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Zamecnik CR, Sowa GM, Abdelhak A, Dandekar R, Bair RD, Wade KJ, Bartley CM, Kizer K, Augusto DG, Tubati A, Gomez R, Fouassier C, Gerungan C, Caspar CM, Alexander J, Wapniarski AE, Loudermilk RP, Eggers EL, Zorn KC, Ananth K, Jabassini N, Mann SA, Ragan NR, Santaniello A, Henry RG, Baranzini SE, Zamvil SS, Sabatino JJ, Bove RM, Guo CY, Gelfand JM, Cuneo R, von Büdingen HC, Oksenberg JR, Cree BAC, Hollenbach JA, Green AJ, Hauser SL, Wallin MT, DeRisi JL, Wilson MR. An autoantibody signature predictive for multiple sclerosis. Nat Med 2024; 30:1300-1308. [PMID: 38641750 DOI: 10.1038/s41591-024-02938-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Although B cells are implicated in multiple sclerosis (MS) pathophysiology, a predictive or diagnostic autoantibody remains elusive. In this study, the Department of Defense Serum Repository (DoDSR), a cohort of over 10 million individuals, was used to generate whole-proteome autoantibody profiles of hundreds of patients with MS (PwMS) years before and subsequently after MS onset. This analysis defines a unique cluster in approximately 10% of PwMS who share an autoantibody signature against a common motif that has similarity with many human pathogens. These patients exhibit antibody reactivity years before developing MS symptoms and have higher levels of serum neurofilament light (sNfL) compared to other PwMS. Furthermore, this profile is preserved over time, providing molecular evidence for an immunologically active preclinical period years before clinical onset. This autoantibody reactivity was validated in samples from a separate incident MS cohort in both cerebrospinal fluid and serum, where it is highly specific for patients eventually diagnosed with MS. This signature is a starting point for further immunological characterization of this MS patient subset and may be clinically useful as an antigen-specific biomarker for high-risk patients with clinically or radiologically isolated neuroinflammatory syndromes.
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Affiliation(s)
- Colin R Zamecnik
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Gavin M Sowa
- University of California, San Francisco School of Medicine, San Francisco, CA, USA
- Department of Medicine, McGaw Medical Center of Northwestern University, Chicago, IL, USA
| | - Ahmed Abdelhak
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Ravi Dandekar
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Rebecca D Bair
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kristen J Wade
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher M Bartley
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kerry Kizer
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Danillo G Augusto
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Asritha Tubati
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Refujia Gomez
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Camille Fouassier
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Chloe Gerungan
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Colette M Caspar
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jessica Alexander
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Anne E Wapniarski
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Rita P Loudermilk
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Erica L Eggers
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Kirtana Ananth
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Nora Jabassini
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA
| | - Nicholas R Ragan
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Adam Santaniello
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Roland G Henry
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sergio E Baranzini
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Scott S Zamvil
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph J Sabatino
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Riley M Bove
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Chu-Yueh Guo
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey M Gelfand
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Richard Cuneo
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - H-Christian von Büdingen
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jorge R Oksenberg
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Bruce A C Cree
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jill A Hollenbach
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Ari J Green
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen L Hauser
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mitchell T Wallin
- Department of Veterans Affairs, Multiple Sclerosis Center of Excellence, Washington, DC, USA
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA
| | - Michael R Wilson
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
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Das R, Panigrahi GK. Messenger RNA Surveillance: Current Understanding, Regulatory Mechanisms, and Future Implications. Mol Biotechnol 2024:10.1007/s12033-024-01062-4. [PMID: 38411790 DOI: 10.1007/s12033-024-01062-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/02/2024] [Indexed: 02/28/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved surveillance mechanism in eukaryotes primarily deployed to ensure RNA quality control by eliminating aberrant transcripts and also involved in modulating the expression of several physiological transcripts. NMD, the mRNA surveillance pathway, is a major form of gene regulation in eukaryotes. NMD serves as one of the most significant quality control mechanisms as it primarily scans the newly synthesized transcripts and differentiates the aberrant and non-aberrant transcripts. The synthesis of truncated proteins is restricted, which would otherwise lead to cellular dysfunctions. The up-frameshift factors (UPFs) play a central role in executing the NMD event, largely by recognizing and recruiting multiple protein factors that result in the decay of non-physiological mRNAs. NMD exhibits astounding variability in its ability across eukaryotes in an array of pathological and physiological contexts. The detailed understanding of NMD and the underlying molecular mechanisms remains blurred. This review outlines our current understanding of NMD, in regulating multifaceted cellular events during development and disease. It also attempts to identify unanswered questions that deserve further investigation.
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Affiliation(s)
- Rutupurna Das
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India
| | - Gagan Kumar Panigrahi
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India.
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Yu CL, Chuang TW, Samuel SY, Lou YC, Tarn WY. Co-phase separation of Y14 and RNA in vitro and its implication for DNA repair. RNA (NEW YORK, N.Y.) 2023; 29:1007-1019. [PMID: 37001915 DOI: 10.1261/rna.079514.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
The multifunctional RNA recognition motif-containing protein Y14/RBM8A participates in mRNA metabolism and is essential for the efficient repair of DNA double-strand breaks (DSBs). Y14 contains highly charged, low-complexity sequences in both the amino- and carboxy-terminal domains. The feature of charge segregation suggests that Y14 may undergo liquid-liquid phase separation (LLPS). Recombinant Y14 formed phase-separated droplets, which were sensitive to pH and salt concentration. Domain mapping suggested that LLPS of Y14 involves multivalent electrostatic interactions and is partly determined by the net charge of its low-complexity regions. Phospho-mimicry of the carboxy-terminal arginine-serine dipeptides of Y14 suppressed phase separation. Moreover, RNA could phase separate into Y14 droplets and modulate Y14 LLPS in a concentration-dependent manner. Finally, the capacity of Y14 in LLPS and coacervation with RNA in vitro correlated with its activity in DSB repair. These results reveal a molecular rule for LLPS of Y14 in vitro and an implication for its co-condensation with RNA in genome stability.
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Affiliation(s)
- Chia-Lin Yu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Tzu-Wei Chuang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Sabrina Yeo Samuel
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yuan-Chao Lou
- Biomedical Translation Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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Zamecnik CR, Sowa GM, Abdelhak A, Dandekar R, Bair RD, Wade KJ, Bartley CM, Tubati A, Gomez R, Fouassier C, Gerungan C, Alexander J, Wapniarski AE, Loudermilk RP, Eggers EL, Zorn KC, Ananth K, Jabassini N, Mann SA, Ragan NR, Santaniello A, Henry RG, Baranzini SE, Zamvil SS, Bove RM, Guo CY, Gelfand JM, Cuneo R, von Büdingen HC, Oksenberg JR, Cree BAC, Hollenbach JA, Green AJ, Hauser SL, Wallin MT, DeRisi JL, Wilson MR. A Predictive Autoantibody Signature in Multiple Sclerosis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.01.23288943. [PMID: 37205595 PMCID: PMC10187343 DOI: 10.1101/2023.05.01.23288943] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Although B cells are implicated in multiple sclerosis (MS) pathophysiology, a predictive or diagnostic autoantibody remains elusive. Here, the Department of Defense Serum Repository (DoDSR), a cohort of over 10 million individuals, was used to generate whole-proteome autoantibody profiles of hundreds of patients with MS (PwMS) years before and subsequently after MS onset. This analysis defines a unique cluster of PwMS that share an autoantibody signature against a common motif that has similarity with many human pathogens. These patients exhibit antibody reactivity years before developing MS symptoms and have higher levels of serum neurofilament light (sNfL) compared to other PwMS. Furthermore, this profile is preserved over time, providing molecular evidence for an immunologically active prodromal period years before clinical onset. This autoantibody reactivity was validated in samples from a separate incident MS cohort in both cerebrospinal fluid (CSF) and serum, where it is highly specific for patients eventually diagnosed with MS. This signature is a starting point for further immunological characterization of this MS patient subset and may be clinically useful as an antigen-specific biomarker for high-risk patients with clinically- or radiologically-isolated neuroinflammatory syndromes.
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Affiliation(s)
- Colin R. Zamecnik
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Gavin M. Sowa
- Department of Medicine, McGaw Medical Center of Northwestern University, Chicago, IL, USA
| | - Ahmed Abdelhak
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Ravi Dandekar
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Rebecca D. Bair
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Kristen J. Wade
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Christopher M. Bartley
- UCSF Weill Institute for Neurosciences, Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, USA
| | - Asritha Tubati
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Refujia Gomez
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Camille Fouassier
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Chloe Gerungan
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Jessica Alexander
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Anne E. Wapniarski
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Rita P. Loudermilk
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Erica L. Eggers
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Kelsey C. Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Kirtana Ananth
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Nora Jabassini
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Sabrina A. Mann
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Nicholas R. Ragan
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Adam Santaniello
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Roland G. Henry
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Sergio E. Baranzini
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Scott S. Zamvil
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Riley M. Bove
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Chu-Yueh Guo
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Jeffrey M. Gelfand
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Richard Cuneo
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - H.-Christian von Büdingen
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Jorge R. Oksenberg
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Bruce AC Cree
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Jill A. Hollenbach
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA USA
| | - Ari J. Green
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Stephen L. Hauser
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Mitchell T. Wallin
- Veterans Affairs, Multiple Sclerosis Center of Excellence, Washington, DC and University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Michael R. Wilson
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
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Wei L, Zou C, Chen L, Lin Y, Liang L, Hu B, Mao Y, Zou D. Molecular Insights and Prognosis Associated With RBM8A in Glioblastoma. Front Mol Biosci 2022; 9:876603. [PMID: 35573726 PMCID: PMC9098818 DOI: 10.3389/fmolb.2022.876603] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/04/2022] [Indexed: 12/31/2022] Open
Abstract
Background: Glioblastoma (GBM) is the most invasive brain tumors, and it is associated with high rates of recurrence and mortality. The purpose of this study was to investigate the expression of RBM8A in GBM and the potential influence of its expression on the disease. Methods: Levels of RBM8A mRNA in GBM patients and controls were examined in The Cancer Genome Atlas (TCGA), GSE16011 and GSE90604 databases. GBM samples in TCGA were divided into RBM8Ahigh and RBM8Alow groups. Differentially expressed genes (DEGs) between GBM patients and controls were identified, as were DEGs between RBM8Ahigh and RBM8Alow groups. DEGs common to both of these comparisons were analyzed for coexpression and regression analyses. In addition, we identified potential effects of RBM8A on competing endogenous RNAs, immune cell infiltration, methylation modifications, and somatic mutations. Results: RBM8A is expressed at significantly higher levels in GBM than control samples, and its level correlates with tumor purity. We identified a total of 488 mRNAs that differed between GBM and controls as well as between RBM8Ahigh and RBM8Alow groups, which enrichment analysis revealed to be associated mainly with neuroblast proliferation, and T cell immune responses. We identified 174 mRNAs that gave areas under the receiver operating characteristic curve >0.7 among coexpression module genes, of which 13 were significantly associated with overall survival of GBM patients. We integrated 11 candidate mRNAs through LASSO algorithm, then nomogram, risk score, and decision curve analyses were analyzed. We found that RBM8A may compete with DLEU1 for binding to miR-128-1-5p, and aberrant RBM8A expression was associations with tumor infiltration by immune cells. Some mRNAs associated with GBM prognosis also appear to be methylated or mutated. Conclusions: Our study strongly links RBM8A expression to GBM pathobiology and patient prognosis. The candidate mRNAs identified here may lead to therapeutic targets against the disease.
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Affiliation(s)
- Lei Wei
- Department of Neurology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chun Zou
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Liechun Chen
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yan Lin
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Lucong Liang
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Beiquan Hu
- Department of Neurosurgery, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yingwei Mao
- Department of Biology, Pennsylvania State University, University Park, PA, United States
- *Correspondence: Donghua Zou, ; Yingwei Mao,
| | - Donghua Zou
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- *Correspondence: Donghua Zou, ; Yingwei Mao,
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Kanellis DC, Espinoza JA, Zisi A, Sakkas E, Bartkova J, Katsori AM, Boström J, Dyrskjøt L, Broholm H, Altun M, Elsässer SJ, Lindström MS, Bartek J. The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output. SCIENCE ADVANCES 2021; 7:eabf7561. [PMID: 34348895 PMCID: PMC8336962 DOI: 10.1126/sciadv.abf7561] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/14/2021] [Indexed: 05/22/2023]
Abstract
Eukaryotic initiation factor 4A-III (eIF4A3), a core helicase component of the exon junction complex, is essential for splicing, mRNA trafficking, and nonsense-mediated decay processes emerging as targets in cancer therapy. Here, we unravel eIF4A3's tumor-promoting function by demonstrating its role in ribosome biogenesis (RiBi) and p53 (de)regulation. Mechanistically, eIF4A3 resides in nucleoli within the small subunit processome and regulates rRNA processing via R-loop clearance. EIF4A3 depletion induces cell cycle arrest through impaired RiBi checkpoint-mediated p53 induction and reprogrammed translation of cell cycle regulators. Multilevel omics analysis following eIF4A3 depletion pinpoints pathways of cell death regulation and translation of alternative mouse double minute homolog 2 (MDM2) transcript isoforms that control p53. EIF4A3 expression and subnuclear localization among clinical cancer specimens correlate with the RiBi status rendering eIF4A3 an exploitable vulnerability in high-RiBi tumors. We propose a concept of eIF4A3's unexpected role in RiBi, with implications for cancer pathogenesis and treatment.
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Affiliation(s)
- Dimitris C Kanellis
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Jaime A Espinoza
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Asimina Zisi
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Elpidoforos Sakkas
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jirina Bartkova
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Anna-Maria Katsori
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm 17165, Sweden
| | - Johan Boström
- Science for Life Laboratory, Division of Clinical Physiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, SE-141 52 Huddinge, Sweden
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Helle Broholm
- Department of Pathology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mikael Altun
- Science for Life Laboratory, Division of Clinical Physiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, SE-141 52 Huddinge, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm 17165, Sweden
| | - Mikael S Lindström
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden.
| | - Jiri Bartek
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden.
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
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7
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A Comprehensive Pan-Cancer Analysis of RBM8A Based on Data Mining. JOURNAL OF ONCOLOGY 2021; 2021:9983354. [PMID: 34326876 PMCID: PMC8277506 DOI: 10.1155/2021/9983354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/02/2021] [Indexed: 01/01/2023]
Abstract
Background As a member of the exon junction complex (EJC), RNA-binding motif protein 8A (RBM8A) plays a crucial role in the maintenance of mRNA and multiple activities of an organism. Immunotherapy has been proven to be a staple type of cancer treatment. However, the role of RBM8A and immunity across cancer types is unclear. Objective This study aims to visualize the expression, prognosis, mutations, and coexpressed gene results of RBM8A across cancer types and to explore the link between RBM8A expression and immunity. Methods In this study, data were collected from multiple online databases. We analyzed the data using the HPA, UALCAN Database, COSMIC, cBioPortal, Cancer Regulome tools, Kaplan–Meier Plotter, and TIMER website. Results For the expression of RBM8A in normal tissues, higher expression of RBM8A was observed in immune-related cells than in nonimmune organs. The expression level of RBM8A was related to tumor type. Missense mutations in RBM8A were found in most tumors and affected the prognosis of carcinomas with coexpressed genes. RBM8A was strongly associated with immune-infiltrating cells and immune checkpoint inhibitors, especially in LIHC. Conclusions RBM8A is a gene worth exploring and may be a unique immune target in the future.
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Zhou Y, Li Z, Wu X, Tou L, Zheng J, Zhou D. MAGOH/MAGOHB Inhibits the Tumorigenesis of Gastric Cancer via Inactivation of b-RAF/MEK/ERK Signaling. Onco Targets Ther 2020; 13:12723-12735. [PMID: 33328743 PMCID: PMC7735944 DOI: 10.2147/ott.s263913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Background Gastric cancer is one of the most malignant tumors all over the world. It has been reported that proteins play key roles during the tumorigenesis of gastric cancer. To identify novel potential targets for gastric cancer, differential expressed proteins between gastric cancer and adjacent normal tissues were analyzed with proteomics and bioinformatics tool. Methods The differentially expressed proteins between gastric cancer and adjacent normal tissues were analyzed by Omicsbean (multi-omics data analysis tool). Cell viability was tested by CCK-8 assay. Flow cytometry was used to measure cell apoptosis and cycle. Transwell assay was used to test cell migration and invasion. Gene and protein expressions were detected by RT-qPCR, immunohistochemistry and Western blot, respectively. Results MAGOH and MAGOHB were found to be notably upregulated in gastric cancer tissues compared with that in normal tissues. Knockdown of MAGOH significantly inhibited the proliferation of gastric cancer cells via inducing the cell apoptosis. In addition, MAGOH knockdown induced G2 phase arrest in gastric cancer cells. Moreover, MAGOH knockdown notably inhibited migration and invasion of gastric cancer cells. Importantly, double knockdown of MAGOH and MAGOHB exhibited much better anti-tumor effects on gastric cancer compared with alone treatment. Finally, double knockdown of MAGOH and MAGOHB mediated the tumorigenesis of gastric cancer via regulation of RAF/MEK/ERK signaling. Conclusion MAGOH knockdown inhibited the tumorigenesis of gastric cancer via mediation of b-RAF/MEK/ERK signaling, and double knockdown of MAGOH and MAGOHB exhibited much better anti-tumor effects. This finding might provide us a new strategy for the treatment of gastric cancer.
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Affiliation(s)
- Yong Zhou
- Department of Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, People's Republic of China
| | - Zhongqi Li
- Department of Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, People's Republic of China
| | - Xuan Wu
- Department of Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, People's Republic of China
| | - Laizhen Tou
- Department of Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, People's Republic of China
| | - Jingjing Zheng
- Department of General Surgery, Lishui Municipal Central Hospital, Lishui, Zhejiang 323000, People's Republic of China
| | - Donghui Zhou
- Department of Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, People's Republic of China
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The Branched Nature of the Nonsense-Mediated mRNA Decay Pathway. Trends Genet 2020; 37:143-159. [PMID: 33008628 DOI: 10.1016/j.tig.2020.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/11/2020] [Accepted: 08/18/2020] [Indexed: 12/16/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a conserved translation-coupled quality control mechanism in all eukaryotes that regulates the expression of a significant fraction of both the aberrant and normal transcriptomes. In vertebrates, NMD has become an essential process owing to expansion of the diversity of NMD-regulated transcripts, particularly during various developmental processes. Surprisingly, however, some core NMD factors that are essential for NMD in simpler organisms appear to be dispensable for vertebrate NMD. At the same time, numerous NMD enhancers and suppressors have been identified in multicellular organisms including vertebrates. Collectively, the available data suggest that vertebrate NMD is a complex, branched pathway wherein individual branches regulate specific mRNA subsets to fulfill distinct physiological functions.
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Lv X, Cheng H. Prognostic value of increased expression of RBM8A in gastric cancer. ACTA ACUST UNITED AC 2020; 53:e9290. [PMID: 32294703 PMCID: PMC7164227 DOI: 10.1590/1414-431x20209290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/09/2020] [Indexed: 01/17/2023]
Abstract
This study was designed to investigate the expression of RBM8A protein in patients with gastric cancer (GC) and to explore its correlation with clinical pathological features as well as prognosis. One hundred pairs of gastric carcinoma tissues and adjacent tissues from patients undergoing gastrectomy for GC were included in this study. The protein expression level of RBM8A was determined by immunohistochemistry using tissue microarrays. We also detected the mRNA expression level of RBM8A in 16 pairs of gastric carcinoma tissues and adjacent tissues. Meanwhile, we predicted the potential correlation between RBM8A and tumor stages as well as survival condition in patents with GC based on The Cancer Genome Atlas (TCGA) database. The correlation of RBM8A with the clinical pathological features and prognosis of the 100 patients with GC was also elucidated. The expression level of RBM8A was significantly higher in gastric carcinoma tissues compared to the adjacent tissues. The protein level of RBM8A was correlated with tumor size (P=0.031), depth of invasion (P<0.001), lymph node metastasis (P<0.001), TNM stage (<0.001), and distant metastasis (P=0.001). Patients with increased RBM8A expression (P<0.0018, 95%CI=0.322−0.871), higher TNM stage (P<0.001, 95%CI=4.990−11.283), and lymph node metastasis (P<0.001, 95%CI=2.873−4.002) had a lower overall survival. Taken together, our study demonstrated that RBM8A may act as a proto-oncogene, which could be a promising biomarker and therapeutic target in the diagnosis and treatment of GC.
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Affiliation(s)
- Xinting Lv
- Department of Surgery, The First People's Hospital of Yongkang, Zhejiang, China
| | - Huifei Cheng
- Department of Radiotherapy, Lishui Municipal Central Hospital, Zhejiang, China
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Ma Q, Tatsuno T, Nakamura Y, Ishigaki Y. The stability of Magoh and Y14 depends on their heterodimer formation and nuclear localization. Biochem Biophys Res Commun 2019; 511:631-636. [PMID: 30826064 DOI: 10.1016/j.bbrc.2019.02.097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 02/19/2019] [Indexed: 01/10/2023]
Abstract
Reduced expression of the Y14 gene is a cause of Thrombocytopenia-absent radius (TAR) syndrome. This gene contains a conserved RNA recognition motif (RRM) in the central region and nuclear localization/export sequences (NLS/NES) in the N-terminal. Y14 and Magoh proteins form tight heterodimers and are the core of exon junction complexes (EJCs), which mediate various processes of mRNA metabolism after transcription. In this report, we found that protein expression levels of exogenously expressed Magoh L136R and Y14 L118R (leucine-to-arginine substitution at amino acid residue 136 and 118 respectively, that results in the formation of the complex being lost) are lower than their wild-types. This reduction is likely caused by protein levels, as no difference in mRNA levels was detected. Meanwhile, a cycloheximide chase assay determined that the degradation rates of Magoh L136R and Y14 L118R were faster than their wild-types. Both Y14 L118R and Magoh L136R lost the ability to form heterodimers with corresponding wild-type proteins. However, Y14 L118R is able to still localize in the nucleus which causes the stability of Y14 L118R to be higher than Magoh L136R. These results reveal that the stability of Magoh and Y14 is not only dependent on the heterodimer structure, but also dependent on nuclear localization.
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Affiliation(s)
- Qingfeng Ma
- Medical Research Institute, Kanazawa Medical University, Uchinada, Kahoku, Japan; Department of Clinical Laboratory, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Takanori Tatsuno
- Medical Research Institute, Kanazawa Medical University, Uchinada, Kahoku, Japan
| | - Yuka Nakamura
- Medical Research Institute, Kanazawa Medical University, Uchinada, Kahoku, Japan
| | - Yasuhito Ishigaki
- Medical Research Institute, Kanazawa Medical University, Uchinada, Kahoku, Japan.
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12
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Ma Q, Tatsuno T, Nakamura Y, Izumi S, Tomosugi N, Ishigaki Y. Immuno‐detection of mRNA‐binding protein complex in human cells under transmission electron microscopy. Microsc Res Tech 2019; 82:680-688. [DOI: 10.1002/jemt.23214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 12/13/2018] [Accepted: 12/15/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Qingfeng Ma
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
- Department of Clinical Laboratory, Liyuan Hospital, Tongji Medical CollegeHuazhong University of Science and Technology Wuhan China
| | - Takanori Tatsuno
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
| | - Yuka Nakamura
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
| | - Shin‐Ichi Izumi
- Department of Cell Biology, Unit of Biomedical SciencesNagasaki University Graduate School of Biomedical Sciences Sakamoto Nagasaki Japan
| | - Naohisa Tomosugi
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
- Medical Care Proteomics Biotechnology Co., Ltd. Uchinada Kahoku Japan
| | - Yasuhito Ishigaki
- Medical Research InstituteKanazawa Medical University Uchinada Kahoku Japan
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