1
|
Li X, Wang J, Wang P, Qi S, Amalraj J, Zhou J, Ding Z. The role of circular RNAs in autoimmune diseases: Potential diagnostic biomarkers and therapeutic targets. FASEB J 2025; 39:e70263. [PMID: 39873909 PMCID: PMC11774230 DOI: 10.1096/fj.202401764r] [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: 07/30/2024] [Revised: 11/12/2024] [Accepted: 12/09/2024] [Indexed: 01/30/2025]
Abstract
With the emergence of high-quality sequencing technologies, further research on transcriptomes has become possible. Circular RNA (circRNA), a novel type of endogenous RNA molecule with a covalently closed circular structure through "back-splicing," is reported to be widely present in eukaryotic cells and participates mainly in regulating gene and protein expression in various ways. It is becoming a research hotspot in the non-coding RNA field. CircRNA shows close relation to several varieties of autoimmune diseases (AIDs) in both the physiological and pathological level and could potentially be used clinically in terms of diagnosis and treatment. Here, we focus on reviewing the importance of circRNA in various AIDs, with the aim of establishing new biomarkers and providing novel insights into understanding the role and functions of circRNA in AIDs. Specific signaling pathways of how circular RNAs are regulated in AIDs will also be illustrated in this review.
Collapse
Affiliation(s)
- Xin’ai Li
- Dongzhimen HospitalBeijing University of Chinese MedicineBeijingChina
- Tongchuan City Thyroid Disease Prevention CenterTongchuanChina
| | - Junhui Wang
- Thyropathy Hospital, Sun Simiao HospitalBeijing University of Chinese MedicineTongchuanChina
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Peng Wang
- The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of CardiologyQilu Hospital of Shandong UniversityJinanChina
| | - Shuo Qi
- Dongzhimen HospitalBeijing University of Chinese MedicineBeijingChina
- Tongchuan City Thyroid Disease Prevention CenterTongchuanChina
- Thyropathy Hospital, Sun Simiao HospitalBeijing University of Chinese MedicineTongchuanChina
| | | | - Jingwei Zhou
- The 1st Ward, Department of Nephrology and Endocrinology, Dongzhimen HospitalBeijing University of Chinese MedicineBeijingChina
| | - Zhiguo Ding
- Dongzhimen HospitalBeijing University of Chinese MedicineBeijingChina
- Tongchuan City Thyroid Disease Prevention CenterTongchuanChina
- Thyropathy Hospital, Sun Simiao HospitalBeijing University of Chinese MedicineTongchuanChina
| |
Collapse
|
2
|
Tosic N, Tomic Vujovic K, Vukovic V, Kotur N, Stankovic B, Marjanovic I, Antic D, Sarac S, Bibic T, Ivanovic J, Zukic B, Karan-Djurasevic T. High Expression Levels of the Long Non-Coding RNAs Lnc-IRF2-3 and Lnc-KIAA1755-4 Are Markers of Poor Prognosis in Chronic Lymphocytic Leukemia. Int J Mol Sci 2025; 26:1153. [PMID: 39940921 PMCID: PMC11817519 DOI: 10.3390/ijms26031153] [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: 12/27/2024] [Revised: 01/22/2025] [Accepted: 01/27/2025] [Indexed: 02/16/2025] Open
Abstract
Long non-coding RNAs (lncRNAs) play complex roles at multiple levels of gene regulation, thus modulating key cellular processes involved in the pathogenesis and progression of cancer. Aberrant expression of lncRNAs has been reported in various malignancies, including chronic lymphocytic leukemia (CLL). We investigated the expression of lnc-IRF2-3 and lnc-KIAA1755-4 in peripheral blood mononuclear cells of 112 previously untreated CLL patients by quantitative reverse-transcriptase polymerase chain reaction. Both lncRNAs were found to be overexpressed in CLL samples in comparison to healthy controls, and their high levels were associated with adverse clinico-biological characteristics of patients at diagnosis. High lnc-IRF2-3 expression was associated with high leukocyte and lymphocyte counts, high β2-microglobulin, advanced Binet stage, unfavorable cytogenetics, CD38-positivity and IGHV-unmutated status. Regarding lnc-KIAA1755-4, its high expression was associated with high leukocyte count, lymphocyte count, β2-microglobulin, lactate dehydrogenase and low hemoglobin, as well as with IGHV-unmutated status. In addition, we observed shorter time to first treatment and overall survival of patients expressing high levels of both lncRNAs in comparison to low-expressing patients. In summary, our study showed that high lnc-IRF2-3 and lnc-KIAA1755-4 expression at diagnosis predicts poor survival in CLL. The mechanisms of their upregulation, as well as their specific targets in CLL cells, remain to be elucidated.
Collapse
MESH Headings
- Humans
- RNA, Long Noncoding/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Male
- Female
- Prognosis
- Middle Aged
- Aged
- Biomarkers, Tumor/genetics
- Gene Expression Regulation, Leukemic
- Aged, 80 and over
- Adult
- Leukocytes, Mononuclear/metabolism
- beta 2-Microglobulin
Collapse
Affiliation(s)
- Natasa Tosic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (N.T.); (N.K.); (B.S.); (I.M.); (B.Z.)
| | - Kristina Tomic Vujovic
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (D.A.); (S.S.); (T.B.); (J.I.)
| | - Vojin Vukovic
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (D.A.); (S.S.); (T.B.); (J.I.)
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Nikola Kotur
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (N.T.); (N.K.); (B.S.); (I.M.); (B.Z.)
| | - Biljana Stankovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (N.T.); (N.K.); (B.S.); (I.M.); (B.Z.)
| | - Irena Marjanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (N.T.); (N.K.); (B.S.); (I.M.); (B.Z.)
| | - Darko Antic
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (D.A.); (S.S.); (T.B.); (J.I.)
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Sofija Sarac
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (D.A.); (S.S.); (T.B.); (J.I.)
| | - Tamara Bibic
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (D.A.); (S.S.); (T.B.); (J.I.)
| | - Jelena Ivanovic
- Clinic for Hematology, University Clinical Center of Serbia, 11000 Belgrade, Serbia; (K.T.V.); (V.V.); (D.A.); (S.S.); (T.B.); (J.I.)
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (N.T.); (N.K.); (B.S.); (I.M.); (B.Z.)
| | - Teodora Karan-Djurasevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (N.T.); (N.K.); (B.S.); (I.M.); (B.Z.)
| |
Collapse
|
3
|
Isshiki Y, Chen X, Teater M, Karagiannidis I, Nam H, Cai W, Meydan C, Xia M, Shen H, Gutierrez J, Easwar Kumar V, Carrasco SE, Ouseph MM, Yamshon S, Martin P, Griess O, Shema E, Porazzi P, Ruella M, Brentjens RJ, Inghirami G, Zappasodi R, Chadburn A, Melnick AM, Béguelin W. EZH2 inhibition enhances T cell immunotherapies by inducing lymphoma immunogenicity and improving T cell function. Cancer Cell 2025; 43:49-68.e9. [PMID: 39642889 PMCID: PMC11732734 DOI: 10.1016/j.ccell.2024.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 10/02/2024] [Accepted: 11/13/2024] [Indexed: 12/09/2024]
Abstract
T cell-based immunotherapies have demonstrated effectiveness in treating diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL) but predicting response and understanding resistance remains a challenge. To address this, we developed syngeneic models reflecting the genetics, epigenetics, and immunology of human FL and DLBCL. We show that EZH2 inhibitors reprogram these models to re-express T cell engagement genes and render them highly immunogenic. EZH2 inhibitors do not harm tumor-controlling T cells or CAR-T cells. Instead, they reduce regulatory T cells, promote memory chimeric antigen receptor (CAR) CD8 phenotypes, and reduce exhaustion, resulting in a decreased tumor burden. Intravital 2-photon imaging shows increased CAR-T recruitment and interaction within the tumor microenvironment, improving lymphoma cell killing. Therefore, EZH2 inhibition enhances CAR-T cell efficacy through direct effects on CAR-T cells, in addition to rendering lymphoma B cells immunogenic. This approach is currently being evaluated in two clinical trials, NCT05934838 and NCT05994235, to improve immunotherapy outcomes in B cell lymphoma patients.
Collapse
MESH Headings
- Enhancer of Zeste Homolog 2 Protein/antagonists & inhibitors
- Humans
- Animals
- Mice
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/therapy
- Lymphoma, Large B-Cell, Diffuse/pathology
- Tumor Microenvironment/immunology
- Tumor Microenvironment/drug effects
- Lymphoma, Follicular/immunology
- Lymphoma, Follicular/therapy
- Lymphoma, Follicular/pathology
- T-Lymphocytes/immunology
- T-Lymphocytes/drug effects
- Immunotherapy, Adoptive/methods
- Immunotherapy/methods
- Cell Line, Tumor
- Receptors, Chimeric Antigen/immunology
Collapse
Affiliation(s)
- Yusuke Isshiki
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Xi Chen
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ioannis Karagiannidis
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Henna Nam
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Winson Cai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cem Meydan
- Institute for Computational Biomedicine, Weill Cornell Medicine, Cornell University, New York, NY, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Min Xia
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Hao Shen
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Johana Gutierrez
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Vigneshwari Easwar Kumar
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sebastián E Carrasco
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA; Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine, and Rockefeller University, New York City, NY, USA
| | - Madhu M Ouseph
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Samuel Yamshon
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Peter Martin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ofir Griess
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Efrat Shema
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Patrizia Porazzi
- Division of Hematology and Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marco Ruella
- Division of Hematology and Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Renier J Brentjens
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Roberta Zappasodi
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
| |
Collapse
|
4
|
Valcárcel LV, San José-Enériz E, Ordoñez R, Apaolaza I, Olaverri-Mendizabal D, Barrena N, Valcárcel A, Garate L, San Miguel J, Pineda-Lucena A, Agirre X, Prósper F, Planes FJ. An automated network-based tool to search for metabolic vulnerabilities in cancer. Nat Commun 2024; 15:8685. [PMID: 39394196 PMCID: PMC11470099 DOI: 10.1038/s41467-024-52725-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/18/2024] [Indexed: 10/13/2024] Open
Abstract
The development of computational tools for the systematic prediction of metabolic vulnerabilities of cancer cells constitutes a central question in systems biology. Here, we present gmctool, a freely accessible online tool that allows us to accomplish this task in a simple, efficient and intuitive environment. gmctool exploits the concept of genetic Minimal Cut Sets (gMCSs), a theoretical approach to synthetic lethality based on genome-scale metabolic networks, including a unique database of synthetic lethals computed from Human1, the most recent metabolic reconstruction of human cells. gmctool introduces qualitative and quantitative improvements over our previously developed algorithms to predict, visualize and analyze metabolic vulnerabilities in cancer, demonstrating a superior performance than competing algorithms. A detailed illustration of gmctool is presented for multiple myeloma (MM), an incurable hematological malignancy. We provide in vitro experimental evidence for the essentiality of CTPS1 (CTPS synthase) and UAP1 (UDP-N-Acetylglucosamine Pyrophosphorylase 1) in specific MM patient subgroups.
Collapse
Affiliation(s)
- Luis V Valcárcel
- University of Navarra, Tecnun School of Engineering, Manuel de Lardizábal 13, 20018, San Sebastián, Spain
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
| | - Edurne San José-Enériz
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- CIBERONC Centro de Investigación Biomédica en Red de Cáncer, 28029, Madrid, Spain
| | - Raquel Ordoñez
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- CIBERONC Centro de Investigación Biomédica en Red de Cáncer, 28029, Madrid, Spain
| | - Iñigo Apaolaza
- University of Navarra, Tecnun School of Engineering, Manuel de Lardizábal 13, 20018, San Sebastián, Spain
| | - Danel Olaverri-Mendizabal
- University of Navarra, Tecnun School of Engineering, Manuel de Lardizábal 13, 20018, San Sebastián, Spain
| | - Naroa Barrena
- University of Navarra, Tecnun School of Engineering, Manuel de Lardizábal 13, 20018, San Sebastián, Spain
| | - Ana Valcárcel
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
| | - Leire Garate
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- CIBERONC Centro de Investigación Biomédica en Red de Cáncer, 28029, Madrid, Spain
| | - Jesús San Miguel
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- CIBERONC Centro de Investigación Biomédica en Red de Cáncer, 28029, Madrid, Spain
- Departmento de Hematología, Clínica Universidad de Navarra and CCUN, Universidad de Navarra, Avenida Pío XII 36, 31008, Pamplona, Spain
| | - Antonio Pineda-Lucena
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- CIBERONC Centro de Investigación Biomédica en Red de Cáncer, 28029, Madrid, Spain
| | - Xabier Agirre
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain
- CIBERONC Centro de Investigación Biomédica en Red de Cáncer, 28029, Madrid, Spain
| | - Felipe Prósper
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), Universidad de Navarra, IDISNA, CCUN, Avenida Pío XII 55, 31008, Pamplona, Spain.
- CIBERONC Centro de Investigación Biomédica en Red de Cáncer, 28029, Madrid, Spain.
- Departmento de Hematología, Clínica Universidad de Navarra and CCUN, Universidad de Navarra, Avenida Pío XII 36, 31008, Pamplona, Spain.
| | - Francisco J Planes
- University of Navarra, Tecnun School of Engineering, Manuel de Lardizábal 13, 20018, San Sebastián, Spain.
- Biomedical Engineering Center, University of Navarra, 31008, Pamplona, Navarra, Spain.
- University of Navarra, Instituto de Ciencia de los Datos e Inteligencia Artificial (DATAI), Campus Universitario, 31008, Pamplona, Spain.
| |
Collapse
|
5
|
Amir N, Taube R. Role of long noncoding RNA in regulating HIV infection-a comprehensive review. mBio 2024; 15:e0192523. [PMID: 38179937 PMCID: PMC10865847 DOI: 10.1128/mbio.01925-23] [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] [Indexed: 01/06/2024] Open
Abstract
A complete cure against human immunodeficiency virus (HIV) infection remains out of reach, as the virus persists in stable cell reservoirs that are resistant to antiretroviral therapy. The key to eliminating these reservoirs lies in deciphering the processes that govern viral gene expression and latency. However, while we comprehensively understand how host proteins influence HIV gene expression and viral latency, the emerging role of long noncoding RNAs (lncRNAs) in the context of T cell activation, HIV gene expression, and viral latency remain unexplored. This review dives into the evolving significance of lncRNAs and their impact on HIV gene expression and viral latency. We provide an overview of the current knowledge regarding how lncRNAs regulate HIV gene expression, categorizing them as either activators or inhibitors of viral gene expression and infectivity. Furthermore, we offer insights into the potential therapeutic applications of lncRNAs in combatting HIV. A deeper understanding of how lncRNAs modulate HIV gene transcription holds promise for developing novel RNA-based therapies to complement existing treatment strategies to eradicate HIV reservoirs.
Collapse
Affiliation(s)
- Noa Amir
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Negev, Israel
| | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Negev, Israel
| |
Collapse
|
6
|
Massoni-Badosa R, Aguilar-Fernández S, Nieto JC, Soler-Vila P, Elosua-Bayes M, Marchese D, Kulis M, Vilas-Zornoza A, Bühler MM, Rashmi S, Alsinet C, Caratù G, Moutinho C, Ruiz S, Lorden P, Lunazzi G, Colomer D, Frigola G, Blevins W, Romero-Rivero L, Jiménez-Martínez V, Vidal A, Mateos-Jaimez J, Maiques-Diaz A, Ovejero S, Moreaux J, Palomino S, Gomez-Cabrero D, Agirre X, Weniger MA, King HW, Garner LC, Marini F, Cervera-Paz FJ, Baptista PM, Vilaseca I, Rosales C, Ruiz-Gaspà S, Talks B, Sidhpura K, Pascual-Reguant A, Hauser AE, Haniffa M, Prosper F, Küppers R, Gut IG, Campo E, Martin-Subero JI, Heyn H. An atlas of cells in the human tonsil. Immunity 2024; 57:379-399.e18. [PMID: 38301653 PMCID: PMC10869140 DOI: 10.1016/j.immuni.2024.01.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/07/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of immunological defense against inhaled or ingested pathogens. We generated an atlas of the human tonsil composed of >556,000 cells profiled across five different data modalities, including single-cell transcriptome, epigenome, proteome, and immune repertoire sequencing, as well as spatial transcriptomics. This census identified 121 cell types and states, defined developmental trajectories, and enabled an understanding of the functional units of the tonsil. Exemplarily, we stratified myeloid slan-like subtypes, established a BCL6 enhancer as locally active in follicle-associated T and B cells, and identified SIX5 as putative transcriptional regulator of plasma cell maturation. Analyses of a validation cohort confirmed the presence, annotation, and markers of tonsillar cell types and provided evidence of age-related compositional shifts. We demonstrate the value of this resource by annotating cells from B cell-derived mantle cell lymphomas, linking transcriptional heterogeneity to normal B cell differentiation states of the human tonsil.
Collapse
Affiliation(s)
| | | | - Juan C Nieto
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Paula Soler-Vila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Amaia Vilas-Zornoza
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marco Matteo Bühler
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Sonal Rashmi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Clara Alsinet
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Ginevra Caratù
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Catia Moutinho
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Sara Ruiz
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Patricia Lorden
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Giulia Lunazzi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Gerard Frigola
- Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Will Blevins
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Lucia Romero-Rivero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Anna Vidal
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Judith Mateos-Jaimez
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alba Maiques-Diaz
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sara Ovejero
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France; Department of Clinical Hematology, CHU Montpellier, Montpellier, France
| | - Sara Palomino
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - David Gomez-Cabrero
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain; Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Xabier Agirre
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Hamish W King
- Epigenetics and Development Division, Walter and Eliza Hall Institute, Parkville, Australia
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany; Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Peter M Baptista
- Department of Otorhinolaryngology, University of Navarra, Pamplona, Spain
| | - Isabel Vilaseca
- Otorhinolaryngology Head-Neck Surgery Department, Hospital Clínic, IDIBAPS Universitat de Barcelona, Barcelona, Spain
| | - Cecilia Rosales
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Silvia Ruiz-Gaspà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Benjamin Talks
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Department of Otolaryngology, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Keval Sidhpura
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Anna Pascual-Reguant
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Anja E Hauser
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Felipe Prosper
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Departamento de Hematología, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Ivo Glynne Gut
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - José Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
7
|
Miglierina E, Ordanoska D, Le Noir S, Laffleur B. RNA processing mechanisms contribute to genome organization and stability in B cells. Oncogene 2024; 43:615-623. [PMID: 38287115 PMCID: PMC10890934 DOI: 10.1038/s41388-024-02952-2] [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: 08/29/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
RNA processing includes post-transcriptional mechanisms controlling RNA quality and quantity to ensure cellular homeostasis. Noncoding (nc) RNAs that are regulated by these dynamic processes may themselves fulfill effector and/or regulatory functions, and recent studies demonstrated the critical role of RNAs in organizing both chromatin and genome architectures. Furthermore, RNAs can threaten genome integrity when accumulating as DNA:RNA hybrids, but could also facilitate DNA repair depending on the molecular context. Therefore, by qualitatively and quantitatively fine-tuning RNAs, RNA processing contributes directly or indirectly to chromatin states, genome organization, and genome stability. B lymphocytes represent a unique model to study these interconnected mechanisms as they express ncRNAs transcribed from key specific sequences before undergoing physiological genetic remodeling processes, including V(D)J recombination, somatic hypermutation, and class switch recombination. RNA processing actors ensure the regulation and degradation of these ncRNAs for efficient DNA repair and immunoglobulin gene remodeling while failure leads to B cell development alterations, aberrant DNA repair, and pathological translocations. This review highlights how RNA processing mechanisms contribute to genome architecture and stability, with emphasis on their critical roles during B cell development, enabling physiological DNA remodeling while preventing lymphomagenesis.
Collapse
Affiliation(s)
- Emma Miglierina
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Delfina Ordanoska
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Sandrine Le Noir
- UMR CNRS 7276, Inserm 1262, Université de Limoges: Contrôle de la Réponse Immune B et des Lymphoproliférations, Team 2, B-NATION: B cell Nuclear Architecture, Immunoglobulin genes and Oncogenes, Limoges, France
| | - Brice Laffleur
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France.
| |
Collapse
|
8
|
Dézé O, Ordanoska D, Rossille D, Miglierina E, Laffleur B, Cogné M. Unique repetitive nucleic acid structures mirror switch regions in the human IgH locus. Biochimie 2023; 214:167-175. [PMID: 37678746 DOI: 10.1016/j.biochi.2023.08.017] [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: 07/06/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/09/2023]
Abstract
Immunoglobulin (Ig) genes carry the unique ability to be reshaped in peripheral B lymphocytes after these cells encounter a specific antigen. B cells can then further improve their affinity, acquire new functions as memory cells and eventually end up as antibody-secreting cells. Ig class switching is an important change that occurs in this context, thanks to local DNA lesions initiated by the enzyme activation-induced deaminase (AID). Several cis-acting elements of the Ig heavy (IgH) chain locus make it accessible to the AID-mediated lesions that promote class switch recombination (CSR). DNA repeats, with a non-template strand rich in G-quadruplexes (G4)-DNA, are prominent cis-targets of AID and define the so-called "switch" (S) regions specifically targeted for CSR. By analyzing the structure of the human IgH locus, we uncover that abundant DNA repeats, some with a putative G4-rich template strand, are additionally present in downstream portions of the IgH coding genes. These like-S (LS) regions stand as 3' mirror-images of S regions and also show analogies to some previously reported repeats associated with the IgH locus 3' super-enhancer. A regulatory role of LS repeats is strongly suggested by their specific localization close to exons encoding the membrane form of Ig molecules, and by their conservation during mammalian evolution.
Collapse
Affiliation(s)
- Ophélie Dézé
- Institut National de La Santé et de La Recherche Médicale, Unité Mixte de Recherche U1236, Université de Rennes, Etablissement Français Du Sang Bretagne, F-35000, Rennes, France
| | - Delfina Ordanoska
- Institut National de La Santé et de La Recherche Médicale, Unité Mixte de Recherche U1236, Université de Rennes, Etablissement Français Du Sang Bretagne, F-35000, Rennes, France
| | - Delphine Rossille
- Centre Hospitalier Universitaire de Rennes, SITI, Pôle Biologie, F-35033, Rennes, France
| | - Emma Miglierina
- Institut National de La Santé et de La Recherche Médicale, Unité Mixte de Recherche U1236, Université de Rennes, Etablissement Français Du Sang Bretagne, F-35000, Rennes, France
| | - Brice Laffleur
- Institut National de La Santé et de La Recherche Médicale, Unité Mixte de Recherche U1236, Université de Rennes, Etablissement Français Du Sang Bretagne, F-35000, Rennes, France
| | - Michel Cogné
- Institut National de La Santé et de La Recherche Médicale, Unité Mixte de Recherche U1236, Université de Rennes, Etablissement Français Du Sang Bretagne, F-35000, Rennes, France; Centre Hospitalier Universitaire de Rennes, SITI, Pôle Biologie, F-35033, Rennes, France.
| |
Collapse
|
9
|
Lin Y, Sun Q, Zhang B, Zhao W, Shen C. The regulation of lncRNAs and miRNAs in SARS-CoV-2 infection. Front Cell Dev Biol 2023; 11:1229393. [PMID: 37576600 PMCID: PMC10416254 DOI: 10.3389/fcell.2023.1229393] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) was a global endemic that continues to cause a large number of severe illnesses and fatalities. There is increasing evidence that non-coding RNAs (ncRNAs) are crucial regulators of viral infection and antiviral immune response and the role of non-coding RNAs in SARS-CoV-2 infection has now become the focus of scholarly inquiry. After SARS-CoV-2 infection, some ncRNAs' expression levels are regulated to indirectly control the expression of antiviral genes and viral gene replication. However, some other ncRNAs are hijacked by SARS-CoV-2 in order to help the virus evade the immune system by suppressing the expression of type I interferon (IFN-1) and controlling cytokine levels. In this review, we summarize the recent findings of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) among non-coding RNAs in SARS-CoV-2 infection and antiviral response, discuss the potential mechanisms of actions, and prospects for the detection, treatment, prevention and future directions of SARS-CoV-2 infection research.
Collapse
Affiliation(s)
| | | | | | - Wei Zhao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Chenguang Shen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|
10
|
Singh B, Dopkins N, Fei T, Marston JL, Michael S, Reyes-Gopar H, Curty G, Heymann JJ, Chadburn A, Martin P, Leal FE, Cesarman E, Nixon DF, Bendall ML. Locus specific human endogenous retroviruses reveal new lymphoma subtypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544208. [PMID: 37333202 PMCID: PMC10274920 DOI: 10.1101/2023.06.08.544208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The heterogeneity of cancers are driven by diverse mechanisms underlying oncogenesis such as differential 'cell-of-origin' (COO) progenitors, mutagenesis, and viral infections. Classification of B-cell lymphomas have been defined by considering these characteristics. However, the expression and contribution of transposable elements (TEs) to B cell lymphoma oncogenesis or classification have been overlooked. We hypothesized that incorporating TE signatures would increase the resolution of B-cell identity during healthy and malignant conditions. Here, we present the first comprehensive, locus-specific characterization of TE expression in benign germinal center (GC) B-cells, diffuse large B-cell lymphoma (DLBCL), Epstein-Barr virus (EBV)-positive and EBV-negative Burkitt lymphoma (BL), and follicular lymphoma (FL). Our findings demonstrate unique human endogenous retrovirus (HERV) signatures in the GC and lymphoma subtypes whose activity can be used in combination with gene expression to define B-cell lineage in lymphoid malignancies, highlighting the potential of retrotranscriptomic analyses as a tool in lymphoma classification, diagnosis, and the identification of novel treatment groups.
Collapse
Affiliation(s)
- Bhavya Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tongyi Fei
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jez L. Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Stephanie Michael
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Helena Reyes-Gopar
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Genómica Computacional, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Gislaine Curty
- Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Jonas J. Heymann
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Peter Martin
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Fabio E. Leal
- Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Douglas F. Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew L. Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| |
Collapse
|
11
|
Elazazy O, Midan HM, Shahin RK, Elesawy AE, Elballal MS, Sallam AAM, Elbadry AMM, Elrebehy MA, Bhnsawy A, Doghish AS. Long non-coding RNAs and rheumatoid arthritis: Pathogenesis and clinical implications. Pathol Res Pract 2023; 246:154512. [PMID: 37172525 DOI: 10.1016/j.prp.2023.154512] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a class of noncoding RNAs with a length larger than 200 nucleotides that participate in various diseases and biological processes as they can control gene expression by different mechanisms. Rheumatoid arthritis (RA) is an inflammatory autoimmune disorder characterized by symmetrical destructive destruction of distal joints as well as extra-articular involvement. Different studies have documented and proven the abnormal expression of lncRNAs in RA patients. Various lncRNAs have proven potential as biomarkers and targets for diagnosing, prognosis and treating RA. This review will focus on RA pathogenesis, clinical implications, and related lncRNA expressions that help to identify new biomarkers and treatment targets.
Collapse
Affiliation(s)
- Ola Elazazy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr, Cairo 11829, Egypt
| | - Heba M Midan
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr, Cairo 11829, Egypt
| | - Reem K Shahin
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr, Cairo 11829, Egypt
| | - Ahmed E Elesawy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr, Cairo 11829, Egypt
| | - Mohammed S Elballal
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr, Cairo 11829, Egypt
| | - Al-Aliaa M Sallam
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr, Cairo 11829, Egypt
| | - Abdullah M M Elbadry
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr, Cairo 11829, Egypt
| | - Mahmoud A Elrebehy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr, Cairo 11829, Egypt.
| | - Abdelmenem Bhnsawy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr, Cairo 11829, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr, Cairo 11829, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr, Cairo 11231, Egypt.
| |
Collapse
|
12
|
Duns G, Winkle M, Chong L, Ennishi D, Morin RD, Diepstra A, Scott DW, Kluiver JL, Steidl C, van den Berg A. Long non-coding RNAs associated with transcriptomic signatures and treatment outcome in diffuse large B-cell lymphoma. Br J Haematol 2023. [PMID: 37190862 DOI: 10.1111/bjh.18870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/29/2023] [Accepted: 05/06/2023] [Indexed: 05/17/2023]
Affiliation(s)
- Gerben Duns
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Melanie Winkle
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Lauren Chong
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daisuke Ennishi
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Arjan Diepstra
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Joost L Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| |
Collapse
|
13
|
Xiong Z, Ge Y, Xiao J, Wang Y, Li L, Ma S, Lan L, Liu B, Qin B, Luan Y, Yang C, Ye Z, Wang Z. GAS1RR, an immune-related enhancer RNA, is related to biochemical recurrence-free survival in prostate cancer. Exp Biol Med (Maywood) 2023; 248:1-13. [PMID: 36408742 PMCID: PMC9989148 DOI: 10.1177/15353702221131888] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Prostate cancer (PCa) is one of the malignant tumors of urinary system with a high morbidity. Enhancer RNA is a subclass of long non-coding RNA transcribed from active enhancer regions, which plays a critical role in gene transcriptional regulation. However, the role of enhancer RNA (eRNA) in PCa remains extremely mysterious. This study is aimed at exploring key prognostic eRNAs in PCa. First, we downloaded gene expression data and clinical data of 33 cancer types from UCSC Xena platform. Second, we selected reported putative eRNA-target pairs and performed the Kaplan-Meier survival and correlation analysis to determine the crucial eRNAs most related to biochemical recurrence (BCR)-free survival. Third, we explored the clinical characteristics with the key eRNA GAS1 adjacent regulatory RNA (GAS1RR) and performed a computational difference algorithm and the Cox regression analysis. Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to explore the underlying mechanisms. Finally, we used the pan-cancer data from The Cancer Genome Atlas (TCGA) and performed reverse transcription-quantitative polymerase chain reaction (RT-qPCR) of 18 pairs of specimens to prove the results we acquired. Among all 2695 putative eRNAs, 6 pairs of eRNA-target genes were prominently related to BCR-free survival. Growth arrest-specific protein 1 (GAS1) was a target gene of GAS1RR (r = 0.86, P < 0.001). Patients with low GAS1RR expression were likely to have unfavorable clinical characteristics. The result of computational Cox regression analysis demonstrated that GAS1RR may predict the prognosis of PCa independently. RT-qPCR results illuminated that GAS1RR and GAS1 were both downregulated in PCa tissues, and they show a strong positive correlation. GO and KEGG analyses revealed biological processes that GAS1RR was mainly associated with. Immune infiltration analysis indicated that GAS1RR expression is correlated with the infiltration level of six kinds of immune cells. Our results suggest that GAS1RR may be clinically useful in the prediction of PCa prognosis. Moreover, it may also be a prognostic predictor and theoretic target with great promise in PCa.
Collapse
Affiliation(s)
- Zezhong Xiong
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yue Ge
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jun Xiao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yanan Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Le Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Sheng Ma
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lingning Lan
- Queen Mary college of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Bo Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Baolong Qin
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yang Luan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chunguang Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhihua Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| |
Collapse
|
14
|
Bilbao-Arribas M, Jugo BM. Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep. Front Genet 2022; 13:1067350. [PMID: 36482891 PMCID: PMC9725098 DOI: 10.3389/fgene.2022.1067350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in several biological processes, including the immune system response to pathogens and vaccines. The annotation and functional characterization of lncRNAs is more advanced in humans than in livestock species. Here, we take advantage of the increasing number of high-throughput functional experiments deposited in public databases in order to uniformly analyse, profile unannotated lncRNAs and integrate 422 ovine RNA-seq samples from the ovine immune system. We identified 12302 unannotated lncRNA genes with support from independent CAGE-seq and histone modification ChIP-seq assays. Unannotated lncRNAs showed low expression levels and sequence conservation across other mammal species. There were differences in expression levels depending on the genomic location-based lncRNA classification. Differential expression analyses between unstimulated and samples stimulated with pathogen infection or vaccination resulted in hundreds of lncRNAs with changed expression. Gene co-expression analyses revealed immune gene-enriched clusters associated with immune system activation and related to interferon signalling, antiviral response or endoplasmic reticulum stress. Besides, differential co-expression networks were constructed in order to find condition-specific relationships between coding genes and lncRNAs. Overall, using a diverse set of immune system samples and bioinformatic approaches we identify several ovine lncRNAs associated with the response to an external stimulus. These findings help in the improvement of the ovine lncRNA catalogue and provide sheep-specific evidence for the implication in the general immune response for several lncRNAs.
Collapse
|
15
|
Gan Y, Yang Y, Wu Y, Li T, Liu L, Liang F, Qi J, Liang P, Pan D. Comprehensive transcriptomic analysis of immune-related eRNAs associated with prognosis and immune microenvironment in melanoma. Front Surg 2022; 9:917061. [PMID: 36338651 PMCID: PMC9632973 DOI: 10.3389/fsurg.2022.917061] [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: 04/10/2022] [Accepted: 08/17/2022] [Indexed: 11/30/2022] Open
Abstract
Background Recent evidence suggests that enhancer RNAs (eRNAs) play key roles in cancers. Identification of immune-related eRNAs (ireRNAs) in melanoma can provide novel insights into the mechanisms underlying its genesis and progression, along with potential therapeutic targets. Aim To establish an ireRNA-related prognostic signature for melanoma and identify potential drug candidates. Methods The ireRNAs associated with the overall survival (OS-ireRNAs) of melanoma patients were screened using data from The Cancer Genome Atlas (TCGA) via WGCNA and univariate Cox analysis. A prognostic signature based on these OS-ireRNAs was then constructed by performing the least absolute shrinkage and selection operator (LASSO) Cox regression analysis. The immune landscape associated with the prognostic model was evaluated by the ESTIMATE algorithm and CIBERSORT method. Finally, the potential drug candidates for melanoma were screened through the cMap database. Results A total of 24 OS-ireRNAs were obtained, of which 7 ireRNAs were used to construct a prognostic signature. The ireRNAs-related signature performed well in predicting the overall survival (OS) of melanoma patients. The risk score of the established signature was further verified as an independent risk factor, and was associated with the unique tumor microenvironment in melanoma. We also identified several potential anti-cancer drugs for melanoma, of which corticosterone ranked first. Conclusions The ireRNA-related signature is an effective prognostic predictor and provides reliable information to better understand the mechanism of ireRNAs in the progression of melanoma.
Collapse
Affiliation(s)
- Yuling Gan
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Yuan Yang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yajiao Wu
- Department of Ophthalmology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Tingdong Li
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Libing Liu
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Fudong Liang
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Jianghua Qi
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Peng Liang
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
- Correspondence: Dongsheng Pan Peng Liang
| | - Dongsheng Pan
- The 1st Department of Bone and Soft Tissue Oncology, Gansu Provincial Cancer Hospital, Lanzhou, China
- Correspondence: Dongsheng Pan Peng Liang
| |
Collapse
|
16
|
Xin Y, Zhang J, Jiang Q, Qiu J. Construction of prognostic signature of patients with oral squamous cell carcinoma based on pyroptosis-related long non-coding RNAs. Front Surg 2022; 9:935765. [PMID: 36211292 PMCID: PMC9533653 DOI: 10.3389/fsurg.2022.935765] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/08/2022] [Indexed: 01/05/2023] Open
Abstract
Background and objectiveOral squamous cell carcinoma (OSCC) is the most common malignant tumor in the head and neck, and its morbidity and mortality are increasing year by year. Changes in key genes are thought to be closely related to the occurrence and development of OSCC. Pyroptosis is an inflammatory form of programmed cell death that has been implicated in malignancies and inflammatory diseases. Changes in the expression of long noncoding RNAs may also affect tumorigenesis and progression. In this study, our main objective was to evaluate the association between pyroptosis-related lncRNAs and prognosis in patients with OSCC.MethodsThe RNA-seq data and clinicopathological data of OSCC patients are from The Cancer Genome Atlas database. The pyroptosis gene set is obtained from Gene Set Enrichment Analysis database. Univariate COX, Lasso and multivariate COX regression analyses were used for the construction of risk prognostic models of OSCC, eight lncRNAs were incorporated into prognostic models. The Kaplan-Meier method and log-rank test were used to evaluate the differences of overall survival between patients in high-risk and low-risk groups. The reliability of predictions across the dataset was analyzed by receiver operating characteristic (ROC) curves. The immune signature score was calculated using the single-sample gene set enrichment analysis.ResultsEight pyroptosis-related lncRNAs were used to construct prognostic signature of OSCC, including AC136475.2, AC024075.2, JPX, ZFAS1, TNFRSF10A-AS1, LINC00847, AC099850.3 and IER3-AS1. According to this prognostic signature, patients with OSCC were divided into high-risk and low-risk groups. Kaplan-Meier survival analysis showed that the survival rate of the high-risk group was significantly lower than the low-risk group. ROC area for risk score was 0.716, and ROC area of the 8 lncRNAs are all between 0.5 and 1, implied that these lncRNAs had high accuracy in predicting the prognosis of OSCC patients. Immune Infiltration findings suggested that these lncRNAs affected immune responses in the microenvironment of OSCC.ConclusionThe prognostic signature based on pyroptosis-related lncRNAs potentially serves as an independent prognostic indicator for OSCC patients. And this signature facilitates research on targeted diagnosis and treatment of patients diagnosed with OSCC.
Collapse
Affiliation(s)
- Yuqi Xin
- Department of Stomatology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Medical College, Nanchang University, Nanchang, China
| | - Jieyuan Zhang
- Department of Stomatology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Medical College, Nanchang University, Nanchang, China
| | - Qingkun Jiang
- Department of Stomatology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Medical College, Nanchang University, Nanchang, China
| | - Jiaxuan Qiu
- Department of Stomatology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Correspondence: Jiaxuan Qiu
| |
Collapse
|
17
|
Devadoss D, Acharya A, Manevski M, Houserova D, Cioffi MD, Pandey K, Nair M, Chapagain P, Mirsaeidi M, Borchert GM, Byrareddy SN, Chand HS. Immunomodulatory LncRNA on antisense strand of ICAM-1 augments SARS-CoV-2 infection-associated airway mucoinflammatory phenotype. iScience 2022; 25:104685. [PMID: 35789750 PMCID: PMC9242679 DOI: 10.1016/j.isci.2022.104685] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/25/2022] [Accepted: 06/23/2022] [Indexed: 01/20/2023] Open
Abstract
Noncoding RNAs are important regulators of mucoinflammatory response, but little is known about the contribution of airway long noncoding RNAs (lncRNAs) in COVID-19. RNA-seq analysis showed a more than 4-fold increased expression of IL-6, ICAM-1, CXCL-8, and SCGB1A1 inflammatory factors; MUC5AC and MUC5B mucins; and SPDEF, FOXA3, and FOXJ1 transcription factors in COVID-19 patient nasal samples compared with uninfected controls. A lncRNA on antisense strand to ICAM-1 or LASI was induced 2-fold in COVID-19 patients, and its expression was directly correlated with viral loads. A SARS-CoV-2-infected 3D-airway model largely recapitulated these clinical findings. RNA microscopy and molecular modeling indicated a possible interaction between viral RNA and LASI lncRNA. Notably, blocking LASI lncRNA reduced the SARS-CoV-2 replication and suppressed MUC5AC mucin levels and associated inflammation, and select LASI-dependent miRNAs (e.g., let-7b-5p and miR-200a-5p) were implicated. Thus, LASI lncRNA represents an essential facilitator of SARS-CoV-2 infection and associated airway mucoinflammatory response.
Collapse
Affiliation(s)
- Dinesh Devadoss
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Marko Manevski
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Dominika Houserova
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Michael D. Cioffi
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Madhavan Nair
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Mehdi Mirsaeidi
- Miller School of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of Miami, Miami, FL 33136, USA
| | - Glen M. Borchert
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Hitendra S. Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| |
Collapse
|
18
|
Non-Coding RNA Networks as Potential Novel Biomarker and Therapeutic Target for Sepsis and Sepsis-Related Multi-Organ Failure. Diagnostics (Basel) 2022; 12:diagnostics12061355. [PMID: 35741168 PMCID: PMC9222180 DOI: 10.3390/diagnostics12061355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 02/04/2023] Open
Abstract
According to “Sepsis-3” consensus, sepsis is a life-threatening clinical syndrome caused by a dysregulated inflammatory host response to infection. A rapid identification of sepsis is mandatory, as the extent of the organ damage triggered by both the pathogen itself and the host’s immune response could abruptly evolve to multiple organ failure and ultimately lead to the death of the patient. The most commonly used therapeutic strategy is to provide hemodynamic and global support to the patient and to rapidly initiate broad-spectrum empiric antibiotic therapy. To date, there is no gold standard diagnostic test that can ascertain the diagnosis of sepsis. Therefore, once sepsis is suspected, the presence of organ dysfunction can be assessed using the Sepsis-related Organ Failure Assessment (SOFA) score, although the diagnosis continues to depend primarily on clinical judgment. Clinicians can now rely on several serum biomarkers for the diagnosis of sepsis (e.g., procalcitonin), and promising new biomarkers have been evaluated, e.g., presepsin and adrenomedullin, although their clinical relevance in the hospital setting is still under discussion. Non-codingRNA, including long non-codingRNAs (lncRNAs), circularRNAs (circRNAs) and microRNAs (miRNAs), take part in a complex chain of events playing a pivotal role in several important regulatory processes in humans. In this narrative review we summarize and then analyze the function of circRNAs-miRNA-mRNA networks as putative novel biomarkers and therapeutic targets for sepsis, focusing only on data collected in clinical settings in humans.
Collapse
|
19
|
A Novel Necroptosis-Associated lncRNA Signature Can Impact the Immune Status and Predict the Outcome of Breast Cancer. J Immunol Res 2022; 2022:3143511. [PMID: 35578667 PMCID: PMC9107037 DOI: 10.1155/2022/3143511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/21/2022] Open
Abstract
Breast cancer (BRCA) is one of the leading causes of death among women worldwide, and drug resistance often leads to a poor prognosis. Necroptosis is a type of programmed cell death (PCD) and exhibits regulatory effects on tumor progression, but few studies have focused on the relationships between necroptosis-associated lncRNAs and BRCA. In this study, we established a signature basis of 7 necroptosis-related lncRNAs associated with prognosis and divided BRCA patients into high- and low-risk groups. Kaplan-Meier curves all showed an adverse prognosis for patients in the high-risk group. Cox assays confirmed that risk score was an independent prognostic factor for BRCA patients. The receiver operating characteristic (ROC) curve proved the predictive accuracy of the signature and the area under the curve (AUC) values of the risk score reached 0.722. The nomogram relatively accurately predicted the prognosis of the patients. GSEA analysis suggested that the related signaling pathways and biological processes enriched in the high- and low-risk groups may influence the tumor microenvironment (TME) of BRCA. ssGSEA showed the difference in immune cell infiltration, immune pathway activation, and immune checkpoint expression between the two risk groups, with the low-risk group more suitable for immunotherapy. According to the significant difference in IC50 between risk groups, patients can be guided for an individualized treatment plan. Overall, the authors established a prognostic signature consisting of 7 necroptosis-associated lncRNAs that can independently predict the clinical outcome of BRCA patients. The difference in the tumor immune microenvironment between the low- and high-risk populations may be the reason for the resistance to immunotherapy in some patients.
Collapse
|
20
|
Xu H, Lin C, Li T, Zhu Y, Yang J, Chen S, Chen J, Chen X, Chen Y, Guo A, Hu C. N 6-Methyladenosine-Modified circRNA in the Bovine Mammary Epithelial Cells Injured by Staphylococcus aureus and Escherichia coli. Front Immunol 2022; 13:873330. [PMID: 35444650 PMCID: PMC9014013 DOI: 10.3389/fimmu.2022.873330] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/11/2022] [Indexed: 11/28/2022] Open
Abstract
Mastitis is a common disease that hinders the development of dairy industry and animal husbandry. It leads to the abuse of antibiotics and the emergence of super drug-resistant bacteria, and poses a great threat to human food health and safety. Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) are the most common pathogens of mastitis in dairy cows and usually cause subclinical or clinical mastitis. CircRNAs and N6-methyladenosine (m6A) play important roles in immunological diseases. However, the mechanisms by which m6A modifies circRNA in bovine mammary epithelial cells remain poorly understood. The aim of our study was to investigate m6A-modified circRNAs in bovine mammary epithelial cells (MAC-T cells) injured by S. aureus and E. coli. The profile of m6A-modified circRNA showed a total of 1,599 m6A peaks within 1,035 circRNAs in the control group, 35 peaks within 32 circRNAs in the S. aureus group, and 1,016 peaks within 728 circRNAs in the E. coli group. Compared with the control group, 67 peaks within 63 circRNAs were significantly different in the S. aureus group, and 192 peaks within 137 circRNAs were significantly different in the E. coli group. Furthermore, we found the source genes of these differentially m6A-modified circRNAs in the S. aureus and E. coli groups with similar functions according to GO and KEGG analyses, which were mainly associated with cell injury, such as inflammation, apoptosis, and autophagy. CircRNA–miRNA–mRNA interaction networks predicted the potential circRNA regulation mechanism in S. aureus- and E. coli-induced cell injury. We found that the mRNAs in the networks, such as BCL2, MIF, and TNFAIP8L2, greatly participated in the MAPK, WNT, and inflammation pathways. This is the first report on m6A-modified circRNA regulation of cells under S. aureus and E. coli treatment, and sheds new light on potential mechanisms and targets from the perspective of epigenetic modification in mastitis and other inflammatory diseases.
Collapse
Affiliation(s)
- Haojun Xu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Changjie Lin
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Ting Li
- The Center for Animal Disease Control and Prevention in Wuhan, Wuhan Bureau of Agriculture and Rural Bureau Affairs, Wuhan, China
| | - Yifan Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jinghan Yang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Sijie Chen
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Jianguo Chen
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xi Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yingyu Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Changmin Hu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
21
|
Peltier DC, Roberts A, Reddy P. LNCing RNA to immunity. Trends Immunol 2022; 43:478-495. [DOI: 10.1016/j.it.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 12/29/2022]
|
22
|
Amundarain A, Valcárcel LV, Ordoñez R, Garate L, Miranda E, Cendoya X, Carrasco‐Leon A, Calasanz MJ, Paiva B, Meydan C, Mason CE, Melnick A, Rodriguez‐Otero P, Martín‐Subero JI, San Miguel J, Planes FJ, Prósper F, Agirre X. Landscape and clinical significance of long noncoding RNAs involved in multiple myeloma expressed fusion transcripts. Am J Hematol 2022; 97:E113-E117. [PMID: 34961980 DOI: 10.1002/ajh.26450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 12/31/2022]
Affiliation(s)
- Ane Amundarain
- Hemato‐Oncology Program, Center for Applied Medical Research (CIMA), IDISNA University of Navarra Pamplona Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Pamplona Spain
| | - Luis V. Valcárcel
- Hemato‐Oncology Program, Center for Applied Medical Research (CIMA), IDISNA University of Navarra Pamplona Spain
- Tecnun School of Engineering, Biomedical Engineering Center University of Navarra San Sebastian Spain
| | - Raquel Ordoñez
- Hemato‐Oncology Program, Center for Applied Medical Research (CIMA), IDISNA University of Navarra Pamplona Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Pamplona Spain
| | - Leire Garate
- Hemato‐Oncology Program, Center for Applied Medical Research (CIMA), IDISNA University of Navarra Pamplona Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Pamplona Spain
- Hematology Department, Clínica Universidad de Navarra University of Navarra Pamplona Spain
| | - Estíbaliz Miranda
- Hemato‐Oncology Program, Center for Applied Medical Research (CIMA), IDISNA University of Navarra Pamplona Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Pamplona Spain
| | - Xabier Cendoya
- Tecnun School of Engineering, Biomedical Engineering Center University of Navarra San Sebastian Spain
| | - Arantxa Carrasco‐Leon
- Hemato‐Oncology Program, Center for Applied Medical Research (CIMA), IDISNA University of Navarra Pamplona Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Pamplona Spain
| | - María José Calasanz
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Pamplona Spain
- CIMA LAB Diagnostics University of Navarra Pamplona Spain
| | - Bruno Paiva
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Pamplona Spain
- Hematology Department, Clínica Universidad de Navarra University of Navarra Pamplona Spain
- CIMA LAB Diagnostics University of Navarra Pamplona Spain
- Flow Cytometry Core, CIMA University of Navarra Pamplona Spain
| | - Cem Meydan
- Division of Hematology/Oncology, Department of Medicine Weill Cornell Medical College New York New York USA
- Department of Physiology and Biophysics Weill Cornell Medicine New York New York USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine Weill Cornell Medicine New York New York USA
| | - Christopher E. Mason
- Division of Hematology/Oncology, Department of Medicine Weill Cornell Medical College New York New York USA
- Department of Physiology and Biophysics Weill Cornell Medicine New York New York USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine Weill Cornell Medicine New York New York USA
| | - Ari Melnick
- Division of Hematology/Oncology, Department of Medicine Weill Cornell Medical College New York New York USA
| | - Paula Rodriguez‐Otero
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Pamplona Spain
- Hematology Department, Clínica Universidad de Navarra University of Navarra Pamplona Spain
| | - José I. Martín‐Subero
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Pamplona Spain
- Hospital Clínic de Barcelona and Departament de Fonaments Clínics, Facultat de Medicina Universitat de Barcelona Barcelona Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer IDIBAPS Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats ICREA Barcelona Spain
| | - Jesús San Miguel
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Pamplona Spain
- Hematology Department, Clínica Universidad de Navarra University of Navarra Pamplona Spain
| | - Francisco J. Planes
- Tecnun School of Engineering, Biomedical Engineering Center University of Navarra San Sebastian Spain
| | - Felipe Prósper
- Hemato‐Oncology Program, Center for Applied Medical Research (CIMA), IDISNA University of Navarra Pamplona Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Pamplona Spain
- Hematology Department, Clínica Universidad de Navarra University of Navarra Pamplona Spain
| | - Xabier Agirre
- Hemato‐Oncology Program, Center for Applied Medical Research (CIMA), IDISNA University of Navarra Pamplona Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Pamplona Spain
| |
Collapse
|
23
|
Super enhancers as master gene regulators in the pathogenesis of hematologic malignancies. Biochim Biophys Acta Rev Cancer 2022; 1877:188697. [PMID: 35150791 DOI: 10.1016/j.bbcan.2022.188697] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/20/2022] [Accepted: 02/04/2022] [Indexed: 12/17/2022]
Abstract
Transcriptional deregulation of multiple oncogenes, tumor suppressors and survival pathways is a cancer cell hallmark. Super enhancers (SE) are long stretches of active enhancers in close linear proximity that ensure extraordinarily high expression levels of key genes associated with cell lineage, function and survival. SE landscape is intrinsically prone to changes and reorganization during the course of normal cell differentiation. This functional plasticity is typically utilized by cancer cells, which remodel their SE landscapes to ensure oncogenic transcriptional reprogramming. Multiple recent studies highlighted structural genetic mechanisms in non-coding regions that create new SE or hijack already existing ones. In addition, alterations in abundance/activity of certain SE-associated proteins or certain viral infections can elicit new super enhancers and trigger SE-driven transcriptional changes. For these reasons, SE profiling emerged as a powerful tool for discovering the core transcriptional regulatory circuits in tumor cells. This, in turn, provides new insights into cancer cell biology, and identifies main nodes of key cellular pathways to be potentially targeted. Since SEs are susceptible to inhibition, their disruption results in exponentially amassing 'butterfly' effect on gene expression and cell function. Moreover, many of SE elements are druggable, opening new therapeutic opportunities. Indeed, SE targeting drugs have been studied preclinically in various hematologic malignancies with promising effects. Herein, we review the unique features of SEs, present different cis- and trans-acting mechanisms through which hematologic tumor cells acquire SEs, and finally, discuss the potential of SE targeting in the therapy of hematologic malignancies.
Collapse
|
24
|
Stage-Specific Non-Coding RNA Expression Patterns during In Vitro Human B Cell Differentiation into Antibody Secreting Plasma Cells. Noncoding RNA 2022; 8:ncrna8010015. [PMID: 35202088 PMCID: PMC8878715 DOI: 10.3390/ncrna8010015] [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: 12/13/2021] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 11/17/2022] Open
Abstract
The differentiation of B cells into antibody secreting plasma cells (PCs) is governed by a strict regulatory network that results in expression of specific transcriptomes along the activation continuum. In vitro models yielding significant numbers of PCs phenotypically identical to the in vivo state enable investigation of pathways, metabolomes, and non-coding (ncRNAs) not previously identified. The objective of our study was to characterize ncRNA expression during human B cell activation and differentiation. To achieve this, we used an in vitro system and performed RNA-seq on resting and activated B cells and PCs. Characterization of coding gene transcripts, including immunoglobulin (Ig), validated our system and also demonstrated that memory B cells preferentially differentiated into PCs. Importantly, we identified more than 980 ncRNA transcripts that are differentially expressed across the stages of activation and differentiation, some of which are known to target transcription, proliferation, cytoskeletal, autophagy and proteasome pathways. Interestingly, ncRNAs located within Ig loci may be targeting both Ig and non-Ig-related transcripts. ncRNAs associated with B cell malignancies were also identified. Taken together, this system provides a platform to study the role of specific ncRNAs in B cell differentiation and altered expression of those ncRNAs involved in B cell malignancies.
Collapse
|
25
|
Wen G, Zhou T, Gu W. The potential of using blood circular RNA as liquid biopsy biomarker for human diseases. Protein Cell 2021; 12:911-946. [PMID: 33131025 PMCID: PMC8674396 DOI: 10.1007/s13238-020-00799-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 12/14/2022] Open
Abstract
Circular RNA (circRNA) is a novel class of single-stranded RNAs with a closed loop structure. The majority of circRNAs are formed by a back-splicing process in pre-mRNA splicing. Their expression is dynamically regulated and shows spatiotemporal patterns among cell types, tissues and developmental stages. CircRNAs have important biological functions in many physiological processes, and their aberrant expression is implicated in many human diseases. Due to their high stability, circRNAs are becoming promising biomarkers in many human diseases, such as cardiovascular diseases, autoimmune diseases and human cancers. In this review, we focus on the translational potential of using human blood circRNAs as liquid biopsy biomarkers for human diseases. We highlight their abundant expression, essential biological functions and significant correlations to human diseases in various components of peripheral blood, including whole blood, blood cells and extracellular vesicles. In addition, we summarize the current knowledge of blood circRNA biomarkers for disease diagnosis or prognosis.
Collapse
Affiliation(s)
- Guoxia Wen
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Tong Zhou
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV, 89557, USA.
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China.
| |
Collapse
|
26
|
Zhang Z, Wu Y, Yu C, Li Z, Xu L. Comprehensive analysis of immune related lncRNAs in the tumor microenvironment of stage II-III colorectal cancer. J Gastrointest Oncol 2021; 12:2232-2243. [PMID: 34790388 DOI: 10.21037/jgo-21-594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/19/2021] [Indexed: 11/06/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) associated with immunological function have increasingly been found to act as effective prognostic biomarkers of the overall survival (OS) of colorectal cancer (CRC) patients. We sought to identify a signature of immune-related lncRNAs that offered value as a tool for the prospective prognostic evaluation of patients with stage II-III CRC. Methods The clinical and gene expression data of CRC patients in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases was obtained and separated into a training cohort composed of 202 samples, a test cohort of 124 samples from the GSE72970 dataset, and a validation cohort of 91 samples from the GSE143985 dataset. Results We firstly evaluated intratumoral immune cell infiltration by conducting a Single-sample gene set enrichment analyses (ssGSEA) analysis to separate patient tumors into those with low immune cell infiltration and those with high immune cell infiltration. We then compared lncRNA and mRNA expression profiles between these two tumor types, leading us to focus on eight lncRNAs identified within the resultant mRNA-lncRNA co-expression network. Multivariate Cox regression models were then utilized to detect an immune-associated lncRNA signature that offered value for prognostic model construction. Functional analyses revealed this lncRNA signature to be associated with key immunological pathways including the JAK-STAT signaling, T cell receptor signaling, and Rap1 signaling pathways. Conclusions Together, our results suggest that our immune-related 4 lncRNA signature can reliably predict stage II-III CRC patient prognosis, thereby guiding efforts to better understand this disease and to effectively treat it.
Collapse
Affiliation(s)
- Zan Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yixin Wu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zhengtai Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lida Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| |
Collapse
|
27
|
Arumugam P, Singla M, Lodha R, Rao V. Identification and characterization of novel infection associated transcripts in macrophages. RNA Biol 2021; 18:604-611. [PMID: 34747322 DOI: 10.1080/15476286.2021.1989217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
By analysis of lncRNA expression profiles of macrophages in response to Mycobacterium tuberculosis (Mtb) infection, we identified novel highly expressed transcripts, unique in encompassing a protein coding transcript- Cytidine Monophosphate Kinase 2 (CMPK2) and a previously identified lncRNA- Negative Regulator of Interferon Response (NRIR). While these transcripts (TILT1, 2,3 - TLR4 and Infection induced Long Transcript) are induced by virulent Mtb as well as lipopolysaccharide (LPS) early, lack of/delayed expression in non-viable Mtb/BCG infected cells, respectively, suggest an important role in macrophage responses. The elevated expression by 3 hr in response to fast growing bacteria further emphasizes the importance of these RNAs in the macrophage infection response. Overall, we provide evidence for the presence of multiple transcripts that form a part of the early infection response programme of macrophages.Abbreviations: IFN: Interferon; NRIR: negative regulator of interferon response; CMPK2: cytidine/ uridine monophosphate kinase; LPS: lipopolysaccharide; LAM: Lipoarabinomannan; PIMs: Phosphatidylinositol Mannosides; TILT1, 2,3: TLR4 and Infection induced Long Transcript; TLR4: Toll-like receptor 4; Mtb: Mycobacterium tuberculosis; BCG: Mycobacterium bovis BCG; MDMs: human monocyte derived macrophages.
Collapse
Affiliation(s)
- Prabhakar Arumugam
- Department of Cardio- Respiratory Disease Biology, CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.,Department of Biological Sciences, Academy of Scientific and Innovative Research, CSIR- HRDC campus, Sector 19, Kamla Nehru Nagar, Ghaziabad- 201002, India
| | - Mohit Singla
- Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Vivek Rao
- Department of Cardio- Respiratory Disease Biology, CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.,Department of Biological Sciences, Academy of Scientific and Innovative Research, CSIR- HRDC campus, Sector 19, Kamla Nehru Nagar, Ghaziabad- 201002, India
| |
Collapse
|
28
|
Identification of sheep lncRNAs related to the immune response to vaccines and aluminium adjuvants. BMC Genomics 2021; 22:770. [PMID: 34706639 PMCID: PMC8554944 DOI: 10.1186/s12864-021-08086-z] [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: 03/29/2021] [Accepted: 10/07/2021] [Indexed: 11/10/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are involved in several immune processes, including the immune response to vaccination, but most of them remain uncharacterised in livestock species. The mechanism of action of aluminium adjuvants as vaccine components is neither not fully understood. Results We built a transcriptome from sheep PBMCs RNA-seq data in order to identify unannotated lncRNAs and analysed their expression patterns along protein coding genes. We found 2284 novel lncRNAs and assessed their conservation in terms of sequence and synteny. Differential expression analysis performed between animals inoculated with commercial vaccines or aluminium adjuvant alone and the co-expression analysis revealed lncRNAs related to the immune response to vaccines and adjuvants. A group of co-expressed genes enriched in cytokine signalling and production highlighted the differences between different treatments. A number of differentially expressed lncRNAs were correlated with a divergently located protein-coding gene, such as the OSM cytokine. Other lncRNAs were predicted to act as sponges of miRNAs involved in immune response regulation. Conclusions This work enlarges the lncRNA catalogue in sheep and puts an accent on their involvement in the immune response to repetitive vaccination, providing a basis for further characterisation of the non-coding sheep transcriptome within different immune cells. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08086-z.
Collapse
|
29
|
Bian E, Chen X, Cheng L, Cheng M, Chen Z, Yue X, Zhang Z, Chen J, Sun L, Huang K, Huang C, Fang Z, Zhao B, Li J. Super-enhancer-associated TMEM44-AS1 aggravated glioma progression by forming a positive feedback loop with Myc. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:337. [PMID: 34696771 PMCID: PMC8543865 DOI: 10.1186/s13046-021-02129-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/05/2021] [Indexed: 01/05/2023]
Abstract
Background Long non-coding RNAs (lncRNAs) have been considered as one type of gene expression regulator for cancer development, but it is not clear how these are regulated. This study aimed to identify a specific lncRNA that promotes glioma progression. Methods RNA sequencing (RNA-seq) and quantitative real-time PCR were performed to screen differentially expressed genes. CCK-8, transwell migration, invasion assays, and a mouse xenograft model were performed to determine the functions of TMEM44-AS1. Co-IP, ChIP, Dual-luciferase reporter assays, RNA pulldown, and RNA immunoprecipitation assays were performed to study the molecular mechanism of TMEM44-AS1 and the downstream target. Results We identified a novel lncRNA TMEM44-AS1, which was aberrantly expressed in glioma tissues, and that increased TMEM44-AS1 expression was correlated with malignant progression and poor survival for patients with glioma. Expression of TMEM44-AS1 increased the proliferation, colony formation, migration, and invasion of glioma cells. Knockdown of TMEM44-AS1 in glioma cells reduced cell proliferation, colony formation, migration and invasion, and tumor growth in a nude mouse xenograft model. Mechanistically, TMEM44-AS1 is directly bound to the SerpinB3, and sequentially activated Myc and EGR1/IL-6 signaling; Myc transcriptionally induced TMEM44-AS1 and directly bound to the promoter and super-enhancer of TMEM44-AS1, thus forming a positive feedback loop with TMEM44-AS. Further studies demonstrated that Myc interacts with MED1 regulates the super-enhancer of TMEM44-AS1. More importantly, a novel small-molecule Myc inhibitor, Myci975, alleviated TMEM44-AS1-promoted the growth of glioma cells. Conclusions Our study implicates a crucial role of the TMEM44-AS1-Myc axis in glioma progression and provides a possible anti-glioma therapeutic agent. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02129-9.
Collapse
Affiliation(s)
- Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China. .,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China.
| | - Xueran Chen
- Department of Laboratory Medicine, Hefei Cancer Hospital, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China.,Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China
| | - Li Cheng
- School of pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Meng Cheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Zhigang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Xiaoyu Yue
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Zhengwei Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Jie Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Libo Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Kebing Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Cheng Huang
- School of pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Zhiyou Fang
- Department of Laboratory Medicine, Hefei Cancer Hospital, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China. .,Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, 230031, Anhui, China.
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China. .,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China.
| | - Jun Li
- School of pharmacy, Anhui Medical University, Hefei, 230032, China.
| |
Collapse
|
30
|
OCT2 pre-positioning facilitates cell fate transition and chromatin architecture changes in humoral immunity. Nat Immunol 2021; 22:1327-1340. [PMID: 34556886 PMCID: PMC9829245 DOI: 10.1038/s41590-021-01025-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 08/05/2021] [Indexed: 01/12/2023]
Abstract
During the germinal center (GC) reaction, B cells undergo profound transcriptional, epigenetic and genomic architectural changes. How such changes are established remains unknown. Mapping chromatin accessibility during the humoral immune response, we show that OCT2 was the dominant transcription factor linked to differential accessibility of GC regulatory elements. Silent chromatin regions destined to become GC-specific super-enhancers (SEs) contained pre-positioned OCT2-binding sites in naive B cells (NBs). These preloaded SE 'seeds' featured spatial clustering of regulatory elements enriched in OCT2 DNA-binding motifs that became heavily loaded with OCT2 and its GC-specific coactivator OCAB in GC B cells (GCBs). SEs with high abundance of pre-positioned OCT2 binding preferentially formed long-range chromatin contacts in GCs, to support expression of GC-specifying factors. Gain in accessibility and architectural interactivity of these regions were dependent on recruitment of OCAB. Pre-positioning key regulators at SEs may represent a broadly used strategy for facilitating rapid cell fate transitions.
Collapse
|
31
|
Gao L, Li Q. Identification of Novel Pyroptosis-Related lncRNAs Associated with the Prognosis of Breast Cancer Through Interactive Analysis. Cancer Manag Res 2021; 13:7175-7186. [PMID: 34552353 PMCID: PMC8450763 DOI: 10.2147/cmar.s325710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/12/2021] [Indexed: 01/14/2023] Open
Abstract
Background The role of pyroptosis and lncRNAs in breast cancer remains controversial. This study aimed to explore the pyroptosis-related lncRNAs in breast cancer. Methods All the data used for bioinformatics analysis were downloaded from The Cancer Genome Atlas database. Limma package was used to perform difference analysis, and distinguish mRNA and lncRNA. Survival package was used to conduct prognosis analysis. LASSO algorithm, univariate cox analysis and multivariate cox analysis were used to construct the prognosis model. P value <0.05 was regarded as statistically significant. Results Based on the seven pyroptosis-related lncRNAs tightly associated with patients' prognosis, a prognostic prediction model was finally developed, which showed powerful effectiveness (Training cohort, one-year AUC = 0.82, 95% Cl = 0.69-0.95, three-year AUC = 0.77, 95% Cl = 0.68-0.85, five-year AUC = 0.74, 95% Cl = 0.66-0.82; Validation cohort, one-year AUC = 0.68, 95% Cl = 0.53-0.84, three-year AUC = 0.72, 95% Cl = 0.64-0.81, five-year AUC = 0.67, 95% Cl = 0.57-0.77). GSEA analysis demonstrated that the protein secretion, angiogenesis, TGF-β signaling and MTORC1 signaling might be involved in the high-risk patients. Moreover, immune infiltration analysis showed that the risk score was positively correlated with Tgd and Th2 cells, yet negatively correlated with CD8+ T cells, cytotoxic cells and T helper cells, which might partly explain the poor prognosis of high-risk patients. Finally, the expression level of seven model lncRNAs in the real world was validated by qRT-PCR using four cancer cell lines (MCF-7, T47D, MDA-MB-231, MDA-MB-469). Conclusion In conclusion, our study identified lncRNAs that are remarkably correlated with patients' survival and might participate in the pyroptosis process, which might be underlying tumor biomarker and therapeutic targets. This study may provide direction for future research.
Collapse
Affiliation(s)
- Lili Gao
- Department of Pathology, Pudong New Area People's Hospital, Shanghai, People's Republic of China
| | - Qing Li
- Department of Pathology, Pudong New Area People's Hospital, Shanghai, People's Republic of China
| |
Collapse
|
32
|
Rivas MA, Durmaz C, Kloetgen A, Chin CR, Chen Z, Bhinder B, Koren A, Viny AD, Scharer CD, Boss JM, Elemento O, Mason CE, Melnick AM. Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes. Front Immunol 2021; 12:688493. [PMID: 34621263 PMCID: PMC8490713 DOI: 10.3389/fimmu.2021.688493] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/24/2021] [Indexed: 01/10/2023] Open
Abstract
The cohesin complex plays critical roles in genomic stability and gene expression through effects on 3D architecture. Cohesin core subunit genes are mutated across a wide cross-section of cancers, but not in germinal center (GC) derived lymphomas. In spite of this, haploinsufficiency of cohesin ATPase subunit Smc3 was shown to contribute to malignant transformation of GC B-cells in mice. Herein we explored potential mechanisms and clinical relevance of Smc3 deficiency in GC lymphomagenesis. Transcriptional profiling of Smc3 haploinsufficient murine lymphomas revealed downregulation of genes repressed by loss of epigenetic tumor suppressors Tet2 and Kmt2d. Profiling 3D chromosomal interactions in lymphomas revealed impaired enhancer-promoter interactions affecting genes like Tet2, which was aberrantly downregulated in Smc3 deficient lymphomas. Tet2 plays important roles in B-cell exit from the GC reaction, and single cell RNA-seq profiles and phenotypic trajectory analysis in Smc3 mutant mice revealed a specific defect in commitment to the final steps of plasma cell differentiation. Although Smc3 deficiency resulted in structural abnormalities in GC B-cells, there was no increase of somatic mutations or structural variants in Smc3 haploinsufficient lymphomas, suggesting that cohesin deficiency largely induces lymphomas through disruption of enhancer-promoter interactions of terminal differentiation and tumor suppressor genes. Strikingly, the presence of the Smc3 haploinsufficient GC B-cell transcriptional signature in human patients with GC-derived diffuse large B-cell lymphoma (DLBCL) was linked to inferior clinical outcome and low expression of cohesin core subunits. Reciprocally, reduced expression of cohesin subunits was an independent risk factor for worse survival int DLBCL patient cohorts. Collectively, the data suggest that Smc3 functions as a bona fide tumor suppressor for lymphomas through non-genetic mechanisms, and drives disease by disrupting the commitment of GC B-cells to the plasma cell fate.
Collapse
MESH Headings
- Animals
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/immunology
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Cells, Cultured
- Chondroitin Sulfate Proteoglycans/genetics
- Chondroitin Sulfate Proteoglycans/immunology
- Chondroitin Sulfate Proteoglycans/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/immunology
- Chromosomal Proteins, Non-Histone/metabolism
- Coculture Techniques
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Databases, Genetic
- Dioxygenases/genetics
- Dioxygenases/metabolism
- Gene Dosage
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Germinal Center/immunology
- Germinal Center/metabolism
- Haploinsufficiency
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Humans
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Mice, Knockout
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Phenotype
- Plasma Cells/immunology
- Plasma Cells/metabolism
- Transcription, Genetic
- Mice
Collapse
Affiliation(s)
- Martin A. Rivas
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Ceyda Durmaz
- Graduate Program on Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, New York, NY, United States
| | - Andreas Kloetgen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Cristopher R. Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Department of Population Health Sciences, Weill Cornell Medical College, New York, NY, United States
| | - Bhavneet Bhinder
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Aaron D. Viny
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, United States
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY, United States
| | - Christopher D. Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Jeremy M. Boss
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, United States
| | - Ari M. Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| |
Collapse
|
33
|
Martinez-Calle N, Isbell LK, Cwynarski K, Schorb E. Advances in treatment of elderly primary central nervous system lymphoma. Br J Haematol 2021; 196:473-487. [PMID: 34448202 DOI: 10.1111/bjh.17799] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The management of older individuals (≥60 years) with primary central nervous system lymphoma remains a clinical challenge. Identification of optimal therapy and delivering adequate dose intensity are two of the major issues in treating elderly patients. Premorbid performance status and comorbidities influence individualised treatment approaches and geriatric assessment tools are increasingly utilised. Optimal induction treatment remains high-dose methotrexate-based immunochemotherapy, delivery is feasible in the majority of patients and the goal of treatment remains achieving complete remission. Consolidation strategies are also relevant in the elderly, aiming to maximise duration of response and quality of life (QoL). Potential options include high-dose therapy with haematopoietic stem cell consolidation, non-myeloablative chemotherapy and whole-brain radiotherapy. Efficacy of novel agents, such as Bruton tyrosine kinase inhibitors and lenalidomide, have been reported; these represent an alternative for elderly patients unfit for chemotherapy. Prognosis remains poor, improvement of outcomes in this age group is urgently needed.
Collapse
Affiliation(s)
- Nicolas Martinez-Calle
- Clinical Haematology Department, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Lisa K Isbell
- Department of Haematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kate Cwynarski
- Department of Haematology, University College Hospital, London, UK
| | - Elisabeth Schorb
- Department of Haematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| |
Collapse
|
34
|
Wang M, Dai M, Wang D, Tang T, Xiong F, Xiang B, Zhou M, Li X, Li Y, Xiong W, Li G, Zeng Z, Guo C. The long noncoding RNA AATBC promotes breast cancer migration and invasion by interacting with YBX1 and activating the YAP1/Hippo signaling pathway. Cancer Lett 2021; 512:60-72. [PMID: 33951538 DOI: 10.1016/j.canlet.2021.04.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022]
Abstract
Long noncoding RNAs (lncRNAs) play an important role in the regulation of gene expression and are involved in several pathological responses. However, many important lncRNAs in breast cancer have not been identified and their expression levels and functions in breast cancer remain unknown. In this study, the lncRNA apoptosis-associated transcript in bladder cancer (AATBC) was found to be significantly highly expressed in breast cancer patients. In vitro and in vivo experiments indicated that AATBC promoted breast cancer metastasis. Further studies revealed that AATBC activated the YAP1/Hippo signaling pathway through the AATBC-YBX1-MST1 axis. This is also an important supplement to the composition of the YAP1/Hippo signaling pathway. The model of "AATBC-YAP1" may bring a new dawn to the treatment of breast cancer.
Collapse
Affiliation(s)
- Maonan Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Manli Dai
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Dan Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Ting Tang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Fang Xiong
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Xiaoling Li
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Yong Li
- Department of Medicine, Comprehensive Cancer Center Baylor College of Medicine, Houston, TX, USA
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Can Guo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
| |
Collapse
|
35
|
Luo H, Bu D, Shao L, Li Y, Sun L, Wang C, Wang J, Yang W, Yang X, Dong J, Zhao Y, Li F. Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:377-393. [PMID: 34284134 PMCID: PMC8864193 DOI: 10.1016/j.gpb.2021.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 12/03/2020] [Accepted: 03/06/2021] [Indexed: 01/08/2023]
Abstract
The development of new biomarkers or therapeutic targets for cancer immunotherapies requires deep understanding of T cells. To date, the complete landscape and systematic characterization of long noncoding RNAs (lncRNAs) in T cells in cancer immunity are lacking. Here, by systematically analyzing full-length single-cell RNA sequencing (scRNA-seq) data of more than 20,000 libraries of T cells across three cancer types, we provided the first comprehensive catalog and the functional repertoires of lncRNAs in human T cells. Specifically, we developed a custom pipeline for de novotranscriptome assembly and obtained a novel lncRNA catalog containing 9433 genes. This increased the number of current human lncRNA catalog by 16% and nearly doubled the number of lncRNAs expressed in T cells. We found that a portion of expressed genes in single T cells were lncRNAs which had been overlooked by the majority of previous studies. Based on metacell maps constructed by the MetaCell algorithm that partitions scRNA-seq datasets into disjointed and homogenous groups of cells (metacells), 154 signature lncRNA genes were identified. They were associated with effector, exhausted, and regulatory T cell states. Moreover, 84 of them were functionally annotated based on the co-expression networks, indicating that lncRNAs might broadly participate in the regulation of T cell functions. Our findings provide a new point of view and resource for investigating the mechanisms of T cell regulation in cancer immunity as well as for novel cancer-immune biomarker development and cancer immunotherapies
Collapse
Affiliation(s)
- Haitao Luo
- Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China; Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen 518020, China; Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou 510632, China.
| | - Dechao Bu
- Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computing Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Lijuan Shao
- Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China; Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen 518020, China; Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou 510632, China
| | - Yang Li
- Department of Gastrointestinal Surgery, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China
| | - Liang Sun
- Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computing Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Ce Wang
- Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China; Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen 518020, China
| | - Jing Wang
- Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China; Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen 518020, China; Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou 510632, China
| | - Wei Yang
- Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China; Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen 518020, China
| | - Xiaofei Yang
- Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China; Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen 518020, China
| | - Jun Dong
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou 510632, China.
| | - Yi Zhao
- Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computing Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.
| | - Furong Li
- Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China; Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen 518020, China.
| |
Collapse
|
36
|
Sun X, Cheng L, Liu J, Xie C, Yang J, Li F. Predicting lncRNA-Protein Interaction With Weighted Graph-Regularized Matrix Factorization. Front Genet 2021; 12:690096. [PMID: 34335693 PMCID: PMC8322775 DOI: 10.3389/fgene.2021.690096] [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: 04/02/2021] [Accepted: 05/21/2021] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are widely concerned because of their close associations with many key biological activities. Though precise functions of most lncRNAs are unknown, research works show that lncRNAs usually exert biological function by interacting with the corresponding proteins. The experimental validation of interactions between lncRNAs and proteins is costly and time-consuming. In this study, we developed a weighted graph-regularized matrix factorization (LPI-WGRMF) method to find unobserved lncRNA-protein interactions (LPIs) based on lncRNA similarity matrix, protein similarity matrix, and known LPIs. We compared our proposed LPI-WGRMF method with five classical LPI prediction methods, that is, LPBNI, LPI-IBNRA, LPIHN, RWR, and collaborative filtering (CF). The results demonstrate that the LPI-WGRMF method can produce high-accuracy performance, obtaining an AUC score of 0.9012 and AUPR of 0.7324. The case study showed that SFPQ, SNHG3, and PRPF31 may associate with Q9NUL5, Q9NUL5, and Q9UKV8 with the highest linking probabilities and need to further experimental validation.
Collapse
Affiliation(s)
- Xibo Sun
- Yidu Central Hospital of Weifang, Weifang, China
| | | | - Jinyang Liu
- Geneis Beijing Co., Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Cuinan Xie
- Geneis Beijing Co., Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Jiasheng Yang
- Academician Workstation, Changsha Medical University, Changsha, China
| | - Fu Li
- Department of Thoracic Surgery, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| |
Collapse
|
37
|
Napoli S, Cascione L, Rinaldi A, Spriano F, Guidetti F, Zhang F, Cacciapuoti MT, Mensah AA, Sartori G, Munz N, Forcato M, Bicciato S, Chiappella A, Ghione P, Elemento O, Cerchietti L, Inghirami G, Bertoni F. Characterization of GECPAR, a noncoding RNA that regulates the transcriptional program of diffuse large B-cell lymphoma. Haematologica 2021; 107:1131-1143. [PMID: 34162177 PMCID: PMC9052922 DOI: 10.3324/haematol.2020.267096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 01/09/2023] Open
Abstract
Enhancers are regulatory regions of DNA, which play a key role in cell-type specific differentiation and development. Most active enhancers are transcribed into enhancer RNA (eRNA) that can regulate transcription of target genes by means of in cis as well as in trans action. eRNA stabilize contacts between distal genomic regions and mediate the interaction of DNA with master transcription factors. Here, we characterized an enhancer eRNA, GECPAR (germinal center proliferative adapter RNA), which is specifically transcribed in normal and neoplastic germinal center B cells from the super-enhancer of POU2AF1, a key regulatory gene of the germinal center reaction. Using diffuse large B-cell lymphoma cell line models, we demonstrated the tumor suppressor activity of GECPAR, which is mediated via its transcriptional regulation of proliferation and differentiation genes, particularly MYC and the Wnt pathway.
Collapse
Affiliation(s)
- Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,SARA NAPOLI
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Filippo Spriano
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Francesca Guidetti
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Fangwen Zhang
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | | | - Afua Adjeiwaa Mensah
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Giulio Sartori
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Nicolas Munz
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Mattia Forcato
- Center for Genome Research, Department of Life Sciences University of Modena and Reggio, Modena, Italy
| | - Silvio Bicciato
- Center for Genome Research, Department of Life Sciences University of Modena and Reggio, Modena, Italy
| | - Annalisa Chiappella
- Ematologia, A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy
| | - Paola Ghione
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Leandro Cerchietti
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Giorgio Inghirami
- Pathology and Laboratory Medicine Department, Weill Cornell Medicine, New York, NY, USA
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,Oncology Institute of Southern Switzerland, Bellinzona, Switzerland,FRANCESCO BERTONI
| |
Collapse
|
38
|
Zhang Z, Yan C, Li K, Bao S, Li L, Chen L, Zhao J, Sun J, Zhou M. Pan-cancer characterization of lncRNA modifiers of immune microenvironment reveals clinically distinct de novo tumor subtypes. NPJ Genom Med 2021; 6:52. [PMID: 34140519 PMCID: PMC8211863 DOI: 10.1038/s41525-021-00215-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/25/2021] [Indexed: 01/20/2023] Open
Abstract
The emerging field of long noncoding RNA (lncRNA)-immunity has provided a new perspective on cancer immunity and immunotherapies. The lncRNA modifiers of infiltrating immune cells in the tumor immune microenvironment (TIME) and their impact on tumor behavior and disease prognosis remain largely uncharacterized. In the present study, a systems immunology framework integrating the noncoding transcriptome and immunogenomics profiles of 9549 tumor samples across 30 solid cancer types was used, and 36 lncRNAs were identified as modifier candidates underlying immune cell infiltration in the TIME at the pan-cancer level. These TIME lncRNA modifiers (TIL-lncRNAs) were able to subclassify various tumors into three de novo pan-cancer subtypes characterized by distinct immunological features, biological behaviors, and disease prognoses. Finally, a TIL-lncRNA-derived immune state index (TISI) that was reflective of immunological and oncogenic states but also predictive of patients' prognosis was proposed. Furthermore, the TISI provided additional prognostic value for existing tumor immunological and molecular subtypes. By applying the TISI to tumors from different clinical immunotherapy cohorts, the TISI was found to be significantly negatively correlated with immune-checkpoint genes and to have the ability to predict the effectiveness of immunotherapy. In conclusion, the present study provided comprehensive resources and insights for future functional and mechanistic studies on lncRNA-mediated cancer immunity and highlighted the potential of the clinical application of lncRNA-based immunotherapeutic strategies in precision immunotherapy.
Collapse
Affiliation(s)
- Zicheng Zhang
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Congcong Yan
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Ke Li
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Siqi Bao
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Lei Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Lu Chen
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jingting Zhao
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jie Sun
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China.
| | - Meng Zhou
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, China.
| |
Collapse
|
39
|
Diversity of Rainbow Trout Blood B Cells Revealed by Single Cell RNA Sequencing. BIOLOGY 2021; 10:biology10060511. [PMID: 34207643 PMCID: PMC8227096 DOI: 10.3390/biology10060511] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/03/2021] [Accepted: 06/06/2021] [Indexed: 01/13/2023]
Abstract
Simple Summary Although evolutionarily jawed fish constitute the first group of animals in which a complete adaptive immune system based on immunoglobulins (Igs) is present, many structural immune differences between fish and mammals predict important functional and phenotypical differences between B cells in these two animal groups. However, to date, very few tools are available to study B cell heterogeneity and functionality in fish. Hence, thus far, antibodies targeting the different Igs have been almost exclusively applied as tools to investigate B cell functionality in fish. In the current study, we used the newly developed 10× Genomics single cell RNA sequencing technology and used it to analyze the transcriptional pattern of single B cells from peripheral blood. The results obtained provide us with a transcriptional profile at single cell level of what seem to correspond to different B cell subsets or B cells in different stages of maturation or differentiation. The information provided will not only help us understand the biology of teleost B cells, but also provides us with a repertoire of potential markers that could be used in the future to differentiate trout B cell subsets. Abstract Single-cell sequencing technologies capable of providing us with immune information from dozens to thousands of individual cells simultaneously have revolutionized the field of immunology these past years. However, to date, most of these novel technologies have not been broadly applied to non-model organisms such as teleost fish. In this study, we used the 10× Genomics single cell RNA sequencing technology and used it to analyze for the first time in teleost fish the transcriptional pattern of single B cells from peripheral blood. The analysis of the data obtained in rainbow trout revealed ten distinct cell clusters that seem to be associated with different subsets and/or maturation/differentiation stages of circulating B cells. The potential characteristics and functions of these different B cell subpopulations are discussed on the basis of their transcriptomic profile. The results obtained provide us with valuable information to understand the biology of teleost B cells and offer us a repertoire of potential markers that could be used in the future to differentiate trout B cell subsets.
Collapse
|
40
|
Zeni PF, Mraz M. LncRNAs in adaptive immunity: role in physiological and pathological conditions. RNA Biol 2021; 18:619-632. [PMID: 33094664 PMCID: PMC8078528 DOI: 10.1080/15476286.2020.1838783] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022] Open
Abstract
The adaptive immune system is responsible for generating immunological response and immunological memory. Regulation of adaptive immunity including B cell and T cell biology was mainly understood from the protein and microRNA perspective. However, long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs (ncRNAs) that influence key factors in lymphocyte biology such as NOTCH, PAX5, MYC and EZH2. LncRNAs were described to modulate lymphocyte activation by regulating pathways such as NFAT, NFκB, MYC, interferon and TCR/BCR signalling (NRON, NKILA, BCALM, GAS5, PVT1), and cell effector functions (IFNG-AS1, TH2-LCR). Here we review lncRNA involvement in adaptive immunity and the implications for autoimmune diseases (multiple sclerosis, inflammatory bowel disease, rheumatoid arthritis) and T/B cell leukaemias and lymphomas (CLL, MCL, DLBCL, T-ALL). It is becoming clear that lncRNAs are important in adaptive immune response and provide new insights into its orchestration.
Collapse
Affiliation(s)
- Pedro Faria Zeni
- Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| |
Collapse
|
41
|
The Role of lncRNAs in the Pathobiology and Clinical Behavior of Multiple Myeloma. Cancers (Basel) 2021; 13:cancers13081976. [PMID: 33923983 PMCID: PMC8074217 DOI: 10.3390/cancers13081976] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Multiple myeloma (MM), the second most common hematological neoplasm, is still considered an incurable disease. Long non-coding RNAs (lncRNAs), genes that do not encode proteins, participate in numerous biological processes, but their deregulation, like that of coding genes, can contribute to carcinogenesis. Increasing evidence points to the relevant role of lncRNAs in the development of human tumors, such that they emerge as attractive biomarkers and therapeutic targets for cancer treatment, including MM. Here we review the oncogenic or tumor-suppressor functions of lncRNAs in MM and provide an overview of novel therapeutic approaches based on lncRNAs that will help to improve the management of these patients. Abstract MM is a hematological neoplasm that is still considered an incurable disease. Besides established genetic alterations, recent studies have shown that MM pathogenesis is also characterized by epigenetic aberrations, such as the gain of de novo active chromatin marks in promoter and enhancer regions and extensive DNA hypomethylation of intergenic regions, highlighting the relevance of these non-coding genomic regions. A recent study described how long non-coding RNAs (lncRNAs) correspond to 82% of the MM transcriptome and an increasing number of studies have demonstrated the importance of deregulation of lncRNAs in MM. In this review we focus on the deregulated lncRNAs in MM, including their biological or functional mechanisms, their role as biomarkers to improve the prognosis and monitoring of MM patients, and their participation in drug resistance. Furthermore, we also discuss the evidence supporting the role of lncRNAs as therapeutic targets through different novel RNA-based strategies.
Collapse
|
42
|
Long, Noncoding RNA Dysregulation in Glioblastoma. Cancers (Basel) 2021; 13:cancers13071604. [PMID: 33807183 PMCID: PMC8037018 DOI: 10.3390/cancers13071604] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/20/2021] [Accepted: 03/24/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Developing effective therapies for glioblastoma (GBM), the most common primary brain cancer, remains challenging due to the heterogeneity within tumors and therapeutic resistance that drives recurrence. Noncoding RNAs are transcribed from a large proportion of the genome and remain largely unexplored in their contribution to the evolution of GBM tumors. Here, we will review the general mechanisms of long, noncoding RNAs and the current knowledge of how these impact heterogeneity and therapeutic resistance in GBM. A better understanding of the molecular drivers required for these aggressive tumors is necessary to improve the management and outcomes of this challenging disease. Abstract Transcription occurs across more than 70% of the human genome and more than half of currently annotated genes produce functional noncoding RNAs. Of these transcripts, the majority—long, noncoding RNAs (lncRNAs)—are greater than 200 nucleotides in length and are necessary for various roles in the cell. It is increasingly appreciated that these lncRNAs are relevant in both health and disease states, with the brain expressing the largest number of lncRNAs compared to other organs. Glioblastoma (GBM) is an aggressive, fatal brain tumor that demonstrates remarkable intratumoral heterogeneity, which has made the development of effective therapies challenging. The cooperation between genetic and epigenetic alterations drives rapid adaptation that allows therapeutic evasion and recurrence. Given the large repertoire of lncRNAs in normal brain tissue and the well-described roles of lncRNAs in molecular and cellular processes, these transcripts are important to consider in the context of GBM heterogeneity and treatment resistance. Herein, we review the general mechanisms and biological roles of lncRNAs, with a focus on GBM, as well as RNA-based therapeutics currently in development.
Collapse
|
43
|
Arora L, Pal D. Remodeling of Stromal Cells and Immune Landscape in Microenvironment During Tumor Progression. Front Oncol 2021; 11:596798. [PMID: 33763348 PMCID: PMC7982455 DOI: 10.3389/fonc.2021.596798] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/29/2021] [Indexed: 12/12/2022] Open
Abstract
The molecular understanding of carcinogenesis and tumor progression rests in intra and inter-tumoral heterogeneity. Solid tumors confined with vast diversity of genetic abnormalities, epigenetic modifications, and environmental cues that differ at each stage from tumor initiation, progression, and metastasis. Complexity within tumors studied by conventional molecular techniques fails to identify different subclasses in stromal and immune cells in individuals and that affects immunotherapies. Here we focus on diversity of stromal cell population and immune inhabitants, whose subtypes create the complexity of tumor microenvironment (TME), leading primary tumors towards advanced-stage cancers. Recent advances in single-cell sequencing (epitope profiling) approach circumscribes phenotypic markers, molecular pathways, and evolutionary trajectories of an individual cell. We discussed the current knowledge of stromal and immune cell subclasses at different stages of cancer development with the regulatory role of non-coding RNAs. Finally, we reported the current therapeutic options in immunotherapies, advances in therapies targeting heterogeneity, and possible outcomes.
Collapse
Affiliation(s)
- Leena Arora
- Tissue Engineering and Regenerative Medicine Lab, Indian Institute of Technology Ropar, Rupnagar, India
| | - Durba Pal
- Tissue Engineering and Regenerative Medicine Lab, Indian Institute of Technology Ropar, Rupnagar, India
| |
Collapse
|
44
|
He H, Wu S, Ai K, Xu R, Zhong Z, Wang Y, Zhang L, Zhao X, Zhu X. LncRNA ZNF503-AS1 acts as a tumor suppressor in bladder cancer by up-regulating Ca 2+ concentration via transcription factor GATA6. Cell Oncol (Dordr) 2021; 44:219-233. [PMID: 33001357 DOI: 10.1007/s13402-020-00563-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Ca2+ homeostasis plays a pivotal role in regulating proliferation and apoptosis during cancer development. This study intended to examine the potential tumor-suppressing role of ZNF503 antisense RNA 1 (ZNF503-AS1) in bladder cancer, which may be implicated in the regulation of Ca2+ homeostasis. METHODS Differentially expressed long non-coding RNAs (lncRNAs) related to bladder cancer were identified using microarray analysis, followed by the verification of transcription factors to which they bind. The relationship between ZNF503-AS1, GATA6 and SLC8A1 was assessed using dual luciferase reporter, RIP and ChIP assays. The expression levels of ZNF503-AS1, GATA6 and SLC8A1 were modulated to examine their effects on the tumorigenic potential, intracellular Ca2+ concentration and Ca2+-ATPase activity in bladder cancer cells. The in vivo tumorigenic ability was validated in nude mice. RESULTS Microarray-based expression profile analysis of the GEO GSE61615 dataset revealed that the expression of ZNF503-AS1 was decreased in bladder cancer. Subsequently, we found that ZNF503-AS1 can bind to the transcription factor GATA6 to up-regulate the expression of SLC8A1. ZNF503-AS1 and SLC8A1 were found to be down-regulated in both primary bladder cancer tissues and cells. Exogenous overexpression of ZNF503-AS1 or SLC8A1 attenuated bladder cancer cell proliferation, invasion and migration, but promoted their apoptosis, accompanied by decreased Ca2+-ATPase activities and increased intracellular Ca2+ concentrations. Additional in vivo experiments validated the inhibitory effect of ZNF503-AS1 overexpression on the tumorigenic capacity of bladder cancer cells in nude mice. CONCLUSION ZNF503-AS1 can recruit transcription factor GATA6 to up-regulate SLC8A1 expression, thereby increasing the intracellular Ca2+ concentration and repressing the proliferation, invasion and migration, and enhancing the apoptosis of bladder cancer cells.
Collapse
Affiliation(s)
- Haiqing He
- Department of Urology, The Second Xiangya Hospital, Central South University, No.139 Renmin Road, Changsha, 410011, Hunan Province, People's Republic of China
| | - Shuiqing Wu
- Department of Urology, The Second Xiangya Hospital, Central South University, No.139 Renmin Road, Changsha, 410011, Hunan Province, People's Republic of China
| | - Kai Ai
- Department of Urology, The Second Xiangya Hospital, Central South University, No.139 Renmin Road, Changsha, 410011, Hunan Province, People's Republic of China
| | - Ran Xu
- Department of Urology, The Second Xiangya Hospital, Central South University, No.139 Renmin Road, Changsha, 410011, Hunan Province, People's Republic of China
| | - Zhaohui Zhong
- Department of Urology, The Second Xiangya Hospital, Central South University, No.139 Renmin Road, Changsha, 410011, Hunan Province, People's Republic of China
| | - Yinhuai Wang
- Department of Urology, The Second Xiangya Hospital, Central South University, No.139 Renmin Road, Changsha, 410011, Hunan Province, People's Republic of China
| | - Lei Zhang
- Department of Urology, The Second Xiangya Hospital, Central South University, No.139 Renmin Road, Changsha, 410011, Hunan Province, People's Republic of China
| | - Xiaokun Zhao
- Department of Urology, The Second Xiangya Hospital, Central South University, No.139 Renmin Road, Changsha, 410011, Hunan Province, People's Republic of China.
| | - Xuan Zhu
- Department of Urology, The Second Xiangya Hospital, Central South University, No.139 Renmin Road, Changsha, 410011, Hunan Province, People's Republic of China.
| |
Collapse
|
45
|
Rivas MA, Meydan C, Chin CR, Challman MF, Kim D, Bhinder B, Kloetgen A, Viny AD, Teater MR, McNally DR, Doane AS, Béguelin W, Fernández MTC, Shen H, Wang X, Levine RL, Chen Z, Tsirigos A, Elemento O, Mason CE, Melnick AM. Smc3 dosage regulates B cell transit through germinal centers and restricts their malignant transformation. Nat Immunol 2021; 22:240-253. [PMID: 33432228 PMCID: PMC7855695 DOI: 10.1038/s41590-020-00827-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 10/25/2020] [Indexed: 01/28/2023]
Abstract
During the germinal center (GC) reaction, B cells undergo extensive redistribution of cohesin complex and three-dimensional reorganization of their genomes. Yet, the significance of cohesin and architectural programming in the humoral immune response is unknown. Herein we report that homozygous deletion of Smc3, encoding the cohesin ATPase subunit, abrogated GC formation, while, in marked contrast, Smc3 haploinsufficiency resulted in GC hyperplasia, skewing of GC polarity and impaired plasma cell (PC) differentiation. Genome-wide chromosomal conformation and transcriptional profiling revealed defects in GC B cell terminal differentiation programs controlled by the lymphoma epigenetic tumor suppressors Tet2 and Kmt2d and failure of Smc3-haploinsufficient GC B cells to switch from B cell- to PC-defining transcription factors. Smc3 haploinsufficiency preferentially impaired the connectivity of enhancer elements controlling various lymphoma tumor suppressor genes, and, accordingly, Smc3 haploinsufficiency accelerated lymphomagenesis in mice with constitutive Bcl6 expression. Collectively, our data indicate a dose-dependent function for cohesin in humoral immunity to facilitate the B cell to PC phenotypic switch while restricting malignant transformation.
Collapse
MESH Headings
- Animals
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cell Cycle Proteins/deficiency
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Cells, Cultured
- Chondroitin Sulfate Proteoglycans/deficiency
- Chondroitin Sulfate Proteoglycans/genetics
- Chondroitin Sulfate Proteoglycans/metabolism
- Chromosomal Proteins, Non-Histone/deficiency
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Dioxygenases
- Gene Deletion
- Gene Dosage
- Gene Expression Regulation, Neoplastic
- Germinal Center/immunology
- Germinal Center/metabolism
- Germinal Center/pathology
- Haploinsufficiency
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Humans
- Immunity, Humoral
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/pathology
- Mice, Inbred C57BL
- Mice, Knockout
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Signal Transduction
- Cohesins
- Mice
Collapse
Affiliation(s)
- Martín A Rivas
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher R Chin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matt F Challman
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Daleum Kim
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Bhavneet Bhinder
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Aaron D Viny
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matt R Teater
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dylan R McNally
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ashley S Doane
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Wendy Béguelin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Hao Shen
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xiang Wang
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ross L Levine
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Institute for Computational Medicine, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
46
|
Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation. Nat Commun 2021; 12:651. [PMID: 33510161 PMCID: PMC7844026 DOI: 10.1038/s41467-020-20849-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
To investigate the three-dimensional (3D) genome architecture across normal B cell differentiation and in neoplastic cells from different subtypes of chronic lymphocytic leukemia and mantle cell lymphoma patients, here we integrate in situ Hi-C and nine additional omics layers. Beyond conventional active (A) and inactive (B) compartments, we uncover a highly-dynamic intermediate compartment enriched in poised and polycomb-repressed chromatin. During B cell development, 28% of the compartments change, mostly involving a widespread chromatin activation from naive to germinal center B cells and a reversal to the naive state upon further maturation into memory B cells. B cell neoplasms are characterized by both entity and subtype-specific alterations in 3D genome organization, including large chromatin blocks spanning key disease-specific genes. This study indicates that 3D genome interactions are extensively modulated during normal B cell differentiation and that the genome of B cell neoplasias acquires a tumor-specific 3D genome architecture.
Collapse
|
47
|
Valcárcel LV, Amundarain A, Kulis M, Charalampopoulou S, Melnick A, San Miguel J, Martín-Subero JI, Planes FJ, Agirre X, Prosper F. Gene expression derived from alternative promoters improves prognostic stratification in multiple myeloma. Leukemia 2021; 35:3012-3016. [PMID: 33972667 PMCID: PMC8478642 DOI: 10.1038/s41375-021-01263-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/08/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
Clinical and genetic risk factors are currently used in multiple myeloma (MM) to stratify patients and to design specific therapies. However, these systems do not capture the heterogeneity of the disease supporting the development of new prognostic factors. In this study, we identified active promoters and alternative active promoters in 6 different B cell subpopulations, including bone-marrow plasma cells, and 32 MM patient samples, using RNA-seq data. We find that expression initiated at both regular and alternative promoters was specific of each B cell subpopulation or MM plasma cells, showing a remarkable level of consistency with chromatin-based promoter definition. Interestingly, using 595 MM patient samples from the CoMMpass dataset, we observed that the expression derived from some alternative promoters was associated with lower progression-free and overall survival in MM patients independently of genetic alterations. Altogether, our results define cancer-specific alternative active promoters as new transcriptomic features that can provide a new avenue for prognostic stratification possibilities in patients with MM.
Collapse
Affiliation(s)
- Luis V. Valcárcel
- grid.5924.a0000000419370271Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, IDISNA, Pamplona, Spain ,grid.5924.a0000000419370271Tecnun School of Engineering, Universidad de Navarra, San Sebastian, Spain
| | - Ane Amundarain
- grid.5924.a0000000419370271Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, IDISNA, Pamplona, Spain ,grid.510933.d0000 0004 8339 0058Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Pamplona, Spain
| | - Marta Kulis
- grid.428756.a0000 0004 0412 0974Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain ,grid.10403.36Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Stella Charalampopoulou
- grid.428756.a0000 0004 0412 0974Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain ,grid.10403.36Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Ari Melnick
- grid.5386.8000000041936877XDivision of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY USA
| | - Jesús San Miguel
- grid.5924.a0000000419370271Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, IDISNA, Pamplona, Spain ,grid.510933.d0000 0004 8339 0058Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Pamplona, Spain ,grid.411730.00000 0001 2191 685XServicio de Hematología, Clínica Universidad de Navarra, Pamplona, Spain
| | - José I. Martín-Subero
- grid.510933.d0000 0004 8339 0058Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Pamplona, Spain ,grid.10403.36Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain ,grid.425902.80000 0000 9601 989XInstitució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain ,grid.5841.80000 0004 1937 0247Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
| | - Francisco J. Planes
- grid.5924.a0000000419370271Tecnun School of Engineering, Universidad de Navarra, San Sebastian, Spain
| | - Xabier Agirre
- grid.5924.a0000000419370271Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, IDISNA, Pamplona, Spain ,grid.510933.d0000 0004 8339 0058Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Pamplona, Spain
| | - Felipe Prosper
- grid.5924.a0000000419370271Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, IDISNA, Pamplona, Spain ,grid.510933.d0000 0004 8339 0058Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Pamplona, Spain ,grid.411730.00000 0001 2191 685XServicio de Hematología, Clínica Universidad de Navarra, Pamplona, Spain
| |
Collapse
|
48
|
Characterization of complete lncRNAs transcriptome reveals the functional and clinical impact of lncRNAs in multiple myeloma. Leukemia 2021; 35:1438-1450. [PMID: 33597729 PMCID: PMC8102198 DOI: 10.1038/s41375-021-01147-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 12/03/2020] [Accepted: 01/21/2021] [Indexed: 02/07/2023]
Abstract
Multiple myeloma (MM) is an incurable disease, whose clinical heterogeneity makes its management challenging, highlighting the need for biological features to guide improved therapies. Deregulation of specific long non-coding RNAs (lncRNAs) has been shown in MM, nevertheless, the complete lncRNA transcriptome has not yet been elucidated. In this work, we identified 40,511 novel lncRNAs in MM samples. lncRNAs accounted for 82% of the MM transcriptome and were more heterogeneously expressed than coding genes. A total of 10,351 overexpressed and 9,535 downregulated lncRNAs were identified in MM patients when compared with normal bone-marrow plasma cells. Transcriptional dynamics study of lncRNAs in the context of normal B-cell maturation revealed 989 lncRNAs with exclusive expression in MM, among which 89 showed de novo epigenomic activation. Knockdown studies on one of these lncRNAs, SMILO (specific myeloma intergenic long non-coding RNA), resulted in reduced proliferation and induction of apoptosis of MM cells, and activation of the interferon pathway. We also showed that the expression of lncRNAs, together with clinical and genetic risk alterations, stratified MM patients into several progression-free survival and overall survival groups. In summary, our global analysis of the lncRNAs transcriptome reveals the presence of specific lncRNAs associated with the biological and clinical behavior of the disease.
Collapse
|
49
|
Intron retention-induced neoantigen load correlates with unfavorable prognosis in multiple myeloma. Oncogene 2021; 40:6130-6138. [PMID: 34504297 PMCID: PMC8426332 DOI: 10.1038/s41388-021-02005-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/17/2021] [Accepted: 08/27/2021] [Indexed: 02/08/2023]
Abstract
Neoantigen peptides arising from genetic alterations may serve as targets for personalized cancer vaccines and as positive predictors of response to immune checkpoint therapy. Mutations in genes regulating RNA splicing are common in hematological malignancies leading to dysregulated splicing and intron retention (IR). In this study, we investigated IR as a potential source of tumor neoantigens in multiple myeloma (MM) patients and the relationship of IR-induced neoantigens (IR-neoAg) with clinical outcomes. MM-specific IR events were identified in RNA-sequencing data from the Multiple Myeloma Research Foundation CoMMpass study after removing IR events that also occurred in normal plasma cells. We quantified the IR-neoAg load by assessing IR-induced novel peptides that were predicted to bind to major histocompatibility complex (MHC) molecules. We found that high IR-neoAg load was associated with poor overall survival in both newly diagnosed and relapsed MM patients. Further analyses revealed that poor outcome in MM patients with high IR-neoAg load was associated with high expression levels of T-cell co-inhibitory molecules and elevated interferon signaling activity. We also found that MM cells exhibiting high IR levels had lower MHC-II protein abundance and treatment of MM cells with a spliceosome inhibitor resulted in increased MHC-I protein abundance. Our findings suggest that IR-neoAg may represent a novel biomarker of MM patient clinical outcome and further that targeting RNA splicing may serve as a potential therapeutic strategy to prevent MM immune escape and promote response to checkpoint blockade.
Collapse
|
50
|
LINC00968 can inhibit the progression of lung adenocarcinoma through the miR-21-5p/SMAD7 signal axis. Aging (Albany NY) 2020; 12:21904-21922. [PMID: 33147570 PMCID: PMC7695398 DOI: 10.18632/aging.104011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 07/30/2020] [Indexed: 12/16/2022]
Abstract
Background: Long non-coding RNAs (LncRNAs) have been associated with several types of cancer. However, little is known about their role in lung adenocarcinoma (LUAD). Results: LINC00968 was significantly differentially expressed in LUAD tissues. Downregulated LINC00968 was associated with clinicopathological features of LUAD. LINC00968 inhibited cell growth and metastasis by regulating the Hippo signaling pathway We demonstrated that LINC00968 acts as a ceRNA to consume miR-21-5p, enhancing the accumulation of SMAD7, a miR-21-5p target. Conclusions: LINC00968 limits LUAD progression via the miR-21-5p/SMAD7 axis and may serve as a prognostic biomarker and therapeutic target for LUAD. Methods: We conducted comprehensive data mining on LINC00968 based on the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. The expression of LINC00968 in LUAD cells was determined using in situ hybridization. We detected LINC00968 function in LUAD cells using the MTT, clone formation, and transwell assays, and tumor xenografts. Label-free quantitative proteomics, western blotting, a dual-luciferase reporter assay, immunofluorescence, and RNA immunoprecipitation assays were used to determine the correlations among LINC00968, miR-21-5p, and SMAD7. Gain- and loss-function approaches were used to explore the effects of LINC00968, miR-21-5p, and SMAD7 on cell proliferation, migration, and invasion.
Collapse
|