 340 Light Hall, 2215 Garland Ave, Nashville, TN 37232, United States
- Epithelial Biology Center, Vanderbilt University Medical Center, MRBIV 10415-E, 2213 Garland Avenue, Nashville, TN 37232, United States
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Road, Tarrytown, NY 10591, United States
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 10475 Medical Research Building IV, 2215 Garland Avenue, Nashville, TN 37232, United States
| | - Simon Vandekar
- Department of Biostatistics, Vanderbilt University, 2525 West End Avenue, Suite 1100, Nashville, TN 37203-1741, United States
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Jia Y, Feng G, Chen S, Li W, Jia Z, Wang J, Li H, Hong S, Dai F. Metabolic Heterogeneity of Tumor Cells and its Impact on Colon Cancer Metastasis: Insights from Single-Cell and Bulk Transcriptome Analyses. J Cancer 2024; 15:4175-4196. [PMID: 38947396 PMCID: PMC11212087 DOI: 10.7150/jca.94630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/17/2024] [Indexed: 07/02/2024] Open
Abstract
Background: Metabolic reprogramming plays a crucial role in the development of colorectal cancer (CRC), influencing tumor heterogeneity, the tumor microenvironment, and metastasis. While the interaction between metabolism and CRC is critical for developing personalized treatments, gaps remain in understanding how tumor cell metabolism affects prognosis. Our study introduces novel insights by integrating single-cell and bulk transcriptome analyses to explore the metabolic landscape within CRC cells and its mechanisms influencing disease progression. This approach allows us to uncover metabolic heterogeneity and identify specific metabolic genes impacting metastasis, which have not been thoroughly examined in previous studies. Methods: We sourced microarray and single-cell RNA sequencing datasets from the Gene Expression Omnibus (GEO) and bulk sequencing data for CRC from The Cancer Genome Atlas (TCGA). We employed Gene Set Variation Analysis (GSVA) to assess metabolic pathway activity, consensus clustering to identify CRC-specific transcriptome subtypes in bulkseq, and rigorous quality controls, including the exclusion of cells with high mitochondrial gene expression in scRNA seq. Advanced analyses such as AUCcell, infercnvCNV, Non-negative Matrix Factorization (NMF), and CytoTRACE were utilized to dissect the cellular landscape and evaluate pathway activities and tumor cell stemness. The hdWGCNA algorithm helped identify prognosis-related hub genes, integrating these findings using a random forest machine learning model. Results: Kaplan-Meier survival curves identified 21 significant metabolic pathways linked to prognosis, with consensus clustering defining three CRC subtypes (C3, C2, C1) based on metabolic activity, which correlated with distinct clinical outcomes. The metabolic activity of the 13 cell subpopulations, particularly the epithelial cell subpopulation with active metabolic levels, was evaluated using AUCcell in scRNA seq. To further analyze tumor cells using infercnv, NMF disaggregated these cells into 10 cellular subpopulations. Among these, the C2 subpopulation exhibited higher stemness and tended to have a poorer prognosis compared to C6 and C0. Conversely, the C8, C3, and C1 subpopulations demonstrated a higher level of the five metabolic pathways, and the C3 and C8 subpopulations tended to have a more favorable prognosis. hdWGCNA identified 20 modules, from which we selected modules primarily expressed in high metabolic tumor subgroups and highly correlated with clinical information, including blue and cyan. By applying variable downscaling of RF to a total of 50 hub genes, seven gene signatures were obtained. Furthermore, molecules that were validated to be protective in GEO were screened alongside related molecules, resulting in the identification of prognostically relevant molecules such as UQCRFS1 and GRSF1. Additionally, the expression of GRSF1 was examined in colon cancer cell lines using qPCR and phenotypically verified by in vitro experiments. Conclusion: Our findings emphasize that high activity in specific metabolic pathways, including pyruvate metabolism and the tricarboxylic acid cycle, correlates with improved colon cancer outcomes, presenting new avenues for metabolic-based therapies. The identification of hub genes like GRSF1 and UQCRFS1 and their link to favorable metabolic profiles offers novel insights into tumor neovascularization and metastasis, with significant clinical implications for targeting metabolic pathways in CRC therapy.
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Affiliation(s)
- Yiwen Jia
- Department of Gastroenterology, The Third Affiliated Hospital of Anhui Medical University (Hefei first people's Hospital), Hefei, China
| | - Guangming Feng
- Department of Gastroenterology, The Third Affiliated Hospital of Anhui Medical University (Hefei first people's Hospital), Hefei, China
| | - Siyuan Chen
- Department of Gastroenterology, The Third Affiliated Hospital of Anhui Medical University (Hefei first people's Hospital), Hefei, China
| | - Wenhao Li
- Department of Pulmonology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Zeguo Jia
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Jian Wang
- Department of Pathology, The Third Affiliated Hospital of Anhui Medical University (Hefei first people's Hospital), Hefei, 230032, China
| | - Hongxia Li
- Department of Oncology, The Third Affiliated Hospital of Anhui Medical University (Hefei first people's Hospital), Hefei, 230032, China
| | - Shaocheng Hong
- Department of Gastroenterology, The Third Affiliated Hospital of Anhui Medical University (Hefei first people's Hospital), Hefei, China
| | - Fu Dai
- Department of Gastroenterology, The Third Affiliated Hospital of Anhui Medical University (Hefei first people's Hospital), Hefei, China
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18
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LaBella KA, Hsu WH, Li J, Qi Y, Liu Y, Liu J, Wu CC, Liu Y, Song Z, Lin Y, Blecher JM, Jiang S, Shang X, Han J, Spring DJ, Zhang J, Xia Y, DePinho RA. Telomere dysfunction alters intestinal stem cell dynamics to promote cancer. Dev Cell 2024; 59:1475-1486.e5. [PMID: 38574731 DOI: 10.1016/j.devcel.2024.03.020] [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: 11/26/2023] [Revised: 01/22/2024] [Accepted: 03/11/2024] [Indexed: 04/06/2024]
Abstract
Telomere dynamics are linked to aging hallmarks, and age-associated telomere loss fuels the development of epithelial cancers. In Apc-mutant mice, the onset of DNA damage associated with telomere dysfunction has been shown to accelerate adenoma initiation via unknown mechanisms. Here, we observed that Apc-mutant mice engineered to experience telomere dysfunction show accelerated adenoma formation resulting from augmented cell competition and clonal expansion. Mechanistically, telomere dysfunction induces the repression of EZH2, resulting in the derepression of Wnt antagonists, which causes the differentiation of adjacent stem cells and a relative growth advantage to Apc-deficient telomere dysfunctional cells. Correspondingly, in this mouse model, GSK3β inhibition countered the actions of Wnt antagonists on intestinal stem cells, resulting in impaired adenoma formation of telomere dysfunctional Apc-mutant cells. Thus, telomere dysfunction contributes to cancer initiation through altered stem cell dynamics, identifying an interception strategy for human APC-mutant cancers with shortened telomeres.
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Affiliation(s)
- Kyle A LaBella
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wen-Hao Hsu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiexi Li
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yutao Qi
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yonghong Liu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jingjing Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chia-Chin Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yang Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yiyun Lin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jonathan M Blecher
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shan Jiang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaoying Shang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jincheng Han
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Denise J Spring
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yan Xia
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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19
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Liu S, Liu M, Li Y, Song Q. N6-methyladenosine-dependent signaling in colorectal cancer: Functions and clinical potential. Crit Rev Oncol Hematol 2024; 198:104360. [PMID: 38615872 DOI: 10.1016/j.critrevonc.2024.104360] [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: 10/30/2023] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024] Open
Abstract
Colorectal cancer (CRC) ranks as the third most prevalent malignancy worldwide. Despite the gradual expansion of therapeutic options for CRC, its clinical management remains a formidable challenge. And, because of the current dearth of technical means for early CRC screening, most patients are diagnosed at an advanced stage. Therefore, it is imperative to develop novel diagnostic and therapeutic tools for this disease. N6-methyladenosine (m6A), the predominant RNA modification in eukaryotes, can be recognized by m6A-specific methylated reading proteins to modulate gene expression. Studies have revealed that CRC disrupts m6A homeostasis through various mechanisms, thereby sustaining aberrant signal transduction and promoting its own progression. Consequently, m6A-based diagnostic and therapeutic strategies have garnered widespread attention. Although utilizing m6A as a biomarker and drug target has demonstrated promising feasibility, existing observations primarily stem from preclinical models; henceforth necessitating further investigation and resolution of numerous outstanding issues.
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Affiliation(s)
- Shaojun Liu
- Department of Oncology, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese medicine, Suzhou, Jiangsu, China
| | - Min Liu
- Department of Oncology, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese medicine, Suzhou, Jiangsu, China
| | - Yuxuan Li
- Department of Oncology, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese medicine, Suzhou, Jiangsu, China
| | - Qing Song
- Department of Oncology, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese medicine, Suzhou, Jiangsu, China.
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20
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Kalla J, Pfneissl J, Mair T, Tran L, Egger G. A systematic review on the culture methods and applications of 3D tumoroids for cancer research and personalized medicine. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00960-8. [PMID: 38806997 DOI: 10.1007/s13402-024-00960-8] [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] [Accepted: 05/11/2024] [Indexed: 05/30/2024] Open
Abstract
Cancer is a highly heterogeneous disease, and thus treatment responses vary greatly between patients. To improve therapy efficacy and outcome for cancer patients, more representative and patient-specific preclinical models are needed. Organoids and tumoroids are 3D cell culture models that typically retain the genetic and epigenetic characteristics, as well as the morphology, of their tissue of origin. Thus, they can be used to understand the underlying mechanisms of cancer initiation, progression, and metastasis in a more physiological setting. Additionally, co-culture methods of tumoroids and cancer-associated cells can help to understand the interplay between a tumor and its tumor microenvironment. In recent years, tumoroids have already helped to refine treatments and to identify new targets for cancer therapy. Advanced culturing systems such as chip-based fluidic devices and bioprinting methods in combination with tumoroids have been used for high-throughput applications for personalized medicine. Even though organoid and tumoroid models are complex in vitro systems, validation of results in vivo is still the common practice. Here, we describe how both animal- and human-derived tumoroids have helped to identify novel vulnerabilities for cancer treatment in recent years, and how they are currently used for precision medicine.
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Affiliation(s)
- Jessica Kalla
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Janette Pfneissl
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Theresia Mair
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Loan Tran
- Department of Pathology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria
| | - Gerda Egger
- Department of Pathology, Medical University of Vienna, Vienna, Austria.
- Ludwig Boltzmann Institute Applied Diagnostics, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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21
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Zhu Y, Koleilat MKI, Roszik J, Kwong MK, Wang Z, Maru DM, Kopetz S, Kwong LN. A Gold Standard-Derived Modular Barcoding Approach to Cancer Transcriptomics. Cancers (Basel) 2024; 16:1886. [PMID: 38791964 PMCID: PMC11120226 DOI: 10.3390/cancers16101886] [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: 03/01/2024] [Revised: 04/22/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
A challenge with studying cancer transcriptomes is in distilling the wealth of information down into manageable portions of information. In this resource, we develop an approach that creates and assembles cancer type-specific gene expression modules into flexible barcodes, allowing for adaptation to a wide variety of uses. Specifically, we propose that modules derived organically from high-quality gold standards such as The Cancer Genome Atlas (TCGA) can accurately capture and describe functionally related genes that are relevant to specific cancer types. We show that such modules can: (1) uncover novel gene relationships and nominate new functional memberships, (2) improve and speed up analysis of smaller or lower-resolution datasets, (3) re-create and expand known cancer subtyping schemes, (4) act as a "decoder" to bridge seemingly disparate established gene signatures, and (5) efficiently apply single-cell RNA sequencing information to other datasets. Moreover, such modules can be used in conjunction with native spreadsheet program commands to create a powerful and rapid approach to hypothesis generation and testing that is readily accessible to non-bioinformaticians. Finally, we provide tools for users to create and interpret their own modules. Overall, the flexible modular nature of the proposed barcoding provides a user-friendly approach to rapidly decoding transcriptome-wide data for research or, potentially, clinical uses.
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Affiliation(s)
- Yan Zhu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
| | - Mohamad Karim I. Koleilat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Man Kam Kwong
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China;
| | - Zhonglin Wang
- Social Science Research Institute, Duke University, Durham, NC 27708, USA;
| | - Dipen M. Maru
- Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Lawrence N. Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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22
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Loh JJ, Ma S. Hallmarks of cancer stemness. Cell Stem Cell 2024; 31:617-639. [PMID: 38701757 DOI: 10.1016/j.stem.2024.04.004] [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: 12/31/2023] [Revised: 03/11/2024] [Accepted: 04/03/2024] [Indexed: 05/05/2024]
Abstract
Cancer stemness is recognized as a key component of tumor development. Previously coined "cancer stem cells" (CSCs) and believed to be a rare population with rigid hierarchical organization, there is good evidence to suggest that these cells exhibit a plastic cellular state influenced by dynamic CSC-niche interplay. This revelation underscores the need to reevaluate the hallmarks of cancer stemness. Herein, we summarize the techniques used to identify and characterize the state of these cells and discuss their defining and emerging hallmarks, along with their enabling and associated features. We also highlight potential future directions in this field of research.
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Affiliation(s)
- Jia-Jian Loh
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Stephanie Ma
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong SAR, China; Laboratory of Synthetic Chemistry and Chemical Biology, Hong Kong Science and Technology Park, Hong Kong SAR, China; Centre for Translational and Stem Cell Biology, Hong Kong Science and Technology Park, Hong Kong SAR, China.
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23
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An M, Mehta A, Min BH, Heo YJ, Wright SJ, Parikh M, Bi L, Lee H, Kim TJ, Lee SY, Moon J, Park RJ, Strickland MR, Park WY, Kang WK, Kim KM, Kim ST, Klempner SJ, Lee J. Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer. Cancer Discov 2024; 14:766-785. [PMID: 38319303 PMCID: PMC11061611 DOI: 10.1158/2159-8290.cd-23-0857] [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: 08/01/2023] [Revised: 11/28/2023] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Adding anti-programmed cell death protein 1 (anti-PD-1) to 5-fluorouracil (5-FU)/platinum improves survival in some advanced gastroesophageal adenocarcinomas (GEA). To understand the effects of chemotherapy and immunotherapy, we conducted a phase II first-line trial (n = 47) sequentially adding pembrolizumab to 5-FU/platinum in advanced GEA. Using serial biopsy of the primary tumor at baseline, after one cycle of 5-FU/platinum, and after the addition of pembrolizumab, we transcriptionally profiled 358,067 single cells to identify evolving multicellular tumor microenvironment (TME) networks. Chemotherapy induced early on-treatment multicellular hubs with tumor-reactive T-cell and M1-like macrophage interactions in slow progressors. Faster progression featured increased MUC5A and MSLN containing treatment resistance programs in tumor cells and M2-like macrophages with immunosuppressive stromal interactions. After pembrolizumab, we observed increased CD8 T-cell infiltration and development of an immunity hub involving tumor-reactive CXCL13 T-cell program and epithelial interferon-stimulated gene programs. Strategies to drive increases in antitumor immune hub formation could expand the portion of patients benefiting from anti-PD-1 approaches. SIGNIFICANCE The benefit of 5-FU/platinum with anti-PD-1 in first-line advanced gastric cancer is limited to patient subgroups. Using a trial with sequential anti-PD-1, we show coordinated induction of multicellular TME hubs informs the ability of anti-PD-1 to potentiate T cell-driven responses. Differential TME hub development highlights features that underlie clinical outcomes. This article is featured in Selected Articles from This Issue, p. 695.
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Affiliation(s)
- Minae An
- Experimental Therapeutics Development Center, Samsung Medical Center, Seoul, Korea
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Arnav Mehta
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Byung Hoon Min
- Department of Medicine, Division of Gastroenterology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Samuel J. Wright
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Milan Parikh
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Lynn Bi
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Hyuk Lee
- Department of Medicine, Division of Gastroenterology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae Jun Kim
- Department of Medicine, Division of Gastroenterology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Song-Yi Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeonghyeon Moon
- Departments of Neurology and Immunology, Yale School of Medicine, New Haven, Connecticut
| | - Ryan J. Park
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Division of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Matthew R. Strickland
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | | | - Won Ki Kang
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Samuel J. Klempner
- Department of Medicine, Division of Hematology-Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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24
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Zheng J, Jin H, Tu Y. Differences in circulating lymphocyte subpopulations among patients with inflammatory polyps, colorectal adenomas and colorectal cancer. Arab J Gastroenterol 2024; 25:129-134. [PMID: 38413325 DOI: 10.1016/j.ajg.2023.12.013] [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: 06/16/2022] [Revised: 09/06/2023] [Accepted: 12/31/2023] [Indexed: 02/29/2024]
Abstract
BACKGROUND AND STUDY AIMS Colorectal cancer (CRC) may develop from focal changes within benign or precancerous polyps. The immune system's failure to detect and eradicate tumor cells due to immune surveillance evasion, allows cancer to develop and spread. This study aims to analyze the differences in circulating lymphocyte subpopulations in patients with colorectal inflammatory polyps, colorectal adenomas and CRC. PATIENTS AND METHODS We retrospectively reviewed patients from September 2016 to December 2019 at the Shaoxing Second Hospital. Using flow cytometry, the subset distribution and immunophenotype of T cells, CD4+ T cells, CD8+ T cells, B cells and NK cells were investigated in peripheral blood mononuclear cell samples. The counts of lymphocytes were determined by white blood cell counts. RESULTS In total, 518 patients were included in this study. The counts of lymphocytes, T cells and NK cells in patients with inflammatory polyps, colorectal adenomas and CRC were lower than controls. The counts and percentages of CD8+ T cells in patients with inflammatory polyps, colorectal adenomas and CRC were lower than controls. The counts of CD4+ T cells were lower in patients with CRC than inflammatory polyps. The percentages of CD4+ T cells in patients with inflammatory polyps, colorectal adenomas and CRC were higher than controls, but lower in the CRC than inflammatory polyps, colorectal adenomas. The counts and percentages of B cells were lower in CRC patients than colorectal adenomas patients. In addition, the percentages of B cells were higher in patients with inflammatory polyps and colorectal adenomas than in controls. CONCLUSIONS The decrease in counts of lymphocyte, T cells, CD8+ T cells and NK cells in patients may be related to the dysplasia of epithelial cells. Furthermore, the B cells and CD4+ T cells may be related to the malignant growth of the dysplastic epithelial cells.
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Affiliation(s)
- Jialai Zheng
- Departments of Molecular Medicine, Shaoxing Second Hospital, Shaoxing, Zhejiang, China.
| | - Haiyong Jin
- Departments of Laboratory Medicine, Shaoxing Second Hospital, Shaoxing, Zhejiang, China
| | - Yongtao Tu
- Departments of Molecular Medicine, Shaoxing Second Hospital, Shaoxing, Zhejiang, China
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25
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Higa T, Nakayama KI. Cell cycle heterogeneity and plasticity of colorectal cancer stem cells. Cancer Sci 2024; 115:1370-1377. [PMID: 38413370 PMCID: PMC11093209 DOI: 10.1111/cas.16117] [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: 11/26/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 02/29/2024] Open
Abstract
Cancer stem cells (CSCs) are a long-lived and self-renewing cancer cell population that drives tumor propagation and maintains cancer heterogeneity. They are also implicated in the therapeutic resistance of various types of cancer. Recent studies of CSCs in colorectal cancer (CRC) have uncovered fundamental paradigms that have increased understanding of CSC systems in solid tumors. Colorectal CSCs share multiple biological properties with normal intestinal stem cells (ISCs), including expression of the stem cell marker Lgr5. New evidence suggests that colorectal CSCs manifest substantial heterogeneity, as exemplified by the existence of both actively cycling Lgr5+ CSCs as well as quiescent Lgr5+ CSCs that are resistant to conventional anticancer therapies. The classical view of a rigid cell hierarchy and irreversible cell differentiation trajectory in normal and neoplastic tissues is now challenged by the finding that differentiated cells have the capacity to revert to stem cells through dynamic physiological reprogramming events. Such plasticity of CSC systems likely underlies both carcinogenesis and therapeutic resistance in CRC. Further characterization of the mechanisms underpinning the heterogeneity and plasticity of CSCs should inform future development of eradicative therapeutic strategies for CRC.
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Affiliation(s)
- Tsunaki Higa
- Department of Molecular and Cellular Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Keiichi I. Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
- Anticancer Strategies Laboratory, TMDU Advanced Research InstituteTokyo Medical and Dental UniversityTokyoJapan
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26
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Chen Z, Guo X, Tao R, Huyghe JR, Law PJ, Fernandez-Rozadilla C, Ping J, Jia G, Long J, Li C, Shen Q, Xie Y, Timofeeva MN, Thomas M, Schmit SL, Díez-Obrero V, Devall M, Moratalla-Navarro F, Fernandez-Tajes J, Palles C, Sherwood K, Briggs SEW, Svinti V, Donnelly K, Farrington SM, Blackmur J, Vaughan-Shaw PG, Shu XO, Lu Y, Broderick P, Studd J, Harrison TA, Conti DV, Schumacher FR, Melas M, Rennert G, Obón-Santacana M, Martín-Sánchez V, Oh JH, Kim J, Jee SH, Jung KJ, Kweon SS, Shin MH, Shin A, Ahn YO, Kim DH, Oze I, Wen W, Matsuo K, Matsuda K, Tanikawa C, Ren Z, Gao YT, Jia WH, Hopper JL, Jenkins MA, Win AK, Pai RK, Figueiredo JC, Haile RW, Gallinger S, Woods MO, Newcomb PA, Duggan D, Cheadle JP, Kaplan R, Kerr R, Kerr D, Kirac I, Böhm J, Mecklin JP, Jousilahti P, Knekt P, Aaltonen LA, Rissanen H, Pukkala E, Eriksson JG, Cajuso T, Hänninen U, Kondelin J, Palin K, Tanskanen T, Renkonen-Sinisalo L, Männistö S, Albanes D, Weinstein SJ, Ruiz-Narvaez E, Palmer JR, Buchanan DD, Platz EA, Visvanathan K, Ulrich CM, Siegel E, Brezina S, Gsur A, Campbell PT, Chang-Claude J, Hoffmeister M, Brenner H, Slattery ML, Potter JD, Tsilidis KK, Schulze MB, Gunter MJ, Murphy N, Castells A, Castellví-Bel S, Moreira L, Arndt V, Shcherbina A, Bishop DT, Giles GG, Southey MC, Idos GE, McDonnell KJ, Abu-Ful Z, Greenson JK, Shulman K, Lejbkowicz F, Offit K, Su YR, Steinfelder R, Keku TO, van Guelpen B, Hudson TJ, Hampel H, Pearlman R, Berndt SI, Hayes RB, Martinez ME, Thomas SS, Pharoah PDP, Larsson SC, Yen Y, Lenz HJ, White E, Li L, Doheny KF, Pugh E, Shelford T, Chan AT, Cruz-Correa M, Lindblom A, Hunter DJ, Joshi AD, Schafmayer C, Scacheri PC, Kundaje A, Schoen RE, Hampe J, Stadler ZK, Vodicka P, Vodickova L, Vymetalkova V, Edlund CK, Gauderman WJ, Shibata D, Toland A, Markowitz S, Kim A, Chanock SJ, van Duijnhoven F, Feskens EJM, Sakoda LC, Gago-Dominguez M, Wolk A, Pardini B, FitzGerald LM, Lee SC, Ogino S, Bien SA, Kooperberg C, Li CI, Lin Y, Prentice R, Qu C, Bézieau S, Yamaji T, Sawada N, Iwasaki M, Le Marchand L, Wu AH, Qu C, McNeil CE, Coetzee G, Hayward C, Deary IJ, Harris SE, Theodoratou E, Reid S, Walker M, Ooi LY, Lau KS, Zhao H, Hsu L, Cai Q, Dunlop MG, Gruber SB, Houlston RS, Moreno V, Casey G, Peters U, Tomlinson I, Zheng W. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes. Nat Commun 2024; 15:3557. [PMID: 38670944 PMCID: PMC11053150 DOI: 10.1038/s41467-024-47399-x] [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: 10/16/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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Affiliation(s)
- Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, 37232, TN, USA
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Philip J Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Ceres Fernandez-Rozadilla
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
- Genomic Medicine Group, Instituto de Investigacion Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chao Li
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quanhu Shen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuhan Xie
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Maria N Timofeeva
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Danish Institute for Advanced Study, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Minta Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Stephanie L Schmit
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
- Population and Cancer Prevention Program, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Virginia Díez-Obrero
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Matthew Devall
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Ferran Moratalla-Navarro
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Juan Fernandez-Tajes
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Kitty Sherwood
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Sarah E W Briggs
- Department of Public Health, Richard Doll Building, University of Oxford, Oxford, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kevin Donnelly
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Susan M Farrington
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James Blackmur
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Peter G Vaughan-Shaw
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - James Studd
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David V Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Fredrick R Schumacher
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Gad Rennert
- Clalit National Cancer Control Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Mireia Obón-Santacana
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Vicente Martín-Sánchez
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Biomedicine Institute, University of León, León, Spain
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center Hospital, National Cancer Center, Gyeonggi-do, South Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Gyeonggi-do, South Korea
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Keum Ji Jung
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Aesun Shin
- Cancer Research Institute, Seoul National University, Seoul, South Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Yoon-Ok Ahn
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Dong-Hyun Kim
- Department of Social and Preventive Medicine, Hallym University College of Medicine, Okcheon-dong, South Korea
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keitaro Matsuo
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Zefang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yu-Tang Gao
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Rish K Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Jane C Figueiredo
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robert W Haile
- Division of Oncology, Department of Medicine, Cedars-Sinai Cancer Research Center for Health Equity, Los Angeles, CA, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Michael O Woods
- Division of Biomedical Sciences, Memorial University of Newfoundland, St. John, ON, Canada
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA, USA
| | - David Duggan
- City of Hope National Medical Center, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Richard Kaplan
- MRC Clinical Trials Unit, Medical Research Council, Cardiff, UK
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Oxford, UK
| | - David Kerr
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Iva Kirac
- Department of Surgical Oncology, University Hospital for Tumors, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Jan Böhm
- Department of Pathology, Central Finland Health Care District, Jyväskylä, Finland
| | | | - Pekka Jousilahti
- Department of Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Paul Knekt
- Department of Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Harri Rissanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Eero Pukkala
- Faculty of Social Sciences, Tampere University, Tampere, Finland
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
| | - Johan G Eriksson
- Folkhälsan Research Centre, University of Helsinki, Helsinki, Finland
- Human Potential Translational Research Programme, National University of Singapore, Singapore, Singapore
- Unit of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tatiana Cajuso
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Ulrika Hänninen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Johanna Kondelin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Tomas Tanskanen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | | | - Satu Männistö
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Edward Ruiz-Narvaez
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Julie R Palmer
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Slone Epidemiology Center at Boston University, Boston, MA, USA
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Erin Siegel
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Peter T Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
- University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg, Hamburg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Kostas K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Neil Murphy
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Leticia Moreira
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Anna Shcherbina
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Gregory E Idos
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Kevin J McDonnell
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Zomoroda Abu-Ful
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Joel K Greenson
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Katerina Shulman
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Flavio Lejbkowicz
- Clalit National Cancer Control Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit Health Services, Personalized Genomic Service, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Yu-Ru Su
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Robert Steinfelder
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Bethany van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | | | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Marie Elena Martinez
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
- Population Sciences, Disparities and Community Engagement, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
| | | | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Susanna C Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yun Yen
- Taipei Medical University, Taipei, Taiwan
| | - Heinz-Josef Lenz
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| | - Li Li
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tameka Shelford
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew T Chan
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Marcia Cruz-Correa
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | - Zsofia K Stadler
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Christopher K Edlund
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - W James Gauderman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David Shibata
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Amanda Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - Sanford Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, USA
| | - Andre Kim
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Franzel van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Edith J M Feskens
- Division of Human Nutrition, Wageningen University and Research, Wageningen, The Netherlands
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Public Foundation of Genomic Medicine, Servicio Galego de Saude, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Barbara Pardini
- Candiolo Cancer Institute FPO-IRCCS, Candiolo, (TO), Italy
- Italian Institute for Genomic Medicine, Candiolo Cancer Institute FPO-IRCCS, Candiolo, (TO), Italy
| | - Liesel M FitzGerald
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Soo Chin Lee
- National University Cancer Institute, Singapore, Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cancer Immunology Program, Dana-Farber Harvard Cancer Center, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ross Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, Nantes, France
| | - Taiki Yamaji
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Norie Sawada
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | | | - Anna H Wu
- Preventative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chenxu Qu
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Caroline E McNeil
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Sarah E Harris
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Stuart Reid
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Marion Walker
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Li Yin Ooi
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Stephen B Gruber
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Victor Moreno
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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Daly AC, Cambuli F, Äijö T, Lötstedt B, Marjanovic N, Kuksenko O, Smith-Erb M, Fernandez S, Domovic D, Van Wittenberghe N, Drokhlyansky E, Griffin GK, Phatnani H, Bonneau R, Regev A, Vickovic S. Tissue and cellular spatiotemporal dynamics in colon aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590125. [PMID: 38712088 PMCID: PMC11071407 DOI: 10.1101/2024.04.22.590125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Tissue structure and molecular circuitry in the colon can be profoundly impacted by systemic age-related effects, but many of the underlying molecular cues remain unclear. Here, we built a cellular and spatial atlas of the colon across three anatomical regions and 11 age groups, encompassing ~1,500 mouse gut tissues profiled by spatial transcriptomics and ~400,000 single nucleus RNA-seq profiles. We developed a new computational framework, cSplotch, which learns a hierarchical Bayesian model of spatially resolved cellular expression associated with age, tissue region, and sex, by leveraging histological features to share information across tissue samples and data modalities. Using this model, we identified cellular and molecular gradients along the adult colonic tract and across the main crypt axis, and multicellular programs associated with aging in the large intestine. Our multi-modal framework for the investigation of cell and tissue organization can aid in the understanding of cellular roles in tissue-level pathology.
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Affiliation(s)
- Aidan C. Daly
- New York Genome Center, New York, NY, USA
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | | | - Tarmo Äijö
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - Britta Lötstedt
- New York Genome Center, New York, NY, USA
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Nemanja Marjanovic
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Olena Kuksenko
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | | | | | | | | | - Eugene Drokhlyansky
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriel K Griffin
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Hemali Phatnani
- New York Genome Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Center for Data Science, New York University, New York, NY, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Sanja Vickovic
- New York Genome Center, New York, NY, USA
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Engineering and Herbert Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Beijer Laboratory for Gene and Neuro Research, Uppsala University, Uppsala, Sweden
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28
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Olkinuora A, Mäki-Nevala S, Ukwattage S, Ristimäki A, Ahtiainen M, Mecklin JP, Peltomäki P. Novel insights into tumorigenesis revealed by molecular analysis of Lynch syndrome cases with multiple colorectal tumors. Front Oncol 2024; 14:1378392. [PMID: 38725616 PMCID: PMC11079657 DOI: 10.3389/fonc.2024.1378392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/01/2024] [Indexed: 05/12/2024] Open
Abstract
Background Lynch syndrome (LS) is an autosomal dominant multi-organ cancer syndrome with a high lifetime risk of cancer. The number of cumulative colorectal adenomas in LS does not generally exceed ten, and removal of adenomas via routine screening minimizes the cancer burden. However, abnormal phenotypes may mislead initial diagnosis and subsequently cause suboptimal treatment. Aim Currently, there is no standard guide for the care of multiple colorectal adenomas in LS individuals. We aimed to shed insight into the molecular features and reasons for multiplicity of adenomas in LS patients. Methods We applied whole exome sequencing on nine adenomas (ten samples) and three assumed primary carcinomas (five samples) of an LS patient developing the tumors during a 21-year follow-up period. We compared the findings to the tumor profiles of two additional LS cases ascertained through colorectal tumor multiplicity, as well as to ten adenomas and 15 carcinomas from 23 unrelated LS patients with no elevated adenoma burden from the same population. As LS associated cancers can arise via several molecular pathways, we also profiled the tumors for CpG Island Methylator Phenotype (CIMP), and LINE-1 methylation. Results All tumors were microsatellite unstable (MSI), and MSI was present in several samples derived from normal mucosa as well. Interestingly, frequent frameshift variants in RNF43 were shared among substantial number of the tumors of our primary case and the tumors of LS cases with multiple tumors but almost absent in our control LS cases. The RNF43 variants were completely absent in the normal tissue, indicating tumor-associated mutational hotspots. The RNF43 status correlated with the mutational signature SBS96. Contrary to LS tumors from the reference set with no elevated colorectal tumor burden, the somatic variants occurred significantly more frequently at C>T in the CpG context, irrespective of CIMP or LINE-1 status, potentially indicating other, yet unknown methylation-related mechanisms. There were no signs of somatic mosaicism affecting the MMR genes. Somatic variants in APC and CTNNB1 were unique to each tumor. Conclusion Frequent somatic RNF43 hot spot variants combined with SBS96 signature and increased tendency to DNA methylation may contribute to tumor multiplicity in LS.
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Affiliation(s)
- Alisa Olkinuora
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Satu Mäki-Nevala
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Sanjeevi Ukwattage
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Ari Ristimäki
- Department of Pathology, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, HUS, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Maarit Ahtiainen
- Department of Pathology, Wellbeing Services County of Central Finland, Jyväskylä, Finland
| | - Jukka-Pekka Mecklin
- Department of Education and Science, Nova Hospital, Central Finland Health Care District, Jyväskylä, Finland
- Faculty of Sports and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- HUSLAB Laboratory of Genetics, HUS Diagnostic Center, HUS, Helsinki University Hospital, Helsinki, Finland
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29
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Luo R, Liu J, Wen J, Zhou X. Single-cell Landscape of Malignant Transition: Unraveling Cancer Cell-of-Origin and Heterogeneous Tissue Microenvironment. RESEARCH SQUARE 2024:rs.3.rs-4085185. [PMID: 38645221 PMCID: PMC11030487 DOI: 10.21203/rs.3.rs-4085185/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Understanding disease progression and sophisticated tumor ecosystems is imperative for investigating tumorigenesis mechanisms and developing novel prevention strategies. Here, we dissected heterogeneous microenvironments during malignant transitions by leveraging data from 1396 samples spanning 13 major tissues. Within transitional stem-like subpopulations highly enriched in precancers and cancers, we identified 30 recurring cellular states strongly linked to malignancy, including hypoxia and epithelial senescence, revealing a high degree of plasticity in epithelial stem cells. By characterizing dynamics in stem-cell crosstalk with the microenvironment along the pseudotime axis, we found differential roles of ANXA1 at different stages of tumor development. In precancerous stages, reduced ANXA1 levels promoted monocyte differentiation toward M1 macrophages and inflammatory responses, whereas during malignant progression, upregulated ANXA1 fostered M2 macrophage polarization and cancer-associated fibroblast transformation by increasing TGF-β production. Our spatiotemporal analysis further provided insights into mechanisms responsible for immunosuppression and a potential target to control evolution of precancer and mitigate the risk for cancer development.
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Affiliation(s)
| | - Jiajia Liu
- The University of Texas Health Science Center at Houston
| | - Jianguo Wen
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston
| | - Xiaobo Zhou
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston
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30
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Tan C, Qin G, Wang QQ, Zhou YC, Yao SK. Clinicopathologic and endoscopic features of sessile serrated lesions and conventional adenomas: a large inpatient population-based study in China. Front Oncol 2024; 14:1337035. [PMID: 38638861 PMCID: PMC11024220 DOI: 10.3389/fonc.2024.1337035] [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: 11/16/2023] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
Objectives Sessile serrated lesions (SSLs) are precursors of sporadic colorectal cancer (CRC) and have distinct characteristics compared with conventional adenomas (CAs). Several lifestyle and environmental factors may play critical roles in the development of advanced lesions. Our aim is to describe the features of SSLs and CAs and further explore risk factors for advanced lesions. Methods This is an observational study that collected demographic, endoscopic, and histological data from the China-Japan Friendship Hospital among the inpatient population with pathologically reported as SSL or CA between 2015 and 2022. We analyzed the clinicopathology and endoscopic differences between SSL alone, CA alone, and synchronous SSL+CA groups, and identified risk factors using multiple regression analysis. Results A total of 9236 polyps from 6598 patients were included in the cohort. Patients with SSL+CA were more likely to be older (p=0.008), while individuals with SSL alone had a higher proportion of early-onset polyps (p<0.001), and SSLs were more common in advanced polyps than CAs (p<0.001). A greater proportion of advanced polyps in the SSL and CA groups were diagnosed as Yamada III, Yamada IV, and laterally spreading tumor (p=0.002, p<0.001, respectively), and multiple SSLs and CAs were more represented in nonadvanced polyps than in advanced polyps. In multiple regression analysis, older patients were more likely to develop advanced SSLs (aOR 1.05, 95% CI 1.02-1.09, p=0.005). Conclusion SSLs and CAs have diverse demographic, endoscopic, and histological characteristics, and their advanced lesions share different risk factors, which advances the understanding of the etiology and progression of SSLs.
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Affiliation(s)
- Chang Tan
- Graduate School, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Geng Qin
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Qian-Qian Wang
- Graduate School, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Yuan-Chen Zhou
- Graduate School, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Shu-Kun Yao
- Graduate School, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
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31
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Stangis MM, Chen Z, Min J, Glass SE, Jackson JO, Radyk MD, Hoi XP, Brennen WN, Yu M, Dinh HQ, Coffey RJ, Shrubsole MJ, Chan KS, Grady WM, Yegnasubramanian S, Lyssiotis CA, Maitra A, Halberg RB, Dey N, Lau KS. The Hallmarks of Precancer. Cancer Discov 2024; 14:683-689. [PMID: 38571435 PMCID: PMC11170686 DOI: 10.1158/2159-8290.cd-23-1550] [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] [Indexed: 04/05/2024]
Abstract
Research on precancers, as defined as at-risk tissues and early lesions, is of high significance given the effectiveness of early intervention. We discuss the need for risk stratification to prevent overtreatment, an emphasis on the role of genetic and epigenetic aging when considering risk, and the importance of integrating macroenvironmental risk factors with molecules and cells in lesions and at-risk normal tissues for developing effective intervention and health policy strategies.
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Affiliation(s)
- Mary M. Stangis
- Department of Oncology – McArdle Laboratory for Cancer Research, University of Wisconsin-Madison
- Department of Medicine – Gastroenterology Division, University of Wisconsin-Madison
- Carbone Cancer Center, University of Wisconsin-Madison
| | - Zhengyi Chen
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine
- Epithelial Biology Center, Vanderbilt University Medical Center
| | - Jimin Min
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center
| | - Sarah E. Glass
- Epithelial Biology Center, Vanderbilt University Medical Center
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine
| | - Jordan O. Jackson
- Department of Laboratory Medicine and Pathology, University of Washington
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center
| | - Megan D. Radyk
- Department of Molecular & Integrative Physiology, University of Michigan Medical School
| | - Xen Ping Hoi
- Department of Urology, Houston Methodist Research Institute
- Neal Cancer Center, Houston Methodist Research Institute
| | - W. Nathaniel Brennen
- Department of Oncology – Genitourinary Cancer Disease Division, Johns Hopkins Medicine
- Department of Pharmacology and Molecular Sciences, Johns Hopkins Medicine
- Department of Urology, Johns Hopkins Medicine
| | - Ming Yu
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center
- Department of Medicine – Division of Gastroenterology, University of Washington
- Public Health Sciences Division, Fred Hutchinson Cancer Center
| | - Huy Q. Dinh
- Department of Oncology – McArdle Laboratory for Cancer Research, University of Wisconsin-Madison
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison
| | - Robert J. Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine
- Department of Medicine – Division of Gastroenterology, Hepatology, & Nutrition, Vanderbilt University Medical Center
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center
| | - Martha J. Shrubsole
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center
- Department of Medicine – Division of Epidemiology, Vanderbilt University Medical Center
| | - Keith S. Chan
- Department of Urology, Houston Methodist Research Institute
- Neal Cancer Center, Houston Methodist Research Institute
| | - William M. Grady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center
- Department of Medicine – Division of Gastroenterology, University of Washington
- Public Health Sciences Division, Fred Hutchinson Cancer Center
| | - Srinivasan Yegnasubramanian
- Department of Oncology – Genitourinary Cancer Disease Division, Johns Hopkins Medicine
- Radiation Oncology and Molecular Radiation Sciences – Molecular Radiation Science Division, Johns Hopkins Medicine
- Department of Pathology – Kidney-Urologic Pathology Division, Johns Hopkins Medicine
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine
| | - Costas A. Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan Medical School
- Internal Medicine – Division of Gastroenterology, University of Michigan Medical School
- Rogel Cancer Center, University of Michigan Medical School
| | - Anirban Maitra
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center
| | - Richard B. Halberg
- Department of Oncology – McArdle Laboratory for Cancer Research, University of Wisconsin-Madison
- Department of Medicine – Gastroenterology Division, University of Wisconsin-Madison
- Carbone Cancer Center, University of Wisconsin-Madison
| | - Neelendu Dey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center
- Department of Medicine – Division of Gastroenterology, University of Washington
| | - Ken S. Lau
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine
- Epithelial Biology Center, Vanderbilt University Medical Center
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center
- Department of Surgery, Vanderbilt University Medical Center
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32
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Sadien ID, Davies RJ, Wheeler JMD. The genomics of sporadic and hereditary colorectal cancer. Ann R Coll Surg Engl 2024; 106:313-320. [PMID: 38555871 PMCID: PMC10981993 DOI: 10.1308/rcsann.2024.0024] [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] [Accepted: 01/20/2024] [Indexed: 04/02/2024] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. Over the past three decades, extensive efforts have sought to elucidate the genomic landscape of CRC. These studies reveal that CRC is highly heterogeneous at the molecular level, with different subtypes characterised by distinct somatic mutational profiles, epigenetic aberrations and transcriptomic signatures. This review summarises our current understanding of the genomic and epigenomic alterations implicated in CRC development and progression. Particular focus is given to how characterisation of CRC genomes is leading to more personalised approaches to diagnosis and treatment.
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Affiliation(s)
| | | | - JMD Wheeler
- Cambridge University Hospitals NHS Foundation Trust, UK
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33
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Tong QY, Pang MJ, Hu XH, Huang XZ, Sun JX, Wang XY, Burclaff J, Mills JC, Wang ZN, Miao ZF. Gastric intestinal metaplasia: progress and remaining challenges. J Gastroenterol 2024; 59:285-301. [PMID: 38242996 DOI: 10.1007/s00535-023-02073-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/26/2023] [Indexed: 01/21/2024]
Abstract
Most gastric cancers arise in the setting of chronic inflammation which alters gland organization, such that acid-pumping parietal cells are lost, and remaining cells undergo metaplastic change in differentiation patterns. From a basic science perspective, recent progress has been made in understanding how atrophy and initial pyloric metaplasia occur. However, pathologists and cancer biologists have long been focused on the development of intestinal metaplasia patterns in this setting. Arguably, much less progress has been made in understanding the mechanisms that lead to the intestinalization seen in chronic atrophic gastritis and pyloric metaplasia. One plausible explanation for this disparity lies in the notable absence of reliable and reproducible small animal models within the field, which would facilitate the investigation of the mechanisms underlying the development of gastric intestinal metaplasia (GIM). This review offers an in-depth exploration of the current state of research in GIM, shedding light on its pivotal role in tumorigenesis. We delve into the histological subtypes of GIM and explore their respective associations with tumor formation. We present the current repertoire of biomarkers utilized to delineate the origins and progression of GIM and provide a comprehensive survey of the available, albeit limited, mouse lines employed for modeling GIM and engage in a discussion regarding potential cell lineages that serve as the origins of GIM. Finally, we expound upon the myriad signaling pathways recognized for their activity in GIM and posit on their potential overlap and interactions that contribute to the ultimate manifestation of the disease phenotype. Through our exhaustive review of the progression from gastric disease to GIM, we aim to establish the groundwork for future research endeavors dedicated to elucidating the etiology of GIM and developing strategies for its prevention and treatment, considering its potential precancerous nature.
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Affiliation(s)
- Qi-Yue Tong
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China
| | - Min-Jiao Pang
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China
| | - Xiao-Hai Hu
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China
| | - Xuan-Zhang Huang
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China
| | - Jing-Xu Sun
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China
| | - Xin-Yu Wang
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina, USA
| | - Jason C Mills
- Section of Gastroenterology and Hepatology, Department of Medicine, Departments of Pathology and Immunology, Molecular and Cellular Biology, Baylor College of Medicine, Houston, USA
| | - Zhen-Ning Wang
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China.
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China.
| | - Zhi-Feng Miao
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China.
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 N. Nanjing Street, Shenyang, 110001, Liaoning, China.
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Mei J, Liu X, Tian H, Chen Y, Cao Y, Zeng J, Liu Y, Chen Y, Gao Y, Yin J, Wang P. Tumour organoids and assembloids: Patient-derived cancer avatars for immunotherapy. Clin Transl Med 2024; 14:e1656. [PMID: 38664597 PMCID: PMC11045561 DOI: 10.1002/ctm2.1656] [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: 09/27/2023] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Organoid technology is an emerging and rapidly growing field that shows promise in studying organ development and screening therapeutic regimens. Although organoids have been proposed for a decade, concerns exist, including batch-to-batch variations, lack of the native microenvironment and clinical applicability. MAIN BODY The concept of organoids has derived patient-derived tumour organoids (PDTOs) for personalized drug screening and new drug discovery, mitigating the risks of medication misuse. The greater the similarity between the PDTOs and the primary tumours, the more influential the model will be. Recently, 'tumour assembloids' inspired by cell-coculture technology have attracted attention to complement the current PDTO technology. High-quality PDTOs must reassemble critical components, including multiple cell types, tumour matrix, paracrine factors, angiogenesis and microorganisms. This review begins with a brief overview of the history of organoids and PDTOs, followed by the current approaches for generating PDTOs and tumour assembloids. Personalized drug screening has been practised; however, it remains unclear whether PDTOs can predict immunotherapies, including immune drugs (e.g. immune checkpoint inhibitors) and immune cells (e.g. tumour-infiltrating lymphocyte, T cell receptor-engineered T cell and chimeric antigen receptor-T cell). PDTOs, as cancer avatars of the patients, can be expanded and stored to form a biobank. CONCLUSION Fundamental research and clinical trials are ongoing, and the intention is to use these models to replace animals. Pre-clinical immunotherapy screening using PDTOs will be beneficial to cancer patients. KEY POINTS The current PDTO models have not yet constructed key cellular and non-cellular components. PDTOs should be expandable and editable. PDTOs are promising preclinical models for immunotherapy unless mature PDTOs can be established. PDTO biobanks with consensual standards are urgently needed.
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Affiliation(s)
- Jie Mei
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of AgingWenzhou Medical UniversityWenzhouPeople's Republic of China
- Department of Clinical Pharmacology, Xiangya HospitalCentral South UniversityChangshaPeople's Republic of China
- Institute of Clinical Pharmacology, Hunan Key Laboratory of PharmacogeneticsCentral South UniversityChangshaPeople's Republic of China
- Engineering Research Center of Applied Technology of PharmacogenomicsMinistry of EducationChangshaPeople's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaPeople's Republic of China
| | - Xingjian Liu
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of AgingWenzhou Medical UniversityWenzhouPeople's Republic of China
| | - Hui‐Xiang Tian
- Department of Clinical Pharmacology, Xiangya HospitalCentral South UniversityChangshaPeople's Republic of China
- Institute of Clinical Pharmacology, Hunan Key Laboratory of PharmacogeneticsCentral South UniversityChangshaPeople's Republic of China
| | - Yixuan Chen
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of AgingWenzhou Medical UniversityWenzhouPeople's Republic of China
| | - Yang Cao
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of AgingWenzhou Medical UniversityWenzhouPeople's Republic of China
| | - Jun Zeng
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of AgingWenzhou Medical UniversityWenzhouPeople's Republic of China
- Department of Thoracic Surgery, Xiangya HospitalCentral South UniversityChangshaPeople's Republic of China
| | - Yung‐Chiang Liu
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of AgingWenzhou Medical UniversityWenzhouPeople's Republic of China
| | - Yaping Chen
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of AgingWenzhou Medical UniversityWenzhouPeople's Republic of China
| | - Yang Gao
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaPeople's Republic of China
- Department of Thoracic Surgery, Xiangya HospitalCentral South UniversityChangshaPeople's Republic of China
- Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis and Treatment, Xiangya HospitalCentral South UniversityChangshaPeople's Republic of China
- Xiangya Lung Cancer Center, Xiangya HospitalCentral South UniversityChangshaPeople's Republic of China
| | - Ji‐Ye Yin
- Department of Clinical Pharmacology, Xiangya HospitalCentral South UniversityChangshaPeople's Republic of China
- Institute of Clinical Pharmacology, Hunan Key Laboratory of PharmacogeneticsCentral South UniversityChangshaPeople's Republic of China
- Engineering Research Center of Applied Technology of PharmacogenomicsMinistry of EducationChangshaPeople's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaPeople's Republic of China
| | - Peng‐Yuan Wang
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of AgingWenzhou Medical UniversityWenzhouPeople's Republic of China
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de Souza N, Zhao S, Bodenmiller B. Multiplex protein imaging in tumour biology. Nat Rev Cancer 2024; 24:171-191. [PMID: 38316945 DOI: 10.1038/s41568-023-00657-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/08/2023] [Indexed: 02/07/2024]
Abstract
Tissue imaging has become much more colourful in the past decade. Advances in both experimental and analytical methods now make it possible to image protein markers in tissue samples in high multiplex. The ability to routinely image 40-50 markers simultaneously, at single-cell or subcellular resolution, has opened up new vistas in the study of tumour biology. Cellular phenotypes, interaction, communication and spatial organization have become amenable to molecular-level analysis, and application to patient cohorts has identified clinically relevant cellular and tissue features in several cancer types. Here, we review the use of multiplex protein imaging methods to study tumour biology, discuss ongoing attempts to combine these approaches with other forms of spatial omics, and highlight challenges in the field.
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Affiliation(s)
- Natalie de Souza
- University of Zurich, Department of Quantitative Biomedicine, Zurich, Switzerland
- ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland
- ETH Zurich, Institute of Molecular Health Sciences, Zurich, Switzerland
| | - Shan Zhao
- University of Zurich, Department of Quantitative Biomedicine, Zurich, Switzerland
- ETH Zurich, Institute of Molecular Health Sciences, Zurich, Switzerland
| | - Bernd Bodenmiller
- University of Zurich, Department of Quantitative Biomedicine, Zurich, Switzerland.
- ETH Zurich, Institute of Molecular Health Sciences, Zurich, Switzerland.
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Adkins-Threats M, Huang YZ, Mills JC. Highlights of how single-cell analyses are illuminating differentiation and disease in the gastric corpus. Am J Physiol Gastrointest Liver Physiol 2024; 326:G205-G215. [PMID: 38193187 PMCID: PMC11211037 DOI: 10.1152/ajpgi.00164.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/18/2023] [Accepted: 12/23/2023] [Indexed: 01/10/2024]
Abstract
Single-cell RNA-sequencing (scRNA-seq) has emerged as a powerful technique to identify novel cell markers, developmental trajectories, and transcriptional changes during cell differentiation and disease onset and progression. In this review, we highlight recent scRNA-seq studies of the gastric corpus in both human and murine systems that have provided insight into gastric organogenesis, identified novel markers for the various gastric lineages during development and in adults, and revealed transcriptional changes during regeneration and tumorigenesis. Overall, by elucidating transcriptional states and fluctuations at the cellular level in healthy and disease contexts, scRNA-seq may lead to better, more personalized clinical treatments for disease progression.
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Affiliation(s)
- Mahliyah Adkins-Threats
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States
| | - Yang-Zhe Huang
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States
- Graduate School of Biomedical Sciences, Cancer and Cell Biology Program, Baylor College of Medicine, Houston, Texas, United States
| | - Jason C Mills
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States
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Schiavoni G, Messina B, Scalera S, Memeo L, Colarossi C, Mare M, Blandino G, Ciliberto G, Bon G, Maugeri-Saccà M. Role of Hippo pathway dysregulation from gastrointestinal premalignant lesions to cancer. J Transl Med 2024; 22:213. [PMID: 38424512 PMCID: PMC10903154 DOI: 10.1186/s12967-024-05027-8] [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: 07/21/2023] [Accepted: 02/25/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND First identified in Drosophila melanogaster, the Hippo pathway is considered a major regulatory cascade controlling tissue homeostasis and organ development. Hippo signaling components include kinases whose activity regulates YAP and TAZ final effectors. In response to upstream stimuli, YAP and TAZ control transcriptional programs involved in cell proliferation, cytoskeletal reorganization and stemness. MAIN TEXT While fine tuning of Hippo cascade components is essential for maintaining the balance between proliferative and non-proliferative signals, pathway signaling is frequently dysregulated in gastrointestinal cancers. Also, YAP/TAZ aberrant activation has been described in conditions characterized by chronic inflammation that precede cancer development, suggesting a role of Hippo effectors in triggering carcinogenesis. In this review, we summarize the architecture of the Hippo pathway and discuss the involvement of signaling cascade unbalances in premalignant lesions of the gastrointestinal tract, providing a focus on the underlying molecular mechanisms. CONCLUSIONS The biology of premalignant Hippo signaling dysregulation needs further investigation in order to elucidate the evolutionary trajectories triggering cancer inititation and develop effective early therapeutic strategies targeting the Hippo/YAP pathway.
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Affiliation(s)
- Giulia Schiavoni
- Clinical Trial Center, Biostatistics and Bioinformatics Unit, Department of Research, Diagnosis and Innovative Technologies, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Beatrice Messina
- Clinical Trial Center, Biostatistics and Bioinformatics Unit, Department of Research, Diagnosis and Innovative Technologies, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Stefano Scalera
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Lorenzo Memeo
- Pathology Unit, Mediterranean Institute of Oncology, Viagrande, Italy
| | | | - Marzia Mare
- Medical Oncology Unit, Mediterranean Institute of Oncology, Viagrande, Italy
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, Messina, Italy
| | - Giovanni Blandino
- Translational Oncology Research Unit, Department of Research, Diagnosis and Innovative Technologies, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Gennaro Ciliberto
- Scientific Directorate, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giulia Bon
- Cellular Network and Molecular Therapeutic Target Unit, Department of Research, Diagnosis and Innovative Technologies, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
| | - Marcello Maugeri-Saccà
- Clinical Trial Center, Biostatistics and Bioinformatics Unit, Department of Research, Diagnosis and Innovative Technologies, IRCCS Regina Elena National Cancer Institute, Rome, Italy
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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Trinh VQH, Ankenbauer KE, Liu J, Batardiere M, Maurer HC, Copeland C, Wong J, Ben-Levy O, Torbit SM, Jarvis B, Revetta F, Ivanov S, Jyotsana N, Makino Y, Ruelas AM, Means AL, Maitra A, Tan MCB, DelGiorno KE. Oncogenic GNAS drives a gastric pylorus program in intraductal papillary mucinous neoplasms of the pancreas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.25.581948. [PMID: 38464029 PMCID: PMC10925208 DOI: 10.1101/2024.02.25.581948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
OBJECTIVE Intraductal Papillary Mucinous Neoplasms (IPMNs) are cystic lesions and bona fide precursors for pancreatic ductal adenocarcinoma (PDAC). Recently, we showed that acinar to ductal metaplasia, an injury repair program, is characterized by a transcriptomic program similar to gastric spasmolytic polypeptide expressing metaplasia (SPEM), suggesting common mechanisms of reprogramming between the stomach and pancreas. The aims of this study were to assay IPMN for pyloric markers and to identify molecular drivers of this program. DESIGN We analyzed RNA-seq studies of IPMN for pyloric markers, which were validated by immunostaining in patient samples. Cell lines expressing Kras G12D +/- GNAS R201C were manipulated to identify distinct and overlapping transcriptomic programs driven by each oncogene. A PyScenic-based regulon analysis was performed to identify molecular drivers in the pancreas. Expression of candidate drivers was evaluated by RNA-seq and immunostaining. RESULTS Pyloric markers were identified in human IPMN. GNAS R201C drove expression of these markers in cell lines and siRNA targeting of GNAS R201C or Kras G12D demonstrates that GNAS R201C amplifies a mucinous, pyloric phenotype. Regulon analysis identified a role for transcription factors SPDEF, CREB3L1, and CREB3L4, which are expressed in patient samples. siRNA-targeting of Spdef inhibited mucin production. CONCLUSION De novo expression of a SPEM phenotype has been identified in pancreatitis and a pyloric phenotype in Kras G12D -driven PanIN and Kras G12D ;GNAS R201C -driven IPMN, suggesting common mechanisms of reprogramming between these lesions and the stomach. A transition from a SPEM to pyloric phenotype may reflect disease progression and/or oncogenic mutation. IPMN-specific GNAS R201C amplifies a mucinous phenotype, in part, through SPDEF.
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Lin G, Gao Z, Wu S, Zheng J, Guo X, Zheng X, Chen R. scRNA-seq revealed high stemness epithelial malignant cell clusters and prognostic models of lung adenocarcinoma. Sci Rep 2024; 14:3709. [PMID: 38355636 PMCID: PMC10867035 DOI: 10.1038/s41598-024-54135-4] [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: 12/05/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the sole causes of death in lung cancer patients. This study combined with single-cell RNA-seq analysis to identify tumor stem-related prognostic models to predict the prognosis of lung adenocarcinoma, chemotherapy agents, and immunotherapy efficacy. mRNA expression-based stemness index (mRNAsi) was determined by One Class Linear Regression (OCLR). Differentially expressed genes (DEGs) were detected by limma package. Single-cell RNA-seq analysis in GSE123902 dataset was performed using Seurat package. Weighted Co-Expression Network Analysis (WGCNA) was built by rms package. Cell differentiation ability was determined by CytoTRACE. Cell communication analysis was performed by CellCall and CellChat package. Prognosis model was constructed by 10 machine learning and 101 combinations. Drug predictive analysis was conducted by pRRophetic package. Immune microenvironment landscape was determined by ESTIMATE, MCP-Counter, ssGSEA analysis. Tumor samples have higher mRNAsi, and the high mRNAsi group presents a worse prognosis. Turquoise module was highly correlated with mRNAsi in TCGA-LUAD dataset. scRNA analysis showed that 22 epithelial cell clusters were obtained, and higher CSCs malignant epithelial cells have more complex cellular communication with other cells and presented dedifferentiation phenomenon. Cellular senescence and Hippo signaling pathway are the major difference pathways between high- and low CSCs malignant epithelial cells. The pseudo-temporal analysis shows that cluster1, 2, high CSC epithelial cells, are concentrated at the end of the differentiation trajectory. Finally, 13 genes were obtained by intersecting genes in turquoise module, Top200 genes in hdWGCNA, DEGs in high- and low- mRNAsi group as well as DEGs in tumor samples vs. normal group. Among 101 prognostic models, average c-index (0.71) was highest in CoxBoost + RSF model. The high-risk group samples had immunosuppressive status, higher tumor malignancy and low benefit from immunotherapy. This work found that malignant tumors and malignant epithelial cells have high CSC characteristics, and identified a model that could predict the prognosis, immune microenvironment, and immunotherapy of LUAD, based on CSC-related genes. These results provided reference value for the clinical diagnosis and treatment of LUAD.
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Affiliation(s)
- GuoYong Lin
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China
| | - ZhiSen Gao
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China
| | - Shun Wu
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China
| | - JianPing Zheng
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China
| | - XiangQiong Guo
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China
| | - XiaoHong Zheng
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China
| | - RunNan Chen
- Department of Respiratory and Critical Illness Medicine, The First Hospital of Putian, Putian, 351100, China.
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Dunne PD, Arends MJ. Molecular pathological classification of colorectal cancer-an update. Virchows Arch 2024; 484:273-285. [PMID: 38319359 PMCID: PMC10948573 DOI: 10.1007/s00428-024-03746-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/07/2024]
Abstract
Colorectal cancer (CRC) has a broad range of molecular alterations with two major mechanisms of genomic instability (chromosomal instability and microsatellite instability) and has been subclassified into 4 consensus molecular subtypes (CMS) based on bulk RNA sequence data. Here, we update the molecular pathological classification of CRC with an overview of more recent bulk and single-cell RNA data analysis for development of transcriptional classifiers and risk stratification methods, taking into account the marked inter-tumoural and intra-tumoural heterogeneity of CRC. The importance of the stromal and immune components or tumour microenvironment (TME) to prognosis has emerged from these analyses. Attempts to remove the contribution of the tumour microenvironment and reveal neoplastic-specific transcriptional traits involved identification of the CRC intrinsic subtypes (CRIS). The use of immunohistochemistry and digital pathology to implement classification systems are evolving fields. Conventional adenoma versus serrated polyp pathway transcriptomic analysis and characterisation of canonical LGR5+ crypt base columnar stem cell versus ANXA1+ regenerative stem cell phenotypes emerged as key properties for improved understanding of transcriptional signals involved in molecular subclassification of colorectal cancers. Recently, classification by three pathway-derived subtypes (PDS1-3) has been developed, revealing a continuum of intrinsic biology associated with biological, stem cell, histopathological, and clinical attributes.
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Affiliation(s)
- Philip D Dunne
- Patrick G. Johnston Centre for Cancer Research, Queens University Belfast, Belfast, Northern Ireland, BT8 7AE, UK
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, G61 1QH, UK
| | - Mark J Arends
- Edinburgh Pathology & Cancer Research UK Scotland Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XR, UK.
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Ye J, Zhang J, Ding W. DNA methylation modulates epigenetic regulation in colorectal cancer diagnosis, prognosis and precision medicine. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:34-53. [PMID: 38464391 PMCID: PMC10918240 DOI: 10.37349/etat.2024.00203] [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: 09/25/2023] [Accepted: 12/11/2023] [Indexed: 03/12/2024] Open
Abstract
Colorectal cancer (CRC) is a multifaceted disease influenced by the interplay of genetic and environmental factors. The clinical heterogeneity of CRC cannot be attributed exclusively to genetic diversity and environmental exposures, and epigenetic markers, especially DNA methylation, play a critical role as key molecular markers of cancer. This review compiles a comprehensive body of evidence underscoring the significant involvement of DNA methylation modifications in the pathogenesis of CRC. Moreover, this review explores the potential utility of DNA methylation in cancer diagnosis, prognostics, assessment of disease activity, and prediction of drug responses. Recognizing the impact of DNA methylation will enhance the ability to identify distinct CRC subtypes, paving the way for personalized treatment strategies and advancing precision medicine in the management of CRC.
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Affiliation(s)
- Jingxin Ye
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
- Department of Gastroenterology, The Affiliated Suqian Hospital of Xuzhou Medical University, Suqian 223800, Jiangsu Province, China
| | - Jianfeng Zhang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Weifeng Ding
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
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Mortezaee K. WNT/β-catenin regulatory roles on PD-(L)1 and immunotherapy responses. Clin Exp Med 2024; 24:15. [PMID: 38280119 PMCID: PMC10822012 DOI: 10.1007/s10238-023-01274-z] [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: 10/18/2023] [Accepted: 11/29/2023] [Indexed: 01/29/2024]
Abstract
Dysregulation of WNT/β-catenin is a hallmark of many cancer types and a key mediator of metastasis in solid tumors. Overactive β-catenin signaling hampers dendritic cell (DC) recruitment, promotes CD8+ T cell exclusion and increases the population of regulatory T cells (Tregs). The activity of WNT/β-catenin also induces the expression of programmed death-ligand 1 (PD-L1) on tumor cells and promotes programmed death-1 (PD-1) upregulation. Increased activity of WNT/β-catenin signaling after anti-PD-1 therapy is indicative of a possible implication of this signaling in bypassing immune checkpoint inhibitor (ICI) therapy. This review is aimed at giving a comprehensive overview of the WNT/β-catenin regulatory roles on PD-1/PD-L1 axis in tumor immune ecosystem, discussing about key mechanistic events contributed to the WNT/β-catenin-mediated bypass of ICI therapy, and representing inhibitors of this signaling as promising combinatory regimen to go with anti-PD-(L)1 in cancer immunotherapy. Ideas presented in this review imply the synergistic efficacy of such combination therapy in rendering durable anti-tumor immunity.
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Affiliation(s)
- Keywan Mortezaee
- Department of Anatomy, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran.
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Meng Q, Zhao Y, Xu M, Wang P, Li J, Cui R, Fu W, Ding S. Increased circulating regulatory T cells and decreased follicular T helper cells are associated with colorectal carcinogenesis. Front Immunol 2024; 15:1287632. [PMID: 38343544 PMCID: PMC10853383 DOI: 10.3389/fimmu.2024.1287632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/10/2024] [Indexed: 02/15/2024] Open
Abstract
Objective Colorectal cancer (CRC) is the third most prevalent cancer worldwide and is associated with high morbidity and mortality rates. Colorectal carcinogenesis occurs via the conventional adenoma-to-carcinoma and serrated pathways. Conventional T helper (Th) and innate lymphoid cells (ILCs) play vital roles in maintaining intestinal homeostasis. However, the contribution of these two major lymphoid cell populations and their associated cytokines to CRC development is unclear. Therefore, we aimed to analyze peripheral lymphocyte profiles during colorectal carcinogenesis. Methods We collected 86 blood samples concurrently, and pathologists confirmed the presence of various pathological conditions (i.e., HPs, adenoma, and carcinoma) using hematoxylin and eosin staining. Ten healthy donors were recruited as healthy controls (HCs) from the physical examination center. We performed flow cytometry on peripheral blood mononuclear cells collected from patients with various pathological conditions and the HCs, and cytokines (interleukin-2, interleukin-4, interleukin-5, interleukin-13, interleukin-17A, interleukin-17F, interleukin-22, interferon-γ, and tumor necrosis factor-α) were quantified. We also analyzed the published single-cell RNA sequence data derived from tissue samples from different stages of colorectal carcinogenesis. Results The cytokine response in peripheral CD4+ T cells was upregulated during the carcinoma process. The frequency of peripheral regulatory T cells (Tregs) increased in the adenoma and carcinoma stages. While the T follicular helper (Tfh) cell proportion was downregulated in the adenoma and carcinoma processes. Thus, Th cell subsets, especially Tregs and Tfh cells, were involved in colonic diseases. Moreover, the immunological profile characteristics in the HPs were clarified. Conclusion We comprehensively analyzed circulating ILCs and adaptive T-cell lymphocyte subtypes in colorectal carcinoma progression. Our results show the immunological profile characteristics and support the involvement of Th subsets, especially Treg and Tfh cell populations, in colonic diseases. These findings significantly enhance our understanding of the immune mechanisms underlying CRC and its precancerous lesions. Further investigation of the Treg and Tfh cells' function in colorectal disease development will provide potential therapeutic targets for monitoring and preventing CRC development.
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Affiliation(s)
- Qiao Meng
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases, Beijing, China
| | - Yang Zhao
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Miao Xu
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Pingzhang Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, NHC Key Laboratory of Medical Immunology (Peking University), Beijing, China
| | - Jun Li
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Rongli Cui
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Weiwei Fu
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases, Beijing, China
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases, Beijing, China
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44
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Valdeolivas A, Amberg B, Giroud N, Richardson M, Gálvez EJC, Badillo S, Julien-Laferrière A, Túrós D, Voith von Voithenberg L, Wells I, Pesti B, Lo AA, Yángüez E, Das Thakur M, Bscheider M, Sultan M, Kumpesa N, Jacobsen B, Bergauer T, Saez-Rodriguez J, Rottenberg S, Schwalie PC, Hahn K. Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics. NPJ Precis Oncol 2024; 8:10. [PMID: 38200223 PMCID: PMC10781769 DOI: 10.1038/s41698-023-00488-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 12/04/2023] [Indexed: 01/12/2024] Open
Abstract
The consensus molecular subtypes (CMS) of colorectal cancer (CRC) is the most widely-used gene expression-based classification and has contributed to a better understanding of disease heterogeneity and prognosis. Nevertheless, CMS intratumoral heterogeneity restricts its clinical application, stressing the necessity of further characterizing the composition and architecture of CRC. Here, we used Spatial Transcriptomics (ST) in combination with single-cell RNA sequencing (scRNA-seq) to decipher the spatially resolved cellular and molecular composition of CRC. In addition to mapping the intratumoral heterogeneity of CMS and their microenvironment, we identified cell communication events in the tumor-stroma interface of CMS2 carcinomas. This includes tumor growth-inhibiting as well as -activating signals, such as the potential regulation of the ETV4 transcriptional activity by DCN or the PLAU-PLAUR ligand-receptor interaction. Our study illustrates the potential of ST to resolve CRC molecular heterogeneity and thereby help advance personalized therapy.
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Affiliation(s)
- Alberto Valdeolivas
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
| | - Bettina Amberg
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nicolas Giroud
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Marion Richardson
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Eric J C Gálvez
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Solveig Badillo
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Alice Julien-Laferrière
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Demeter Túrós
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Isabelle Wells
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Benedek Pesti
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Amy A Lo
- Genentech, Inc, San Francisco, CA, USA
| | - Emilio Yángüez
- Roche Pharma Research and Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | | | - Michael Bscheider
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Marc Sultan
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Nadine Kumpesa
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Björn Jacobsen
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Tobias Bergauer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Julio Saez-Rodriguez
- Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine (BCPM), University of Bern, Bern, Switzerland
| | - Petra C Schwalie
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Kerstin Hahn
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
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45
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Peters L, Venkatachalam A, Ben-Neriah Y. Tissue-Predisposition to Cancer Driver Mutations. Cells 2024; 13:106. [PMID: 38247798 PMCID: PMC10814991 DOI: 10.3390/cells13020106] [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: 12/08/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
Driver mutations are considered the cornerstone of cancer initiation. They are defined as mutations that convey a competitive fitness advantage, and hence, their mutation frequency in premalignant tissue is expected to exceed the basal mutation rate. In old terms, that translates to "the survival of the fittest" and implies that a selective process underlies the frequency of cancer driver mutations. In that sense, each tissue is its own niche that creates a molecular selective pressure that may favor the propagation of a mutation or not. At the heart of this stands one of the biggest riddles in cancer biology: the tissue-predisposition to cancer driver mutations. The frequency of cancer driver mutations among tissues is non-uniform: for instance, mutations in APC are particularly frequent in colorectal cancer, and 99% of chronic myeloid leukemia patients harbor the driver BCR-ABL1 fusion mutation, which is rarely found in solid tumors. Here, we provide a mechanistic framework that aims to explain how tissue-specific features, ranging from epigenetic underpinnings to the expression of viral transposable elements, establish a molecular basis for selecting cancer driver mutations in a tissue-specific manner.
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Affiliation(s)
| | | | - Yinon Ben-Neriah
- Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research (IMRIC), The Faculty of Medicine, Hebrew University of Jerusalem, P.O. Box 12272, Jerusalem 91120, Israel; (L.P.); (A.V.)
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46
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Rzasa P, Rufini A. Cholesterol metabolism and colorectal cancer: the plot thickens. Cell Death Discov 2024; 10:3. [PMID: 38177141 PMCID: PMC10766946 DOI: 10.1038/s41420-023-01784-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/21/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024] Open
Affiliation(s)
- Paulina Rzasa
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Alessandro Rufini
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK.
- Dipartimento di Bioscienze, University of Milan, Milan, Italy.
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47
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Musulen E, Gené M, Cuatrecasas M, Amat I, Veiga JA, Fernández-Aceñero MJ, Chimisana VF, Tarragona J, Jurado I, Fernández-Victoria R, Martínez-Ciarpaglini C, Alenda González C, Zac C, Fernández-Figueras MT, Esteller M. Gastric metaplasia as a precursor of nonconventional dysplasia in inflammatory bowel disease. Hum Pathol 2024; 143:50-61. [PMID: 38000679 DOI: 10.1016/j.humpath.2023.11.011] [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: 07/24/2023] [Revised: 10/18/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Gastric metaplasia in colonic mucosa with inflammatory bowel disease (IBD) develops as an adaptation mechanism. The association between gastric metaplasia and nonconventional and/or conventional dysplasia as precursors of colitis-associated colorectal cancer is unknown. To address this question, we retrospectively reviewed a series of 33 IBD colectomies to identify gastric metaplasia in 76 precursor lesions. We obtained 61 nonconventional and 15 conventional dysplasias. Among nonconventional dysplasia, 31 (50.8 %) were low-grade (LGD), 4 (6.5 %) were high-grade (HGD), 9 (14.8 %) had both LGD and HGD, and 17 (27.9 %) had no dysplasia (ND), while 14 (93 %) conventional dysplasias had LGD, and 1 (7 %) had LGD and HGD. Gastric metaplasia was assessed by concomitant immunoexpression of MUC5AC and loss of CDX2 staining. Expression of a p53-mut pattern was considered as a surrogate for gene mutation, and complete loss of MLH1 staining as presence of MLH1 hypermethylation. In nonconventional dysplasia, MUC5AC immunoexpression decreased as the degree of dysplasia increased, being 78 % in LGD and 39 % in HGD (p = 0.006). CDX2 was lost in epithelial glands with high expression of MUC5AC (p < 0.001). The p53-mut pattern was observed in 77 % HGD, 45 % LGD, and in 6 % with ND (p < 0.001). Neither nonconventional nor conventional dysplasia showed complete loss of MLH1 staining. Gastric metaplasia was also present in mucosa adjacent to nonconventional dysplasia with chronic changes or active inflammation. Our results show that gastric metaplasia appears in IBD-inflamed colon mucosa, it is the substrate of most nonconventional dysplasia and occurs prior to p53 alterations.
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Affiliation(s)
- Eva Musulen
- Pathology Department, Hospital Universitari General de Catalunya-Grupo QuironSalud, 08915 Sant Cugat Del Vallès, Barcelona, Spain; Institut de Recerca Contra La Leucèmia Josep Carreras (IJC), 08916 Badalona, Barcelona, Spain.
| | - Míriam Gené
- Pathology Department, Hospital Universitari Joan XXIII, 43005 Tarragona, Spain; Surgery Department, Programme of Surgery and Morphological Sciences, Universitat Autònoma de Barcelona (UAB), 08193 Cerdanyola Del Vallès, Spain
| | - Míriam Cuatrecasas
- Pathology Department, Hospital Clínic, 08036 Barcelona, Spain; Department of Basic Clinical Practice, University of Barcelona (UB), 08036 Barcelona, Spain
| | - Irene Amat
- Pathology Department, Complejo Hospitalario de Navarra, 31008 Navarra, Spain
| | - Jesús Alberto Veiga
- Pathology Department, Complejo Hospitalario Universitario de Ferrol, 15405 Ferrol, Spain
| | | | | | - Jordi Tarragona
- Pathology Department, Hospital Universitari Arnau de Vilanova, 25198 Lleida, Spain
| | - Ismael Jurado
- Pathology Department, Consorci Sanitari de Terrassa, 08227 Terrassa, Spain
| | | | - Carolina Martínez-Ciarpaglini
- Pathology Department, Hospital Clínico Universitario de Valencia, INCLIVA- Instituto de Investigación Sanitaria, Universidad de Valencia, 46010 Valencia, Spain
| | - Cristina Alenda González
- Pathology Department, Hospital General Universitario Dr. Balmis, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 031010 Alicante, Spain
| | - Carlos Zac
- Pathology Department, Hospital Universitari I Politècnic La Fe, 46026 Valencia, Spain
| | - María Teresa Fernández-Figueras
- Pathology Department, Hospital Universitari General de Catalunya-Grupo QuironSalud, 08915 Sant Cugat Del Vallès, Barcelona, Spain; School of Medicine, Campus Sant Cugat Del Vallès, Universitat Internacional de Catalunya (UIC), 08917 Sant Cugat Del Vallès, Spain
| | - Manel Esteller
- Institut de Recerca Contra La Leucèmia Josep Carreras (IJC), 08916 Badalona, Barcelona, Spain; Institució Catalana de Recerca I Estudis Avançats (ICREA), 08010 Barcelona, Spain; Faculty of Medicine and Health Sciences, Department of Physiological Sciences, Universitat de Barcelona (UB), 08007 Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
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48
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Yan S, Zhang J, Li L, Chen G, Chen Z, Zhan W. Bioinformatics analysis of markers based on m6A related to prognosis combined with immune invasion of rectal adenocarcinoma. Cancer Biomark 2024; 40:95-109. [PMID: 38306025 PMCID: PMC11191489 DOI: 10.3233/cbm-230123] [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: 03/29/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) is a common form of cancer, with rectal cancer accounting for approximately one-third of all cases. Among rectal cancers, 95% are classified as rectal adenocarcinoma (READ). Emerging evidence suggests that long noncoding RNAs (lncRNAs) play a significant role in the development and progression of various cancers. In our study, we aimed to identify differentially expressed lncRNAs potentially associated with m6A and establish a risk assessment model to predict clinical outcomes for READ patients. METHODS The READ dataset from the TCGA database was utilized in this study to synergistically and logically integrate m6A and lncRNA, while employing bioinformatics technology for the identification of suitable biomarkers. A risk prediction model comprising m6A-associated lncRNAs was constructed to investigate the prognostic, diagnostic, and biological functional relevance of these m6A-related lncRNAs. RESULTS Our research builds a composed of three related to m6A lncRNA rectal gland cancer prognosis model, and the model has been proved in the multi-dimensional can serve as the potential of the prognosis of rectal gland cancer biomarkers. Our study constructed a prognostic model of rectal adenocarcinoma consisting of three related m6A lncRNAs: linc00702, ac106900.1 and al583785.1. CONCLUSION The model has been validated as a potential prognostic biomarker for rectal cancer in multiple dimensions, aiming to provide clinicians with an indicator to assess the duration of straight adenocarcinoma. This enables early detection of rectal cancer and offers a promising target for immunotherapy.
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Affiliation(s)
- Shunkang Yan
- Department of Anorectal Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Jiandong Zhang
- Department of Anorectal Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Lianghe Li
- Department of Anorectal Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Gang Chen
- Department of Anorectal Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Zhongsheng Chen
- Department of Anorectal Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Wei Zhan
- Department of Anorectal Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
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49
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Aiderus A, Barker N, Tergaonkar V. Serrated colorectal cancer: preclinical models and molecular pathways. Trends Cancer 2024; 10:76-91. [PMID: 37880007 DOI: 10.1016/j.trecan.2023.09.011] [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: 08/15/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/27/2023]
Abstract
Serrated lesions are histologically heterogeneous, and detection can be challenging as these lesions have subtle features that may be missed by endoscopy. Furthermore, while approximately 30% of colorectal cancers (CRCs) arise from serrated lesions, only 8-10% of invasive serrated CRCs exhibit serrated morphology at presentation, suggesting potential loss of apparent characteristics with increased malignancy. Thus, understanding the genetic basis driving serrated CRC initiation and progression is critical to improve diagnosis and identify therapeutic biomarkers and targets to guide disease management. This review discusses the preclinical models of serrated CRCs reported to date and how these systems have been used to provide mechanistic insights into tumor initiation, progression, and novel treatment targets.
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Affiliation(s)
- Aziz Aiderus
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore.
| | - Nick Barker
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 2 Medical Drive, MD9, Singapore 117593, Republic of Singapore; Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Vinay Tergaonkar
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, MD7, Singapore 117596, Republic of Singapore
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50
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Su JY, Wang Y, Wu SS, Li WK, Wang CY, Ma JY, Qiu YT, Zhou MS, Wang Z, Li P, Liu CT, Wu J. Association between new plasma inflammatory markers and risk of colorectal neoplasms in individuals over 50 years old. Carcinogenesis 2023; 44:824-836. [PMID: 37713476 DOI: 10.1093/carcin/bgad064] [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: 01/12/2023] [Revised: 07/02/2023] [Accepted: 09/14/2023] [Indexed: 09/17/2023] Open
Abstract
OBJECTIVE(S) The prognostic value of systemic cytokine profiles and inflammatory markers in colorectal cancer were explored by several studies. We want to know more about inflammatory biomarkers in colorectal adenoma and early cancer. METHOD The level of 38 inflammatory markers in the plasma of 112 adenoma patients, 72 Tis-T1 staging of colorectal carcinoma patients, 34 T2-T4 staging of colorectal carcinoma patients and 53 normal subjects were detected and compared. RESULT(S) Eight inflammatory biomarkers (Eotaxin, GCSF, IL-4, IL-5, IL-17E, MCP-1, TNF-α and VEGF-A) have higher plasma concentrations in colorectal adenoma and cancer patients compared with normal participants over 50 years old. CONCLUSION(S) Inflammatory markers may have the prognostic value for colorectal adenoma and early-stage carcinoma.
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Affiliation(s)
- Jia-Yi Su
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- National Clinical Research Center for Digestive Diseases, Beijing 100050, China
- Beijing Digestive Disease Center, Beijing 100050, China
| | - Yun Wang
- Department of Presbyatrics, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Shang-Shang Wu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- National Clinical Research Center for Digestive Diseases, Beijing 100050, China
- Beijing Digestive Disease Center, Beijing 100050, China
- Department of Clinical Epidemiology and Evidence-based Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Wen-Kun Li
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- National Clinical Research Center for Digestive Diseases, Beijing 100050, China
- Beijing Digestive Disease Center, Beijing 100050, China
| | - Cheng-Yao Wang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- National Clinical Research Center for Digestive Diseases, Beijing 100050, China
- Beijing Digestive Disease Center, Beijing 100050, China
| | - Jiu-Yue Ma
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- National Clinical Research Center for Digestive Diseases, Beijing 100050, China
- Beijing Digestive Disease Center, Beijing 100050, China
| | - Yu-Ting Qiu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- National Clinical Research Center for Digestive Diseases, Beijing 100050, China
- Beijing Digestive Disease Center, Beijing 100050, China
| | - Min-Si Zhou
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- National Clinical Research Center for Digestive Diseases, Beijing 100050, China
- Beijing Digestive Disease Center, Beijing 100050, China
| | - Zhan Wang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- National Clinical Research Center for Digestive Diseases, Beijing 100050, China
- Beijing Digestive Disease Center, Beijing 100050, China
| | - Peng Li
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- National Clinical Research Center for Digestive Diseases, Beijing 100050, China
- Beijing Digestive Disease Center, Beijing 100050, China
| | - Chun-Tao Liu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- National Clinical Research Center for Digestive Diseases, Beijing 100050, China
- Beijing Digestive Disease Center, Beijing 100050, China
| | - Jing Wu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- National Clinical Research Center for Digestive Diseases, Beijing 100050, China
- Beijing Digestive Disease Center, Beijing 100050, China
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