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Zhang Y, Liu D, Guo D, Lin W, Lu W, Hu L, Chen S, Chen C. CPSF3 regulates alternative polyadenylation of CNIH2 to promote esophageal squamous cell carcinoma progression. Cancer Lett 2024; 593:216925. [PMID: 38718887 DOI: 10.1016/j.canlet.2024.216925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/26/2024] [Accepted: 04/27/2024] [Indexed: 05/19/2024]
Abstract
Alternative polyadenylation (APA), an important post-transcriptional regulatory mechanism, is aberrantly activated in cancer,but how APA functions in tumorigenesis remains elusive. We analyzed APA events in RNA-seq data in TCGA and reported 3'UTR alterations associated with esophageal squamous cell carcinoma (ESCC) patient prognosis and gene expression changes involving loss of tumor-suppressive miRNA binding sites. Moreover, we investigated the expression and function of cleavage and polyadenylation specific factor 3 (CPSF3), a key APA regulator in ESCC. By immunohistochemistry and qRT-PCR, we found that CPSF3 was highly expressed in ESCC tissues and associated with poor patient prognosis. Overexpression of CPSF3 enhanced, while knockdown of CPSF3 inhibited ESCC cell proliferation and migration in vitro and in vivo, as determined by colony formation, transwell assays and animal experiments. Iso-Seq and RNA-seq data analysis indicated that knockdown of CPSF3 favored use of the distal poly (A) site in the 3'UTR of Cornichon family AMPA receptor auxiliary protein 2 (CNIH2), resulting in a long-3'UTR CNIH2 isoform that produced less CNIH2 protein due to miR-125a-5p targeting and downregulating CNIH2 mRNA through a miR-125a-5p binding site in the long CNIH2 mRNA 3'UTR. Moreover, CPSF3-induced ESCC tumorigenicity was mediated by CNIH2. Taken together, CPSF3 promotes ESCC progression by upregulating CNIH2 expression through loss of miR-125a-5p-mediated CNIH2 repression through alternative splicing and polyadenylation of the CNIH2 mRNA 3'UTR.
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Affiliation(s)
- Ying Zhang
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou, Guangdong, 515041, China; Department of Clinical Research Center, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou, Guangdong, 515041, China.
| | - Dongchen Liu
- Department of Clinical Research Center, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou, Guangdong, 515041, China
| | - Dan Guo
- Department of Pathology, Shantou University Medical College, No.22 Xinling Road, Shantou, Guangdong, 515041, China
| | - Wenting Lin
- Department of Pathology, Shantou University Medical College, No.22 Xinling Road, Shantou, Guangdong, 515041, China
| | - Weiqing Lu
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou, Guangdong, 515041, China
| | - Lan Hu
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou, Guangdong, 515041, China
| | - Shuqin Chen
- Department of Pathology, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou, Guangdong, 515041, China
| | - Chuangzhen Chen
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, No. 7 Raoping Road, Shantou, Guangdong, 515041, China.
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2
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Naro C, Antonioni A, Medici V, Caggiano C, Jolly A, de la Grange P, Bielli P, Paronetto MP, Sette C. Splicing targeting drugs highlight intron retention as an actionable vulnerability in advanced prostate cancer. J Exp Clin Cancer Res 2024; 43:58. [PMID: 38413979 PMCID: PMC10898177 DOI: 10.1186/s13046-024-02986-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Advanced prostate cancer (PC) is characterized by insensitivity to androgen deprivation therapy and chemotherapy, resulting in poor outcome for most patients. Thus, advanced PC urgently needs novel therapeutic strategies. Mounting evidence points to splicing dysregulation as a hallmark of advanced PC. Moreover, pharmacologic inhibition of the splicing process is emerging as a promising option for this disease. METHOD By using a representative androgen-insensitive PC cell line (22Rv1), we have investigated the genome-wide transcriptomic effects underlying the cytotoxic effects exerted by three splicing-targeting drugs: Pladienolide B, indisulam and THZ531. Bioinformatic analyses were performed to uncover the gene structural features underlying sensitivity to transcriptional and splicing regulation by these treatments. Biological pathways altered by these treatments were annotated by gene ontology analyses and validated by functional experiments in cell models. RESULTS Although eliciting similar cytotoxic effects on advanced PC cells, Pladienolide B, indisulam and THZ531 modulate specific transcriptional and splicing signatures. Drug sensitivity is associated with distinct gene structural features, expression levels and cis-acting sequence elements in the regulated exons and introns. Importantly, we identified PC-relevant genes (i.e. EZH2, MDM4) whose drug-induced splicing alteration exerts an impact on cell survival. Moreover, computational analyses uncovered a widespread impact of splicing-targeting drugs on intron retention, with enrichment in genes implicated in pre-mRNA 3'-end processing (i.e. CSTF3, PCF11). Coherently, advanced PC cells displayed high sensitivity to a specific inhibitor of the cleavage and polyadenylation complex, which enhances the effects of chemotherapeutic drugs that are already in use for this cancer. CONCLUSIONS Our study uncovers intron retention as an actionable vulnerability for advanced PC, which may be exploited to improve therapeutic management of this currently incurable disease.
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Affiliation(s)
- Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy
- GSTeP Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168, Rome, Italy
| | - Ambra Antonioni
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Vanessa Medici
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Cinzia Caggiano
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy
- GSTeP Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168, Rome, Italy
| | | | | | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Fondazione Santa Lucia, 00143, Rome, Italy
- University of Rome Foro Italico, 00135, Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy.
- GSTeP Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168, Rome, Italy.
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3
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Alahmari AA, Chaubey AH, Jonnakuti VS, Tisdale AA, Schwarz CD, Cornwell AC, Maraszek KE, Paterson EJ, Kim M, Venkat S, Gomez EC, Wang J, Gurova KV, Yalamanchili HK, Feigin ME. CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing. RNA (NEW YORK, N.Y.) 2024; 30:281-297. [PMID: 38191171 PMCID: PMC10870380 DOI: 10.1261/rna.079931.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited effective treatment options, potentiating the importance of uncovering novel drug targets. Here, we target cleavage and polyadenylation specificity factor 3 (CPSF3), the 3' endonuclease that catalyzes mRNA cleavage during polyadenylation and histone mRNA processing. We find that CPSF3 is highly expressed in PDAC and is associated with poor prognosis. CPSF3 knockdown blocks PDAC cell proliferation and colony formation in vitro and tumor growth in vivo. Chemical inhibition of CPSF3 by the small molecule JTE-607 also attenuates PDAC cell proliferation and colony formation, while it has no effect on cell proliferation of nontransformed immortalized control pancreatic cells. Mechanistically, JTE-607 induces transcriptional readthrough in replication-dependent histones, reduces core histone expression, destabilizes chromatin structure, and arrests cells in the S-phase of the cell cycle. Therefore, CPSF3 represents a potential therapeutic target for the treatment of PDAC.
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Affiliation(s)
- Abdulrahman A Alahmari
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Aditi H Chaubey
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Venkata S Jonnakuti
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Arwen A Tisdale
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Carla D Schwarz
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Abigail C Cornwell
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Kathryn E Maraszek
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Emily J Paterson
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Minsuh Kim
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Swati Venkat
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Eduardo Cortes Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Katerina V Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michael E Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
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4
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Liu L, Yu AM, Wang X, Soles LV, Teng X, Chen Y, Yoon Y, Sarkan KSK, Valdez MC, Linder J, England W, Spitale R, Yu Z, Marazzi I, Qiao F, Li W, Seelig G, Shi Y. The anticancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3' processing machinery. Nat Struct Mol Biol 2023; 30:1947-1957. [PMID: 38087090 DOI: 10.1038/s41594-023-01161-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
JTE-607 is an anticancer and anti-inflammatory compound and its active form, compound 2, directly binds to and inhibits CPSF73, the endonuclease for the cleavage step in pre-messenger RNA (pre-mRNA) 3' processing. Surprisingly, compound 2-mediated inhibition of pre-mRNA cleavage is sequence specific and the drug sensitivity is predominantly determined by sequences flanking the cleavage site (CS). Using massively parallel in vitro assays, we identified key sequence features that determine drug sensitivity. We trained a machine learning model that can predict poly(A) site (PAS) relative sensitivity to compound 2 and provide the molecular basis for understanding the impact of JTE-607 on PAS selection and transcription termination genome wide. We propose that CPSF73 and associated factors bind to the CS region in a sequence-dependent manner and the interaction affinity determines compound 2 sensitivity. These results have not only elucidated the mechanism of action of JTE-607, but also unveiled an evolutionarily conserved sequence specificity of the mRNA 3' processing machinery.
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Affiliation(s)
- Liang Liu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
- Center for Virus Research, University of California, Irvine, Irvine, CA, USA
| | - Angela M Yu
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Seattle, WA, USA
| | - Xiuye Wang
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
- Guangzhou Laboratory, Guangdong, China
| | - Lindsey V Soles
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Xueyi Teng
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yiling Chen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yoseop Yoon
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kristianna S K Sarkan
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Marielle Cárdenas Valdez
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Johannes Linder
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Whitney England
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
| | - Robert Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Zhaoxia Yu
- Department of Statistics, University of California, Irvine, Irvine, CA, USA
| | - Ivan Marazzi
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Feng Qiao
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Wei Li
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Georg Seelig
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Seattle, WA, USA.
- Paul G Allen School of Computer Science and Engineering, University of Washington, Seattle, Seattle, WA, USA.
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA.
- Center for Virus Research, University of California, Irvine, Irvine, CA, USA.
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5
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Cui Y, Wang L, Ding Q, Shin J, Cassel J, Liu Q, Salvino JM, Tian B. Elevated pre-mRNA 3' end processing activity in cancer cells renders vulnerability to inhibition of cleavage and polyadenylation. Nat Commun 2023; 14:4480. [PMID: 37528120 PMCID: PMC10394034 DOI: 10.1038/s41467-023-39793-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/27/2023] [Indexed: 08/03/2023] Open
Abstract
Cleavage and polyadenylation (CPA) is responsible for 3' end processing of eukaryotic poly(A)+ RNAs and preludes transcriptional termination. JTE-607, which targets CPSF-73, is the first known CPA inhibitor (CPAi) in mammalian cells. Here we show that JTE-607 perturbs gene expression through both transcriptional readthrough and alternative polyadenylation (APA). Sensitive genes are associated with features similar to those previously identified for PCF11 knockdown, underscoring a unified transcriptomic signature of CPAi. The degree of inhibition of an APA site by JTE-607 correlates with its usage level and, consistently, cells with elevated CPA activities, such as those with induced overexpression of FIP1, display greater transcriptomic disturbances when treated with JTE-607. Moreover, JTE-607 causes S phase crisis and is hence synergistic with inhibitors of DNA damage repair pathways. Together, our data reveal CPA activity and proliferation rate as determinants of CPAi-mediated cell death, raising the possibility of using CPAi as an adjunct therapy to suppress certain cancers.
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Affiliation(s)
- Yange Cui
- Gene Expression and Regulation Program, and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Luyang Wang
- Gene Expression and Regulation Program, and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Qingbao Ding
- Gene Expression and Regulation Program, and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Jihae Shin
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Joel Cassel
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Qin Liu
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Joseph M Salvino
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Bin Tian
- Gene Expression and Regulation Program, and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, 19104, USA.
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6
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Abstract
Formation of the 3' end of a eukaryotic mRNA is a key step in the production of a mature transcript. This process is mediated by a number of protein factors that cleave the pre-mRNA, add a poly(A) tail, and regulate transcription by protein dephosphorylation. Cleavage and polyadenylation specificity factor (CPSF) in humans, or cleavage and polyadenylation factor (CPF) in yeast, coordinates these enzymatic activities with each other, with RNA recognition, and with transcription. The site of pre-mRNA cleavage can strongly influence the translation, stability, and localization of the mRNA. Hence, cleavage site selection is highly regulated. The length of the poly(A) tail is also controlled to ensure that every transcript has a similar tail when it is exported from the nucleus. In this review, we summarize new mechanistic insights into mRNA 3'-end processing obtained through structural studies and biochemical reconstitution and outline outstanding questions in the field.
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Affiliation(s)
- Vytautė Boreikaitė
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom;
| | - Lori A Passmore
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom;
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7
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Liu L, Yu AM, Wang X, Soles LV, Chen Y, Yoon Y, Sarkan KSK, Valdez MC, Linder J, Marazzi I, Yu Z, Qiao F, Li W, Seelig G, Shi Y. The anti-cancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3' processing machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536453. [PMID: 37090613 PMCID: PMC10120630 DOI: 10.1101/2023.04.11.536453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
JTE-607 is a small molecule compound with anti-inflammation and anti-cancer activities. Upon entering the cell, it is hydrolyzed to Compound 2, which directly binds to and inhibits CPSF73, the endonuclease for the cleavage step in pre-mRNA 3' processing. Although CPSF73 is universally required for mRNA 3' end formation, we have unexpectedly found that Compound 2- mediated inhibition of pre-mRNA 3' processing is sequence-specific and that the sequences flanking the cleavage site (CS) are a major determinant for drug sensitivity. By using massively parallel in vitro assays, we have measured the Compound 2 sensitivities of over 260,000 sequence variants and identified key sequence features that determine drug sensitivity. A machine learning model trained on these data can predict the impact of JTE-607 on poly(A) site (PAS) selection and transcription termination genome-wide. We propose a biochemical model in which CPSF73 and other mRNA 3' processing factors bind to RNA of the CS region in a sequence-specific manner and the affinity of such interaction determines the Compound 2 sensitivity of a PAS. As the Compound 2-resistant CS sequences, characterized by U/A-rich motifs, are prevalent in PASs from yeast to human, the CS region sequence may have more fundamental functions beyond determining drug resistance. Together, our study not only characterized the mechanism of action of a compound with clinical implications, but also revealed a previously unknown and evolutionarily conserved sequence-specificity of the mRNA 3' processing machinery.
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8
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Borišek J, Aupič J, Magistrato A. Establishing the catalytic and regulatory mechanism of
RNA
‐based machineries. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jure Borišek
- Theory Department National Institute of Chemistry Ljubljana Slovenia
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9
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Interleukin Inhibitors in Cytokine Release Syndrome and Neurotoxicity Secondary to CAR-T Therapy. Diseases 2022; 10:diseases10030041. [PMID: 35892735 PMCID: PMC9326641 DOI: 10.3390/diseases10030041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
Introduction: Chimeric antigen receptor T-cell (CAR-T) therapy is an innovative therapeutic option for addressing certain recurrent or refractory hematological malignancies. However, CAR-T cells also cause the release of pro-inflammatory cytokines that lead to life-threatening cytokine release syndrome and neurotoxicity. Objective: To study the efficacy of interleukin inhibitors in addressing cytokine release syndrome (CRS) and neurotoxicity secondary to CAR-T therapy. Methodology: The authors conducted a bibliographic review in which 10 articles were analyzed. These included cut-off studies, case reports, and clinical trials involving 11 cancer centers and up to 475 patients over 18 years of age. Results: Tocilizumab is the only interleukin inhibitor approved to address CRS secondary to CAR-T therapy due to its efficacy and safety. Other inhibitors, such as siltuximab and anakinra, could be useful in combination with tocilizumab for preventing severe cytokine release and neurotoxicity. In addition, the new specific inhibitors could be effective in mitigating CRS without affecting the cytotoxic efficacy of CAR-T therapy. Conclusion: More lines of research should be opened to elucidate the true implications of these drugs in treating the side effects of CAR-T therapy.
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10
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RBBP6 activates the pre-mRNA 3' end processing machinery in humans. Genes Dev 2022; 36:210-224. [PMID: 35177536 PMCID: PMC8887125 DOI: 10.1101/gad.349223.121] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/01/2022] [Indexed: 11/25/2022]
Abstract
In this study, Boreikaite et al. reconstituted specific and efficient 3′ endonuclease activity of human CPSF with purified proteins. This required the seven-subunit CPSF as well as three additional protein factors: cleavage stimulatory factor (CStF), cleavage factor IIm (CFIIm), and, importantly, the multidomain protein RBBP6. 3′ end processing of most human mRNAs is carried out by the cleavage and polyadenylation specificity factor (CPSF; CPF in yeast). Endonucleolytic cleavage of the nascent pre-mRNA defines the 3′ end of the mature transcript, which is important for mRNA localization, translation, and stability. Cleavage must therefore be tightly regulated. Here, we reconstituted specific and efficient 3′ endonuclease activity of human CPSF with purified proteins. This required the seven-subunit CPSF as well as three additional protein factors: cleavage stimulatory factor (CStF), cleavage factor IIm (CFIIm), and, importantly, the multidomain protein RBBP6. Unlike its yeast homolog Mpe1, which is a stable subunit of CPF, RBBP6 does not copurify with CPSF and is recruited in an RNA-dependent manner. Sequence and mutational analyses suggest that RBBP6 interacts with the WDR33 and CPSF73 subunits of CPSF. Thus, it is likely that the role of RBBP6 is conserved from yeast to humans. Overall, our data are consistent with CPSF endonuclease activation and site-specific pre-mRNA cleavage being highly controlled to maintain fidelity in mRNA processing.
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11
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Population-level deficit of homozygosity unveils CPSF3 as an intellectual disability syndrome gene. Nat Commun 2022; 13:705. [PMID: 35121750 PMCID: PMC8817032 DOI: 10.1038/s41467-022-28330-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/20/2022] [Indexed: 02/05/2023] Open
Abstract
AbstractPredicting the pathogenicity of biallelic missense variants can be challenging. Here, we use a deficit of observed homozygous carriers of missense variants, versus an expected number in a set of 153,054 chip-genotyped Icelanders, to identify potentially pathogenic genotypes. We follow three missense variants with a complete deficit of homozygosity and find that their pathogenic effect in homozygous state ranges from severe childhood disease to early embryonic lethality. One of these variants is in CPSF3, a gene not previously linked to disease. From a set of clinically sequenced Icelanders, and by sequencing archival samples targeted through the Icelandic genealogy, we find four homozygous carriers. Additionally, we find two homozygous carriers of Mexican descent of another missense variant in CPSF3. All six homozygous carriers of missense variants in CPSF3 show severe intellectual disability, seizures, microcephaly, and abnormal muscle tone. Here, we show how the absence of certain homozygous genotypes from a large population set can elucidate causes of previously unexplained recessive diseases and early miscarriage.
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12
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Davis AG, Johnson DT, Zheng D, Wang R, Jayne ND, Liu M, Shin J, Wang L, Stoner SA, Zhou JH, Ball ED, Tian B, Zhang DE. Alternative polyadenylation dysregulation contributes to the differentiation block of acute myeloid leukemia. Blood 2022; 139:424-438. [PMID: 34482400 PMCID: PMC8777198 DOI: 10.1182/blood.2020005693] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/16/2021] [Indexed: 01/22/2023] Open
Abstract
Posttranscriptional regulation has emerged as a driver for leukemia development and an avenue for therapeutic targeting. Among posttranscriptional processes, alternative polyadenylation (APA) is globally dysregulated across cancer types. However, limited studies have focused on the prevalence and role of APA in myeloid leukemia. Furthermore, it is poorly understood how altered poly(A) site usage of individual genes contributes to malignancy or whether targeting global APA patterns might alter oncogenic potential. In this study, we examined global APA dysregulation in patients with acute myeloid leukemia (AML) by performing 3' region extraction and deep sequencing (3'READS) on a subset of AML patient samples along with healthy hematopoietic stem and progenitor cells (HSPCs) and by analyzing publicly available data from a broad AML patient cohort. We show that patient cells exhibit global 3' untranslated region (UTR) shortening and coding sequence lengthening due to differences in poly(A) site (PAS) usage. Among APA regulators, expression of FIP1L1, one of the core cleavage and polyadenylation factors, correlated with the degree of APA dysregulation in our 3'READS data set. Targeting global APA by FIP1L1 knockdown reversed the global trends seen in patients. Importantly, FIP1L1 knockdown induced differentiation of t(8;21) cells by promoting 3'UTR lengthening and downregulation of the fusion oncoprotein AML1-ETO. In non-t(8;21) cells, FIP1L1 knockdown also promoted differentiation by attenuating mechanistic target of rapamycin complex 1 (mTORC1) signaling and reducing MYC protein levels. Our study provides mechanistic insights into the role of APA in AML pathogenesis and indicates that targeting global APA patterns can overcome the differentiation block in patients with AML.
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Affiliation(s)
- Amanda G Davis
- Moores Cancer Center and
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Daniel T Johnson
- Moores Cancer Center and
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ
| | - Ruijia Wang
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ
| | - Nathan D Jayne
- Moores Cancer Center and
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Mengdan Liu
- Moores Cancer Center and
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Jihae Shin
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ
| | - Luyang Wang
- Program in Gene Expression and Regulation, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA
| | | | - Jie-Hua Zhou
- Division of Blood and Marrow Transplantation, Department of Medicine; and
| | - Edward D Ball
- Division of Blood and Marrow Transplantation, Department of Medicine; and
| | - Bin Tian
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ
- Program in Gene Expression and Regulation, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA
| | - Dong-Er Zhang
- Moores Cancer Center and
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
- Department of Pathology, University of California San Diego, La Jolla, CA
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13
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Mars JC, Ghram M, Culjkovic-Kraljacic B, Borden KLB. The Cap-Binding Complex CBC and the Eukaryotic Translation Factor eIF4E: Co-Conspirators in Cap-Dependent RNA Maturation and Translation. Cancers (Basel) 2021; 13:6185. [PMID: 34944805 PMCID: PMC8699206 DOI: 10.3390/cancers13246185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/26/2022] Open
Abstract
The translation of RNA into protein is a dynamic process which is heavily regulated during normal cell physiology and can be dysregulated in human malignancies. Its dysregulation can impact selected groups of RNAs, modifying protein levels independently of transcription. Integral to their suitability for translation, RNAs undergo a series of maturation steps including the addition of the m7G cap on the 5' end of RNAs, splicing, as well as cleavage and polyadenylation (CPA). Importantly, each of these steps can be coopted to modify the transcript signal. Factors that bind the m7G cap escort these RNAs through different steps of maturation and thus govern the physical nature of the final transcript product presented to the translation machinery. Here, we describe these steps and how the major m7G cap-binding factors in mammalian cells, the cap binding complex (CBC) and the eukaryotic translation initiation factor eIF4E, are positioned to chaperone transcripts through RNA maturation, nuclear export, and translation in a transcript-specific manner. To conceptualize a framework for the flow and integration of this genetic information, we discuss RNA maturation models and how these integrate with translation. Finally, we discuss how these processes can be coopted by cancer cells and means to target these in malignancy.
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Affiliation(s)
- Jean-Clement Mars
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Mehdi Ghram
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
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14
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Safarzadeh Kozani P, Safarzadeh Kozani P, Rahbarizadeh F. Optimizing the Clinical Impact of CAR-T Cell Therapy in B-Cell Acute Lymphoblastic Leukemia: Looking Back While Moving Forward. Front Immunol 2021; 12:765097. [PMID: 34777381 PMCID: PMC8581403 DOI: 10.3389/fimmu.2021.765097] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
Chimeric antigen receptor T-cell (CAR-T) therapy has been successful in creating extraordinary clinical outcomes in the treatment of hematologic malignancies including relapsed or refractory (R/R) B-cell acute lymphoblastic leukemia (B-ALL). With several FDA approvals, CAR-T therapy is recognized as an alternative treatment option for particular patients with certain conditions of B-ALL, diffuse large B-cell lymphoma, mantle cell lymphoma, follicular lymphoma, or multiple myeloma. However, CAR-T therapy for B-ALL can be surrounded by challenges such as various adverse events including the life-threatening cytokine release syndrome (CRS) and neurotoxicity, B-cell aplasia-associated hypogammaglobulinemia and agammaglobulinemia, and the alloreactivity of allogeneic CAR-Ts. Furthermore, recent advances such as improvements in media design, the reduction of ex vivo culturing duration, and other phenotype-determining factors can still create room for a more effective CAR-T therapy in R/R B-ALL. Herein, we review preclinical and clinical strategies with a focus on novel studies aiming to address the mentioned hurdles and stepping further towards a milestone in CAR-T therapy of B-ALL.
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Affiliation(s)
- Pouya Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran.,Student Research Committee, Medical Biotechnology Research Center, School of Nursing, Midwifery, and Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Pooria Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.,Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran
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15
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Hunt AG, Howe DK, Brown A, Yeargan M. Transcriptional dynamics in the protozoan parasite Sarcocystis neurona and mammalian host cells after treatment with a specific inhibitor of apicomplexan mRNA polyadenylation. PLoS One 2021; 16:e0259109. [PMID: 34710156 PMCID: PMC8553156 DOI: 10.1371/journal.pone.0259109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/12/2021] [Indexed: 11/19/2022] Open
Abstract
In recent years, a class of chemical compounds (benzoxaboroles) that are active against a range of parasites has been shown to target mRNA polyadenylation by inhibiting the activity of CPSF73, the endonucleolytic core of the eukaryotic polyadenylation complex. One particular compound, termed AN3661, is active against several apicomplexan parasites that cause disease in humans. In this study, we report that AN3661 is active against an apicomplexan that causes disease in horses and marine mammals (Sarcocystis neurona), with an approximate IC50 value of 14.99 nM. Consistent with the reported mode of action of AN3661 against other apicomplexans, S. neurona mutants resistant to AN3661 had an alteration in CPSF73 that was identical to a mutation previously documented in AN3661-resistant Toxoplasma gondii and Plasmodium falciparum. AN3661 had a wide-ranging effect on poly(A) site choice in S. neurona, with more than half of all expressed genes showing some alteration in mRNA 3' ends. This was accompanied by changes in the relative expression of more than 25% of S. neurona genes and an overall 5-fold reduction of S. neurona transcripts in infected cells. In contrast, AN3661 had no discernible effect on poly(A) site choice or gene expression in the host cells. These transcriptomic studies indicate that AN3661 is exceedingly specific for the parasite CPSF73 protein, and has the potential to augment other therapies for the control of apicomplexan parasites in domestic animals.
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Affiliation(s)
- Arthur G. Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States of America
- * E-mail:
| | - Daniel K. Howe
- Department of Veterinary Science, University of Kentucky, Lexington, KY, United States of America
| | - Ashley Brown
- Department of Veterinary Science, University of Kentucky, Lexington, KY, United States of America
| | - Michelle Yeargan
- Department of Veterinary Science, University of Kentucky, Lexington, KY, United States of America
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16
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Gutierrez PA, Baughman K, Sun Y, Tong L. A real-time fluorescence assay for CPSF73, the nuclease for pre-mRNA 3'-end processing. RNA (NEW YORK, N.Y.) 2021; 27:1148-1154. [PMID: 34230059 PMCID: PMC8457007 DOI: 10.1261/rna.078764.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/17/2021] [Indexed: 05/09/2023]
Abstract
CPSF73 is the endonuclease that catalyzes the cleavage reaction for 3'-end processing of mRNA precursors (pre-mRNAs) in two distinct machineries, a canonical machinery for the majority of pre-mRNAs and a U7 snRNP (U7 machinery) for replication-dependent histone pre-mRNAs in animal cells. CPSF73 also possesses 5'-3' exonuclease activity in the U7 machinery, degrading the downstream cleavage product after the endonucleolytic cleavage. Recent studies show that CPSF73 is a potential target for developing anticancer, antimalarial, and antiprotozoal drugs, spurring interest in identifying new small-molecule inhibitors against this enzyme. CPSF73 nuclease activity has so far been demonstrated using a gel-based end-point assay, using radiolabeled or fluorescently labeled RNA substrates. By taking advantage of unique properties of the U7 machinery, we have developed a novel, real-time fluorescence assay for the nuclease activity of CPSF73. This assay is facile and high-throughput, and should also be helpful for the discovery of new CPSF73 inhibitors.
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Affiliation(s)
- Pedro A Gutierrez
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Kirk Baughman
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Yadong Sun
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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17
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Liu H, Moore CL. On the Cutting Edge: Regulation and Therapeutic Potential of the mRNA 3' End Nuclease. Trends Biochem Sci 2021; 46:772-784. [PMID: 33941430 PMCID: PMC8364479 DOI: 10.1016/j.tibs.2021.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/18/2021] [Accepted: 04/02/2021] [Indexed: 12/24/2022]
Abstract
Cleavage of nascent transcripts is a fundamental process for eukaryotic mRNA maturation and for the production of different mRNA isoforms. In eukaryotes, cleavage of mRNA precursors by the highly conserved endonuclease CPSF73 is critical for mRNA stability, export from the nucleus, and translation. As an essential enzyme in the cell, CPSF73 surprisingly shows promise as a drug target for specific cancers and for protozoan parasites. In this review, we cover our current understanding of CPSF73 in cleavage and polyadenylation, histone pre-mRNA processing, and transcription termination. We discuss the potential of CPSF73 as a target for novel therapeutics and highlight further research into the regulation of CPSF73 that will be critical to understanding its role in cancer and other diseases.
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Affiliation(s)
- Huiyun Liu
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Claire L Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA.
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18
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Sun Y, Aik WS, Yang XC, Marzluff WF, Dominski Z, Tong L. Reconstitution and biochemical assays of an active human histone pre-mRNA 3'-end processing machinery. Methods Enzymol 2021; 655:291-324. [PMID: 34183127 DOI: 10.1016/bs.mie.2021.03.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In animal cells, replication-dependent histone pre-mRNAs are processed at the 3'-end by an endonucleolytic cleavage carried out by the U7 snRNP, a machinery that contains the U7 snRNA and many protein subunits. Studies on the composition of this machinery and understanding of its role in 3'-end processing were greatly facilitated by the development of an in vitro system utilizing nuclear extracts from mammalian cells 35 years ago and later from Drosophila cells. Most recently, recombinant expression and purification of the components of the machinery have enabled the full reconstitution of an active machinery and its complex with a model pre-mRNA substrate, using 13 proteins and 2 RNAs, and the determination of the structure of this active machinery. This chapter presents protocols for preparing nuclear extracts containing endogenous processing machinery, for assembling semi-recombinant and fully reconstituted machineries, and for histone pre-mRNA 3'-end processing assays with these samples.
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Affiliation(s)
- Yadong Sun
- Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Wei Shen Aik
- Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - William F Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Zbigniew Dominski
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY, United States.
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19
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Spinello A, Borišek J, Pavlin M, Janoš P, Magistrato A. Computing Metal-Binding Proteins for Therapeutic Benefit. ChemMedChem 2021; 16:2034-2049. [PMID: 33740297 DOI: 10.1002/cmdc.202100109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Indexed: 01/18/2023]
Abstract
Over one third of biomolecules rely on metal ions to exert their cellular functions. Metal ions can play a structural role by stabilizing the structure of biomolecules, a functional role by promoting a wide variety of biochemical reactions, and a regulatory role by acting as messengers upon binding to proteins regulating cellular metal-homeostasis. These diverse roles in biology ascribe critical implications to metal-binding proteins in the onset of many diseases. Hence, it is of utmost importance to exhaustively unlock the different mechanistic facets of metal-binding proteins and to harness this knowledge to rationally devise novel therapeutic strategies to prevent or cure pathological states associated with metal-dependent cellular dysfunctions. In this compendium, we illustrate how the use of a computational arsenal based on docking, classical, and quantum-classical molecular dynamics simulations can contribute to extricate the minutiae of the catalytic, transport, and inhibition mechanisms of metal-binding proteins at the atomic level. This knowledge represents a fertile ground and an essential prerequisite for selectively targeting metal-binding proteins with small-molecule inhibitors aiming to (i) abrogate deregulated metal-dependent (mis)functions or (ii) leverage metal-dyshomeostasis to selectively trigger harmful cells death.
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Affiliation(s)
- Angelo Spinello
- National Research Council of Italy (CNR)-, Institute of Materials (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy
| | - Jure Borišek
- National Institute of Chemistry Institution Hajdrihova ulica 19, 1000, Ljubljana, Slovenia
| | - Matic Pavlin
- Laboratory of Microsensor Structures and Electronics Faculty of Electrical Engineering, University of Ljubljana Tržaška cesta 25, 1000, Ljubljana, Slovenia
| | - Pavel Janoš
- National Research Council of Italy (CNR)-, Institute of Materials (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR)-, Institute of Materials (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy
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20
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Borišek J, Magistrato A. An Expanded Two-Zn2+-Ion Motif Orchestrates Pre-mRNA Maturation in the 3′-End Processing Endonuclease Machinery. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jure Borišek
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o SISSA, Via Bonomea 265, 34136 Trieste, Italy
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21
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Li N, Jiang S, Fu R, Lv J, Yao J, Mai J, Hua X, Chen H, Liu J, Lu M. Cleavage and polyadenylation-specific factor 3 induces cell cycle arrest via PI3K/Akt/GSK-3β signaling pathways and predicts a negative prognosis in hepatocellular carcinoma. Biomark Med 2021; 15:347-358. [PMID: 33666519 DOI: 10.2217/bmm-2021-0039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: Recent studies have shown that cleavage and polyadenylation-specific factor 3 (CPSF3) is a promising antitumor therapeutic target, but its potential role in hepatocellular carcinoma (HCC) has not been reported. Materials & methods: We explored the expression pattern of CPSF3 in HCC through bioinformatics analysis, quantitative polymerase chain reaction (qPCR) and western blot. The potential role of CPSF3 as a biomarker for HCC was evaluated by Kaplan-Meier analysis. Next, changes in HCC cell lines in the CPSF3 knockdown model group and the control group were assessed by Cell Counting Kit-8, clonal formation, flow cytometry and EdU staining. Western blot detected changes in protein levels of the PI3K/Akt/GSK-3β axis of two HCC cell lines in the knockdown group and the control group. Results: The results showed that the transcription and protein levels of CPSF3 were significantly higher in HCC tissues than in adjacent normal tissues (p < 0.05). The HCC cohort with increased expression of CPSF3 is associated with advanced stage and differentiation and predicts poorer prognosis (p < 0.05). CPSF3 knockdown significantly inhibited proliferation and clone formation of HepG2 and SMMC-7721 cell lines. Flow cytometry analysis showed G1-S cell cycle arrest in the CPSF3 knockdown group, and the results of EdU staining were consistent with this. Compared with the control group, p-Akt and cyclin D1 were decreased, and GSK-3β was increased in the knockdown group. Conclusion: CPSF3 may be a potential diagnostic biomarker and candidate therapeutic target for HCC.
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Affiliation(s)
- Ning Li
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Shaotao Jiang
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Rongdang Fu
- Department of Hepatic Surgery, The First People's Hospital of Foshan, Affiliated Foshan Hospital of Sun Yat-sen University, Foshan, 528000, China
| | - Jin Lv
- Department of Pathology, The First People's Hospital of Foshan, Affiliated Foshan Hospital of Sun Yat-sen University, Foshan, 528000, China
| | - Jiyou Yao
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Jialuo Mai
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Xuefeng Hua
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Huan Chen
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Jie Liu
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Minqiang Lu
- Department of HBP Surgery II, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
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22
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Sun Y, Hamilton K, Tong L. Recent molecular insights into canonical pre-mRNA 3'-end processing. Transcription 2020; 11:83-96. [PMID: 32522085 DOI: 10.1080/21541264.2020.1777047] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The majority of eukaryotic messenger RNA precursors (pre-mRNAs) undergo cleavage and polyadenylation at their 3' end. This canonical 3'-end processing depends on sequence elements in the pre-mRNA as well as a mega-dalton protein machinery. The cleavage site in mammalian pre-mRNAs is located between an upstream poly(A) signal, most frequently an AAUAAA hexamer, and a GU-rich downstream sequence element. This review will summarize recent advances from the studies on this canonical 3'-end processing machinery. They have revealed the molecular mechanism for the recognition of the poly(A) signal and provided the first glimpse into the overall architecture of the machinery. The studies also show that the machinery is highly dynamic conformationally, and extensive re-arrangements are necessary for its activation. Inhibitors targeting the active site of the CPSF73 nuclease of this machinery have anti-cancer, anti-inflammatory and anti-protozoal effects, indicating that CPSF73 and pre-mRNA 3'-end processing in general are attractive targets for drug discovery. ABBREVIATIONS APA: alternative polyadenylation; β-CASP: metallo-β-lactamase-associated CPSF Artemis SNM1/PSO2; CTD: C-terminal domain; CF: cleavage factor; CPF: cleavage and polyadenylation factor; CPSF: cleavage and polyadenylation specificity factor; CstF: cleavage stimulation factor; DSE: downstream element; HAT: half a TPR; HCC: histone pre-mRNA cleavage complex; mCF: mammalian cleavage factor; mPSF: mammalian polyadenylation specificity factor; mRNA: messenger RNA; nt: nucleotide; NTD: N-terminal domain; PAP: polyadenylate polymerase; PAS: polyadenylation signal; PIM: mPSF interaction motif; Poly(A): polyadenylation, polyadenylate; Pol II: RNA polymerase II; pre-mRNA: messenger RNA precursor; RRM: RNA recognition module, RNA recognition motif; snRNP: small nuclear ribonucleoprotein; TPR: tetratricopeptide repeat; UTR: untranslated region; ZF: zinc finger.
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Affiliation(s)
- Yadong Sun
- Department of Biological Sciences, Columbia University , New York, NY, USA
| | - Keith Hamilton
- Department of Biological Sciences, Columbia University , New York, NY, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University , New York, NY, USA
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23
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Futami M, Suzuki K, Kato S, Ohmae S, Tahara Y, Nojima M, Imai Y, Mimura T, Watanabe Y, Tojo A. The novel multi-cytokine inhibitor TO-207 specifically inhibits pro-inflammatory cytokine secretion in monocytes without affecting the killing ability of CAR T cells. PLoS One 2020; 15:e0231896. [PMID: 32320454 PMCID: PMC7176125 DOI: 10.1371/journal.pone.0231896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/02/2020] [Indexed: 12/14/2022] Open
Abstract
Cancer immunotherapy using chimeric antigen receptor–armed T (CAR T) cells have been shown to improve outcomes significantly in patients with hematological malignancies. However, cytokine release syndrome (CRS) remains a risk. CRS is characterized by the excessive activation of CAR T cells and macrophages. Signs and symptoms of CRS are usually resolved after steroid administration, but steroids abrogate the expansion and persistence of CAR T cell populations. Tocilizumab is a humanized monoclonal antibody (mAb) that attenuates CRS without significant loss of CAR T cell activity. However, interleukin-6 (IL-6)/IL-6 receptor (IL-6R) blockade alone cannot relieve CRS symptoms fully, and novel treatments are needed to prevent or cure CRS. TO-207 is an N-benzoyl-L-phenylalanine derivative that significantly inhibits inflammatory cytokine production in human monocyte and macrophage-specific manner. We investigated whether TO-207 could inhibit cytokine production without impairing CAR T cell function in a CRS-simulating co-culture system.
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Affiliation(s)
- Muneyoshi Futami
- Division of Molecular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- * E-mail:
| | - Keisuke Suzuki
- Research laboratories, Torii Pharmaceutical., Sakura-shi, Japan
| | - Satomi Kato
- Division of Molecular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Saori Ohmae
- Research laboratories, Torii Pharmaceutical., Sakura-shi, Japan
| | - Yoshio Tahara
- Research laboratories, Torii Pharmaceutical., Sakura-shi, Japan
| | - Masanori Nojima
- Center for Translational Research, The Institute of Medical Science Hospital, The University of Tokyo, Tokyo, Japan
| | - Yoichi Imai
- Department of Hematology/Oncology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takayuki Mimura
- Research laboratories, Torii Pharmaceutical., Sakura-shi, Japan
| | - Yoshihiro Watanabe
- Research laboratories, Torii Pharmaceutical., Sakura-shi, Japan
- Innovative Clinical Research Center, Kanazawa University, Kanazawa, Japan
| | - Arinobu Tojo
- Division of Molecular Therapy, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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24
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Processing for destruction. Nat Chem Biol 2019; 16:3-4. [PMID: 31819275 DOI: 10.1038/s41589-019-0428-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Ross NT, Lohmann F, Carbonneau S, Fazal A, Weihofen WA, Gleim S, Salcius M, Sigoillot F, Henault M, Carl SH, Rodríguez-Molina JB, Miller HR, Brittain SM, Murphy J, Zambrowski M, Boynton G, Wang Y, Chen A, Molind GJ, Wilbertz JH, Artus-Revel CG, Jia M, Akinjiyan FA, Turner J, Knehr J, Carbone W, Schuierer S, Reece-Hoyes JS, Xie K, Saran C, Williams ET, Roma G, Spencer M, Jenkins J, George EL, Thomas JR, Michaud G, Schirle M, Tallarico J, Passmore LA, Chao JA, Beckwith REJ. CPSF3-dependent pre-mRNA processing as a druggable node in AML and Ewing's sarcoma. Nat Chem Biol 2019; 16:50-59. [PMID: 31819276 DOI: 10.1038/s41589-019-0424-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/01/2019] [Indexed: 02/07/2023]
Abstract
The post-genomic era has seen many advances in our understanding of cancer pathways, yet resistance and tumor heterogeneity necessitate multiple approaches to target even monogenic tumors. Here, we combine phenotypic screening with chemical genetics to identify pre-messenger RNA endonuclease cleavage and polyadenylation specificity factor 3 (CPSF3) as the target of JTE-607, a small molecule with previously unknown target. We show that CPSF3 represents a synthetic lethal node in a subset of acute myeloid leukemia (AML) and Ewing's sarcoma cancer cell lines. Inhibition of CPSF3 by JTE-607 alters expression of known downstream effectors in AML and Ewing's sarcoma lines, upregulates apoptosis and causes tumor-selective stasis in mouse xenografts. Mechanistically, it prevents the release of newly synthesized pre-mRNAs, resulting in read-through transcription and the formation of DNA-RNA hybrid R-loop structures. This study implicates pre-mRNA processing, and specifically CPSF3, as a druggable target providing an avenue to therapeutic intervention in cancer.
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Affiliation(s)
- Nathan T Ross
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.,Vertex Pharmaceuticals, Boston, MA, USA
| | - Felix Lohmann
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Seth Carbonneau
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Aleem Fazal
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Scott Gleim
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Michael Salcius
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Martin Henault
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Howard R Miller
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Jason Murphy
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Mark Zambrowski
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Yuan Wang
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Aye Chen
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Johannes H Wilbertz
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Min Jia
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Jonathan Turner
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Judith Knehr
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Kevin Xie
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Chitra Saran
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Eric T Williams
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Matt Spencer
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Jeremy Jenkins
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Jason R Thomas
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Gregory Michaud
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John Tallarico
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Lori A Passmore
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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