1
|
Joanito I, Wirapati P, Zhao N, Nawaz Z, Yeo G, Lee F, Eng CLP, Macalinao DC, Kahraman M, Srinivasan H, Lakshmanan V, Verbandt S, Tsantoulis P, Gunn N, Venkatesh PN, Poh ZW, Nahar R, Oh HLJ, Loo JM, Chia S, Cheow LF, Cheruba E, Wong MT, Kua L, Chua C, Nguyen A, Golovan J, Gan A, Lim WJ, Guo YA, Yap CK, Tay B, Hong Y, Chong DQ, Chok AY, Park WY, Han S, Chang MH, Seow-En I, Fu C, Mathew R, Toh EL, Hong LZ, Skanderup AJ, DasGupta R, Ong CAJ, Lim KH, Tan EKW, Koo SL, Leow WQ, Tejpar S, Prabhakar S, Tan IB. Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer. Nat Genet 2022; 54:963-975. [PMID: 35773407 PMCID: PMC9279158 DOI: 10.1038/s41588-022-01100-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 05/16/2022] [Indexed: 12/12/2022]
Abstract
The consensus molecular subtype (CMS) classification of colorectal cancer is based on bulk transcriptomics. The underlying epithelial cell diversity remains unclear. We analyzed 373,058 single-cell transcriptomes from 63 patients, focusing on 49,155 epithelial cells. We identified a pervasive genetic and transcriptomic dichotomy of malignant cells, based on distinct gene expression, DNA copy number and gene regulatory network. We recapitulated these subtypes in bulk transcriptomes from 3,614 patients. The two intrinsic subtypes, iCMS2 and iCMS3, refine CMS. iCMS3 comprises microsatellite unstable (MSI-H) cancers and one-third of microsatellite-stable (MSS) tumors. iCMS3 MSS cancers are transcriptomically more similar to MSI-H cancers than to other MSS cancers. CMS4 cancers had either iCMS2 or iCMS3 epithelium; the latter had the worst prognosis. We defined the intrinsic epithelial axis of colorectal cancer and propose a refined ‘IMF’ classification with five subtypes, combining intrinsic epithelial subtype (I), microsatellite instability status (M) and fibrosis (F). A single-cell transcriptomic analysis of 63 patients with colorectal cancer classifies tumor cells into two epithelial subtypes. An improved tumor classification based on epithelial subtype, microsatellite stability and fibrosis reveals differences in pathway activation and metastasis.
Collapse
Affiliation(s)
- Ignasius Joanito
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Pratyaksha Wirapati
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nancy Zhao
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zahid Nawaz
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Grace Yeo
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Fiona Lee
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National Cancer Centre, Singapore, Singapore
| | - Christine L P Eng
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National Cancer Centre, Singapore, Singapore
| | | | - Merve Kahraman
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Harini Srinivasan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National Cancer Centre, Singapore, Singapore
| | | | - Sara Verbandt
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Petros Tsantoulis
- Hôpitaux Universitaires de Genève, Geneva, Switzerland.,University of Geneva, Geneva, Switzerland
| | - Nicole Gunn
- National Cancer Centre, Singapore, Singapore
| | - Prasanna Nori Venkatesh
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zhong Wee Poh
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Rahul Nahar
- MSD International GmbH (Singapore Branch), Singapore, Singapore
| | | | - Jia Min Loo
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shumei Chia
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Elsie Cheruba
- National University of Singapore, Singapore, Singapore
| | | | - Lindsay Kua
- National Cancer Centre, Singapore, Singapore
| | | | | | | | - Anna Gan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wan-Jun Lim
- National Cancer Centre, Singapore, Singapore
| | - Yu Amanda Guo
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Choon Kong Yap
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Brenda Tay
- National Cancer Centre, Singapore, Singapore
| | - Yourae Hong
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Dawn Qingqing Chong
- National Cancer Centre, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Aik-Yong Chok
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Shuting Han
- National Cancer Centre, Singapore, Singapore
| | - Mei Huan Chang
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Isaac Seow-En
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Cherylin Fu
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Ronnie Mathew
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Ee-Lin Toh
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore.,EL Toh Colorectal & Minimally Invasive Surgery, Singapore, Singapore
| | - Lewis Z Hong
- MSD International GmbH (Singapore Branch), Singapore, Singapore
| | - Anders Jacobsen Skanderup
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ramanuj DasGupta
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chin-Ann Johnny Ong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.,SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.,SingHealth Duke-NUS Surgery Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.,Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore
| | - Kiat Hon Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Emile K W Tan
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Si-Lin Koo
- National Cancer Centre, Singapore, Singapore
| | - Wei Qiang Leow
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Sabine Tejpar
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium.
| | - Shyam Prabhakar
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Iain Beehuat Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,National Cancer Centre, Singapore, Singapore. .,Duke-National University of Singapore Medical School, Singapore, Singapore.
| |
Collapse
|
2
|
Li Y, Gunn NA, Kua L, Lee FYX, Koo SL, Chua CWL, Tan E, Toh EL, Mathew R, Lee SY, Tan WS, Dasgupta R, Tan IB. Characterization of a patient-specific T-cell and tumor cell coculture model of immuno-cytotoxicity in colorectal cancer. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e14178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e14178 Background: Colorectal Cancer (CRC) is the third most commonly diagnosed cancer in the world. Yet, CRC has been difficult to treat with immunotherapy, as majority (85%) of CRC are Microsatellite stable (MSS), lowly immunogenic and do not respond well. To investigate immuno-cytotoxicity in MSS cancers, we set up an ex vivo co-culture model using patient-derived tumor epithelial cells and autologous tumor-infiltrating lymphocytes (TILs). Aims: To perform phenotypic and functional characterisation of the model, and show we are able to modulate immuno-cytotoxicity. Methods: Fresh tumor, adjacent normal and/or liver metastasis samples were collected and freshly dissociated from 29 colorectal cancer patients undergoing surgery. TILs and tumor epithelial cells were grown in culture. Weekly immunophenotyping of TILs was performed via flow cytometry and data was analysed to identify temporal changes in proportions of cell types. To modulate cytotoxicity, epithelial cell lines were co-cultured with autologous and allogeneic TILs at various effector:target ratios with and without anti-PD1 (Pembrolizumab). Caspase dye was used to detect apoptosis and measure cell death. Results: TILs from most patients were successfully expanded, with a theoretical potential of up to 10,000 times. CD4+ T cells were selectively expanded, while CD8+ T cells decreased in proportion over time. A select group of patients showed an opposite trend. Cell type proportions in metastases mirrored those of the primary tumour while NK cells expanded more in tumour samples than normal samples. Selection proceeded up to 3 weeks then decreased. In the cytotoxicity experiment, we show that cell death is increased at higher effector:target ratios in the presence of autologous TILs. Addition of Pembrolizumab further modulates cytotoxicity in vitro. Conclusions: We have developed and characterised an autologous T cell and epithelial cell co-culture system to evaluate immuno-cytotoxicity in colorectal cancer. This will allow screening of perturbations for improved immuno-cytotoxicity in colorectal cancer.
Collapse
Affiliation(s)
- Yanhui Li
- Duke-NUS Medical School, Singapore, Singapore
| | | | - Lindsay Kua
- Genome Institute of Singapore, Singapore, Singapore
| | | | - Si-Lin Koo
- National Cancer Center, Singapore, Singapore
| | | | | | - Ee-Lin Toh
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | | | - Ser Yee Lee
- Department of Surgical Oncology, National Cancer Centre, Singapore, Singapore
| | - Wah Siew Tan
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | | | - Iain B. Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| |
Collapse
|
3
|
Tan SQ, Lee Y, Lee FYX, Wang WW, Bok KX, Kua L, Lim WJ, Teo HM(V, Chia S, Loo JM, Yeo ESA, Tan WS, Toh EL, Chua C, Koo SL, Toh YC, Biswas SK, Toh HC, Dasgupta R, Tan IB. Ex vivo co-culture models for immunotherapy with patient-derived tumor infiltrating lymphocytes, peripheral blood mononuclear cells and autologous patient colorectal cancer (CRC) cell lines. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.e15531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Si Qi Tan
- Duke-NUS Medical School, Singapore, Singapore
| | - Yunqin Lee
- Singapore Immunology Network, Singapore, Singapore
| | | | | | - Ke Xin Bok
- Duke-NUS Medical School, Singapore, Singapore
| | - Lindsay Kua
- Genome Institute of Singapore, Singapore, Singapore
| | - Wan Jun Lim
- National Cancer Center Singapore, Singapore, Singapore
| | | | - Shumei Chia
- Genome Institute of Singapore, Singapore, Singapore
| | - Jia Min Loo
- Genome Institute of Singapore, Singapore, Singapore
| | - Eugene Shen Ann Yeo
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Wah Siew Tan
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Ee-Lin Toh
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Clarinda Chua
- National Cancer Center Singapore, Singapore, Singapore
| | - Si-Lin Koo
- National Cancer Centre Singapore, Singapore, Singapore
| | - Yi-Chin Toh
- National University of Singapore, Singapore, Singapore
| | | | | | | | | |
Collapse
|
4
|
Geva-Zatorsky N, Sefik E, Kua L, Pasman L, Tan TG, Ortiz-Lopez A, Yanortsang TB, Yang L, Jupp R, Mathis D, Benoist C, Kasper DL. Mining the Human Gut Microbiota for Immunomodulatory Organisms. Cell 2017; 168:928-943.e11. [PMID: 28215708 DOI: 10.1016/j.cell.2017.01.022] [Citation(s) in RCA: 472] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/01/2016] [Accepted: 01/19/2017] [Indexed: 12/16/2022]
Abstract
Within the human gut reside diverse microbes coexisting with the host in a mutually advantageous relationship. Evidence has revealed the pivotal role of the gut microbiota in shaping the immune system. To date, only a few of these microbes have been shown to modulate specific immune parameters. Herein, we broadly identify the immunomodulatory effects of phylogenetically diverse human gut microbes. We monocolonized mice with each of 53 individual bacterial species and systematically analyzed host immunologic adaptation to colonization. Most microbes exerted several specialized, complementary, and redundant transcriptional and immunomodulatory effects. Surprisingly, these were independent of microbial phylogeny. Microbial diversity in the gut ensures robustness of the microbiota's ability to generate a consistent immunomodulatory impact, serving as a highly important epigenetic system. This study provides a foundation for investigation of gut microbiota-host mutualism, highlighting key players that could identify important therapeutics.
Collapse
Affiliation(s)
- Naama Geva-Zatorsky
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Esen Sefik
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Lindsay Kua
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Lesley Pasman
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Tze Guan Tan
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Adriana Ortiz-Lopez
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Tsering Bakto Yanortsang
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Liang Yang
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ray Jupp
- UCB Pharma, Slough, Berkshire SL1 3WE, UK
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis L Kasper
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|