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Wardman R, Keles M, Pachkiv I, Hemanna S, Grein S, Schwarz J, Stein F, Ola R, Dobreva G, Hentze MW, Heineke J. RNA-Binding Proteins Regulate Post-Transcriptional Responses to TGF-β to Coordinate Function and Mesenchymal Activation of Murine Endothelial Cells. Arterioscler Thromb Vasc Biol 2023; 43:1967-1989. [PMID: 37650327 PMCID: PMC10521797 DOI: 10.1161/atvbaha.123.319925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023]
Abstract
BACKGROUND Endothelial cells (ECs) are primed to respond to various signaling cues. For example, TGF (transforming growth factor)-β has major effects on EC function and phenotype by driving ECs towards a more mesenchymal state (ie, triggering endothelial to mesenchymal activation), a dynamic process associated with cardiovascular diseases. Although transcriptional regulation triggered by TGF-β in ECs is well characterized, post-transcriptional regulatory mechanisms induced by TGF-β remain largely unknown. METHODS Using RNA interactome capture, we identified global TGF-β driven changes in RNA-binding proteins in ECs. We investigated specific changes in the RNA-binding patterns of hnRNP H1 (heterogeneous nuclear ribonucleoprotein H1) and Csde1 (cold shock domain containing E1) using RNA immunoprecipitation and overlapped this with RNA-sequencing data after knockdown of either protein for functional insight. Using a modified proximity ligation assay, we visualized the specific interactions between hnRNP H1 and Csde1 and target RNAs in situ both in vitro and in mouse heart sections. RESULTS Characterization of TGF-β-regulated RBPs (RNA-binding proteins) revealed hnRNP H1 and Csde1 as key regulators of the cellular response to TGF-β at the post-transcriptional level, with loss of either protein-promoting mesenchymal activation in ECs. We found that TGF-β drives an increase in binding of hnRNP H1 to its target RNAs, offsetting mesenchymal activation, but a decrease in Csde1 RNA-binding, facilitating this process. Both, hnRNP H1 and Csde1, dynamically bind and regulate specific subsets of mRNAs related to mesenchymal activation and endothelial function. CONCLUSIONS Together, we show that RBPs play a key role in the endothelial response to TGF-β stimulation at the post-transcriptional level and that the RBPs hnRNP H1 and Csde1 serve to maintain EC function and counteract mesenchymal activation. We propose that TGF-β profoundly modifies RNA-protein interaction entailing feedback and feed-forward control at the post-transcriptional level, to fine-tune mesenchymal activation in ECs.
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Affiliation(s)
- Rhys Wardman
- Department of Cardiovascular Physiology (R.W., M.K., I.P., S.H., S.G., J.H.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim (R.W., M.K., S.H., S.G., G.D., J.H.)
| | - Merve Keles
- Department of Cardiovascular Physiology (R.W., M.K., I.P., S.H., S.G., J.H.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim (R.W., M.K., S.H., S.G., G.D., J.H.)
| | - Ihor Pachkiv
- Department of Cardiovascular Physiology (R.W., M.K., I.P., S.H., S.G., J.H.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
| | - Shruthi Hemanna
- Department of Cardiovascular Physiology (R.W., M.K., I.P., S.H., S.G., J.H.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim (R.W., M.K., S.H., S.G., G.D., J.H.)
| | - Steve Grein
- Department of Cardiovascular Physiology (R.W., M.K., I.P., S.H., S.G., J.H.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim (R.W., M.K., S.H., S.G., G.D., J.H.)
| | - Jennifer Schwarz
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany (J.S., F.S.)
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany (J.S., F.S.)
| | - Roxana Ola
- Cardiovascular Pharmacology (R.O.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
| | - Gergana Dobreva
- Cardiovascular Genomics and Epigenomics (G.D.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim (R.W., M.K., S.H., S.G., G.D., J.H.)
| | - Matthias W. Hentze
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany (M.W.H.)
| | - Joerg Heineke
- Department of Cardiovascular Physiology (R.W., M.K., I.P., S.H., S.G., J.H.), European Center for Angioscience (ECAS), Medical Faculty Mannheim of Heidelberg University, Germany
- German Center for Cardiovascular Research (DZHK), partner site Heidelberg/Mannheim (R.W., M.K., S.H., S.G., G.D., J.H.)
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Brownmiller T, Caplen NJ. The HNRNPF/H RNA binding proteins and disease. Wiley Interdiscip Rev RNA 2023; 14:e1788. [PMID: 37042074 PMCID: PMC10523889 DOI: 10.1002/wrna.1788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 04/13/2023]
Abstract
The members of the HNRNPF/H family of heterogeneous nuclear RNA proteins-HNRNPF, HNRNPH1, HNRNPH2, HNRNPH3, and GRSF1, are critical regulators of RNA maturation. Documented functions of these proteins include regulating splicing, particularly alternative splicing, 5' capping and 3' polyadenylation of RNAs, and RNA export. The assignment of these proteins to the HNRNPF/H protein family members relates to differences in the amino acid composition of their RNA recognition motifs, which differ from those of other RNA binding proteins (RBPs). HNRNPF/H proteins typically bind RNA sequences enriched with guanine (G) residues, including sequences that, in the presence of a cation, have the potential to form higher-order G-quadruplex structures. The need to further investigate members of the HNRNPF/H family of RBPs has intensified with the recent descriptions of their involvement in several disease states, including the pediatric tumor Ewing sarcoma and the hematological malignancy mantle cell lymphoma; newly described groups of developmental syndromes; and neuronal-related disorders, including addictive behavior. Here, to foster the study of the HNRNPF/H family of RBPs, we discuss features of the genes encoding these proteins, their structures and functions, and emerging contributions to disease. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Tayvia Brownmiller
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland, USA
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland, USA
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Velayutham S, Seerattan R, Sultan M, Seal T, Danthurthy S, Chinnappan B, Landi J, Pearl K, Singh A, Smalley KSM, Zaias J, Choi JY, Minond D. Novel Anti-Melanoma Compounds Are Efficacious in A375 Cell Line Xenograft Melanoma Model in Nude Mice. Biomolecules 2023; 13:1276. [PMID: 37759675 PMCID: PMC10526148 DOI: 10.3390/biom13091276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/20/2023] [Accepted: 08/17/2023] [Indexed: 09/29/2023] Open
Abstract
Despite the successes of immunotherapy, melanoma remains one of the deadliest cancers, therefore, the need for innovation remains high. We previously reported anti-melanoma compounds that work by downregulating spliceosomal proteins hnRNPH1 and H2. In a separate study, we reported that these compounds were non-toxic to Balb/C mice at 50 mg/kg suggesting their utility in in vivo studies. In the present study, we aimed to assess the efficacy of these compounds by testing them in A375 cell-line xenograft in nude athymic mice. Animals were randomized into four groups (n = 12/group): 10 mg/kg vemurafenib, and 25 mg/kg 2155-14 and 2155-18 thrice a week for 15 days along with a control group. The results revealed that both 2155-14 and 2155-18 significantly decreased the growth of A375 tumors, which was comparable to vemurafenib. These results were confirmed by tumor volume, weight, and histopathological examination. In conclusion, these results demonstrate the therapeutic potential of targeting spliceosomal proteins hnRNPH1 and H2.
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Affiliation(s)
- Sadeeshkumar Velayutham
- College of Pharmacy, Nova Southeastern University, 3321 College Avenue, Fort Lauderdale, FL 33314, USA
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, 3321 College Avenue, CCR r.605, Fort Lauderdale, FL 33314, USA;
| | - Ryan Seerattan
- Department of Chemistry and Biochemistry, Queens College, 65-30 Kissena Boulevard, Flushing, NY 11367, USA
| | - Maab Sultan
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, 3321 College Avenue, CCR r.605, Fort Lauderdale, FL 33314, USA;
| | - Trisha Seal
- Halmos College of Arts and Sciences, Nova Southeastern University, 3301 College Avenue, Fort Lauderdale, FL 33314, USA
| | - Samaya Danthurthy
- Honors College, Nova Southeastern University, 8000 N Ocean Dr., Dania Beach, FL 33004, USA
| | - Baskaran Chinnappan
- College of Pharmacy, Nova Southeastern University, 3321 College Avenue, Fort Lauderdale, FL 33314, USA
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, 3321 College Avenue, CCR r.605, Fort Lauderdale, FL 33314, USA;
| | - Jessica Landi
- Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, 3321 College Avenue, Fort Lauderdale, FL 33314, USA
| | - Kaitlyn Pearl
- Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, 3321 College Avenue, Fort Lauderdale, FL 33314, USA
| | - Aveta Singh
- Department of Chemistry and Biochemistry, Queens College, 65-30 Kissena Boulevard, Flushing, NY 11367, USA
| | - Keiran S. M. Smalley
- Department of Tumor Biology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA;
| | - Julia Zaias
- Division of Comparative Pathology, University of Miami, 1501 NW 10th Ave, Miami, FL 33136, USA;
| | - Jun Yong Choi
- Department of Chemistry and Biochemistry, Queens College, 65-30 Kissena Boulevard, Flushing, NY 11367, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, 365 5th Ave, New York, NY 10016, USA
| | - Dmitriy Minond
- College of Pharmacy, Nova Southeastern University, 3321 College Avenue, Fort Lauderdale, FL 33314, USA
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, 3321 College Avenue, CCR r.605, Fort Lauderdale, FL 33314, USA;
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Wang P, Wang J, Yao S, Cui M, Cheng Y, Liu W, Gao Z, Hu J, Zhang J, Zhang H. Deubiquitinase USP9X stabilizes RNA m 6A demethylase ALKBH5 and promotes acute myeloid leukemia cell survival. J Biol Chem 2023; 299:105055. [PMID: 37454738 PMCID: PMC10424212 DOI: 10.1016/j.jbc.2023.105055] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Post-translational modifications including protein ubiquitination regulate a plethora of cellular processes in distinct manners. RNA N6-methyladenosine is the most abundant post-transcriptional modification on mammalian mRNAs and plays important roles in various physiological and pathological conditions including hematologic malignancies. We previously determined that the RNA N6-methyladenosine eraser ALKBH5 is necessary for the maintenance of acute myeloid leukemia (AML) stem cell function, but the post-translational modifications involved in ALKBH5 regulation remain elusive. Here, we show that deubiquitinase ubiquitin-specific peptidase 9X (USP9X) stabilizes ALKBH5 and promotes AML cell survival. Through the use of mass spectrometry as an unbiased approach, we identify USP9X and confirm that it directly binds to ALKBH5. USP9X stabilizes ALKBH5 by removing the K48-linked polyubiquitin chain at K57. Using human myeloid leukemia cells and a murine AML model, we find that genetic knockdown or pharmaceutical inhibition of USP9X inhibits leukemia cell proliferation, induces apoptosis, and delays AML development. Ectopic expression of ALKBH5 partially mediates the function of USP9X in AML. Overall, this study uncovers deubiquitinase USP9X as a key for stabilizing ALKBH5 expression and reveals the important role of USP9X in AML, which provides a promising therapeutic strategy for AML treatment in the clinic.
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Affiliation(s)
- Peipei Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Jing Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China
| | - Shuxin Yao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Manman Cui
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Ying Cheng
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Weidong Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China
| | - Zhuying Gao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Jin Hu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Jinfang Zhang
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Haojian Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
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5
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Li JS, Chen X, Luo A, Chen D. TFRC-RNA interactions show the regulation of gene expression and alternative splicing associated with IgAN in human renal tubule mesangial cells. Front Genet 2023; 14:1176118. [PMID: 37547464 PMCID: PMC10397801 DOI: 10.3389/fgene.2023.1176118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction: IgA nephropathy (IgAN) is the most common primary glomerular disease (PGD) which could progress to renal failure and is characterized by aberrant IgA immune complex deposition. Transferrin receptor1 (TFRC), an IgA receptor, is a potential RNA binding protein (RBP) which regulates expression of genes positively associated with the cell cycle and proliferation and is involved in IgAN. Molecular mechanisms by which TFRC affects IgAN development remain unclear. Methods: In this study, TFRC was overexpressed in human renal tubular mesangial cells (HRMCs) and RNA-sequencing (RNA-seq) and improved RNA immunoprecipitation sequencing (iRIP-seq) were performed. The aim was to identify potential RNA targets of TFRC at transcriptional and alternative splicing (AS) levels. Results: TFRC-regulated AS genes were enriched in mRNA splicing and DNA repair, consistent with global changes due to TFRC overexpression (TFRC-OE). Expression of TFRC-regulated genes potentially associated with IgAN, including CENPH, FOXM1, KIFC1, TOP2A, FABP4, ID1, KIF20A, ATF3, H19, IRF7, and H1-2, and with AS, CYGB, MCM7 and HNRNPH1, were investigated by RT-qPCR and iRIP-seq data analyzed to identify TFRC-bound RNA targets. RCC1 and RPPH1 were found to be TFRC-bound RNA targets involved in cell proliferation. Discussion: In conclusion, molecular TFRC targets were identified in HRMCs and TFRC found to regulate gene transcription and AS. TFRC is considered to have potential as a clinical therapeutic target.
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Affiliation(s)
- Jian-Si Li
- Department of Nephrology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiao Chen
- Heilongjiang Provincial Hospital Affiliated to Harbin Institute of Technology, Harbin, China
| | - Ailing Luo
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., Wuhan, China
| | - Dong Chen
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., Wuhan, China
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6
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Mas AM, Huarte M. Long Noncoding RNA Signatures as Cancer Biomarkers. J Clin Oncol 2023; 41:3059-3062. [PMID: 37043713 DOI: 10.1200/jco.23.00381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Affiliation(s)
- Aina M Mas
- Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Maite Huarte
- Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
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Feng S, Wen H, Liu K, Xiong M, Li J, Gui Y, Lv C, Zhang J, Ma X, Wang X, Yuan S. hnRNPH1 establishes Sertoli-germ cell crosstalk through cooperation with PTBP1 and AR, and is essential for male fertility in mice. Development 2023; 150:dev201040. [PMID: 36718792 DOI: 10.1242/dev.201040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/03/2023] [Indexed: 02/01/2023]
Abstract
Spermatogenesis depends on the crosstalk of Sertoli cells (SCs) and germ cells. However, the gene regulatory network establishing the communications between SCs and germ cells remains unclear. Here, we report that heterogeneous nuclear ribonucleoprotein H1 (hnRNPH1) in SCs is essential for the establishment of crosstalk between SCs and germ cells. Conditional knockout of hnRNPH1 in mouse SCs leads to compromised blood-testis barrier function, delayed meiotic progression, increased germ cell apoptosis, sloughing of germ cells and, eventually, infertility of mice. Mechanistically, we discovered that hnRNPH1 could interact with the splicing regulator PTBP1 in SCs to regulate the pre-mRNA alternative splicing of the target genes functionally related to cell adhesion. Interestingly, we also found hnRNPH1 could cooperate with the androgen receptor, one of the SC-specific transcription factors, to modulate the transcription level of a group of genes associated with the cell-cell junction and EGFR pathway by directly binding to the gene promoters. Collectively, our findings reveal a crucial role for hnRNPH1 in SCs during spermatogenesis and uncover a potential molecular regulatory network involving hnRNPH1 in establishing Sertoli-germ cell crosstalk.
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Affiliation(s)
- Shenglei Feng
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hui Wen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kuan Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengneng Xiong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jinmei Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yiqian Gui
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chunyu Lv
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jin Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xixiang Ma
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Laboratory of Animal Center, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Laboratory of Animal Center, Huazhong University of Science and Technology, Wuhan 430030, China
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong 518057, China
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8
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Velayutham S, Seal T, Danthurthy S, Zaias J, Smalley KSM, Minond D. In Vivo Acute Toxicity Studies of Novel Anti-Melanoma Compounds Downregulators of hnRNPH1/H2. Biomolecules 2023; 13:biom13020349. [PMID: 36830718 PMCID: PMC9953269 DOI: 10.3390/biom13020349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Despite the recent advances in melanoma therapy, the need for new targets and novel approaches to therapy is urgent. We previously reported melanoma actives that work via binding and downregulating spliceosomal proteins hnRNPH1 and H2. Given the lack of knowledge about the side effects of using spliceosomal binders in humans, an acute toxicity study was conducted to evaluate these compounds in mice. Male and female mice were treated with compounds 2155-14 and 2155-18 at 50 mg/kg/day via subcutaneous injections, and the clinical signs of distress were monitored for 21 days and compared with control mice. Additionally, the effect of the leads on blood chemistry, blood cell counts, and organs was evaluated. No significant changes were observed in the body weight, blood cell count, blood chemistry, or organs of the mice following the compound treatment. The results show that our compounds, 2155-14 and 2155-18, are not toxic for the study period of three weeks.
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Affiliation(s)
- Sadeeshkumar Velayutham
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, 3321 College Avenue, CCR r.605, Fort Lauderdale, FL 33314, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, 3321 College Avenue, Fort Lauderdale, FL 33314, USA
| | - Trisha Seal
- Halmos College of Arts and Sciences, Nova Southeastern University, 3301 College Avenue, Fort Lauderdale, FL 33314, USA
| | - Samaya Danthurthy
- Honors College, Nova Southeastern University, 8000 N Ocean Dr., Dania Beach, FL 33004, USA
| | - Julia Zaias
- Division of Comparative Pathology, University of Miami, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - Keiran S. M. Smalley
- Moffitt Cancer Center, Department of Tumor Biology, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Dmitriy Minond
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, 3321 College Avenue, CCR r.605, Fort Lauderdale, FL 33314, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, 3321 College Avenue, Fort Lauderdale, FL 33314, USA
- Correspondence:
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Qureshi QUA, Audas TE, Morin RD, Coyle KM. Emerging roles for heterogeneous ribonuclear proteins in normal and malignant B cells. Biochem Cell Biol 2023; 101:160-171. [PMID: 36745874 DOI: 10.1139/bcb-2022-0332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are among the most abundantly expressed RNA binding proteins in the cell and play major roles in all facets of RNA metabolism. hnRNPs are increasingly appreciated as essential for mammalian B cell development by regulating the carefully ordered expression of specific genes. Due to this tight regulation of the hnRNP-RNA network, it is no surprise that a growing number of genes encoding hnRNPs have been causally associated with the onset or progression of many cancers, including B cell neoplasms. Here we discuss our current understanding of hnRNP-driven regulation in normal, perturbed, and malignant B cells, and the most recent and emerging therapeutic innovations aimed at targeting the hnRNP-RNA network in lymphoma.
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Affiliation(s)
- Qurat Ul Ain Qureshi
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Timothy E Audas
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Ryan D Morin
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Krysta M Coyle
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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Nasrullah U, Stanke K, Recknagel V, Bozkurt S, Wurzel P, Gauer S, Imre G, Münch C, Pfeilschifter J, Eberhardt W. The E3 Ligase TRIM25 Impairs Apoptotic Cell Death in Colon Carcinoma Cells via Destabilization of Caspase-7 mRNA: A Possible Role of hnRNPH1. Cells 2023; 12. [PMID: 36611995 DOI: 10.3390/cells12010201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Therapy resistance is still a major reason for treatment failure in colorectal cancer (CRC). Previously, we identified the E3 ubiquitin ligase TRIM25 as a novel suppressor of caspase-2 translation which contributes to the apoptosis resistance of CRC cells towards chemotherapeutic drugs. Here, we report the executioner caspase-7 as being a further target of TRIM25. The results from the gain- and loss-of-function approaches and the actinomycin D experiments indicate that TRIM25 attenuates caspase-7 expression mainly through a decrease in mRNA stability. The data from the RNA pulldown assays with immunoprecipitated TRIM25 truncations indicate a direct TRIM25 binding to caspase-7 mRNA, which is mediated by the PRY/SPRY domain, which is also known to be highly relevant for protein-protein interactions. By employing TRIM25 immunoprecipitation, we identified the heterogeneous nuclear ribonucleoprotein H1 (hnRNPH1) as a novel TRIM25 binding protein with a functional impact on caspase-7 mRNA stability. Notably, the interaction of both proteins was highly sensitive to RNase A treatment and again depended on the PRY/SPRY domain, thus indicating an indirect interaction of both proteins which is achieved through a common RNA binding. Ubiquitin affinity chromatography showed that both proteins are targets of ubiquitin modification. Functionally, the ectopic expression of caspase-7 in CRC cells caused an increase in poly ADP-ribose polymerase (PARP) cleavage concomitant with a significant increase in apoptosis. Collectively, the negative regulation of caspase-7 by TRIM25, which is possibly executed by hnRNPH1, implies a novel survival mechanism underlying the chemotherapeutic drug resistance of CRC cells. The targeting of TRIM25 could therefore offer a promising strategy for the reduction in therapy resistance in CRC patients.
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11
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Feng S, Li J, Wen H, Liu K, Gui Y, Wen Y, Wang X, Yuan S. hnRNPH1 recruits PTBP2 and SRSF3 to modulate alternative splicing in germ cells. Nat Commun 2022; 13:3588. [PMID: 35739118 DOI: 10.1038/s41467-022-31364-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/14/2022] [Indexed: 12/03/2022] Open
Abstract
Coordinated regulation of alternative pre-mRNA splicing is essential for germ cell development. However, the underlying molecular mechanism that controls alternative mRNA expression during germ cell development remains elusive. Herein, we show that hnRNPH1 is highly expressed in the reproductive system and recruits the PTBP2 and SRSF3 to modulate the alternative splicing in germ cells. Conditional knockout Hnrnph1 in spermatogenic cells causes many abnormal splicing events, thus affecting the genes related to meiosis and communication between germ cells and Sertoli cells. This is characterized by asynapsis of chromosomes and impairment of germ-Sertoli communications, which ultimately leads to male sterility. Markedly, Hnrnph1 germline-specific mutant female mice are also infertile, and Hnrnph1-deficient oocytes exhibit a similar defective synapsis and cell-cell junction as seen in Hnrnph1-deficient male germ cells. Collectively, our data support a molecular model wherein hnRNPH1 governs a network of alternative splicing events in germ cells via recruitment of PTBP2 and SRSF3. Coordinated regulation of alternative splicing is essential for germ cell development. Here, the authors report that hnRNPH1 interacts with alternative splicing factors PTBP2 and SRSF3 in the germline to regulate pre-mRNA alternative splicing.
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12
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Ma H, de Zwaan E, Guo YE, Cejas P, Thiru P, van de Bunt M, Jeppesen JF, Syamala S, Dall'Agnese A, Abraham BJ, Fu D, Garrett-Engele C, Lee TI, Long HW, Griffith LG, Young RA, Jaenisch R. The nuclear receptor THRB facilitates differentiation of human PSCs into more mature hepatocytes. Cell Stem Cell 2022; 29:795-809.e11. [PMID: 35452598 PMCID: PMC9466295 DOI: 10.1016/j.stem.2022.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/23/2021] [Accepted: 03/28/2022] [Indexed: 12/15/2022]
Abstract
To understand the mechanisms regulating the in vitro maturation of hPSC-derived hepatocytes, we developed a 3D differentiation system and compared gene regulatory elements in human primary hepatocytes with those in hPSC-hepatocytes that were differentiated in 2D or 3D conditions by RNA-seq, ATAC-seq, and H3K27Ac ChIP-seq. Regulome comparisons showed a reduced enrichment of thyroid receptor THRB motifs in accessible chromatin and active enhancers without a reduced transcription of THRB. The addition of thyroid hormone T3 increased the binding of THRB to the CYP3A4 proximal enhancer, restored the super-enhancer status and gene expression of NFIC, and reduced the expression of AFP. The resultant hPSC-hepatocytes showed gene expression, epigenetic status, and super-enhancer landscape closer to primary hepatocytes and activated regulatory regions including non-coding SNPs associated with liver-related diseases. Transplanting the hPSC-hepatocytes resulted in the engraftment of human hepatocytes into the mouse liver without disrupting normal liver histology. This work implicates the environmental factor-nuclear receptor axis in regulating the maturation of hPSC-hepatocytes.
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Affiliation(s)
- Haiting Ma
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Esmée de Zwaan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yang Eric Guo
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Prathapan Thiru
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Jacob F Jeppesen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Global Drug Discovery, Novo Nordisk, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sudeepa Syamala
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Dongdong Fu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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13
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Le Bras M, Gorelick N, Pautet S, Tyler B, Manenti S, Skuli N, Millevoi S, Cammas A. Translational Regulation by hnRNP H/F Is Essential for the Proliferation and Survival of Glioblastoma. Cancers (Basel) 2022; 14:1283. [PMID: 35267591 DOI: 10.3390/cancers14051283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/21/2022] [Indexed: 02/05/2023] Open
Abstract
Deregulation of mRNA translation is a widespread characteristic of glioblastoma (GBM), aggressive malignant brain tumors that are resistant to conventional therapies. RNA-binding proteins (RBPs) play a critical role in translational regulation, yet the mechanisms and impact of these regulations on cancer development, progression and response to therapy remain to be fully understood. Here, we showed that hnRNP H/F RBPs are potent regulators of translation through several mechanisms that converge to modulate the expression and/or the activity of translation initiation factors. Among these, hnRNP H/F regulate the phosphorylation of eIF4E and its translational targets by controlling RNA splicing of the A-Raf kinase mRNA, which in turn modulates the MEK-ERK/MAPK signaling pathway. The underlying mechanism involves RNA G-quadruplex (RG4s), RNA structures whose modulation phenocopies hnRNP H/F translation regulation in GBM cells. Our results highlighted that hnRNP H/F are essential for key functional pathways regulating proliferation and survival of GBM, highlighting its targeting as a promising strategy for improving therapeutic outcomes.
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14
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Tanu T, Taniue K, Imamura K, Onoguchi-Mizutani R, Han H, Jensen TH, Akimitsu N. hnRNPH1-MTR4 complex-mediated regulation of NEAT1v2 stability is critical for IL8 expression. RNA Biol 2021; 18:537-547. [PMID: 34470577 DOI: 10.1080/15476286.2021.1971439] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many long noncoding RNAs (lncRNAs) are localized in the nucleus and play important roles in various biological processes, including cell proliferation, differentiation and antiviral response. Yet, it remains unclear how some nuclear lncRNAs are turned over. Here we show that the heterogeneous nuclear ribonucleoprotein H1 (hnRNPH1) controls expression levels of NEAT1v2, a lncRNA involved in the formation of nuclear paraspeckles. hnRNPH1 associates, in an RNA-independent manner, with the RNA helicase MTR4/MTREX, an essential co-factor of the nuclear ribonucleolytic RNA exosome. hnRNPH1 localizes in nuclear speckles and depletion of hnRNPH1 enhances NEAT1v2-mediated expression of the IL8 mRNA, encoding a cytokine involved in the innate immune response. Taken together, our results indicate that the hnRNPH1-MTR4 linkage regulates IL8 expression through the degradation of NEAT1v2 RNA.
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Affiliation(s)
- Tanzina Tanu
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Kenzui Taniue
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Katsutoshi Imamura
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | | | - Han Han
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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15
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Schonfeld M, Villar MT, Artigues A, Weinman SA, Tikhanovich I. Arginine Methylation of Hepatic hnRNPH Suppresses Complement Activation and Systemic Inflammation in Alcohol-Fed Mice. Hepatol Commun 2021; 5:812-829. [PMID: 34027271 PMCID: PMC8122385 DOI: 10.1002/hep4.1674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/29/2020] [Accepted: 12/17/2020] [Indexed: 01/16/2023] Open
Abstract
Protein arginine methyl transferase 1 (PRMT1) is the main enzyme for cellular arginine methylation. It regulates many aspects of liver biology including inflammation, lipid metabolism, and proliferation. Previously we identified that PRMT1 is necessary for protection from alcohol-induced liver injury. However, many PRMT1 targets in the liver after alcohol exposure are not yet identified. We studied the changes in the PRMT1-dependent arginine methylated proteome after alcohol feeding in mouse liver using mass spectrometry. We found that arginine methylation of the RNA-binding protein (heterogeneous nuclear ribonucleoprotein [hnRNP]) H1 is mediated by PRMT1 and is altered in alcohol-fed mice. PRMT1-dependent methylation suppressed hnRNP H1 binding to several messenger RNAs of complement pathway including complement component C3. We found that PRMT1-dependent hnRNP H methylation suppressed complement component expression in vitro, and phosphorylation is required for this function of PRMT1. In agreement with that finding, hepatocyte-specific PRMT1 knockout mice had an increase in complement component expression in the liver. Excessive complement expression in alcohol-fed PRMT1 knockout mice resulted in further complement activation and an increase in serum C3a and C5a levels, which correlated with inflammation in multiple organs including lung and adipose tissue. Using specific inhibitors to block C3aR and C5aR receptors, we were able to prevent lung and adipose tissue inflammation without affecting inflammation in the liver or liver injury. Conclusion: Taken together, these data suggest that PRMT1-dependent suppression of complement production in the liver is necessary for prevention of systemic inflammation in alcohol-fed mice. C3a and C5a play a role in this liver-lung and liver-adipose interaction in alcohol-fed mice deficient in liver arginine methylation.
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Affiliation(s)
- Michael Schonfeld
- Department of Internal MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Maria T Villar
- Department of BiochemistryUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Antonio Artigues
- Department of BiochemistryUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Steven A Weinman
- Department of Internal MedicineUniversity of Kansas Medical CenterKansas CityKSUSA.,Liver CenterUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Irina Tikhanovich
- Department of Internal MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
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16
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17
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Jacinto JGP, Häfliger IM, Borel N, Zanolari P, Drögemüller C, Veiga IMB. Clinicopathological and Genomic Characterization of a Simmental Calf with Generalized Bovine Juvenile Angiomatosis. Animals (Basel) 2021; 11:ani11030624. [PMID: 33652974 PMCID: PMC7996833 DOI: 10.3390/ani11030624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Vascular anomalies represent a heterogeneous group of rare disorders encompassing both vascular malformations and tumors, which can be congenital or arise shortly after birth. They often pose a diagnostic challenge in human and veterinary medicine, and the referring nomenclature is equivocal. Bovine juvenile angiomatosis (BJA), a clinical condition belonging to this group of disorders, encompasses vascular malformations and tumors arising in calves. Usually, such vascular anomalies are not further investigated on a molecular genetic level, mainly because of a lack of resources and diagnostic tools, as well as the low value and short lifespan of the affected animals. Here we report the clinical, pathological, immunohistochemical, and genetic features of a Simmental calf that displayed multiple cutaneous, subcutaneous, and visceral vascular hamartomas compatible with a generalized form of BJA. Whole-genome sequencing identified six coding variants, including four heterozygous variants in the PREX1, UBE3B, PCDHGA2, and ZSWIM6 genes, which occurred only in the BJA-affected calf and were absent in the global control cohort of more than 4500 cattle. Assuming a germline mutation as etiology, one of these variants might be responsible for the vascular malformations identified in this calf. Abstract Bovine juvenile angiomatosis (BJA) comprises a group of single or multiple proliferative vascular anomalies in the skin and viscera of affected calves. The purpose of this study was to characterize the clinicopathological phenotype of a 1.5-month-old Simmental calf with multiple cutaneous, subcutaneous, and visceral vascular hamartomas, which were compatible with a generalized form of BJA, and to identify genetic cause for this phenotype by whole-genome sequencing (WGS). The calf was referred to the clinics as a result of its failure to thrive and the presence of multiple cutaneous and subcutaneous nodules, some of which bled abundantly following spontaneous rupture. Gross pathology revealed similar lesions at the inner thoracic wall, diaphragm, mediastinum, pericardium, inner abdominal wall, and mesentery. Histologically, variably sized cavities lined by a single layer of plump cells and supported by a loose stroma with occasional acute hemorrhage were observed. Determined by immunochemistry, the plump cells lining the cavities displayed a strong cytoplasmic signal for PECAM-1, von Willebrand factor, and vimentin. WGS revealed six private protein-changing variants affecting different genes present in the calf and absent in more than 4500 control genomes. Assuming a spontaneous de novo mutation event, one of the identified variants found in the PREX1, UBE3B, PCDHGA2, and ZSWIM6 genes may represent a possible candidate pathogenic variant for this rare form of vascular malformation.
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Affiliation(s)
- Joana G. P. Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano Emilia (BO), Italy;
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | - Irene M. Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | - Nicole Borel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland;
| | - Patrik Zanolari
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
- Correspondence: ; Tel.: +41-31-631-2529
| | - Inês M. B. Veiga
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
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18
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Wang Q, Conlon EG, Manley JL, Rio DC. Widespread intron retention impairs protein homeostasis in C9orf72 ALS brains. Genome Res 2020; 30:1705-1715. [PMID: 33055097 PMCID: PMC7706729 DOI: 10.1101/gr.265298.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022]
Abstract
The GGGGCC hexanucleotide expansion in C9orf72 (C9) is the most frequent known cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), yet a clear understanding of how C9 fits into the broader context of ALS/FTD pathology has remained lacking. The repetitive RNA derived from the C9 repeat is known to sequester hnRNPH, a splicing regulator, into insoluble aggregates, resulting in aberrant alternative splicing. Furthermore, hnRNPH insolubility and altered splicing of a robust set of targets have been observed to correlate in C9 and sporadic ALS/FTD patients alike, suggesting that changes along this axis are a core feature of disease pathogenesis. Here, we characterize previously uncategorized RNA splicing defects involving widespread intron retention affecting almost 2000 transcripts in C9ALS/FTD brains exhibiting a high amount of sequestered, insoluble hnRNPH. These intron retention events appear not to alter overall expression levels of the affected transcripts but rather the protein-coding regions. These retained introns affect transcripts in multiple cellular pathways predicted to be involved in C9 as well as sporadic ALS/FTD etiology, including the proteasomal and autophagy systems. The retained intron pre-mRNAs display a number of characteristics, including enrichment of hnRNPH-bound splicing enhancer motifs and a propensity for G-quadruplex (G-Q) formation, linking the defective splicing directly to high amounts of sequestered hnRNPH. Together, our results reveal previously undetected splicing defects in high insoluble hnRNPH-associated C9ALS brains, suggesting a feedback between effective RNA-binding protein dosage and protein quality control in C9, and perhaps all, ALS/FTD.
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Affiliation(s)
- Qingqing Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Erin G Conlon
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Donald C Rio
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
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19
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Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood 2020; 136:572-584. [PMID: 32160292 PMCID: PMC7440974 DOI: 10.1182/blood.2019002385] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 02/20/2020] [Indexed: 12/11/2022] Open
Abstract
Mantle cell lymphoma (MCL) is an uncommon B-cell non-Hodgkin lymphoma (NHL) that is incurable with standard therapies. The genetic drivers of this cancer have not been firmly established, and the features that contribute to differences in clinical course remain limited. To extend our understanding of the biological pathways involved in this malignancy, we performed a large-scale genomic analysis of MCL using data from 51 exomes and 34 genomes alongside previously published exome cohorts. To confirm our findings, we resequenced the genes identified in the exome cohort in 191 MCL tumors, each having clinical follow-up data. We confirmed the prognostic association of TP53 and NOTCH1 mutations. Our sequencing revealed novel recurrent noncoding mutations surrounding a single exon of the HNRNPH1gene. In RNA-seq data from 103 of these cases, MCL tumors with these mutations had a distinct imbalance of HNRNPH1 isoforms. This altered splicing of HNRNPH1 was associated with inferior outcomes in MCL and showed a significant increase in protein expression by immunohistochemistry. We describe a functional role for these recurrent noncoding mutations in disrupting an autoregulatory feedback mechanism, thereby deregulating HNRNPH1 protein expression. Taken together, these data strongly imply a role for aberrant regulation of messenger RNA processing in MCL pathobiology.
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Affiliation(s)
- Prasath Pararajalingam
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Krysta M Coyle
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Sarah E Arthur
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Nicole Thomas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Miguel Alcaide
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Barbara Meissner
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Merrill Boyle
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Quratulain Qureshi
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Christopher Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Graham W Slack
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | | | - Constantine S Tam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Rishu Agarwal
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Georg Lenz
- Department of Medicine A, Hematology, Oncology, and Pneumology, University Hospital Münster, Münster, Germany
| | | | - Randy D Gascoyne
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Christian Steidl
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Joseph Connors
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Diego Villa
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Timothy E Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Marco A Marra
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | | | - David W Scott
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
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20
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Mineo M, Lyons SM, Zdioruk M, von Spreckelsen N, Ferrer-Luna R, Ito H, Alayo QA, Kharel P, Giantini Larsen A, Fan WY, Auduong S, Grauwet K, Passaro C, Khalsa JK, Shah K, Reardon DA, Ligon KL, Beroukhim R, Nakashima H, Ivanov P, Anderson PJ, Lawler SE, Chiocca EA. Tumor Interferon Signaling Is Regulated by a lncRNA INCR1 Transcribed from the PD-L1 Locus. Mol Cell 2020; 78:1207-1223.e8. [PMID: 32504554 DOI: 10.1016/j.molcel.2020.05.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 03/03/2020] [Accepted: 05/11/2020] [Indexed: 01/22/2023]
Abstract
Tumor interferon (IFN) signaling promotes PD-L1 expression to suppress T cell-mediated immunosurveillance. We identify the IFN-stimulated non-coding RNA 1 (INCR1) as a long noncoding RNA (lncRNA) transcribed from the PD-L1 locus and show that INCR1 controls IFNγ signaling in multiple tumor types. Silencing INCR1 decreases the expression of PD-L1, JAK2, and several other IFNγ-stimulated genes. INCR1 knockdown sensitizes tumor cells to cytotoxic T cell-mediated killing, improving CAR T cell therapy. We discover that PD-L1 and JAK2 transcripts are negatively regulated by binding to HNRNPH1, a nuclear ribonucleoprotein. The primary transcript of INCR1 binds HNRNPH1 to block its inhibitory effects on the neighboring genes PD-L1 and JAK2, enabling their expression. These findings introduce a mechanism of tumor IFNγ signaling regulation mediated by the lncRNA INCR1 and suggest a therapeutic target for cancer immunotherapy.
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Affiliation(s)
- Marco Mineo
- Harvey W. Cushing Neuro-oncology Laboratories (HCNL), Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Shawn M Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mykola Zdioruk
- Harvey W. Cushing Neuro-oncology Laboratories (HCNL), Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Niklas von Spreckelsen
- Harvey W. Cushing Neuro-oncology Laboratories (HCNL), Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Neurosurgery, Center for Neurosurgery, Faculty of Medicine, and University Hospital, University of Cologne, 50937 Cologne, Germany
| | - Ruben Ferrer-Luna
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hirotaka Ito
- Harvey W. Cushing Neuro-oncology Laboratories (HCNL), Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Quazim A Alayo
- Harvey W. Cushing Neuro-oncology Laboratories (HCNL), Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Prakash Kharel
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandra Giantini Larsen
- Harvey W. Cushing Neuro-oncology Laboratories (HCNL), Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - William Y Fan
- Harvey W. Cushing Neuro-oncology Laboratories (HCNL), Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sophia Auduong
- Harvey W. Cushing Neuro-oncology Laboratories (HCNL), Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Korneel Grauwet
- Harvey W. Cushing Neuro-oncology Laboratories (HCNL), Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Carmela Passaro
- Harvey W. Cushing Neuro-oncology Laboratories (HCNL), Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jasneet K Khalsa
- Center for Stem Cell Therapeutics and Imaging, Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Khalid Shah
- Center for Stem Cell Therapeutics and Imaging, Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - David A Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Keith L Ligon
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston Children's Hospital, and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Neuro-Oncology, Dana-Farber Cancer Institute, and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Hiroshi Nakashima
- Harvey W. Cushing Neuro-oncology Laboratories (HCNL), Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Paul J Anderson
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Sean E Lawler
- Harvey W. Cushing Neuro-oncology Laboratories (HCNL), Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - E Antonio Chiocca
- Harvey W. Cushing Neuro-oncology Laboratories (HCNL), Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
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21
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Pawar S, Liew TO, Stanam A, Lahiri C. Common cancer biomarkers of breast and ovarian types identified through artificial intelligence. Chem Biol Drug Des 2020; 96:995-1004. [DOI: 10.1111/cbdd.13672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Shrikant Pawar
- Yale Center for Genome Analysis (YCGA) Yale University New Haven CT USA
| | - Tuck Onn Liew
- Department of Biological Sciences Sunway University Petaling Jaya Malaysia
| | - Aditya Stanam
- College of Public Health The University of Iowa Iowa City IA USA
| | - Chandrajit Lahiri
- Department of Biological Sciences Sunway University Petaling Jaya Malaysia
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22
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Konishi H, Fujiya M, Kashima S, Sakatani A, Dokoshi T, Ando K, Ueno N, Iwama T, Moriichi K, Tanaka H, Okumura T. A tumor-specific modulation of heterogeneous ribonucleoprotein A0 promotes excessive mitosis and growth in colorectal cancer cells. Cell Death Dis 2020; 11:245. [PMID: 32303675 DOI: 10.1038/s41419-020-2439-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 11/11/2022]
Abstract
RNA regulation mediating RNA-binding proteins (RBPs) have been shown to be related to the maintenance of homeostasis as well as cancer progression. However, the tumor-associated functions as well as the detailed mechanisms underlying the anti-tumor effects of most RBPs have yet to be explored. We herein report that the phosphorylated heterogeneous ribonucleoprotein (hnRNP) A0 promotes mitosis through the RAS-associated protein 3 GTPase-activating protein catalytic subunit 1 (RAB3GAP1)-Zeste white 10 interactor (ZWINT1) cascade. The downregulation assay of 20 representative hnRNPs, a major family of RNA-binding proteins, in colorectal cancer cells revealed that hnRNPA0 is a strong regulator of cancer cell growth. The tumor promotive function of hnRNPA0 was confirmed in gastrointestinal cancer cells, including pancreatic, esophageal, and gastric cancer cells, but not in non-cancerous cells. Flow cytometry and Western blotting analyses revealed that hnRNPA0 inhibited the apoptosis through the maintenance of G2/M phase promotion in colorectal cancer cells. A comprehensive analysis of mRNAs regulated by hnRNP A0 and immunostaining revealed that mitotic events were regulated by the hnRNPA0-RAB3GAP1 mRNA-mediated ZWINT-1 stabilization in colorectal cancer cells, but not in non-tumorous cells. The interaction of hnRNP A0 with mRNAs was dramatically changed by the deactivation of its phosphorylation site in cancer cells, but not in non-tumorous cells. Therefore, the tumor-specific biological functions characterized by the abnormal phosphorylation of RBPs are considered to be an attractive target for tumor treatment.
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23
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Neckles C, Boer RE, Aboreden N, Cross AM, Walker RL, Kim BH, Kim S, Schneekloth JS, Caplen NJ. HNRNPH1-dependent splicing of a fusion oncogene reveals a targetable RNA G-quadruplex interaction. RNA 2019; 25:1731-1750. [PMID: 31511320 PMCID: PMC6859848 DOI: 10.1261/rna.072454.119] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/08/2019] [Indexed: 05/05/2023]
Abstract
The primary oncogenic event in ∼85% of Ewing sarcomas is a chromosomal translocation that generates a fusion oncogene encoding an aberrant transcription factor. The exact genomic breakpoints within the translocated genes, EWSR1 and FLI1, vary; however, in EWSR1, breakpoints typically occur within introns 7 or 8. We previously found that in Ewing sarcoma cells harboring EWSR1 intron 8 breakpoints, the RNA-binding protein HNRNPH1 facilitates a splicing event that excludes EWSR1 exon 8 from the EWS-FLI1 pre-mRNA to generate an in-frame mRNA. Here, we show that the processing of distinct EWS-FLI1 pre-mRNAs by HNRNPH1, but not other homologous family members, resembles alternative splicing of transcript variants of EWSR1 We demonstrate that HNRNPH1 recruitment is driven by guanine-rich sequences within EWSR1 exon 8 that have the potential to fold into RNA G-quadruplex structures. Critically, we demonstrate that an RNA mimetic of one of these G-quadruplexes modulates HNRNPH1 binding and induces a decrease in the growth of an EWSR1 exon 8 fusion-positive Ewing sarcoma cell line. Finally, we show that EWSR1 exon 8 fusion-positive cell lines are more sensitive to treatment with the pan-quadruplex binding molecule, pyridostatin (PDS), than EWSR1 exon 8 fusion-negative lines. Also, the treatment of EWSR1 exon 8 fusion-positive cells with PDS decreases EWS-FLI1 transcriptional activity, reversing the transcriptional deregulation driven by EWS-FLI1. Our findings illustrate that modulation of the alternative splicing of EWS-FLI1 pre-mRNA is a novel strategy for future therapeutics against the EWSR1 exon 8 containing fusion oncogenes present in a third of Ewing sarcoma.
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Affiliation(s)
- Carla Neckles
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Robert E Boer
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Nicholas Aboreden
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Allison M Cross
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Robert L Walker
- Molecular Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Bong-Hyun Kim
- CCR Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702, USA
| | - Suntae Kim
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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24
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Palrasu M, Knapinska AM, Diez J, Smith L, LaVoi T, Giulianotti M, Houghten RA, Fields GB, Minond D. A Novel Probe for Spliceosomal Proteins that Induces Autophagy and Death of Melanoma Cells Reveals New Targets for Melanoma Drug Discovery. Cell Physiol Biochem 2019; 53:656-686. [PMID: 31573152 PMCID: PMC6990463 DOI: 10.33594/000000164] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 09/25/2019] [Indexed: 12/24/2022] Open
Abstract
Background/Aims: Despite recent advances in melanoma drug discovery, the average overall survival of patients with late stage metastatic melanoma is approximately 3 years, suggesting a need for approaches that identify new melanoma targets. We have previously reported a discovery of novel anti-melanoma compound 2155–14 (Onwuha-Ekpete et al., J Med Chem. 2014 Feb 27; 57(4):1599–608). In the report presented herein we aim to identify its target(s) and mechanism of action. Methods: We utilized biotinylated analog of 2155–14 to pull down its targets from melanoma cells. Proteomics in combination with western blot were used to identify the targets. Mechanism of action of 2155–14 was determined using flow cytometry, RT-PCR, microscopy, western blot, and enzymatic activity assays. Where applicable, one-way analysis of variance (ANOVA) was used followed by Dunnett post hoc test. Results: In the present study, we identified ATP-dependent RNA helicase DDX1 and heterogeneous nuclear ribonucleoproteins (hnRNPs) H1, H2 and A2/B1 as targets of anti-melanoma compound 2155–14. To the best of our knowledge, this is a first report suggesting that these proteins could be targeted for melanoma therapy. Mechanistic investigations showed that 2155–14 induces ER stress leading to potentiation of basal autophagy resulting in melanoma cell death in BRAF and NRAS mutated melanoma cells. Conclusion: Identification of mode of action of 2155–14 may provide insight into novel therapies against a broad range of melanoma subtypes. These studies were enabled by the novel probe derived from a mixture-based library, an important class of chemical biology tools for discovering novel targets.
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Affiliation(s)
- Manikandan Palrasu
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Anna M Knapinska
- Department of Chemistry & Biochemistry, Center for Molecular Biology & Biotechnology, Florida Atlantic University, Jupiter, FL, USA
| | - Juan Diez
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Lyndsay Smith
- Department of Chemistry & Biochemistry, Center for Molecular Biology & Biotechnology, Florida Atlantic University, Jupiter, FL, USA
| | - Travis LaVoi
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL, USA
| | - Marc Giulianotti
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL, USA
| | | | - Gregg B Fields
- Department of Chemistry & Biochemistry, Center for Molecular Biology & Biotechnology, Florida Atlantic University, Jupiter, FL, USA
| | - Dmitriy Minond
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, Fort Lauderdale, FL, USA.,Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA,
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25
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Hale MA, Johnson NE, Berglund JA. Repeat-associated RNA structure and aberrant splicing. Biochim Biophys Acta Gene Regul Mech 2019; 1862:194405. [PMID: 31323433 DOI: 10.1016/j.bbagrm.2019.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
Over 30 hereditary disorders attributed to the expansion of microsatellite repeats have been identified. Despite variant nucleotide content, number of consecutive repeats, and different locations in the genome, many of these diseases have pathogenic RNA gain-of-function mechanisms. The repeat-containing RNAs can form structures in vitro predicted to contribute to the disease through assembly of intracellular RNA aggregates termed foci. The expanded repeat RNAs within these foci sequester RNA binding proteins (RBPs) with important roles in the regulation of RNA metabolism, most notably alternative splicing (AS). These deleterious interactions lead to downstream alterations in transcriptome-wide AS directly linked with disease symptoms. This review summarizes existing knowledge about the association between the repeat RNA structures and RBPs as well as the resulting aberrant AS patterns, specifically in the context of myotonic dystrophy. The connection between toxic, structured RNAs and dysregulation of AS in other repeat expansion diseases is also discussed. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Melissa A Hale
- Department of Neurology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nicholas E Johnson
- Department of Neurology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - J Andrew Berglund
- The RNA Institute, Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA.
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26
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Velasco MX, Kosti A, Guardia GDA, Santos MC, Tegge A, Qiao M, Correa BRS, Hernández G, Kokovay E, Galante PAF, Penalva LOF. Antagonism between the RNA-binding protein Musashi1 and miR-137 and its potential impact on neurogenesis and glioblastoma development. RNA 2019; 25:768-782. [PMID: 31004009 PMCID: PMC6573790 DOI: 10.1261/rna.069211.118] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
RNA-binding proteins (RBPs) and miRNAs are critical gene expression regulators that interact with one another in cooperative and antagonistic fashions. We identified Musashi1 (Msi1) and miR-137 as regulators of a molecular switch between self-renewal and differentiation. Msi1 and miR-137 have opposite expression patterns and functions, and Msi1 is repressed by miR-137. Msi1 is a stem-cell protein implicated in self-renewal while miR-137 functions as a proneuronal differentiation miRNA. In gliomas, miR-137 functions as a tumor suppressor while Msi1 is a prooncogenic factor. We suggest that the balance between Msi1 and miR-137 is a key determinant in cell fate decisions and disruption of this balance could contribute to neurodegenerative diseases and glioma development. Genomic analyses revealed that Msi1 and miR-137 share 141 target genes associated with differentiation, development, and morphogenesis. Initial results pointed out that these two regulators have an opposite impact on the expression of their target genes. Therefore, we propose an antagonistic model in which this network of shared targets could be either repressed by miR-137 or activated by Msi1, leading to different outcomes (self-renewal, proliferation, tumorigenesis).
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Affiliation(s)
- Mitzli X Velasco
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
- Translation and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City 14080, Mexico
| | - Adam Kosti
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Gabriela D A Guardia
- Centro de Oncologia Molecular-Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Marcia C Santos
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Allison Tegge
- Department of Statistics, Virginia Tech, Blacksburg, Virginia 14080, USA
| | - Mei Qiao
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Bruna R S Correa
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
- Centro de Oncologia Molecular-Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Greco Hernández
- Translation and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City 14080, Mexico
| | - Erzsebet Kokovay
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Pedro A F Galante
- Centro de Oncologia Molecular-Hospital Sírio-Libanês, São Paulo 01308-050, Brazil
| | - Luiz O F Penalva
- Greheey Children's Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
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27
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Barton SK, Gregory JM, Chandran S, Turner BJ. Could an Impairment in Local Translation of mRNAs in Glia be Contributing to Pathogenesis in ALS? Front Mol Neurosci 2019; 12:124. [PMID: 31164803 PMCID: PMC6536688 DOI: 10.3389/fnmol.2019.00124] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/26/2019] [Indexed: 12/13/2022] Open
Abstract
One of the key pathways implicated in amyotrophic lateral sclerosis (ALS) pathogenesis is abnormal RNA processing. Studies to date have focussed on defects in RNA stability, splicing, and translation, but this review article will focus on the largely overlooked RNA processing mechanism of RNA trafficking, with particular emphasis on the importance of glia. In the central nervous system (CNS), oligodendrocytes can extend processes to myelinate and metabolically support up to 50 axons and astrocytes can extend processes to cover up to 100,000 synapses, all with differing local functional requirements. Furthermore, many of the proteins required in these processes are large, aggregation-prone proteins which would be difficult to transport in their fully translated, terminally-folded state. This, therefore, highlights a critical requirement in these cells for local control of protein translation, which is achieved through specific trafficking of mRNAs to each process and local translation therein. Given that a large number of RNA-binding proteins have been implicated in ALS, and RNA-binding proteins are essential for trafficking mRNAs from the nucleus to glial processes for local translation, RNA misprocessing in glial cells is a likely source of cellular dysfunction in ALS. To date, neurons have been the focus of ALS research, but an intrinsic deficit in glia, namely astrocytes and oligodendrocytes, could have an additive effect on declining neuronal function in ALS. This review article aims to highlight the key evidence that supports the contention that RNA trafficking deficits in astrocytes and oligodendrocytes may contribute to in ALS.
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Affiliation(s)
- Samantha K Barton
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jenna M Gregory
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, United Kingdom
| | - Siddharthan Chandran
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, United Kingdom
| | - Bradley J Turner
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
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28
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Penumutchu S, Chiu LY, Meagher JL, Hansen AL, Stuckey JA, Tolbert BS. Differential Conformational Dynamics Encoded by the Linker between Quasi RNA Recognition Motifs of Heterogeneous Nuclear Ribonucleoprotein H. J Am Chem Soc 2018; 140:11661-11673. [PMID: 30122033 PMCID: PMC6648666 DOI: 10.1021/jacs.8b05366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Members of the heterogeneous nuclear ribonucleoprotein (hnRNP) F/H family are multipurpose RNA binding proteins that participate in most stages of RNA metabolism. Despite having similar RNA sequence preferences, hnRNP F/H proteins function in overlapping and, in some cases, distinct cellular processes. The domain organization of hnRNP F/H proteins is modular, consisting of N-terminal tandem quasi-RNA recognition motifs (F/HqRRM1,2) and a third C-terminal qRRM3 embedded between glycine-rich repeats. The tandem qRRMs are connected through a 10-residue linker, with several amino acids strictly conserved between hnRNP H and F. A significant difference occurs at position 105 of the linker, where hnRNP H contains a proline and hnRNP F an alanine. To investigate the influence of P105 on the conformational properties of hnRNP H, we probed the structural dynamics of its HqRRM1,2 domain with X-ray crystallography, NMR spectroscopy, and small-angle X-ray scattering. The collective results best describe that HqRRM1,2 exists in a conformational equilibrium between compact and extended structures. The compact structure displays an electropositive surface formed at the qRRM1-qRRM2 interface. Comparison of NMR relaxation parameters, including Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion, between HqRRM1,2 and FqRRM1,2 indicates that FqRRM1,2 primarily adopts a more extended and flexible conformation. Introducing the P105A mutation into HqRRM1,2 alters its conformational dynamics to favor an extended structure. Thus, our work demonstrates that the linker compositions confer different structural properties between hnRNP F/H family members that might contribute to their functional diversity.
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Affiliation(s)
- Srinivasa
R. Penumutchu
- Department
of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Liang-Yuan Chiu
- Department
of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Jennifer L. Meagher
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alexandar L. Hansen
- Campus
Chemical Instrument Center, The Ohio State
University, Columbus, Ohio 43210, United States
| | - Jeanne A. Stuckey
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Blanton S. Tolbert
- Department
of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States,
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29
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Braun S, Enculescu M, Setty ST, Cortés-López M, de Almeida BP, Sutandy FXR, Schulz L, Busch A, Seiler M, Ebersberger S, Barbosa-Morais NL, Legewie S, König J, Zarnack K. Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis. Nat Commun 2018; 9:3315. [PMID: 30120239 PMCID: PMC6098099 DOI: 10.1038/s41467-018-05748-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 07/19/2018] [Indexed: 01/22/2023] Open
Abstract
Mutations causing aberrant splicing are frequently implicated in human diseases including cancer. Here, we establish a high-throughput screen of randomly mutated minigenes to decode the cis-regulatory landscape that determines alternative splicing of exon 11 in the proto-oncogene MST1R (RON). Mathematical modelling of splicing kinetics enables us to identify more than 1000 mutations affecting RON exon 11 skipping, which corresponds to the pathological isoform RON∆165. Importantly, the effects correlate with RON alternative splicing in cancer patients bearing the same mutations. Moreover, we highlight heterogeneous nuclear ribonucleoprotein H (HNRNPH) as a key regulator of RON splicing in healthy tissues and cancer. Using iCLIP and synergy analysis, we pinpoint the functionally most relevant HNRNPH binding sites and demonstrate how cooperative HNRNPH binding facilitates a splicing switch of RON exon 11. Our results thereby offer insights into splicing regulation and the impact of mutations on alternative splicing in cancer.
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Affiliation(s)
- Simon Braun
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Mihaela Enculescu
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Samarth T Setty
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | | | - Bernardo P de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal.,Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus Gambelas, 8005-139, Faro, Portugal
| | | | - Laura Schulz
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Markus Seiler
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | | | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Stefan Legewie
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany.
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30
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Lee SJ, Oses-Prieto JA, Kawaguchi R, Sahoo PK, Kar AN, Rozenbaum M, Oliver D, Chand S, Ji H, Shtutman M, Miller-Randolph S, Taylor RJ, Fainzilber M, Coppola G, Burlingame AL, Twiss JL. hnRNPs Interacting with mRNA Localization Motifs Define Axonal RNA Regulons. Mol Cell Proteomics 2018; 17:2091-2106. [PMID: 30038033 DOI: 10.1074/mcp.ra118.000603] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 07/05/2018] [Indexed: 12/30/2022] Open
Abstract
mRNA translation in axons enables neurons to introduce new proteins at sites distant from their cell body. mRNA-protein interactions drive this post-transcriptional regulation, yet knowledge of RNA binding proteins (RBP) in axons is limited. Here we used proteomics to identify RBPs interacting with the axonal localizing motifs of Nrn1, Hmgb1, Actb, and Gap43 mRNAs, revealing many novel RBPs in axons. Interestingly, no RBP is shared between all four RNA motifs, suggesting graded and overlapping specificities of RBP-mRNA pairings. A systematic assessment of axonal mRNAs interacting with hnRNP H1, hnRNP F, and hnRNP K, proteins that bound with high specificity to Nrn1 and Hmgb1, revealed that axonal mRNAs segregate into axon growth-associated RNA regulons based on hnRNP interactions. Axotomy increases axonal transport of hnRNPs H1, F, and K, depletion of these hnRNPs decreases axon growth and reduces axonal mRNA levels and axonal protein synthesis. Thus, subcellular hnRNP-interacting RNA regulons support neuronal growth and regeneration.
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Affiliation(s)
- Seung Joon Lee
- From the ‡Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208
| | - Juan A Oses-Prieto
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158
| | - Riki Kawaguchi
- ¶Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095
| | - Pabitra K Sahoo
- From the ‡Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208
| | - Amar N Kar
- From the ‡Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208
| | - Meir Rozenbaum
- ‖Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - David Oliver
- **Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208
| | - Shreya Chand
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158
| | - Hao Ji
- **Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208
| | - Michael Shtutman
- **Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208
| | | | - Ross J Taylor
- From the ‡Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208
| | - Mike Fainzilber
- ‖Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Giovanni Coppola
- ¶Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095.,‡‡Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095
| | - Alma L Burlingame
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158
| | - Jeffery L Twiss
- From the ‡Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208;
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31
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Ruan QT, Yazdani N, Beierle JA, Hixson KM, Hokenson KE, Apicco DJ, Luttik KP, Zheng K, Maziuk BF, Ash PEA, Szumlinski KK, Russek SJ, Wolozin B, Bryant CD. Changes in neuronal immunofluorescence in the C- versus N-terminal domains of hnRNP H following D1 dopamine receptor activation. Neurosci Lett 2018; 684:109-114. [PMID: 30003938 DOI: 10.1016/j.neulet.2018.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/04/2018] [Accepted: 07/08/2018] [Indexed: 12/23/2022]
Abstract
RNA binding proteins are a diverse class of proteins that regulate all aspects of RNA metabolism. Accumulating studies indicate that heterogeneous nuclear ribonucleoproteins are associated with cellular adaptations in response to drugs of abuse. We recently mapped and validated heterogeneous nuclear ribonucleoprotein H1 (Hnrnph1) as a quantitative trait gene underlying differential behavioral sensitivity to methamphetamine. The molecular mechanisms by which hnRNP H1 alters methamphetamine behaviors are unknown but could involve pre- and/or post-synaptic changes in protein localization and function. Methamphetamine initiates post-synaptic D1 dopamine receptor signaling indirectly by binding to pre-synaptic dopamine transporters and vesicular monoamine transporters of midbrain dopaminergic neurons which triggers reverse transport and accumulation of dopamine at the synapse. Here, we examined changes in neuronal localization of hnRNP H in primary rat cortical neurons that express dopamine receptors that can be modulated by the D1 or D2 dopamine receptor agonists SKF38393 and (-)-Quinpirole HCl, respectively. Basal immunostaining of hnRNP H was localized primarily to the nucleus. D1 dopamine receptor activation induced an increase in hnRNP H nuclear immunostaining as detected by immunocytochemistry with a C-domain directed antibody containing epitope near the glycine-rich domain but not with an N-domain specific antibody. Although there was no change in hnRNP H protein in the nucleus or cytoplasm, there was a decrease in Hnrnph1 transcript following D1 receptor stimulation. Taken together, these results suggest that D1 receptor activation increases availability of the hnRNP H C-terminal epitope, which could potentially reflect changes in protein-protein interactions. Thus, D1 receptor signaling could represent a key molecular post-synaptic event linking Hnrnph1 polymorphisms to drug-induced behavior.
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Affiliation(s)
- Qiu T Ruan
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, United States; Biomolecular Pharmacology Training Program, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, United States; Transformative Training Program in Addiction Science, Boston University, United States
| | - Neema Yazdani
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, United States; Biomolecular Pharmacology Training Program, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, United States; Transformative Training Program in Addiction Science, Boston University, United States
| | - Jacob A Beierle
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, United States; Biomolecular Pharmacology Training Program, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, United States; Transformative Training Program in Addiction Science, Boston University, United States
| | - Kathryn M Hixson
- Biomolecular Pharmacology Training Program, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, United States; Laboratory of Translational Epilepsy, Department of Pharmacology and Experimental Therapeutics and Biology, Boston University School of Medicine, United States
| | - Kristen E Hokenson
- Biomolecular Pharmacology Training Program, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, United States; Laboratory of Translational Epilepsy, Department of Pharmacology and Experimental Therapeutics and Biology, Boston University School of Medicine, United States
| | - Daniel J Apicco
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, United States; Laboratory of Neurodegeneration, Department of Pharmacology and Experimental Therapeutics and Neurology, Boston University School of Medicine, United States
| | - Kimberly P Luttik
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, United States
| | - Karen Zheng
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, United States
| | - Brandon F Maziuk
- Laboratory of Neurodegeneration, Department of Pharmacology and Experimental Therapeutics and Neurology, Boston University School of Medicine, United States
| | - Peter E A Ash
- Laboratory of Neurodegeneration, Department of Pharmacology and Experimental Therapeutics and Neurology, Boston University School of Medicine, United States
| | - Karen K Szumlinski
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, United States
| | - Shelley J Russek
- Laboratory of Translational Epilepsy, Department of Pharmacology and Experimental Therapeutics and Biology, Boston University School of Medicine, United States
| | - Benjamin Wolozin
- Laboratory of Neurodegeneration, Department of Pharmacology and Experimental Therapeutics and Neurology, Boston University School of Medicine, United States
| | - Camron D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, United States.
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32
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Reeme AE, Claeys TA, Aggarwal P, Turner AJ, Routes JM, Broeckel U, Robinson RT. Human IL12RB1 expression is allele-biased and produces a novel IL12 response regulator. Genes Immun 2018; 20:181-197. [PMID: 29599514 PMCID: PMC6165718 DOI: 10.1038/s41435-018-0023-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/21/2017] [Accepted: 01/02/2018] [Indexed: 12/30/2022]
Abstract
Human IL12RB1 is an autosomal gene that is essential for mycobacterial disease resistance and T cell differentiation. Using primary human tissue and PBMCs, we demonstrate that lung and T cell IL12RB1 expression is allele-biased, and the extent to which cells express one IL12RB1 allele is unaffected by activation. Furthermore, following its expression the IL12RB1 pre-mRNA is processed into either IL12RB1 Isoform 1 (IL12Rβ1, a positive regulator of IL12-responsiveness) or IL12RB1 Isoform 2 (a protein of heretofore unknown function). T cells’ choice to process pre-mRNA into Isoform 1 or Isoform 2 is controlled by intragenic competition of IL12RB1 exon 9-10 splicing with IL12RB1 exon 9b splicing, as well as an IL12RB1 exon 9b-associated polyadenylation site. Heterogeneous nuclear ribonucleoprotein H (hnRNP H) binds near the regulated polyadenylation site, but is not required for exon 9b polyadenylation. Finally, microRNA-mediated knockdown experiments demonstrated that IL12RB1 Isoform 2 promotes T cell IL12 responses. Collectively, our data support a model wherein tissue expression of human IL12RB1 is allele-biased and produces an hnRNP H bound pre-mRNA, the processing of which generates a novel IL12 response regulator.
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Affiliation(s)
- Allison E Reeme
- Department of Microbiology and Immunology, The Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Tiffany A Claeys
- Department of Microbiology and Immunology, The Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Praful Aggarwal
- Department of Pediatrics, Section of Genomic Pediatrics and Children's Research Institute, The Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Amy J Turner
- Department of Pediatrics, Section of Genomic Pediatrics and Children's Research Institute, The Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - John M Routes
- Department of Pediatrics, Section of Asthma, Allergy and Clinical Immunology, The Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Ulrich Broeckel
- Department of Pediatrics, Section of Genomic Pediatrics and Children's Research Institute, The Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Richard T Robinson
- Department of Microbiology and Immunology, The Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
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33
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Meyer K, Köster T, Nolte C, Weinholdt C, Lewinski M, Grosse I, Staiger D. Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7. Genome Biol 2017; 18:204. [PMID: 29084609 PMCID: PMC5663106 DOI: 10.1186/s13059-017-1332-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/29/2017] [Indexed: 12/11/2022] Open
Abstract
Background Functions for RNA-binding proteins in orchestrating plant development and environmental responses are well established. However, the lack of a genome-wide view of their in vivo binding targets and binding landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we adapt individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) genome-wide to determine the binding repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7. Results iCLIP identifies 858 transcripts with significantly enriched crosslink sites in plants expressing AtGRP7-GFP that are absent in plants expressing an RNA-binding-dead AtGRP7 variant or GFP alone. To independently validate the targets, we performed RNA immunoprecipitation (RIP)-sequencing of AtGRP7-GFP plants subjected to formaldehyde fixation. Of the iCLIP targets, 452 were also identified by RIP-seq and represent a set of high-confidence binders. AtGRP7 can bind to all transcript regions, with a preference for 3′ untranslated regions. In the vicinity of crosslink sites, U/C-rich motifs are overrepresented. Cross-referencing the targets against transcriptome changes in AtGRP7 loss-of-function mutants or AtGRP7-overexpressing plants reveals a predominantly negative effect of AtGRP7 on its targets. In particular, elevated AtGRP7 levels lead to damping of circadian oscillations of transcripts, including DORMANCY/AUXIN ASSOCIATED FAMILY PROTEIN2 and CCR-LIKE. Furthermore, several targets show changes in alternative splicing or polyadenylation in response to altered AtGRP7 levels. Conclusions We have established iCLIP for plants to identify target transcripts of the RNA-binding protein AtGRP7. This paves the way to investigate the dynamics of posttranscriptional networks in response to exogenous and endogenous cues. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1332-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katja Meyer
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Christine Nolte
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Claus Weinholdt
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Martin Lewinski
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
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34
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Abstract
Neurodegeneration is a leading cause of death in the developed world and a natural, albeit unfortunate, consequence of longer-lived populations. Despite great demand for therapeutic intervention, it is often the case that these diseases are insufficiently understood at the basic molecular level. What little is known has prompted much hopeful speculation about a generalized mechanistic thread that ties these disparate conditions together at the subcellular level and can be exploited for broad curative benefit. In this review, we discuss a prominent theory supported by genetic and pathological changes in an array of neurodegenerative diseases: that neurons are particularly vulnerable to disruption of RNA-binding protein dosage and dynamics. Here we synthesize the progress made at the clinical, genetic, and biophysical levels and conclude that this perspective offers the most parsimonious explanation for these mysterious diseases. Where appropriate, we highlight the reciprocal benefits of cross-disciplinary collaboration between disease specialists and RNA biologists as we envision a future in which neurodegeneration declines and our understanding of the broad importance of RNA processing deepens.
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Affiliation(s)
- Erin G Conlon
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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35
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Marcelino Meliso F, Hubert CG, Favoretto Galante PA, Penalva LO. RNA processing as an alternative route to attack glioblastoma. Hum Genet 2017; 136:1129-41. [PMID: 28608251 DOI: 10.1007/s00439-017-1819-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/02/2017] [Indexed: 02/07/2023]
Abstract
Genomic analyses have become an important tool to identify new avenues for therapy. This is especially true for cancer types with extremely poor outcomes, since our lack of effective therapies offers no tangible clinical starting point to build upon. The highly malignant brain tumor glioblastoma (GBM) exemplifies such a refractory cancer, with only 15 month average patient survival. Analyses of several hundred GBM samples compiled by the TCGA (The Cancer Genome Atlas) have produced an extensive transcriptomic map, identified prevalent chromosomal alterations, and defined important driver mutations. Unfortunately, clinical trials based on these results have not yet delivered an improvement on outcome. It is, therefore, necessary to characterize other regulatory routes known for playing a role in tumor relapse and response to treatment. Alternative splicing affects more than 90% of the human coding genes and it is an important source for transcript variation and gene regulation. Mutations and alterations in splicing factors are highly prevalent in multiple cancers, demonstrating the potential for splicing to act as a tumor driver. As a result, numerous genes are expressed as cancer-specific splicing isoforms that are functionally distinct from the canonical isoforms found in normal tissue. These include genes that regulate cancer-critical pathways such as apoptosis, DNA repair, cell proliferation, and migration. Splicing defects can even induce genomic instability, a common characteristic of cancer, and a driver of tumor evolution. Importantly, components of the splicing machinery are targetable; multiple drugs can inhibit splicing factors or promote changes in splicing which could be exploited to begin improving clinical outcomes. Here, we review the current literature and present a case for exploring RNA processing as therapeutic route for the treatment of GBM.
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36
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Nicholson CO, Friedersdorf M, Keene JD. Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq. RNA 2017; 23:32-46. [PMID: 27742911 PMCID: PMC5159647 DOI: 10.1261/rna.058115.116] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/30/2016] [Indexed: 05/27/2023]
Abstract
RNA-binding proteins (RBPs) and noncoding RNAs orchestrate post-transcriptional processes through the recognition of specific sites on targeted transcripts. Thus, understanding the connection between binding to specific sites and active regulation of the whole transcript is essential. Many immunoprecipitation techniques have been developed that identify either whole transcripts or binding sites of RBPs on each transcript using cell lysates. However, none of these methods simultaneously measures the strength of each binding site and quantifies binding to whole transcripts. In this study, we compare current procedures and present digestion optimized (DO)-RIP-seq, a simple method that locates and quantifies RBP binding sites using a continuous metric. We have used the RBP HuR/ELAVL1 to demonstrate that DO-RIP-seq can quantify HuR binding sites with high coverage across the entire human transcriptome, thereby generating metrics of relative RNA binding strength. We demonstrate that this quantitative enrichment of binding sites is proportional to the relative in vitro binding strength for these sites. In addition, we used DO-RIP-seq to quantify and compare HuR's binding to whole transcripts, thus allowing for seamless integration of binding site data with whole-transcript measurements. Finally, we demonstrate that DO-RIP-seq is useful for identifying functional mRNA target sets and binding sites where combinatorial interactions between HuR and AGO-microRNAs regulate the fate of the transcripts. Our data indicate that DO-RIP-seq will be useful for quantifying RBP binding events that regulate dynamic biological processes.
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Affiliation(s)
- Cindo O Nicholson
- Department of Molecular Genetics and Microbiology, Center for RNA Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Matthew Friedersdorf
- Department of Molecular Genetics and Microbiology, Center for RNA Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Jack D Keene
- Department of Molecular Genetics and Microbiology, Center for RNA Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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37
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Nicholson CO, Friedersdorf MB, Bisogno LS, Keene JD. DO-RIP-seq to quantify RNA binding sites transcriptome-wide. Methods 2016; 118-119:16-23. [PMID: 27840290 DOI: 10.1016/j.ymeth.2016.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/21/2016] [Accepted: 11/07/2016] [Indexed: 01/20/2023] Open
Abstract
Post-transcriptional processes orchestrate gene expression through dynamic protein-RNA interactions. These interactions occur at specific sites determined by RNA sequence, secondary structure, or nucleotide modifications. Methods have been developed either to quantify binding of whole transcripts or to identify the binding sites, but there is none proven to quantify binding at both the whole transcript and binding site levels. Here we describe digestion optimized RNA immunoprecipitation with deep sequencing (DO-RIP-seq) as a method that quantitates at the whole transcript target (RIP-Seq-Like or RSL) level and at the binding site level (BSL) using continuous metrics. DO-RIP-seq methodology was developed using the RBP HuR/ELAVL1 as a test case (Nicholson et al., 2016). DO-RIP-seq employs treatment of cell lysates with a nuclease under optimized conditions to yield partially digested RNA fragments bound by RNA binding proteins, followed by immunoprecipitations that capture the digested RNA-protein complexes and assess non-specific or background interactions. Analyses of sequenced cDNA libraries made from the bound RNA fragments yielded two types of enrichment scores; one for RSL binding events and the other for BSL events (Nicholson et al., 2016). These analyses plus the extensive read coverage of DO-RIP-seq allows seamless integration of binding site and whole transcript information. Therefore, DO-RIP-seq is useful for quantifying RBP binding events that are regulated during dynamic biological processes.
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Affiliation(s)
- Cindo O Nicholson
- Department of Molecular Genetics & Microbiology, USA; Duke University Medical Center, Durham, NC 27710, USA.
| | - Matthew B Friedersdorf
- Department of Molecular Genetics & Microbiology, USA; Duke University Medical Center, Durham, NC 27710, USA.
| | | | - Jack D Keene
- Department of Molecular Genetics & Microbiology, USA; Duke University Medical Center, Durham, NC 27710, USA.
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38
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Abstract
Gene expression patterns change dramatically during neuronal development. Proliferating cells, including neural stem cells (NSCs), express telomere repeat-binding factor 2 (TRF2), a nuclear protein that associates with telomeric proteins, DNA, and RNA telomeres. In NSCs TRF2 also binds to the transcription regulator REST to facilitate repression of numerous neuron-specific genes, thereby keeping the NSCs in a self-renewing state. Upon neuronal differentiation, TRF2 levels decline, REST-regulated neuronal genes are derepressed, and a short isoform of TRF2 arises (TRF2-S) which localizes in the cytoplasm, associates with different subsets of proteins and transcripts, and mobilizes axonal G-rich mRNAs. We recently identified two RNA-binding proteins, HNRNPH1 and H2 (referred to jointly as HNRNPH due to their high homology), which mediate the alternative splicing of an exon required for the expression of full-length TRF2. As HNRNPH levels decline during neurogenesis, TRF2 abundance decreases and TRF2-S accumulates. Here, we discuss the shared and unique functions of TRF2 and TRF2-S, the distinct subcellular compartment in which each isoform resides, the subsets of proteins and nucleic acids with which each interacts, and the functional consequences of these ribonucleoprotein interactions. This paradigm illustrates the dynamic mechanisms through which splicing regulation by factors like HNRNPH enable distinct protein functions as cells adapt to developmental programs such as neurogenesis.
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Affiliation(s)
- Ioannis Grammatikakis
- a Laboratory of Genetics, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Peisu Zhang
- b Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Mark P Mattson
- b Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Myriam Gorospe
- a Laboratory of Genetics, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
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39
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Ennajdaoui H, Howard JM, Sterne-Weiler T, Jahanbani F, Coyne DJ, Uren PJ, Dargyte M, Katzman S, Draper JM, Wallace A, Cazarez O, Burns SC, Qiao M, Hinck L, Smith AD, Toloue MM, Blencowe BJ, Penalva LO, Sanford JR. IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC. Cell Rep 2016; 15:1876-83. [PMID: 27210763 DOI: 10.1016/j.celrep.2016.04.083] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 02/08/2016] [Accepted: 04/21/2016] [Indexed: 11/21/2022] Open
Abstract
Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) expression correlates with malignancy, but its role(s) in pathogenesis remains enigmatic. We interrogated the IGF2BP3-RNA interaction network in pancreatic ductal adenocarcinoma (PDAC) cells. Using a combination of genome-wide approaches, we have identified 164 direct mRNA targets of IGF2BP3. These transcripts encode proteins enriched for functions such as cell migration, proliferation, and adhesion. Loss of IGF2BP3 reduced PDAC cell invasiveness and remodeled focal adhesion junctions. Individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) revealed significant overlap of IGF2BP3 and microRNA (miRNA) binding sites. IGF2BP3 promotes association of the RNA-induced silencing complex (RISC) with specific transcripts. Our results show that IGF2BP3 influences a malignancy-associated RNA regulon by modulating miRNA-mRNA interactions.
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40
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Grammatikakis I, Zhang P, Panda AC, Kim J, Maudsley S, Abdelmohsen K, Yang X, Martindale JL, Motiño O, Hutchison ER, Mattson MP, Gorospe M. Alternative Splicing of Neuronal Differentiation Factor TRF2 Regulated by HNRNPH1/H2. Cell Rep 2016; 15:926-934. [PMID: 27117401 DOI: 10.1016/j.celrep.2016.03.080] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 02/18/2016] [Accepted: 03/22/2016] [Indexed: 10/21/2022] Open
Abstract
During neuronal differentiation, use of an alternative splice site on the rat telomere repeat-binding factor 2 (TRF2) mRNA generates a short TRF2 protein isoform (TRF2-S) capable of derepressing neuronal genes. However, the RNA-binding proteins (RBPs) controlling this splicing event are unknown. Here, using affinity pull-down analysis, we identified heterogeneous nuclear ribonucleoproteins H1 and H2(HNRNPH) as RBPs specifically capable of interacting with the spliced RNA segment (exon 7) of Trf2 pre-mRNA. HNRNPH proteins prevent the production of the short isoform of Trf2 mRNA, as HNRNPH silencing selectively elevates TRF2-S levels. Accordingly, HNRNPH levels decline while TRF2-S levels increase during neuronal differentiation. In addition, CRISPR/Cas9-mediated deletion of hnRNPH2 selectively accelerates the NGF-triggered differentiation of rat pheochromocytoma cells into neurons. In sum, HNRNPH is a splicing regulator of Trf2 pre-mRNA that prevents the expression of TRF2-S, a factor implicated in neuronal differentiation.
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Affiliation(s)
- Ioannis Grammatikakis
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Peisu Zhang
- Laboratory of Neurosciences, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Amaresh C Panda
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Jiyoung Kim
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Stuart Maudsley
- Translational Neurobiology Group, VIB Department of Molecular Genetics, University of Antwerp, 2610 Antwerpen, Belgium
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Xiaoling Yang
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Omar Motiño
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Emmette R Hutchison
- Laboratory of Neurosciences, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Mark P Mattson
- Laboratory of Neurosciences, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA.
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