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Rao F, Cao J, Wang C, Xiang S, Wu K, Lin D, Lv J, Wang X, Wang M, Xiang L. Overexpression of miR-96 leads to retinal degeneration in mice. Biochem Biophys Res Commun 2024; 719:150048. [PMID: 38763044 DOI: 10.1016/j.bbrc.2024.150048] [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: 04/22/2024] [Accepted: 05/01/2024] [Indexed: 05/21/2024]
Abstract
Double knockout of miR-183 and miR-96 results in retinal degeneration in mice; however, single knockout of miR-96 leads to developmental delay but not substantial retinal degeneration. To further explore the role of miR-96, we overexpressed this miRNA in mouse retinas. Interestingly, we found that overexpression of miR-96 at a safe dose results in retinal degeneration in the mouse retina. The retinal photoreceptors dramatically degenerated in the miR-96-overexpressing group, as shown by OCT, ERG and cryosectioning at one month after subretinal injection. Degenerative features such as TUNEL signals and reactive gliosis were observed in the miR-96-overexpressing retina. RNA-seq data revealed that immune responses and microglial activation occurred in the degenerating retina. Further qRT‒PCR and immunostaining experiments verified the microglial activation. Moreover, the number of microglia in the miR-96-overexpressing retinas was significantly increased. Our findings demonstrate that appropriate miR-96 expression is required for mouse retinal homeostasis.
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Affiliation(s)
- Fengqin Rao
- Department of Anesthesiology, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai 317000, China; Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; College of Nursing, Wenzhou Medical University, Wenzhou 325035, China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Jianbin Cao
- Department of Anesthesiology, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai 317000, China
| | - Chenyu Wang
- Department of Preventive Medicine, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shengjin Xiang
- Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Kunchao Wu
- Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; Department of Ophthalmology, The First People's Hospital of Guiyang, China
| | - Dan Lin
- Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Jineng Lv
- Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Xiaojie Wang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
| | - Mingcang Wang
- Department of Anesthesiology, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai 317000, China.
| | - Lue Xiang
- Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China.
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2
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Ur Rehman A, Wang Z, Qin Q, Zhang X, Akhtar A, Liu H, Mao B, Khan N, Tang L, Li X. Enhancing antitumor immunity and achieving tumor eradication with IL11RA mRNA immunotherapy. Int Immunopharmacol 2024; 134:112205. [PMID: 38718659 DOI: 10.1016/j.intimp.2024.112205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 06/03/2024]
Abstract
Current methods for delivering genes to target tumors face significant challenges, including off-target effects and immune responses against delivery vectors. In this study, we developed a novel approach using messenger RNA (mRNA) to encode IL11RA for local immunotherapy, aiming to harness the immune system to combat tumors. Our research uncovered a compelling correlation between IL11RA expression and CD8 + T cell levels across multiple tumor types, with elevated IL11RA expression correlating with improved overall survival. Examination of the Pan-Cancer Atlas dataset showed a significant reduction in IL11RA expression in various cancer types compared to normal tissue, raising questions about its potential role in tumorigenesis. To achieve efficient in vivo expression of IL11RA, we synthesized two mRNA sequences mimicking the wild-type protein. These mRNA sequences were formulated and capped to ensure effective delivery, resulting in robust expression within tumor sites. Our investigation into IL11RA mRNA therapy demonstrated its effectiveness in controlling tumor growth when administered both intratumorally and intravenously in mouse models. Additionally, IL11RA mRNA treatment significantly stimulated the expansion of CD8 + T cells within tumors, draining lymph nodes, and the spleen. Transcriptome analysis revealed distinct transcriptional patterns associated with T cell functions. Using multiple deconvolution algorithms, we found substantial infiltration of CD8 + T cells following IL11RA mRNA treatment, highlighting its immunomodulatory effects within the tumor microenvironment. In conclusion, IL11RA mRNA therapy presents a promising strategy for tumor regression with potential immunomodulatory effects and clinical implications for improved survival outcomes.
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Affiliation(s)
- Adeel Ur Rehman
- Clinical Molecular Medicine Testing Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Key Laboratory of Major Brain Disease and Aging Research (Ministry of Education), Institute for Brain Science and Disease, Chongqing Medical University, Chongqing 400016, China.
| | - Zhihuai Wang
- Department of General Surgery, Changzhou No.2 People's Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, 213000, China
| | - Qianshan Qin
- Suzhou Abogen Biosciences Co., Ltd., Suzhou, Jiangsu, 215123, China
| | - Xiaojing Zhang
- Suzhou Abogen Biosciences Co., Ltd., Suzhou, Jiangsu, 215123, China
| | - Aleena Akhtar
- Clinical Molecular Medicine Testing Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Hanyang Liu
- Charité‑University Medical Center, Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molecular Cancer Research Center, D‑13353 Berlin, Germany
| | - Binli Mao
- Clinical Molecular Medicine Testing Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Naveed Khan
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Korea
| | - Liming Tang
- Department of General Surgery, Changzhou No.2 People's Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, 213000, China
| | - Xiaosong Li
- Clinical Molecular Medicine Testing Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Key Laboratory of Major Brain Disease and Aging Research (Ministry of Education), Institute for Brain Science and Disease, Chongqing Medical University, Chongqing 400016, China.
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3
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Boufaied N, Chetta P, Hallal T, Cacciatore S, Lalli D, Luthold C, Homsy K, Imada EL, Syamala S, Photopoulos C, Di Matteo A, de Polo A, Storaci AM, Huang Y, Giunchi F, Sheridan PA, Michelotti G, Nguyen QD, Zhao X, Liu Y, Davicioni E, Spratt DE, Sabbioneda S, Maga G, Mucci LA, Ghigna C, Marchionni L, Butler LM, Ellis L, Bordeleau F, Loda M, Vaira V, Labbé DP, Zadra G. Obesogenic High-Fat Diet and MYC Cooperate to Promote Lactate Accumulation and Tumor Microenvironment Remodeling in Prostate Cancer. Cancer Res 2024; 84:1834-1855. [PMID: 38831751 PMCID: PMC11148549 DOI: 10.1158/0008-5472.can-23-0519] [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: 02/17/2023] [Revised: 12/29/2023] [Accepted: 04/05/2024] [Indexed: 06/05/2024]
Abstract
Cancer cells exhibit metabolic plasticity to meet oncogene-driven dependencies while coping with nutrient availability. A better understanding of how systemic metabolism impacts the accumulation of metabolites that reprogram the tumor microenvironment (TME) and drive cancer could facilitate development of precision nutrition approaches. Using the Hi-MYC prostate cancer mouse model, we demonstrated that an obesogenic high-fat diet (HFD) rich in saturated fats accelerates the development of c-MYC-driven invasive prostate cancer through metabolic rewiring. Although c-MYC modulated key metabolic pathways, interaction with an obesogenic HFD was necessary to induce glycolysis and lactate accumulation in tumors. These metabolic changes were associated with augmented infiltration of CD206+ and PD-L1+ tumor-associated macrophages (TAM) and FOXP3+ regulatory T cells, as well as with the activation of transcriptional programs linked to disease progression and therapy resistance. Lactate itself also stimulated neoangiogenesis and prostate cancer cell migration, which were significantly reduced following treatment with the lactate dehydrogenase inhibitor FX11. In patients with prostate cancer, high saturated fat intake and increased body mass index were associated with tumor glycolytic features that promote the infiltration of M2-like TAMs. Finally, upregulation of lactate dehydrogenase, indicative of a lactagenic phenotype, was associated with a shorter time to biochemical recurrence in independent clinical cohorts. This work identifies cooperation between genetic drivers and systemic metabolism to hijack the TME and promote prostate cancer progression through oncometabolite accumulation. This sets the stage for the assessment of lactate as a prognostic biomarker and supports strategies of dietary intervention and direct lactagenesis blockade in treating advanced prostate cancer. SIGNIFICANCE Lactate accumulation driven by high-fat diet and MYC reprograms the tumor microenvironment and promotes prostate cancer progression, supporting the potential of lactate as a biomarker and therapeutic target in prostate cancer. See related commentary by Frigo, p. 1742.
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Affiliation(s)
- Nadia Boufaied
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Paolo Chetta
- University of Milan, Residency Program in Pathology, Milan, Italy
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Tarek Hallal
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, Québec, Canada
| | - Stefano Cacciatore
- Bionformatics Unit, International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa
| | - Daniela Lalli
- Department of Science and Technological Innovation, University of Piemonte Orientale “A. Avogadro,” Alessandria, Italy
| | - Carole Luthold
- CHU de Québec-Université Laval Research Center (Oncology Division) and Cancer Research Center, Centre de Recherche en Organogénèse Expérimentale/LOEX, Université Laval, Québec, Canada
| | - Kevin Homsy
- CHU de Québec-Université Laval Research Center (Oncology Division) and Cancer Research Center, Centre de Recherche en Organogénèse Expérimentale/LOEX, Université Laval, Québec, Canada
| | - Eddie L. Imada
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York Presbyterian-Weill Cornell Campus, New York, New York
| | - Sudeepa Syamala
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Cornelia Photopoulos
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Anna Di Matteo
- Institute of Molecular Genetics, National Research Council (CNR-IGM), Pavia, Italy
| | - Anna de Polo
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | | | - Ying Huang
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Francesca Giunchi
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | | | - Quang-De Nguyen
- Department of Imaging, Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Xin Zhao
- Veracyte, South San Francisco, California
| | - Yang Liu
- Veracyte, South San Francisco, California
| | | | - Daniel E. Spratt
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Simone Sabbioneda
- Institute of Molecular Genetics, National Research Council (CNR-IGM), Pavia, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics, National Research Council (CNR-IGM), Pavia, Italy
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Claudia Ghigna
- Institute of Molecular Genetics, National Research Council (CNR-IGM), Pavia, Italy
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York Presbyterian-Weill Cornell Campus, New York, New York
| | - Lisa M. Butler
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Leigh Ellis
- Department of Surgery, Center for Prostate Disease Research, Murtha Cancer Center Research Program, 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, Maryland
| | - François Bordeleau
- CHU de Québec-Université Laval Research Center (Oncology Division) and Cancer Research Center, Centre de Recherche en Organogénèse Expérimentale/LOEX, Université Laval, Québec, Canada
- Department of Molecular Biology, Clinical Biochemistry, and Pathology, Laval University, Québec, Canada
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York Presbyterian-Weill Cornell Campus, New York, New York
| | - Valentina Vaira
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - David P. Labbé
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, Québec, Canada
- Division of Urology, Department of Surgery, McGill University, Montréal, Québec, Canada
| | - Giorgia Zadra
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Institute of Molecular Genetics, National Research Council (CNR-IGM), Pavia, Italy
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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Nasr S, Li L, Asad M, Moridi M, Wang M, Zemp FJ, Mahoney DJ, Wang E. A computational pipeline for identifying gene targets and signalling pathways in cancer cells to improve lymphocyte infiltration and immune checkpoint therapy efficacy. EBioMedicine 2024; 104:105167. [PMID: 38805852 PMCID: PMC11154126 DOI: 10.1016/j.ebiom.2024.105167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/28/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Tumour-infiltrating lymphocytes (TILs) are crucial for effective immune checkpoint blockade (ICB) therapy in solid tumours. However, ∼70% of these tumours exhibit poor lymphocyte infiltration, rendering ICB therapies less effective. METHODS We developed a bioinformatics pipeline integrating multiple previously unconsidered factors or datasets, including tumour cell immune-related pathways, copy number variation (CNV), and single tumour cell sequencing data, as well as tumour mRNA-seq data and patient survival data, to identify targets that can potentially improve T cell infiltration and enhance ICB efficacy. Furthermore, we conducted wet-lab experiments and successfully validated one of the top-identified genes. FINDINGS We applied this pipeline in solid tumours of the Cancer Genome Atlas (TCGA) and identified a set of genes in 18 cancer types that might potentially improve lymphocyte infiltration and ICB efficacy, providing a valuable drug target resource to be further explored. Importantly, we experimentally validated SUN1, which had not been linked to T cell infiltration and ICB therapy previously, but was one of the top-identified gene targets among 3 cancer types based on the pipeline, in a mouse colon cancer syngeneic model. We showed that Sun1 KO could significantly enhance antigen presentation, increase T-cell infiltration, and improve anti-PD1 treatment efficacy. Moreover, with a single-cell multiome analysis, we identified subgene regulatory networks (sub-GRNs) showing Stat proteins play important roles in enhancing the immune-related pathways in Sun1-KO cancer cells. INTERPRETATION This study not only established a computational pipeline for discovering new gene targets and signalling pathways in cancer cells that block T-cell infiltration, but also provided a gene target pool for further exploration in improving lymphocyte infiltration and ICB efficacy in solid tumours. FUNDING A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.
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Affiliation(s)
- Sahar Nasr
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Lin Li
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 1N4, Canada; Faculty of Medicine, Dalian University of Technology, Dalian, Liaoning, 116024, China.
| | - Mohammad Asad
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Mahroo Moridi
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Megan Wang
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Franz J Zemp
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Douglas J Mahoney
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Edwin Wang
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 1N4, Canada.
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Ye Y, Wang H, Chen W, Chen Z, Wu D, Zhang F, Hu F. Dynamic changes of immunocyte subpopulations in thermogenic activation of adipose tissues. Front Immunol 2024; 15:1375138. [PMID: 38812501 PMCID: PMC11133676 DOI: 10.3389/fimmu.2024.1375138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024] Open
Abstract
Objectives The effects of cold exposure on whole-body metabolism in humans have gained increasing attention. Brown or beige adipose tissues are crucial in cold-induced thermogenesis to dissipate energy and thus have the potential to combat metabolic disorders. Despite the immune regulation of thermogenic adipose tissues, the overall changes in vital immune cells during distinct cold periods remain elusive. This study aimed to discuss the overall changes in immune cells under different cold exposure periods and to screen several potential immune cell subpopulations on thermogenic regulation. Methods Cibersort and mMCP-counter algorithms were employed to analyze immune infiltration in two (brown and beige) thermogenic adipose tissues under distinct cold periods. Changes in some crucial immune cell populations were validated by reanalyzing the single-cell sequencing dataset (GSE207706). Flow cytometry, immunofluorescence, and quantitative real-time PCR assays were performed to detect the proportion or expression changes in mouse immune cells of thermogenic adipose tissues under cold challenge. Results The proportion of monocytes, naïve, and memory T cells increased, while the proportion of NK cells decreased under cold exposure in brown adipose tissues. Conclusion Our study revealed dynamic changes in immune cell profiles in thermogenic adipose tissues and identified several novel immune cell subpopulations, which may contribute to thermogenic activation of adipose tissues under cold exposure.
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Affiliation(s)
| | | | | | | | | | | | - Fang Hu
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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Mi N, Li Z, Zhang X, Gao Y, Wang Y, Liu S, Wang S. Identification of potential immunotherapeutic targets and prognostic biomarkers in Graves' disease using weighted gene co-expression network analysis. Heliyon 2024; 10:e27175. [PMID: 38468967 PMCID: PMC10926144 DOI: 10.1016/j.heliyon.2024.e27175] [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: 07/21/2023] [Revised: 12/11/2023] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Graves' disease (GD) is an autoimmune disorder characterized by hyperthyroidism resulting from autoantibody-induced stimulation of the thyroid gland. Despite recent advancements in understanding GD's pathogenesis, the molecular processes driving disease progression and treatment response remain poorly understood. In this study, we aimed to identify crucial immunogenic factors associated with GD prognosis and immunotherapeutic response. To achieve this, we implemented a comprehensive screening strategy that combined computational immunogenicity-potential scoring with multi-parametric cluster analysis to assess the immunomodulatory genes in GD-related subtypes involving stromal and immune cells. Utilizing weighted gene co-expression network analysis (WGCNA), we identified co-expressed gene modules linked to cellular senescence and immune infiltration in CD4+ and CD8+ GD samples. Additionally, gene set enrichment analysis enabled the identification of hallmark pathways distinguishing high- and low-immune subtypes. Our WGCNA analysis revealed 21 gene co-expression modules comprising 1,541 genes associated with immune infiltration components in various stages of GD, including T cells, M1 and M2 macrophages, NK cells, and Tregs. These genes primarily participated in T cell proliferation through purinergic signaling pathways, particularly neuroactive ligand-receptor interactions, and DNA binding transcription factor activity. Three genes, namely PRSS1, HCRTR1, and P2RY4, exhibited robustness in GD patients across multiple stages and were involved in immune cell infiltration during the late stage of GD (p < 0.05). Importantly, HCRTR1 and P2RY4 emerged as potential prognostic signatures for predicting overall survival in high-immunocore GD patients (p < 0.05). Overall, our study provides novel insights into the molecular mechanisms driving GD progression and highlights potential key immunogens for further investigation. These findings underscore the significance of immune infiltration-related cellular senescence in GD therapy and present promising targets for the development of new immunotherapeutic strategies.
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Affiliation(s)
- Nianrong Mi
- Department of General Practice, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, 250013, China
| | - Zhe Li
- Department of Health Management Center, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, 250013, China
| | - Xueling Zhang
- Department of Integrated Chinese and Western Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, 250013, China
| | - Yingjing Gao
- Department of Endocrinology, Shandong First Medical University, Jinan, Shandong Province, 250013, China
| | - Yanan Wang
- Department of Endocrinology, Shandong First Medical University, Jinan, Shandong Province, 250013, China
| | - Siyan Liu
- Department of Endocrinology, Shandong First Medical University, Jinan, Shandong Province, 250013, China
| | - Shaolian Wang
- Department of Integrated Chinese and Western Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, 250013, China
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Flümann R, Hansen J, Meinel J, Pfeiffer P, Goldfarb Wittkopf H, Lütz A, Wirtz J, Möllmann M, Zhou T, Tabatabai A, Lohmann T, Jauch M, Beleggia F, Pelzer B, Ullrich F, Höfmann S, Arora A, Persigehl T, Büttner R, von Tresckow B, Klein S, Jachimowicz RD, Reinhardt HC, Knittel G. An inducible Cd79b mutation confers ibrutinib sensitivity in mouse models of Myd88-driven diffuse large B-cell lymphoma. Blood Adv 2024; 8:1063-1074. [PMID: 38060829 PMCID: PMC10907402 DOI: 10.1182/bloodadvances.2023011213] [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: 07/14/2023] [Accepted: 11/26/2023] [Indexed: 02/29/2024] Open
Abstract
ABSTRACT Diffuse large B-cell lymphoma (DLBCL) is the most common aggressive lymphoma and constitutes a highly heterogenous disease. Recent comprehensive genomic profiling revealed the identity of numerous molecularly defined DLBCL subtypes, including a cluster which is characterized by recurrent aberrations in MYD88, CD79B, and BCL2, as well as various lesions promoting a block in plasma cell differentiation, including PRDM1, TBL1XR1, and SPIB. Here, we generated a series of autochthonous mouse models to mimic this DLBCL cluster and specifically focused on the impact of Cd79b mutations in this setting. We show that canonical Cd79b immunoreceptor tyrosine-based activation motif (ITAM) mutations do not accelerate Myd88- and BCL2-driven lymphomagenesis. Cd79b-mutant murine DLBCL were enriched for IgM surface expression, reminiscent of their human counterparts. Moreover, Cd79b-mutant lymphomas displayed a robust formation of cytoplasmic signaling complexes involving MYD88, CD79B, MALT1, and BTK. These complexes were disrupted upon pharmacological BTK inhibition. The BTK inhibitor-mediated disruption of these signaling complexes translated into a selective ibrutinib sensitivity of lymphomas harboring combined Cd79b and Myd88 mutations. Altogether, this in-depth cross-species comparison provides a framework for the development of molecularly targeted therapeutic intervention strategies in DLBCL.
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Affiliation(s)
- Ruth Flümann
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Julia Hansen
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Jörn Meinel
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Pauline Pfeiffer
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Hannah Goldfarb Wittkopf
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Anna Lütz
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Jessica Wirtz
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Michael Möllmann
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Tanja Zhou
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Areya Tabatabai
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Tim Lohmann
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Maximilian Jauch
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Filippo Beleggia
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Benedikt Pelzer
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY
| | - Fabian Ullrich
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Svenja Höfmann
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Aastha Arora
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Thorsten Persigehl
- Department of Radiology and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Bastian von Tresckow
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sebastian Klein
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ron D. Jachimowicz
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Gero Knittel
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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8
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Merotto L, Sturm G, Dietrich A, List M, Finotello F. Making mouse transcriptomics deconvolution accessible with immunedeconv. BIOINFORMATICS ADVANCES 2024; 4:vbae032. [PMID: 38464974 PMCID: PMC10924280 DOI: 10.1093/bioadv/vbae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/01/2024] [Accepted: 02/26/2024] [Indexed: 03/12/2024]
Abstract
Summary Transcriptome deconvolution has emerged as a reliable technique to estimate cell-type abundances from bulk RNA sequencing data. Unlike their human equivalents, methods to quantify the cellular composition of complex tissues from murine transcriptomics are sparse and sometimes not easy to use. We extended the immunedeconv R package to facilitate the deconvolution of mouse transcriptomics, enabling the quantification of murine immune-cell types using 13 different methods. Through immunedeconv, we further offer the possibility of tweaking cell signatures used by deconvolution methods, providing custom annotations tailored for specific cell types and tissues. These developments strongly facilitate the study of the immune-cell composition of mouse models and further open new avenues in the investigation of the cellular composition of other tissues and organisms. Availability and implementation The R package and the documentation are available at https://github.com/omnideconv/immunedeconv.
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Affiliation(s)
- Lorenzo Merotto
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck 6020, Austria
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck 6020, Austria
- Boehringer Ingelheim International Pharma GmbH & Co KG, Biberach 88400, Germany
| | - Alexander Dietrich
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Markus List
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Francesca Finotello
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck 6020, Austria
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Jiang A, Zheng X, Yan S, Yan J, Yao Y, He W. Advancing the Boundaries of Immunotherapy in Lung Adenocarcinoma with Idiopathic Pulmonary Fibrosis by a Biomimetic Proteinoid Enabling Selective Endocytosis. ACS NANO 2024. [PMID: 38319028 PMCID: PMC10883119 DOI: 10.1021/acsnano.3c09852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
The coexistence of lung adenocarcinoma (LUAD) with idiopathic pulmonary fibrosis (IPF), which has been extensively documented as a prominent risk factor for checkpoint inhibitor-related pneumonitis (CIP) in patients undergoing immunotherapy, has long been considered a restricted domain for the use of immune checkpoint inhibitors (ICIs). To overcome it, an approach was employed herein to specifically target PD-L1 within the cellular interior, surpassing the conventional focus solely on the cytomembrane, thereby facilitating the development of ICIs capable of distinguishing between LUAD cells and noncancerous cells based on their distinctive endocytic propensities. By exploiting the aurophilicity-driven self-assembly of a PD-L1 binding peptide (PDBP) and subsequently encapsulating it within erythrocyte membranes (EM), the resulting biomimetic ICIs protein EMS-PDBP exhibited extraordinary selectivity in internalizing LUAD cells, effectively targeting PD-L1 within cancer cells while hindering its membrane translocation. The EMS-PDBP treatment not only reactivated the antitumor immune response in the LUAD orthotopic allograft mouse model but also demonstrated a favorable safety profile by effectively eliminating any immune-related adverse events (irAEs). Most significantly, EMS-PDBP successfully and safely restored the antitumor immune response in a mouse model of LUAD with coexistent IPF, thus shattering the confines of ICIs immunotherapy. The reported EMS-PDBP collectively offers a potential strategy for immune reactivation to overcome the limitations of immunotherapy in LUAD coexisting with IPF.
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Affiliation(s)
- Aimin Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Xiaoqiang Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
- Institute for Stem Cell & Regenerative Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Siqi Yan
- Institute for Stem Cell & Regenerative Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Jin Yan
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Yu Yao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Wangxiao He
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
- Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an 710061, China
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10
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Ferrena A, Wang J, Zhang R, Karadal-Ferrena B, Al-Hardan W, Singh S, Borjihan H, Schwartz EL, Zhao H, Oktay MH, Yang R, Geller DS, Hoang BH, Zheng D. SKP2 Knockout in Rb1/p53-Deficient Mouse Models of Osteosarcoma Induces Immune Infiltration and Drives a Transcriptional Program with a Favorable Prognosis. Mol Cancer Ther 2024; 23:223-234. [PMID: 37871911 PMCID: PMC10842346 DOI: 10.1158/1535-7163.mct-23-0173] [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: 03/24/2023] [Revised: 08/27/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023]
Abstract
Osteosarcoma is an aggressive bone malignancy with a poor prognosis. One putative proto-oncogene in osteosarcoma is SKP2, encoding a substrate recognition factor of the SCF E3 ubiquitin ligase. We previously demonstrated that Skp2 knockout in murine osteosarcoma improved survival and delayed tumorigenesis. Here, we performed RNA sequencing (RNA-seq) on tumors from a transgenic osteosarcoma mouse model with conditional Trp53 and Rb1 knockouts in the osteoblast lineage ("DKO": Osx1-Cre;Rb1lox/lox;p53lox/lox) and a triple-knockout model with additional Skp2 germline knockout ("TKO": Osx1-Cre;Rb1lox/lox;p53lox/lox;Skp2-/-), followed by qPCR and immunohistochemistry validation. To investigate the clinical implications of our results, we analyzed a human osteosarcoma patient cohort ("NCI-TARGET OS") with RNA-seq and clinical data. We found large differences in gene expression after SKP2 knockout. Surprisingly, we observed increased expression of genes related to immune microenvironment infiltration in TKO tumors, especially the signature genes for macrophages and to a lesser extent, T cells, B cells, and vascular cells. We also uncovered a set of relevant transcription factors that may mediate these changes. In osteosarcoma patient cohorts, high expression of genes upregulated in TKO was correlated with favorable overall survival, which was largely explained by the macrophage gene signatures. This relationship was further supported by our finding that SKP2 expression was negatively correlated with macrophage infiltration in the NCI-TARGET osteosarcoma and the TCGA Sarcoma cohorts. Overall, our findings indicate that SKP2 may mediate immune exclusion from the osteosarcoma tumor microenvironment, suggesting that SKP2 modulation in osteosarcoma may induce antitumor immune activation.
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Affiliation(s)
- Alexander Ferrena
- Institute for Clinical and Translational Research, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jichuan Wang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ranxin Zhang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Waleed Al-Hardan
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Swapnil Singh
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hasibagan Borjihan
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Edward L. Schwartz
- Department of Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hongling Zhao
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Maja H. Oktay
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
- Gruss-Lipper Biophotonics Center, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
- Integrated Imaging Program, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rui Yang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - David S Geller
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bang H Hoang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
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11
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Yasinoglu SA, Kuipers TB, Suidgeest E, van der Weerd L, Mei H, Baelde HJ, Peters DJM. Transcriptomic profiling of Polycystic Kidney Disease identifies paracrine factors in the early cyst microenvironment. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166987. [PMID: 38070582 DOI: 10.1016/j.bbadis.2023.166987] [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: 08/23/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
Initial cysts that are formed upon Pkd1 loss in mice impose persistent stress on surrounding tissue and trigger a cystic snowball effect, in which local aberrant PKD-related signaling increases the likelihood of new cyst formation, ultimately leading to accelerated disease progression. Although many pathways have been associated with PKD progression, the knowledge of early changes near initial cysts is limited. To perform an unbiased analysis of transcriptomic alterations in the cyst microenvironment, microdomains were collected from kidney sections of iKsp-Pkd1del mice with scattered Pkd1-deletion using Laser Capture Microdissection. These microdomains were defined as F4/80-low cystic, representing early alterations in the cyst microenvironment, F4/80-high cystic, with more advanced alterations, or non-cystic. RNA sequencing and differential gene expression analysis revealed 953 and 8088 dysregulated genes in the F4/80-low and F4/80-high cyst microenvironment, respectively, when compared to non-cystic microdomains. In the early cyst microenvironment, several injury-repair, growth, and tissue remodeling-related pathways were activated, accompanied by mild metabolic changes. In the more advanced F4/80-high microdomains, these pathways were potentiated and the metabolism was highly dysregulated. Upstream regulator analysis revealed a series of paracrine factors with increased activity in the early cyst microenvironment, including TNFSF12 and OSM. In line with the upstream regulator analysis, TWEAK and Oncostatin-M promoted cell proliferation and inflammatory gene expression in renal epithelial cells and fibroblasts in vitro. Collectively, our data provide an overview of molecular alterations that specifically occur in the cyst microenvironment and identify paracrine factors that may mediate early and advanced alterations in the cyst microenvironment.
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Affiliation(s)
- Sevtap A Yasinoglu
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Thomas B Kuipers
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Ernst Suidgeest
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Louise van der Weerd
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans J Baelde
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
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12
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Cao K, Zhu J, Lu M, Zhang J, Yang Y, Ling X, Zhang L, Qi C, Wei S, Zhang Y, Ma J. Analysis of multiple programmed cell death-related prognostic genes and functional validations of necroptosis-associated genes in oesophageal squamous cell carcinoma. EBioMedicine 2024; 99:104920. [PMID: 38101299 PMCID: PMC10733113 DOI: 10.1016/j.ebiom.2023.104920] [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: 06/13/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Oesophageal squamous cell carcinoma (ESCC) is a lethal malignancy. Immune checkpoint inhibitors (ICIs) showed great clinical benefits for patients with ESCC. We aimed to construct a model predicting prognosis and response to ICIs by integrating diverse programmed cell death (PCD) forms. METHODS Genes related to 14 PCDs were collected to generate multi-gene signatures, including apoptosis, necroptosis, pyroptosis, ferroptosis, and cuproptosis. Bulk and single-cell RNA transcriptome datasets were used to develop and validate the model. We assessed the functions of two necroptosis-related genes in ESCC cells by Western blot, co-immunoprecipitation (Co-IP), LDH release assay, CCK-8, and migration assay, followed by immunohistochemistry (IHC) staining on samples of patients with ESCC (n = 67). FINDINGS We built and validated a 16-gene prognostic combined cell death index (CCDI) by combining immunogenic cell death (ICD) and necroptosis signatures. The CCDI could also predict response to ICIs in cancer, as shown by Tumour Immune Dysfunction and Exclusion (TIDE) analysis, confirmed in four independent ICI clinical trials. Trajectory analysis revealed that HOOK1 and CUL4A might affect ESCC cell fate. We found that HOOK1 induced necroptosis and inhibited the proliferation and migration of ESCC cells, while CUL4A exhibited the opposite effects. Co-IP assay confirmed that HOOK1 and CUL4A promoted and reduced necrosome formation in ESCC cells. Data from patients with ESCC further supported that HOOK1 and CUL4A might be a tumour suppressor and oncogene, respectively. INTERPRETATION We constructed a CCDI model with potential in predicting prognosis and response to ICIs in cancer. HOOK1 and CUL4A in the CCDI model are crucial prognostic biomarkers in ESCC. FUNDING The Natural Science Foundation of China [82172786], The National Cancer Center Climbing Fund of China [NCC201908B06], The Natural Science Foundation of Heilongjiang Province [LH2021H077].
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Affiliation(s)
- Kui Cao
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Jinhong Zhu
- Biobank, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China; Department of Clinical Laboratory, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Mengdi Lu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Jinfeng Zhang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Yingnan Yang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Xiaodong Ling
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Luquan Zhang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Cuicui Qi
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Shenshui Wei
- Biobank, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China
| | - Yanqiao Zhang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China; Clinical Research Center for Colorectal Cancer in Heilongjiang, Harbin, China; Key Laboratories of Tumor Immunology in Heilongjiang, Harbin, China; Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.
| | - Jianqun Ma
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, Heilongjiang, China.
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13
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Iorgulescu JB, Ruthen N, Ahn R, Panagioti E, Gokhale PC, Neagu M, Speranza MC, Eschle BK, Soroko KM, Piranlioglu R, Datta M, Krishnan S, Yates KB, Baker GJ, Jain RK, Suvà ML, Neuberg D, White FM, Chiocca EA, Freeman GJ, Sharpe AH, Wu CJ, Reardon DA. Antigen presentation deficiency, mesenchymal differentiation, and resistance to immunotherapy in the murine syngeneic CT2A tumor model. Front Immunol 2023; 14:1297932. [PMID: 38213329 PMCID: PMC10782385 DOI: 10.3389/fimmu.2023.1297932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/11/2023] [Indexed: 01/13/2024] Open
Abstract
Background The GL261 and CT2A syngeneic tumor lines are frequently used as immunocompetent orthotopic mouse models of human glioblastoma (huGBM) but demonstrate distinct differences in their responses to immunotherapy. Methods To decipher the cell-intrinsic mechanisms that drive immunotherapy resistance in CT2A-luc and to define the aspects of human cancer biology that these lines can best model, we systematically compared their characteristics using whole exome and transcriptome sequencing, and protein analysis through immunohistochemistry, Western blot, flow cytometry, immunopeptidomics, and phosphopeptidomics. Results The transcriptional profiles of GL261-luc2 and CT2A-luc tumors resembled those of some huGBMs, despite neither line sharing the essential genetic or histologic features of huGBM. Both models exhibited striking hypermutation, with clonal hotspot mutations in RAS genes (Kras p.G12C in GL261-luc2 and Nras p.Q61L in CT2A-luc). CT2A-luc distinctly displayed mesenchymal differentiation, upregulated angiogenesis, and multiple defects in antigen presentation machinery (e.g. Tap1 p.Y488C and Psmb8 p.A275P mutations) and interferon response pathways (e.g. copy number losses of loci including IFN genes and reduced phosphorylation of JAK/STAT pathway members). The defect in MHC class I expression could be overcome in CT2A-luc by interferon-γ treatment, which may underlie the modest efficacy of some immunotherapy combinations. Additionally, CT2A-luc demonstrated substantial baseline secretion of the CCL-2, CCL-5, and CCL-22 chemokines, which play important roles as myeloid chemoattractants. Conclusion Although the clinical contexts that can be modeled by GL261 and CT2A for huGBM are limited, CT2A may be an informative model of immunotherapy resistance due to its deficits in antigen presentation machinery and interferon response pathways.
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Affiliation(s)
- J. Bryan Iorgulescu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Neil Ruthen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Ryuhjin Ahn
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Eleni Panagioti
- Department of Neurosurgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Prafulla C. Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Martha Neagu
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Maria C. Speranza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Benjamin K. Eschle
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Kara M. Soroko
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Raziye Piranlioglu
- Department of Neurosurgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Meenal Datta
- Edwin L. Steele Laboratories for Tumor Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Shanmugarajan Krishnan
- Edwin L. Steele Laboratories for Tumor Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Kathleen B. Yates
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, United States
| | - Gregory J. Baker
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA, United States
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, United States
| | - Rakesh K. Jain
- Edwin L. Steele Laboratories for Tumor Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Mario L. Suvà
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, United States
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Donna Neuberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Forest M. White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - E. Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Gordon J. Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Arlene H. Sharpe
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - David A. Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
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14
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Wang P, Zhang Q, Zhang H, Shao J, Zhang H, Wang Z. Molecular and clinical characterization of ICOS expression in breast cancer through large-scale transcriptome data. PLoS One 2023; 18:e0293469. [PMID: 38127899 PMCID: PMC10734928 DOI: 10.1371/journal.pone.0293469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/13/2023] [Indexed: 12/23/2023] Open
Abstract
ICOS (Inducible T Cell Costimulator), one of the co-stimulatory B7 superfamily members, was characterized as a co-stimulatory receptor for T-cell enhancement. However, the role of ICOS in breast cancer remains largely unknown. The present study systematically investigated the expression pattern and its relation to clinical characteristics and immunotherapy by integrating multiple clinical cohorts and large-scale gene expression data. This study included 2994 breast tumor samples with transcriptome data and matched clinical data. To make our findings more reliable, we set the TCGA cohort as the discovery set and the METABRIC cohort as the validation set. The expression of ICOS in breast cancer is strongly associated with major clinical and molecular characteristics. There is an association between higher ICOS expression and malignant subtypes and grades of tumors. In addition, gene ontology analysis based on genes significantly correlated with ICOS expression indicated that the expression of ICOS is mainly associated with immune responses and inflammation. We also observed strong correlations between ICOS and other promising immune-checkpoint molecules, including PD1, PDL1, CTLA4, and IDO1. Furthermore, we found that ICOS expression is associated with the response to anti-PDL1 immunotherapy and may serve as a biomarker for immunotherapy prediction. Our results indicated higher ICOS expression is significantly associated with favorable survival in triple-negative breast cancer (TNBC) patients, but not for all subtypes of breast cancer patients. In summary, ICOS correlates with higher malignant breast cancers, and it contributes to the regulation of the immune microenvironment of breast tumors, making it a potential biomarker and immunotherapy target.
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Affiliation(s)
- Peng Wang
- Thyroid and Breast Department III, Cangzhou Central Hospital, Cangzhou, Hebei Province, China
| | - Qin Zhang
- Thyroid and Breast Department III, Cangzhou Central Hospital, Cangzhou, Hebei Province, China
| | - Hengle Zhang
- Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Jianqiang Shao
- Thyroid and Breast Department III, Cangzhou Central Hospital, Cangzhou, Hebei Province, China
| | - Hui Zhang
- Thyroid and Breast Department III, Cangzhou Central Hospital, Cangzhou, Hebei Province, China
| | - Zunyi Wang
- Thyroid and Breast Department III, Cangzhou Central Hospital, Cangzhou, Hebei Province, China
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15
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Bao Y, Qiao Y, Choi JE, Zhang Y, Mannan R, Cheng C, He T, Zheng Y, Yu J, Gondal M, Cruz G, Grove S, Cao X, Su F, Wang R, Chang Y, Kryczek I, Cieslik M, Green MD, Zou W, Chinnaiyan AM. Targeting the lipid kinase PIKfyve upregulates surface expression of MHC class I to augment cancer immunotherapy. Proc Natl Acad Sci U S A 2023; 120:e2314416120. [PMID: 38011559 PMCID: PMC10710078 DOI: 10.1073/pnas.2314416120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023] Open
Abstract
Despite the remarkable clinical success of immunotherapies in a subset of cancer patients, many fail to respond to treatment and exhibit resistance. Here, we found that genetic or pharmacologic inhibition of the lipid kinase PIKfyve, a regulator of autophagic flux and lysosomal biogenesis, upregulated surface expression of major histocompatibility complex class I (MHC-I) in cancer cells via impairing autophagic flux, resulting in enhanced cancer cell killing mediated by CD8+ T cells. Genetic depletion or pharmacologic inhibition of PIKfyve elevated tumor-specific MHC-I surface expression, increased intratumoral functional CD8+ T cells, and slowed tumor progression in multiple syngeneic mouse models. Importantly, enhanced antitumor responses by Pikfyve-depletion were CD8+ T cell- and MHC-I-dependent, as CD8+ T cell depletion or B2m knockout rescued tumor growth. Furthermore, PIKfyve inhibition improved response to immune checkpoint blockade (ICB), adoptive cell therapy, and a therapeutic vaccine. High expression of PIKFYVE was also predictive of poor response to ICB and prognostic of poor survival in ICB-treated cohorts. Collectively, our findings show that targeting PIKfyve enhances immunotherapies by elevating surface expression of MHC-I in cancer cells, and PIKfyve inhibitors have potential as agents to increase immunotherapy response in cancer patients.
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Affiliation(s)
- Yi Bao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI48109
| | - Jae Eun Choi
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Caleb Cheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Tongchen He
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Yang Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Jiali Yu
- Department of Surgery, University of Michigan, Ann Arbor, MI48109
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI48109
| | - Mahnoor Gondal
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI48109
| | - Gabriel Cruz
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
| | - Sara Grove
- Department of Surgery, University of Michigan, Ann Arbor, MI48109
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI48109
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Yu Chang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Ilona Kryczek
- Department of Surgery, University of Michigan, Ann Arbor, MI48109
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI48109
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI48109
| | - Michael D. Green
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI48109
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI48109
- Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, MI48109
| | - Weiping Zou
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI48109
- Department of Surgery, University of Michigan, Ann Arbor, MI48109
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI48109
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI48109
- HHMI, University of Michigan, Ann Arbor, MI48109
- Department of Urology, University of Michigan, Ann Arbor, MI48109
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Xia Y, Gao Y, Liu MY, Li L, Pan W, Mao LZ, Yang Z, Yang M, Guo AY. ICBcomb: a comprehensive expression database for immune checkpoint blockade combination therapy. Brief Bioinform 2023; 25:bbad457. [PMID: 38095856 PMCID: PMC10753530 DOI: 10.1093/bib/bbad457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/19/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
The success of immune checkpoint blockade (ICB) promotes the immunotherapy to be a new pillar in cancer treatment. However, the low response rate of the ICB therapy limits its application. To increase the response rate and enhance efficacy, the ICB combination therapy has emerged and its clinical trials are increasing. Nevertheless, the gene expression profile and its pattern of ICB combination were not comprehensively studied, which limits the understanding of the ICB combination therapy and the identification of new drugs. Here, we constructed ICBcomb (http://bioinfo.life.hust.edu.cn/ICBcomb/), a comprehensive database, by analyzing the human and mouse expression data of the ICB combination therapy and comparing them between groups treated with ICB, other drugs or their combinations. ICBcomb contains 1399 samples across 29 cancer types involving 52 drugs. It provides a user-friendly web interface for demonstrating the results of the available comparisons in the ICB combination therapy datasets with five functional modules: [1, 2] the 'Dataset/Disease' modules for browsing the expression, enrichment and comparison results in each dataset or disease; [3] the 'Gene' module for inputting a gene symbol and displaying its expression and comparison results across datasets/diseases; [4] the 'Gene Set' module for GSVA/GSEA enrichment analysis on the built-in gene sets and the user-input gene sets in different comparisons; [5] the 'Immune Cell' module for immune cell infiltration comparison between different groups by immune cell abundance analysis. The ICBcomb database provides the first resource for gene expression profile and comparison in ICB combination therapy, which may provide clues for discovering the mechanism of effective combination strategies and new combinatory drugs.
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Affiliation(s)
- Yun Xia
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yan Gao
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Ming-Yu Liu
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Lei Li
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wen Pan
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Ling-Zi Mao
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhongzheng Yang
- Wuhan Biobank Co., Ltd., Wuhan Institute of Biotechnology, Wuhan, 430000, China
| | - Mei Yang
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - An-Yuan Guo
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Department of Thoracic Surgery, West China Biomedical Big Data Center, Med-X Center for Informatics, West China Hospital, Sichuan University, Chengdu, 610041, China
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17
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Chen H, Xu C, Zeng H, Zhang Z, Wang N, Guo Y, Zheng Y, Xia S, Zhou H, Yu X, Fu X, Tang T, Wu X, Chen Z, Peng Y, Cai J, Li J, Yan F, Gu C, Chen G, Chen J. Ly6C-high monocytes alleviate brain injury in experimental subarachnoid hemorrhage in mice. J Neuroinflammation 2023; 20:270. [PMID: 37978532 PMCID: PMC10657171 DOI: 10.1186/s12974-023-02939-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: 07/30/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Subarachnoid hemorrhage (SAH) is an uncommon type of potentially fatal stroke. The pathophysiological mechanisms of brain injury remain unclear, which hinders the development of drugs for SAH. We aimed to investigate the pathophysiological mechanisms of SAH and to elucidate the cellular and molecular biological response to SAH-induced injury. METHODS A cross-species (human and mouse) multiomics approach combining high-throughput data and bioinformatic analysis was used to explore the key pathophysiological processes and cells involved in SAH-induced brain injury. Patient data were collected from the hospital (n = 712). SAH was established in adult male mice via endovascular perforation, and flow cytometry, a bone marrow chimera model, qPCR, and microglial depletion experiments were conducted to explore the origin and chemotaxis mechanism of the immune cells. To investigate cell effects on SAH prognosis, murine neurological function was evaluated based on a modified Garcia score, pole test, and rotarod test. RESULTS The bioinformatics analysis confirmed that inflammatory and immune responses were the key pathophysiological processes after SAH. Significant increases in the monocyte levels were observed in both the mouse brains and the peripheral blood of patients after SAH. Ly6C-high monocytes originated in the bone marrow, and the skull bone marrow contribute a higher proportion of these monocytes than neutrophils. The mRNA level of Ccl2 was significantly upregulated after SAH and was greater in CD11b-positive than CD11b-negative cells. Microglial depletion, microglial inhibition, and CCL2 blockade reduced the numbers of Ly6C-high monocytes after SAH. With CCR2 antagonization, the neurological function of the mice exhibited a slow recovery. Three days post-SAH, the monocyte-derived dendritic cell (moDC) population had a higher proportion of TNF-α-positive cells and a lower proportion of IL-10-positive cells than the macrophage population. The ratio of moDCs to macrophages was higher on day 3 than on day 5 post-SAH. CONCLUSIONS Inflammatory and immune responses are significantly involved in SAH-induced brain injury. Ly6C-high monocytes derived from the bone marrow, including the skull bone marrow, infiltrated into mouse brains via CCL2 secreted from microglia. Moreover, Ly6C-high monocytes alleviated neurological dysfunction after SAH.
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Affiliation(s)
- Huaijun Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Chaoran Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Hanhai Zeng
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Zhihua Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Ning Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Yinghan Guo
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Yonghe Zheng
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Siqi Xia
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Hang Zhou
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Xiaobo Yu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Xiongjie Fu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Tianchi Tang
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Xinyan Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Zihang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Yucong Peng
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Jing Cai
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Jianru Li
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Feng Yan
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China
| | - Chi Gu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China.
| | - Gao Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China.
| | - Jingyin Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, China.
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18
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Morita K, Mizuno T, Azuma I, Suzuki Y, Kusuhara H. Rat Deconvolution as Knowledge Miner for Immune Cell Trafficking from Toxicogenomics Databases. Toxicol Sci 2023; 197:kfad117. [PMID: 37941435 PMCID: PMC10823770 DOI: 10.1093/toxsci/kfad117] [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] [Indexed: 11/10/2023] Open
Abstract
Toxicogenomics databases are useful for understanding biological responses in individuals because they include a diverse spectrum of biological responses. Although these databases contain no information regarding immune cells in the liver, which are important in the progression of liver injury, deconvolution that estimates cell-type proportions from bulk transcriptome could extend immune information. However, deconvolution has been mainly applied to humans and mice and less often to rats, which are the main target of toxicogenomics databases. Here, we developed a deconvolution method for rats to retrieve information regarding immune cells from toxicogenomics databases. The rat-specific deconvolution showed high correlations for several types of immune cells between spleen and blood, and between liver treated with toxicants compared with those based on human and mouse data. Additionally, we found 4 clusters of compounds in Open TG-GATEs database based on estimated immune cell trafficking, which are different from those based on transcriptome data itself. The contributions of this work are three-fold. First, we obtained the gene expression profiles of 6 rat immune cells necessary for deconvolution. Second, we clarified the importance of species differences on deconvolution. Third, we retrieved immune cell trafficking from toxicogenomics databases. Accumulated and comparable immune cell profiles of massive data of immune cell trafficking in rats could deepen our understanding of enable us to clarify the relationship between the order and the contribution rate of immune cells, chemokines and cytokines, and pathologies. Ultimately, these findings will lead to the evaluation of organ responses in Adverse Outcome Pathway.
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Affiliation(s)
- Katsuhisa Morita
- Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Tadahaya Mizuno
- Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Iori Azuma
- Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hiroyuki Kusuhara
- Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
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19
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Liu XD, Zhang YT, McGrail DJ, Zhang X, Lam T, Hoang A, Hasanov E, Manyam G, Peterson CB, Zhu H, Kumar SV, Akbani R, Pilie PG, Tannir NM, Peng G, Jonasch E. SETD2 Loss and ATR Inhibition Synergize to Promote cGAS Signaling and Immunotherapy Response in Renal Cell Carcinoma. Clin Cancer Res 2023; 29:4002-4015. [PMID: 37527013 PMCID: PMC10592192 DOI: 10.1158/1078-0432.ccr-23-1003] [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: 04/05/2023] [Revised: 04/13/2023] [Accepted: 07/27/2023] [Indexed: 08/03/2023]
Abstract
PURPOSE Immune checkpoint blockade (ICB) demonstrates durable clinical benefits in a minority of patients with renal cell carcinoma (RCC). We aimed to identify the molecular features that determine the response and develop approaches to enhance it. EXPERIMENTAL DESIGN We investigated the effects of SET domain-containing protein 2 (SETD2) loss on the DNA damage response pathway, the cytosolic DNA-sensing pathway, the tumor immune microenvironment, and the response to ataxia telangiectasia and rad3-related (ATR) and checkpoint inhibition in RCC. RESULTS ATR inhibition activated the cyclic GMP-AMP synthase (cGAS)-interferon regulatory factor 3 (IRF3)-dependent cytosolic DNA-sensing pathway, resulting in the concurrent expression of inflammatory cytokines and immune checkpoints. Among the common RCC genotypes, SETD2 loss is associated with preferential ATR activation and sensitizes cells to ATR inhibition. SETD2 knockdown promoted the cytosolic DNA-sensing pathway in response to ATR inhibition. Treatment with the ATR inhibitor VE822 concurrently upregulated immune cell infiltration and immune checkpoint expression in Setd2 knockdown Renca tumors, providing a rationale for ATR inhibition plus ICB combination therapy. Setd2-deficient Renca tumors demonstrated greater vulnerability to ICB monotherapy or combination therapy with VE822 than Setd2-proficient tumors. Moreover, SETD2 mutations were associated with a higher response rate and prolonged overall survival in patients with ICB-treated RCC but not in patients with non-ICB-treated RCC. CONCLUSIONS SETD2 loss and ATR inhibition synergize to promote cGAS signaling and enhance immune cell infiltration, providing a mechanistic rationale for the combination of ATR and checkpoint inhibition in patients with RCC with SETD2 mutations.
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Affiliation(s)
- Xian-De Liu
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- These authors contributed equally
| | - Yan-Ting Zhang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- These authors contributed equally
| | - Daniel J. McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44195, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Xuesong Zhang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Truong Lam
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anh Hoang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elshad Hasanov
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ganiraju Manyam
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Haifeng Zhu
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shwetha V Kumar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick G. Pilie
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention at The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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20
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Shimizu K, Kahramanian A, Jabbar MADA, Turna Demir F, Gokyer D, Uthamacumaran A, Rajan A, Saad MA, Gorham J, Wakimoto H, Martuza RL, Rabkin SD, Hasan T, Wakimoto H. Photodynamic augmentation of oncolytic virus therapy for central nervous system malignancies. Cancer Lett 2023; 572:216363. [PMID: 37619813 PMCID: PMC10529118 DOI: 10.1016/j.canlet.2023.216363] [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] [Revised: 08/09/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023]
Abstract
Oncolytic viruses (OVs) have emerged as a clinical therapeutic modality potentially effective for cancers that evade conventional therapies, including central nervous system malignancies. Rationally designed combinatorial strategies can augment the efficacy of OVs by boosting tumor-selective cytotoxicity and modulating the tumor microenvironment (TME). Photodynamic therapy (PDT) of cancer not only mediates direct neoplastic cell death but also primes the TME to sensitize the tumor to secondary therapies, allowing for the combination of two potentially synergistic therapies with broader targets. Here, we created G47Δ-KR, clinical oncolytic herpes simplex virus G47Δ that expresses photosensitizer protein KillerRed (KR). Optical properties and cytotoxic effects of G47Δ-KR infection followed by amber LED illumination (peak wavelength: 585-595 nm) were examined in human glioblastoma (GBM) and malignant meningioma (MM) models in vitro. G47Δ-KR infection of tumor cells mediated KR expression that was activated by LED and produced reactive oxygen species, leading to cell death that was more robust than G47Δ-KR without light. In vivo, we tested photodynamic-oncolytic virus (PD-OV) therapy employing intratumoral injection of G47Δ-KR followed by laser light tumor irradiation (wavelength: 585 nm) in GBM and MM xenografts. PD-OV therapy was feasible in these models and resulted in potent anti-tumor effects that were superior to G47Δ-KR alone (without laser light) or laser light alone. RNA sequencing analysis of post-treatment tumor samples revealed PD-OV therapy-induced increases in TME infiltration of variable immune cell types. This study thus demonstrated the proof-of-concept that G47Δ-KR enables PD-OV therapy for neuro-oncological malignancies and warrants further research to advance potential clinical translation.
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Affiliation(s)
- Kazuhide Shimizu
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA; Department of Neurosurgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Andranik Kahramanian
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA; Department of Neurosurgery, Royal Melbourne Hospital, Melbourne, Australia
| | | | - Fatma Turna Demir
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA; Department of Medical Services and Techniques, Medical Laboratory Techniques Programme, Vocational School of Health Services, Antalya Bilim University, Antalya, Turkey
| | - Dilan Gokyer
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Abicumaran Uthamacumaran
- McGill University, McGill Genome Center, Montreal, Canada; Douglas Mental Health University Institute, Department of Psychiatry, Montreal, Canada
| | - Anant Rajan
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Mohammad Ahsan Saad
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Joshua Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Robert L Martuza
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Samuel D Rabkin
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Tayyaba Hasan
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA; Division of Health Sciences and Technology, Harvard University and Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
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21
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Luo J, Pei J, Yu CJ, Tian XM, Zhang J, Shen LJ, Hua Y, Wei GH. Exploring the role of Hmox1 in ferroptosis and immune infiltration during renal ischemia-reperfusion injury. Ren Fail 2023; 45:2257801. [PMID: 38532724 DOI: 10.1080/0886022x.2023.2257801] [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: 06/02/2023] [Accepted: 09/06/2023] [Indexed: 03/28/2024] Open
Abstract
Ischemia-reperfusion injury (IRI) is inevitable in kidney transplantations and, as a complex pathophysiological process, it can be greatly impacted by ferroptosis and immune inflammation. Our study aimed to identify the biomarkers of renal IRI (RIRI) and elucidate their relationship with immune infiltration. In this study, the GSE148420 database was used as a training set to analyze differential genes and overlap them with ferroptosis-related genes to identify hub genes using a protein-protein interaction (PPI) network, the least absolute shrinkage and selection operator (LASSO), and random forest algorithm (RFA). We verified the hub gene and ferroptosis-related phenotypes in a verification set and animal experiments involving unilateral IRI with contralateral nephrectomy in rats. Gene set enrichment analysis (GSEA) of single genes was conducted according to the hub gene to predict related endogenous RNAs (ceRNAs) and drugs to establish a network. Finally, we used the Cibersort to analyze immunological infiltration and conducted Spearman's correlation analysis. We identified 5456 differential genes and obtained 26 ferroptosis-related differentially expressed genes. Through PPI, LASSO, and RFA, Hmox1 was identified as the only hub gene and its expression levels were verified using verification sets. In animal experiments, Hmox1 was verified as a key biomarker. GSEA of single genes revealed the seven most related pathways, and the ceRNAs network included 138 mRNAs and miRNAs. We predicted 11 related drugs and their three-dimensional structural maps. Thus, Hmox1 was identified as a key biomarker and regulator of ferroptosis in RIRI and its regulation of ferroptosis was closely related to immune infiltration.
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Affiliation(s)
- Jin Luo
- Department of Urology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Jun Pei
- Department of Urology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Cheng-Jun Yu
- Department of Urology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Xiao-Mao Tian
- Department of Urology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Jie Zhang
- Department of Urology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Lian-Ju Shen
- Department of Urology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Yi Hua
- Department of Urology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Guang-Hui Wei
- Department of Urology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
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Pandya Shesh B, Walter V, Palsa K, Slagle-Webb B, Neely E, Schell T, Connor JR. Sexually dimorphic effect of H-ferritin genetic manipulation on survival and tumor microenvironment in a mouse model of glioblastoma. J Neurooncol 2023; 164:569-586. [PMID: 37812288 DOI: 10.1007/s11060-023-04415-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/03/2023] [Indexed: 10/10/2023]
Abstract
PURPOSE Iron plays a crucial role in various biological mechanisms and has been found to promote tumor growth. Recent research has shown that the H-ferritin (FTH1) protein, traditionally recognized as an essential iron storage protein, can transport iron to GBM cancer stem cells, reducing their invasion activity. Moreover, the binding of extracellular FTH1 to human GBM tissues, and brain iron delivery in general, has been found to have a sex bias. These observations raise questions, addressed in this study, about whether H-ferritin levels extrinsic to the tumor can affect tumor cell pathways and if this impact is sex-specific. METHODS To interrogate the role of systemic H-ferritin in GBM we introduce a mouse model in which H-ferritin levels are genetically manipulated. Mice that were genetically manipulated to be heterozygous for H-ferritin (Fth1+/-) gene expression were orthotopically implanted with a mouse GBM cell line (GL261). Littermate Fth1 +/+ mice were used as controls. The animals were evaluated for survival and the tumors were subjected to RNA sequencing protocols. We analyzed the resulting data utilizing the murine Microenvironment Cell Population (mMCP) method for in silico immune deconvolution. mMCP analysis estimates the abundance of tissue infiltrating immune and stromal populations based on cell-specific gene expression signatures. RESULTS There was a clear sex bias in survival. Female Fth1+/- mice had significantly poorer survival than control females (Fth1+/+). The Fth1 genetic status did not affect survival in males. The mMCP analysis revealed a significant reduction in T cells and CD8 + T cell infiltration in the tumors of females with Fth1+/- background as compared to the Fth1+/+. Mast and fibroblast cell infiltration was increased in females and males with Fth1+/- background, respectively, compared to Fth1+/+ mice. CONCLUSION Genetic manipulation of Fth1 which leads to reduced systemic levels of FTH1 protein had a sexually dimorphic impact on survival. Fth1 heterozygosity significantly worsened survival in females but did not affect survival in male GBMs. Furthermore, the genetic manipulation of Fth1 significantly affected tumor infiltration of T-cells, CD8 + T cells, fibroblasts, and mast cells in a sexually dimorphic manner. These results demonstrate a role for FTH1 and presumably iron status in establishing the tumor cellular landscape that ultimately impacts survival and further reveals a sex bias that may inform the population studies showing a sex effect on the prevalence of brain tumors.
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Affiliation(s)
| | - Vonn Walter
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Kondaiah Palsa
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
| | - Becky Slagle-Webb
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
| | - Elizabeth Neely
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
| | - Todd Schell
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA, USA
| | - James R Connor
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA.
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23
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Croft D, Lodhia P, Lourenco S, MacKay C. Effectively utilizing publicly available databases for cancer target evaluation. NAR Cancer 2023; 5:zcad035. [PMID: 37457379 PMCID: PMC10346432 DOI: 10.1093/narcan/zcad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/12/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
The majority of compounds designed against cancer drug targets do not progress to become approved drugs, mainly due to lack of efficacy and/or unmanageable toxicity. Robust target evaluation is therefore required before progressing through the drug discovery process to reduce the high attrition rate. There are a wealth of publicly available databases that can be mined to generate data as part of a target evaluation. It can, however, be challenging to learn what databases are available, how and when they should be used, and to understand the associated limitations. Here, we have compiled and present key, freely accessible and easy-to-use databases that house informative datasets from in vitro, in vivo and clinical studies. We also highlight comprehensive target review databases that aim to bring together information from multiple sources into one-stop portals. In the post-genomics era, a key objective is to exploit the extensive cell, animal and patient characterization datasets in order to deliver precision medicine on a patient-specific basis. Effective utilization of the highlighted databases will go some way towards supporting the cancer research community achieve these aims.
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Affiliation(s)
- Daniel Croft
- Cancer Research Horizons, The Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Puja Lodhia
- Cancer Research Horizons, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sofia Lourenco
- Cancer Research Horizons, The Francis Crick Institute, London, NW1 1AT, UK
| | - Craig MacKay
- Cancer Research Horizons, The Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
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24
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Sun C, Qi Y, Fowlkes N, Lazic N, Su X, Lozano G, Wasylishen AR. The histone chaperone function of Daxx is dispensable for embryonic development. Cell Death Dis 2023; 14:565. [PMID: 37633949 PMCID: PMC10460429 DOI: 10.1038/s41419-023-06089-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 08/28/2023]
Abstract
Daxx functions as a histone chaperone for the histone H3 variant, H3.3, and is essential for embryonic development. Daxx interacts with Atrx to form a protein complex that deposits H3.3 into heterochromatic regions of the genome, including centromeres, telomeres, and repeat loci. To advance our understanding of histone chaperone activity in vivo, we developed two Daxx mutant alleles in the mouse germline, which abolish the interactions between Daxx and Atrx (DaxxY130A), and Daxx and H3.3 (DaxxS226A). We found that the interaction between Daxx and Atrx is dispensable for viability; mice are born at the expected Mendelian ratio and are fertile. The loss of Daxx-Atrx interaction, however, does cause dysregulated expression of endogenous retroviruses. In contrast, the interaction between Daxx and H3.3, while not required for embryonic development, is essential for postnatal viability. Transcriptome analysis of embryonic tissues demonstrates that this interaction is important for silencing endogenous retroviruses and for maintaining proper immune cell composition. Overall, these results clearly demonstrate that Daxx has both Atrx-dependent and independent functions in vivo, advancing our understanding of this epigenetic regulatory complex.
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Affiliation(s)
- Chang Sun
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Yuan Qi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Natalie Fowlkes
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Nina Lazic
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Guillermina Lozano
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
| | - Amanda R Wasylishen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, 45267, USA.
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25
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Liu L, Xie Y, Yang H, Lin A, Dong M, Wang H, Zhang C, Liu Z, Cheng Q, Zhang J, Yuan S, Luo P. HPVTIMER: A shiny web application for tumor immune estimation in human papillomavirus-associated cancers. IMETA 2023; 2:e130. [PMID: 38867938 PMCID: PMC10989930 DOI: 10.1002/imt2.130] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 06/14/2024]
Abstract
The tumor immune microenvironment (TIME) is closely associated with tumor formation, particularly linked to the human papillomavirus (HPV), and regulates tumor initiation, proliferation, infiltration, and metastasis. With the rise of immunotherapy, an increasing amount of sample data used for TIME exploration is available in databases. However, no currently available web tool enables a comprehensive exploration of the TIME of HPV-associated cancers by leveraging these data. We have developed a web tool called HPV-associated Tumor Immune MicroEnvironment ExploreR (HPVTIMER), which provides a comprehensive analysis platform that integrates over 10,000 genes and 2290 tumor samples from 65 transcriptome data sets across 8 cancer types sourced from the Gene Expression Omnibus (GEO) database. The tool features four built-in analysis modules, namely, the differential expression analysis module, correlation analysis module, immune infiltration analysis module, and pathway analysis module. These modules enable users to perform systematic and vertical analyses. We used several analytical modules in HPVTIMER to briefly explore the role of CDKN2A in head and neck squamous cell carcinomas. We expect that HPVTIMER will help users explore the immune microenvironment of HPV-associated cancers and uncover potential immune regulatory mechanisms and immunotherapeutic targets. HPVTIMER is available at http://www.hpvtimer.com/.
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Affiliation(s)
- Liying Liu
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
- The First Clinical Medical SchoolSouthern Medical UniversityGuangzhouGuangdongChina
| | - Yanan Xie
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
- The Second Clinical Medicine SchoolSouthern Medical UniversityGuangzhouGuangdongChina
| | - Hong Yang
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
| | - Anqi Lin
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
| | - Minjun Dong
- Department of Surgical OncologySir Run Run Shaw Hospital Affiliated to Zhejiang University, School of MedicineHang ZhouChina
| | - Haitao Wang
- Thoracic Surgery BranchCenter for Cancer Research, National Institutes of HealthBethesdaMarylandUSA
| | - Cangang Zhang
- Department of Pathogenic Microbiology and ImmunologyXi'an Jiaotong UniversityXi'anShaanxiChina
| | - Zaoqu Liu
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Quan Cheng
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityHunanChina
| | - Jian Zhang
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
| | - Shuofeng Yuan
- Department of Infectious Disease and MicrobiologyThe University of Hong Kong‐Shenzhen HospitalShenzhenChina
- State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologySchool of Clinical Medicine, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
| | - Peng Luo
- Department of OncologyZhujiang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
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26
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Yang J, Bergdorf K, Yan C, Luo W, Chen SC, Ayers GD, Liu Q, Liu X, Boothby M, Weiss VL, Groves SM, Oleskie AN, Zhang X, Maeda DY, Zebala JA, Quaranta V, Richmond A. CXCR2 expression during melanoma tumorigenesis controls transcriptional programs that facilitate tumor growth. Mol Cancer 2023; 22:92. [PMID: 37270599 PMCID: PMC10239119 DOI: 10.1186/s12943-023-01789-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/16/2023] [Indexed: 06/05/2023] Open
Abstract
BACKGROUND Though the CXCR2 chemokine receptor is known to play a key role in cancer growth and response to therapy, a direct link between expression of CXCR2 in tumor progenitor cells during induction of tumorigenesis has not been established. METHODS To characterize the role of CXCR2 during melanoma tumorigenesis, we generated tamoxifen-inducible tyrosinase-promoter driven BrafV600E/Pten-/-/Cxcr2-/- and NRasQ61R/INK4a-/-/Cxcr2-/- melanoma models. In addition, the effects of a CXCR1/CXCR2 antagonist, SX-682, on melanoma tumorigenesis were evaluated in BrafV600E/Pten-/- and NRasQ61R/INK4a-/- mice and in melanoma cell lines. Potential mechanisms by which Cxcr2 affects melanoma tumorigenesis in these murine models were explored using RNAseq, mMCP-counter, ChIPseq, and qRT-PCR; flow cytometry, and reverse phosphoprotein analysis (RPPA). RESULTS Genetic loss of Cxcr2 or pharmacological inhibition of CXCR1/CXCR2 during melanoma tumor induction resulted in key changes in gene expression that reduced tumor incidence/growth and increased anti-tumor immunity. Interestingly, after Cxcr2 ablation, Tfcp2l1, a key tumor suppressive transcription factor, was the only gene significantly induced with a log2 fold-change greater than 2 in these three different melanoma models. CONCLUSIONS Here, we provide novel mechanistic insight revealing how loss of Cxcr2 expression/activity in melanoma tumor progenitor cells results in reduced tumor burden and creation of an anti-tumor immune microenvironment. This mechanism entails an increase in expression of the tumor suppressive transcription factor, Tfcp2l1, along with alteration in the expression of genes involved in growth regulation, tumor suppression, stemness, differentiation, and immune modulation. These gene expression changes are coincident with reduction in the activation of key growth regulatory pathways, including AKT and mTOR.
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Affiliation(s)
- J Yang
- TVHS Department of Veterans Affairs, Nashville, TN, 37212, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
| | - K Bergdorf
- TVHS Department of Veterans Affairs, Nashville, TN, 37212, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
| | - C Yan
- TVHS Department of Veterans Affairs, Nashville, TN, 37212, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
| | - W Luo
- TVHS Department of Veterans Affairs, Nashville, TN, 37212, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
| | - S C Chen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203-1742, USA
| | - G D Ayers
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203-1742, USA
| | - Q Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203-1742, USA
| | - X Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203-1742, USA
| | - M Boothby
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - V L Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - S M Groves
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - A N Oleskie
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
| | - X Zhang
- Department of Genomic Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, 77030, USA
| | - D Y Maeda
- Syntrix Pharmaceuticals, Auburn, WA, 98001, USA
| | - J A Zebala
- Syntrix Pharmaceuticals, Auburn, WA, 98001, USA
| | - V Quaranta
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
- Department of Biochemistry, Vanderbilt University, TN, 37240, Nashville, USA
| | - A Richmond
- TVHS Department of Veterans Affairs, Nashville, TN, 37212, USA.
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA.
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27
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Ferrena A, Wang J, Zhang R, Karadal-Ferrena B, Al-Hardan W, Singh S, Borjihan H, Schwartz E, Zhao H, Yang R, Geller D, Hoang B, Zheng D. SKP2 knockout in Rb1/p53 deficient mouse models of osteosarcoma induces immune infiltration and drives a transcriptional program with a favorable prognosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540053. [PMID: 37214958 PMCID: PMC10197654 DOI: 10.1101/2023.05.09.540053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Purpose Osteosarcoma (OS) is an aggressive bone malignancy with a poor prognosis. One putative proto-oncogene in OS is SKP2, encoding a substrate recognition factor of the SCF E3 ubiquitin ligase. We previously demonstrated that SKP2 knockout in murine OS improved survival and delayed tumorigenesis. Here we aim to define the SKP2 drives transcriptional program and its clinical implication in OS. Experimental Design We performed RNA-sequencing (RNA-seq) on tumors from a transgenic OS mouse model with conditional Trp53 and Rb1 knockouts in the osteoblast lineage ("DKO": Osx1-Cre;Rb1lox/lox;p53lox/lox) and a triple-knockout model with additional Skp2 germline knockout ("TKO": Osx1-Cre;Rb1lox/lox;p53lox/lox;SKP2-/-). We validated our RNA-seq findings using qPCR and immunohistochemistry. To investigate the clinical implications of our results, we analyzed a human OS patient cohort ("NCI-TARGET OS") with RNA-seq and clinical data. Results We found large differences in gene expression after SKP2 knockout. Strikingly, we observed increased expression of genes related to immune microenvironment infiltration in TKO tumors. We observed significant increases in signature genes for macrophages and to a lesser extent, T cells, B cells and vascular cells. We also uncovered a set of relevant transcription factors that may mediate the changes. In OS patient cohorts, high expression of genes upregulated in TKO was correlated with favorable overall survival, which was largely explained by the macrophage gene signatures. This relationship was further supported by our finding that SKP2 expression was negatively correlated with macrophage infiltration in the NCI-TARGET OS and the TCGA Sarcoma cohort. Conclusion Our findings indicate that SKP2 may mediate immune exclusion from the OS tumor microenvironment, suggesting that SKP2 modulation in OS may induce anti-tumor immune activation.
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Affiliation(s)
- Alexander Ferrena
- Institute for Clinical and Translational Research, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jichuan Wang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ranxin Zhang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Waleed Al-Hardan
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Swapnil Singh
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hasibagan Borjihan
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Edward Schwartz
- Department of Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hongling Zhao
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rui Yang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - David Geller
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bang Hoang
- Department of Orthopedic Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
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28
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Pasupuleti SK, Chao K, Ramdas B, Kanumuri R, Palam LR, Liu S, Wan J, Annesley C, Loh ML, Stieglitz E, Burke MJ, Kapur R. Potential clinical use of azacitidine and MEK inhibitor combination therapy in PTPN11-mutated juvenile myelomonocytic leukemia. Mol Ther 2023; 31:986-1001. [PMID: 36739480 PMCID: PMC10124140 DOI: 10.1016/j.ymthe.2023.01.030] [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: 09/13/2022] [Revised: 01/17/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a rare myeloproliferative neoplasm of childhood. The molecular hallmark of JMML is hyperactivation of the Ras/MAPK pathway with the most common cause being mutations in the gene PTPN11, encoding the protein tyrosine phosphatase SHP2. Current strategies for treating JMML include using the hypomethylating agent, 5-azacitidine (5-Aza) or MEK inhibitors trametinib and PD0325901 (PD-901), but none of these are curative as monotherapy. Utilizing an Shp2E76K/+ murine model of JMML, we show that the combination of 5-Aza and PD-901 modulates several hematologic abnormalities often seen in JMML patients, in part by reducing the burden of leukemic hematopoietic stem and progenitor cells (HSC/Ps). The reduced JMML features in drug-treated mice were associated with a decrease in p-MEK and p-ERK levels in Shp2E76K/+ mice treated with the combination of 5-Aza and PD-901. RNA-sequencing analysis revealed a reduction in several RAS and MAPK signaling-related genes. Additionally, a decrease in the expression of genes associated with inflammation and myeloid leukemia was also observed in Shp2E76K/+ mice treated with the combination of the two drugs. Finally, we report two patients with JMML and PTPN11 mutations treated with 5-Aza, trametinib, and chemotherapy who experienced a clinical response because of the combination treatment.
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Affiliation(s)
- Santhosh Kumar Pasupuleti
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut Street, R4-168, Indianapolis, IN 46202, USA
| | - Karen Chao
- Department of Pediatrics, Children's Wisconsin, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Stanford University School of Medicine, Lucile Packard Children's Hospital, Palo Alto, CA, USA
| | - Baskar Ramdas
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut Street, R4-168, Indianapolis, IN 46202, USA
| | - Rahul Kanumuri
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut Street, R4-168, Indianapolis, IN 46202, USA
| | - Lakshmi Reddy Palam
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut Street, R4-168, Indianapolis, IN 46202, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | | | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Michael J Burke
- Department of Pediatrics, Children's Wisconsin, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Reuben Kapur
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut Street, R4-168, Indianapolis, IN 46202, USA; Department of Microbiology & Immunology, Indiana University School of Medicine, 1044 W. Walnut Street, R4-168, Indianapolis, IN 46202, USA.
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Yang J, Bergdorf K, Yan C, Luo W, Chen SC, Ayers D, Liu Q, Liu X, Boothby M, Groves SM, Oleskie AN, Zhang X, Maeda DY, Zebala JA, Quaranta V, Richmond A. CXCR2 expression during melanoma tumorigenesis controls transcriptional programs that facilitate tumor growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529548. [PMID: 36865260 PMCID: PMC9980137 DOI: 10.1101/2023.02.22.529548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Background Though the CXCR2 chemokine receptor is known to play a key role in cancer growth and response to therapy, a direct link between expression of CXCR2 in tumor progenitor cells during induction of tumorigenesis has not been established. Methods To characterize the role of CXCR2 during melanoma tumorigenesis, we generated tamoxifen-inducible tyrosinase-promoter driven Braf V600E /Pten -/- /Cxcr2 -/- and NRas Q61R /INK4a -/- /Cxcr2 -/- melanoma models. In addition, the effects of a CXCR1/CXCR2 antagonist, SX-682, on melanoma tumorigenesis were evaluated in Braf V600E /Pten -/- and NRas Q61R /INK4a -/- mice and in melanoma cell lines. Potential mechanisms by which Cxcr2 affects melanoma tumorigenesis in these murine models were explored using RNAseq, mMCP-counter, ChIPseq, and qRT-PCR; flow cytometry, and reverse phosphoprotein analysis (RPPA). Results Genetic loss of Cxcr2 or pharmacological inhibition of CXCR1/CXCR2 during melanoma tumor induction resulted in key changes in gene expression that reduced tumor incidence/growth and increased anti-tumor immunity. Interestingly, after Cxcr2 ablation, Tfcp2l1 , a key tumor suppressive transcription factor, was the only gene significantly induced with a log 2 fold-change greater than 2 in these three different melanoma models. Conclusions Here, we provide novel mechanistic insight revealing how loss of Cxcr2 expression/activity in melanoma tumor progenitor cells results in reduced tumor burden and creation of an anti-tumor immune microenvironment. This mechanism entails an increase in expression of the tumor suppressive transcription factor, Tfcp2l1, along with alteration in the expression of genes involved in growth regulation, tumor suppression, stemness, differentiation, and immune modulation. These gene expression changes are coincident with reduction in the activation of key growth regulatory pathways, including AKT and mTOR.
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30
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Sun D, Dai T, Ji Y, Shen W, Bian W. COL11A1-driven positive feedback loop modulates fibroblast transformation and activates pancreatic cancer progression. Cell Biol Int 2023; 47:1081-1091. [PMID: 36861686 DOI: 10.1002/cbin.12009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/04/2023] [Accepted: 01/25/2023] [Indexed: 03/03/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most common leading causes of cancer death. The cancer-associated fibroblasts (CAFs) in the tumor microenvironment (TME) aggravate the malignant behavior of PDAC. However, it is still unknown how PDAC induces normal fibroblasts (NFs) to CAFs. In present research, we found that PDAC-derived collagen type XI alpha 1 (COL11A1) promoted the conversion of NFs to CAF-like cells. It included morphological and corresponding molecular marker changes. Activation of the nuclear factor-κB (NF-κB) pathway was involved in this process. Corresponding, CAFs cells could secrete interleukin 6 (IL-6), which promoted the invasion and the epithelial-mesenchymal transition of PDAC cells. Furthermore, IL-6 promoted the expression of transcription factor Activating Transcription Factor 4 by activating the Mitogen-Activated Protein Kinase/extracellular-signal-regulated kinase pathway. The latter directly promotes the expression of COL11A1. This way, a feedback loop of mutual influence was constructed between PDAC and CAFs. Our research proposed a novel concept for PDAC-educated NFs. PDAC-COL11A1-fibroblast-IL-6-PDAC axis might contribute to the cascade between PDAC and TME.
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Affiliation(s)
- Defeng Sun
- Department of Hepatobiliary Surgery, Affiliated Wuxi 2 People's Hospital, Nanjing Medical University, Wuxi, Jiangsu, People's Republic of China.,Department of Hepatobiliary, Wuxi Clinical College, Nantong University, Wuxi, Jiangsu, People's Republic of China
| | - Tu Dai
- Department of Hepatobiliary Surgery, Affiliated Wuxi 2 People's Hospital, Nanjing Medical University, Wuxi, Jiangsu, People's Republic of China.,Department of Hepatobiliary, Wuxi Clinical College, Nantong University, Wuxi, Jiangsu, People's Republic of China
| | - Yuan Ji
- Department of Hepatobiliary Surgery, Affiliated Wuxi 2 People's Hospital, Nanjing Medical University, Wuxi, Jiangsu, People's Republic of China.,Department of Hepatobiliary, Wuxi Clinical College, Nantong University, Wuxi, Jiangsu, People's Republic of China
| | - Weibo Shen
- Department of Hepatobiliary Surgery, Affiliated Wuxi 2 People's Hospital, Nanjing Medical University, Wuxi, Jiangsu, People's Republic of China.,Department of Hepatobiliary, Wuxi Clinical College, Nantong University, Wuxi, Jiangsu, People's Republic of China
| | - Wuyang Bian
- Department of Hepatobiliary Surgery, Affiliated Wuxi 2 People's Hospital, Nanjing Medical University, Wuxi, Jiangsu, People's Republic of China.,Department of Hepatobiliary, Wuxi Clinical College, Nantong University, Wuxi, Jiangsu, People's Republic of China
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31
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Amirkhah R, Gilroy K, Malla SB, Lannagan TRM, Byrne RM, Fisher NC, Corry SM, Mohamed NE, Naderi-Meshkin H, Mills ML, Campbell AD, Ridgway RA, Ahmaderaghi B, Murray R, Llergo AB, Sanz-Pamplona R, Villanueva A, Batlle E, Salazar R, Lawler M, Sansom OJ, Dunne PD. MmCMS: mouse models' consensus molecular subtypes of colorectal cancer. Br J Cancer 2023; 128:1333-1343. [PMID: 36717674 PMCID: PMC10050155 DOI: 10.1038/s41416-023-02157-6] [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: 06/03/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) primary tumours are molecularly classified into four consensus molecular subtypes (CMS1-4). Genetically engineered mouse models aim to faithfully mimic the complexity of human cancers and, when appropriately aligned, represent ideal pre-clinical systems to test new drug treatments. Despite its importance, dual-species classification has been limited by the lack of a reliable approach. Here we utilise, develop and test a set of options for human-to-mouse CMS classifications of CRC tissue. METHODS Using transcriptional data from established collections of CRC tumours, including human (TCGA cohort; n = 577) and mouse (n = 57 across n = 8 genotypes) tumours with combinations of random forest and nearest template prediction algorithms, alongside gene ontology collections, we comprehensively assess the performance of a suite of new dual-species classifiers. RESULTS We developed three approaches: MmCMS-A; a gene-level classifier, MmCMS-B; an ontology-level approach and MmCMS-C; a combined pathway system encompassing multiple biological and histological signalling cascades. Although all options could identify tumours associated with stromal-rich CMS4-like biology, MmCMS-A was unable to accurately classify the biology underpinning epithelial-like subtypes (CMS2/3) in mouse tumours. CONCLUSIONS When applying human-based transcriptional classifiers to mouse tumour data, a pathway-level classifier, rather than an individual gene-level system, is optimal. Our R package enables researchers to select suitable mouse models of human CRC subtype for their experimental testing.
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Affiliation(s)
- Raheleh Amirkhah
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | - Sudhir B Malla
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | - Ryan M Byrne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Natalie C Fisher
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Shania M Corry
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | - Hojjat Naderi-Meshkin
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | | | | | | | - Baharak Ahmaderaghi
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, UK
| | - Richard Murray
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Antoni Berenguer Llergo
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Alberto Villanueva
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ramon Salazar
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), CIBERONC and Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Mark Lawler
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Philip D Dunne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.
- Cancer Research UK Beatson Institute, Glasgow, UK.
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32
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Säisä-Borreill S, Davidson G, Kleiber T, Thevenot A, Martin E, Mondot S, Blottière H, Helleux A, Mengus G, Plateroti M, Duluc I, Davidson I, Freund JN. General transcription factor TAF4 antagonizes epigenetic silencing by Polycomb to maintain intestine stem cell functions. Cell Death Differ 2023; 30:839-853. [PMID: 36639541 PMCID: PMC9984434 DOI: 10.1038/s41418-022-01109-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023] Open
Abstract
Taf4 (TATA-box binding protein-associated factor 4) is a subunit of the general transcription factor TFIID, a component of the RNA polymerase II pre-initiation complex that interacts with tissue-specific transcription factors to regulate gene expression. Properly regulated gene expression is particularly important in the intestinal epithelium that is constantly renewed from stem cells. Tissue-specific inactivation of Taf4 in murine intestinal epithelium during embryogenesis compromised gut morphogenesis and the emergence of adult-type stem cells. In adults, Taf4 loss impacted the stem cell compartment and associated Paneth cells in the stem cell niche, epithelial turnover and differentiation of mature cells, thus exacerbating the response to inflammatory challenge. Taf4 inactivation ex vivo in enteroids prevented budding formation and maintenance and caused broad chromatin remodeling and a strong reduction in the numbers of stem and progenitor cells with a concomitant increase in an undifferentiated cell population that displayed high activity of the Ezh2 and Suz12 components of Polycomb Repressive Complex 2 (PRC2). Treatment of Taf4-mutant enteroids with a specific Ezh2 inhibitor restored buddings, cell proliferation and the stem/progenitor compartment. Taf4 loss also led to increased PRC2 activity in cells of adult crypts associated with modification of the immune/inflammatory microenvironment that potentiated Apc-driven tumorigenesis. Our results reveal a novel function of Taf4 in antagonizing PRC2-mediated repression of the stem cell gene expression program to assure normal development, homeostasis, and immune-microenvironment of the intestinal epithelium.
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Affiliation(s)
- Susanna Säisä-Borreill
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Thomas Kleiber
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
- Orphazyme, Ole Maaloes 3, 2200, Copenhagen, Denmark
| | - Andréa Thevenot
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Elisabeth Martin
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Stanislas Mondot
- University Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Hervé Blottière
- University Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Alexandra Helleux
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Gabrielle Mengus
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Michelina Plateroti
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Isabelle Duluc
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Jean-Noel Freund
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France.
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Stern E, Caruso S, Meiller C, Mishalian I, Hirsch TZ, Bayard Q, Tadmor CT, Wald H, Jean D, Wald O. Deep dive into the immune response against murine mesothelioma permits design of novel anti-mesothelioma therapeutics. Front Immunol 2023; 13:1026185. [PMID: 36685577 PMCID: PMC9846605 DOI: 10.3389/fimmu.2022.1026185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/31/2022] [Indexed: 01/06/2023] Open
Abstract
Given the need to improve the efficacy of standard-of-care immunotherapy (anti-CTLA-4 + anti-PD-1) in human malignant pleural mesothelioma (hMPM), we thoroughly characterized the immunobiology of the AB12 murine mesothelioma (MM) model, aiming to increase its accuracy in predicting the response of hMPM to immunotherapy and in designing novel anti-hMPM treatments. Specifically, we used immunologic, transcriptomic and survival analyses, to synchronize the MM tumor growth phases and immune evolution with the histo-molecular and immunological characteristics of hMPM while also determining the anti-MM efficacy of standard-of-care anti-hMPM immunotherapy as a benchmark that novel therapeutics should meet. We report that early-, intermediate- and advanced- AB12 tumors are characterized by a bell-shaped anti-tumor response that peaks in intermediate tumors and decays in advanced tumors. We further show that intermediate- and advanced- tumors match with immune active ("hot") and immune inactive ("cold") hMPM respectively, and that they respond to immunotherapy in a manner that corresponds well with its performance in real-life settings. Finally, we show that in advanced tumors, addition of cisplatin to anti CTLA-4 + anti PD-1 can extend mice survival and invigorate the decaying anti-tumor response. Therefore, we highlight this triple combination as a worthy candidate to improve clinical outcomes in hMPM.
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Affiliation(s)
- Esther Stern
- Gene Therapy Institute, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Stefano Caruso
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, Université Paris Cité, team Functional Genomics of Solid Tumors, Paris, France
| | - Clément Meiller
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, Université Paris Cité, team Functional Genomics of Solid Tumors, Paris, France
| | - Inbal Mishalian
- Gene Therapy Institute, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Theo Z. Hirsch
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, Université Paris Cité, team Functional Genomics of Solid Tumors, Paris, France
| | - Quentin Bayard
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, Université Paris Cité, team Functional Genomics of Solid Tumors, Paris, France
| | - Carmit T. Tadmor
- Gene Therapy Institute, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Tel Aviv University, Tel Aviv, Israel
| | - Hanna Wald
- Gene Therapy Institute, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Didier Jean
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, Université Paris Cité, team Functional Genomics of Solid Tumors, Paris, France
| | - Ori Wald
- Gene Therapy Institute, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Cardiothoracic Surgery, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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Gu Y, Lin X, Dong Y, Wood G, Seidah NG, Werstuck G, Major P, Bonert M, Kapoor A, Tang D. PCSK9 facilitates melanoma pathogenesis via a network regulating tumor immunity. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2023; 42:2. [PMID: 36588164 PMCID: PMC9806914 DOI: 10.1186/s13046-022-02584-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/26/2022] [Indexed: 01/03/2023]
Abstract
BACKGROUND PCSK9 regulates cholesterol homeostasis and promotes tumorigenesis. However, the relevance of these two actions and the mechanisms underlying PCSK9's oncogenic roles in melanoma and other cancers remain unclear. METHODS PCSK9's association with melanoma was analysed using the TCGA dataset. Empty vector (EV), PCSK9, gain-of-function (D374Y), and loss-of-function (Q152H) PCSK9 mutant were stably-expressed in murine melanoma B16 cells and studied for impact on B16 cell-derived oncogenesis in vitro and in vivo using syngeneic C57BL/6 and Pcsk9-/- mice. Intratumoral accumulation of cholesterol was determined. RNA-seq was performed on individual tumor types. Differentially-expressed genes (DEGs) were derived from the comparisons of B16 PCSK9, B16 D374Y, or B16 Q152H tumors to B16 EV allografts and analysed for pathway alterations. RESULTS PCSK9 expression and its network negatively correlated with the survival probability of patients with melanoma. PCSK9 promoted B16 cell proliferation, migration, and growth in soft agar in vitro, formation of tumors in C57BL/6 mice in vivo, and accumulation of intratumoral cholesterol in a manner reflecting its regulation of the low-density lipoprotein receptor (LDLR): Q152H, EV, PCSK9, and D374Y. Tumor-associated T cells, CD8 + T cells, and NK cells were significantly increased in D374Y tumors along with upregulations of multiple immune checkpoints, IFNγ, and 143 genes associated with T cell dysfunction. Overlap of 36 genes between the D374Y DEGs and the PCSK9 DEGs predicted poor prognosis of melanoma and resistance to immune checkpoint blockade (ICB) therapy. CYTH4, DENND1C, AOAH, TBC1D10C, EPSTI1, GIMAP7, and FASL (FAS ligand) were novel predictors of ICB therapy and displayed high level of correlations with multiple immune checkpoints in melanoma and across 30 human cancers. We observed FAS ligand being among the most robust biomarkers of ICB treatment and constructed two novel and effective multigene panels predicting response to ICB therapy. The profiles of allografts produced by B16 EV, PCSK9, D374Y, and Q152H remained comparable in C57BL/6 and Pcsk9-/- mice. CONCLUSIONS Tumor-derived PCSK9 plays a critical role in melanoma pathogenesis. PCSK9's oncogenic actions are associated with intratumoral cholesterol accumulation. PCSK9 systemically affects the immune system, contributing to melanoma immune evasion. Novel biomarkers derived from the PCSK9-network effectively predicted ICB therapy responses.
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Affiliation(s)
- Yan Gu
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
| | - Xiaozeng Lin
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
| | - Ying Dong
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
| | - Geoffrey Wood
- grid.34429.380000 0004 1936 8198Department of Pathology, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Nabil G. Seidah
- grid.511547.30000 0001 2106 1695Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute, University of Montreal, Montreal, QC H2W 1R7 Canada
| | - Geoff Werstuck
- grid.25073.330000 0004 1936 8227Department of Medicine, McMaster University, Hamilton, ON L8S 4K1 Canada
| | - Pierre Major
- grid.25073.330000 0004 1936 8227Department of Oncology, McMaster University, Hamilton, ON L8S 4K1 Canada
| | - Michael Bonert
- grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4K1 Canada
| | - Anil Kapoor
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
| | - Damu Tang
- grid.416721.70000 0001 0742 7355Urological Cancer Center for Research and Innovation (UCCRI), T3310, St. Joseph’s Hospital, 50 Charlton Ave East, Hamilton, ON L8N 4A6 Canada ,grid.25073.330000 0004 1936 8227Department of Surgery, McMaster University, Hamilton, ON L8S 4K1 Canada ,grid.416721.70000 0001 0742 7355The Research Institute of St Joe’s Hamilton, G344, St. Joseph’s Hospital, Hamilton, ON L8N 4A6 Canada
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35
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Yan Q, Zheng W, Jiang Y, Zhou P, Lai Y, Liu C, Wu P, Zhuang H, Huang H, Li G, Zhan S, Lao Z, Liu X. Transcriptomic reveals the ferroptosis features of host response in a mouse model of Zika virus infection. J Med Virol 2023; 95:e28386. [PMID: 36477858 DOI: 10.1002/jmv.28386] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
Zika virus (ZIKV) is a neurotropic flavivirus. The outbreak of ZIKV in 2016 created a global health emergency. However, the underlying pathogenic mechanisms remain elusive. We investigated the host response features of in vivo replication in a mouse model of ZIKV infection, by performing a series of transcriptomic and bioinformatic analyses of ZIKV and mock-infected brain tissue. Tissue damage, inflammatory cells infiltration and high viral replication were observed in the brain tissue of ZIKV infected mice. RNA-Seq of the brain indicated the activation of ferroptosis pathways. Enrichment analysis of ferroptosis regulators revealed their involvement in pathways such as mineral absorption, fatty acid biosynthesis, fatty acid degradation, PPAR signaling pathway, peroxidase, and adipokinesine signalling pathway. We then identified 12 interacted hub ferroptosis regulators (CYBB, HMOX1, CP, SAT1, TF, SLC39A14, FTL, LPCAT3, FTH1, SLC3A2, TP53, and SLC40A1) that were related to the differential expression of CD8+ T cells, microglia and monocytes. CYBB, HMOX1, SALT, and SLAC40A1 were selected as potential biomarkers of ZIKV infection. Finally, we validated our results using RT-qPCR and outside available datasets. For the first time, we proposed a possible mechanism of ferroptosis in brain tissue infected by ZIKV in mice and identified the four key ferroptosis regulators.
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Affiliation(s)
- Qian Yan
- Department of Internal Medicine of Traditional Chinese Medicine (TCM), The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Pulmonary and Critical Care Medicine (PCCM), The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.,Animal Biosafety Level 2 laboratory (ABSL-2), Animal Laboratory Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wenjiang Zheng
- Department of Internal Medicine of Traditional Chinese Medicine (TCM), The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Pulmonary and Critical Care Medicine (PCCM), The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.,Animal Biosafety Level 2 laboratory (ABSL-2), Animal Laboratory Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yong Jiang
- Traditional Chinese Medicine Innovation Research Center and Department of Respiratory Medicine, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| | - Peiwen Zhou
- Animal Biosafety Level 3 laboratory (ABSL-3), Foshan Institute of Medical Microbiology, Foshan, China
| | - Yanni Lai
- Department of Diagnostics of Traditional Chinese Medicine (TCM), Basic Medical Sciences School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chengxin Liu
- Department of Internal Medicine of Traditional Chinese Medicine (TCM), The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peng Wu
- Department of Internal Medicine of Traditional Chinese Medicine (TCM), The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hongfa Zhuang
- Department of Pulmonary and Critical Care Medicine (PCCM), The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huiting Huang
- Department of Pulmonary and Critical Care Medicine (PCCM), The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Geng Li
- Animal Biosafety Level 2 laboratory (ABSL-2), Animal Laboratory Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shaofeng Zhan
- Department of Internal Medicine of Traditional Chinese Medicine (TCM), The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Pulmonary and Critical Care Medicine (PCCM), The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zizhao Lao
- Animal Biosafety Level 2 laboratory (ABSL-2), Animal Laboratory Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Traditional Chinese Medicine Innovation Research Center and Department of Respiratory Medicine, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| | - Xiaohong Liu
- Department of Internal Medicine of Traditional Chinese Medicine (TCM), The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Pulmonary and Critical Care Medicine (PCCM), The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
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36
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Zeng Z, Gu SS, Ouardaoui N, Tymm C, Yang L, Wong CJ, Li D, Zhang W, Wang X, Weirather JL, Rodig SJ, Hodi FS, Brown M, Liu XS. Hippo Signaling Pathway Regulates Cancer Cell-Intrinsic MHC-II Expression. Cancer Immunol Res 2022; 10:1559-1569. [PMID: 36219700 DOI: 10.1158/2326-6066.cir-22-0227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 07/02/2022] [Accepted: 10/06/2022] [Indexed: 01/10/2023]
Abstract
MHC-II is known to be mainly expressed on the surface of antigen-presenting cells. Evidence suggests MHC-II is also expressed by cancer cells and may be associated with better immunotherapy responses. However, the role and regulation of MHC-II in cancer cells remain unclear. In this study, we leveraged data mining and experimental validation to elucidate the regulation of MHC-II in cancer cells and its role in modulating the response to immunotherapy. We collated an extensive collection of omics data to examine cancer cell-intrinsic MHC-II expression and its association with immunotherapy outcomes. We then tested the functional relevance of cancer cell-intrinsic MHC-II expression using a syngeneic transplantation model. Finally, we performed data mining to identify pathways potentially involved in the regulation of MHC-II expression, and experimentally validated candidate regulators. Analyses of preimmunotherapy clinical samples in the CheckMate 064 trial revealed that cancer cell-intrinsic MHC-II protein was positively correlated with more favorable immunotherapy outcomes. Comprehensive meta-analyses of multiomics data from an exhaustive collection of data revealed that MHC-II is heterogeneously expressed in various solid tumors, and its expression is particularly high in melanoma. Using a syngeneic transplantation model, we further established that melanoma cells with high MHC-II responded better to anti-PD-1 treatment. Data mining followed by experimental validation revealed the Hippo signaling pathway as a potential regulator of melanoma MHC-II expression. In summary, we identified the Hippo signaling pathway as a novel regulator of cancer cell-intrinsic MHC-II expression. These findings suggest modulation of MHC-II in melanoma could potentially improve immunotherapy response.
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Affiliation(s)
- Zexian Zeng
- Department of Data Science, Dana Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Shengqing Stan Gu
- Department of Data Science, Dana Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nofal Ouardaoui
- Department of Data Science, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Carly Tymm
- Department of Data Science, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Lin Yang
- Department of Data Science, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Cheryl J Wong
- Department of Data Science, Dana Farber Cancer Institute, Boston, Massachusetts
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Dian Li
- Department of Data Science, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Wubing Zhang
- Department of Data Science, Dana Farber Cancer Institute, Boston, Massachusetts
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Xiaoqing Wang
- Department of Data Science, Dana Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jason L Weirather
- Department of Data Science, Dana Farber Cancer Institute, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Scott J Rodig
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - X Shirley Liu
- Department of Data Science, Dana Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
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37
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Li Y, Peng G, Qin C, Wang X, Li Y, Li Y. Positive regulators of T cell proliferation as biomarkers for predicting prognosis and characterizing the immune landscape in lung adenocarcinoma. Front Genet 2022; 13:1003754. [PMID: 36506303 PMCID: PMC9732442 DOI: 10.3389/fgene.2022.1003754] [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: 07/26/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the one of the most prevalent and fatal form of malignant tumors worldwide. Recently, immunotherapy is widely used in the treatment of patients with LUAD and has proved to be clinically effective in improve the prognosis of patients. But there still has been a tremendous thrust to further improve the efficacy of immunotherapy in individual patients with LUAD. The suppression of T cells and their effector functions in the tumor microenvironment (TME) of LUAD is one of the primary reasons for the low efficacy of immunotherapy in some patients with LUAD. Therefore, identifying positive regulators of T cell proliferation (TPRs) may offer novel avenues for LUAD immunotherapy. In this study, we comprehensively evaluated the infiltration patterns of TPRs in 1,066 patients with LUAD using unsupervised consensus clustering and identified correlations with genomic and clinicopathological characteristics. Three infiltrating TPR clusters were defined, and a TPR-related risk signature composed of nine TPRs was constructed using least absolute shrinkage and selection operator-Cox regression algorithms to classify the individual TPR infiltration patterns. Cluster 1 exhibited high levels of T cell infiltration and activation of immune-related signaling pathways, whereas cluster 2 was characterized by robust T cell immune infiltration and enrichment of pathways associated with carcinogenic gene sets and tumor immunity. Cluster 3 was characterized as an immune-desert phenotype. Moreover, the TPR signature was confirmed as an independent prognostic biomarker for drug sensitivity in patients with LUAD. In conclusion, the TPR signature may serve as a novel tool for effectively characterizing immune characteristics and evaluating the prognosis of patients with LUAD.
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Affiliation(s)
- Yang Li
- Department of Laboratory Medicine, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Gang Peng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chaoying Qin
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiangyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yue Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yueran Li
- Department of Laboratory Medicine, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Gynecology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Yueran Li,
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Wilmouth JJ, Olabe J, Garcia-Garcia D, Lucas C, Guiton R, Roucher-Boulez F, Dufour D, Damon-Soubeyrand C, Sahut-Barnola I, Pointud JC, Renaud Y, Levasseur A, Tauveron I, Lefrançois-Martinez AM, Martinez A, Val P. Sexually dimorphic activation of innate antitumor immunity prevents adrenocortical carcinoma development. SCIENCE ADVANCES 2022; 8:eadd0422. [PMID: 36240276 PMCID: PMC9565812 DOI: 10.1126/sciadv.add0422] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/25/2022] [Indexed: 05/31/2023]
Abstract
Unlike most cancers, adrenocortical carcinomas (ACCs) are more frequent in women than in men, but the underlying mechanisms of this sexual dimorphism remain elusive. Here, we show that inactivation of Znrf3 in the mouse adrenal cortex, recapitulating the most frequent alteration in ACC patients, is associated with sexually dimorphic tumor progression. Although female knockouts develop metastatic carcinomas at 18 months, adrenal hyperplasia regresses in male knockouts. This male-specific phenotype is associated with androgen-dependent induction of senescence, recruitment, and differentiation of highly phagocytic macrophages that clear out senescent cells. In contrast, in females, macrophage recruitment is delayed and dampened, which allows for aggressive tumor progression. Consistently, analysis of TCGA-ACC data shows that phagocytic macrophages are more prominent in men and are associated with better prognosis. Together, these data show that phagocytic macrophages are key players in the sexual dimorphism of ACC that could be previously unidentified allies in the fight against this devastating cancer.
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Affiliation(s)
- James J. Wilmouth
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Julie Olabe
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Diana Garcia-Garcia
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Cécily Lucas
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Rachel Guiton
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Florence Roucher-Boulez
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
- Laboratoire de Biochimie et Biologie Moléculaire, UM Pathologies Endocriniennes, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Université Claude Bernard Lyon 1, Lyon, France
| | - Damien Dufour
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Christelle Damon-Soubeyrand
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Isabelle Sahut-Barnola
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Jean-Christophe Pointud
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Yoan Renaud
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Adrien Levasseur
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Igor Tauveron
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
- Endocrinologie Diabétologie CHU Clermont Ferrand, 58 rue Montalembert, F63000 Clermont-Ferrand, France
| | - Anne-Marie Lefrançois-Martinez
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Antoine Martinez
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Pierre Val
- Institut GReD (Genetics, Reproduction and Development), CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
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Mao Y, Xu J, Xu X, Qiu J, Hu Z, Jiang F, Zhou G. Comprehensive analysis for cellular senescence-related immunogenic characteristics and immunotherapy prediction of acute myeloid leukemia. Front Pharmacol 2022; 13:987398. [PMID: 36225590 PMCID: PMC9548549 DOI: 10.3389/fphar.2022.987398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/23/2022] [Indexed: 01/10/2023] Open
Abstract
In malignancies, cellular senescence is critical for carcinogenesis, development, and immunological regulation. Patients with acute myeloid leukemia (AML) have not investigated a reliable cellular senescence-associated profile and its significance in outcomes and therapeutic response. Cellular senescence-related genes were acquired from the CellAge database, while AML data were obtained from the GEO and TCGA databases. The TCGA-AML group served as a training set to construct a prognostic risk score signature, while the GSE71014 set was used as a testing set to validate the accuracy of the signature. Through exploring the expression profiles of cellular senescence-related genes (SRGs) in AML patients, we used Lasso and Cox regression analysis to establish the SRG-based signature (SRGS), which was validated as an independent prognostic predictor for AML patients via clinical correlation. Survival analysis showed that AML patients in the low-risk score group had a longer survival time. Tumor immune infiltration and functional enrichment analysis demonstrated that AML patients with low-risk scores had higher immune infiltration and active immune-related pathways. Meanwhile, drug sensitivity analysis and the TIDE algorithm showed that the low-risk score group was more susceptible to chemotherapy and immunotherapy. Cell line analysis in vitro further confirmed that the SRGs in the proposed signature played roles in the susceptibility to cytarabine and YM155. Our results indicated that SRGS, which regulates the immunological microenvironment, is a reliable predictor of the clinical outcome and immunotherapeutic response in AML.
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Affiliation(s)
- Yan Mao
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinwen Xu
- Department of Pediatric Nephrology, Wuxi Children’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Xuejiao Xu
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiayun Qiu
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhengyun Hu
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Pediatrics, Shanghai Songjiang District Central Hospital, Shanghai, China
| | - Feng Jiang
- Department of Neonatology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- *Correspondence: Guoping Zhou, ; Feng Jiang,
| | - Guoping Zhou
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Guoping Zhou, ; Feng Jiang,
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Dietrich A, Sturm G, Merotto L, Marini F, Finotello F, List M. SimBu: bias-aware simulation of bulk RNA-seq data with variable cell-type composition. Bioinformatics 2022; 38:ii141-ii147. [PMID: 36124800 DOI: 10.1093/bioinformatics/btac499] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION As complex tissues are typically composed of various cell types, deconvolution tools have been developed to computationally infer their cellular composition from bulk RNA sequencing (RNA-seq) data. To comprehensively assess deconvolution performance, gold-standard datasets are indispensable. Gold-standard, experimental techniques like flow cytometry or immunohistochemistry are resource-intensive and cannot be systematically applied to the numerous cell types and tissues profiled with high-throughput transcriptomics. The simulation of 'pseudo-bulk' data, generated by aggregating single-cell RNA-seq expression profiles in pre-defined proportions, offers a scalable and cost-effective alternative. This makes it feasible to create in silico gold standards that allow fine-grained control of cell-type fractions not conceivable in an experimental setup. However, at present, no simulation software for generating pseudo-bulk RNA-seq data exists. RESULTS We developed SimBu, an R package capable of simulating pseudo-bulk samples based on various simulation scenarios, designed to test specific features of deconvolution methods. A unique feature of SimBu is the modeling of cell-type-specific mRNA bias using experimentally derived or data-driven scaling factors. Here, we show that SimBu can generate realistic pseudo-bulk data, recapitulating the biological and statistical features of real RNA-seq data. Finally, we illustrate the impact of mRNA bias on the evaluation of deconvolution tools and provide recommendations for the selection of suitable methods for estimating mRNA content. SimBu is a user-friendly and flexible tool for simulating realistic pseudo-bulk RNA-seq datasets serving as in silico gold-standard for assessing cell-type deconvolution methods. AVAILABILITY AND IMPLEMENTATION SimBu is freely available at https://github.com/omnideconv/SimBu as an R package under the GPL-3 license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alexander Dietrich
- Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lorenzo Merotto
- Institute of Molecular Biology, University of Innsbruck, 6020 Innsbruck, Austria.,Digital Science Center (DiSC), University of Innsbruck, 6020 Innsbruck, Austria
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany.,Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Francesca Finotello
- Institute of Molecular Biology, University of Innsbruck, 6020 Innsbruck, Austria.,Digital Science Center (DiSC), University of Innsbruck, 6020 Innsbruck, Austria
| | - Markus List
- Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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Cheng S, Liu Y, Jing Y, Jiang B, Wang D, Chu X, Jia L, Xin S. Identification of key monocytes/macrophages related gene set of the early-stage abdominal aortic aneurysm by integrated bioinformatics analysis and experimental validation. Front Cardiovasc Med 2022; 9:950961. [PMID: 36186997 PMCID: PMC9515382 DOI: 10.3389/fcvm.2022.950961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022] Open
Abstract
Objective Abdominal aortic aneurysm (AAA) is a lethal peripheral vascular disease. Inflammatory immune cell infiltration is a central part of the pathogenesis of AAA. It’s critical to investigate the molecular mechanisms underlying immune infiltration in early-stage AAA and look for a viable AAA marker. Methods In this study, we download several mRNA expression datasets and scRNA-seq datasets of the early-stage AAA models from the NCBI-GEO database. mMCP-counter and CIBERSORT were used to assess immune infiltration in early-stage experimental AAA. The scRNA-seq datasets were then utilized to analyze AAA-related gene modules of monocytes/macrophages infiltrated into the early-stage AAA by Weighted Correlation Network analysis (WGCNA). After that, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis for the module genes was performed by ClusterProfiler. The STRING database was used to create the protein-protein interaction (PPI) network. The Differentially Expressed Genes (DEGs) of the monocytes/macrophages were explored by Limma-Voom and the key gene set were identified. Then We further examined the expression of key genes in the human AAA dataset and built a logistic diagnostic model for distinguishing AAA patients and healthy people. Finally, real-time quantitative polymerase chain reaction (RT-qPCR) and Enzyme Linked Immunosorbent Assay (ELISA) were performed to validate the gene expression and serum protein level between the AAA and healthy donor samples in our cohort. Results Monocytes/macrophages were identified as the major immune cells infiltrating the early-stage experimental AAA. After pseudocell construction of monocytes/macrophages from scRNA-seq datasets and WGCNA analysis, four gene modules from two datasets were identified positively related to AAA, mainly enriched in Myeloid Leukocyte Migration, Collagen-Containing Extracellular matrix, and PI3K-Akt signaling pathway by functional enrichment analysis. Thbs1, Clec4e, and Il1b were identified as key genes among the hub genes in the modules, and the high expression of Clec4e, Il1b, and Thbs1 was confirmed in the other datasets. Then, in human AAA transcriptome datasets, the high expression of CLEC4E, IL1B was confirmed and a logistic regression model based on the two gene expressions was built, with an AUC of 0.9 in the train set and 0.79 in the validated set. Additionally, in our cohort, we confirmed the increased serum protein levels of IL-1β and CLEC4E in AAA patients as well as the increased expression of these two genes in AAA aorta samples. Conclusion This study identified monocytes/macrophages as the main immune cells infiltrated into the early-stage AAA and constructed a logistic regression model based on monocytes/macrophages related gene set. This study could aid in the early diagnostic of AAA.
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Affiliation(s)
- Shuai Cheng
- Department of Vascular and Thyroid Surgery, The First Hospital, China Medical University, Shenyang, China
- Key Laboratory of Pathogenesis, Prevention, and Therapeutics of Aortic Aneurysm in Liaoning Province, Shenyang, China
- Regenerative Medicine Research Center of China Medical University, Shenyang, China
| | - Yuanlin Liu
- Department of Vascular and Thyroid Surgery, The First Hospital, China Medical University, Shenyang, China
- Key Laboratory of Pathogenesis, Prevention, and Therapeutics of Aortic Aneurysm in Liaoning Province, Shenyang, China
- Regenerative Medicine Research Center of China Medical University, Shenyang, China
| | - Yuchen Jing
- Department of Vascular and Thyroid Surgery, The First Hospital, China Medical University, Shenyang, China
- Key Laboratory of Pathogenesis, Prevention, and Therapeutics of Aortic Aneurysm in Liaoning Province, Shenyang, China
- Regenerative Medicine Research Center of China Medical University, Shenyang, China
| | - Bo Jiang
- Department of Vascular and Thyroid Surgery, The First Hospital, China Medical University, Shenyang, China
- Key Laboratory of Pathogenesis, Prevention, and Therapeutics of Aortic Aneurysm in Liaoning Province, Shenyang, China
- Regenerative Medicine Research Center of China Medical University, Shenyang, China
| | - Ding Wang
- Department of Vascular and Thyroid Surgery, The First Hospital, China Medical University, Shenyang, China
- Key Laboratory of Pathogenesis, Prevention, and Therapeutics of Aortic Aneurysm in Liaoning Province, Shenyang, China
- Regenerative Medicine Research Center of China Medical University, Shenyang, China
| | - Xiangyu Chu
- Department of Vascular and Thyroid Surgery, The First Hospital, China Medical University, Shenyang, China
- Key Laboratory of Pathogenesis, Prevention, and Therapeutics of Aortic Aneurysm in Liaoning Province, Shenyang, China
- Regenerative Medicine Research Center of China Medical University, Shenyang, China
| | - Longyuan Jia
- Department of Vascular and Thyroid Surgery, The First Hospital, China Medical University, Shenyang, China
- Key Laboratory of Pathogenesis, Prevention, and Therapeutics of Aortic Aneurysm in Liaoning Province, Shenyang, China
- Regenerative Medicine Research Center of China Medical University, Shenyang, China
| | - Shijie Xin
- Department of Vascular and Thyroid Surgery, The First Hospital, China Medical University, Shenyang, China
- Key Laboratory of Pathogenesis, Prevention, and Therapeutics of Aortic Aneurysm in Liaoning Province, Shenyang, China
- Regenerative Medicine Research Center of China Medical University, Shenyang, China
- *Correspondence: Shijie Xin,
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Yu J, Wu X, Song J, Zhao Y, Li H, Luo M, Liu X. Loss of MHC-I antigen presentation correlated with immune checkpoint blockade tolerance in MAPK inhibitor-resistant melanoma. Front Pharmacol 2022; 13:928226. [PMID: 36091815 PMCID: PMC9459091 DOI: 10.3389/fphar.2022.928226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/27/2022] [Indexed: 11/20/2022] Open
Abstract
Immune checkpoint blockade and MAPK-targeted combined therapy is a promising regimen for advanced melanoma patients. However, the clinical benefit from this combo regimen remains limited, especially in patients who acquired resistance to MAPK-targeted therapy. Here, we systematically characterized the immune landscape during MAPK-targeted therapy in patients and mouse melanoma models. We observed that both the abundance of tumor-infiltrated T cells and the expression of immune-related genes were upregulated in the drug-responsive period, but downregulated in the resistance period, implying that acquired drug resistance dampens the antitumor immune response. Further transcriptomic dissection indicated that loss of MHC-I antigen presentation on tumor cells plays a critical role in the reduction of T cell infiltration during drug resistance. Survival analysis demonstrates that loss of antigen presentation and reduction of T-cell infiltration during acquired drug resistance are associated with poorer clinical response and prognosis of anti-PD-1 therapy in melanoma patients. In addition, we identified that alterations in the MAPK inhibitor resistance-related oncogenic signaling pathway closely correlated with deficiency of MHC-I antigen presentation, including activation of the PI3K-mTOR, MAPK, and Wnt pathways. In conclusion, our research illuminates that decreased infiltration of T cells is associated with acquired drug resistance during MAPK-targeted therapy, which may underlie the cross-resistance to immune checkpoint blockade.
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Affiliation(s)
- Jing Yu
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Xi Wu
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Jinen Song
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Yujie Zhao
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Huifang Li
- Research Core Facility, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Min Luo
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
- *Correspondence: Xiaowei Liu, ; Min Luo,
| | - Xiaowei Liu
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
- *Correspondence: Xiaowei Liu, ; Min Luo,
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43
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Yang X, Li Q. Pan-Cancer Analysis of the Oncogenic and Immunological Role of Solute Carrier Family 6 Member 8 (SLC6A8). Front Genet 2022; 13:916439. [PMID: 36061183 PMCID: PMC9428493 DOI: 10.3389/fgene.2022.916439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
There is mounting evidence on the implication of SLC6A8 in the initiation and progression of human cancers. However, a comprehensive understanding of the role of SLC6A8 in pan-cancer remains elusive yet. Bioinformatics analysis was performed to investigate the expression and mutation profiles of SLC6A8 in cancers, and the association of SLC6A8 expression with cancer patients’ survival and immune cell infiltration. In general, SLC6A8 is significantly upregulated across multiple cancers. SLC6A8 expression was inconsistently prognostic in different types of cancer, albeit associated with favorable survival in the vast majority of cancers. The receiver operating characteristic curves showed that SLC6A8 was relatively accurate in identifying possible cancer patients. The genetic alteration of SLC6A8, including mutation, amplification and deletion, was frequently present across various types of cancer. Mechanistically, SLC6A8 might be involved in tumorigenesis through “carbon metabolism” and “HIF-1 signaling pathway.” Besides, SLC6A8 expression had significant correlation with immune checkpoints genes and tumor-infiltrating immune cell abundances. The present study offers a novel insight into the roles of SLC6A8 in the oncogenesis and development of multiple common cancers.
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Affiliation(s)
- Xin Yang
- Department of Surgery, People’s Hospital of Deyang City, Deyang, China
| | - Qiao Li
- Department of Pathology, People’s Hospital of Deyang City, Deyang, China
- *Correspondence: Qiao Li,
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Ruffolo LI, Jackson KM, Kuhlers PC, Dale BS, Figueroa Guilliani NM, Ullman NA, Burchard PR, Qin SS, Juviler PG, Keilson JM, Morrison AB, Georger M, Jewell R, Calvi LM, Nywening TM, O'Dell MR, Hezel AF, De Las Casas L, Lesinski GB, Yeh JJ, Hernandez-Alejandro R, Belt BA, Linehan DC. GM-CSF drives myelopoiesis, recruitment and polarisation of tumour-associated macrophages in cholangiocarcinoma and systemic blockade facilitates antitumour immunity. Gut 2022; 71:1386-1398. [PMID: 34413131 PMCID: PMC8857285 DOI: 10.1136/gutjnl-2021-324109] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 07/28/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Intrahepatic cholangiocarcinoma (iCCA) is rising in incidence, and at present, there are limited effective systemic therapies. iCCA tumours are infiltrated by stromal cells, with high prevalence of suppressive myeloid populations including tumour-associated macrophages (TAMs) and myeloid-derived suppressor cells (MDSCs). Here, we show that tumour-derived granulocyte-macrophage colony-stimulating factor (GM-CSF) and the host bone marrow is central for monopoiesis and potentiation of TAMs, and abrogation of this signalling axis facilitates antitumour immunity in a novel model of iCCA. METHODS Blood and tumours were analysed from iCCA patients and controls. Treatment and correlative studies were performed in mice with autochthonous and established orthotopic iCCA tumours treated with anti-GM-CSF monoclonal antibody. RESULTS Systemic elevation in circulating myeloid cells correlates with poor prognosis in patients with iCCA, and patients who undergo resection have a worse overall survival if tumours are more infiltrated with CD68+ TAMs. Mice with spontaneous iCCA demonstrate significant elevation of monocytic myeloid cells in the tumour microenvironment and immune compartments, and tumours overexpress GM-CSF. Blockade of GM-CSF with a monoclonal antibody decreased tumour growth and spread. Mice bearing orthotopic tumours treated with anti-GM-CSF demonstrate repolarisation of immunosuppressive TAMs and MDSCs, facilitating T cell response and tumour regression. GM-CSF blockade dampened inflammatory gene networks in tumours and TAMs. Human tumours with decreased GM-CSF expression exhibit improved overall survival after resection. CONCLUSIONS iCCA uses the GM-CSF-bone marrow axis to establish an immunosuppressive tumour microenvironment. Blockade of the GM-CSF axis promotes antitumour T cell immunity.
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Affiliation(s)
- Luis I Ruffolo
- Department of Surgery, University of Rochester Medical Center, Rochester, New York, USA
| | - Katherine M Jackson
- Department of Surgery, University of Rochester Medical Center, Rochester, New York, USA
| | - Peyton C Kuhlers
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Benjamin S Dale
- Department of Surgery, University of Rochester Medical Center, Rochester, New York, USA
| | | | - Nicholas A Ullman
- Department of Surgery, University of Rochester Medical Center, Rochester, New York, USA
| | - Paul R Burchard
- Department of Surgery, University of Rochester Medical Center, Rochester, New York, USA
| | - Shuyang S Qin
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Peter G Juviler
- Department of Surgery, University of Rochester Medical Center, Rochester, New York, USA
| | - Jessica Millian Keilson
- Division of Surgical Oncology, Department of Surgery, Emory University, Atlanta, Georgia, USA
| | - Ashley B Morrison
- Lineberger Comprehensive Cancer Center, University of North Carolina System, Chapel Hill, North Carolina, USA
| | - Mary Georger
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Rachel Jewell
- Department of Surgery, University of Rochester Medical Center, Rochester, New York, USA
| | - Laura M Calvi
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Timothy M Nywening
- Division of Surgical Oncology, Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Michael R O'Dell
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Aram F Hezel
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Luis De Las Casas
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Gregory B Lesinski
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Jen Jen Yeh
- Departments of Surgery and Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina System, Chapel Hill, North Carolina, USA
| | | | - Brian A Belt
- Department of Surgery, University of Rochester Medical Center, Rochester, New York, USA
| | - David C Linehan
- Department of Surgery, University of Rochester Medical Center, Rochester, New York, USA
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Cancer Stem Cell-Associated Immune Microenvironment in Recurrent Glioblastomas. Cells 2022; 11:cells11132054. [PMID: 35805138 PMCID: PMC9265559 DOI: 10.3390/cells11132054] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 02/04/2023] Open
Abstract
Glioblastoma multiforme (GBM) is the most incurable tumor (due to the difficulty in complete surgical resection and the resistance to conventional chemo/radiotherapies) that displays a high relapse frequency. Cancer stem cells (CSCs) have been considered as a promising target responsible for therapy resistance and cancer recurrence. CSCs are known to organize a self-advantageous microenvironment (niche) for their maintenance and expansion. Therefore, understanding how the microenvironment is reconstructed by the remaining CSCs after conventional treatments and how it eventually causes recurrence should be essential to inhibit cancer recurrence. However, the number of studies focusing on recurrence is limited, particularly those related to tumor immune microenvironment, while numerous data have been obtained from primary resected samples. Here, we summarize recent investigations on the immune microenvironment from the viewpoint of recurrent GBM (rGBM). Based on the recurrence-associated immune cell composition reported so far, we will discuss how CSCs manipulate host immunity and create the special microenvironment for themselves to regrow. An integrated understanding of the interactions between CSCs and host immune cells at the recurrent phase will lead us to develop innovative therapies and diagnoses to achieve GBM eradication.
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Extracellular vimentin mimics VEGF and is a target for anti-angiogenic immunotherapy. Nat Commun 2022; 13:2842. [PMID: 35606362 PMCID: PMC9126915 DOI: 10.1038/s41467-022-30063-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 04/14/2022] [Indexed: 12/12/2022] Open
Abstract
Anti-angiogenic cancer therapies possess immune-stimulatory properties by counteracting pro-angiogenic molecular mechanisms. We report that tumor endothelial cells ubiquitously overexpress and secrete the intermediate filament protein vimentin through type III unconventional secretion mechanisms. Extracellular vimentin is pro-angiogenic and functionally mimics VEGF action, while concomitantly acting as inhibitor of leukocyte-endothelial interactions. Antibody targeting of extracellular vimentin shows inhibition of angiogenesis in vitro and in vivo. Effective and safe inhibition of angiogenesis and tumor growth in several preclinical and clinical studies is demonstrated using a vaccination strategy against extracellular vimentin. Targeting vimentin induces a pro-inflammatory condition in the tumor, exemplified by induction of the endothelial adhesion molecule ICAM1, suppression of PD-L1, and altered immune cell profiles. Our findings show that extracellular vimentin contributes to immune suppression and functions as a vascular immune checkpoint molecule. Targeting of extracellular vimentin presents therefore an anti-angiogenic immunotherapy strategy against cancer. The pro-tumorigenic effects of vimentin have been attributed to intracellular functions in tumour cells so far. Here, the authors show that tumour endothelial cells can secrete vimentin as a pro-angiogenic factor and that targeting of vimentin can be used as an immunotherapeutic strategy.
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Xu C, Huang J, Yang Y, Li L, Li G. Increased Expression of Homeobox 5 Predicts Poor Prognosis: A Potential Prognostic Biomarker for Glioma. Int J Gen Med 2022; 15:4399-4407. [PMID: 35502183 PMCID: PMC9056058 DOI: 10.2147/ijgm.s350454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 04/05/2022] [Indexed: 11/25/2022] Open
Abstract
Background The homeobox gene 5 (HOXB5) encodes a transcription factor that regulates the embryonic development of the central nervous system. Notably, its expression pattern and prognostic role in glioma remain unelucidated. Methods This study identified the relationship between HOXB5 and glioma by investigating HOXB5 expression data from The Cancer Genome Atlas and the Genotype Tissue Expression databases and validating the obtained data using the Chinese Glioma Genome Atlas database. Western blots were used to identify HOXB5 expression levels in glioma cells and clinical samples. Kaplan-Meier and multivariate Cox regression analyses were performed to assess the prognostic value of HOXB5. The key functions and signaling pathways related to HOXB5 were analyzed using GO, KEGG, and GSEA. Immune infiltration was calculated using the microenvironment cell populations-counter, estimate the proportion of immune and cancer, and ESTIMATE algorithms. Results The expression of HOXB5 was upregulated in glioma and generally increased with malignancy. HOXB5 was an independent prognostic factor for glioma patients. A nomogram was further built that integrated HOXB5, and it showed stratifying prediction accuracy and efficiency. HOXB5 was associated with the regulation of cell growth, endothelial cell growth, and the IL-6/JAK-STAT3 pathway, and was determined to possibly promote stomatal specimen enrichment and angiogenesis. Conclusion HOXB5 protein is overexpressed in glioma and might serve as a good predictive factor of this disease.
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Affiliation(s)
- Chengran Xu
- Department of Neurosurgery, First Affiliated Hospital of China Medical University, Shenyang, People’s Republic of China
| | - Jinhai Huang
- Department of Neurosurgery, First Affiliated Hospital of China Medical University, Shenyang, People’s Republic of China
| | - Yi Yang
- Department of Neurosurgery, First Affiliated Hospital of China Medical University, Shenyang, People’s Republic of China
| | - Lun Li
- Department of Neurosurgery, Anshan Hospital of the First Hospital of China Medical University, Anshan, People’s Republic of China
| | - Guangyu Li
- Department of Neurosurgery, First Affiliated Hospital of China Medical University, Shenyang, People’s Republic of China
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Ahmaderaghi B, Amirkhah R, Jackson J, Lannagan TRM, Gilroy K, Malla SB, Redmond KL, Quinn G, McDade SS, ACRCelerate Consortium, Maughan T, Leedham S, Campbell ASD, Sansom OJ, Lawler M, Dunne PD. Molecular Subtyping Resource: a user-friendly tool for rapid biological discovery from transcriptional data. Dis Model Mech 2022; 15:dmm049257. [PMID: 35112706 PMCID: PMC8990914 DOI: 10.1242/dmm.049257] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/24/2022] [Indexed: 11/20/2022] Open
Abstract
Generation of transcriptional data has dramatically increased in the past decade, driving the development of analytical algorithms that enable interrogation of the biology underpinning the profiled samples. However, these resources require users to have expertise in data wrangling and analytics, reducing opportunities for biological discovery by 'wet-lab' users with a limited programming skillset. Although commercial solutions exist, costs for software access can be prohibitive for academic research groups. To address these challenges, we have developed an open source and user-friendly data analysis platform for on-the-fly bioinformatic interrogation of transcriptional data derived from human or mouse tissue, called Molecular Subtyping Resource (MouSR). This internet-accessible analytical tool, https://mousr.qub.ac.uk/, enables users to easily interrogate their data using an intuitive 'point-and-click' interface, which includes a suite of molecular characterisation options including quality control, differential gene expression, gene set enrichment and microenvironmental cell population analyses from RNA sequencing. The MouSR online tool provides a unique freely available option for users to perform rapid transcriptomic analyses and comprehensive interrogation of the signalling underpinning transcriptional datasets, which alleviates a major bottleneck for biological discovery. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Baharak Ahmaderaghi
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Raheleh Amirkhah
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - James Jackson
- Information Services, Queen's University Belfast, Belfast BT7 1NN, UK
| | | | - Kathryn Gilroy
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
| | - Sudhir B. Malla
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Keara L. Redmond
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Gerard Quinn
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Simon S. McDade
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | | | - Tim Maughan
- Oxford Institute of Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Simon Leedham
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | - Owen J. Sansom
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow OX3 7DQ, UK
| | - Mark Lawler
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Philip D. Dunne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
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Wang S, Ying JH, Xu H. Identification of Diagnostic Biomarkers Associated with Stromal and Immune Cell Infiltration in Fatty Infiltration After Rotator Cuff Tear by Integrating Bioinformatic Analysis and Machine-Learning. Int J Gen Med 2022; 15:1805-1819. [PMID: 35221715 PMCID: PMC8865865 DOI: 10.2147/ijgm.s354741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/11/2022] [Indexed: 11/26/2022] Open
Abstract
Purpose The present study aimed to explore potential diagnostic biomarkers for fatty infiltration (FI) of the rotator cuff muscles after rotator cuff tear (RCT) and investigate the influence of stromal and immune cell infiltration on this pathology. Methods The GSE130447 and GSE103266 datasets were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified, and gene set enrichment analyses were performed by R software. Two machine learning algorithms, random forest and multiple support vector machine recursive feature elimination (mSVM-RFE), were used to screen candidate biomarkers. The diagnostic value of the screened biomarkers was further validated by the area under the ROC curve (AUC) in the GSE103266 dataset. Murine microenvironment cell population counter (mMCP-counter) method was employed to estimate stromal and immune cell infiltration of FI. The correlation between biomarkers and infiltrated immune and stromal cell subsets was further analyzed. Results A total of 2123 DEGs were identified. The identified DEGs were predominantly linked to immune system process, extracellular matrix organization and PPAR signalling pathway. FABP5 (AUC = 0.958) and MGP (AUC = 1) were screened as diagnostic biomarkers of FI. Stromal and immune cell infiltration analysis showed that monocytes, mast cells, vessels, endothelial cells and fibroblasts may be related to the process of FI. FABP5 and MGP were positively correlated with vessels whereas negatively correlated with monocytes and mast cells. Conclusion FABP5 and MGP can serve as diagnostic biomarkers of FI after RCT, and stromal and immune cell infiltration may play a crucial role in this pathology.
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Affiliation(s)
- Si Wang
- Department of Information Centre, Lishui Hospital, Zhejiang University School of Medicine, Lishui, 323000, Zhejiang, People’s Republic of China
| | - Jin-He Ying
- Department of Joint Surgery, Lishui Hospital, Zhejiang University School of Medicine, Lishui, 323000, Zhejiang, People’s Republic of China
| | - Huan Xu
- Department of Joint Surgery, Lishui Hospital, Zhejiang University School of Medicine, Lishui, 323000, Zhejiang, People’s Republic of China
- Correspondence: Huan Xu, Tel +86 578 2285310, Fax +865782133457, Email
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Li J, Bi D, Zhang X, Cao Y, Lv K, Jiang L. Network Pharmacology and Inflammatory Microenvironment Strategy Approach to Finding the Potential Target of Siraitia grosvenorii (Luo Han Guo) for Glioblastoma. Front Genet 2022; 12:799799. [PMID: 34987553 PMCID: PMC8721149 DOI: 10.3389/fgene.2021.799799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/15/2021] [Indexed: 01/04/2023] Open
Abstract
Background: Glioblastoma (GBM) is the most common and aggressive primary intracranial tumor of the central nervous system, and the prognosis of GBM remains a challenge using the standard methods of treatment—TMZ, radiation, and surgical resection. Traditional Chinese medicine (TCM) is a helpful complementary and alternative medicine. However, there are relatively few studies on TCM for GBM. Purpose: We aimed to find the connection between TCM and anti-GBM. Study design: Network pharmacology and inflammatory microenvironment strategy were used to predict Siraitia grosvenorii (Luo Han Guo) target for treating glioblastoma. Methods: We mainly used network pharmacology and bioinformatics. Results: CCL5 was significantly highly expressed in GBM with poor prognostics. Uni-cox and randomForest were used to determine that CCL5 was especially a biomarker in GBM. CCL5 was also the target for SG and TMZ. The active ingredient of Luo Han Guo — squalene and CCL5 —showed high binding efficiency. CCL5, a chemotactic ligand, was enriched and positively correlated in eosinophils. CCL5 was also the target of Luo Han Guo, and its effective active integrate compound –— squalene — might act on CCL5. Conclusion: SG might be a new complementary therapy of the same medicine and food, working on the target CCL5 and playing an anti-GBM effect. CCL5 might affect the immune microenvironment of GBM.
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Affiliation(s)
- Juan Li
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - De Bi
- Suzhou Polytechnic Institute of Agriculture, Suzhou, China
| | - Xin Zhang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Yunpeng Cao
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Kun Lv
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Yijishan Hospital of Wannan Medical College, Wuhu, China.,Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Lan Jiang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Yijishan Hospital of Wannan Medical College, Wuhu, China.,Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu, China
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