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Liu Y, Gao J, Xu Q, Wang X, Zhong W, Wu F, Lin X, Zhang Q, Ye Q. Long non-coding RNA NEAT1 exacerbates NLRP3-mediated pyroptosis in allergic rhinitis through regulating the PTBP1/FOXP1 cascade. Int Immunopharmacol 2024; 137:112337. [PMID: 38861915 DOI: 10.1016/j.intimp.2024.112337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND Allergic Rhinitis (AR) is a prevalent chronic non-infectious inflammation affecting the nasal mucosa. NLRP3-mediated pyroptosis of epithelial cells plays a pivotal role in AR pathogenesis. Herein, we evaluated the impact of the long non-coding RNA nuclear paraspeckle assembly transcript 1 (lncRNA NEAT1) on NLR family pyrin domain containing 3 (NLRP3)-mediated pyroptosis in AR. METHODS Nasal inflammation levels in ovalbumin (OVA)-induced AR mice were assessed using HE staining, and NLRP3 expression was evaluated through immunohistochemistry. ELISA was utilized to detect OVA-specific IgE, IL-6, IL-5, and inflammatory cytokines (IL-1β, IL-18). Human nasal epithelial cells (HNEpCs) stimulated with IL4/IL13 were used to analyze the mRNA and protein levels of associated genes utilizing RT-qPCR and western blot, respectively. Cell viability and pyroptosis were assessed by CCK-8 and flow cytometry. The targeting relationship between NEAT1, PTBP1 and FOXP1 were analyzed by RIP and RNA pull down assays. FISH and IF analysis were performed to assess the co-localization of NEAT1 and PTBP1. RESULTS In both the AR mouse and cellular models, increased levels of NEAT1, PTBP1 and FOXP1 were observed. AR mice exhibited elevated inflammatory infiltration and pyroptosis, evidenced by enhanced expressions of OVA-specific IgE, IL-6, and IL-5, NLRP3, Cleaved-caspase 1, GSDMD-N, IL-1β and IL-18. Functional assays revealed that knockdown of PTBP1 or NEAT1 inhibited pyroptosis while promoting the proliferation of IL4/IL13-treated HNEpCs. Mechanistically, NEAT1 directly interacted with PTBP1, thereby maintaining FOXP1 mRNA stability. Rescue assays demonstrated that FOXP1 upregulation reversed the inhibitory effects of silencing NEAT1 or PTBP1 on IL4/IL13-stimulated pyroptosis activation in HNEpCs. CONCLUSION NEAT1 acts as a RNA scaffold for PTBP1, activating the PTBP1/FOXP1 signaling cascade, subsequently triggering NLRP3-mediated pyroptosis in HNEpCs, and ultimately promoting AR progression. These findings highlight some new insights into the pathogenesis of AR.
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MESH Headings
- Animals
- NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
- NLR Family, Pyrin Domain-Containing 3 Protein/genetics
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Pyroptosis
- Rhinitis, Allergic/immunology
- Rhinitis, Allergic/pathology
- Rhinitis, Allergic/genetics
- Rhinitis, Allergic/metabolism
- Humans
- Mice
- Forkhead Transcription Factors/metabolism
- Forkhead Transcription Factors/genetics
- Nasal Mucosa/immunology
- Nasal Mucosa/pathology
- Nasal Mucosa/metabolism
- Mice, Inbred BALB C
- Ovalbumin/immunology
- Heterogeneous-Nuclear Ribonucleoproteins/metabolism
- Heterogeneous-Nuclear Ribonucleoproteins/genetics
- Signal Transduction
- Disease Models, Animal
- Female
- Cytokines/metabolism
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Affiliation(s)
- Yunliang Liu
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, Fujian Province, PR China; Department of Otolaryngology, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, Fujian Province, PR China; Department of Otolaryngology, Fujian Children's Hospital, Fuzhou 350000, Fujian Province, PR China
| | - Jing Gao
- Health Medicine Department, The 900th Hospital of Chinese PLA Joint Logistics Support Force, Fuzhou 350025, Fujian Province, PR China
| | - Qingqing Xu
- Department of Otolaryngology, Fujian Children's Hospital, Fuzhou 350000, Fujian Province, PR China
| | - Xiaoyan Wang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, Fujian Province, PR China; Department of Otorhinolaryngology-Head & Neck Surgery, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, Fujian Province, PR China
| | - Wenhui Zhong
- Department of Clinical Laboratory, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, Fujian Province, PR China
| | - Fengfang Wu
- Department of Otorhinolaryngology-Head & Neck Surgery, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou 362000, Fujian Province, PR China
| | - Xianghang Lin
- Department of Otolaryngology, Fujian Children's Hospital, Fuzhou 350000, Fujian Province, PR China
| | - Qiuyun Zhang
- Department of Otolaryngology, Fujian Children's Hospital, Fuzhou 350000, Fujian Province, PR China
| | - Qing Ye
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, Fujian Province, PR China; Department of Otorhinolaryngology-Head & Neck Surgery, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, Fujian Province, PR China.
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Tawfik MM, Betancor MB, McMillan S, Norambuena F, Tocher DR, Douglas A, Martin SAM. Modulation of metabolic and immunoregulatory pathways in the gut transcriptome of Atlantic salmon ( Salmo salar L.) after early nutritional programming during first feeding with plant-based diet. Front Immunol 2024; 15:1412821. [PMID: 39015564 PMCID: PMC11249740 DOI: 10.3389/fimmu.2024.1412821] [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: 04/05/2024] [Accepted: 05/27/2024] [Indexed: 07/18/2024] Open
Abstract
Introduction Plant-based nutritional programming is the concept of exposing fish at very early life stages to a plant-based diet for a short duration to improve physiological responses when exposed to a similar plant-rich diet at a later developmental stage. The mechanisms of action underlying nutritional programming have not been fully deciphered, and the responses may be controlled at multiple levels. Methods This 22-week study examines gut transcriptional changes after nutritional programming. Triplicate groups of Atlantic salmon were fed with a plant (V) vs. a marine-rich (M, control) diet for 2 weeks (stimulus phase) at the first exogenous feeding. Both stimulus fish groups (M and V fish) were then fed the M diet for 12 weeks (intermediate phase) and lastly fed the V diet (challenge phase) for 6 weeks, generating two dietary regimes (MMV and VMV) across phases. This study used a whole-transcriptome approach to analyse the effects of the V diet at the end of stimulus (short-term effects) and 22 weeks post-first feeding (long-term effects). After the stimulus, due to its developmental stage, the whole intestine was used, whereas, after the challenge, pyloric caeca and middle and distal intestines were examined. Results and discussion At the stimulus end, genes with increased expression in V fish enriched pathways including regulatory epigenetic responses and lipid metabolism, and genes involved in innate immune response were downregulated. In the middle intestine at the end of the challenge, expression levels of genes of lipid, carbohydrate, and energy metabolism were increased in V fish, while M fish revealed increased expression of genes associated with autoimmune and acute adaptive immune response. The distal intestine of V fish showed increased expression of genes associated with immune response and potential immune tolerance. Conversely, the distal intestine of M fish at challenge revealed upregulation of lipid and carbohydrate metabolic pathways, tissue degeneration, and apoptotic responses. The present study demonstrated nutritional programming-associated changes in the intestinal transcriptome, with altered expression of genes involved in both immune responses and different metabolic processes. While there were limited changes in growth between the groups, the results show that there were transcriptional differences, suggesting a programming response, although the mechanism of this response still requires to be fully elucidated.
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Affiliation(s)
- Marwa Mamdouh Tawfik
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
- Hydrobiology Department, Veterinary Research Institute, National Research Centre, Giza, Egypt
| | - Mónica B. Betancor
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Stuart McMillan
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | | | - Douglas R. Tocher
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, Guangdong, China
| | - Alex Douglas
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Samuel A. M. Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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de Winter N, Ji J, Sintou A, Forte E, Lee M, Noseda M, Li A, Koenig AL, Lavine KJ, Hayat S, Rosenthal N, Emanueli C, Srivastava PK, Sattler S. Persistent transcriptional changes in cardiac adaptive immune cells following myocardial infarction: New evidence from the re-analysis of publicly available single cell and nuclei RNA-sequencing data sets. J Mol Cell Cardiol 2024; 192:48-64. [PMID: 38734060 DOI: 10.1016/j.yjmcc.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 03/17/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
INTRODUCTION Chronic immunopathology contributes to the development of heart failure after a myocardial infarction. Both T and B cells of the adaptive immune system are present in the myocardium and have been suggested to be involved in post-MI immunopathology. METHODS We analyzed the B and T cell populations isolated from previously published single cell RNA-sequencing data sets (PMID: 32130914, PMID: 35948637, PMID: 32971526 and PMID: 35926050), of the mouse and human heart, using differential expression analysis, functional enrichment analysis, gene regulatory inferences, and integration with autoimmune and cardiovascular GWAS. RESULTS Already at baseline, mature effector B and T cells are present in the human and mouse heart, having increased activity in transcription factors maintaining tolerance (e.g. DEAF1, JDP2, SPI-B). Following MI, T cells upregulate pro-inflammatory transcript levels (e.g. Cd11, Gzmk, Prf1), while B cells upregulate activation markers (e.g. Il6, Il1rn, Ccl6) and collagen (e.g. Col5a2, Col4a1, Col1a2). Importantly, pro-inflammatory and fibrotic transcription factors (e.g. NFKB1, CREM, REL) remain active in T cells, while B cells maintain elevated activity in transcription factors related to immunoglobulin production (e.g. ERG, REL) in both mouse and human post-MI hearts. Notably, genes differentially expressed in post-MI T and B cells are associated with cardiovascular and autoimmune disease. CONCLUSION These findings highlight the varied and time-dependent dynamic roles of post-MI T and B cells. They appear ready-to-go and are activated immediately after MI, thus participate in the acute wound healing response. However, they subsequently remain in a state of pro-inflammatory activation contributing to persistent immunopathology.
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Affiliation(s)
- Natasha de Winter
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, United Kingdom
| | - Jiahui Ji
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, United Kingdom
| | - Amalia Sintou
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, United Kingdom
| | - Elvira Forte
- The Jackson Laboratory, Bar Harbor, United States
| | - Michael Lee
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, United Kingdom
| | - Michela Noseda
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, United Kingdom; British Heart Foundation Centre For Research Excellence, Imperial College London, United Kingdom
| | - Aoxue Li
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, United Kingdom; Department of Medicine Solna, Division of Cardiovascular Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Andrew L Koenig
- Center for Cardiovascular Research, Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, United States
| | - Kory J Lavine
- Center for Cardiovascular Research, Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, United States
| | | | - Nadia Rosenthal
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, United Kingdom; The Jackson Laboratory, Bar Harbor, United States
| | - Costanza Emanueli
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, United Kingdom; British Heart Foundation Centre For Research Excellence, Imperial College London, United Kingdom
| | - Prashant K Srivastava
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, United Kingdom
| | - Susanne Sattler
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, United Kingdom; Department of Cardiology, Medical University of Graz, Austria; Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Austria.
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Lucibello F, Lalanne AI, Le Gac AL, Soumare A, Aflaki S, Cyrta J, Dubreuil L, Mestdagh M, Salou M, Houy A, Ekwegbara C, Jamet C, Gardrat S, Le Ven A, Bernardeau K, Cassoux N, Matet A, Malaise D, Pierron G, Piperno-Neumann S, Stern MH, Rodrigues M, Lantz O. Divergent local and systemic antitumor response in primary uveal melanomas. J Exp Med 2024; 221:e20232094. [PMID: 38563818 PMCID: PMC10986814 DOI: 10.1084/jem.20232094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/08/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Uveal melanoma (UM) is the most common cancer of the eye. The loss of chromosome 3 (M3) is associated with a high risk of metastases. M3 tumors are more infiltrated by T-lymphocytes than low-risk disomic-3 (D3) tumors, contrasting with other tumor types in which T cell infiltration correlates with better prognosis. Whether these T cells represent an antitumor response and how these T cells would be primed in the eye are both unknown. Herein, we characterized the T cells infiltrating primary UMs. CD8+ and Treg cells were more abundant in M3 than in D3 tumors. CD39+PD-1+CD8+ T cells were enriched in M3 tumors, suggesting specific responses to tumor antigen (Ag) as confirmed using HLA-A2:Melan-A tetramers. scRNAseq-VDJ analysis of T cells evidenced high numbers of proliferating CD39+PD1+CD8+ clonal expansions, suggesting in situ antitumor Ag responses. TCRseq and tumor-Ag tetramer staining characterized the recirculation pattern of the antitumor responses in M3 and D3 tumors. Thus, tumor-Ag responses occur in localized UMs, raising the question of the priming mechanisms in the absence of known lymphatic drainage.
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Affiliation(s)
- Francesca Lucibello
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Ana I. Lalanne
- Laboratoire d’Immunologie Clinique, Institut Curie, Paris, France
- Centre d’investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428), Paris, France
| | - Anne-Laure Le Gac
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Abdoulaye Soumare
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Setareh Aflaki
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Joanna Cyrta
- Departments of Pathology, Institut Curie, Paris, France
| | - Lea Dubreuil
- Laboratoire d’Immunologie Clinique, Institut Curie, Paris, France
| | - Martin Mestdagh
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Marion Salou
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Alexandre Houy
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Christina Ekwegbara
- Laboratoire d’Immunologie Clinique, Institut Curie, Paris, France
- Centre d’investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428), Paris, France
| | - Camille Jamet
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | | | - Anais Le Ven
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Karine Bernardeau
- Centre Hospitalier Universitaire (CHU) Nantes, Centre National de la Recherche Scientifique, Inserm, BioCore, US16, Nantes Université, Nantes, France
| | - Nathalie Cassoux
- Department of Surgical Oncology, University of Paris, Institut Curie, Paris, France
| | - Alexandre Matet
- Department of Surgical Oncology, University of Paris, Institut Curie, Paris, France
| | - Denis Malaise
- Department of Surgical Oncology, University of Paris, Institut Curie, Paris, France
| | | | | | - Marc-Henri Stern
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Manuel Rodrigues
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Olivier Lantz
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
- Laboratoire d’Immunologie Clinique, Institut Curie, Paris, France
- Centre d’investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428), Paris, France
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Chasov V, Zmievskaya E, Ganeeva I, Gilyazova E, Davletshin D, Filimonova M, Valiullina A, Kudriaeva A, Bulatov E. Systemic lupus erythematosus therapeutic strategy: From immunotherapy to gut microbiota modulation. J Biomed Res 2024; 38:1-16. [PMID: 38828853 DOI: 10.7555/jbr.38.20240009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
Abstract
Systemic lupus erythematosus (SLE) is characterized by a systemic dysfunction of the innate and adaptive immune systems, leading to an attack on healthy tissues of the body. During the development of SLE, pathogenic features, such as the formation of autoantibodies to self-nuclear antigens, caused tissue damage including necrosis and fibrosis, with an increased expression of type Ⅰ interferon (IFN) regulated genes. Treatment of lupus with immunosuppressants and glucocorticoids, which are used as the standard therapy, is not effective enough and causes side effects. As an alternative, more effective immunotherapies have been developed, including monoclonal and bispecific antibodies that target B cells, T cells, co-stimulatory molecules, cytokines or their receptors, and signaling molecules. Encouraging results have been observed in clinical trials with some of these therapies. Furthermore, a chimeric antigen receptor T cells (CAR-T) therapy has emerged as the most effective, safe, and promising treatment option for SLE, as demonstrated by successful pilot studies. Additionally, emerging evidence suggests that gut microbiota dysbiosis may play a significant role in the severity of SLE, and the use of methods to normalize the gut microbiota, particularly fecal microbiota transplantation (FMT), opens up new opportunities for effective treatment of SLE.
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Affiliation(s)
- Vitaly Chasov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Ekaterina Zmievskaya
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Irina Ganeeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Elvina Gilyazova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Damir Davletshin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Maria Filimonova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Aygul Valiullina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Anna Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Emil Bulatov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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Theofilatos D, Ho T, Waitt G, Äijö T, Schiapparelli LM, Soderblom EJ, Tsagaratou A. Deciphering the TET3 interactome in primary thymic developing T cells. iScience 2024; 27:109782. [PMID: 38711449 PMCID: PMC11070343 DOI: 10.1016/j.isci.2024.109782] [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: 11/11/2023] [Revised: 03/04/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024] Open
Abstract
Ten-eleven translocation (TET) proteins are DNA dioxygenases that mediate active DNA demethylation. TET3 is the most highly expressed TET protein in thymic developing T cells. TET3, either independently or in cooperation with TET1 or TET2, has been implicated in T cell lineage specification by regulating DNA demethylation. However, TET-deficient mice exhibit complex phenotypes, suggesting that TET3 exerts multifaceted roles, potentially by interacting with other proteins. We performed liquid chromatography with tandem mass spectrometry in primary developing T cells to identify TET3 interacting partners in endogenous, in vivo conditions. We discover TET3 interacting partners. Our data establish that TET3 participates in a plethora of fundamental biological processes, such as transcriptional regulation, RNA polymerase elongation, splicing, DNA repair, and DNA replication. This resource brings in the spotlight emerging functions of TET3 and sets the stage for systematic studies to dissect the precise mechanistic contributions of TET3 in shaping T cell biology.
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Affiliation(s)
- Dimitris Theofilatos
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tricia Ho
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Greg Waitt
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Tarmo Äijö
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Erik J. Soderblom
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Josi R, Ogrina A, Rothen D, Balke I, Casaramona AS, de Brot S, Mohsen MO. Intranodal Injection of Immune Activator Demonstrates Antitumor Efficacy in an Adjuvant Approach. Vaccines (Basel) 2024; 12:355. [PMID: 38675737 PMCID: PMC11054762 DOI: 10.3390/vaccines12040355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
The tumor-draining lymph nodes (tdLN) are the initial site of metastases and are the prime site for generating robust antitumor responses. In this study, we explored the efficacy of a universal immune activator (ImmAct) targeted to the tdLN. This approach can be viewed as an attempt to turn a cold, unresponsive tdLN into a hot, responsive site. The adjuvant antitumor efficacy of our novel intranodal injection was evaluated in an aggressive metastatic mammary carcinoma murine model. The cancer cells were inoculated subcutaneously in the lower quadrant of the mouse to provoke the tdLN (inguinal lymph node). The study encompasses a range of methodologies, including in vivo and in vitro assays and high-dimensional flow cytometry analysis. Our findings demonstrated that intranodal administration of ImmAct following the dissection of the primary tumor led to improved tumor-free survival and minimized weight loss. ImmAct led to both local and systemic alterations in the cellular and humoral immunity. Additionally, after ImmAct treatment, non-responders showed a higher rate of exhausted CD8+ T cells compared to responders. Indeed, our innovative approach surpassed the gold standard surgery of sentinel lymph node excision. Overall, intranodal administration of ImmAct yielded a robust antitumor immune response, offering protection against micrometastases and relapse.
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Affiliation(s)
- Romano Josi
- Department of BioMedical Research, University of Bern, 3008 Bern, Switzerland (M.O.M.)
- Department of Rheumatology and Immunology RIA, University Hospital Bern, 3010 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, 3012 Bern, Switzerland
| | - Anete Ogrina
- Plant Virology Laboratory, Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia (I.B.)
| | - Dominik Rothen
- Department of BioMedical Research, University of Bern, 3008 Bern, Switzerland (M.O.M.)
- Department of Rheumatology and Immunology RIA, University Hospital Bern, 3010 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, 3012 Bern, Switzerland
| | - Ina Balke
- Plant Virology Laboratory, Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia (I.B.)
| | - Arnau Solé Casaramona
- Department of BioMedical Research, University of Bern, 3008 Bern, Switzerland (M.O.M.)
- Department of Rheumatology and Immunology RIA, University Hospital Bern, 3010 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, 3012 Bern, Switzerland
| | - Simone de Brot
- COMPATH, Institute of Animal Pathology, University of Bern, 3012 Bern, Switzerland;
| | - Mona O. Mohsen
- Department of BioMedical Research, University of Bern, 3008 Bern, Switzerland (M.O.M.)
- Department of Rheumatology and Immunology RIA, University Hospital Bern, 3010 Bern, Switzerland
- Tajarub Research & Development, Doha P.O. Box 12627, Qatar
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Srirat T, Hayakawa T, Mise-Omata S, Nakagawara K, Ando M, Shichino S, Ito M, Yoshimura A. NR4a1/2 deletion promotes accumulation of TCF1 + stem-like precursors of exhausted CD8 + T cells in the tumor microenvironment. Cell Rep 2024; 43:113898. [PMID: 38451819 DOI: 10.1016/j.celrep.2024.113898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/28/2023] [Accepted: 02/15/2024] [Indexed: 03/09/2024] Open
Abstract
T cell exhaustion impairs tumor immunity and contributes to resistance against immune checkpoint inhibitors. The nuclear receptor subfamily 4 group A (NR4a) family of nuclear receptors plays a crucial role in driving T cell exhaustion. In this study, we observe that NR4a1 and NR4a2 deficiency in CD8+ tumor-infiltrating lymphocytes (TILs) results in potent tumor eradication and exhibits not only reduced exhaustion characteristics but also an increase in the precursors/progenitors of exhausted T (Pre-Tex) cell fraction. Serial transfers of NR4a1-/-NR4a2-/-CD8+ TILs into tumor-bearing mice result in the expansion of TCF1+ (Tcf7+) stem-like Pre-Tex cells, whereas wild-type TILs are depleted upon secondary transfer. NR4a1/2-deficient CD8+ T cells express higher levels of stemness/memory-related genes and illustrate potent mitochondrial oxidative phosphorylation. Collectively, these findings suggest that inhibiting NR4a in tumors represents a potent immuno-oncotherapy strategy by increasing stem-like Pre-Tex cells and reducing exhaustion of CD8+ T cells.
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Affiliation(s)
- Tanakorn Srirat
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| | - Taeko Hayakawa
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Setsuko Mise-Omata
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kensuke Nakagawara
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Makoto Ando
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda City, Chiba 278-0022, Japan
| | - Minako Ito
- Division of Allergy and Immunology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
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9
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Yan Z, Luan Y, Wang Y, Ren Y, Li Z, Zhao L, Shen L, Yang X, Liu T, Gao Y, Sun W. Constructing a Novel Amino Acid Metabolism Signature: A New Perspective on Pheochromocytoma Diagnosis, Immune Landscape, and Immunotherapy. Biochem Genet 2024:10.1007/s10528-024-10733-5. [PMID: 38526709 DOI: 10.1007/s10528-024-10733-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/05/2024] [Indexed: 03/27/2024]
Abstract
Pheochromocytoma/paraganglioma (PGPG) is a rare neuroendocrine tumor. Amino acid metabolism is crucial for energy production, redox balance, and metabolic pathways in tumor cell proliferation. This study aimed to build a risk model using amino acid metabolism-related genes, enhancing PGPG diagnosis and treatment decisions. We analyzed RNA-sequencing data from the PCPG cohort in the GEO dataset as our training set and validated our findings using the TCGA dataset and an additional clinical cohort. WGCNA and LASSO were utilized to identify hub genes and develop risk prediction models. The single-sample gene set enrichment analysis, MCPCOUNTER, and ESTIMATE algorithm calculated the relationship between amino acid metabolism and immune cell infiltration in PCPG. The TIDE algorithm predicted the immunotherapy efficacy for PCPG patients. The analysis identified 292 genes with differential expression, which are involved in amino acid metabolism and immune pathways. Six genes (DDC, SYT11, GCLM, PSMB7, TYRO3, AGMAT) were identified as crucial for the risk prediction model. Patients with a high-risk profile demonstrated reduced immune infiltration but potentially higher benefits from immunotherapy. Notably, DDC and SYT11 showed strong diagnostic and prognostic potential. Validation through quantitative Real-Time Polymerase Chain Reaction and immunohistochemistry confirmed their differential expression, underscoring their significance in PCPG diagnosis and in predicting immunotherapy response. This study's integration of amino acid metabolism-related genes into a risk prediction model offers critical clinical insights for PCPG risk stratification, potential immunotherapy responses, drug development, and treatment planning, marking a significant step forward in the management of this complex condition.
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Affiliation(s)
- Zechen Yan
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Henan Engineering Research Center of Tumor Molecular Diagnosis and Treatment, Zhengzhou, 450001, Henan, People's Republic of China
- Institute of Molecular Cancer Surgery, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Yongkun Luan
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Henan Engineering Research Center of Tumor Molecular Diagnosis and Treatment, Zhengzhou, 450001, Henan, People's Republic of China
- Institute of Molecular Cancer Surgery, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Yu Wang
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Institute of Molecular Cancer Surgery, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Yilin Ren
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Henan Engineering Research Center of Tumor Molecular Diagnosis and Treatment, Zhengzhou, 450001, Henan, People's Republic of China
| | - Zhiyuan Li
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Henan Engineering Research Center of Tumor Molecular Diagnosis and Treatment, Zhengzhou, 450001, Henan, People's Republic of China
| | - Luyang Zhao
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Henan Engineering Research Center of Tumor Molecular Diagnosis and Treatment, Zhengzhou, 450001, Henan, People's Republic of China
- Institute of Molecular Cancer Surgery, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Linnuo Shen
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Henan Engineering Research Center of Tumor Molecular Diagnosis and Treatment, Zhengzhou, 450001, Henan, People's Republic of China
- Institute of Molecular Cancer Surgery, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Xiaojie Yang
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- Henan Engineering Research Center of Tumor Molecular Diagnosis and Treatment, Zhengzhou, 450001, Henan, People's Republic of China
- Institute of Molecular Cancer Surgery, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Tonghu Liu
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
- Henan Engineering Research Center of Tumor Molecular Diagnosis and Treatment, Zhengzhou, 450001, Henan, People's Republic of China.
- Institute of Molecular Cancer Surgery, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
| | - Yukui Gao
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
- Institute of Molecular Cancer Surgery, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
| | - Weibo Sun
- Department of Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
- Institute of Molecular Cancer Surgery, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
- Department of Radiation Oncology and Oncology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450000, China.
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10
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Ham SD, Abraham MN, Deutschman CS, Taylor MD. Single-cell RNA sequencing reveals Immune Education promotes T cell survival in mice subjected to the cecal ligation and puncture sepsis model. Front Immunol 2024; 15:1366955. [PMID: 38562928 PMCID: PMC10982361 DOI: 10.3389/fimmu.2024.1366955] [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: 01/07/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
Background Individual T cell responses vary significantly based on the microenvironment present at the time of immune response and on prior induced T cell memory. While the cecal ligation and puncture (CLP) model is the most commonly used murine sepsis model, the contribution of diverse T cell responses has not been explored. We defined T cell subset responses to CLP using single-cell RNA sequencing and examined the effects of prior induced T cell memory (Immune Education) on these responses. We hypothesized that Immune Education prior to CLP would alter T cell responses at the single cell level at a single, early post-CLP time point. Methods Splenic T cells were isolated from C57BL/6 mice. Four cohorts were studied: Control, Immune-Educated, CLP, and Immune-Educated CLP. At age 8 weeks, Immune-Educated and Immune-Educated CLP mice received anti-CD3ϵ antibody; Control and CLP mice were administered an isotype control. CLP (two punctures with a 22-gauge needle) was performed at 12-13 weeks of life. Mice were sacrificed at baseline or 24-hours post-CLP. Unsupervised clustering of the transcriptome library identified six distinct T cell subsets: quiescent naïve CD4+, primed naïve CD4+, memory CD4+, naïve CD8+, activated CD8+, and CD8+ cytotoxic T cell subsets. T cell subset specific gene set enrichment analysis and Hurdle analysis for differentially expressed genes (DEGs) were performed. Results T cell responses to CLP were not uniform - subsets of activated and suppressed T cells were identified. Immune Education augmented specific T cell subsets and led to genomic signatures favoring T cell survival in unoperated and CLP mice. Additionally, the combination of Immune Education and CLP effected the expression of genes related to T cell activity in ways that differed from CLP alone. Validating our finding that IL7R pathway markers were upregulated in Immune-Educated CLP mice, we found that Immune Education increased T cell surface IL7R expression in post-CLP mice. Conclusion Immune Education enhanced the expression of genes associated with T cell survival in unoperated and CLP mice. Induction of memory T cell compartments via Immune Education combined with CLP may increase the model's concordance to human sepsis.
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Affiliation(s)
- Steven D. Ham
- The Division of Critical Care Medicine, Department of Pediatrics, Cohen Children’s Medical Center/Northwell Health, New Hyde Park, NY, United States
- Sepsis Research Laboratory, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Mabel N. Abraham
- The Division of Critical Care Medicine, Department of Pediatrics, Cohen Children’s Medical Center/Northwell Health, New Hyde Park, NY, United States
- Sepsis Research Laboratory, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Clifford S. Deutschman
- The Division of Critical Care Medicine, Department of Pediatrics, Cohen Children’s Medical Center/Northwell Health, New Hyde Park, NY, United States
- Sepsis Research Laboratory, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Matthew D. Taylor
- The Division of Critical Care Medicine, Department of Pediatrics, Cohen Children’s Medical Center/Northwell Health, New Hyde Park, NY, United States
- Sepsis Research Laboratory, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
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11
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Cinciripini PM, Wetter DW, Wang J, Yu R, Kypriotakis G, Kumar T, Robinson JD, Cui Y, Green CE, Bergen AW, Kosten TR, Scherer SE, Shete S. Deep sequencing of candidate genes identified 14 variants associated with smoking abstinence in an ethnically diverse sample. Sci Rep 2024; 14:6385. [PMID: 38493193 PMCID: PMC10944542 DOI: 10.1038/s41598-024-56750-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
Despite the large public health toll of smoking, genetic studies of smoking cessation have been limited with few discoveries of risk or protective loci. We investigated common and rare variant associations with success in quitting smoking using a cohort from 8 randomized controlled trials involving 2231 participants and a total of 10,020 common and 24,147 rare variants. We identified 14 novel markers including 6 mapping to genes previously related to psychiatric and substance use disorders, 4 of which were protective (CYP2B6 (rs1175607105), HTR3B (rs1413172952; rs1204720503), rs80210037 on chr15), and 2 of which were associated with reduced cessation (PARP15 (rs2173763), SCL18A2 (rs363222)). The others mapped to areas associated with cancer including FOXP1 (rs1288980) and ZEB1 (rs7349). Network analysis identified significant canonical pathways for the serotonin receptor signaling pathway, nicotine and bupropion metabolism, and several related to tumor suppression. Two novel markers (rs6749438; rs6718083) on chr2 are flanked by genes associated with regulation of bodyweight. The identification of novel loci in this study can provide new targets of pharmacotherapy and inform efforts to develop personalized treatments based on genetic profiles.
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Affiliation(s)
- Paul M Cinciripini
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - David W Wetter
- Department of Department of Population Health Sciences, University of Utah and Huntsman Cancer Institute, Salt Lake City, Utah, 84112, USA
| | - Jian Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Robert Yu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - George Kypriotakis
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Tapsi Kumar
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jason D Robinson
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yong Cui
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Charles E Green
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX, 77030, USA
| | | | - Thomas R Kosten
- Department of Psychiatry, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Steven E Scherer
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sanjay Shete
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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12
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Gholami N, Khalaji A, Mehri M, Mehrtabar S, Habibzade E. Acute myeloid leukemia with unreported translocation (x; 3) (q24; p13): A case report. Clin Case Rep 2024; 12:e8543. [PMID: 38385056 PMCID: PMC10879643 DOI: 10.1002/ccr3.8543] [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: 05/17/2023] [Revised: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Key Clinical Message Novel and rare chromosomal aberrations in AML are important to understand, particularly if associated with tumorigenesis and how they contribute to prognostic risk. It is important that acute leukemia be treated right away. Herein, novel (x; 3) (q24; p13) is described. Abstract Acute myeloid leukemia (AML) is a cancer of the blood and bone marrow. It is the most common type of acute leukemia in adults. This type of cancer usually gets worse quickly if it is not treated. Here, we report an unusual case of AML with an unreported translocation associated with AML.
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Affiliation(s)
- Nasrin Gholami
- Hematology and Oncology Research CenterTabriz University of Medical SciencesTabrizIran
| | - Amirreza Khalaji
- Connective Tissue Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Immunology Research CenterTabriz University of Medical SciencesTabrizIran
| | - Maghsood Mehri
- Hematology and Oncology Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Medical GeneticsTabriz University of Medical SciencesTabrizIran
| | - Saba Mehrtabar
- Immunology Research CenterTabriz University of Medical SciencesTabrizIran
- Student Research CommitteeTabriz University of Medical SciencesTabrizIran
| | - Elham Habibzade
- Faculty of MedicineTabriz University of Medical SciencesTabrizIran
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13
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Chasov V, Zmievskaya E, Ganeeva I, Gilyazova E, Davletshin D, Khaliulin M, Kabwe E, Davidyuk YN, Valiullina A, Rizvanov A, Bulatov E. Immunotherapy Strategy for Systemic Autoimmune Diseases: Betting on CAR-T Cells and Antibodies. Antibodies (Basel) 2024; 13:10. [PMID: 38390871 PMCID: PMC10885098 DOI: 10.3390/antib13010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/24/2024] Open
Abstract
Systemic autoimmune diseases (SAIDs), such as systemic lupus erythematosus (SLE), systemic sclerosis (SSc) and rheumatoid arthritis (RA), are fully related to the unregulated innate and adaptive immune systems involved in their pathogenesis. They have similar pathogenic characteristics, including the interferon signature, loss of tolerance to self-nuclear antigens, and enhanced tissue damage like necrosis and fibrosis. Glucocorticoids and immunosuppressants, which have limited specificity and are prone to tolerance, are used as the first-line therapy. A plethora of novel immunotherapies have been developed, including monoclonal and bispecific antibodies, and other biological agents to target cellular and soluble factors involved in disease pathogenesis, such as B cells, co-stimulatory molecules, cytokines or their receptors, and signaling molecules. Many of these have shown encouraging results in clinical trials. CAR-T cell therapy is considered the most promising technique for curing autoimmune diseases, with recent successes in the treatment of SLE and SSc. Here, we overview novel therapeutic approaches based on CAR-T cells and antibodies for targeting systemic autoimmune diseases.
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Affiliation(s)
- Vitaly Chasov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Ekaterina Zmievskaya
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Irina Ganeeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Elvina Gilyazova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Damir Davletshin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Marat Khaliulin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Emmanuel Kabwe
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Yuriy N Davidyuk
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Aygul Valiullina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Albert Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- Division of Medical and Biological Sciences, Tatarstan Academy of Sciences, 420111 Kazan, Russia
| | - Emil Bulatov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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14
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Xu S, Shi C, Zhou R, Han Y, Li N, Qu C, Xia R, Zhang C, Hu Y, Tian Z, Liu S, Wang L, Li J, Zhang Z. Mapping the landscape of HPV integration and characterising virus and host genome interactions in HPV-positive oropharyngeal squamous cell carcinoma. Clin Transl Med 2024; 14:e1556. [PMID: 38279874 PMCID: PMC10819103 DOI: 10.1002/ctm2.1556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND Human papillomavirus (HPV) integration into the host genome is an important factor in HPV(+)OPSCC carcinogenesis, in conjunction with HPV oncoproteins E6/E7. However, a well-studied investigation about virus-host interaction still needs to be completed. Our objective is to characterise HPV integration to investigate potential mechanisms of tumourigenesis independent of E6/E7 oncoproteins. MATERIALS AND METHODS High-throughput viral integration detection was performed on 109 HPV(+)OPSCC tumours with relevant clinicopathological information. Of these tumours, 38 tumours underwent targeted gene sequencing, 29 underwent whole exome sequencing and 26 underwent RNA sequencing. RESULTS HPV integration was detected in 94% of tumours (with a mean integration count of 337). Tumours occurring at the tonsil/oropharyngeal wall that exhibit higher PD-L1 expression demonstrated increased integration sites (p = .024). HPV exhibited a propensity for integration at genomic sites located within specific fragile sites (FRA19A) or genes associated with functional roles such as cell proliferation and differentiation (PTEN, AR), immune evasion (CD274) and glycoprotein biosynthesis process (FUT8). The viral oncogenes E2, E4, E6 and E7 tended to remain intact. HPV fragments displayed enrichment within host copy number variation (CNV) regions. However, insertions into genes related to altered homologous recombination repair were infrequent. Genes with integration had distinct expression levels. Fifty-nine genes whose expression level was affected by viral integration were identified, for example, EPHB1, which was reported to be involved in cellular protein metabolic process. CONCLUSIONS HPV can promote oncogenesis through recurrent integration into functional host genome regions, leading to subsequent genomic aberrations and gene expression disruption. This study characterises viral integrations and virus-host interactions, enhancing our understanding of HPV-related carcinogenesis mechanisms.
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Affiliation(s)
- Shengming Xu
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Chaoji Shi
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Rong Zhou
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Yong Han
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - NianNian Li
- Department of BioinfomaticsSequantaShanghaiChina
| | - Chuxiang Qu
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Ronghui Xia
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Chunye Zhang
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Yuhua Hu
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Zhen Tian
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Shuli Liu
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Lizhen Wang
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Jiang Li
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Zhiyuan Zhang
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
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Elhage A, Cuthbertson P, Sligar C, Watson D, Sluyter R. A Species-Specific Anti-Human P2X7 Monoclonal Antibody Reduces Graft-versus-Host Disease in Humanised Mice. Pharmaceutics 2023; 15:2263. [PMID: 37765233 PMCID: PMC10536354 DOI: 10.3390/pharmaceutics15092263] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/29/2023] Open
Abstract
Graft-versus-host disease (GVHD) is a T cell-mediated inflammatory disorder that arises from allogeneic haematopoietic stem cell transplantation and is often fatal. The P2X7 receptor is an extracellular adenosine 5'-triphosphate-gated cation channel expressed on immune cells. Blockade of this receptor with small molecule inhibitors impairs GVHD in a humanised mouse model. A species-specific blocking monoclonal antibody (mAb) (clone L4) for human P2X7 is available, affording the opportunity to determine whether donor (human) P2X7 contributes to the development of GVHD in humanised mice. Using flow cytometric assays of human RPMI 8266 and murine J774 cells, this study confirmed that this mAb bound and impaired human P2X7. Furthermore, this mAb prevented the loss of human regulatory T cells (hTregs) and natural killer (hNK) T cells in vitro. NOD-scid IL2Rγnull mice were injected with 10 × 106 human peripheral blood mononuclear cells (Day 0) and an anti-hP2X7 or control mAb (100 μg i.p. per mouse, Days 0, 2, 4, 6, and 8). The anti-hP2X7 mAb increased hTregs and hNK cells at Day 21. Moreover, anti-hP2X7 mAb-treatment reduced clinical and histological GVHD in the liver and lung compared to the control treatment at disease endpoint. hTregs, hNK, and hNK T cell proportions were increased, and human T helper 17 cell proportions were decreased at endpoint. These studies indicate that blockade of human (donor) P2X7 reduces GVHD development in humanised mice, providing the first direct evidence of a role for donor P2X7 in GVHD.
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Affiliation(s)
- Amal Elhage
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; (A.E.); (P.C.); (C.S.); (D.W.)
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Peter Cuthbertson
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; (A.E.); (P.C.); (C.S.); (D.W.)
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Chloe Sligar
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; (A.E.); (P.C.); (C.S.); (D.W.)
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Debbie Watson
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; (A.E.); (P.C.); (C.S.); (D.W.)
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Ronald Sluyter
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; (A.E.); (P.C.); (C.S.); (D.W.)
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
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Nicola Candia AJ, Garcia Fallit M, Peña Agudelo JA, Pérez Küper M, Gonzalez N, Moreno Ayala MA, De Simone E, Giampaoli C, Casares N, Seilicovich A, Lasarte JJ, Zanetti FA, Candolfi M. Targeting FOXP3 Tumor-Intrinsic Effects Using Adenoviral Vectors in Experimental Breast Cancer. Viruses 2023; 15:1813. [PMID: 37766222 PMCID: PMC10537292 DOI: 10.3390/v15091813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The regulatory T cell master transcription factor, Forkhead box P3 (Foxp3), has been detected in cancer cells; however, its role in breast tumor pathogenesis remains controversial. Here we assessed Foxp3 tumor intrinsic effects in experimental breast cancer using a Foxp3 binder peptide (P60) that impairs Foxp3 nuclear translocation. Cisplatin upregulated Foxp3 expression in HER2+ and triple-negative breast cancer (TNBC) cells. Foxp3 inhibition with P60 enhanced chemosensitivity and reduced cell survival and migration in human and murine breast tumor cells. We also developed an adenoviral vector encoding P60 (Ad.P60) that efficiently transduced breast tumor cells, reduced cell viability and migration, and improved the cytotoxic response to cisplatin. Conditioned medium from transduced breast tumor cells contained lower levels of IL-10 and improved the activation of splenic lymphocytes. Intratumoral administration of Ad.P60 in breast-tumor-bearing mice significantly reduced tumor infiltration of Tregs, delayed tumor growth, and inhibited the development of spontaneous lung metastases. Our results suggest that Foxp3 exerts protumoral intrinsic effects in breast cancer cells and that gene-therapy-mediated blockade of Foxp3 could constitute a therapeutic strategy to improve the response of these tumors to standard treatment.
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Affiliation(s)
- Alejandro J. Nicola Candia
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121A6B, Argentina; (A.J.N.C.); (A.S.)
| | - Matías Garcia Fallit
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121A6B, Argentina; (A.J.N.C.); (A.S.)
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1121A6B, Argentina
| | - Jorge A. Peña Agudelo
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121A6B, Argentina; (A.J.N.C.); (A.S.)
| | - Melanie Pérez Küper
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121A6B, Argentina; (A.J.N.C.); (A.S.)
| | - Nazareno Gonzalez
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121A6B, Argentina; (A.J.N.C.); (A.S.)
| | - Mariela A. Moreno Ayala
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121A6B, Argentina; (A.J.N.C.); (A.S.)
| | - Emilio De Simone
- Cátedra de Fisiología Animal, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires C1428BFA, Argentina
| | - Carla Giampaoli
- Cátedra de Fisiología Animal, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires C1428BFA, Argentina
| | - Noelia Casares
- Program Immunology and Immunotherapy, Centro de Investigación Médica Aplicada (CIMA, CUN), 31008 Pamplona, Spain; (N.C.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
| | - Adriana Seilicovich
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121A6B, Argentina; (A.J.N.C.); (A.S.)
| | - Juan José Lasarte
- Program Immunology and Immunotherapy, Centro de Investigación Médica Aplicada (CIMA, CUN), 31008 Pamplona, Spain; (N.C.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
| | - Flavia A. Zanetti
- Instituto de Ciencia y Tecnología “Dr. Cesar Milstein”, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Saladillo C1440FFX, Buenos Aires, Argentina;
| | - Marianela Candolfi
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121A6B, Argentina; (A.J.N.C.); (A.S.)
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Yang T, Luo Y, Liu J, Liu F, Ma Z, Liu G, LI H, Wen J, Chen C, Zeng X. A novel signature incorporating lipid metabolism- and immune-related genes to predict the prognosis and immune landscape in hepatocellular carcinoma. Front Oncol 2023; 13:1182434. [PMID: 37346073 PMCID: PMC10279962 DOI: 10.3389/fonc.2023.1182434] [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: 03/08/2023] [Accepted: 05/23/2023] [Indexed: 06/23/2023] Open
Abstract
Background Liver hepatocellular carcinoma (LIHC) is a highly malignant tumor with high metastasis and recurrence rates. Due to the relation between lipid metabolism and the tumor immune microenvironment is constantly being elucidated, this work is carried out to produce a new prognostic gene signature that incorporates immune profiles and lipid metabolism of LIHC patients. Methods We used the "DEseq2" R package and the "Venn" R package to identify differentially expressed genes related to lipid metabolism (LRDGs) in LIHC. Additionally, we performed unsupervised clustering of LIHC patients based on LRDGs to identify their subgroups and immuno-infiltration and Gene Ontology (GO) enrichment analysis on the subgroups. Next, we employed multivariate, LASSO and univariate Cox regression analyses to determine variables and to create a prognostic profile on the basis of immune- and lipid metabolism-related differential genes (IRDGs and LRDGs). We separated patients into low- and high-risk groups in accordance with the best cut-off value of risk score. We conducted Decision Curve Analysis (DCA), Receiver Operating Characteristic curve analysis as a function of time as well as Survival Analysis to evaluate this signature's prognostic value. We incorporated the clinical characteristics of patients into the risk model to obtain a nomogram prognostic model. GEO14520 and ICGC-LIRI JP datasets were employed to externally confirm the accuracy and robustness of signature. The gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were applied for investigating the underlying mechanisms. Immune infiltration analysis was implemented to examine the differences in immune between both risk groups. Single-cell RNA sequencing (scRNA-SEQ) was utilized to characterize the genes that were involved in the distribution of signature and expression characteristics of different LIHC cell types. The patients' sensitivity in both risk groups to commonly used chemotherapeutic agents and semi-inhibitory concentrations (IC50) of the drugs was assessed using the GDSC database. On the basis of the differentially expressed genes (DEGs) in the two groups, the CMAP database was adopted for the prediction of potential small-molecule compounds. Small-molecule compounds were molecularly docked with prognostic markers. Lastly, we investigated the prognostic gene expression levels in normal and LIHC tissues with immunohistochemistry (IHC) and quantitative reverse transcription polymerase chain reaction(qRT-PCR). Results We built and verified a prognostic signature with seven genes that incorporated immune profiles and lipid metabolism. Patients were classified as low- and high-risk groups depending on their prognostic profiles. The overall survival (OS) was markedly lower in the high-risk group as compared to low-risk group. Time-dependent ROC curves more precisely predicted patients' survival at 1, 3 and 5 years; the area under the ROC curve was 0.81 (1 year), 0.75 (3 years) and 0.77 (5 years). The DCA curves showed the value of the prognostic genes in this signature for clinical applications. We included the patients' clinical characteristics in the risk model for both multivariate and univariate Cox regression analyses, and the findings revealed that the risk model represents an independent factor that influences OS in LIHC patients. With immune analysis, GSVA and GSEA, we identified that there are remarkable differences between the two risk groups in immune pathways, lipid metabolism, tumor development, immune cell infiltration and immune microenvironment, response to immunotherapy, and sensitivity to chemotherapy. Moreover, those with higher risk scores presented greater sensitivity to the chemotherapeutic agents. Experiments in vitro further elucidated the roles of SPP1 and FLT3 in the LIHC immune microenvironment. Furthermore, four small-molecule drugs that could target LIHC were screened. In vitro qRT-PCR , IHC revealed that the SPP1,KIF18A expressions were raised in LIHC in tumor samples, whereas FLT3,SOCS2 showed the opposite trend. Conclusions We developed and verified a new signature comprising immune- and lipid metabolism-associated markers and to assess the prognosis and the immune status of LIHC patients. This signature can be applied to survival prediction, individualized chemotherapy, and immunotherapeutic guidance for patients with liver cancer. This study also provides potential targeted therapeutics and novel ideas for the immune evasion and progression of LIHC.
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Affiliation(s)
- Ti Yang
- Department of Hepatobiliary-Pancreatic and Hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yurong Luo
- Department of Hepatobiliary-Pancreatic and Hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Junhao Liu
- Department of Hepatobiliary-Pancreatic and Hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Fang Liu
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zengxin Ma
- Department of Hepatobiliary-Pancreatic and Hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Gai Liu
- Department of Hepatobiliary-Pancreatic and Hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Hailiang LI
- Department of Hepatobiliary-Pancreatic and Hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Jianfan Wen
- Department of Hepatobiliary-Pancreatic and Hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Chengcong Chen
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Xiancheng Zeng
- Department of Hepatobiliary-Pancreatic and Hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
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Purzycka-Bohdan D, Nedoszytko B, Sobalska-Kwapis M, Zabłotna M, Żmijewski MA, Wierzbicka J, Gleń J, Strapagiel D, Szczerkowska-Dobosz A, Nowicki RJ. Assessment of the Potential Role of Selected Single Nucleotide Polymorphisms (SNPs) of Genes Related to the Functioning of Regulatory T Cells in the Pathogenesis of Psoriasis. Int J Mol Sci 2023; 24:ijms24076061. [PMID: 37047033 PMCID: PMC10094301 DOI: 10.3390/ijms24076061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Recent studies have indicated a key role of the impaired suppressive capacity of regulatory T cells (Tregs) in psoriasis (PsO) pathogenesis. However, the genetic background of Treg dysfunctions remains unknown. The aim of this study was to evaluate the association of PsO development with selected single nucleotide polymorphisms (SNPs) of genes in which protein products play a significant role in the regulation of differentiation and function of Tregs. There were three study groups in our research and each consisted of different unrelated patients and controls: 192 PsO patients and 5605 healthy volunteers in the microarray genotyping group, 150 PsO patients and 173 controls in the ARMS-PCR method group, and 6 PsO patients and 6 healthy volunteers in the expression analysis group. The DNA microarrays analysis (283 SNPs of 57 genes) and ARMS-PCR method (8 SNPs in 7 genes) were used to determine the frequency of occurrence of SNPs in selected genes. The mRNA expression of selected genes was determined in skin samples. There were statistically significant differences in the allele frequencies of four SNPs in three genes (TNF, IL12RB2, and IL12B) between early-onset PsO patients and controls. The lowest p-value was observed for rs3093662 (TNF), and the G allele carriers had a 2.73 times higher risk of developing early-onset PsO. Moreover, the study revealed significant differences in the frequency of SNPs and their influence on PsO development between early- and late-onset PsO. Based on the ARMS-PCR method, the association between some polymorphisms of four genes (IL4, IL10, TGFB1, and STAT3) and the risk of developing PsO was noticed. Psoriatic lesions were characterized with a lower mRNA expression of FOXP3, CTLA4, and IL2, and a higher expression of TNF and IL1A in comparison with unaffected skin. In conclusion, the genetic background associated with properly functioning Tregs seems to play a significant role in PsO pathogenesis and could have diagnostic value.
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Affiliation(s)
- Dorota Purzycka-Bohdan
- Department of Dermatology, Venereology and Allergology, Medical University of Gdansk, 80-210 Gdansk, Poland
| | - Bogusław Nedoszytko
- Department of Dermatology, Venereology and Allergology, Medical University of Gdansk, 80-210 Gdansk, Poland
- Molecular Laboratory, Invicta Fertility and Reproductive Centre, 81-740 Sopot, Poland
| | - Marta Sobalska-Kwapis
- Biobank Laboratory, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland
| | - Monika Zabłotna
- Department of Dermatology, Venereology and Allergology, Medical University of Gdansk, 80-210 Gdansk, Poland
| | - Michał A Żmijewski
- Department of Histology, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Justyna Wierzbicka
- Department of Histology, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Jolanta Gleń
- Department of Dermatology, Venereology and Allergology, Medical University of Gdansk, 80-210 Gdansk, Poland
| | - Dominik Strapagiel
- Biobank Laboratory, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland
| | - Aneta Szczerkowska-Dobosz
- Department of Dermatology, Venereology and Allergology, Medical University of Gdansk, 80-210 Gdansk, Poland
| | - Roman J Nowicki
- Department of Dermatology, Venereology and Allergology, Medical University of Gdansk, 80-210 Gdansk, Poland
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Liu C, Liu D, Wang F, Liu Y, Xie J, Xie J, Xie Y. Construction of a novel choline metabolism-related signature to predict prognosis, immune landscape, and chemotherapy response in colon adenocarcinoma. Front Immunol 2022; 13:1038927. [PMID: 36451813 PMCID: PMC9701742 DOI: 10.3389/fimmu.2022.1038927] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2023] Open
Abstract
BACKGROUND Colon adenocarcinoma (COAD) is a common digestive system malignancy with high mortality and poor prognosis. Accumulating evidence indicates that choline metabolism is closely related to tumorigenesis and development. However, the efficacy of choline metabolism-related signature in predicting patient prognosis, immune microenvironment and chemotherapy response has not been fully clarified. METHODS Choline metabolism-related differentially expressed genes (DEGs) between normal and COAD tissues were screened using datasets from The Cancer Genome Atlas (TCGA), Kyoto Encyclopedia of Genes and Genomes (KEGG), AmiGO2 and Reactome Pathway databases. Two choline metabolism-related genes (CHKB and PEMT) were identified by univariate and multivariate Cox regression analyses. TCGA-COAD was the training cohort, and GSE17536 was the validation cohort. Patients in the high- and low-risk groups were distinguished according to the optimal cutoff value of the risk score. A nomogram was used to assess the prognostic accuracy of the choline metabolism-related signature. Calibration curves, decision curve analysis (DCA), and clinical impact curve (CIC) were used to improve the clinical applicability of the prognostic signature. Gene Ontology (GO) and KEGG pathway enrichment analyses of DEGs in the high- and low-risk groups were performed. KEGG cluster analysis was conducted by the KOBAS-i database. The distribution and expression of CHKB and PEMT in various types of immune cells were analyzed based on single-cell RNA sequencing (scRNA-seq). The CIBERSORT and ESTIMATE algorithms evaluated tumor immune cell infiltration in the high- and low-risk groups. Evaluation of the half maximal inhibitory concentration (IC50) of common chemotherapeutic drugs based on the choline metabolism-related signature was performed. Small molecule compounds were predicted using the Connectivity Map (CMap) database. Molecular docking is used to simulate the binding conformation of small molecule compounds and key targets. By immunohistochemistry (IHC), Western blot, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) experiments, the expression levels of CHKB and PEMT in human, mouse, and cell lines were detected. RESULTS We constructed and validated a choline metabolism-related signature containing two genes (CHKB and PEMT). The overall survival (OS) of patients in the high-risk group was significantly worse than that of patients in the low-risk group. The nomogram could effectively and accurately predict the OS of COAD patients at 1, 3, and 5 years. The DCA curve and CIC demonstrate the clinical utility of the nomogram. scRNA-seq showed that CHKB was mainly distributed in endothelial cells, while PEMT was mainly distributed in CD4+ T cells and CD8+ T cells. In addition, multiple types of immune cells expressing CHKB and PEMT differed significantly. There were significant differences in the immune microenvironment, immune checkpoint expression and chemotherapy response between the two risk groups. In addition, we screened five potential small molecule drugs that targeted treatment for COAD. Finally, the results of IHC, Western blot, and qRT-PCR consistently showed that the expression of CHKB in human, mouse, and cell lines was elevated in normal samples, while PMET showed the opposite trend. CONCLUSION In conclusion, we constructed a choline metabolism-related signature in COAD and revealed its potential application value in predicting the prognosis, immune microenvironment, and chemotherapy response of patients, which may lay an important theoretical basis for future personalized precision therapy.
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Affiliation(s)
- Cong Liu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Dingwei Liu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Fangfei Wang
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Yang Liu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Jun Xie
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Jinliang Xie
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Yong Xie
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
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