101
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Qi T, Song L, Guo Y, Chen C, Yang J. From genetic associations to genes: methods, applications, and challenges. Trends Genet 2024; 40:642-667. [PMID: 38734482 DOI: 10.1016/j.tig.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/13/2024]
Abstract
Genome-wide association studies (GWASs) have identified numerous genetic loci associated with human traits and diseases. However, pinpointing the causal genes remains a challenge, which impedes the translation of GWAS findings into biological insights and medical applications. In this review, we provide an in-depth overview of the methods and technologies used for prioritizing genes from GWAS loci, including gene-based association tests, integrative analysis of GWAS and molecular quantitative trait loci (xQTL) data, linking GWAS variants to target genes through enhancer-gene connection maps, and network-based prioritization. We also outline strategies for generating context-dependent xQTL data and their applications in gene prioritization. We further highlight the potential of gene prioritization in drug repurposing. Lastly, we discuss future challenges and opportunities in this field.
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Affiliation(s)
- Ting Qi
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China.
| | - Liyang Song
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yazhou Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Chang Chen
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Jian Yang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China.
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102
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Kim GD, Lim C, Park J. A practical handbook on single-cell RNA sequencing data quality control and downstream analysis. Mol Cells 2024; 47:100103. [PMID: 39094968 DOI: 10.1016/j.mocell.2024.100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/19/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
Advancements in single-cell analysis have facilitated high-resolution observation of the transcriptome in individual cells. However, standards for obtaining high-quality cells and data analysis pipelines remain variable. Here, we provide the groundwork for improving the quality of single-cell analysis by delineating guidelines for selecting high-quality cells and considerations throughout the analysis. This review will streamline researchers' access to single-cell analysis and serve as a valuable guide for analysis.
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Affiliation(s)
- Gyeong Dae Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Chaemin Lim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea.
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103
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Zhou Z, Li T, Li J, Lin W, Zheng Q. Exosomal transfer of HCC-derived miR-17-5p downregulates NK cell function by targeting RUNX1-NKG2D axis. Int Immunopharmacol 2024; 136:112361. [PMID: 38820961 DOI: 10.1016/j.intimp.2024.112361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/06/2024] [Accepted: 05/26/2024] [Indexed: 06/02/2024]
Abstract
OBJECTIVE Natural killer (NK) cells are an integral part of the staunch defense line against malignant tumors within the tumor microenvironment. Existing research indicates that miRNAs can influence the development of NK cells by negatively modulating gene expression. In this study, we aim to explore how the miR-17-5p in Hepatocellular Carcinoma (HCC) exosomes regulates the killing function of NK cells towards HCC cells through the transcription factor RNX1. METHODS The exosomes were isolated from HCC tissues and cell lines, followed by a second generation sequencing to compare differential miRNAs. Verification was performed using qRT-PCR and Western blot methods. The mutual interactions between miR-17-5p and RUNX1, as well as between RUNX1 and NKG2D, were authenticated using techniques like luciferase reporter gene assays, Western blotting, and Chromatin Immunoprecipitation (ChIP). The cytotoxic activity of NK cells towards HCC cells in vitro was measured using methods such as RTCA and ELISPOT. The zebrafish xenotransplantation was utilized to assess the in vivo killing capacity of NK cells against HCC cells. RESULTS The level of miR-17-5p in exosomes from HCC tissue increased compared to adjacent tissues. We verified that RUNX1 was a target of miR-17-5p and that RUNX1 enhances the transcription of NKG2D. MiR-17-5p was found to downregulate the expression of RUNX1 and NKG2D, subsequently reducing the in vitro and in vivo cytotoxic capabilities of NK cells against HCC cells. CONCLUSIONS The miR-17-5p found within HCC exosomes can target RUNX1, subsequently attenuating the cytotoxic activity of NK cells.
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Affiliation(s)
- Zhifeng Zhou
- Laboratory of Immuno-Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, China; School of Basic Medical Sciences, Fujian Medical University, Fuzhu, Fujian, China
| | - Tianchuan Li
- Department of Integrated Traditional and Western Medicine, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, China
| | - Jieyu Li
- Laboratory of Immuno-Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, China; School of Basic Medical Sciences, Fujian Medical University, Fuzhu, Fujian, China
| | - Wansong Lin
- Laboratory of Immuno-Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, China; School of Basic Medical Sciences, Fujian Medical University, Fuzhu, Fujian, China.
| | - Qingfeng Zheng
- Department of Thoracic Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, China.
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104
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Singh A, Khiabanian H. Feature selection followed by a novel residuals-based normalization that includes variance stabilization simplifies and improves single-cell gene expression analysis. BMC Bioinformatics 2024; 25:248. [PMID: 39080559 PMCID: PMC11290295 DOI: 10.1186/s12859-024-05872-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
Normalization is a crucial step in the analysis of single-cell RNA-sequencing (scRNA-seq) counts data. Its principal objectives are reduction of systematic biases primarily introduced through technical sources and transformation of counts to make them more amenable for the application of established statistical frameworks. In the standard workflows, normalization is followed by feature selection to identify highly variable genes (HVGs) that capture most of the biologically meaningful variation across the cells. Here, we make the case for a revised workflow by proposing a simple feature selection method and showing that we can perform feature selection before normalization by relying on observed counts. We highlight that the feature selection step can be used to not only select HVGs but to also identify stable genes. We further propose a novel variance stabilization transformation inclusive residuals-based normalization method that in fact relies on the stable genes to inform the reduction of systematic biases. We demonstrate significant improvements in downstream clustering analyses through the application of our proposed methods on biological truth-known as well as simulated counts datasets. We have implemented this novel workflow for analyzing high-throughput scRNA-seq data in an R package called Piccolo.
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Affiliation(s)
- Amartya Singh
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA.
| | - Hossein Khiabanian
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
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105
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Cao S, Nguyen K, Ma K, Du X, Liu X, Antonova AU, Rood RP, Gremida A, Chen CH, Gutierrez A, Rubin DC, Gregory MH, Gergely M, Escudero GO, Huang K, Jaeger N, Cella M, Newberry RD, Davidson NO, Ciorba MA, Deepak P, Colonna M. Mucosal Single-Cell Profiling of Crohn's-Like Disease of the Pouch Reveals Unique Pathogenesis and Therapeutic Targets. Gastroenterology 2024:S0016-5085(24)05284-3. [PMID: 39084267 DOI: 10.1053/j.gastro.2024.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/11/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND & AIMS The pathophysiology of Crohn's-like disease of the pouch (CDP) in patients with a history of ulcerative colitis (UC) is unknown. We examined mucosal cells from patients with and without CDP using single-cell analyses. METHODS Endoscopic samples were collected from pouch body and prepouch ileum (pouch/ileum) of 50 patients with an ileal pouch-anal anastomosis. Single-cell RNA sequencing was performed on pouch/ileal tissues of patients with normal pouch/ileum and CDP. Mass cytometry was performed on mucosal immune cells from patients with UC with normal pouch/ileum, CDP, pouchitis, and those with familial adenomatous polyposis after pouch formation. Findings were independently validated using immunohistochemistry. RESULTS The cell populations/states in the pouch body differed from those in the prepouch ileum, likely secondary to increased microbial burden. Compared with the familial adenomatous polyposis pouch, the UC pouch was enriched in colitogenic immune cells even without inflammation. CDP was characterized by increases in T helper 17 cells, inflammatory fibroblasts, inflammatory monocytes, TREM1+ monocytes, clonal expansion of effector T cells, and overexpression of T helper 17 cells-inducing cytokine genes such as IL23, IL1B, and IL6 by mononuclear phagocytes. Ligand-receptor analysis further revealed a stromal-mononuclear phagocytes-lymphocyte circuit in CDP. Integrated analysis showed that up-regulated immune mediators in CDP were similar to those in CD and pouchitis, but not UC. Additionally, CDP pouch/ileum exhibited heightened endoplasmic reticulum stress across all major cell compartments. CONCLUSIONS CDP likely represents a distinct entity of inflammatory bowel disease with heightened endoplasmic reticulum stress in both immune and nonimmune cells, which may become a novel diagnostic biomarker and therapeutic target for CDP.
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Affiliation(s)
- Siyan Cao
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri.
| | - Khai Nguyen
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Kaiming Ma
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Xiaotang Du
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Xiuli Liu
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Alina Ulezko Antonova
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Richard P Rood
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Anas Gremida
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Chien-Huan Chen
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Alexandra Gutierrez
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Deborah C Rubin
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Martin H Gregory
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Mate Gergely
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Guadalupe Oliva Escudero
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Katherine Huang
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Natalia Jaeger
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Marina Cella
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Rodney D Newberry
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Nicholas O Davidson
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Matthew A Ciorba
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Parakkal Deepak
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri.
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106
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Abedi Kichi Z, Dini N, Rojhannezhad M, Shirvani Farsani Z. Noncoding RNAs in B cell non-Hodgkins lymphoma. Gene 2024; 917:148480. [PMID: 38636814 DOI: 10.1016/j.gene.2024.148480] [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: 01/05/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
B-cell non-Hodgkins lymphomas (BCNHLs) are a category of B-cell cancers that show heterogeneity. These blood disorders are derived from different levels of B-cell maturity. Among NHL cases, ∼80-90 % are derived from B-cells. Recent studies have demonstrated that noncoding RNAs (ncRNAs) contribute to almost all parts of mechanisms and are essential in tumorigenesis, including B-cell non-Hodgkins lymphomas. The study of ncRNA dysregulations in B-cell lymphoma unravels important mysteries in lymphoma's molecular etiology. It seems also necessary for discovering novel trials as well as investigating the potential of ncRNAs as markers for their diagnosis and prognosis. In the current study, we summarize the role of ncRNAs involving miRNAs, long noncoding RNAs, as well as circular RNAs in the development or progression of BCNHLs.
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Affiliation(s)
- Zahra Abedi Kichi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IR Iran; Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University Munich, Germany
| | - Niloofar Dini
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Mahbubeh Rojhannezhad
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IR Iran
| | - Zeinab Shirvani Farsani
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
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107
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Shang Y, Cui P, Chen Y, Zhang Z, Li S, Chen Z, Ma A, Jia Y. Study on the mechanism of mitigating radiation damage by improving the hematopoietic system and intestinal barrier with Tenebrio molitor peptides. Food Funct 2024; 15:8116-8127. [PMID: 39011610 DOI: 10.1039/d4fo01141d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Research on plant and animal peptides has garnered significant attention, but there is a lack of studies on the functional properties of Tenebrio molitor peptides, particularly in relation to their potential mitigating effect on radiation damage and the underlying mechanisms. This study aims to explore the protective effects of Tenebrio molitor peptides against radiation-induced damage. Mice were divided into five groups: normal, radiation model, and low-, medium-, and high-dose Tenebrio molitor peptide (TMP) groups (0.15 g per kg BW, 0.30 g per kg BW, and 0.60 g per kg BW). Various parameters such as blood cell counts, bone marrow DNA content, immune organ indices, serum levels of D-lactic acid, diamine oxidase (DAO), endotoxin (LPS), and inflammatory factors were assessed at 3 and 15 days post gamma irradiation. Additionally, the intestinal tissue morphology was examined through H&E staining, RT-qPCR experiments were conducted to analyze the expression of inflammatory factors in the intestine, and immunohistochemistry was utilized to evaluate the expression of tight junction proteins ZO-1 and Occludin in the intestine. The findings revealed that high-dose TMP significantly enhanced the hematopoietic system function in mice post radiation exposure, leading to increased spleen index, thymus index, blood cell counts, and bone marrow DNA production (p < 0.05). Moreover, TMP improved the intestinal barrier integrity and reduced the intestinal permeability. Mechanistic insights suggested that these peptides may safeguard intestinal barrier function by downregulating the gene expression of inflammatory factors TNF-α, IL-1β, and IL-6, while upregulating the expression of tight junction proteins ZO-1 and Occludin (p < 0.05). Overall, supplementation with TMP mitigates radiation-induced intestinal damage by enhancing the hematopoietic system and the intestinal barrier, offering valuable insights for further investigations into the mechanisms underlying the protective effects of these peptides against ionizing radiation.
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Affiliation(s)
- Yuting Shang
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China.
| | - Pengfei Cui
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China.
| | - Yachun Chen
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China.
| | - Ziqi Zhang
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China.
| | - Siting Li
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China.
| | - Zhou Chen
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China.
| | - Aijin Ma
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China.
| | - Yingmin Jia
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, PR China.
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108
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Xing Z, Li X, He J, Chen Y, Zhu L, Zhang X, Huang Z, Tang J, Guo Y, He Y. OLFM4 modulates intestinal inflammation by promoting IL-22 +ILC3 in the gut. Commun Biol 2024; 7:914. [PMID: 39075283 PMCID: PMC11286877 DOI: 10.1038/s42003-024-06601-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: 01/21/2024] [Accepted: 07/18/2024] [Indexed: 07/31/2024] Open
Abstract
Group 3 innate lymphoid cells (ILC3s) play key roles in intestinal inflammation. Olfactomedin 4 (OLFM4) is highly expressed in the colon and has a potential role in dextran sodium sulfate-induced colitis. However, the detailed mechanisms underlying the effects of OLFM4 on ILC3-mediated colitis remain unclear. In this study, we identify OLFM4 as a positive regulator of IL-22+ILC3. OLFM4 expression in colonic ILC3s increases substantially during intestinal inflammation in humans and mice. Compared to littermate controls, OLFM4-deficient (OLFM4-/-) mice are more susceptible to bacterial infection and display greater resistance to anti-CD40 induced innate colitis, together with impaired IL-22 production by ILC3, and ILC3s from OLFM4-/-mice are defective in pathogen resistance. Besides, mice with OLFM4 deficiency in the RORγt compartment exhibit the same trend as in OLFM4-/-mice, including colonic inflammation and IL-22 production. Mechanistically, the decrease in IL-22+ILC3 caused by OLFM4 deficiency involves the apoptosis signal-regulating kinase 1 (ASK1)- p38 MAPK signaling-dependent downregulation of RAR-related orphan receptor gamma (RORγt) protein. The OLFM4-metadherin (MTDH) complex upregulates p38/RORγt signaling, which is necessary for IL-22+ILC3 activation. The findings indicate that OLFM4 is a novel regulator of IL-22+ILC3 and essential for modulating intestinal inflammation and tissue homeostasis.
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Affiliation(s)
- Zhe Xing
- Pediatric Intensive Care Unit, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences); Department of Immunology, School of Basic Medical Sciences; Department of Clinical Laboratory, the Third Affiliated Hospital of Southern Medical University, Southern Medical University, Guangzhou, China
| | - Xinyao Li
- Department of Immunology; Guangdong Provincial Key Laboratory of Single Cell Technology and Application, School of Basic Medical Sciences; Southern Medical University, Guangzhou, China
| | - Junyu He
- Department of Immunology; Guangdong Provincial Key Laboratory of Single Cell Technology and Application, School of Basic Medical Sciences; Southern Medical University, Guangzhou, China
| | - Yimin Chen
- Department of Immunology; Guangdong Provincial Key Laboratory of Single Cell Technology and Application, School of Basic Medical Sciences; Southern Medical University, Guangzhou, China
| | - Lei Zhu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaogang Zhang
- Department of Immunology; Guangdong Provincial Key Laboratory of Single Cell Technology and Application, School of Basic Medical Sciences; Southern Medical University, Guangzhou, China
| | - Zhengcong Huang
- Department of Immunology; Guangdong Provincial Key Laboratory of Single Cell Technology and Application, School of Basic Medical Sciences; Southern Medical University, Guangzhou, China
| | - Jian Tang
- Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Yuxiong Guo
- Pediatric Intensive Care Unit, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University; Guangdong Provincial Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
| | - Yumei He
- Pediatric Intensive Care Unit, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences); Department of Immunology, School of Basic Medical Sciences; Department of Clinical Laboratory, the Third Affiliated Hospital of Southern Medical University, Southern Medical University, Guangzhou, China.
- Department of Immunology; Guangdong Provincial Key Laboratory of Single Cell Technology and Application, School of Basic Medical Sciences; Southern Medical University, Guangzhou, China.
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109
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Schipper M, Ulirsch J, Posthuma D, Ripke S, Heilbron K. Simplifying causal gene identification in GWAS loci. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.26.24311057. [PMID: 39132490 PMCID: PMC11312651 DOI: 10.1101/2024.07.26.24311057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Genome-wide association studies (GWAS) help to identify disease-linked genetic variants, but pinpointing the most likely causal genes in GWAS loci remains challenging. Existing GWAS gene prioritization tools are powerful, but often use complex black box models trained on datasets containing unaddressed biases. Here we present CALDERA, a gene prioritization tool that achieves similar or better performance than state-of-the-art methods, but uses just 12 features and a simple logistic regression model with L1 regularization. We use a data-driven approach to construct a truth set of causal genes in 406 GWAS loci and correct for potential confounders. We demonstrate that CALDERA is well-calibrated in external datasets and prioritizes genes with expected properties, such as being mutation-intolerant (OR = 1.751 for pLI > 90%, P = 8.45×10-3). CALDERA facilitates the prioritization of potentially causal genes in GWAS loci and may help identify novel genetics-driven drug targets.
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Affiliation(s)
- Marijn Schipper
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jacob Ulirsch
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry and Pediatric Psychology, Section Complex Trait Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam, The Netherlands
| | - Stephan Ripke
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Mental Health (DZPG), partner site Berlin/Potsdam, Berlin, Germany
| | - Karl Heilbron
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Mental Health (DZPG), partner site Berlin/Potsdam, Berlin, Germany
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110
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Huang L, Hu W, Huang LQ, Zhou QX, Song ZY, Tao HY, Xu B, Zhang CY, Wang Y, Xing XH. "Two-birds-one-stone" oral nanotherapeutic designed to target intestinal integrins and regulate redox homeostasis for UC treatment. SCIENCE ADVANCES 2024; 10:eado7438. [PMID: 39047093 PMCID: PMC11268407 DOI: 10.1126/sciadv.ado7438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
Designing highly efficient orally administrated nanotherapeutics with specific inflammatory site-targeting functions in the gastrointestinal tract for ulcerative colitis (UC) management is a noteworthy challenge. Here, we focused on exploring a specific targeting oral nanotherapy, serving as "one stone," for the directed localization of inflammation and the regulation of redox homeostasis, thereby achieving effects against "two birds" for UC treatment. Our designed nanotherapeutic agent OPNs@LMWH (oxidation-sensitive ε-polylysine nanoparticles at low-molecular weight heparin) exhibited specific active targeting effects and therapeutic efficacy simultaneously. Our results indicate that OPNs@LMWH had high integrin αM-mediated immune cellular uptake efficiency and preferentially accumulated in inflamed tissues. We also confirmed its effectiveness in the treatment experiment of colitis in mice by ameliorating oxidative stress and inhibiting the activation of inflammation-associated signaling pathways while simultaneously bolstering the protective mechanisms of the colonic epithelium. Overall, these findings underscore the compelling dual functionalities of OPNs@LMWH, which enable effective oral delivery to inflamed sites, thereby facilitating precise UC management.
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Affiliation(s)
- Long Huang
- Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Institute of Biopharmaceutical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Wei Hu
- Institute of Biopharmaceutical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Long Qun Huang
- Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Qin Xuan Zhou
- Institute of Biopharmaceutical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Zheng Yang Song
- Institute of Biopharmaceutical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Heng Yu Tao
- Institute of Biopharmaceutical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Bing Xu
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Can Yang Zhang
- Institute of Biopharmaceutical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Yi Wang
- Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Xin-Hui Xing
- Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Institute of Biopharmaceutical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518118, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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Deka A, Kumar N, Basu S, Chawla M, Bhattacharya N, Ali SA, Bhawna, Madan U, Kumar S, Das B, Sengupta D, Awasthi A, Basak S. Non-canonical NF-κB signaling limits the tolerogenic β-catenin-Raldh2 axis in gut dendritic cells to exacerbate intestinal pathologies. EMBO J 2024:10.1038/s44318-024-00182-6. [PMID: 39060515 DOI: 10.1038/s44318-024-00182-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 07/12/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Dendritic cell (DC) dysfunction is known to exacerbate intestinal pathologies, but the mechanisms compromising DC-mediated immune regulation in this context remain unclear. Here, we show that intestinal dendritic cells from a mouse model of experimental colitis exhibit significant levels of noncanonical NF-κB signaling, which activates the RelB:p52 heterodimer. Genetic inactivation of this pathway in DCs alleviates intestinal pathologies in mice suffering from colitis. Deficiency of RelB:p52 diminishes transcription of Axin1, a critical component of the β-catenin destruction complex, reinforcing β-catenin-dependent expression of Raldh2, which imparts tolerogenic DC attributes by promoting retinoic acid synthesis. DC-specific impairment of noncanonical NF-κB signaling leads to increased colonic numbers of Tregs and IgA+ B cells, which promote luminal IgA production and foster eubiosis. Experimentally introduced β-catenin haploinsufficiency in DCs with deficient noncanonical NF-κB signaling moderates Raldh2 activity, reinstating colitogenic sensitivity in mice. Finally, inflammatory bowel-disease patients also display a deleterious noncanonical NF-κB signaling signature in intestinal DCs. In sum, we establish how noncanonical NF-κB signaling in dendritic cells can subvert retinoic acid synthesis to fuel intestinal inflammation.
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Affiliation(s)
- Alvina Deka
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Kumar
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swapnava Basu
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Meenakshi Chawla
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Namrata Bhattacharya
- Indraprastha Institute of Information Technology Delhi, New Delhi, India
- Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Sk Asif Ali
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Bhawna
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Upasna Madan
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Shakti Kumar
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Bhabatosh Das
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Debarka Sengupta
- Indraprastha Institute of Information Technology Delhi, New Delhi, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Soumen Basak
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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112
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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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113
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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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114
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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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115
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Petran EM, Periferakis A, Troumpata L, Periferakis AT, Scheau AE, Badarau IA, Periferakis K, Caruntu A, Savulescu-Fiedler I, Sima RM, Calina D, Constantin C, Neagu M, Caruntu C, Scheau C. Capsaicin: Emerging Pharmacological and Therapeutic Insights. Curr Issues Mol Biol 2024; 46:7895-7943. [PMID: 39194685 DOI: 10.3390/cimb46080468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 07/19/2024] [Accepted: 07/22/2024] [Indexed: 08/29/2024] Open
Abstract
Capsaicin, the most prominent pungent compound of chilli peppers, has been used in traditional medicine systems for centuries; it already has a number of established clinical and industrial applications. Capsaicin is known to act through the TRPV1 receptor, which exists in various tissues; capsaicin is hepatically metabolised, having a half-life correlated with the method of application. Research on various applications of capsaicin in different formulations is still ongoing. Thus, local capsaicin applications have a pronounced anti-inflammatory effect, while systemic applications have a multitude of different effects because their increased lipophilic character ensures their augmented bioavailability. Furthermore, various teams have documented capsaicin's anti-cancer effects, proven both in vivo and in vitro designs. A notable constraint in the therapeutic effects of capsaicin is its increased toxicity, especially in sensitive tissues. Regarding the traditional applications of capsaicin, apart from all the effects recorded as medicinal effects, the application of capsaicin in acupuncture points has been demonstrated to be effective and the combination of acupuncture and capsaicin warrants further research. Finally, capsaicin has demonstrated antimicrobial effects, which can supplement its anti-inflammatory and anti-carcinogenic actions.
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Affiliation(s)
- Elena Madalina Petran
- Department of Biochemistry, The "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Toxicology, Grigore Alexandrescu Emergency Children's Hospital, 011743 Bucharest, Romania
| | - Argyrios Periferakis
- Department of Physiology, The "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Akadimia of Ancient Greek and Traditional Chinese Medicine, 16675 Athens, Greece
- Elkyda, Research & Education Centre of Charismatheia, 17675 Athens, Greece
| | - Lamprini Troumpata
- Department of Physiology, The "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Aristodemos-Theodoros Periferakis
- Department of Physiology, The "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Elkyda, Research & Education Centre of Charismatheia, 17675 Athens, Greece
| | - Andreea-Elena Scheau
- Department of Radiology and Medical Imaging, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Ioana Anca Badarau
- Department of Physiology, The "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Konstantinos Periferakis
- Akadimia of Ancient Greek and Traditional Chinese Medicine, 16675 Athens, Greece
- Pan-Hellenic Organization of Educational Programs (P.O.E.P), 17236 Athens, Greece
| | - Ana Caruntu
- Department of Oral and Maxillofacial Surgery, The "Carol Davila" Central Military Emergency Hospital, 010825 Bucharest, Romania
- Department of Oral and Maxillofacial Surgery, Faculty of Dental Medicine, "Titu Maiorescu" University, 031593 Bucharest, Romania
| | - Ilinca Savulescu-Fiedler
- Department of Internal Medicine, The "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Internal Medicine and Cardiology, Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Romina-Marina Sima
- Department of Obstetrics and Gynecology, The "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- The "Bucur" Maternity, "Saint John" Hospital, 040294 Bucharest, Romania
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Carolina Constantin
- Immunology Department, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania
- Department of Pathology, Colentina University Hospital, 020125 Bucharest, Romania
| | - Monica Neagu
- Immunology Department, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania
- Department of Pathology, Colentina University Hospital, 020125 Bucharest, Romania
- Faculty of Biology, University of Bucharest, 76201 Bucharest, Romania
| | - Constantin Caruntu
- Department of Physiology, The "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Dermatology, "Prof. N.C. Paulescu" National Institute of Diabetes, Nutrition and Metabolic Diseases, 011233 Bucharest, Romania
| | - Cristian Scheau
- Department of Physiology, The "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Radiology and Medical Imaging, "Foisor" Clinical Hospital of Orthopaedics, Traumatology and Osteoarticular TB, 021382 Bucharest, Romania
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116
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Xing X, Rodeo SA. Emerging roles of non-coding RNAs in fibroblast to myofibroblast transition and fibrotic diseases. Front Pharmacol 2024; 15:1423045. [PMID: 39114349 PMCID: PMC11303237 DOI: 10.3389/fphar.2024.1423045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/01/2024] [Indexed: 08/10/2024] Open
Abstract
The transition of fibroblasts to myofibroblasts (FMT) represents a pivotal process in wound healing, tissue repair, and fibrotic diseases. This intricate transformation involves dynamic changes in cellular morphology, gene expression, and extracellular matrix remodeling. While extensively studied at the molecular level, recent research has illuminated the regulatory roles of non-coding RNAs (ncRNAs) in orchestrating FMT. This review explores the emerging roles of ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), in regulating this intricate process. NcRNAs interface with key signaling pathways, transcription factors, and epigenetic mechanisms to fine-tune gene expression during FMT. Their functions are critical in maintaining tissue homeostasis, and disruptions in these regulatory networks have been linked to pathological fibrosis across various tissues. Understanding the dynamic roles of ncRNAs in FMT bears therapeutic promise. Targeting specific ncRNAs holds potential to mitigate exaggerated myofibroblast activation and tissue fibrosis. However, challenges in delivery and specificity of ncRNA-based therapies remain. In summary, ncRNAs emerge as integral regulators in the symphony of FMT, orchestrating the balance between quiescent fibroblasts and activated myofibroblasts. As research advances, these ncRNAs appear to be prospects for innovative therapeutic strategies, offering hope in taming the complexities of fibrosis and restoring tissue equilibrium.
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Affiliation(s)
- Xuewu Xing
- Department of Orthopaedics, Tianjin First Central Hospital, Tianjin, China
- Orthopedic Soft Tissue Research Program, Hospital for Special Surgery, New York, NY, United States
| | - Scott A. Rodeo
- Orthopedic Soft Tissue Research Program, Hospital for Special Surgery, New York, NY, United States
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117
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Ke BJ, Abdurahiman S, Biscu F, Zanella G, Dragoni G, Santhosh S, De Simone V, Zouzaf A, van Baarle L, Stakenborg M, Bosáková V, Van Rymenant Y, Verhulst E, Verstockt S, Klein E, Bislenghi G, Wolthuis A, Frič J, Breynaert C, D’Hoore A, Van der Veken P, De Meester I, Lovisa S, Hawinkels LJ, Verstockt B, De Hertogh G, Vermeire S, Matteoli G. Intercellular interaction between FAP+ fibroblasts and CD150+ inflammatory monocytes mediates fibrostenosis in Crohn's disease. J Clin Invest 2024; 134:e173835. [PMID: 39042469 PMCID: PMC11324301 DOI: 10.1172/jci173835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 06/14/2024] [Indexed: 07/25/2024] Open
Abstract
Crohn's disease (CD) is marked by recurring intestinal inflammation and tissue injury, often resulting in fibrostenosis and bowel obstruction, necessitating surgical intervention with high recurrence rates. To elucidate the mechanisms underlying fibrostenosis in CD, we analyzed the transcriptome of cells isolated from the transmural ileum of patients with CD, including a trio of lesions from each patient: non-affected, inflamed, and stenotic ileum samples, and compared them with samples from patients without CD. Our computational analysis revealed that profibrotic signals from a subset of monocyte-derived cells expressing CD150 induced a disease-specific fibroblast population, resulting in chronic inflammation and tissue fibrosis. The transcription factor TWIST1 was identified as a key modulator of fibroblast activation and extracellular matrix (ECM) deposition. Genetic and pharmacological inhibition of TWIST1 prevents fibroblast activation, reducing ECM production and collagen deposition. Our findings suggest that the myeloid-stromal axis may offer a promising therapeutic target to prevent fibrostenosis in CD.
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Affiliation(s)
- Bo-Jun Ke
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Saeed Abdurahiman
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Francesca Biscu
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Gaia Zanella
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Gabriele Dragoni
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Gastroenterology Research Unit, Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Sneha Santhosh
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Veronica De Simone
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Anissa Zouzaf
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Lies van Baarle
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Michelle Stakenborg
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Veronika Bosáková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Brno, Czech Republic
| | - Yentl Van Rymenant
- Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Emile Verhulst
- Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sare Verstockt
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Elliott Klein
- Department of Immunology and Respiratory Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut, USA
| | - Gabriele Bislenghi
- Department of Abdominal Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Albert Wolthuis
- Department of Abdominal Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Jan Frič
- International Clinical Research Center, St. Anne’s University Hospital Brno, Brno, Czech Republic
- International Clinical Research Center, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Christine Breynaert
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Andre D’Hoore
- Department of Abdominal Surgery, University Hospitals Leuven, Leuven, Belgium
| | | | - Ingrid De Meester
- Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sara Lovisa
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Lukas J.A.C. Hawinkels
- Department of Gastroenterology-Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Bram Verstockt
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Gert De Hertogh
- Laboratory of Pathology, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Séverine Vermeire
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Gianluca Matteoli
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
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118
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Qian C, Yang Q, Rotinen M, Huang R, Kim H, Gallent B, Yan Y, Cadaneanu R, Zhang B, Kaochar S, Freedland S, Posadas E, Ellis L, Di Vizio D, Morrissey C, Nelson P, Brady L, Murali R, Campbell M, Yang W, Knudsen B, Mostaghel E, Ye H, Garraway I, You S, Freeman M. ONECUT2 acts as a lineage plasticity driver in adenocarcinoma as well as neuroendocrine variants of prostate cancer. Nucleic Acids Res 2024; 52:7740-7760. [PMID: 38932701 PMCID: PMC11260453 DOI: 10.1093/nar/gkae547] [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: 02/02/2024] [Revised: 06/06/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024] Open
Abstract
Androgen receptor- (AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that ONECUT2 (OC2) activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. Direct OC2 gene targets include the glucocorticoid receptor (GR; NR3C1) and the NE splicing factor SRRM4, which are key drivers of lineage plasticity. Thus, OC2, despite its previously described NEPC driver function, can indirectly activate a portion of the AR cistrome through epigenetic activation of GR. Mechanisms by which OC2 regulates gene expression include promoter binding, enhancement of genome-wide chromatin accessibility, and super-enhancer reprogramming. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC and support enhanced efforts to therapeutically target OC2 as a means of suppressing treatment-resistant disease.
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Affiliation(s)
- Chen Qian
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Qian Yang
- Departments of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mirja Rotinen
- Department of Health Sciences, Public University of Navarre, Pamplona, Navarra, Spain
| | - Rongrong Huang
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Hyoyoung Kim
- Departments of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Brad Gallent
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yiwu Yan
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Radu M Cadaneanu
- Department of Surgical and Perioperative Care, VA Greater Los Angeles; Department of Urology and Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA 90095, USA
| | - Baohui Zhang
- Department of Surgical and Perioperative Care, VA Greater Los Angeles; Department of Urology and Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA 90095, USA
| | - Salma Kaochar
- Department of Medicine Section Hematology/Oncology Baylor College of Medicine, Houston, 77030 TX, USA
| | - Stephen J Freedland
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Edwin M Posadas
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Leigh Ellis
- Center for Prostate Disease Research, Mutha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and the Walter Reed National Military Medical Center; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20814, USA
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Dolores Di Vizio
- Departments of Urology, Pathology and Laboratory Medicine, and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lauren Brady
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ramachandran Murali
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Moray J Campbell
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Wei Yang
- Department of Pathology and Cancer Center, Stony Brook University, NY 11794, USA
| | - Beatrice S Knudsen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84108, USA
- Department of Pathology, University of Utah, Salt Lake City, UT 84108, USA
| | - Elahe A Mostaghel
- Geriatric Research, Education and Clinical Center (GRECC), U.S. Department of Veterans Affairs Puget Sound Health Care System, Seattle, WA 98133, USA
| | - Huihui Ye
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Isla P Garraway
- Department of Surgical and Perioperative Care, VA Greater Los Angeles; Department of Urology and Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA 90095, USA
| | - Sungyong You
- Departments of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Michael R Freeman
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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119
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Liu X, Li Z, Shan J, Wang F, Li Z, Luo S, Wu J. PM 2.5 Exposure Inhibits Transepithelial Anion Short-circuit Current by Downregulating P2Y2 Receptor/CFTR Pathway. Int J Med Sci 2024; 21:1929-1944. [PMID: 39113893 PMCID: PMC11302563 DOI: 10.7150/ijms.96777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 07/06/2024] [Indexed: 08/10/2024] Open
Abstract
Fine particulate matter (PM2.5) can damage airway epithelial barriers. The anion transport system plays a crucial role in airway epithelial barriers. However, the detrimental effect and mechanism of PM2.5 on the anion transport system are still unclear. In this study, airway epithelial cells and ovalbumin (OVA)-induced asthmatic mice were used. In transwell model, the adenosine triphosphate (ATP)-induced transepithelial anion short-circuit current (Isc) and airway surface liquid (ASL) significantly decreased after PM2.5 exposure. In addition, PM2.5 exposure decreased the expression levels of P2Y2R, CFTR and cytoplasmic free-calcium, but ATP can increase the expressions of these proteins. PM2.5 exposure increased the levels of Th2-related cytokines of bronchoalveolar lavage fluid, lung inflammation, collagen deposition and hyperplasisa of goblet cells. Interestingly, the administration of ATP showed an inhibitory effect on lung inflammation induced by PM2.5. Together, our study reveals that PM2.5 impairs the ATP-induced transepithelial anion Isc through downregulating P2Y2R/CFTR pathway, and this process may participate in aggravating airway hyperresponsiveness and airway inflammation. These findings may provide important insights on PM2.5-mediated airway epithelial injury.
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Affiliation(s)
- Xiaolong Liu
- Second Department of Elderly Respiratory, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 510080, Guangzhou, China
| | - Zhangwen Li
- School of Medicine, South China University of Technology, Guangzhou, 510000, China
| | - Jiajie Shan
- School of Medicine, South China University of Technology, Guangzhou, 510000, China
| | - Fang Wang
- Second Department of Elderly Respiratory, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 510080, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, 510000, China
| | - Zhongpeng Li
- Second Department of Elderly Respiratory, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 510080, Guangzhou, China
| | - Shaohua Luo
- Second Department of Elderly Respiratory, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 510080, Guangzhou, China
| | - Jian Wu
- Second Department of Elderly Respiratory, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 510080, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, 510000, China
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120
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Sinha S, McLaren E, Mullick M, Singh S, Boland BS, Ghosh P. FORWARD: A Learning Framework for Logical Network Perturbations to Prioritize Targets for Drug Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.602603. [PMID: 39071297 PMCID: PMC11275938 DOI: 10.1101/2024.07.16.602603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Despite advances in artificial intelligence (AI), target-based drug development remains a costly, complex and imprecise process. We introduce F.O.R.W.A.R.D [ Framework for Outcome-based Research and Drug Development ], a network-based target prioritization approach and test its utility in the challenging therapeutic area of Inflammatory Bowel Diseases (IBD), which is a chronic condition of multifactorial origin. F.O.R.W.A.R.D leverages real-world outcomes, using a machine-learning classifier trained on transcriptomic data from seven prospective randomized clinical trials involving four drugs. It establishes a molecular signature of remission as the therapeutic goal and computes, by integrating principles of network connectivity, the likelihood that a drug's action on its target(s) will induce the remission-associated genes. Benchmarking F.O.R.W.A.R.D against 210 completed clinical trials on 52 targets showed a perfect predictive accuracy of 100%. The success of F.O.R.W.A.R.D was achieved despite differences in targets, mechanisms, and trial designs. F.O.R.W.A.R.D-driven in-silico phase '0' trials revealed its potential to inform trial design, justify re-trialing failed drugs, and guide early terminations. With its extendable applications to other therapeutic areas and its iterative refinement with emerging trials, F.O.R.W.A.R.D holds the promise to transform drug discovery by generating foresight from hindsight and impacting research and development as well as human-in-the-loop clinical decision-making.
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121
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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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122
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Wei TT, Blanc E, Peidli S, Bischoff P, Trinks A, Horst D, Sers C, Blüthgen N, Beule D, Morkel M, Obermayer B. High-confidence calling of normal epithelial cells allows identification of a novel stem-like cell state in the colorectal cancer microenvironment. Int J Cancer 2024. [PMID: 39031967 DOI: 10.1002/ijc.35079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/29/2024] [Accepted: 06/10/2024] [Indexed: 07/22/2024]
Abstract
Single-cell analyses can be confounded by assigning unrelated groups of cells to common developmental trajectories. For instance, cancer cells and admixed normal epithelial cells could adopt similar cell states thus complicating analyses of their developmental potential. Here, we develop and benchmark CCISM (for Cancer Cell Identification using Somatic Mutations) to exploit genomic single nucleotide variants for the disambiguation of cancer cells from genomically normal non-cancer cells in single-cell data. We find that our method and others based on gene expression or allelic imbalances identify overlapping sets of colorectal cancer versus normal colon epithelial cells, depending on molecular characteristics of individual cancers. Further, we define consensus cell identities of normal and cancer epithelial cells with higher transcriptome cluster homogeneity than those derived using existing tools. Using the consensus identities, we identify significant shifts of cell state distributions in genomically normal epithelial cells developing in the cancer microenvironment, with immature states increased at the expense of terminal differentiation throughout the colon, and a novel stem-like cell state arising in the left colon. Trajectory analyses show that the new cell state extends the pseudo-time range of normal colon stem-like cells in a cancer context. We identify cancer-associated fibroblasts as sources of WNT and BMP ligands potentially contributing to increased plasticity of stem cells in the cancer microenvironment. Our analyses advocate careful interpretation of cell heterogeneity and plasticity in the cancer context and the consideration of genomic information in addition to gene expression data when possible.
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Affiliation(s)
- Tzu-Ting Wei
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Peidli
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Philip Bischoff
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium Partner Site Berlin, German Cancer Research Center, Heidelberg, Germany
| | - Alexandra Trinks
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Unit Bioportal Single Cells, Berlin, Germany
| | - David Horst
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium Partner Site Berlin, German Cancer Research Center, Heidelberg, Germany
| | - Christine Sers
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium Partner Site Berlin, German Cancer Research Center, Heidelberg, Germany
| | - Nils Blüthgen
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
- German Cancer Consortium Partner Site Berlin, German Cancer Research Center, Heidelberg, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Morkel
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Unit Bioportal Single Cells, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
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123
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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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124
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Rahman MF, Kurlovs AH, Vodnala M, Meibalan E, Means TK, Nouri N, de Rinaldis E, Savova V. Immune disease dialogue of chemokine-based cell communications as revealed by single-cell RNA sequencing meta-analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603936. [PMID: 39071425 PMCID: PMC11275869 DOI: 10.1101/2024.07.17.603936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Immune-mediated diseases are characterized by aberrant immune responses, posing significant challenges to global health. In both inflammatory and autoimmune diseases, dysregulated immune reactions mediated by tissue-residing immune and non-immune cells precipitate chronic inflammation and tissue damage that is amplified by peripheral immune cell extravasation into the tissue. Chemokine receptors are pivotal in orchestrating immune cell migration, yet deciphering the signaling code across cell types, diseases and tissues remains an open challenge. To delineate disease-specific cell-cell communications involved in immune cell migration, we conducted a meta-analysis of publicly available single-cell RNA sequencing (scRNA-seq) data across diverse immune diseases and tissues. Our comprehensive analysis spanned multiple immune disorders affecting major organs: atopic dermatitis and psoriasis (skin), chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis (lung), ulcerative colitis (colon), IgA nephropathy and lupus nephritis (kidney). By interrogating ligand-receptor (L-R) interactions, alterations in cell proportions, and differential gene expression, we unveiled intricate disease-specific and common immune cell chemoattraction and extravasation patterns. Our findings delineate disease-specific L-R networks and shed light on shared immune responses across tissues and diseases. Insights gleaned from this analysis hold promise for the development of targeted therapeutics aimed at modulating immune cell migration to mitigate inflammation and tissue damage. This nuanced understanding of immune cell dynamics at the single-cell resolution opens avenues for precision medicine in immune disease management.
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Affiliation(s)
- Mouly F. Rahman
- Precision Medicine and Computational Biology, Sanofi US, Cambridge, MA 02141, United States
| | - Andre H. Kurlovs
- Precision Medicine and Computational Biology, Sanofi US, Cambridge, MA 02141, United States
| | - Munender Vodnala
- Precision Medicine and Computational Biology, Sanofi US, Cambridge, MA 02141, United States
| | - Elamaran Meibalan
- Precision Medicine and Computational Biology, Sanofi US, Cambridge, MA 02141, United States
| | - Terry K. Means
- Immunology & Inflammation Research Therapeutic Area, Sanofi US, Cambridge, MA 02141, United States
| | - Nima Nouri
- Precision Medicine and Computational Biology, Sanofi US, Cambridge, MA 02141, United States
| | - Emanuele de Rinaldis
- Precision Medicine and Computational Biology, Sanofi US, Cambridge, MA 02141, United States
| | - Virginia Savova
- Precision Medicine and Computational Biology, Sanofi US, Cambridge, MA 02141, United States
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125
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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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126
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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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127
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Neale I, Reddy C, Tan ZY, Li B, Nag PP, Park J, Park J, Carey KL, Graham DB, Xavier RJ. Small-molecule probe for IBD risk variant GPR65 I231L alters cytokine signaling networks through positive allosteric modulation. SCIENCE ADVANCES 2024; 10:eadn2339. [PMID: 39028811 PMCID: PMC11259170 DOI: 10.1126/sciadv.adn2339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 06/13/2024] [Indexed: 07/21/2024]
Abstract
The proton-sensing heterotrimeric guanine nucleotide-binding protein-coupled receptor GPR65 is expressed in immune cells and regulates tissue homeostasis in response to decreased extracellular pH, which occurs in the context of inflammation and tumorigenesis. Genome-wide association studies linked GPR65 to several autoimmune and inflammatory diseases such as multiple sclerosis and inflammatory bowel disease (IBD). The loss-of-function GPR65 I231L IBD risk variant alters cellular metabolism, impairs protective tissue functions, and increases proinflammatory cytokine production. Hypothesizing that a small molecule designed to potentiate GPR65 at subphysiological pH could decrease inflammatory responses, we found positive allosteric modulators of GPR65 that engage and activate both human and mouse orthologs of the receptor. We observed that the chemical probe BRD5075 alters cytokine and chemokine programs in dendritic cells, establishing that immune signaling can be modulated by targeting GPR65. Our investigation offers improved chemical probes to further interrogate the biology of human GPR65 and its clinically relevant genetic variants.
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Affiliation(s)
- Ilona Neale
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Clark Reddy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zher Yin Tan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Bihua Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Partha P. Nag
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joshua Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jihye Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Daniel B. Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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128
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Missarova A, Dann E, Rosen L, Satija R, Marioni J. Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE. Genome Biol 2024; 25:189. [PMID: 39026254 PMCID: PMC11256449 DOI: 10.1186/s13059-024-03334-3] [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: 09/01/2023] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
Single-cell RNA-sequencing enables testing for differential expression (DE) between conditions at a cell type level. While powerful, one of the limitations of such approaches is that the sensitivity of DE testing is dictated by the sensitivity of clustering, which is often suboptimal. To overcome this, we present miloDE-a cluster-free framework for DE testing (available as an open-source R package). We illustrate the performance of miloDE on both simulated and real data. Using miloDE, we identify a transient hemogenic endothelia-like state in mouse embryos lacking Tal1 and detect distinct programs during macrophage activation in idiopathic pulmonary fibrosis.
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Affiliation(s)
- Alsu Missarova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leah Rosen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Rahul Satija
- Center for Genomics and Systems Biology, NYU, New York, USA.
- New York Genome Center, New York, USA.
| | - John Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
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129
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Wang L, Wen X, Morrison J. Imperfect gold standard gene sets yield inaccurate evaluation of causal gene identification methods. Commun Biol 2024; 7:873. [PMID: 39020054 PMCID: PMC11255313 DOI: 10.1038/s42003-024-06482-1] [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: 11/17/2023] [Accepted: 06/21/2024] [Indexed: 07/19/2024] Open
Abstract
Causal gene discovery methods are often evaluated using reference sets of causal genes, which are treated as gold standards (GS) for the purposes of evaluation. However, evaluation methods typically treat genes not in the GS positive set as known negatives rather than unknowns. This leads to inaccurate estimates of sensitivity, specificity, and AUC. Labeling biases in GS gene sets can also lead to inaccurate ordering of alternative causal gene discovery methods. We argue that the evaluation of causal gene discovery methods should rely on statistical techniques like those used for variant discovery rather than on comparison with GS gene sets.
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Affiliation(s)
- Lijia Wang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
| | - Jean Morrison
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
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130
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Zagoren E, Dias N, Smith ZD, Ameen NA, Sumigray K. A second wave of Notch signaling diversifies the intestinal secretory lineage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603542. [PMID: 39071399 PMCID: PMC11275776 DOI: 10.1101/2024.07.15.603542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The small intestine is well known for the function of its nutrient-absorbing enterocytes; yet equally critical for the maintenance of homeostasis is a diverse set of secretory cells, all of which are presumed to differentiate from the same intestinal stem cell. Despite major roles in intestinal function and health, understanding how the full spectrum of secretory cell types arises remains a longstanding challenge, largely due to their comparative rarity. Here, we investigate the fate specification of a rare and distinct population of small intestinal epithelial cells found in rats and humans but not mice: C FTR Hi gh E xpressers (CHEs). We use pseudotime trajectory analysis of single-cell RNA-seq data from rat intestinal jejunum to provide evidence that CHEs are specified along the secretory lineage and appear to employ a second wave of Notch-based signal transduction to distinguish these cells from other secretory cell types. We further validate the general order of transcription factors that direct these cells from unspecified progenitors within the crypt and experimentally demonstrate that Notch signaling is necessary to induce CHE fate both in vivo and in vitro . Our results suggest a model in which Notch is reactivated along the secretory lineage to specify the CHE population: a rare secretory cell type with putative functions in localized coordination of luminal pH and direct relevance to cystic fibrosis pathophysiology.
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131
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Cantoni C, Falco M, Vitale M, Pietra G, Munari E, Pende D, Mingari MC, Sivori S, Moretta L. Human NK cells and cancer. Oncoimmunology 2024; 13:2378520. [PMID: 39022338 PMCID: PMC11253890 DOI: 10.1080/2162402x.2024.2378520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024] Open
Abstract
The long story of NK cells started about 50 y ago with the first demonstration of a natural cytotoxic activity within an undefined subset of circulating leukocytes, has involved an ever-growing number of researchers, fascinated by the apparently easy-to-reach aim of getting a "universal anti-tumor immune tool". In fact, in spite of the impressive progress obtained in the first decades, these cells proved far more complex than expected and, paradoxically, the accumulating findings have continuously moved forward the attainment of a complete control of their function for immunotherapy. The refined studies of these latter years have indicated that NK cells can epigenetically calibrate their functional potential, in response to specific environmental contexts, giving rise to extraordinarily variegated subpopulations, comprehensive of memory-like cells, tissue-resident cells, or cells in various differentiation stages, or distinct functional states. In addition, NK cells can adapt their activity in response to a complex body of signals, spanning from the interaction with either suppressive or stimulating cells (myeloid-derived suppressor cells or dendritic cells, respectively) to the engagement of various receptors (specific for immune checkpoints, cytokines, tumor/viral ligands, or mediating antibody-dependent cell-mediated cytotoxicity). According to this picture, the idea of an easy and generalized exploitation of NK cells is changing, and the way is opening toward new carefully designed, combined and personalized therapeutic strategies, also based on the use of genetically modified NK cells and stimuli capable of strengthening and redirecting their effector functions against cancer.
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Affiliation(s)
- Claudia Cantoni
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy
- Laboratory of Clinical and Experimental Immunology, Integrated Department of Services and Laboratories, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Michela Falco
- Laboratory of Clinical and Experimental Immunology, Integrated Department of Services and Laboratories, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Massimo Vitale
- UO Pathology and Experimental Immunology, IRCCS Ospedale Policlinico, San Martino, Genova, Italy
| | - Gabriella Pietra
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy
- UO Pathology and Experimental Immunology, IRCCS Ospedale Policlinico, San Martino, Genova, Italy
| | - Enrico Munari
- Pathology Unit, Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Daniela Pende
- UO Pathology and Experimental Immunology, IRCCS Ospedale Policlinico, San Martino, Genova, Italy
| | - Maria Cristina Mingari
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy
- UO Pathology and Experimental Immunology, IRCCS Ospedale Policlinico, San Martino, Genova, Italy
| | - Simona Sivori
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico, San Martino, Genova, Italy
| | - Lorenzo Moretta
- Tumor Immunology Unit, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
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Rahmani S, Galipeau HJ, Clarizio AV, Wang X, Hann A, Rueda GH, Kirtikar UN, Constante M, Wulczynski M, Su HM, Burchett R, Bramson JL, Pinto-Sanchez MI, Stefanolo JP, Niveloni S, Surette MG, Murray JA, Anderson RP, Bercik P, Caminero A, Chirdo FG, Didar TF, Verdu EF. Gluten dependent activation of CD4 + T cells by MHC class II-expressing epithelium. Gastroenterology 2024:S0016-5085(24)05211-9. [PMID: 39128638 DOI: 10.1053/j.gastro.2024.07.008] [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: 09/07/2023] [Revised: 06/28/2024] [Accepted: 07/07/2024] [Indexed: 08/13/2024]
Abstract
BACKGROUND AND AIMS Intestinal epithelial cell (IEC) damage is a hallmark of celiac disease (CeD); however, its role in gluten-dependent T-cell activation is unknown. We investigated IEC-gluten-T cell interactions in organoid monolayers expressing human MHC class II (HLA-DQ2.5), which facilitates gluten antigen recognition by CD4+ T cells in CeD. METHODS Epithelial MHC class II (MHCII) was determined in active and treated CeD, and in non-immunized and gluten-immunized DR3-DQ2.5 transgenic mice, lacking mouse MHCII molecules. Organoid monolayers from DR3-DQ2.5 mice were treated with or without IFN-γ, and MHCII expression was evaluated by flow cytometry. Organoid monolayers and CD4+ T cell co-cultures were incubated with gluten, pre-digested, or not by elastase-producing Pseudomonas aeruginosa or its lasB mutant. T cell function was assessed based on proliferation, expression of activation markers, and cytokine release in the co-culture supernatants. RESULTS Active CeD patients and gluten-immunized DR3-DQ2.5 mice demonstrated epithelial MHCII expression. Organoid monolayers derived from gluten-immunized DR3-DQ2.5 mice expressed MHCII, which was upregulated by IFN-γ. In organoid monolayer-T cell co-cultures, gluten increased the proliferation of CD4+ T cells, expression of T cell activation markers, and the release of IL-2, IFN-γ, and IL-15 in co-culture supernatants. Gluten metabolized by P. aeruginosa, but not the lasB mutant, enhanced CD4+ T cell proliferation and activation. CONCLUSIONS Gluten antigens are efficiently presented by MHCII-expressing IECs, resulting in the activation of gluten-specific CD4+ T cells, which is enhanced by gluten pre-digestion with microbial elastase. Therapeutics directed at IECs may offer a novel approach for modulating both adaptive and innate immunity in CeD patients.
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Affiliation(s)
- Sara Rahmani
- School of Biomedical Engineering, McMaster University; Hamilton, Ontario, Canada; Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada
| | - Heather J Galipeau
- Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada
| | - Alexandra V Clarizio
- Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada
| | - Xuanyu Wang
- Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada
| | - Amber Hann
- Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada
| | - Gaston H Rueda
- Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada
| | - Utkarshini N Kirtikar
- Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada
| | - Marco Constante
- Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada
| | - Mark Wulczynski
- Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada
| | - Hsuan-Ming Su
- Department of Mechanical Engineering, McMaster University; Hamilton, Ontario, Canada
| | - Rebecca Burchett
- Department of Medicine, McMaster University; Hamilton, ON, Canada
| | | | - Maria Ines Pinto-Sanchez
- Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada
| | | | | | - Michael G Surette
- Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada
| | - Joseph A Murray
- Division of Gastroenterology and Hepatology, Department of Immunology, Mayo Clinic College of Medicine; Rochester, Minnesota, USA
| | | | - Premysl Bercik
- Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada
| | - Alberto Caminero
- Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada
| | - Fernando G Chirdo
- Instituto de Estudios Inmunológicos y Fisiopatológicos - IIFP (UNLP-CONICET). Facultad de Ciencias Exactas, Universidad Nacional de La Plata; La Plata, Argentina.
| | - Tohid F Didar
- School of Biomedical Engineering, McMaster University; Hamilton, Ontario, Canada; Department of Mechanical Engineering, McMaster University; Hamilton, Ontario, Canada.
| | - Elena F Verdu
- Farncombe Family Digestive Health Research Institute, McMaster University; Hamilton, Ontario, Canada; Department of Medicine, McMaster University; Hamilton, ON, Canada.
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Urzúa-Traslaviña CG, van Lieshout T, Boulogne F, Domanegg K, Zidan M, Bakker OB, Claringbould A, de Ridder J, Zwart W, Westra HJ, Deelen P, Franke L. Co-expression in tissue-specific gene networks links genes in cancer-susceptibility loci to known somatic driver genes. BMC Med Genomics 2024; 17:186. [PMID: 39010058 PMCID: PMC11247850 DOI: 10.1186/s12920-024-01941-4] [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: 05/01/2024] [Accepted: 06/18/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND The genetic background of cancer remains complex and challenging to integrate. Many somatic mutations within genes are known to cause and drive cancer, while genome-wide association studies (GWAS) of cancer have revealed many germline risk factors associated with cancer. However, the overlap between known somatic driver genes and positional candidate genes from GWAS loci is surprisingly small. We hypothesised that genes from multiple independent cancer GWAS loci should show tissue-specific co-regulation patterns that converge on cancer-specific driver genes. RESULTS We studied recent well-powered GWAS of breast, prostate, colorectal and skin cancer by estimating co-expression between genes and subsequently prioritising genes that show significant co-expression with genes mapping within susceptibility loci from cancer GWAS. We observed that the prioritised genes were strongly enriched for cancer drivers defined by COSMIC, IntOGen and Dietlein et al. The enrichment of known cancer driver genes was most significant when using co-expression networks derived from non-cancer samples of the relevant tissue of origin. CONCLUSION We show how genes within risk loci identified by cancer GWAS can be linked to known cancer driver genes through tissue-specific co-expression networks. This provides an important explanation for why seemingly unrelated sets of genes that harbour either germline risk factors or somatic mutations can eventually cause the same type of disease.
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Affiliation(s)
- Carlos G Urzúa-Traslaviña
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Tijs van Lieshout
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Floranne Boulogne
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Kevin Domanegg
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Mahmoud Zidan
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Olivier B Bakker
- Wellcome Sanger Institute, Human Genetics, Hinxton, UK
- Open Targets, Hinxton, UK
| | - Annique Claringbould
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
- EMBL Heidelberg, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Jeroen de Ridder
- Oncode Institute, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wilbert Zwart
- Oncode Institute, Utrecht, The Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
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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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Li K, Song Z, Yue Q, Wang Q, Li Y, Zhu Y, Chen H. Disease-specific transcriptional programs govern airway goblet cell metaplasia. Heliyon 2024; 10:e34105. [PMID: 39071568 PMCID: PMC11283004 DOI: 10.1016/j.heliyon.2024.e34105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/02/2024] [Accepted: 07/03/2024] [Indexed: 07/30/2024] Open
Abstract
Hypersecretion of airway mucus caused by goblet cell metaplasia is a characteristic of chronic pulmonary inflammatory diseases including asthma, cystic fibrosis (CF), and chronic obstructive pulmonary disease (COPD). Goblet cells originate from airway progenitor club cells. However, the molecular mechanisms and features of goblet cell metaplasia in lung disease are poorly understood. Herein, public single-cell RNA sequencing datasets of human lungs were reanalyzed to explore the transitional phase as club cells differentiate into goblet cells in asthma, CF, and COPD. We found that changes in club and goblet cells during pathogenesis and cellular transition were associated with signalling pathways related to immune response, oxidative stress, and apoptosis. Moreover, other key drivers of goblet cell specification appeared to be pathologically specific, with interleukin (IL)-13 and hypoxia inducible factor 1 (HIF-1)-induced genetic changes in asthma, cystic fibrosis transmembrane conductance regulator (CFTR) mutation being present in CF, and interactions with CD8+ T cells, mitophagy, and mitochondria-induced apoptosis in COPD. In conclusion, this study revealed the similarities and differences in goblet cell metaplasia in asthma, CF, and COPD at the transcriptome level, thereby providing insights into possible novel therapeutic approaches for these diseases.
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Affiliation(s)
- Kuan Li
- Department of Respiratory Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Tianjin Institute of Respiratory Diseases, 300350, Tianjin, China
| | - Zhaoyu Song
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Department of Clinical Lab, Tianjin First Central Hospital, 300192, Tianjin, China
| | - Qing Yue
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
| | - Qi Wang
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
| | - Yu Li
- Department of Respiratory Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Department of Tuberculosis, Haihe Clinical School, Tianjin Medical University, 300350, Tianjin, China
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Tianjin Institute of Respiratory Diseases, 300350, Tianjin, China
| | - Yu Zhu
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Department of Clinical Laboratory, Haihe Hospital, Tianjin University, 300350, Tianjin, China
| | - Huaiyong Chen
- Department of Respiratory Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Department of Tuberculosis, Haihe Clinical School, Tianjin Medical University, 300350, Tianjin, China
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, 300350, Tianjin, China
- Tianjin Institute of Respiratory Diseases, 300350, Tianjin, China
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136
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Quach H, Farrell S, Wu MJM, Kanagarajah K, Leung JWH, Xu X, Kallurkar P, Turinsky AL, Bear CE, Ratjen F, Kalish B, Goyal S, Moraes TJ, Wong AP. Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity. Nat Commun 2024; 15:5898. [PMID: 39003323 PMCID: PMC11246468 DOI: 10.1038/s41467-024-50281-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 07/05/2024] [Indexed: 07/15/2024] Open
Abstract
Studying human fetal lungs can inform how developmental defects and disease states alter the function of the lungs. Here, we sequenced >150,000 single cells from 19 healthy human pseudoglandular fetal lung tissues ranging between gestational weeks 10-19. We capture dynamic developmental trajectories from progenitor cells that express abundant levels of the cystic fibrosis conductance transmembrane regulator (CFTR). These cells give rise to multiple specialized epithelial cell types. Combined with spatial transcriptomics, we show temporal regulation of key signalling pathways that may drive the temporal and spatial emergence of specialized epithelial cells including ciliated and pulmonary neuroendocrine cells. Finally, we show that human pluripotent stem cell-derived fetal lung models contain CFTR-expressing progenitor cells that capture similar lineage developmental trajectories as identified in the native tissue. Overall, this study provides a comprehensive single-cell atlas of the developing human lung, outlining the temporal and spatial complexities of cell lineage development and benchmarks fetal lung cultures from human pluripotent stem cell differentiations to similar developmental window.
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Affiliation(s)
- Henry Quach
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Spencer Farrell
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Ming Jia Michael Wu
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kayshani Kanagarajah
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Joseph Wai-Hin Leung
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xiaoqiao Xu
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Prajkta Kallurkar
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrei L Turinsky
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christine E Bear
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Felix Ratjen
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brian Kalish
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Neonatology, Department of Paediatrics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sidhartha Goyal
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Theo J Moraes
- Program in Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amy P Wong
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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137
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Berdnikovs S, Newcomb DC, McKernan KE, Kuehnle SN, Haruna NF, Gebretsadik T, McKennan C, Ma S, Cephus JY, Rosas-Salazar C, Anderson LJ, Gern JE, Hartert T. Single cell profiling to determine influence of wheeze and early-life viral infection on developmental programming of airway epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602506. [PMID: 39026695 PMCID: PMC11257436 DOI: 10.1101/2024.07.08.602506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Although childhood asthma is in part an airway epithelial disorder, the development of the airway epithelium in asthma is not understood. We sought to characterize airway epithelial developmental phenotypes in those with and without recurrent wheeze and the impact of infant infection with respiratory syncytial virus (RSV). Nasal airway epithelial cells (NAECs) were collected at age 2-3 years from an a priori designed nested birth cohort of children from four mutually exclusive groups of wheezers/non-wheezers and RSV-infected/uninfected in the first year of life. NAECs were cultured in air-liquid interface differentiation conditions followed by a combined analysis of single cell RNA sequencing (scRNA-seq) and in vitro infection with respiratory syncytial virus (RSV). NAECs from children with a wheeze phenotype were characterized by abnormal differentiation and basal cell activation of developmental pathways, plasticity in precursor differentiation and a delayed onset of maturation. NAECs from children with wheeze also had increased diversity of currently known RSV receptors and blunted anti-viral immune responses to in vitro infection. The most dramatic changes in differentiation of cultured epithelium were observed in NAECs derived from children that had both wheeze and RSV in the first year of life. Together this suggests that airway epithelium in children with wheeze is developmentally reprogrammed and characterized by increased barrier permeability, decreased antiviral response, and increased RSV receptors, which may predispose to and amplify the effects of RSV infection in infancy and susceptibility to other asthma risk factors that interact with the airway mucosa. SUMMARY Nasal airway epithelial cells from children with wheeze are characterized by altered development and increased susceptibility to RSV infection.
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138
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Eaton AF, Danielson EC, Capen D, Merkulova M, Brown D. Dmxl1 Is an Essential Mammalian Gene that Is Required for V-ATPase Assembly and Function In Vivo. FUNCTION 2024; 5:zqae025. [PMID: 38984989 PMCID: PMC11237898 DOI: 10.1093/function/zqae025] [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: 04/16/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 07/11/2024] Open
Abstract
The proton pumping V-ATPase drives essential biological processes, such as acidification of intracellular organelles. Critically, the V-ATPase domains, V1 and VO, must assemble to produce a functional holoenzyme. V-ATPase dysfunction results in cancer, neurodegeneration, and diabetes, as well as systemic acidosis caused by reduced activity of proton-secreting kidney intercalated cells (ICs). However, little is known about the molecular regulation of V-ATPase in mammals. We identified a novel interactor of the mammalian V-ATPase, Drosophila melanogaster X chromosomal gene-like 1 (Dmxl1), aka Rabconnectin-3A. The yeast homologue of Dmxl1, Rav1p, is part of a complex that catalyzes the reversible assembly of the domains. We, therefore,hypothesized that Dmxl1 is a mammalian V-ATPase assembly factor. Here, we generated kidney IC-specific Dmxl1 knockout (KO) mice, which had high urine pH, like B1 V-ATPase KO mice, suggesting impaired V-ATPase function. Western blotting showed decreased B1 expression and B1 (V1) and a4 (VO) subunits were more intracellular and less colocalized in Dmxl1 KO ICs. In parallel, subcellular fractionation revealed less V1 associated B1 in the membrane fraction of KO cells relative to the cytosol. Furthermore, a proximity ligation assay performed using probes against B1 and a4 V-ATPase subunits also revealed decreased association. We propose that loss of Dmxl1 reduces V-ATPase holoenzyme assembly, thereby inhibiting proton pumping function. Dmxl1 may recruit the V1 domain to the membrane and facilitate assembly with the VO domain and in its absence V1 may be targeted for degradation. We conclude that Dmxl1 is a bona fide mammalian V-ATPase assembly factor.
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Affiliation(s)
- Amity F Eaton
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Elizabeth C Danielson
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Diane Capen
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Maria Merkulova
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Dennis Brown
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
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139
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Reedy JL, Jensen KN, Crossen AJ, Basham KJ, Ward RA, Reardon CM, Brown Harding H, Hepworth OW, Simaku P, Kwaku GN, Tone K, Willment JA, Reid DM, Stappers MHT, Brown GD, Rajagopal J, Vyas JM. Fungal melanin suppresses airway epithelial chemokine secretion through blockade of calcium fluxing. Nat Commun 2024; 15:5817. [PMID: 38987270 PMCID: PMC11237042 DOI: 10.1038/s41467-024-50100-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: 04/02/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Respiratory infections caused by the human fungal pathogen Aspergillus fumigatus are a major cause of mortality for immunocompromised patients. Exposure to these pathogens occurs through inhalation, although the role of the respiratory epithelium in disease pathogenesis has not been fully defined. Employing a primary human airway epithelial model, we demonstrate that fungal melanins potently block the post-translational secretion of the chemokines CXCL1 and CXCL8 independent of transcription or the requirement of melanin to be phagocytosed, leading to a significant reduction in neutrophil recruitment to the apical airway both in vitro and in vivo. Aspergillus-derived melanin, a major constituent of the fungal cell wall, dampened airway epithelial chemokine secretion in response to fungi, bacteria, and exogenous cytokines. Furthermore, melanin muted pathogen-mediated calcium fluxing and hindered actin filamentation. Taken together, our results reveal a critical role for melanin interaction with airway epithelium in shaping the host response to fungal and bacterial pathogens.
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Affiliation(s)
- Jennifer L Reedy
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kirstine Nolling Jensen
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Arianne J Crossen
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Kyle J Basham
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Rebecca A Ward
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher M Reardon
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Hannah Brown Harding
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Olivia W Hepworth
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Patricia Simaku
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Geneva N Kwaku
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Kazuya Tone
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
- Division of Respiratory Diseases, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Janet A Willment
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Delyth M Reid
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Mark H T Stappers
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Gordon D Brown
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Jatin M Vyas
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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140
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Hung CT, Ma C, Panda SK, Trsan T, Hodel M, Frein J, Foster A, Sun S, Wu HT, Kern J, Mishra R, Jain U, Ho YC, Colonna M, Stappenbeck TS, Liu TC. Western diet reduces small intestinal intraepithelial lymphocytes via FXR-Interferon pathway. Mucosal Immunol 2024:S1933-0219(24)00067-9. [PMID: 38992433 DOI: 10.1016/j.mucimm.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/13/2024]
Abstract
The prevalence of obesity in the United States has continued to increase over the past several decades. Understanding how diet-induced obesity modulates mucosal immunity is of clinical relevance. We previously showed that consumption of a high fat, high sugar "Western" diet (WD) reduces the density and function of small intestinal Paneth cells, a small intestinal epithelial cell type with innate immune function. We hypothesized that obesity could also result in repressed gut adaptive immunity. Using small intestinal intraepithelial lymphocytes (IEL) as a readout, we found that in non-inflammatory bowel disease (IBD) subjects, high body mass index correlated with reduced IEL density. We recapitulated this in wild type (WT) mice fed with WD. A 4-week WD consumption was able to reduce IEL but not splenic, blood, or bone marrow lymphocytes, and the effect was reversible after another 2 weeks of standard diet (SD) washout. Importantly, WD-associated IEL reduction was not dependent on the presence of gut microbiota, as WD-fed germ-free mice also showed IEL reduction. We further found that WD-mediated Farnesoid X Receptor (FXR) activation in the gut triggered IEL reduction, and this was partially mediated by intestinal phagocytes. Activated FXR signaling stimulated phagocytes to secrete type I IFN, and inhibition of either FXR or type I IFN signaling within the phagocytes prevented WD-mediated IEL loss. Therefore, WD consumption represses both innate and adaptive immunity in the gut. These findings have significant clinical implications in the understanding of how diet modulates mucosal immunity.
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Affiliation(s)
- Chen-Ting Hung
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Changqing Ma
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Santosh K Panda
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Tihana Trsan
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Miki Hodel
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Jennifer Frein
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Amanda Foster
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Shengxiang Sun
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Hung-Ting Wu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Justin Kern
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Richa Mishra
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, United States
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, United States
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, United States.
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141
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Zaidi S, Park J, Chan JM, Roudier MP, Zhao JL, Gopalan A, Wadosky KM, Patel RA, Sayar E, Karthaus WR, Kates DH, Chaudhary O, Xu T, Masilionis I, Mazutis L, Chaligné R, Obradovic A, Linkov I, Barlas A, Jungbluth AA, Rekhtman N, Silber J, Manova-Todorova K, Watson PA, True LD, Morrissey C, Scher HI, Rathkopf DE, Morris MJ, Goodrich DW, Choi J, Nelson PS, Haffner MC, Sawyers CL. Single-cell analysis of treatment-resistant prostate cancer: Implications of cell state changes for cell surface antigen-targeted therapies. Proc Natl Acad Sci U S A 2024; 121:e2322203121. [PMID: 38968122 PMCID: PMC11252802 DOI: 10.1073/pnas.2322203121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/09/2024] [Indexed: 07/07/2024] Open
Abstract
Targeting cell surface molecules using radioligand and antibody-based therapies has yielded considerable success across cancers. However, it remains unclear how the expression of putative lineage markers, particularly cell surface molecules, varies in the process of lineage plasticity, wherein tumor cells alter their identity and acquire new oncogenic properties. A notable example of lineage plasticity is the transformation of prostate adenocarcinoma (PRAD) to neuroendocrine prostate cancer (NEPC)-a growing resistance mechanism that results in the loss of responsiveness to androgen blockade and portends dismal patient survival. To understand how lineage markers vary across the evolution of lineage plasticity in prostate cancer, we applied single-cell analyses to 21 human prostate tumor biopsies and two genetically engineered mouse models, together with tissue microarray analysis on 131 tumor samples. Not only did we observe a higher degree of phenotypic heterogeneity in castrate-resistant PRAD and NEPC than previously anticipated but also found that the expression of molecules targeted therapeutically, namely PSMA, STEAP1, STEAP2, TROP2, CEACAM5, and DLL3, varied within a subset of gene-regulatory networks (GRNs). We also noted that NEPC and small cell lung cancer subtypes shared a set of GRNs, indicative of conserved biologic pathways that may be exploited therapeutically across tumor types. While this extreme level of transcriptional heterogeneity, particularly in cell surface marker expression, may mitigate the durability of clinical responses to current and future antigen-directed therapies, its delineation may yield signatures for patient selection in clinical trials, potentially across distinct cancer types.
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MESH Headings
- Male
- Humans
- Single-Cell Analysis/methods
- Animals
- Mice
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Prostatic Neoplasms/drug therapy
- Antigens, Surface/metabolism
- Antigens, Surface/genetics
- Antigens, Neoplasm/metabolism
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Biomarkers, Tumor/metabolism
- Biomarkers, Tumor/genetics
- Adenocarcinoma/genetics
- Adenocarcinoma/pathology
- Adenocarcinoma/metabolism
- Adenocarcinoma/drug therapy
- Carcinoma, Neuroendocrine/genetics
- Carcinoma, Neuroendocrine/pathology
- Carcinoma, Neuroendocrine/metabolism
- Carcinoma, Neuroendocrine/drug therapy
- Gene Expression Regulation, Neoplastic
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Prostatic Neoplasms, Castration-Resistant/pathology
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/drug therapy
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Affiliation(s)
- Samir Zaidi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- Department of Medicine, Division of Solid Tumor Oncology, Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Jooyoung Park
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul02841, Korea
| | - Joseph M. Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | | | | | - Anuradha Gopalan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Kristine M. Wadosky
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY14263
| | - Radhika A. Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98195
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98195
| | - Erolcan Sayar
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98195
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98195
| | - Wouter R. Karthaus
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne1015, Switzerland
| | - D. Henry Kates
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Ojasvi Chaudhary
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Tianhao Xu
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Ignas Masilionis
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Linas Mazutis
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Ronan Chaligné
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Aleksandar Obradovic
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY10032
| | - Irina Linkov
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Afsar Barlas
- Molecular Cytology Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New YorkNY10065
| | - Achim A. Jungbluth
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Natasha Rekhtman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Joachim Silber
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Katia Manova-Todorova
- Molecular Cytology Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New YorkNY10065
| | - Philip A. Watson
- Research Outreach and Compliance, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA98195
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA98195
| | - Howard I. Scher
- Department of Medicine, Division of Solid Tumor Oncology, Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Dana E. Rathkopf
- Department of Medicine, Division of Solid Tumor Oncology, Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Michael J. Morris
- Department of Medicine, Division of Solid Tumor Oncology, Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - David W. Goodrich
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY14263
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul02841, Korea
- Department of Genetics, Yale University School of Medicine, New Haven, CT06510
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98195
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98195
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA98195
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA98195
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA98195
| | - Charles L. Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- HHMI, Memorial Sloan Kettering Cancer Center, New York, NY10065
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142
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Collier CA, Salikhova A, Sabir S, Foncerrada S, Raghavan SA. Crisis in the gut: navigating gastrointestinal challenges in Gulf War Illness with bioengineering. Mil Med Res 2024; 11:45. [PMID: 38978144 PMCID: PMC11229309 DOI: 10.1186/s40779-024-00547-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/26/2024] [Indexed: 07/10/2024] Open
Abstract
Gulf War Illness (GWI) is characterized by a wide range of symptoms that manifests largely as gastrointestinal symptoms. Among these gastrointestinal symptoms, motility disorders are highly prevalent, presenting as chronic constipation, stomach pain, indigestion, diarrhea, and other conditions that severely impact the quality of life of GWI veterans. However, despite a high prevalence of gastrointestinal impairments among these veterans, most research attention has focused on neurological disturbances. This perspective provides a comprehensive overview of current in vivo research advancements elucidating the underlying mechanisms contributing to gastrointestinal disorders in GWI. Generally, these in vivo and in vitro models propose that neuroinflammation alters gut motility and drives the gastrointestinal symptoms reported in GWI. Additionally, this perspective highlights the potential and challenges of in vitro bioengineering models, which could be a crucial contributor to understanding and treating the pathology of gastrointestinal related-GWI.
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Affiliation(s)
- Claudia A Collier
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Aelita Salikhova
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Sufiyan Sabir
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Steven Foncerrada
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Shreya A Raghavan
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA.
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143
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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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144
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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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145
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Bakht MK, Beltran H. Biological determinants of PSMA expression, regulation and heterogeneity in prostate cancer. Nat Rev Urol 2024:10.1038/s41585-024-00900-z. [PMID: 38977769 DOI: 10.1038/s41585-024-00900-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 07/10/2024]
Abstract
Prostate-specific membrane antigen (PSMA) is an important cell-surface imaging biomarker and therapeutic target in prostate cancer. The PSMA-targeted theranostic 177Lu-PSMA-617 was approved in 2022 for men with PSMA-PET-positive metastatic castration-resistant prostate cancer. However, not all patients respond to PSMA-radioligand therapy, in part owing to the heterogeneity of PSMA expression in the tumour. The PSMA regulatory network is composed of a PSMA transcription complex, an upstream enhancer that loops to the FOLH1 (PSMA) gene promoter, intergenic enhancers and differentially methylated regions. Our understanding of the PSMA regulatory network and the mechanisms underlying PSMA suppression is evolving. Clinically, molecular imaging provides a unique window into PSMA dynamics that occur on therapy and with disease progression, although challenges arise owing to the limited resolution of PET. PSMA regulation and heterogeneity - including intertumoural and inter-patient heterogeneity, temporal changes, lineage dynamics and the tumour microenvironment - affect PSMA theranostics. PSMA response and resistance to radioligand therapy are mediated by a number of potential mechanisms, and complementary biomarkers beyond PSMA are under development. Understanding the biological determinants of cell surface target regulation and heterogeneity can inform precision medicine approaches to PSMA theranostics as well as other emerging therapies.
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Affiliation(s)
- Martin K Bakht
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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146
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Ávila-Arres IE, Rodríguez Hernández E, Gómez Rosales S, Reis de Souza TC, Mariscal-Landín G. Proteomic Identification and Quantification of Basal Endogenous Proteins in the Ileal Digesta of Growing Pigs. Animals (Basel) 2024; 14:2000. [PMID: 38998112 PMCID: PMC11240675 DOI: 10.3390/ani14132000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
The accurate estimation of basal endogenous losses (BEL) of amino acids at the ileum is indispensable to improve nutrient utilization efficiency. This study used a quantitative proteomic approach to identify variations in BEL in the ileal digesta of growing pigs fed a nitrogen-free diet (NFD) or a casein diet (CAS). Eight barrow pigs (39.8 ± 6.3 kg initial body weight (BW)) were randomly assigned to a 2 × 2 crossover design. A total of 348 proteins were identified and quantified in both treatments, of which 101 showed a significant differential abundance between the treatments (p < 0.05). Functional and pathway enrichment analyses revealed that the endogenous proteins were associated with intestinal metabolic function. Furthermore, differentially abundant proteins (DAPs) in the digesta of pigs fed the NFD enriched terms and pathways that suggest intestinal inflammation, the activation of innate antimicrobial host defense, an increase in cellular autophagy and epithelial turnover, and reduced synthesis of pancreatic and intestinal secretions. These findings suggest that casein diets may provide a more accurate estimation of BEL because they promote normal gastrointestinal secretions. Overall, proteomic and bioinformatic analyses provided valuable insights into the composition of endogenous proteins in the ileal digesta and their relationship with the functions, processes, and pathways modified by diet composition.
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Affiliation(s)
- Iris Elisa Ávila-Arres
- Posgrado en Ciencias de la Producción y de la Salud Animal, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
| | - Elba Rodríguez Hernández
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Km 1 Carretera a Colón, Querétaro 76280, Mexico; (E.R.H.); (S.G.R.)
| | - Sergio Gómez Rosales
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Km 1 Carretera a Colón, Querétaro 76280, Mexico; (E.R.H.); (S.G.R.)
| | - Tércia Cesária Reis de Souza
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias s/n, Querétaro 76230, Mexico;
| | - Gerardo Mariscal-Landín
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Km 1 Carretera a Colón, Querétaro 76280, Mexico; (E.R.H.); (S.G.R.)
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147
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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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148
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Sabbaghian M, Gheitasi H, Fadaee M, Javadi Henafard H, Tavakoli A, Shekarchi AA, Poortahmasebi V. Human cytomegalovirus microRNAs: strategies for immune evasion and viral latency. Arch Virol 2024; 169:157. [PMID: 38969819 DOI: 10.1007/s00705-024-06080-w] [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: 12/11/2023] [Accepted: 05/17/2024] [Indexed: 07/07/2024]
Abstract
Viruses use various strategies and mechanisms to deal with cells and proteins of the immune system that form a barrier against infection. One of these mechanisms is the encoding and production of viral microRNAs (miRNAs), whose function is to regulate the gene expression of the host cell and the virus, thus creating a suitable environment for survival and spreading viral infection. miRNAs are short, single-stranded, non-coding RNA molecules that can regulate the expression of host and viral proteins, and due to their non-immunogenic nature, they are not eliminated by the cells of the immune system. More than half of the viral miRNAs are encoded and produced by Orthoherpesviridae family members. Human cytomegalovirus (HCMV) produces miRNAs that mediate various processes in infected cells to contribute to HCMV pathogenicity, including immune escape, viral latency, and cell apoptosis. Here, we discuss which cellular and viral proteins or cellular pathways and processes these mysterious molecules target to evade immunity and support viral latency in infected cells. We also discuss current evidence that their function of bypassing the host's innate and adaptive immune system is essential for the survival and multiplication of the virus and the spread of HCMV infection.
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Affiliation(s)
- Mohammad Sabbaghian
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamidreza Gheitasi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Manouchehr Fadaee
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | | | - Ahmad Tavakoli
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Akbar Shekarchi
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
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149
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Alayoubi Y, Bentsen M, Looso M. Scanpro is a tool for robust proportion analysis of single-cell resolution data. Sci Rep 2024; 14:15581. [PMID: 38971877 PMCID: PMC11227528 DOI: 10.1038/s41598-024-66381-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 07/01/2024] [Indexed: 07/08/2024] Open
Abstract
In higher organisms, individual cells respond to signals and perturbations by epigenetic regulation and transcriptional adaptation. However, in addition to shifting the expression level of individual genes, the adaptive response of cells can also lead to shifts in the proportions of different cell types. Recent methods such as scRNA-seq allow for the interrogation of expression on the single-cell level, and can quantify individual cell type clusters within complex tissue samples. In order to identify clusters showing differential composition between different biological conditions, differential proportion analysis has recently been introduced. However, bioinformatics tools for robust proportion analysis of both replicated and unreplicated single-cell datasets are critically missing. In this manuscript, we present Scanpro, a modular tool for proportion analysis, seamlessly integrating into widely accepted frameworks in the Python environment. Scanpro is fast, accurate, supports datasets without replicates, and is intended to be used by bioinformatics experts and beginners alike.
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Affiliation(s)
- Yousef Alayoubi
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mette Bentsen
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
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150
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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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