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Yu H, Chen Y, Deng J, Cai G, Fu W, Shentu C, Xu Y, Liu J, Zhou Y, Luo Y, Chen Y, Liu X, Wu Y, Xu T. Integrated metabolomics and proteomics analyses to reveal anticancer mechanism of hemp oil extract in colorectal cancer. J Pharm Biomed Anal 2024; 249:116379. [PMID: 39059180 DOI: 10.1016/j.jpba.2024.116379] [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: 05/06/2024] [Revised: 06/17/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024]
Abstract
Cannabis sativa L., with a rich history in Chinese folk medicine, includes hemp strains that offer substantial economic and medical benefits due to their non-addictive properties. Hemp has demonstrated various pharmaceutical activities, including anti-inflammatory, antioxidant, and anti-tumor effects. This study explores the potential of hemp oil extract (HOE) in treating colorectal cancer (CRC). Despite its promise, the specific anticancer mechanisms of HOE have not been well understood. To elucidate these mechanisms, we employed mass spectrometry-based metabolomics and proteomics to investigate the global effects of HOE on CRC cells. Additionally, bioinformatics approaches, including bulk RNA-seq and single-cell RNA-seq, were used to identify gene expression differences and cellular heterogeneity. The results were validated using flow cytometry, western blotting, and immunohistochemistry. Our findings reveal that HOE induces significant alterations in purine metabolism pathways, down-regulates c-MYC, and inhibits the expression of cell cycle-related proteins such as CCND1, CDK4, and CDK6, leading to cell cycle arrest in the G1 phase. This comprehensive analysis demonstrates that HOE effectively blocks the cell cycle in the G1 phase, thereby inhibiting colorectal cancer cell proliferation. These findings provide experimental evidence supporting the potential therapeutic use of hemp in medicine.
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Affiliation(s)
- Hengyuan Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, Wenzhou 325800, China
| | - Yang Chen
- Department of Clinical Pharmacy, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Xihu University School of Medicine, Hangzhou 310006, China
| | - Jiayin Deng
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guoxin Cai
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Weiliang Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chengyu Shentu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Youdong Xu
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jie Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Shandong C.P. Freda Pharmaceutical Co., Ltd., Jinan 250104, China
| | - Yuan Zhou
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Yingjie Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, Wenzhou 325800, China
| | - Yong Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, Wenzhou 325800, China
| | - Xuesong Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, Wenzhou 325800, China
| | - Yongjiang Wu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Tengfei Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, Wenzhou 325800, China.
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2
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Guo Y, Ren C, He Y, Wu Y, Yang X. Deciphering the spatiotemporal transcriptional landscape of intestinal diseases (Review). Mol Med Rep 2024; 30:157. [PMID: 38994768 PMCID: PMC11258600 DOI: 10.3892/mmr.2024.13281] [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: 11/21/2023] [Accepted: 04/19/2024] [Indexed: 07/13/2024] Open
Abstract
The intestines are the largest barrier organ in the human body. The intestinal barrier plays a crucial role in maintaining the balance of the intestinal environment and protecting the intestines from harmful bacterial invasion. Single‑cell RNA sequencing technology allows the detection of the different cell types in the intestine in two dimensions and the exploration of cell types that have not been fully characterized. The intestinal mucosa is highly complex in structure, and its proper functioning is linked to multiple structures in the proximal‑distal intestinal and luminal‑mucosal axes. Spatial localization is at the core of the efforts to explore the interactions between the complex structures. Spatial transcriptomics (ST) is a method that allows for comprehensive tissue analysis and the acquisition of spatially separated genetic information from individual cells, while preserving their spatial location and interactions. This approach also prevents the loss of fragile cells during tissue disaggregation. The emergence of ST technology allows us to spatially dissect enzymatic processes and interactions between multiple cells, genes, proteins and signals in the intestine. This includes the exchange of oxygen and nutrients in the intestine, different gradients of microbial populations and the role of extracellular matrix proteins. This regionally precise approach to tissue studies is gaining more acceptance and is increasingly applied in the investigation of disease mechanisms related to the gastrointestinal tract. Therefore, this review summarized the application of ST in gastrointestinal diseases.
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Affiliation(s)
- Yajing Guo
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610075, P.R. China
| | - Chao Ren
- Graduate School, Hunan University of Traditional Chinese Medicine, Changsha, Hunan 410208, P.R. China
| | - Yuxi He
- Department of Digestive Medicine, Chongqing City Hospital of Traditional Chinese Medicine, Chongqing 400021, P.R. China
| | - Yue Wu
- Department of Digestive Medicine, Chongqing City Hospital of Traditional Chinese Medicine, Chongqing 400021, P.R. China
| | - Xiaojun Yang
- Department of Digestive Medicine, Chongqing City Hospital of Traditional Chinese Medicine, Chongqing 400021, P.R. China
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3
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Teillaud JL, Houel A, Panouillot M, Riffard C, Dieu-Nosjean MC. Tertiary lymphoid structures in anticancer immunity. Nat Rev Cancer 2024; 24:629-646. [PMID: 39117919 DOI: 10.1038/s41568-024-00728-0] [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: 07/02/2024] [Indexed: 08/10/2024]
Abstract
Tertiary lymphoid structures (TLS) are transient ectopic lymphoid aggregates where adaptive antitumour cellular and humoral responses can be elaborated. Initially described in non-small cell lung cancer as functional immune lymphoid structures associated with better clinical outcome, TLS have also been found in many other carcinomas, as well as melanomas and sarcomas, and associated with improved response to immunotherapy. The manipulation of TLS as a therapeutic strategy is now coming of age owing to the likely role of TLS in the improved survival of patients with cancer receiving immune checkpoint inhibitor treatment. TLS have also garnered considerable interest as a predictive biomarker of the response to antitumour therapies, including immune checkpoint blockade and, possibly, chemotherapy. However, several important questions still remain regarding the definition of TLS in terms of both their cellular composition and functions. Here, we summarize the current views on the composition of TLS at different stages of their development. We also discuss the role of B cells and T cells associated with TLS and their dialogue in mounting antibody and cellular antitumour responses, as well as some of the various mechanisms that negatively regulate antitumour activity of TLS. The prognostic value of TLS to the clinical outcome of patients with cancer and the relationship between TLS and the response to therapy are then addressed. Finally, we present some preclinical evidence that favours the idea that manipulating the formation and function of TLS could lead to a potent next-generation cancer immunotherapy.
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Affiliation(s)
- Jean-Luc Teillaud
- Sorbonne University UMRS1135, Paris, France
- Inserm U1135, Paris, France
- Center of Immunology and Microbial Infections (Cimi), Faculty of Health, Paris, France
| | - Ana Houel
- Sorbonne University UMRS1135, Paris, France
- Inserm U1135, Paris, France
- Center of Immunology and Microbial Infections (Cimi), Faculty of Health, Paris, France
- Transgene, Illkirch-Graffenstaden, France
| | - Marylou Panouillot
- Sorbonne University UMRS1135, Paris, France
- Inserm U1135, Paris, France
- Center of Immunology and Microbial Infections (Cimi), Faculty of Health, Paris, France
- Sanofi, Vitry-sur-Seine, France
| | - Clémence Riffard
- Sorbonne University UMRS1135, Paris, France
- Inserm U1135, Paris, France
- Center of Immunology and Microbial Infections (Cimi), Faculty of Health, Paris, France
| | - Marie-Caroline Dieu-Nosjean
- Sorbonne University UMRS1135, Paris, France.
- Inserm U1135, Paris, France.
- Center of Immunology and Microbial Infections (Cimi), Faculty of Health, Paris, France.
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Chen J, Larsson L, Swarbrick A, Lundeberg J. Spatial landscapes of cancers: insights and opportunities. Nat Rev Clin Oncol 2024; 21:660-674. [PMID: 39043872 DOI: 10.1038/s41571-024-00926-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2024] [Indexed: 07/25/2024]
Abstract
Solid tumours comprise many different cell types organized in spatially structured arrangements, with substantial intratumour and intertumour heterogeneity. Advances in spatial profiling technologies over the past decade hold promise to capture the complexity of these cellular architectures to build a holistic view of the intricate molecular mechanisms that shape the tumour ecosystem. Some of these mechanisms act at the cellular scale and are controlled by cell-autonomous programmes or communication between nearby cells, whereas other mechanisms result from coordinated efforts between large networks of cells and extracellular molecules organized into tissues and organs. In this Review we provide insights into the application of single-cell and spatial profiling tools, with a focus on spatially resolved transcriptomic tools developed to understand the cellular architecture of the tumour microenvironment and identify opportunities to use them to improve clinical management of cancers.
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Affiliation(s)
- Julia Chen
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Department of Medical Oncology, St George Hospital, Sydney, New South Wales, Australia
| | - Ludvig Larsson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
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Cao H, Lan T, Kuang S, Wang L, Li J, Li Q, Li Y, Xu Q, Chen Q, Ren S, Lan C, Ouyang N, Liao J, Huang Y, Li J. FAT1 as a tumor mutation burden specific gene affects the immunotherapy effect in head and neck squamous cell cancer. Drug Resist Updat 2024; 76:101095. [PMID: 38986165 DOI: 10.1016/j.drup.2024.101095] [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: 12/10/2023] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 07/12/2024]
Abstract
BACKGROUND Response to immunotherapy is the main challenge of head and neck squamous cancer (HNSCC) treatment. Previous studies have indicated that tumor mutational burden (TMB) is associated with prognosis, but it is not always a precise index. Hence, investigating specific genetic mutations and tumor microenvironment (TME) changes in TMB-high patients is essential for precision therapy of HNSCC. METHODS A total of 33 HNSCC patients were enrolled in this study. We calculated the TMB score based on next-generation sequencing (NGS) sequencing and grouped these patients based on TMB score. Then, we examined the immune microenvironment of HNSCC using assessments of the bulk transcriptome and the single-cell RNA sequence (scRNA-seq) focusing on the molecular nature of TMB and mutations in HNSCC from our cohort. The association of the mutation pattern and TMB was analyzed in The Cancer Genome Atlas (TCGA) and validated by our cohort. RESULTS 33 HNSCC patients were divided into three groups (TMB-low, -medium, and -high) based on TMB score. In the result of 520-gene panel sequencing data, we found that FAT1 and LRP1B mutations were highly prevalent in TMB-high patients. FAT1 mutations are associated with resistance to immunotherapy in HNSCC patients. This involves many metabolism-related pathways like RERE, AIRE, HOMER1, etc. In the scRNA-seq data, regulatory T cells (Tregs), monocytes, and DCs were found mainly enriched in TMB-high samples. CONCLUSION Our analysis unraveled the FAT1 gene as an assistant predictor when we use TMB as a biomarker of drug resistance in HNSCC. Tregs, monocytes, and dendritic cells (DCs) were found mainly enriched in TMB-high samples.
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Affiliation(s)
- Haotian Cao
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510010, China.
| | - Tianjun Lan
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510010, China
| | - Shijia Kuang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510010, China
| | - Liansheng Wang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510010, China
| | - Jintao Li
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510010, China
| | - Qunxin Li
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510010, China
| | - Yanyan Li
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510010, China
| | - Qiuping Xu
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Qian Chen
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120, China
| | - Shuwei Ren
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Chunhong Lan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Nengtai Ouyang
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jianwei Liao
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Yongsheng Huang
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Jinsong Li
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital of Sun Yat-Sen University, Guangzhou 510010, China.
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6
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Cañellas-Socias A, Sancho E, Batlle E. Mechanisms of metastatic colorectal cancer. Nat Rev Gastroenterol Hepatol 2024; 21:609-625. [PMID: 38806657 DOI: 10.1038/s41575-024-00934-z] [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: 04/17/2024] [Indexed: 05/30/2024]
Abstract
Despite extensive research and improvements in understanding colorectal cancer (CRC), its metastatic form continues to pose a substantial challenge, primarily owing to limited therapeutic options and a poor prognosis. This Review addresses the emerging focus on metastatic CRC (mCRC), which has historically been under-studied compared with primary CRC despite its lethality. We delve into two crucial aspects: the molecular and cellular determinants facilitating CRC metastasis and the principles guiding the evolution of metastatic disease. Initially, we examine the genetic alterations integral to CRC metastasis, connecting them to clinically marked characteristics of advanced CRC. Subsequently, we scrutinize the role of cellular heterogeneity and plasticity in metastatic spread and therapy resistance. Finally, we explore how the tumour microenvironment influences metastatic disease, emphasizing the effect of stromal gene programmes and the immune context. The ongoing research in these fields holds immense importance, as its future implications are projected to revolutionize the treatment of patients with mCRC, hopefully offering a promising outlook for their survival.
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Affiliation(s)
- Adrià Cañellas-Socias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
| | - Elena Sancho
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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7
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White BS, de Reyniès A, Newman AM, Waterfall JJ, Lamb A, Petitprez F, Lin Y, Yu R, Guerrero-Gimenez ME, Domanskyi S, Monaco G, Chung V, Banerjee J, Derrick D, Valdeolivas A, Li H, Xiao X, Wang S, Zheng F, Yang W, Catania CA, Lang BJ, Bertus TJ, Piermarocchi C, Caruso FP, Ceccarelli M, Yu T, Guo X, Bletz J, Coller J, Maecker H, Duault C, Shokoohi V, Patel S, Liliental JE, Simon S, Saez-Rodriguez J, Heiser LM, Guinney J, Gentles AJ. Community assessment of methods to deconvolve cellular composition from bulk gene expression. Nat Commun 2024; 15:7362. [PMID: 39191725 DOI: 10.1038/s41467-024-50618-0] [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: 08/28/2023] [Accepted: 07/11/2024] [Indexed: 08/29/2024] Open
Abstract
We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression of tumor samples, through a community-wide DREAM Challenge. We assess six published and 22 community-contributed methods using in vitro and in silico transcriptional profiles of admixed cancer and healthy immune cells. Several published methods predict most cell types well, though they either were not trained to evaluate all functional CD8+ T cell states or do so with low accuracy. Several community-contributed methods address this gap, including a deep learning-based approach, whose strong performance establishes the applicability of this paradigm to deconvolution. Despite being developed largely using immune cells from healthy tissues, deconvolution methods predict levels of tumor-derived immune cells well. Our admixed and purified transcriptional profiles will be a valuable resource for developing deconvolution methods, including in response to common challenges we observe across methods, such as sensitive identification of functional CD4+ T cell states.
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Affiliation(s)
- Brian S White
- Sage Bionetworks, Seattle, WA, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Aurélien de Reyniès
- Centre de Recherche des Cordeliers, INSERM U1138, Université Paris Cité, Paris, France
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Joshua J Waterfall
- INSERM U830 and Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | | | - Florent Petitprez
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
- MRC Centre for Reproductive Health, the Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Yating Lin
- Xiamen University, Xiamen, Fujian, China
| | | | - Martin E Guerrero-Gimenez
- Institute of Biochemistry and Biotechnology, School of Medicine, National University of Cuyo, Mendoza, Argentina
| | | | - Gianni Monaco
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, AV, Italy
| | | | | | - Daniel Derrick
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Alberto Valdeolivas
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Haojun Li
- Xiamen University, Xiamen, Fujian, China
| | - Xu Xiao
- Xiamen University, Xiamen, Fujian, China
| | - Shun Wang
- Department of Pathology, Cancer Hospital, Chinese Aacdemy of Medical Science, Beijing, China
| | | | | | - Carlos A Catania
- Laboratory of Intelligent Systems (LABSIN), Engineering School, National University of Cuyo, Mendoza, Argentina
| | - Benjamin J Lang
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | | | - Francesca P Caruso
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, AV, Italy
| | - Michele Ceccarelli
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, AV, Italy
- Sylvester Comprehensive Cancer Center, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, Florida, USA
| | | | | | | | - John Coller
- Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA, USA
| | - Holden Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Caroline Duault
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Vida Shokoohi
- Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA, USA
| | - Shailja Patel
- Translational Applications Service Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Joanna E Liliental
- Translational Applications Service Center, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Laura M Heiser
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | | | - Andrew J Gentles
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
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8
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Single-cell atlas defines distinct immune escape mechanisms in colorectal cancer. NATURE CANCER 2024:10.1038/s43018-024-00809-x. [PMID: 39179927 DOI: 10.1038/s43018-024-00809-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
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9
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Gulati GS, D'Silva JP, Liu Y, Wang L, Newman AM. Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00768-2. [PMID: 39169166 DOI: 10.1038/s41580-024-00768-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2024] [Indexed: 08/23/2024]
Abstract
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has emerged as a tool to contextualize single cells in multicellular neighbourhoods and to identify spatially recurrent phenotypes, or ecotypes. These technologies have generated vast datasets with targeted-transcriptome and whole-transcriptome profiles of hundreds to millions of cells. Such data have provided new insights into developmental hierarchies, cellular plasticity and diverse tissue microenvironments, and spurred a burst of innovation in computational methods for single-cell analysis. In this Review, we discuss recent advancements, ongoing challenges and prospects in identifying and characterizing cell states and multicellular neighbourhoods. We discuss recent progress in sample processing, data integration, identification of subtle cell states, trajectory modelling, deconvolution and spatial analysis. Furthermore, we discuss the increasing application of deep learning, including foundation models, in analysing single-cell and spatial transcriptomics data. Finally, we discuss recent applications of these tools in the fields of stem cell biology, immunology, and tumour biology, and the future of single-cell and spatial transcriptomics in biological research and its translation to the clinic.
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Affiliation(s)
- Gunsagar S Gulati
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Yunhe Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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10
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Chu X, Li X, Zhang Y, Dang G, Miao Y, Xu W, Wang J, Zhang Z, Cheng S. Integrative single-cell analysis of human colorectal cancer reveals patient stratification with distinct immune evasion mechanisms. NATURE CANCER 2024:10.1038/s43018-024-00807-z. [PMID: 39147986 DOI: 10.1038/s43018-024-00807-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 07/16/2024] [Indexed: 08/17/2024]
Abstract
The tumor microenvironment (TME) considerably influences colorectal cancer (CRC) progression, therapeutic response and clinical outcome, but studies of interindividual heterogeneities of the TME in CRC are lacking. Here, by integrating human colorectal single-cell transcriptomic data from approximately 200 donors, we comprehensively characterized transcriptional remodeling in the TME compared to noncancer tissues and identified a rare tumor-specific subset of endothelial cells with T cell recruitment potential. The large sample size enabled us to stratify patients based on their TME heterogeneity, revealing divergent TME subtypes in which cancer cells exploit different immune evasion mechanisms. Additionally, by associating single-cell transcriptional profiling with risk genes identified by genome-wide association studies, we determined that stromal cells are major effector cell types in CRC genetic susceptibility. In summary, our results provide valuable insights into CRC pathogenesis and might help with the development of personalized immune therapies.
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Affiliation(s)
| | | | - Yu Zhang
- Changping Laboratory, Beijing, China
| | - Guohui Dang
- Changping Laboratory, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | | | - Wenbin Xu
- Changping Laboratory, Beijing, China
| | | | - Zemin Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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11
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Stary V, Pandey RV, List J, Kleissl L, Deckert F, Kabiljo J, Laengle J, Gerakopoulos V, Oehler R, Watzke L, Farlik M, Lukowski SW, Vogt AB, Stary G, Stockinger H, Bergmann M, Pilat N. Dysfunctional tumor-infiltrating Vδ1 + T lymphocytes in microsatellite-stable colorectal cancer. Nat Commun 2024; 15:6949. [PMID: 39138181 PMCID: PMC11322529 DOI: 10.1038/s41467-024-51025-1] [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: 06/23/2023] [Accepted: 07/24/2024] [Indexed: 08/15/2024] Open
Abstract
Although γδ T cells are known to participate in immune dysregulation in solid tumors, their relevance to human microsatellite-stable (MSS) colorectal cancer (CRC) is still undefined. Here, using integrated gene expression analysis and T cell receptor sequencing, we characterized γδ T cells in MSS CRC, with a focus on Vδ1 + T cells. We identified Vδ1+ T cells with shared motifs in the third complementarity-determining region of the δ-chain, reflective of antigen recognition. Changes in gene and protein expression levels suggested a dysfunctional effector state of Vδ1+ T cells in MSS CRC, distinct from Vδ1+ T cells in microsatellite-instable (MSI). Interaction analysis highlighted an immunosuppressive role of fibroblasts in the dysregulation of Vδ1+ T cells in MSS CRC via the TIGIT-NECTIN2 axis. Blocking this pathway with a TIGIT antibody partially restored cytotoxicity of the dysfunctional Vδ1 phenotype. These results define an operative pathway in γδ T cells in MSS CRC.
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MESH Headings
- Humans
- Colorectal Neoplasms/immunology
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/pathology
- Lymphocytes, Tumor-Infiltrating/immunology
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Receptors, Immunologic/immunology
- Microsatellite Instability
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Microsatellite Repeats/genetics
- Gene Expression Regulation, Neoplastic
- Female
- Male
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
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Affiliation(s)
- Victoria Stary
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria.
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria.
| | - Ram V Pandey
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Julia List
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Lisa Kleissl
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Florian Deckert
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Julijan Kabiljo
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Johannes Laengle
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Vasileios Gerakopoulos
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Rudolf Oehler
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Lukas Watzke
- Medical University of Vienna, Department of Pathology, Vienna, Austria
| | - Matthias Farlik
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Samuel W Lukowski
- Department of Human Cancer Immunology, Boehringer Ingelheim RCV GmBH & Co KG., Dr. Boehringer Gasse 5-11, 1120, Vienna, Austria
| | - Anne B Vogt
- Department of Human Cancer Immunology, Boehringer Ingelheim RCV GmBH & Co KG., Dr. Boehringer Gasse 5-11, 1120, Vienna, Austria
| | - Georg Stary
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Hannes Stockinger
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
| | - Michael Bergmann
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Nina Pilat
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
- Medical University of Vienna, Department of Cardiac Surgery, Vienna, Austria
- Medical University of Vienna, Center for Biomedical Research and Translational Surgery, Vienna, Austria
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12
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Zhou Y, Yang M, Fu R, Liu W, Cai Z, Lin H, Li S, Zong C, Chen Y, Tong Z. Interleukin-17F suppressed colon cancer by enhancing caspase 4 mediated pyroptosis of endothelial cells. Sci Rep 2024; 14:18363. [PMID: 39112724 PMCID: PMC11306372 DOI: 10.1038/s41598-024-69436-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: 05/15/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024] Open
Abstract
The combination of anti-angiogenic treatment and immunotherapy presents a promising strategy against colon cancer. Interleukin-17F (IL-17F) emerges as a critical immune cell cytokine expressed in colonic epithelial cells, demonstrating potential in inhibiting angiogenesis. In order to clarify the roles of IL-17F in the colon cancer microenvironment and elucidate its mechanism, we established a mouse colon carcinoma cell line CT26 overexpressing IL-17F and transplanted it subcutaneously into syngeneic BALB/c mice. We also analyzed induced colon tumor in IL-17F knockout and wild type mice. Our results demonstrated that IL-17F could suppress colon tumor growth in vivo with inhibited angiogenesis and enhanced recruitment of cysteine-cysteine motif chemokine receptor 6 (CCR6) positive immune cells. Additionally, IL-17F suppressed the tube formation, cell growth and migration of endothelial cells EOMA in vitro. Comprehensive bioinformatics analysis of transcriptome profiles between EOMA cells and those treated with three different concentrations of IL-17F identified 109 differentially expressed genes. Notably, a potential new target, Caspase 4, showed increased expressions after IL-17F treatment in endothelial cells. Further molecular validation revealed a novel downstream signaling for IL-17F: IL-17F enhanced Caspase 4/GSDMD signaling of endothelial cells, CT26 cells and CT26 transplanted tumors, while IL-17F knockout colon tumors exhibited decreased Caspase 4/GSDMD signaling. The heightened expression of the GSDMD N-terminus, coupled with increased cellular propidium iodide (PI) uptake and lactate dehydrogenase (LDH) release, revealed that IL-17F promoted pyroptosis of endothelial cells. Altogether, IL-17F could modulate the colon tumor microenvironment with inhibited angiogenesis, underscoring its potential as a therapeutic target for colon cancer.
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Affiliation(s)
- Ying Zhou
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Donghu Road, No. 185, Wuhan, 430071, China
| | - Mei Yang
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Donghu Road, No. 185, Wuhan, 430071, China
| | - Rishun Fu
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Donghu Road, No. 185, Wuhan, 430071, China
| | - Weihuang Liu
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Donghu Road, No. 185, Wuhan, 430071, China
| | - Zihan Cai
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Donghu Road, No. 185, Wuhan, 430071, China
| | - Hanyu Lin
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Donghu Road, No. 185, Wuhan, 430071, China
| | - Siheng Li
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Donghu Road, No. 185, Wuhan, 430071, China
| | - Chuanyu Zong
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Donghu Road, No. 185, Wuhan, 430071, China
| | - Yun Chen
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Donghu Road, No. 185, Wuhan, 430071, China
| | - Zan Tong
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Donghu Road, No. 185, Wuhan, 430071, China.
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13
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Jonchère V, Montémont H, Le Scanf E, Siret A, Letourneur Q, Tubacher E, Battail C, Fall A, Labreche K, Renault V, Ratovomanana T, Buhard O, Jolly A, Le Rouzic P, Feys C, Despras E, Zouali H, Nicolle R, Cervera P, Svrcek M, Bourgoin P, Blanché H, Boland A, Lefèvre J, Parc Y, Touat M, Bielle F, Arzur D, Cueff G, Le Jossic-Corcos C, Quéré G, Dujardin G, Blondel M, Le Maréchal C, Cohen R, André T, Coulet F, de la Grange P, de Reyniès A, Fléjou JF, Renaud F, Alentorn A, Corcos L, Deleuze JF, Collura A, Duval A. Microsatellite instability at U2AF-binding polypyrimidic tract sites perturbs alternative splicing during colorectal cancer initiation. Genome Biol 2024; 25:210. [PMID: 39107855 PMCID: PMC11304650 DOI: 10.1186/s13059-024-03340-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Microsatellite instability (MSI) due to mismatch repair deficiency (dMMR) is common in colorectal cancer (CRC). These cancers are associated with somatic coding events, but the noncoding pathophysiological impact of this genomic instability is yet poorly understood. Here, we perform an analysis of coding and noncoding MSI events at the different steps of colorectal tumorigenesis using whole exome sequencing and search for associated splicing events via RNA sequencing at the bulk-tumor and single-cell levels. RESULTS Our results demonstrate that MSI leads to hundreds of noncoding DNA mutations, notably at polypyrimidine U2AF RNA-binding sites which are endowed with cis-activity in splicing, while higher frequency of exon skipping events are observed in the mRNAs of MSI compared to non-MSI CRC. At the DNA level, these noncoding MSI mutations occur very early prior to cell transformation in the dMMR colonic crypt, accounting for only a fraction of the exon skipping in MSI CRC. At the RNA level, the aberrant exon skipping signature is likely to impair colonic cell differentiation in MSI CRC affecting the expression of alternative exons encoding protein isoforms governing cell fate, while also targeting constitutive exons, making dMMR cells immunogenic in early stage before the onset of coding mutations. This signature is characterized by its similarity to the oncogenic U2AF1-S34F splicing mutation observed in several other non-MSI cancer. CONCLUSIONS Overall, these findings provide evidence that a very early RNA splicing signature partly driven by MSI impairs cell differentiation and promotes MSI CRC initiation, far before coding mutations which accumulate later during MSI tumorigenesis.
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Affiliation(s)
- Vincent Jonchère
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | - Hugo Montémont
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | - Enora Le Scanf
- INSERM, UMR 1078, Université de Brest, Génétique Génomique Fonctionnelle Et Biotechnologies, Etablissement Français du Sang, F-29200, Brest, France
- CHU de Brest, Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, F-29200, France
| | - Aurélie Siret
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | - Quentin Letourneur
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | - Emmanuel Tubacher
- Laboratory for Genomics, Foundation Jean Dausset-CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Christophe Battail
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Assane Fall
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | - Karim Labreche
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | - Victor Renault
- Laboratory for Genomics, Foundation Jean Dausset-CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Toky Ratovomanana
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | - Olivier Buhard
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | | | - Philippe Le Rouzic
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | - Cody Feys
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | - Emmanuelle Despras
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | - Habib Zouali
- Laboratory for Genomics, Foundation Jean Dausset-CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Rémy Nicolle
- Programme "Cartes d'Identité Des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Pascale Cervera
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
- Department of Pathology, Sorbonne Université, AP-HP.Sorbonne UniversitéHôpital Saint-Antoine, 47-83 Boulevard de L'hôpital, 75012, Paris, France
| | - Magali Svrcek
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
- Department of Pathology, Sorbonne Université, AP-HP.Sorbonne UniversitéHôpital Saint-Antoine, 47-83 Boulevard de L'hôpital, 75012, Paris, France
| | - Pierre Bourgoin
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
- Department of Pathology, Sorbonne Université, AP-HP.Sorbonne UniversitéHôpital Saint-Antoine, 47-83 Boulevard de L'hôpital, 75012, Paris, France
| | - Hélène Blanché
- Laboratory for Genomics, Foundation Jean Dausset-CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jérémie Lefèvre
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
- Department of Digestive Surgery, Sorbonne Université, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Yann Parc
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
- Department of Digestive Surgery, Sorbonne Université, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Mehdi Touat
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
- Sorbonne Université, Inserm, CNRS, UMR S 1127 and SIRIC CURAMUS, Institut du Cerveau Et de La Moelle Épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2 Mazarin, Paris, France
| | - Franck Bielle
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau Et de La Moelle Épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neuropathologie Laboratoire Escourolle, Paris, France
| | - Danielle Arzur
- INSERM, UMR 1078, Université de Brest, Génétique Génomique Fonctionnelle Et Biotechnologies, Etablissement Français du Sang, F-29200, Brest, France
- CHU de Brest, Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, F-29200, France
| | - Gwennina Cueff
- INSERM, UMR 1078, Université de Brest, Génétique Génomique Fonctionnelle Et Biotechnologies, Etablissement Français du Sang, F-29200, Brest, France
- CHU de Brest, Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, F-29200, France
| | - Catherine Le Jossic-Corcos
- INSERM, UMR 1078, Université de Brest, Génétique Génomique Fonctionnelle Et Biotechnologies, Etablissement Français du Sang, F-29200, Brest, France
- CHU de Brest, Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, F-29200, France
| | - Gaël Quéré
- INSERM, UMR 1078, Université de Brest, Génétique Génomique Fonctionnelle Et Biotechnologies, Etablissement Français du Sang, F-29200, Brest, France
- CHU de Brest, Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, F-29200, France
| | - Gwendal Dujardin
- INSERM, UMR 1078, Université de Brest, Génétique Génomique Fonctionnelle Et Biotechnologies, Etablissement Français du Sang, F-29200, Brest, France
- CHU de Brest, Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, F-29200, France
| | - Marc Blondel
- INSERM, UMR 1078, Université de Brest, Génétique Génomique Fonctionnelle Et Biotechnologies, Etablissement Français du Sang, F-29200, Brest, France
- CHU de Brest, Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, F-29200, France
| | - Cédric Le Maréchal
- INSERM, UMR 1078, Université de Brest, Génétique Génomique Fonctionnelle Et Biotechnologies, Etablissement Français du Sang, F-29200, Brest, France
- CHU de Brest, Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, F-29200, France
| | - Romain Cohen
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
- Department of Medical Oncology, Sorbonne Université, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Thierry André
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
- Department of Medical Oncology, Sorbonne Université, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Florence Coulet
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
- Genetics Department, AP-HP.Sorbonne Université, Paris, France
| | | | - Aurélien de Reyniès
- Programme "Cartes d'Identité Des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Jean-François Fléjou
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
- Department of Pathology, Sorbonne Université, AP-HP.Sorbonne UniversitéHôpital Saint-Antoine, 47-83 Boulevard de L'hôpital, 75012, Paris, France
| | - Florence Renaud
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | - Agusti Alentorn
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | - Laurent Corcos
- INSERM, UMR 1078, Université de Brest, Génétique Génomique Fonctionnelle Et Biotechnologies, Etablissement Français du Sang, F-29200, Brest, France
- CHU de Brest, Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, F-29200, France
| | - Jean-François Deleuze
- Laboratory for Genomics, Foundation Jean Dausset-CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Ada Collura
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France
| | - Alex Duval
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité Des Microsatellites Et Cancer, Equipe Labellisée Par La Ligue Nationale Contre Le Cancer, 75012, Paris, France.
- Genetics Department, AP-HP.Sorbonne Université, Paris, France.
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14
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Wang H, Torous W, Gong B, Purdom E. Visualizing scRNA-Seq Data at Population Scale with GloScope. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.29.542786. [PMID: 37398321 PMCID: PMC10312527 DOI: 10.1101/2023.05.29.542786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Increasingly, scRNA-Seq studies explore cell populations across different samples and the effect of sample heterogeneity on organism's phenotype. However, relatively few bioinformatic methods have been developed which adequately address the variation between samples for such population-level analyses. We propose a framework for representing the entire single-cell profile of a sample, which we call a GloScope representation. We implement GloScope on scRNA-Seq datasets from study designs ranging from 12 to over 300 samples and demonstrate how GloScope allows researchers to perform essential bioinformatic tasks at the sample-level, in particular visualization and quality control assessment.
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Affiliation(s)
- Hao Wang
- Division of Biostatistics, University of California, Berkeley, CA, USA
| | - William Torous
- Department of Statistics, University of California, Berkeley, CA, USA
| | - Boying Gong
- Division of Biostatistics, University of California, Berkeley, CA, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
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15
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Isnard P, Li D, Xuanyuan Q, Wu H, Humphreys BD. Histopathological-Based Analysis of Human Kidney Spatial Transcriptomics Data: Toward Precision Pathology. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00274-8. [PMID: 39097165 DOI: 10.1016/j.ajpath.2024.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 06/04/2024] [Accepted: 06/26/2024] [Indexed: 08/05/2024]
Abstract
The application of spatial transcriptomics (ST) technologies is booming and has already yielded important insights across many different tissues and disease models. In nephrology, ST technologies have helped to decipher the cellular and molecular mechanisms at work in kidney diseases and have allowed the recent creation of spatially anchored human kidney atlases in healthy and diseased kidney tissues. During ST data analysis, the obtained computationally annotated clusters are often superimposed on a histologic image without their initial identification being based on the morphologic and spatial analyses of the tissues and lesions. In this study, we conduct a histopathologic-based analysis of ST data on a human kidney sample corresponding as closely as possible to the reality of the interpretation of a kidney biopsy sample in a health care or research context. This study shows the feasibility of a morphology-based approach to interpreting ST data, helping to improve our understanding of the lesion phenomena at work in chronic kidney disease at both the cellular and the molecular level. Finally, we show that our newly identified pathology-based clusters can be accurately projected onto other slides from nephrectomy or needle biopsy samples. They thus serve as a reference for analyzing other kidney tissues, paving the way for the future of molecular microscopy and precision pathology.
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Affiliation(s)
- Pierre Isnard
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Dian Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Qiao Xuanyuan
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri; Department of Developmental Biology, Washington University in St. Louis, St. Louis, Missouri.
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16
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Tao Y, Feng F, Luo X, Reihsmann CV, Hopkirk AL, Cartailler JP, Brissova M, Parker SCJ, Saunders DC, Liu J. CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images. PLoS Comput Biol 2024; 20:e1012344. [PMID: 39196899 DOI: 10.1371/journal.pcbi.1012344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 07/22/2024] [Indexed: 08/30/2024] Open
Abstract
Recent studies show that cellular neighborhoods play an important role in evolving biological events such as cancer and diabetes. Therefore, it is critical to accurately and efficiently identify cellular neighborhoods from spatially-resolved single-cell transcriptomic data or single-cell resolution tissue imaging data. In this work, we develop CNTools, a computational toolbox for end-to-end cellular neighborhood analysis on annotated cell images, comprising both the identification and analysis steps. It includes state-of-the-art cellular neighborhood identification methods and post-identification smoothing techniques, with our newly proposed Cellular Neighbor Embedding (CNE) method and Naive Smoothing technique, as well as several established downstream analysis approaches. We applied CNTools on three real-world CODEX datasets and evaluated identification methods with smoothing techniques quantitatively and qualitatively. It shows that CNE with Naive Smoothing overall outperformed other methods and revealed more convincing biological insights. We also provided suggestions on how to choose proper identification methods and smoothing techniques according to input data.
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Affiliation(s)
- Yicheng Tao
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Fan Feng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Xin Luo
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Conrad V Reihsmann
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Alexander L Hopkirk
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jean-Philippe Cartailler
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Marcela Brissova
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Diane C Saunders
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jie Liu
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
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17
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Vitale S, Calapà F, Colonna F, Luongo F, Biffoni M, De Maria R, Fiori ME. Advancements in 3D In Vitro Models for Colorectal Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2405084. [PMID: 38962943 PMCID: PMC11348154 DOI: 10.1002/advs.202405084] [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: 05/14/2024] [Indexed: 07/05/2024]
Abstract
The process of drug discovery and pre-clinical testing is currently inefficient, expensive, and time-consuming. Most importantly, the success rate is unsatisfactory, as only a small percentage of tested drugs are made available to oncological patients. This is largely due to the lack of reliable models that accurately predict drug efficacy and safety. Even animal models often fail to replicate human-specific pathologies and human body's complexity. These factors, along with ethical concerns regarding animal use, urge the development of suitable human-relevant, translational in vitro models.
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Affiliation(s)
- Sara Vitale
- Department of Oncology and Molecular Medicine (OMM)Istituto Superiore di SanitàViale Regina Elena 299Rome00161Italy
| | - Federica Calapà
- Dipartimento di Medicina e Chirurgia traslazionaleUniversità Cattolica del Sacro CuoreLargo F. Vito 1RomeItaly
| | - Francesca Colonna
- Department of Oncology and Molecular Medicine (OMM)Istituto Superiore di SanitàViale Regina Elena 299Rome00161Italy
| | - Francesca Luongo
- Dipartimento di Medicina e Chirurgia traslazionaleUniversità Cattolica del Sacro CuoreLargo F. Vito 1RomeItaly
| | - Mauro Biffoni
- Department of Oncology and Molecular Medicine (OMM)Istituto Superiore di SanitàViale Regina Elena 299Rome00161Italy
| | - Ruggero De Maria
- Dipartimento di Medicina e Chirurgia traslazionaleUniversità Cattolica del Sacro CuoreLargo F. Vito 1RomeItaly
- Fondazione Policlinico Universitario “A. Gemelli” – IRCCSLargo F. Vito 1RomeItaly
| | - Micol E. Fiori
- Department of Oncology and Molecular Medicine (OMM)Istituto Superiore di SanitàViale Regina Elena 299Rome00161Italy
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18
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Zebley CC, Zehn D, Gottschalk S, Chi H. T cell dysfunction and therapeutic intervention in cancer. Nat Immunol 2024; 25:1344-1354. [PMID: 39025962 DOI: 10.1038/s41590-024-01896-9] [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: 04/12/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024]
Abstract
Recent advances in immunotherapy have affirmed the curative potential of T cell-based approaches for treating relapsed and refractory cancers. However, the therapeutic efficacy is limited in part owing to the ability of cancers to evade immunosurveillance and adapt to immunological pressure. In this Review, we provide a brief overview of cancer-mediated immunosuppressive mechanisms with a specific focus on the repression of the surveillance and effector function of T cells. We discuss CD8+ T cell exhaustion and functional heterogeneity and describe strategies for targeting the molecular checkpoints that restrict T cell differentiation and effector function to bolster immunotherapeutic effects. We also delineate the emerging contributions of the tumor microenvironment to T cell metabolism and conclude by highlighting discovery-based approaches for developing future cellular therapies. Continued exploration of T cell biology and engineering hold great promise for advancing therapeutic interventions for cancer.
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Affiliation(s)
- Caitlin C Zebley
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Dietmar Zehn
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan and Center for Infection Prevention (ZIP), Technical University of Munich, Freising, Germany
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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19
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Polak R, Zhang ET, Kuo CJ. Cancer organoids 2.0: modelling the complexity of the tumour immune microenvironment. Nat Rev Cancer 2024; 24:523-539. [PMID: 38977835 DOI: 10.1038/s41568-024-00706-6] [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: 05/09/2024] [Indexed: 07/10/2024]
Abstract
The development of neoplasia involves a complex and continuous interplay between malignantly transformed cells and the tumour microenvironment (TME). Cancer immunotherapies targeting the immune TME have been increasingly validated in clinical trials but response rates vary substantially between tumour histologies and are often transient, idiosyncratic and confounded by resistance. Faithful experimental models of the patient-specific tumour immune microenvironment, capable of recapitulating tumour biology and immunotherapy effects, would greatly improve patient selection, target identification and definition of resistance mechanisms for immuno-oncology therapeutics. In this Review, we discuss currently available and rapidly evolving 3D tumour organoid models that capture important immune features of the TME. We highlight diverse opportunities for organoid-based investigations of tumour immunity, drug development and precision medicine.
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Affiliation(s)
- Roel Polak
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Elisa T Zhang
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA.
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20
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Li Y, Xun Z, Long J, Sun H, Yang X, Wang Y, Wang Y, Xue J, Zhang N, Zhang J, Bian J, Shi J, Yang X, Wang H, Zhao H. Immunosuppression and phenotypic plasticity in an atlas of human hepatocholangiocarcinoma. Hepatobiliary Surg Nutr 2024; 13:586-603. [PMID: 39175731 PMCID: PMC11336540 DOI: 10.21037/hbsn-23-400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/30/2023] [Indexed: 08/24/2024]
Abstract
Background Hepatocholangiocarcinoma (H-ChC) has the clinicopathological features of both hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA) and is a more aggressive subtype of primary hepatic carcinoma than HCC or iCCA. Methods We sequenced 91,112 single-cell transcriptomes from 16 human samples to elucidate the molecular mechanisms underlying the coexistence of HCC and iCCA components in H-ChC. Results We observed two molecular subtypes of H-ChC at the whole-transcriptome level (CHP and CIP), where a metabolically active tumour cell subpopulation enriched in CHP was characterized by a cellular pre-differentiation property. To define the heterogeneity of tumours and their associated microenvironments, we observe greater tumour diversity in H-ChC than HCC and iCCA. H-ChC exhibits weaker immune cell infiltration and greater CD8+ exhausted T cell (Tex) dysfunction than HCC and iCCA. Then we defined two broad cell states of 6,852 CD8+ Tex cells: GZMK+ CD8+ Tex cells and terminal CD8+ Tex cells. GZMK+ CD8+ Tex cells exhibited higher infiltration of after treatment in H-ChC, the effector scores and expression of the immune checkpoints of them greatly increased after immunotherapy, which indicated that H-ChC might be more sensitive than HCC or iCCA to immunotherapy. Conclusions In this paper, H-ChC was explored, hoping to contribute to the study of mixed tumours in other cancers.
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Affiliation(s)
- Yiran Li
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Ziyu Xun
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Junyu Long
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Huishan Sun
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xu Yang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Yanyu Wang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Yunchao Wang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Jingnan Xue
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Nan Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Junwei Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Jin Bian
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Jie Shi
- Division of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xiaobo Yang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Hanping Wang
- Division of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Haitao Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
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21
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Chen Y, Liang Z, Lai M. Targeting the devil: Strategies against cancer-associated fibroblasts in colorectal cancer. Transl Res 2024; 270:81-93. [PMID: 38614213 DOI: 10.1016/j.trsl.2024.04.003] [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: 01/30/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
Cancer-associated fibroblasts (CAFs), as significant constituents of the tumor microenvironment (TME), play a pivotal role in the progression of cancers, including colorectal cancer (CRC). In this comprehensive review, we presented the origins and activation mechanisms of CAFs in CRC, elaborating on how CAFs drive tumor progression through their interactions with CRC cells, immune cells, vascular endothelial cells, and the extracellular matrix within the TME. We systematically outline the intricate web of interactions among CAFs, tumor cells, and other TME components, and based on this complex interplay, we summarize various therapeutic strategies designed to target CAFs in CRC. It is also essential to recognize that CAFs represent a highly heterogeneous group, encompassing various subtypes such as myofibroblastic CAF (myCAF), inflammatory CAF (iCAF), antigen-presenting CAF (apCAF), vessel-associated CAF (vCAF). Herein, we provide a summary of studies investigating the heterogeneity of CAFs in CRC and the characteristic expression patterns of each subtype. While the majority of CAFs contribute to the exacerbation of CRC malignancy, recent findings have revealed specific subtypes that exert inhibitory effects on CRC progression. Nevertheless, the comprehensive landscape of CAF heterogeneity still awaits exploration. We also highlight pivotal unanswered questions that need to be addressed before CAFs can be recognized as feasible targets for cancer treatment. In conclusion, the aim of our review is to elucidate the significance and challenges of advancing in-depth research on CAFs, while outlining the pathway to uncover the complex roles of CAFs in CRC and underscore their significant potential as therapeutic targets.
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Affiliation(s)
- Yuting Chen
- Department of Pathology, and Department of Pathology of Sir Run Run Shaw Hospital, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy of Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, 310058, China; Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China; Key Laboratory of Disease Proteomics of Zhejiang Province, Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Zhiyong Liang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Maode Lai
- Department of Pathology, and Department of Pathology of Sir Run Run Shaw Hospital, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy of Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, 310058, China; Key Laboratory of Disease Proteomics of Zhejiang Province, Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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22
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Rodriguez BL, Huang J, Gibson L, Fradette JJ, Chen HIH, Koyano K, Cortez C, Li B, Ho C, Ashique AM, Lin VY, Crawley S, Roda JM, Chen P, Fan B, Kim J, Sissons J, Sitrin J, Kaplan DD, Gibbons DL, Rivera LB. Antitumor Activity of a Novel LAIR1 Antagonist in Combination with Anti-PD1 to Treat Collagen-Rich Solid Tumors. Mol Cancer Ther 2024; 23:1144-1158. [PMID: 38648067 PMCID: PMC11293989 DOI: 10.1158/1535-7163.mct-23-0866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/05/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024]
Abstract
We recently reported that resistance to PD-1 blockade in a refractory lung cancer-derived model involved increased collagen deposition and the collagen-binding inhibitory receptor leukocyte-associated immunoglobulin-like receptor 1 (LAIR1). Thus, we hypothesized that LAIR1 and collagen cooperated to suppress therapeutic response. In this study, we report that LAIR1 is associated with tumor stroma and is highly expressed by intratumoral myeloid cells in both human tumors and mouse models of cancer. Stroma-associated myeloid cells exhibit a suppressive phenotype and correlate with LAIR1 expression in human cancer. NGM438, a novel humanized LAIR1 antagonist mAb, elicits myeloid inflammation and allogeneic T-cell responses by binding to LAIR1 and blocking collagen engagement. Furthermore, a mouse-reactive NGM438 surrogate antibody sensitized refractory KP mouse lung tumors to anti-PD-1 therapy and resulted in increased intratumoral CD8+ T-cell content and inflammatory gene expression. These data place LAIR1 at the intersection of stroma and suppressive myeloid cells and support the notion that blockade of the LAIR1/collagen axis can potentially address resistance to checkpoint inhibitor therapy in the clinic.
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Affiliation(s)
- B. Leticia Rodriguez
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiawei Huang
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Laura Gibson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared J. Fradette
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hung-I H. Chen
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Kikuye Koyano
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Czrina Cortez
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Betty Li
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Carmence Ho
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | | | - Vicky Y. Lin
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | | | - Julie M. Roda
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Peirong Chen
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Bin Fan
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - Jeong Kim
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | - James Sissons
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
| | | | | | - Don L. Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lee B. Rivera
- NGM Biopharmaceuticals Inc. South San Francisco, CA, USA
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Majid U, Bergsland CH, Sveen A, Bruun J, Eilertsen IA, Bækkevold ES, Nesbakken A, Yaqub S, Jahnsen FL, Lothe RA. The prognostic effect of tumor-associated macrophages in stage I-III colorectal cancer depends on T cell infiltration. Cell Oncol (Dordr) 2024; 47:1267-1276. [PMID: 38407700 PMCID: PMC11322253 DOI: 10.1007/s13402-024-00926-w] [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: 02/12/2024] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND Tumor-associated macrophages (TAMs) are associated with unfavorable patient prognosis in many cancer types. However, TAMs are a heterogeneous cell population and subsets have been shown to activate tumor-infiltrating T cells and confer a good patient prognosis. Data on the prognostic value of TAMs in colorectal cancer are conflicting. We investigated the prognostic effect of TAMs in relation to tumor-infiltrating T cells in colorectal cancers. METHODS The TAM markers CD68 and CD163 were analyzed by multiplex fluorescence immunohistochemistry and digital image analysis on tissue microarrays of 1720 primary colorectal cancers. TAM density in the tumor stroma was scored in relation to T cell density (stromal CD3+ and epithelial CD8+ cells) and analyzed in Cox proportional hazards models of 5-year relapse-free survival. Multivariable survival models included clinicopathological factors, MSI status and BRAFV600E mutation status. RESULTS High TAM density was associated with a favorable 5-year relapse-free survival in a multivariable model of patients with stage I-III tumors (p = 0.004, hazard ratio 0.94, 95% confidence interval 0.90-0.98). However, the prognostic effect was dependent on tumoral T-cell density. High TAM density was associated with a good prognosis in patients who also had high T-cell levels in their tumors, while high TAM density was associated with poorer prognosis in patients with low T-cell levels (pinteraction = 0.0006). This prognostic heterogeneity was found for microsatellite stable tumors separately. CONCLUSIONS This study supported a phenotypic heterogeneity of TAMs in colorectal cancer, and showed that combined tumor immunophenotyping of multiple immune cell types improved the prediction of patient prognosis.
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Affiliation(s)
- Umair Majid
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Christian Holst Bergsland
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ina Andrassy Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Espen S Bækkevold
- Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
- Institute of Oral Biology, University of Oslo, Oslo, Norway
| | - Arild Nesbakken
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Sheraz Yaqub
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Hepatobiliary Surgery, Oslo University Hospital, Oslo, Norway
| | - Frode L Jahnsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
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24
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Mi H, Sivagnanam S, Ho WJ, Zhang S, Bergman D, Deshpande A, Baras AS, Jaffee EM, Coussens LM, Fertig EJ, Popel AS. Computational methods and biomarker discovery strategies for spatial proteomics: a review in immuno-oncology. Brief Bioinform 2024; 25:bbae421. [PMID: 39179248 PMCID: PMC11343572 DOI: 10.1093/bib/bbae421] [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: 05/29/2024] [Revised: 07/11/2024] [Accepted: 08/09/2024] [Indexed: 08/26/2024] Open
Abstract
Advancements in imaging technologies have revolutionized our ability to deeply profile pathological tissue architectures, generating large volumes of imaging data with unparalleled spatial resolution. This type of data collection, namely, spatial proteomics, offers invaluable insights into various human diseases. Simultaneously, computational algorithms have evolved to manage the increasing dimensionality of spatial proteomics inherent in this progress. Numerous imaging-based computational frameworks, such as computational pathology, have been proposed for research and clinical applications. However, the development of these fields demands diverse domain expertise, creating barriers to their integration and further application. This review seeks to bridge this divide by presenting a comprehensive guideline. We consolidate prevailing computational methods and outline a roadmap from image processing to data-driven, statistics-informed biomarker discovery. Additionally, we explore future perspectives as the field moves toward interfacing with other quantitative domains, holding significant promise for precision care in immuno-oncology.
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Affiliation(s)
- Haoyang Mi
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Shamilene Sivagnanam
- The Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, United States
- Department of Cell, Development and Cancer Biology, Oregon Health and Science University, Portland, OR 97201, United States
| | - Won Jin Ho
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shuming Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Daniel Bergman
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Atul Deshpande
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Alexander S Baras
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
- Department of Pathology, Johns Hopkins University School of Medicine, MD 21205, United States
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Elizabeth M Jaffee
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Lisa M Coussens
- The Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, United States
- Department of Cell, Development and Cancer Biology, Oregon Health and Science University, Portland, OR 97201, United States
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR 97201, United States
| | - Elana J Fertig
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, United States
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
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Li M, Su Y, Gao Y, Tian W. ReCIDE: robust estimation of cell type proportions by integrating single-reference-based deconvolutions. Brief Bioinform 2024; 25:bbae422. [PMID: 39177263 PMCID: PMC11342246 DOI: 10.1093/bib/bbae422] [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: 04/02/2024] [Revised: 07/16/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
In this study, we introduce Robust estimation of Cell type proportions by Integrating single-reference-based DEconvolutions (ReCIDE), an innovative framework for robust estimation of cell type proportions by integrating single-reference-based deconvolutions. ReCIDE outperforms existing approaches in benchmark and real datasets, particularly excelling in estimating rare cell type proportions. Through exploratory analysis on public bulk data of triple-negative breast cancer (TNBC) patients using ReCIDE, we demonstrate a significant correlation between the prognosis of TNBC patients and the proportions of both T cell and perivascular-like cell subtypes. Built upon this discovery, we develop a prognostic assessment model for TNBC patients. Our contribution presents a novel framework for enhancing deconvolution accuracy, showcasing its effectiveness in medical research.
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Affiliation(s)
- Minghan Li
- State Key Laboratory of Genetic Engineering, Department of Computational Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yuqing Su
- State Key Laboratory of Genetic Engineering, Department of Computational Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yanbo Gao
- Shanghai SPH Jiaolian Pharmaceutical Technology Company, Limited, Buliding 4, 998 Ha Lei Road, Pudong District, Shanghai 201203, China
| | - Weidong Tian
- State Key Laboratory of Genetic Engineering, Department of Computational Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
- Children’s Hospital of Fudan University, 399 Wanyuan Road, Minhang District, Shanghai 201102, China
- Children’s Hospital of Shandong University, 23976 Jingshi Road, Huaiyin District, Jinan, Shandong 250022, China
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Xiao WW, Chen G, Gao YH, Lin JZ, Wu XJ, Luo HL, Lu ZH, Wang QX, Sun R, Cai PQ, Zhu CM, Liu M, Li JB, Wang YR, Jin Y, Wang F, Luo HT, Li CL, Pan ZZ, Xu RH. Effect of neoadjuvant chemoradiotherapy with or without PD-1 antibody sintilimab in pMMR locally advanced rectal cancer: A randomized clinical trial. Cancer Cell 2024:S1535-6108(24)00269-1. [PMID: 39094560 DOI: 10.1016/j.ccell.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 05/26/2024] [Accepted: 07/08/2024] [Indexed: 08/04/2024]
Abstract
Neoadjuvant chemoradiotherapy (NACRT) was the standard treatment for patients with locally advanced rectal cancer (LARC) with proficient mismatch repair (pMMR) proteins. In this randomized phase 2 trial (ClinicalTrial.gov: NCT04304209), 134 pMMR LARC patients were randomly (1:1) assigned to receive NACRT or NACRT and the programmed cell death protein 1 (PD-1) antibody sintilimab. As the primary endpoint, the total complete response (CR) rate is 26.9% (18/67, 95% confidence interval [CI] 16.0%-37.8%) and 44.8% (30/67, 95% CI 32.6%-57.0%) in the control and experimental arm, respectively, with significant difference (p = 0.031 for chi-squared test). Response ratio is 1.667 (95% CI 1.035-2.683). Immunohistochemistry shows PD-1 ligand 1 (PD-L1) combined positive score is associated with the synergistic effect. The safety profile is similar between the arms. Adding the PD-1 antibody sintilimab to NACRT significantly increases the CR rate in pMMR LARC, with a manageable safety profile. PD-L1 positivity may help identify patients who might benefit most from the combination therapy.
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Affiliation(s)
- Wei-Wei Xiao
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China; United Laboratory of Frontier Radiotherapy Technology of Sun Yat-sen University & Chinese Academy of Sciences Ion Medical Technology Co., Ltd, Guangzhou, China
| | - Gong Chen
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Yuan-Hong Gao
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Jun-Zhong Lin
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Xiao-Jun Wu
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Hui-Long Luo
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Zhen-Hai Lu
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Qiao-Xuan Wang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Rui Sun
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Pei-Qiang Cai
- Department of Radiology, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Chong-Mei Zhu
- Department of Pathology, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Min Liu
- Department of Ultrasound, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Ji-Bin Li
- Department of Statistics, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Yi-Rui Wang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Ying Jin
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Feng Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Hai-Tao Luo
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd, Shenzhen, China
| | - Cai-Ling Li
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd, Shenzhen, China
| | - Zhi-Zhong Pan
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Rui-Hua Xu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, The State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, China.
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Ran R, Trapecar M, Brubaker DK. Systematic Analysis of Human Colorectal Cancer scRNA-seq Revealed Limited Pro-tumoral IL-17 Production Potential in Gamma Delta T Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604156. [PMID: 39071278 PMCID: PMC11275756 DOI: 10.1101/2024.07.18.604156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Gamma delta (γδ) T cells play a crucial role in anti-tumor immunity due to their cytotoxic properties. However, the role and extent of γδ T cells in production of pro-tumorigenic interleukin- 17 (IL-17) within the tumor microenvironment (TME) of colorectal cancer (CRC) remains controversial. In this study, we re-analyzed nine published human CRC whole-tissue single-cell RNA sequencing (scRNA-seq) datasets, identifying 18,483 γδ T cells out of 951,785 total cells, in the neoplastic or adjacent normal tissue of 165 human CRC patients. Our results confirm that tumor-infiltrating γδ T cells exhibit high cytotoxicity-related transcription in both tumor and adjacent normal tissues, but critically, none of the γδ T cell clusters showed IL-17 production potential. We also identified various γδ T cell subsets, including Teff, TRM, Tpex, and Tex, and noted an increased expression of cytotoxic molecules in tumor-infiltrating γδ T cells compared to their normal area counterparts. Our work demonstrates that γδ T cells in CRC primarily function as cytotoxic effector cells rather than IL-17 producers, mitigating the concerns about their potential pro-tumorigenic roles in CRC, highlighting the importance of accurately characterizing these cells for cancer immunotherapy research and the unneglectable cross-species discrepancy between the mouse and human immune system in the study of cancer immunology.
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Affiliation(s)
- Ran Ran
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH
| | - Martin Trapecar
- Department of Medicine, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Douglas K. Brubaker
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH
- The Blood, Heart, Lung, and Immunology Research Center, Case Western Reserve University, University Hospitals of Cleveland, Cleveland, OH
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28
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Majumder B, Nataraj NB, Maitreyi L, Datta S. Mismatch repair-proficient tumor footprints in the sands of immune desert: mechanistic constraints and precision platforms. Front Immunol 2024; 15:1414376. [PMID: 39100682 PMCID: PMC11294168 DOI: 10.3389/fimmu.2024.1414376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/17/2024] [Indexed: 08/06/2024] Open
Abstract
Mismatch repair proficient (MMRp) tumors of colorectal origin are one of the prevalent yet unpredictable clinical challenges. Despite earnest efforts, optimal treatment modalities have yet to emerge for this class. The poor prognosis and limited actionability of MMRp are ascribed to a low neoantigen burden and a desert-like microenvironment. This review focuses on the critical roadblocks orchestrated by an immune evasive mechanistic milieu in the context of MMRp. The low density of effector immune cells, their weak spatiotemporal underpinnings, and the high-handedness of the IL-17-TGF-β signaling are intertwined and present formidable challenges for the existing therapies. Microbiome niche decorated by Fusobacterium nucleatum alters the metabolic program to maintain an immunosuppressive state. We also highlight the evolving strategies to repolarize and reinvigorate this microenvironment. Reconstruction of anti-tumor chemokine signaling, rational drug combinations eliciting T cell activation, and reprograming the maladapted microbiome are exciting developments in this direction. Alternative vulnerability of other DNA damage repair pathways is gaining momentum. Integration of liquid biopsy and ex vivo functional platforms provide precision oncology insights. We illustrated the perspectives and changing landscape of MMRp-CRC. The emerging opportunities discussed in this review can turn the tide in favor of fighting the treatment dilemma for this elusive cancer.
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Yang J, Ding X, Fang Z, Wu S, Yuan M, Chen R, Xu Q, Gao X, Wu H, Chen L, Zheng X, Jiang J. Association of CD8 +TILs co-expressing granzyme A and interferon-γ with colon cancer cells in the tumor microenvironment. BMC Cancer 2024; 24:869. [PMID: 39030523 PMCID: PMC11265531 DOI: 10.1186/s12885-024-12605-y] [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: 05/15/2024] [Accepted: 07/04/2024] [Indexed: 07/21/2024] Open
Abstract
CD8+T cells secreting granzyme A (GZMA) can induce pyroptosis in tumor cells by effectively cleaving gasdermin B (GSDMB), which is stimulated by interferon-γ (IFN-γ). However, the interaction between GZMA-expressing CD8+T cells and GSDMB-expressing tumor cells in colon cancer remains poorly understood. Our research employed multi-color immunohistochemistry (mIHC) staining and integrated clinical data to explore the spatial distribution and clinical relevance of GZMA- and IFN-γ-expressing CD8+ tumor-infiltrating lymphocytes (TILs), as well as GSDMB-expressing CK+ cells, within the tumor microenvironment (TME) of human colon cancer samples. Additionally, we utilizing single-cell RNA sequencing (scRNA-seq) data to examine the functional dynamics and interactions among these cell populations. scRNA-seq analysis of colorectal cancer (CRC) tissues revealed that CD8+TILs co-expressed GZMA and IFN-γ, but not other cell types. Our mIHC staining results indicated that a significant reduction in the infiltration of GZMA+IFN-γ+CD8+TILs in colon cancer patients (P < 0.01). Functional analysis results indicated that GZMA+IFN-γ+CD8+TILs demonstrated enhanced activation and effector functions compared to other CD8+TIL subsets. Furthermore, GSDMB-expressing CK+ cells exhibited augmented immunogenicity. Correlation analysis highlighted a positive association between GSDMB+CK+ cells and GZMA+IFN-γ+CD8+TILs (r = 0.221, P = 0.033). Analysis of cell-cell interactions further showed that these interactions were mediated by IFN-γ and transforming growth factor-β (TGF-β), the co-stimulatory molecule ICOS, and immune checkpoint molecules TIGIT and TIM-3. These findings suggested that GZMA+IFN-γ+CD8+TILs modulating GSDMB-expressing tumor cells, significantly impacted the immune microenvironment and patients' prognosis in colon cancer. By elucidating these mechanisms, our present study aims to provide novel insights for the advancement of immunotherapeutic strategies in colon cancer.
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Affiliation(s)
- Jiayi Yang
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, Jiangsu, 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
| | - Xinyi Ding
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, Jiangsu, 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
| | - Zhang Fang
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, Jiangsu, 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
| | - Shaoxian Wu
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, Jiangsu, 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
| | - Maoling Yuan
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, Jiangsu, 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
| | - Rongzhang Chen
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, Jiangsu, 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
| | - Qinlan Xu
- Department of Gastroenterology, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
| | - Xinran Gao
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, Jiangsu, 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
| | - Haoyu Wu
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, Jiangsu, 213003, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China
| | - Lujun Chen
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, Jiangsu, 213003, China.
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China.
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China.
| | - Xiao Zheng
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, Jiangsu, 213003, China.
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China.
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China.
| | - Jingting Jiang
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Jiangsu Changzhou, Jiangsu, 213003, China.
- Jiangsu Engineering Research Center for Tumor Immunotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China.
- Institute of Cell Therapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, 213003, China.
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Ivancevic A, Simpson DM, Joyner OM, Bagby SM, Nguyen LL, Bitler BG, Pitts TM, Chuong EB. Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer. SCIENCE ADVANCES 2024; 10:eado1218. [PMID: 39018396 PMCID: PMC466953 DOI: 10.1126/sciadv.ado1218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/13/2024] [Indexed: 07/19/2024]
Abstract
Cancer cells exhibit rewired transcriptional regulatory networks that promote tumor growth and survival. However, the mechanisms underlying the formation of these pathological networks remain poorly understood. Through a pan-cancer epigenomic analysis, we found that primate-specific endogenous retroviruses (ERVs) are a rich source of enhancers displaying cancer-specific activity. In colorectal cancer and other epithelial tumors, oncogenic MAPK/AP1 signaling drives the activation of enhancers derived from the primate-specific ERV family LTR10. Functional studies in colorectal cancer cells revealed that LTR10 elements regulate tumor-specific expression of multiple genes associated with tumorigenesis, such as ATG12 and XRCC4. Within the human population, individual LTR10 elements exhibit germline and somatic structural variation resulting from a highly mutable internal tandem repeat region, which affects AP1 binding activity. Our findings reveal that ERV-derived enhancers contribute to transcriptional dysregulation in response to oncogenic signaling and shape the evolution of cancer-specific regulatory networks.
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Affiliation(s)
- Atma Ivancevic
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - David M. Simpson
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Olivia M. Joyner
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Stacey M. Bagby
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lily L. Nguyen
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ben G. Bitler
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Todd M. Pitts
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Edward B. Chuong
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
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Liu HX, Feng J, Jiang JJ, Shen WJ, Zheng Y, Liu G, Gao XY. Integrated single-cell and bulk RNA sequencing revealed an epigenetic signature predicts prognosis and tumor microenvironment colorectal cancer heterogeneity. World J Gastrointest Oncol 2024; 16:3032-3054. [PMID: 39072180 PMCID: PMC11271797 DOI: 10.4251/wjgo.v16.i7.3032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/23/2024] [Accepted: 05/07/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) prognosis prediction is currently a major challenge. Epigenetic regulation has been widely reported for its role in cancer development. AIM To construct a robust prognostic signature, we used developed and validated across datasets. METHODS After constructing the signature, the prognostic value of the signature was evaluated in the TCGA cohort and six independent datasets (GSE17526, GSE17537, GSE33113, GSE37892, GSE39048 and GSE39582). The clinical, genomic and transcriptomic features related to the signature were identified. The correlations of the signature score with immune cell infiltration and cell-cell interactions were analyzed. The correlations between the signature score and the sensitivity to different drugs were also predicted. RESULTS In the TCGA cohort, patients in the low-risk group according to the signature score had longer survival than those in the high-risk group, and this finding was validated in the validation datasets. The signature was a prognostic factor independent of age and sex and was correlated with stage and PD-1/PD-L1 expression. Area under the receiving operating characteristic curve was 0.72. Genomic association analyses revealed that samples from high-risk patients exhibited chromosomal instability. Transcriptomic analyses revealed that the signature score was significantly associated with multiple cellular pathways. Bulk RNA-seq and single-cell sequencing data revealed that the signature reflected differences in infiltrating immune cell-tumor cell interactions, especially for macrophages. The signature also predicted the putative drug sensitivity of CRC samples. CONCLUSION The signature is a valuable biomarker for predicting CRC prognosis and reflects multiple features of CRC, especially macrophage infiltration in the microenvironment.
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Affiliation(s)
- Han-Xuan Liu
- Beijing Jinghua Anliang Technology, Beijing 102627, China
| | - Jie Feng
- Department of Clinical Laboratory, The First Medical Centre of Chinese PLA General Hospital, Beijing 100853, China
| | - Jing-Jing Jiang
- Clinical Biological Sample Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China
| | - Wan-Jun Shen
- Department of Nephrology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Yu Zheng
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Gang Liu
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xiang-Yang Gao
- The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
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Chen Y, Wang D, Li Y, Qi L, Si W, Bo Y, Chen X, Ye Z, Fan H, Liu B, Liu C, Zhang L, Zhang X, Li Z, Zhu L, Wu A, Zhang Z. Spatiotemporal single-cell analysis decodes cellular dynamics underlying different responses to immunotherapy in colorectal cancer. Cancer Cell 2024; 42:1268-1285.e7. [PMID: 38981439 DOI: 10.1016/j.ccell.2024.06.009] [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: 07/12/2023] [Revised: 04/10/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
Abstract
Expanding the efficacy of immune checkpoint blockade (ICB) in colorectal cancer (CRC) presses for a comprehensive understanding of treatment responsiveness. Here, we analyze multiple sequential single-cell samples from 22 patients undergoing PD-1 blockade to map the evolution of local and systemic immunity of CRC patients. In tumors, we identify coordinated cellular programs exhibiting distinct response associations. Specifically, exhausted T (Tex) or tumor-reactive-like CD8+ T (Ttr-like) cells are closely related to treatment efficacy, and Tex cells show correlated proportion changes with multiple other tumor-enriched cell types following PD-1 blockade. In addition, we reveal the less-exhausted phenotype of blood-associated Ttr-like cells in tumors and find that their higher abundance suggests better treatment outcomes. Finally, a higher major histocompatibility complex (MHC) II-related signature in circulating CD8+ T cells at baseline is linked to superior responses. Our study provides insights into the spatiotemporal cellular dynamics following neoadjuvant PD-1 blockade in CRC.
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Affiliation(s)
- Yuqing Chen
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dongfang Wang
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China.
| | - Yingjie Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Unit III, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Lu Qi
- Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing, China
| | - Wen Si
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Yufei Bo
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhaochen Ye
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Hongtao Fan
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Baolin Liu
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Chang Liu
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Li Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Pathology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xiaoyan Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Radiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Zhongwu Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Pathology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Linna Zhu
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Aiwen Wu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Unit III, Peking University Cancer Hospital & Institute, Beijing 100142, China.
| | - Zemin Zhang
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China.
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Liang L, Yang Y, Deng K, Wu Y, Li Y, Bai L, Wang Y, Lu C. Type I Interferon Activates PD-1 Expression through Activation of the STAT1-IRF2 Pathway in Myeloid Cells. Cells 2024; 13:1163. [PMID: 38995014 PMCID: PMC11240780 DOI: 10.3390/cells13131163] [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: 04/30/2024] [Revised: 06/18/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024] Open
Abstract
PD-1 (Programmed cell death protein 1) regulates the metabolic reprogramming of myeloid-derived suppressor cells and myeloid cell differentiation, as well as the type I interferon (IFN-I) signaling pathway in myeloid cells in the tumor microenvironment. PD-1, therefore, is a key inhibitory receptor in myeloid cells. However, the regulation of PD-1 expression in myeloid cells is unknown. We report that the expression level of PDCD1, the gene that encodes the PD-1 protein, is positively correlated with the levels of IFNB1 and IFNAR1 in myeloid cells in human colorectal cancer. Treatment of mouse myeloid cell lines with recombinant IFNβ protein elevated PD-1 expression in myeloid cells in vitro. Knocking out IFNAR1, the gene that encodes the IFN-I-specific receptor, diminished the inductive effect of IFNβ on PD-1 expression in myeloid cells in vitro. Treatment of tumor-bearing mice with a lipid nanoparticle-encapsulated IFNβ-encoding plasmid (IFNBCOL01) increased IFNβ expression, resulting in elevated PD-1 expression in tumor-infiltrating myeloid cells. At the molecular level, we determined that IFNβ activates STAT1 (signal transducer and activator of transcription 1) and IRFs (interferon regulatory factors) in myeloid cells. Analysis of the cd279 promoter identified IRF2-binding consensus sequence elements. ChIP (chromatin immunoprecipitation) analysis determined that the pSTAT1 directly binds to the irf2 promoter and that IRF2 directly binds to the cd279 promoter in myeloid cells in vitro and in vivo. In colon cancer patients, the expression levels of STAT1, IRF2 and PDCD1 are positively correlated in tumor-infiltrating myeloid cells. Our findings determine that IFNβ activates PD-1 expression at least in part by an autocrine mechanism via the stimulation of the pSTAT1-IRF2 axis in myeloid cells.
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Affiliation(s)
- Liyan Liang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (L.L.); (Y.Y.); (K.D.); (Y.W.); (Y.L.)
| | - Yingcui Yang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (L.L.); (Y.Y.); (K.D.); (Y.W.); (Y.L.)
| | - Kaidi Deng
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (L.L.); (Y.Y.); (K.D.); (Y.W.); (Y.L.)
| | - Yanmin Wu
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (L.L.); (Y.Y.); (K.D.); (Y.W.); (Y.L.)
| | - Yan Li
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (L.L.); (Y.Y.); (K.D.); (Y.W.); (Y.L.)
| | - Liya Bai
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China; (L.B.); (Y.W.)
| | - Yinsong Wang
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China; (L.B.); (Y.W.)
| | - Chunwan Lu
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (L.L.); (Y.Y.); (K.D.); (Y.W.); (Y.L.)
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Yuan X, Ma Y, Gao R, Cui S, Wang Y, Fa B, Ma S, Wei T, Ma S, Yu Z. HEARTSVG: a fast and accurate method for identifying spatially variable genes in large-scale spatial transcriptomics. Nat Commun 2024; 15:5700. [PMID: 38972896 PMCID: PMC11228050 DOI: 10.1038/s41467-024-49846-1] [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: 06/29/2023] [Accepted: 06/19/2024] [Indexed: 07/09/2024] Open
Abstract
Identifying spatially variable genes (SVGs) is crucial for understanding the spatiotemporal characteristics of diseases and tissue structures, posing a distinctive challenge in spatial transcriptomics research. We propose HEARTSVG, a distribution-free, test-based method for fast and accurately identifying spatially variable genes in large-scale spatial transcriptomic data. Extensive simulations demonstrate that HEARTSVG outperforms state-of-the-art methods with higherF 1 scores (averageF 1 Score=0.948), improved computational efficiency, scalability, and reduced false positives (FPs). Through analysis of twelve real datasets from various spatial transcriptomic technologies, HEARTSVG identifies a greater number of biologically significant SVGs (average AUC = 0.792) than other comparative methods without prespecifying spatial patterns. Furthermore, by clustering SVGs, we uncover two distinct tumor spatial domains characterized by unique spatial expression patterns, spatial-temporal locations, and biological functions in human colorectal cancer data, unraveling the complexity of tumors.
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Affiliation(s)
- Xin Yuan
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China
| | - Yanran Ma
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ruitian Gao
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuya Cui
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China
| | - Yifan Wang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Botao Fa
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Shiyang Ma
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ting Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangge Ma
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China.
- Department of Biostatistics, Yale University, New Haven, USA.
| | - Zhangsheng Yu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China.
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Center for Biomedical Data Science, Translational Science Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Coulton A, Murai J, Qian D, Thakkar K, Lewis CE, Litchfield K. Using a pan-cancer atlas to investigate tumour associated macrophages as regulators of immunotherapy response. Nat Commun 2024; 15:5665. [PMID: 38969631 PMCID: PMC11226649 DOI: 10.1038/s41467-024-49885-8] [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: 02/27/2023] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
The paradigm for macrophage characterization has evolved from the simple M1/M2 dichotomy to a more complex model that encompasses the broad spectrum of macrophage phenotypic diversity, due to differences in ontogeny and/or local stimuli. We currently lack an in-depth pan-cancer single cell RNA-seq (scRNAseq) atlas of tumour-associated macrophages (TAMs) that fully captures this complexity. In addition, an increased understanding of macrophage diversity could help to explain the variable responses of cancer patients to immunotherapy. Our atlas includes well established macrophage subsets as well as a number of additional ones. We associate macrophage composition with tumour phenotype and show macrophage subsets can vary between primary and metastatic tumours growing in sites like the liver. We also examine macrophage-T cell functional cross talk and identify two subsets of TAMs associated with T cell activation. Analysis of TAM signatures in a large cohort of immune checkpoint inhibitor-treated patients (CPI1000 + ) identify multiple TAM subsets associated with response, including the presence of a subset of TAMs that upregulate collagen-related genes. Finally, we demonstrate the utility of our data as a resource and reference atlas for mapping of novel macrophage datasets using projection. Overall, these advances represent an important step in both macrophage classification and overcoming resistance to immunotherapies in cancer.
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Affiliation(s)
- Alexander Coulton
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK
| | - Jun Murai
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK
| | - Danwen Qian
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK
| | - Krupa Thakkar
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK
| | - Claire E Lewis
- Department of Oncology and Metabolism, University of Sheffield Medical School, Beech Hill Road, Sheffield, Yorkshire, S10 2RX, UK.
| | - Kevin Litchfield
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, WC1E 6DD, UK.
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Robinson W, Stone JK, Schischlik F, Gasmi B, Kelly MC, Seibert C, Dadkhah K, Gertz EM, Lee JS, Zhu K, Ma L, Wang XW, Sahinalp SC, Patro R, Leiserson MDM, Harris CC, Schäffer AA, Ruppin E. Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes. SCIENCE ADVANCES 2024; 10:eadj7402. [PMID: 38959321 PMCID: PMC11221508 DOI: 10.1126/sciadv.adj7402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 05/29/2024] [Indexed: 07/05/2024]
Abstract
The study of the tumor microbiome has been garnering increased attention. We developed a computational pipeline (CSI-Microbes) for identifying microbial reads from single-cell RNA sequencing (scRNA-seq) data and for analyzing differential abundance of taxa. Using a series of controlled experiments and analyses, we performed the first systematic evaluation of the efficacy of recovering microbial unique molecular identifiers by multiple scRNA-seq technologies, which identified the newer 10x chemistries (3' v3 and 5') as the best suited approach. We analyzed patient esophageal and colorectal carcinomas and found that reads from distinct genera tend to co-occur in the same host cells, testifying to possible intracellular polymicrobial interactions. Microbial reads are disproportionately abundant within myeloid cells that up-regulate proinflammatory cytokines like IL1Β and CXCL8, while infected tumor cells up-regulate antigen processing and presentation pathways. These results show that myeloid cells with bacteria engulfed are a major source of bacterial RNA within the tumor microenvironment (TME) and may inflame the TME and influence immunotherapy response.
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Affiliation(s)
- Welles Robinson
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20910, USA
- Department of Computer Science, University of Maryland, College Park, MD 20910, USA
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
- Tumour Immunogenomics and Immunosurveillance Laboratory, Department of Oncology, University College London, London, UK
| | - Joshua K. Stone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Fiorella Schischlik
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Billel Gasmi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael C. Kelly
- Center for Cancer Research Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Bethesda, MD 20701, USA
| | - Charlie Seibert
- Center for Cancer Research Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Bethesda, MD 20701, USA
| | - Kimia Dadkhah
- Center for Cancer Research Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Bethesda, MD 20701, USA
| | - E. Michael Gertz
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Joo Sang Lee
- Department of Artificial Intelligence and Department of Precision Medicine, School of Medicine, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Kaiyuan Zhu
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
- Department of Computer Science, Indiana University, Bloomington, IN 47408, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lichun Ma
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - S. Cenk Sahinalp
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Rob Patro
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20910, USA
- Department of Computer Science, University of Maryland, College Park, MD 20910, USA
| | - Mark D. M. Leiserson
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20910, USA
- Department of Computer Science, University of Maryland, College Park, MD 20910, USA
| | - Curtis C. Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alejandro A. Schäffer
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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37
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Wu C, Yu H, Liang F, Huang X, Jiang B, Lou Z, Liu Y, Wu Z, Wang Q, Shen H, Chen M, Wu P, Wu M. Hypoxia inhibits the iMo/cDC2/CD8+ TRMs immune axis in the tumor microenvironment of human esophageal cancer. J Immunother Cancer 2024; 12:e008889. [PMID: 38964786 PMCID: PMC11227851 DOI: 10.1136/jitc-2024-008889] [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: 05/22/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Esophageal cancer (ESCA) is a form of malignant tumor associated with chronic inflammation and immune dysregulation. However, the specific immune status and key mechanisms of immune regulation in this disease require further exploration. METHODS To investigate the features of the human ESCA tumor immune microenvironment and its possible regulation, we performed mass cytometry by time of flight, single-cell RNA sequencing, multicolor fluorescence staining of tissue, and flow cytometry analyses on tumor and paracancerous tissue from treatment-naïve patients. RESULTS We depicted the immune landscape of the ESCA and revealed that CD8+ (tissue-resident memory CD8+ T cells (CD8+ TRMs) were closely related to disease progression. We also revealed the heterogeneity of CD8+ TRMs in the ESCA tumor microenvironment (TME), which was associated with their differentiation and function. Moreover, the subset of CD8+ TRMs in tumor (called tTRMs) that expressed high levels of granzyme B and immune checkpoints was markedly decreased in the TME of advanced ESCA. We showed that tTRMs are tumor effector cells preactivated in the TME. We then demonstrated that conventional dendritic cells (cDC2s) derived from intermediate monocytes (iMos) are essential for maintaining the proliferation of CD8+ TRMs in the TME. Our preliminary study showed that hypoxia can promote the apoptosis of iMos and impede the maturation of cDC2s, which in turn reduces the proliferative capacity of CD8+ TRMs, thereby contributing to the progression of cancer. CONCLUSIONS Our study revealed the essential antitumor roles of CD8+ TRMs and preliminarily explored the regulation of the iMo/cDC2/CD8+ TRM immune axis in the human ESCA TME.
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Affiliation(s)
- Chuanqiang Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Laboratory of Clinical Research Center of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Huan Yu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Fuxiang Liang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Xiancong Huang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang Province, People's Republic of China
| | - Bin Jiang
- Department of Thoracic Surgery, Shandong Provincial Hospital, Jinan, Shandong Province, People's Republic of China
| | - Zhiling Lou
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Yafei Liu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Zixiang Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Qi Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Hong Shen
- Department of Medical Oncology, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Pin Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Ming Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Laboratory of Clinical Research Center of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
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38
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Kunes RZ, Walle T, Land M, Nawy T, Pe'er D. Supervised discovery of interpretable gene programs from single-cell data. Nat Biotechnol 2024; 42:1084-1095. [PMID: 37735262 PMCID: PMC10958532 DOI: 10.1038/s41587-023-01940-3] [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: 12/21/2022] [Accepted: 08/09/2023] [Indexed: 09/23/2023]
Abstract
Factor analysis decomposes single-cell gene expression data into a minimal set of gene programs that correspond to processes executed by cells in a sample. However, matrix factorization methods are prone to technical artifacts and poor factor interpretability. We address these concerns with Spectra, an algorithm that combines user-provided gene programs with the detection of novel programs that together best explain expression covariation. Spectra incorporates existing gene sets and cell-type labels as prior biological information, explicitly models cell type and represents input gene sets as a gene-gene knowledge graph using a penalty function to guide factorization toward the input graph. We show that Spectra outperforms existing approaches in challenging tumor immune contexts, as it finds factors that change under immune checkpoint therapy, disentangles the highly correlated features of CD8+ T cell tumor reactivity and exhaustion, finds a program that explains continuous macrophage state changes under therapy and identifies cell-type-specific immune metabolic programs.
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Affiliation(s)
- Russell Z Kunes
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Statistics, Columbia University, New York, NY, USA
| | - Thomas Walle
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Max Land
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tal Nawy
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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39
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Holder AM, Dedeilia A, Sierra-Davidson K, Cohen S, Liu D, Parikh A, Boland GM. Defining clinically useful biomarkers of immune checkpoint inhibitors in solid tumours. Nat Rev Cancer 2024; 24:498-512. [PMID: 38867074 DOI: 10.1038/s41568-024-00705-7] [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: 05/08/2024] [Indexed: 06/14/2024]
Abstract
Although more than a decade has passed since the approval of immune checkpoint inhibitors (ICIs) for the treatment of melanoma and non-small-cell lung, breast and gastrointestinal cancers, many patients still show limited response. US Food and Drug Administration (FDA)-approved biomarkers include programmed cell death 1 ligand 1 (PDL1) expression, microsatellite status (that is, microsatellite instability-high (MSI-H)) and tumour mutational burden (TMB), but these have limited utility and/or lack standardized testing approaches for pan-cancer applications. Tissue-based analytes (such as tumour gene signatures, tumour antigen presentation or tumour microenvironment profiles) show a correlation with immune response, but equally, these demonstrate limited efficacy, as they represent a single time point and a single spatial assessment. Patient heterogeneity as well as inter- and intra-tumoural differences across different tissue sites and time points represent substantial challenges for static biomarkers. However, dynamic biomarkers such as longitudinal biopsies or novel, less-invasive markers such as blood-based biomarkers, radiomics and the gut microbiome show increasing potential for the dynamic identification of ICI response, and patient-tailored predictors identified through neoadjuvant trials or novel ex vivo tumour models can help to personalize treatment. In this Perspective, we critically assess the multiple new static, dynamic and patient-specific biomarkers, highlight the newest consortia and trial efforts, and provide recommendations for future clinical trials to make meaningful steps forwards in the field.
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Affiliation(s)
- Ashley M Holder
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Sonia Cohen
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - David Liu
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Aparna Parikh
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Genevieve M Boland
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
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40
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Hu M, Chikina M. InstaPrism: an R package for fast implementation of BayesPrism. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae440. [PMID: 38970377 PMCID: PMC11245312 DOI: 10.1093/bioinformatics/btae440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/26/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
SUMMARY Computational cell-type deconvolution is an important analytic technique for modeling the compositional heterogeneity of bulk gene expression data. A conceptually new Bayesian approach to this problem, BayesPrism, has recently been proposed and has subsequently been shown to be superior in accuracy and robustness against model misspecifications by independent studies; however, given that BayesPrism relies on Gibbs sampling, it is orders of magnitude more computationally expensive than standard approaches. Here, we introduce the InstaPrism package which re-implements BayesPrism in a derandomized framework by replacing the time-consuming Gibbs sampling step with a fixed-point algorithm. We demonstrate that the new algorithm is effectively equivalent to BayesPrism while providing a considerable speed and memory advantage. Furthermore, the InstaPrism package is equipped with a precompiled, curated set of references tailored for a variety of cancer types, streamlining the deconvolution process. AVAILABILITY AND IMPLEMENTATION The package InstaPrism is freely available at: https://github.com/humengying0907/InstaPrism. The source code and evaluation pipeline used in this paper can be found at: https://github.com/humengying0907/InstaPrismSourceCode.
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Affiliation(s)
- Mengying Hu
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, 15260, United States
- Joint Carnegie Mellon - University of Pittsburgh Computational Biology PhD Program, University of Pittsburgh, Pittsburgh, 15260, United States
| | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, 15260, United States
- Joint Carnegie Mellon - University of Pittsburgh Computational Biology PhD Program, University of Pittsburgh, Pittsburgh, 15260, United States
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41
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Fortin BM, Pfeiffer SM, Insua-Rodríguez J, Alshetaiwi H, Moshensky A, Song WA, Mahieu AL, Chun SK, Lewis AN, Hsu A, Adam I, Eng OS, Pannunzio NR, Seldin MM, Marazzi I, Marangoni F, Lawson DA, Kessenbrock K, Masri S. Circadian control of tumor immunosuppression affects efficacy of immune checkpoint blockade. Nat Immunol 2024; 25:1257-1269. [PMID: 38806707 DOI: 10.1038/s41590-024-01859-0] [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: 11/09/2023] [Accepted: 04/29/2024] [Indexed: 05/30/2024]
Abstract
The circadian clock is a critical regulator of immunity, and this circadian control of immune modulation has an essential function in host defense and tumor immunosurveillance. Here we use a single-cell RNA sequencing approach and a genetic model of colorectal cancer to identify clock-dependent changes to the immune landscape that control the abundance of immunosuppressive cells and consequent suppression of cytotoxic CD8+ T cells. Of these immunosuppressive cell types, PD-L1-expressing myeloid-derived suppressor cells (MDSCs) peak in abundance in a rhythmic manner. Disruption of the epithelial cell clock regulates the secretion of cytokines that promote heightened inflammation, recruitment of neutrophils and the subsequent development of MDSCs. We also show that time-of-day anti-PD-L1 delivery is most effective when synchronized with the abundance of immunosuppressive MDSCs. Collectively, these data indicate that circadian gating of tumor immunosuppression informs the timing and efficacy of immune checkpoint inhibitors.
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Affiliation(s)
- Bridget M Fortin
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Shannon M Pfeiffer
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Jacob Insua-Rodríguez
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Hamad Alshetaiwi
- Department of Pathology, University of Hail, Hail, Saudi Arabia
- Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Alexander Moshensky
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Wei A Song
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Alisa L Mahieu
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Sung Kook Chun
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Amber N Lewis
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Alex Hsu
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Isam Adam
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Oliver S Eng
- Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
- Department of Surgery, Division of Surgical Oncology, University of California Irvine, Orange, CA, USA
| | - Nicholas R Pannunzio
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
- Department of Medicine, Division of Hematology/Oncology, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA, USA
| | - Marcus M Seldin
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA, USA
| | - Ivan Marazzi
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA, USA
| | - Francesco Marangoni
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Devon A Lawson
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA, USA
| | - Selma Masri
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA.
- Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA.
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA, USA.
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Jin Y, Zuo Y, Li G, Liu W, Pan Y, Fan T, Fu X, Yao X, Peng Y. Advances in spatial transcriptomics and its applications in cancer research. Mol Cancer 2024; 23:129. [PMID: 38902727 PMCID: PMC11188176 DOI: 10.1186/s12943-024-02040-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 06/10/2024] [Indexed: 06/22/2024] Open
Abstract
Malignant tumors have increasing morbidity and high mortality, and their occurrence and development is a complicate process. The development of sequencing technologies enabled us to gain a better understanding of the underlying genetic and molecular mechanisms in tumors. In recent years, the spatial transcriptomics sequencing technologies have been developed rapidly and allow the quantification and illustration of gene expression in the spatial context of tissues. Compared with the traditional transcriptomics technologies, spatial transcriptomics technologies not only detect gene expression levels in cells, but also inform the spatial location of genes within tissues, cell composition of biological tissues, and interaction between cells. Here we summarize the development of spatial transcriptomics technologies, spatial transcriptomics tools and its application in cancer research. We also discuss the limitations and challenges of current spatial transcriptomics approaches, as well as future development and prospects.
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Affiliation(s)
- Yang Jin
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuanli Zuo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Gang Li
- Department of Thoracic Surgery, The Public Health Clinical Center of Chengdu, Chengdu, 610061, China
| | - Wenrong Liu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yitong Pan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ting Fan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xin Fu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaojun Yao
- Department of Thoracic Surgery, The Public Health Clinical Center of Chengdu, Chengdu, 610061, China.
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China.
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Liu B, Li S, Cheng Y, Song P, Xu M, Li Z, Shao W, Xin J, Fu Z, Gu D, Du M, Zhang Z, Wang M. Distinctive multicellular immunosuppressive hubs confer different intervention strategies for left- and right-sided colon cancers. Cell Rep Med 2024; 5:101589. [PMID: 38806057 PMCID: PMC11228667 DOI: 10.1016/j.xcrm.2024.101589] [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: 11/13/2023] [Revised: 03/11/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
Primary colon cancers arising from the left and right sides exhibit distinct clinical and molecular characteristics. Sidedness-associated heterogeneity relies intricately on the oncogenic properties of cancer cells and multicellular interactions in tumor microenvironments. Here, combining transcriptomic profiling of 426,863 single cells from 105 colon cancer patients and validation with spatial transcriptomics and large-scale histological analysis, we capture common transcriptional heterogeneity patterns between left- and right-sided malignant epithelia through delineating two side-specific expression meta-programs. The proliferation stemness meta-program is notably enriched in left-sided malignant epithelia that colocalize with Mph-PLTP cells, activated regulatory T cells (Tregs), and exhausted CD8-LAYN cells, constituting the glucose metabolism reprogramming niche. The immune secretory (IS) meta-program exhibits specific enrichment in right-sided malignant epithelia, especially in smoking patients with right-sided colon cancer. The IShigh malignant epithelia spatially localize in hypoxic regions and facilitate immune evasion through attenuating Mph-SPP1 cell antigen presentation and recruiting innate-like cytotoxicity-reduced CD8-CD161 cells.
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Affiliation(s)
- Bingxin Liu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuwei Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yifei Cheng
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Peng Song
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Menghuan Xu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengyi Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wei Shao
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zan Fu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Dongying Gu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
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Theune WC, Chen J, Theune EV, Ye X, Ménoret A, Vella AT, Wang K. Interleukin-17 directly stimulates tumor infiltrating Tregs to prevent cancer development. Front Immunol 2024; 15:1408710. [PMID: 38947320 PMCID: PMC11211274 DOI: 10.3389/fimmu.2024.1408710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/27/2024] [Indexed: 07/02/2024] Open
Abstract
Background Interleukin-17 (IL-17) family cytokines promote protective inflammation for pathogen resistance, but also facilitate autoimmunity and tumor development. A direct signal of IL-17 to regulatory T cells (Tregs) has not been reported and may help explain these dichotomous responses. Methods We generated a conditional knockout of Il17ra in Tregs by crossing Foxp3-YFP-Cre mice to Il17ra-flox mice (Il17ra ΔTreg mice). Subsequently, we adoptively transferred bone marrow cells from Il17ra ΔTreg mice to a mouse model of sporadic colorectal cancer (Cdx2-Cre +/Apc F/+), to selectively ablate IL-17 direct signaling on Tregs in colorectal cancer. Single cell RNA sequencing and bulk RNA sequencing were performed on purified Tregs from mouse colorectal tumors, and compared to those of human tumor infiltrating Treg cells. Results IL-17 Receptor A (IL-17RA) is expressed in Tregs that reside in mouse mesenteric lymph nodes and colon tumors. Ablation of IL-17RA, specifically in Tregs, resulted in increased Th17 cells, and exacerbated tumor development. Mechanistically, tumor-infiltrating Tregs exhibit a unique gene signature that is linked to their activation, maturation, and suppression function, and this signature is in part supported by the direct signaling of IL-17 to Tregs. To study pathways of Treg programming, we found that loss of IL-17RA in tumor Tregs resulted in reduced RNA splicing, and downregulation of several RNA binding proteins that are known to regulate alternative splicing and promote Treg function. Conclusion IL-17 directly signals to Tregs and promotes their maturation and function. This signaling pathway constitutes a negative feedback loop that controls cancer-promoting inflammation in CRC.
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Affiliation(s)
- William C. Theune
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, United States
| | - Ju Chen
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, United States
- The Eighth Clinical Medical College of Guangzhou University of Chinese Medicine, Foshan Hospital of Traditional Chinese Medicine, Foshan, Guangdong, China
| | - Eileen Victoria Theune
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, United States
| | - Xiaoyang Ye
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, United States
| | - Antoine Ménoret
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, United States
| | - Anthony T. Vella
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, United States
| | - Kepeng Wang
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT, United States
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45
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Du P, Fan R, Zhang N, Wu C, Zhang Y. Advances in Integrated Multi-omics Analysis for Drug-Target Identification. Biomolecules 2024; 14:692. [PMID: 38927095 PMCID: PMC11201992 DOI: 10.3390/biom14060692] [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: 05/11/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
As an essential component of modern drug discovery, the role of drug-target identification is growing increasingly prominent. Additionally, single-omics technologies have been widely utilized in the process of discovering drug targets. However, it is difficult for any single-omics level to clearly expound the causal connection between drugs and how they give rise to the emergence of complex phenotypes. With the progress of large-scale sequencing and the development of high-throughput technologies, the tendency in drug-target identification has shifted towards integrated multi-omics techniques, gradually replacing traditional single-omics techniques. Herein, this review centers on the recent advancements in the domain of integrated multi-omics techniques for target identification, highlights the common multi-omics analysis strategies, briefly summarizes the selection of multi-omics analysis tools, and explores the challenges of existing multi-omics analyses, as well as the applications of multi-omics technology in drug-target identification.
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Affiliation(s)
- Peiling Du
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Rui Fan
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Nana Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Chenyuan Wu
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Yingqian Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
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Fowler H, Clifford RE, Bowden D, Sutton PA, Govindarajah N, Fok M, Glenn M, Wall M, Rubbi C, Buczacki SJA, Mandal A, Francies H, Hughes J, Parsons JL, Vimalachandran D. Myoferlin: A Potential Marker of Response to Radiation Therapy and Survival in Locally Advanced Rectal Cancer. Int J Radiat Oncol Biol Phys 2024:S0360-3016(24)00696-5. [PMID: 38866213 DOI: 10.1016/j.ijrobp.2024.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 05/24/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024]
Abstract
PURPOSE Patients with locally advanced rectal cancer often require neoadjuvant chemoradiation therapy to downstage the disease, but the response is variable with no predictive biomarkers. We have previously revealed through proteomic profiling that myoferlin is associated with response to radiation therapy. The aims of this study were to further validate this finding and explore the potential for myoferlin to act as a prognostic and/or therapeutic target. METHODS AND MATERIALS Immunohistochemical analysis of a tissue microarray (TMA) for 111 patients was used to validate the initial proteomic findings. Manipulation of myoferlin was achieved using small interfering RNA, a small molecular inhibitor (wj460), and a CRISPR-Cas9 knockout cell line. Radiosensitization after treatment was assessed using 2-dimensional clonogenic assays, 3-dimensional spheroid models, and patient-derived organoids. Underlying mechanisms were investigated using electrophoresis, immunofluorescence, and immunoblotting. RESULTS Analysis of both the diagnostic biopsy and tumor resection samples confirmed that low myoferlin expression correlated with a good response to neoadjuvant long-course chemoradiation therapy. High myoferlin expression was associated with spread to local lymph nodes and worse 5-year survival (P = .01; hazard ratio, 3.5; 95% CI, 1.27-10.04). This was externally validated using the Stratification in Colorectal Cancer database. Quantification of myoferlin using immunoblotting in immortalized colorectal cancer cell lines and organoids demonstrated that high myoferlin expression was associated with increased radioresistance. Biological and pharmacologic manipulation of myoferlin resulted in significantly increased radiosensitivity across all cell lines in 2-dimensional and 3-dimensional models. After irradiation, myoferlin knockdown cells had a significantly impaired ability to repair DNA double-strand breaks. This appeared to be mediated via nonhomologous end-joining. CONCLUSIONS We have confirmed that high expression of myoferlin in rectal cancer is associated with poor response to neoadjuvant therapy and worse long-term survival. Furthermore, the manipulation of myoferlin led to increased radiosensitivity in vitro. This suggests that myoferlin could be targeted to enhance the sensitivity of patients with rectal cancer to radiation therapy, and further work is required.
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Affiliation(s)
- Hayley Fowler
- Department of Colorectal Surgery, Countess of Chester National Health Service Foundation Trust, Chester, United Kingdom; Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, William Henry Duncan Building, Liverpool, United Kingdom.
| | - Rachael E Clifford
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, William Henry Duncan Building, Liverpool, United Kingdom
| | - David Bowden
- Department of Colorectal Surgery, Countess of Chester National Health Service Foundation Trust, Chester, United Kingdom
| | - Paul A Sutton
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, William Henry Duncan Building, Liverpool, United Kingdom
| | - Naren Govindarajah
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, William Henry Duncan Building, Liverpool, United Kingdom
| | - Matthew Fok
- Department of Colorectal Surgery, Countess of Chester National Health Service Foundation Trust, Chester, United Kingdom; Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, William Henry Duncan Building, Liverpool, United Kingdom
| | - Mark Glenn
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, William Henry Duncan Building, Liverpool, United Kingdom
| | - Michael Wall
- Department of Colorectal Surgery, Countess of Chester National Health Service Foundation Trust, Chester, United Kingdom
| | - Carlos Rubbi
- Faculty of Health, Social Care & Medicine, Edge Hill University, St Helens Road, Ormskirk, Lancashire, L39 4QP
| | - Simon J A Buczacki
- Nuffield Department of Surgical Sciences (NDS), University of Oxford, Oxford, United Kingdom
| | - Amit Mandal
- Nuffield Department of Surgical Sciences (NDS), University of Oxford, Oxford, United Kingdom
| | - Hayley Francies
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan Hughes
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jason L Parsons
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Dale Vimalachandran
- Department of Colorectal Surgery, Countess of Chester National Health Service Foundation Trust, Chester, United Kingdom; Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, William Henry Duncan Building, Liverpool, United Kingdom
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Warner van Dijk FA, Tong O, O’Neil TR, Bertram KM, Hu K, Baharlou H, Vine EE, Jenns K, Gosselink MP, Toh JW, Papadopoulos T, Barnouti L, Jenkins GJ, Sandercoe G, Haniffa M, Sandgren KJ, Harman AN, Cunningham AL, Nasr N. Characterising plasmacytoid and myeloid AXL+ SIGLEC-6+ dendritic cell functions and their interactions with HIV. PLoS Pathog 2024; 20:e1012351. [PMID: 38924030 PMCID: PMC11233022 DOI: 10.1371/journal.ppat.1012351] [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: 02/15/2024] [Revised: 07/09/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
AXL+ Siglec-6+ dendritic cells (ASDC) are novel myeloid DCs which can be subdivided into CD11c+ and CD123+ expressing subsets. We showed for the first time that these two ASDC subsets are present in inflamed human anogenital tissues where HIV transmission occurs. Their presence in inflamed tissues was supported by single cell RNA analysis of public databases of such tissues including psoriasis diseased skin and colorectal cancer. Almost all previous studies have examined ASDCs as a combined population. Our data revealed that the two ASDC subsets differ markedly in their functions when compared with each other and to pDCs. Relative to their cell functions, both subsets of blood ASDCs but not pDCs expressed co-stimulatory and maturation markers which were more prevalent on CD11c+ ASDCs, thus inducing more T cell proliferation and activation than their CD123+ counterparts. There was also a significant polarisation of naïve T cells by both ASDC subsets toward Th2, Th9, Th22, Th17 and Treg but less toward a Th1 phenotype. Furthermore, we investigated the expression of chemokine receptors that facilitate ASDCs and pDCs migration from blood to inflamed tissues, their HIV binding receptors, and their interactions with HIV and CD4 T cells. For HIV infection, within 2 hours of HIV exposure, CD11c+ ASDCs showed a trend in more viral transfer to T cells than CD123+ ASDCs and pDCs for first phase transfer. However, for second phase transfer, CD123+ ASDCs showed a trend in transferring more HIV than CD11c+ ASDCs and there was no viral transfer from pDCs. As anogenital inflammation is a prerequisite for HIV transmission, strategies to inhibit ASDC recruitment into inflamed tissues and their ability to transmit HIV to CD4 T cells should be considered.
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Affiliation(s)
- Freja A. Warner van Dijk
- The Westmead Institute for Medical Research, Centre for Virus Research, Westmead, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
| | - Orion Tong
- The Westmead Institute for Medical Research, Centre for Virus Research, Westmead, Australia
| | - Thomas R. O’Neil
- The Westmead Institute for Medical Research, Centre for Virus Research, Westmead, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
| | - Kirstie M. Bertram
- The Westmead Institute for Medical Research, Centre for Virus Research, Westmead, Australia
| | - Kevin Hu
- The Westmead Institute for Medical Research, Centre for Virus Research, Westmead, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
| | - Heeva Baharlou
- The Westmead Institute for Medical Research, Centre for Virus Research, Westmead, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
| | - Erica E. Vine
- The Westmead Institute for Medical Research, Centre for Virus Research, Westmead, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
| | - Kate Jenns
- The Westmead Institute for Medical Research, Centre for Virus Research, Westmead, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
| | | | - James W. Toh
- The Westmead Institute for Medical Research, Centre for Virus Research, Westmead, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
- Department of Colorectal Surgery, Westmead Hospital, Westmead, Australia
| | - Tim Papadopoulos
- Department of Plastic, Reconstructive, and Aesthetic Surgery, Westmead Private Hospital, Westmead, Australia
| | - Laith Barnouti
- Department of Plastic, Reconstructive, and Aesthetic Surgery, Westmead Private Hospital, Westmead, Australia
| | - Gregory J. Jenkins
- Department of Obstetrics and Gynaecology, Westmead Hospital, Westmead, Australia
| | - Gavin Sandercoe
- Department of Plastic Surgery, Norwest Private Hospital, Bella Vista, Australia
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Knigdom
- Biosciences Institute, Newcastle University, Newcastle, United Knigdom
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Knigdom
| | - Kerrie J. Sandgren
- The Westmead Institute for Medical Research, Centre for Virus Research, Westmead, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
| | - Andrew N. Harman
- The Westmead Institute for Medical Research, Centre for Virus Research, Westmead, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
| | - Anthony L. Cunningham
- The Westmead Institute for Medical Research, Centre for Virus Research, Westmead, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
| | - Najla Nasr
- The Westmead Institute for Medical Research, Centre for Virus Research, Westmead, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, Australia
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Zhang J, Fu L, Wang H, Yonemura A, Semba T, Yasuda-Yoshihara N, Nishimura A, Tajiri T, Tong Y, Yasuda T, Uchihara T, Yamazaki M, Okamoto Y, Yamasaki J, Nagano O, Baba H, Ishimoto T. RAC1-mediated integrin alpha-6 expression in E-cadherin-deficient gastric cancer cells promotes interactions with the stroma and peritoneal dissemination. Cancer Lett 2024; 591:216901. [PMID: 38641311 DOI: 10.1016/j.canlet.2024.216901] [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: 12/18/2023] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/21/2024]
Abstract
Diffuse-type gastric cancer (DGC) is a subtype of gastric cancer that is prone to peritoneal dissemination, with poor patient prognosis. Although intercellular adhesion loss between cancer cells is a major characteristic of DGCs, the mechanism underlying the alteration in cell-to-extracellular matrix (ECM) adhesion is unclear. We investigated how DGCs progress and cause peritoneal dissemination through interactions between DGC cells and the tumour microenvironment (TME). P53 knockout and KRASG12V-expressing (GAN-KP) cells and Cdh1-deleted GAN-KP (GAN-KPC) cells were orthotopically transplanted into the gastric wall to mimic peritoneal dissemination. The GAN-KPC tumour morphology was similar to that of human DGCs containing abundant stroma. RNA sequencing revealed that pathways related to Rho GTPases and integrin-ECM interactions were specifically increased in GAN-KPC cells compared with GAN-KP cells. Notably, we found that Rac Family Small GTPase 1 (RAC1) induces Integrin Subunit Alpha 6 (ITGA6) trafficking, leading to its enrichment on the GC cell membrane. Fibroblasts activate the FAK/AKT pathway in GC cells by mediating extracellular matrix (ECM)-Itga6 interactions, exacerbating the malignant phenotype. In turn, GC cells induce abnormal expression of fibroblast collagen and its transformation into cancer-associated fibroblasts (CAFs), resulting in DGC-like subtypes. These findings indicate that Cdh1 gene loss leads to abnormal expression and changes in the subcellular localization of ITGA6 through RAC1 signalling. The latter, through interactions with CAFs, allows for peritoneal dissemination.
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Affiliation(s)
- Jun Zhang
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan; Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Lingfeng Fu
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan; Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Huaitao Wang
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan; Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Atsuko Yonemura
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan; Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takashi Semba
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Noriko Yasuda-Yoshihara
- Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan; Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Akiho Nishimura
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Takuya Tajiri
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan; Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yilin Tong
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan; Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tadahito Yasuda
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan; Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tomoyuki Uchihara
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan; Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Masaya Yamazaki
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yuya Okamoto
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Juntaro Yamasaki
- Division of Gene Regulation, Cancer Center, Fujita Health University, Toyoake, Japan
| | - Osamu Nagano
- Division of Gene Regulation, Cancer Center, Fujita Health University, Toyoake, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan; Center for Metabolic Regulation of Healthy Ageing, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takatsugu Ishimoto
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Gastrointestinal Cancer Biology, International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan; Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
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49
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Wen J. Single-cell transcriptomics reveals antigen-presenting capacity and therapeutic resistance potential of immunomodulatory endothelial cells in colorectal cancer. Immun Inflamm Dis 2024; 12:e1311. [PMID: 38874280 PMCID: PMC11177288 DOI: 10.1002/iid3.1311] [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: 11/24/2023] [Revised: 05/10/2024] [Accepted: 05/29/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND The heterogeneity of tumor endothelial cells (TECs) hinders the efficacy of antiangiogenic therapies (AATs). Only a small percentage of angiogenic TECs are considered effective targets for AATs. Immunomodulatory ECs (IMECs), as a newly focused functional subgroup of endothelial cells (ECs), are being evaluated for their ability to regulate tumor immune balance and influence existing AATs. METHODS Based on single-cell transcriptome data from colorectal cancer in a publicly available database, we conducted a wide array of bioinformatic approaches to study EC subsets that meet the IMECs definition. Our investigation encompassed the gene expression signatures of these subsets, cellular composition differences, cell-cell interactions. RESULTS Two subsets that meet the IMECs definition were found in tumors and para-cancerous tissues. Combined with the results of gene ontological analysis and interaction with CD4+ T cells, we found that IMECs can present MHC-II antigens to mature CD4+ T cells. There were differences in the level of interaction between IMECs and different types of mature CD4+ T cell subsets. In addition, IMEC subsets had different expression levels of angiogenesis related genes. The angiogenesis score of IMECs decreased after patients received immunotherapy. IMEC subsets do not depend on a single proangiogenic receptor and are involved in regulating angiogenesis, which may reduce the efficacy of AATs. The adverse effects of specific IMEC subsets on AATs were validated in the RNA-seq dataset of the bevacizumab treatment group. CONCLUSION Our study suggests the potential MHC-II antigen presentation capacity of IMECs and the enhanced angiogenesis characteristics within tumors. The function of IMECs in the vascular network may have a potentially adverse effect on AATs. Controlling the functional properties of IMECs may be a new angle for tumor therapy.
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Affiliation(s)
- Jingyi Wen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
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50
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Bader JE, Wolf MM, Lupica-Tondo GL, Madden MZ, Reinfeld BI, Arner EN, Hathaway ES, Steiner KK, Needle GA, Hatem Z, Landis MD, Faneuff EE, Blackman A, Wolf EM, Cottam MA, Ye X, Bates ME, Smart K, Wang W, Pinheiro LV, Christofides A, Smith D, Boussiotis VA, Haake SM, Beckermann KE, Wellen KE, Reinhart-King CA, Serezani CH, Lee CH, Aubrey C, Chen H, Rathmell WK, Hasty AH, Rathmell JC. Obesity induces PD-1 on macrophages to suppress anti-tumour immunity. Nature 2024; 630:968-975. [PMID: 38867043 DOI: 10.1038/s41586-024-07529-3] [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: 11/04/2022] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Obesity is a leading risk factor for progression and metastasis of many cancers1,2, yet can in some cases enhance survival3-5 and responses to immune checkpoint blockade therapies, including anti-PD-1, which targets PD-1 (encoded by PDCD1), an inhibitory receptor expressed on immune cells6-8. Although obesity promotes chronic inflammation, the role of the immune system in the obesity-cancer connection and immunotherapy remains unclear. It has been shown that in addition to T cells, macrophages can express PD-19-12. Here we found that obesity selectively induced PD-1 expression on tumour-associated macrophages (TAMs). Type I inflammatory cytokines and molecules linked to obesity, including interferon-γ, tumour necrosis factor, leptin, insulin and palmitate, induced macrophage PD-1 expression in an mTORC1- and glycolysis-dependent manner. PD-1 then provided negative feedback to TAMs that suppressed glycolysis, phagocytosis and T cell stimulatory potential. Conversely, PD-1 blockade increased the level of macrophage glycolysis, which was essential for PD-1 inhibition to augment TAM expression of CD86 and major histocompatibility complex I and II molecules and ability to activate T cells. Myeloid-specific PD-1 deficiency slowed tumour growth, enhanced TAM glycolysis and antigen-presentation capability, and led to increased CD8+ T cell activity with a reduced level of markers of exhaustion. These findings show that obesity-associated metabolic signalling and inflammatory cues cause TAMs to induce PD-1 expression, which then drives a TAM-specific feedback mechanism that impairs tumour immune surveillance. This may contribute to increased cancer risk yet improved response to PD-1 immunotherapy in obesity.
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Affiliation(s)
- Jackie E Bader
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melissa M Wolf
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gian Luca Lupica-Tondo
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew Z Madden
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bradley I Reinfeld
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emily N Arner
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emma S Hathaway
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - KayLee K Steiner
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gabriel A Needle
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zaid Hatem
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Madelyn D Landis
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eden E Faneuff
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amondrea Blackman
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elysa M Wolf
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Matthew A Cottam
- Department of Surgery, Division of Surgical Oncology and Endocrine Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Madison E Bates
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Kyra Smart
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Wenjun Wang
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Laura V Pinheiro
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anthos Christofides
- Department of Medicine, Division of Hematology-Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Harvard University, Boston, MA, USA
| | - DuPreez Smith
- Department of Obstetrics and Gynecology, University of Alberta, Edmonton, Alberta, Canada
| | - Vassiliki A Boussiotis
- Department of Medicine, Division of Hematology-Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Scott M Haake
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kathryn E Beckermann
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kathryn E Wellen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - C Henrique Serezani
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cheng-Han Lee
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Christa Aubrey
- Department of Obstetrics and Gynecology, University of Alberta, Edmonton, Alberta, Canada
| | - Heidi Chen
- Department of Biostatistics, Vanderbilt University, Nashville, TN, USA
| | - W Kimryn Rathmell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alyssa H Hasty
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- US Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Jeffrey C Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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