1
|
Saberi F, Dehghan Z, Noori E, Zali H. Identification of Renal Transplantation Rejection Biomarkers in Blood Using the Systems Biology Approach. IRANIAN BIOMEDICAL JOURNAL 2023; 27:375-87. [PMID: 38224029 PMCID: PMC10826908 DOI: 10.52547/ibj.3871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 08/19/2023] [Indexed: 01/16/2024]
Abstract
Background Renal transplantation plays an essential role in the quality of life of patients with end-stage renal disease. At least 12% of the renal patients receiving transplantations show graft rejection. One of the methods used to diagnose renal transplantation rejection is renal allograft biopsy. This procedure is associated with some risks such as bleeding and arteriovenous fistula formation. In this study, we applied a bioinformatics approach to identify serum markers for graft rejection in patients receiving a renal transplantation. Methods Transcriptomic data were first retrieved from the blood of renal transplantation rejection patients using the GEO database. The data were then used to construct the protein-protein interaction and gene regulatory networks using Cytoscape software. Next, network analysis was performed to identify hub-bottlenecks, and key blood markers involved in renal graft rejection. Lastly, the gene ontology and functional pathways related to hub-bottlenecks were detected using PANTHER and DAVID servers. Results In PPIN and GRN, SYNCRIP, SQSTM1, GRAMD1A, FAM104A, ND2, TPGS2, ZNF652, RORA, and MALAT1 were the identified critical genes. In GRN, miR-155, miR17, miR146b, miR-200 family, and GATA2 were the factors that regulated critical genes. The MAPK, neurotrophin, and TNF signaling pathways, IL-17, and human cytomegalovirus infection, human papillomavirus infection, and shigellosis were identified as significant pathways involved in graft rejection. Concusion The above-mentioned genes can be used as diagnostic and therapeutic serum markers of transplantation rejection in renal patients. The newly predicted biomarkers and pathways require further studies.
Collapse
Affiliation(s)
- Fatemeh Saberi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Dehghan
- Department of Comparative Biomedical Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Effat Noori
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hakimeh Zali
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
2
|
Morales ML, García-Vicente R, Rodríguez-García A, Reyes-Palomares A, Vincelle-Nieto Á, Álvarez N, Ortiz-Ruiz A, Garrido-García V, Giménez A, Carreño-Tarragona G, Sánchez R, Ayala R, Martínez-López J, Linares M. Posttranslational splicing modifications as a key mechanism in cytarabine resistance in acute myeloid leukemia. Leukemia 2023; 37:1649-1659. [PMID: 37422594 PMCID: PMC10400425 DOI: 10.1038/s41375-023-01963-4] [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: 02/07/2023] [Revised: 06/14/2023] [Accepted: 06/29/2023] [Indexed: 07/10/2023]
Abstract
Despite the approval of several drugs for AML, cytarabine is still widely used as a therapeutic approach. However, 85% of patients show resistance and only 10% overcome the disease. Using RNA-seq and phosphoproteomics, we show that RNA splicing and serine-arginine-rich (SR) proteins phosphorylation were altered during cytarabine resistance. Moreover, phosphorylation of SR proteins at diagnosis were significantly lower in responder than non-responder patients, pointing to their utility to predict response. These changes correlated with altered transcriptomic profiles of SR protein target genes. Notably, splicing inhibitors were therapeutically effective in treating sensitive and resistant AML cells as monotherapy or combination with other approved drugs. H3B-8800 and venetoclax combination showed the best efficacy in vitro, demonstrating synergistic effects in patient samples and no toxicity in healthy hematopoietic progenitors. Our results establish that RNA splicing inhibition, alone or combined with venetoclax, could be useful for the treatment of newly diagnosed or relapsed/refractory AML.
Collapse
Affiliation(s)
- María Luz Morales
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain.
| | - Roberto García-Vicente
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Alba Rodríguez-García
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Armando Reyes-Palomares
- Department of Biochemistry and Molecular Biology, Veterinary School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain
| | - África Vincelle-Nieto
- Department of Biochemistry and Molecular Biology, Veterinary School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain
| | - Noemí Álvarez
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Alejandra Ortiz-Ruiz
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Vanesa Garrido-García
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Alicia Giménez
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Gonzalo Carreño-Tarragona
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Ricardo Sánchez
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
| | - Rosa Ayala
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
- Department of Medicine, Medicine School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain
| | - Joaquín Martínez-López
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain
- Department of Medicine, Medicine School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain
| | - María Linares
- Department of Translational Hematology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, Hospital 12 de Octubre - Centro Nacional de Investigaciones Oncológicas, CIBERONC, ES 28041, Madrid, Spain.
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040, Madrid, Spain.
| |
Collapse
|
3
|
Choi JO, Ham JH, Hwang SS. RNA Metabolism in T Lymphocytes. Immune Netw 2022; 22:e39. [PMID: 36381959 PMCID: PMC9634142 DOI: 10.4110/in.2022.22.e39] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023] Open
Abstract
RNA metabolism plays a central role in regulating of T cell-mediated immunity. RNA processing, modifications, and regulations of RNA decay influence the tight and rapid regulation of gene expression during T cell phase transition. Thymic selection, quiescence maintenance, activation, differentiation, and effector functions of T cells are dependent on selective RNA modulations. Recent technical improvements have unveiled the complex crosstalk between RNAs and T cells. Moreover, resting T cells contain large amounts of untranslated mRNAs, implying that the regulation of RNA metabolism might be a key step in controlling gene expression. Considering the immunological significance of T cells for disease treatment, an understanding of RNA metabolism in T cells could provide new directions in harnessing T cells for therapeutic implications.
Collapse
Affiliation(s)
- Jin Ouk Choi
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Severance Biomedical Science Institute and Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jeong Hyeon Ham
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Severance Biomedical Science Institute and Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Soo Seok Hwang
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Severance Biomedical Science Institute and Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea.,Chronic Intractable Disease Systems Medicine Research Center, Institute of Genetic Science, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
| |
Collapse
|
4
|
Xu S, Lai SK, Sim DY, Ang W, Li HY, Roca X. SRRM2 organizes splicing condensates to regulate alternative splicing. Nucleic Acids Res 2022; 50:8599-8614. [PMID: 35929045 PMCID: PMC9410892 DOI: 10.1093/nar/gkac669] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/29/2022] [Accepted: 08/04/2022] [Indexed: 12/27/2022] Open
Abstract
SRRM2 is a nuclear-speckle marker containing multiple disordered domains, whose dysfunction is associated with several human diseases. Using mainly EGFP-SRRM2 knock-in HEK293T cells, we show that SRRM2 forms biomolecular condensates satisfying most hallmarks of liquid-liquid phase separation, including spherical shape, dynamic rearrangement, coalescence and concentration dependence supported by in vitro experiments. Live-cell imaging shows that SRRM2 organizes nuclear speckles along the cell cycle. As bona-fide splicing factor present in spliceosome structures, SRRM2 deficiency induces skipping of cassette exons with short introns and weak splice sites, tending to change large protein domains. In THP-1 myeloid-like cells, SRRM2 depletion compromises cell viability, upregulates differentiation markers, and sensitizes cells to anti-leukemia drugs. SRRM2 induces a FES splice isoform that attenuates innate inflammatory responses, and MUC1 isoforms that undergo shedding with oncogenic properties. We conclude that SRRM2 acts as a scaffold to organize nuclear speckles, regulating alternative splicing in innate immunity and cell homeostasis.
Collapse
Affiliation(s)
- Shaohai Xu
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Soak-Kuan Lai
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Donald Yuhui Sim
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | | | - Hoi Yeung Li
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Xavier Roca
- To whom correspondence should be addressed. Tel: +65 65927561;
| |
Collapse
|
5
|
Ibáñez-Costa A, Perez-Sanchez C, Patiño-Trives AM, Luque-Tevar M, Font P, Arias de la Rosa I, Roman-Rodriguez C, Abalos-Aguilera MC, Conde C, Gonzalez A, Pedraza-Arevalo S, Del Rio-Moreno M, Blazquez-Encinas R, Segui P, Calvo J, Ortega Castro R, Escudero-Contreras A, Barbarroja N, Aguirre MA, Castaño JP, Luque RM, Collantes-Estevez E, Lopez-Pedrera C. Splicing machinery is impaired in rheumatoid arthritis, associated with disease activity and modulated by anti-TNF therapy. Ann Rheum Dis 2021; 81:56-67. [PMID: 34625402 PMCID: PMC8762032 DOI: 10.1136/annrheumdis-2021-220308] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 08/18/2021] [Indexed: 12/29/2022]
Abstract
OBJECTIVES To characterise splicing machinery (SM) alterations in leucocytes of patients with rheumatoid arthritis (RA), and to assess its influence on their clinical profile and therapeutic response. METHODS Leucocyte subtypes from 129 patients with RA and 29 healthy donors (HD) were purified, and 45 selected SM elements (SME) were evaluated by quantitative PCR-array based on microfluidic technology (Fluidigm). Modulation by anti-tumour necrosis factor (TNF) therapy and underlying regulatory mechanisms were assessed. RESULTS An altered expression of several SME was found in RA leucocytes. Eight elements (SNRNP70, SNRNP200, U2AF2, RNU4ATAC, RBM3, RBM17, KHDRBS1 and SRSF10) were equally altered in all leucocytes subtypes. Logistic regressions revealed that this signature might: discriminate RA and HD, and anti-citrullinated protein antibodies (ACPAs) positivity; classify high-disease activity (disease activity score-28 (DAS28) >5.1); recognise radiological involvement; and identify patients showing atheroma plaques. Furthermore, this signature was altered in RA synovial fluid and ankle joints of K/BxN-arthritic mice. An available RNA-seq data set enabled to validate data and identified distinctive splicing events and splicing variants among patients with RA expressing high and low SME levels. 3 and 6 months anti-TNF therapy reversed their expression in parallel to the reduction of the inflammatory profile. In vitro, ACPAs modulated SME, at least partially, by Fc Receptor (FcR)-dependent mechanisms. Key inflammatory cytokines further altered SME. Lastly, induced SNRNP70-overexpression and KHDRBS1-overexpression reversed inflammation in lymphocytes, NETosis in neutrophils and adhesion in RA monocytes and influenced activity of RA synovial fibroblasts. CONCLUSIONS Overall, we have characterised for the first time a signature comprising eight dysregulated SME in RA leucocytes from both peripheral blood and synovial fluid, linked to disease pathophysiology, modulated by ACPAs and reversed by anti-TNF therapy.
Collapse
Affiliation(s)
- Alejandro Ibáñez-Costa
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Carlos Perez-Sanchez
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Alejandra María Patiño-Trives
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Maria Luque-Tevar
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Pilar Font
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Ivan Arias de la Rosa
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Cristobal Roman-Rodriguez
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Mª Carmen Abalos-Aguilera
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Carmen Conde
- Laboratorio de Investigación 8, Instituto de Investigación Sanitaria (IDIS), Hospital Clinico de Santiago (CHUS), Santiago de Compostela, Spain
| | - Antonio Gonzalez
- Experimental and Observational Rheumatology, Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Sergio Pedraza-Arevalo
- Department of Cell Biology, Physiology and Immunology, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba and CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Cordoba, Spain
| | - Mercedes Del Rio-Moreno
- Department of Cell Biology, Physiology and Immunology, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba and CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Cordoba, Spain
| | - Ricardo Blazquez-Encinas
- Department of Cell Biology, Physiology and Immunology, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba and CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Cordoba, Spain
| | - Pedro Segui
- Radiology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Jerusalem Calvo
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Rafaela Ortega Castro
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Alejandro Escudero-Contreras
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Nuria Barbarroja
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Mª Angeles Aguirre
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Justo P Castaño
- Department of Cell Biology, Physiology and Immunology, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba and CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Cordoba, Spain
| | - Raul M Luque
- Department of Cell Biology, Physiology and Immunology, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba and CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Cordoba, Spain
| | - Eduardo Collantes-Estevez
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| | - Chary Lopez-Pedrera
- Rheumatology Service, Maimonides Institute of Biomedical Research of Cordoba (IMIBIC),Reina Sofia University Hospital, University of Córdoba, Cordoba, Spain
| |
Collapse
|
6
|
Zhang X, Bustos MA, Gross R, Ramos RI, Takeshima T, Mills GB, Yu Q, Hoon DSB. Interleukin enhancer-binding factor 2 promotes cell proliferation and DNA damage response in metastatic melanoma. Clin Transl Med 2021; 11:e608. [PMID: 34709752 PMCID: PMC8516365 DOI: 10.1002/ctm2.608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND 1q21.3 amplification, which is frequently observed in metastatic melanoma, is associated with cancer progression. Interleukin enhancer-binding factor 2 (ILF2) is located in the 1q21.3 amplified region, but its functional role or contribution to tumour aggressiveness in cutaneous melanoma is unknown. METHODS In silico analyses were performed using the TCGA SKCM dataset with clinical annotations and three melanoma microarray cohorts from the GEO datasets. RNA in situ hybridisation and immunohistochemistry were utilised to validate the gene expression in melanoma tissues. Four stable melanoma cell lines were established for in vitro ILF2 functional characterisation. RESULTS Our results showed that the ILF2 copy number variation (CNV) is positively correlated with ILF2 mRNA expression (r = 0.68, p < .0001). Additionally, ILF2 expression is significantly increased with melanoma progression (p < .0001), and significantly associated with poor overall survival for metastatic melanoma patients (p = .026). The overexpression of ILF2 (ILF2-OV) promotes proliferation in metastatic melanoma cells, whereas ILF2 knockdown decreases proliferation by blocking the cell cycle. Mechanistically, we demonstrated the interaction between ILF2 and the splicing factor U2AF2, whose knockdown reverses the proliferation effects mediated by ILF2-OV. Stage IIIB-C melanoma patients with high ILF2-U2AF2 expression showed significantly shorter overall survival (p = .024). Enhanced ILF2/U2AF2 expression promotes a more efficient DNA-damage repair by increasing RAD50 and ATM mRNA expression. Paradoxically, metastatic melanoma cells with ILF2-OV were more sensitive to ATM inhibitors. CONCLUSION Our study uncovered that ILF2 amplification of the 1q21.3 chromosome is associated with melanoma progression and triggers a functional downstream pathway in metastatic melanoma promoting drug resistance.
Collapse
Affiliation(s)
- Xiaoqing Zhang
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Matias A. Bustos
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Rebecca Gross
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Romela Irene Ramos
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Teh‐Ling Takeshima
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Gordon B. Mills
- Department of Cell Development and Cancer BiologyKnight Cancer InstituteOregon Health and Science UniversityPortlandOregon
| | - Qiang Yu
- Agency for Science Technology and Research (A*STAR)Genome Institute of SingaporeBiopolisSingapore
| | - Dave S. B. Hoon
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| |
Collapse
|
7
|
Freen-van Heeren JJ. Post-transcriptional control of T-cell cytokine production: Implications for cancer therapy. Immunology 2021; 164:57-72. [PMID: 33884612 DOI: 10.1111/imm.13339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/22/2021] [Accepted: 03/30/2021] [Indexed: 01/05/2023] Open
Abstract
As part of the adaptive immune system, T cells are vital for the eradication of infected and malignantly transformed cells. To perform their protective function, T cells produce effector molecules that are either directly cytotoxic, such as granzymes, perforin, interferon-γ and tumour necrosis factor α, or attract and stimulate (immune) cells, such as interleukin-2. As these molecules can also induce immunopathology, tight control of their production is required. Indeed, inflammatory cytokine production is regulated on multiple levels. Firstly, locus accessibility and transcription factor availability and activity determine the amount of mRNA produced. Secondly, post-transcriptional mechanisms, influencing mRNA splicing/codon usage, stability, decay, localization and translation rate subsequently determine the amount of protein that is produced. In the immune suppressive environments of tumours, T cells gradually lose the capacity to produce effector molecules, resulting in tumour immune escape. Recently, the role of post-transcriptional regulation in fine-tuning T-cell effector function has become more appreciated. Furthermore, several groups have shown that exhausted or dysfunctional T cells from cancer patients or murine models possess mRNA for inflammatory mediators, but fail to produce effector molecules, hinting that post-transcriptional events also play a role in hampering tumour-infiltrating lymphocyte effector function. Here, the post-transcriptional regulatory events governing T-cell cytokine production are reviewed, with a specific focus on the importance of post-transcriptional regulation in anti-tumour responses. Furthermore, potential approaches to circumvent tumour-mediated dampening of T-cell effector function through the (dis)engagement of post-transcriptional events are explored, such as CRISPR/Cas9-mediated genome editing or chimeric antigen receptors.
Collapse
|
8
|
Sabo Y, de Los Santos K, Goff SP. IQGAP1 Negatively Regulates HIV-1 Gag Trafficking and Virion Production. Cell Rep 2021; 30:4065-4081.e4. [PMID: 32209469 PMCID: PMC7199802 DOI: 10.1016/j.celrep.2020.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/29/2020] [Accepted: 02/28/2020] [Indexed: 01/21/2023] Open
Abstract
IQGAP1 is a master regulator of many cellular processes, including intracellular vesicle trafficking and endocytosis. We show that depletion of IQGAP1 in a variety of cell types increases the release of HIV-1 infectious virions and that overexpression diminishes virion production, with neither affecting the early stages of infection. IQGAP1 negatively regulates the steady-state levels of HIV-1 Gag at the plasma membrane, the site of assembly. We establish that IQGAP1 interacts with both the nucleocapsid and p6 domains of Gag, and interaction with either domain is sufficient for its regulatory function. Finally, we demonstrate that IQGAP1 regulation is independent of HIV-1 Gag “late-domains” sequences required by the virus to recruit the cellular ESCRT machinery. Thus, we provide evidence that IQGAP1 is a negative regulatory factor inhibiting efficient budding of HIV-1 by reducing Gag accumulation at the plasma membrane. IQGAP1 is a ubiquitously expressed master regulator of many cellular processes, including intracellular trafficking. Sabo et al. demonstrate that in a variety of cell types, IQGAP1 acts as a negative regulator of HIV-1 viral particle release by reducing accumulation of the Gag viral structural protein at the plasma membrane.
Collapse
Affiliation(s)
- Yosef Sabo
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA; Department of Medicine, Division of Infectious Diseases, Columbia University, New York, NY 10032, USA
| | - Kenia de Los Santos
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA
| | - Stephen P Goff
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
9
|
Papadaki M, Rinotas V, Violitzi F, Thireou T, Panayotou G, Samiotaki M, Douni E. New Insights for RANKL as a Proinflammatory Modulator in Modeled Inflammatory Arthritis. Front Immunol 2019; 10:97. [PMID: 30804932 PMCID: PMC6370657 DOI: 10.3389/fimmu.2019.00097] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/14/2019] [Indexed: 01/01/2023] Open
Abstract
Receptor activator of nuclear factor-κB ligand (RANKL), a member of the Tumor Necrosis Factor (TNF) superfamily, constitutes the master regulator of osteoclast formation and bone resorption, whereas its involvement in inflammatory diseases remains unclear. Here, we used the human TNF transgenic mouse model of erosive inflammatory arthritis to determine if the progression of inflammation is affected by either genetic inactivation or overexpression of RANKL in transgenic mouse models. TNF-mediated inflammatory arthritis was significantly attenuated in the absence of functional RANKL. Notably, TNF overexpression could not compensate for RANKL-mediated osteopetrosis, but promoted osteoclastogenesis between the pannus and bone interface, suggesting RANKL-independent mechanisms of osteoclastogenesis in inflamed joints. On the other hand, simultaneous overexpression of RANKL and TNF in double transgenic mice accelerated disease onset and led to severe arthritis characterized by significantly elevated clinical and histological scores as shown by aggressive pannus formation, extended bone resorption, and massive accumulation of inflammatory cells, mainly of myeloid origin. RANKL and TNF cooperated not only in local bone loss identified in the inflamed calcaneous bone, but also systemically in distal femurs as shown by microCT analysis. Proteomic analysis in inflamed ankles from double transgenic mice overexpressing human TNF and RANKL showed an abundance of proteins involved in osteoclastogenesis, pro-inflammatory processes, gene expression regulation, and cell proliferation, while proteins participating in basic metabolic processes were downregulated compared to TNF and RANKL single transgenic mice. Collectively, these results suggest that RANKL modulates modeled inflammatory arthritis not only as a mediator of osteoclastogenesis and bone resorption but also as a disease modifier affecting inflammation and immune activation.
Collapse
Affiliation(s)
- Maria Papadaki
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece.,Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Athens, Greece
| | - Vagelis Rinotas
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece.,Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Athens, Greece
| | - Foteini Violitzi
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece.,Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Athens, Greece
| | - Trias Thireou
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - George Panayotou
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Athens, Greece
| | - Martina Samiotaki
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Athens, Greece
| | - Eleni Douni
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece.,Division of Immunology, Biomedical Sciences Research Center "Alexander Fleming", Athens, Greece
| |
Collapse
|
10
|
Makjaroen J, Somparn P, Hodge K, Poomipak W, Hirankarn N, Pisitkun T. Comprehensive Proteomics Identification of IFN-λ3-regulated Antiviral Proteins in HBV-transfected Cells. Mol Cell Proteomics 2018; 17:2197-2215. [PMID: 30097535 PMCID: PMC6210224 DOI: 10.1074/mcp.ra118.000735] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/10/2018] [Indexed: 12/16/2022] Open
Abstract
Interferon lambda (IFN-λ) is a relatively unexplored, yet promising antiviral agent. IFN-λ has recently been tested in clinical trials of chronic hepatitis B virus infection (CHB), with the advantage that side effects may be limited compared with IFN-α, as IFN-λ receptors are found only in epithelial cells. To date, IFN-λ's downstream signaling pathway remains largely unelucidated, particularly via proteomics methods. Here, we report that IFN-λ3 inhibits HBV replication in HepG2.2.15 cells, reducing levels of both HBV transcripts and intracellular HBV DNA. Quantitative proteomic analysis of HBV-transfected cells was performed following 24-hour IFN-λ3 treatment, with parallel IFN-α2a and PBS treatments for comparison using a dimethyl labeling method. The depth of the study allowed us to map the induction of antiviral proteins to multiple points of the viral life cycle, as well as facilitating the identification of antiviral proteins not previously known to be elicited upon HBV infection (e.g. IFITM3, XRN2, and NT5C3A). This study also shows up-regulation of many effectors involved in antigen processing/presentation indicating that this cytokine exerted immunomodulatory effects through several essential molecules for these processes. Interestingly, the 2 subunits of the immunoproteasome cap (PSME1 and PSME2) were up-regulated whereas cap components of the constitutive proteasome were down-regulated upon both IFN treatments, suggesting coordinated modulation toward the antigen processing/presentation mode. Furthermore, in addition to confirming canonical activation of interferon-stimulated gene (ISG) transcription through the JAK-STAT pathway, we reveal that IFN-λ3 restored levels of RIG-I and RIG-G, proteins known to be suppressed by HBV. Enrichment analysis demonstrated that several biological processes including RNA metabolism, translation, and ER-targeting were differentially regulated upon treatment with IFN-λ3 versus IFN-α2a. Our proteomic data suggests that IFN-λ3 regulates an array of cellular processes to control HBV replication.
Collapse
Affiliation(s)
- Jiradej Makjaroen
- From the ‡Medical Microbiology Interdisciplinary Program, Graduate School, Chulalongkorn University, Bangkok, Thailand
- §Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- ¶Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Poorichaya Somparn
- §Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- ¶Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kenneth Hodge
- ¶Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Witthaya Poomipak
- ¶Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nattiya Hirankarn
- §Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Trairak Pisitkun
- ¶Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| |
Collapse
|
11
|
Baumjohann D, Heissmeyer V. Posttranscriptional Gene Regulation of T Follicular Helper Cells by RNA-Binding Proteins and microRNAs. Front Immunol 2018; 9:1794. [PMID: 30108596 PMCID: PMC6079247 DOI: 10.3389/fimmu.2018.01794] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/20/2018] [Indexed: 12/24/2022] Open
Abstract
T follicular helper (Tfh) cells are critically involved in the establishment of potent antibody responses against infectious pathogens, such as viruses and bacteria, but their dysregulation may also result in aberrant antibody responses that frequently coincide with autoimmune diseases or allergies. The fate and identity of Tfh cells is tightly controlled by gene regulation on the transcriptional and posttranscriptional level. Here, we provide deeper insights into the posttranscriptional mechanisms that regulate Tfh cell differentiation, function, and plasticity through the actions of RNA-binding proteins (RBPs) and small endogenously expressed regulatory RNAs called microRNAs (miRNAs). The Roquin family of RBPs has been shown to dampen spontaneous activation and differentiation of naïve CD4+ T cells into Tfh cells, since CD4+ T cells with Roquin mutations accumulate as Tfh cells and provide inappropriate B cell help in the production of autoantibodies. Moreover, Regnase-1, an endoribonuclease that regulates a set of targets, which strongly overlaps with that of Roquin, is crucial for the prevention of autoantibody production. Interestingly, both Roquin and Regnase-1 proteins are cleaved and inactivated after TCR stimulation by the paracaspase MALT1. miRNAs are expressed in naïve CD4+ T cells and help preventing spontaneous differentiation into effector cells. While most miRNAs are downregulated upon T cell activation, several miRNAs have been shown to regulate the fate of these cells by either promoting (e.g., miR-17-92 and miR-155) or inhibiting (e.g., miR-146a) Tfh cell differentiation. Together, these different aspects highlight a complex and dynamic regulatory network of posttranscriptional gene regulation in Tfh cells that may also be active in other T helper cell populations, including Th1, Th2, Th17, and Treg.
Collapse
Affiliation(s)
- Dirk Baumjohann
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.,Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany
| |
Collapse
|
12
|
Díaz-Muñoz MD, Turner M. Uncovering the Role of RNA-Binding Proteins in Gene Expression in the Immune System. Front Immunol 2018; 9:1094. [PMID: 29875770 PMCID: PMC5974052 DOI: 10.3389/fimmu.2018.01094] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/02/2018] [Indexed: 12/29/2022] Open
Abstract
Fighting external pathogens requires an ever-changing immune system that relies on tight regulation of gene expression. Transcriptional control is the first step to build efficient responses while preventing immunodeficiencies and autoimmunity. Post-transcriptional regulation of RNA editing, location, stability, and translation are the other key steps for final gene expression, and they are all controlled by RNA-binding proteins (RBPs). Nowadays we have a deep understanding of how transcription factors control the immune system but recent evidences suggest that post-transcriptional regulation by RBPs is equally important for both development and activation of immune responses. Here, we review current knowledge about how post-transcriptional control by RBPs shapes our immune system and discuss the perspective of RBPs being the key players of a hidden immune cell epitranscriptome.
Collapse
Affiliation(s)
- Manuel D Díaz-Muñoz
- Centre de Physiopathologie Toulouse-Purpan, INSERM UMR1043/CNRS U5282, Toulouse, France
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
| |
Collapse
|
13
|
Whisenant TC. Gene expression profiling of U2AF2 dependent RNA-protein interactions during CD4 + T cell activation. GENOMICS DATA 2016; 11:77-80. [PMID: 28050347 PMCID: PMC5192059 DOI: 10.1016/j.gdata.2016.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/11/2016] [Indexed: 10/25/2022]
Abstract
CD4 T cell activation is a central component of the mammalian adaptive immune response and is underscored by a dramatic change in the gene expression profile in these cells. The changes in gene expression that occur during T cell activation are regulated in multiple ways including post-transcriptionally by complexes of RNA-binding proteins. Recently, our study explored the role of the RNA-binding protein U2AF2 and its interacting proteins in mediating posttranscriptional changes in constitutive and alternative splicing during T cell activation. First, we used RNA-seq to identify the global changes in gene expression and splicing that occur with T cell activation. Next, we used RIP-seq to identify the specific genes bound to U2AF2 during T cell activation. After identification of the protein interacting partners of U2AF2, we used splicing sensitive microarrays to measure the effects on global gene expression of using siRNAs to knock down a sampling of these proteins. Finally, we used RIP-chip to measure the effects of the same siRNA knockdown on the transcripts specifically bound to U2AF2. Here we provide the experimental details and analysis of the gene expression data for each of these techniques, which have been deposited into Gene Expression Omnibus (GEO) with the Superseries ID: GSE62923.
Collapse
Affiliation(s)
- Thomas C Whisenant
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, United States
| |
Collapse
|