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Kolathur KK, Mallya S, Barve S, Bojja SL, Wagle MM. Moonlighting functions of the ubiquitin-like protein, Hub1/UBL-5. Int J Biochem Cell Biol 2023; 162:106445. [PMID: 37453225 DOI: 10.1016/j.biocel.2023.106445] [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: 03/31/2023] [Revised: 06/28/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
The faithful splicing of pre-mRNA is critical for accurate gene expression. Dysregulation of pre-mRNA splicing has been associated with several human diseases including cancer. The ubiquitin-like protein Hub1/UBL5 binds to the substrates non-covalently and promotes pre-mRNA splicing. Additionally, UBL5 promotes the common fragile sites stability and the Fanconi anemia pathway of DNA damage repair. These functions strongly suggests that UBL5 could potentially be implicated in cancer. Therefore, we analyzed the UBL5 expression in TCGA tumor sample datasets and observed the differences between tumor and normal tissues among different tumor subtypes. We have noticed the alteration frequency of UBL5 in TCGA tumor samples. Altogether, this review summarizes the UBL5 functions and discusses its putative role in tumorigenesis.
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Affiliation(s)
- Kiran Kumar Kolathur
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences (MCOPS), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India.
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Shivmani Barve
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences (MCOPS), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India
| | - Sree Lalitha Bojja
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences (MCOPS), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India
| | - Manoj M Wagle
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
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2
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Tantawy SI, Timofeeva N, Sarkar A, Gandhi V. Targeting MCL-1 protein to treat cancer: opportunities and challenges. Front Oncol 2023; 13:1226289. [PMID: 37601693 PMCID: PMC10436212 DOI: 10.3389/fonc.2023.1226289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023] Open
Abstract
Evading apoptosis has been linked to tumor development and chemoresistance. One mechanism for this evasion is the overexpression of prosurvival B-cell lymphoma-2 (BCL-2) family proteins, which gives cancer cells a survival advantage. Mcl-1, a member of the BCL-2 family, is among the most frequently amplified genes in cancer. Targeting myeloid cell leukemia-1 (MCL-1) protein is a successful strategy to induce apoptosis and overcome tumor resistance to chemotherapy and targeted therapy. Various strategies to inhibit the antiapoptotic activity of MCL-1 protein, including transcription, translation, and the degradation of MCL-1 protein, have been tested. Neutralizing MCL-1's function by targeting its interactions with other proteins via BCL-2 interacting mediator (BIM)S2A has been shown to be an equally effective approach. Encouraged by the design of venetoclax and its efficacy in chronic lymphocytic leukemia, scientists have developed other BCL-2 homology (BH3) mimetics-particularly MCL-1 inhibitors (MCL-1i)-that are currently in clinical trials for various cancers. While extensive reviews of MCL-1i are available, critical analyses focusing on the challenges of MCL-1i and their optimization are lacking. In this review, we discuss the current knowledge regarding clinically relevant MCL-1i and focus on predictive biomarkers of response, mechanisms of resistance, major issues associated with use of MCL-1i, and the future use of and maximization of the benefits from these agents.
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Affiliation(s)
- Shady I. Tantawy
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Natalia Timofeeva
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Aloke Sarkar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Varsha Gandhi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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3
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Wang W, Hawkridge AM, Ma Y, Zhang B, Mangrum JB, Hassan ZH, He T, Blat S, Guo C, Zhou H, Liu J, Wang XY, Fang X. Ubiquitin-like protein 5 is a novel player in the UPR-PERK arm and ER stress-induced cell death. J Biol Chem 2023; 299:104915. [PMID: 37315790 PMCID: PMC10339194 DOI: 10.1016/j.jbc.2023.104915] [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: 09/30/2022] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/16/2023] Open
Abstract
Biological functions of the highly conserved ubiquitin-like protein 5 (UBL5) are not well understood. In Caenorhabditis elegans, UBL5 is induced under mitochondrial stress to mount the mitochondrial unfolded protein response (UPR). However, the role of UBL5 in the more prevalent endoplasmic reticulum (ER) stress-UPR in the mammalian system is unknown. In the present work, we demonstrated that UBL5 was an ER stress-responsive protein, undergoing rapid depletion in mammalian cells and livers of mice. The ER stress-induced UBL5 depletion was mediated by proteasome-dependent yet ubiquitin-independent proteolysis. Activation of the protein kinase R-like ER kinase arm of the UPR was essential and sufficient for inducing UBL5 degradation. RNA-Seq analysis of UBL5-regulated transcriptome revealed that multiple death pathways were activated in UBL5-silenced cells. In agreement with this, UBL5 knockdown induced severe apoptosis in culture and suppressed tumorigenicity of cancer cells in vivo. Furthermore, overexpression of UBL5 protected specifically against ER stress-induced apoptosis. These results identify UBL5 as a physiologically relevant survival regulator that is proteolytically depleted by the UPR-protein kinase R-like ER kinase pathway, linking ER stress to cell death.
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Affiliation(s)
- Wei Wang
- Department of Biochemistry & Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Adam M Hawkridge
- Department of Pharmaceutics, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Yibao Ma
- Department of Biochemistry & Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Bei Zhang
- Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - John B Mangrum
- Department of Pharmaceutics, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Zaneera H Hassan
- Department of Pharmaceutics, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Tianhai He
- Department of Biochemistry & Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Sofiya Blat
- Department of Biochemistry & Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Chunqing Guo
- Department of Human & Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Huiping Zhou
- Department of Microbiology & Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA; Hunter Holmes McGuire VA Medical Center, Richmond, Virginia, USA
| | - Jinze Liu
- Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Xiang-Yang Wang
- Department of Human & Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA; Hunter Holmes McGuire VA Medical Center, Richmond, Virginia, USA
| | - Xianjun Fang
- Department of Biochemistry & Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA.
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4
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Sancho M, Leiva D, Lucendo E, Orzáez M. Understanding MCL1: from cellular function and regulation to pharmacological inhibition. FEBS J 2022; 289:6209-6234. [PMID: 34310025 PMCID: PMC9787394 DOI: 10.1111/febs.16136] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/09/2021] [Accepted: 07/22/2021] [Indexed: 12/30/2022]
Abstract
Myeloid cell leukemia-1 (MCL1), an antiapoptotic member of the BCL2 family characterized by a short half-life, functions as a rapid sensor that regulates cell death and other relevant processes that include cell cycle progression and mitochondrial homeostasis. In cancer, MCL1 overexpression contributes to cell survival and resistance to diverse chemotherapeutic agents; for this reason, several MCL1 inhibitors are currently under preclinical and clinical development for cancer treatment. However, the nonapoptotic functions of MCL1 may influence their therapeutic potential. Overall, the complexity of MCL1 regulation and function represent challenges to the clinical application of MCL1 inhibitors. We now summarize the current knowledge regarding MCL1 structure, regulation, and function that could impact the clinical success of MCL1 inhibitors.
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Affiliation(s)
- Mónica Sancho
- Targeted Therapies on Cancer and Inflammation LaboratoryCentro de Investigación Príncipe FelipeValenciaSpain
| | - Diego Leiva
- Targeted Therapies on Cancer and Inflammation LaboratoryCentro de Investigación Príncipe FelipeValenciaSpain
| | - Estefanía Lucendo
- Targeted Therapies on Cancer and Inflammation LaboratoryCentro de Investigación Príncipe FelipeValenciaSpain
| | - Mar Orzáez
- Targeted Therapies on Cancer and Inflammation LaboratoryCentro de Investigación Príncipe FelipeValenciaSpain
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5
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RNA splicing: a dual-edged sword for hepatocellular carcinoma. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:173. [PMID: 35972700 DOI: 10.1007/s12032-022-01726-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/30/2022] [Indexed: 10/15/2022]
Abstract
RNA splicing is the fundamental process that brings diversity at the transcriptome and proteome levels. The spliceosome complex regulates minor and major processes of RNA splicing. Aberrant regulation is often associated with different diseases, including diabetes, stroke, hypertension, and cancer. In the majority of cancers, dysregulated alternative RNA splicing (ARS) events directly affect tumor progression, invasiveness, and often lead to poor survival of the patients. Alike the rest of the gastrointestinal malignancies, in hepatocellular carcinoma (HCC), which alone contributes to ~ 75% of the liver cancers, a large number of ARS events have been observed, including intron retention, exon skipping, presence of alternative 3'-splice site (3'SS), and alternative 5'-splice site (5'SS). These events are reported in spliceosome and non-spliceosome complexes genes. Molecules such as MCL1, Bcl-X, and BCL2 in different isoforms can behave as anti-apoptotic or pro-apoptotic, making the spliceosome complex a dual-edged sword. The anti-apoptotic isoforms of such molecules bring in resistance to chemotherapy or cornerstone drugs. However, in contrast, multiple malignant tumors, including HCC that target the pro-apoptotic favoring isoforms/variants favor apoptotic induction and make chemotherapy effective. Herein, we discuss different splicing events, aberrations, and antisense oligonucleotides (ASOs) in modulating RNA splicing in HCC tumorigenesis with a possible therapeutic outcome.
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6
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Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities. Int J Mol Sci 2021; 22:ijms22105110. [PMID: 34065983 PMCID: PMC8150589 DOI: 10.3390/ijms22105110] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of messenger RNA (mRNA) processing—in particular mRNA splicing—is a hallmark of cancer. Compared to normal cells, cancer cells frequently present aberrant mRNA splicing, which promotes cancer progression and treatment resistance. This hallmark provides opportunities for developing new targeted cancer treatments. Splicing of precursor mRNA into mature mRNA is executed by a dynamic complex of proteins and small RNAs called the spliceosome. Spliceosomes are part of the supraspliceosome, a macromolecular structure where all co-transcriptional mRNA processing activities in the cell nucleus are coordinated. Here we review the biology of the mRNA splicing machinery in the context of other mRNA processing activities in the supraspliceosome and present current knowledge of its dysregulation in lung cancer. In addition, we review investigations to discover therapeutic targets in the spliceosome and give an overview of inhibitors and modulators of the mRNA splicing process identified so far. Together, this provides insight into the value of targeting the spliceosome as a possible new treatment for lung cancer.
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7
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Nicolaou KC, Rekula SR, Kumar SM, Podilapu AR, Matuszak RP, Jung PM, Lam LT, Phillips AC, Lyssikatos J, Munneke S, Gu C, Sarvaiya H, Sandoval J, Hammond M, Aujay M, Purcell JW, Reilly RM, Gavrilyuk J. Design, Synthesis, and Biological Investigation of Thailanstatin A and Spliceostatin D Analogues Containing Tetrahydropyran, Tetrahydrooxazine, and Fluorinated Structural Motifs. J Org Chem 2021; 86:2499-2521. [PMID: 33417458 DOI: 10.1021/acs.joc.0c02643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thailanstatin A and spliceostatin D, two naturally occurring molecules endowed with potent antitumor activities by virtue of their ability to bind and inhibit the function of the spliceosome, and their natural siblings and designed analogues, constitute an appealing family of compounds for further evaluation and optimization as potential drug candidates for cancer therapies. In this article, the design, synthesis, and biological investigation of a number of novel thailanstatin A analogues, including some accommodating 1,1-difluorocyclopropyl and tetrahydrooxazine structural motifs within their structures, are described. Important findings from these studies paving the way for further investigations include the identification of several highly potent compounds for advancement as payloads for antibody-drug conjugates (ADCs) as potential targeted cancer therapies and/or small molecule drugs, either alone or in combination with other anticancer agents.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Santhosh Reddy Rekula
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - S Mothish Kumar
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Ananda Rao Podilapu
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Ryan P Matuszak
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Paul M Jung
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Lloyd T Lam
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Andrew C Phillips
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Joseph Lyssikatos
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Stefan Munneke
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Christine Gu
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Hetal Sarvaiya
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Joseph Sandoval
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Mikhail Hammond
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Monette Aujay
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - James W Purcell
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Regina M Reilly
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Julia Gavrilyuk
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
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8
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Henson HE, Taylor MR. A sart1 Zebrafish Mutant Results in Developmental Defects in the Central Nervous System. Cells 2020; 9:cells9112340. [PMID: 33105605 PMCID: PMC7690441 DOI: 10.3390/cells9112340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
The spliceosome consists of accessory proteins and small nuclear ribonucleoproteins (snRNPs) that remove introns from RNA. As splicing defects are associated with degenerative conditions, a better understanding of spliceosome formation and function is essential. We provide insight into the role of a spliceosome protein U4/U6.U5 tri-snRNP-associated protein 1, or Squamous cell carcinoma antigen recognized by T-cells (Sart1). Sart1 recruits the U4.U6/U5 tri-snRNP complex to nuclear RNA. The complex then associates with U1 and U2 snRNPs to form the spliceosome. A forward genetic screen identifying defects in choroid plexus development and whole-exome sequencing (WES) identified a point mutation in exon 12 of sart1 in Danio rerio (zebrafish). This mutation caused an up-regulation of sart1. Using RNA-Seq analysis, we identified additional upregulated genes, including those involved in apoptosis. We also observed increased activated caspase 3 in the brain and eye and down-regulation of vision-related genes. Although splicing occurs in numerous cells types, sart1 expression in zebrafish was restricted to the brain. By identifying sart1 expression in the brain and cell death within the central nervous system (CNS), we provide additional insights into the role of sart1 in specific tissues. We also characterized sart1's involvement in cell death and vision-related pathways.
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Affiliation(s)
- Hannah E. Henson
- Chemical Biology and Therapeutics Department, St. Jude Children’s Research Hospital, Memphis, TN 38015, USA
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Correspondence: ; Tel.: +1-731-661-5520
| | - Michael R. Taylor
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA;
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Streletskaia AY, Senichkin VV, Prikazchikova TA, Zatsepin TS, Zhivotovsky B, Kopeina GS. Upregulation of Mcl-1S Causes Cell-Cycle Perturbations and DNA Damage Accumulation. Front Cell Dev Biol 2020; 8:543066. [PMID: 33072738 PMCID: PMC7544834 DOI: 10.3389/fcell.2020.543066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 08/19/2020] [Indexed: 12/04/2022] Open
Abstract
As an important regulator of apoptosis, Mcl-1 protein, a member of the Bcl-2 family, represents an attractive target for cancer treatment. The recent development of novel small molecule compounds has allowed Mcl-1-inhibitory therapy to proceed to clinical trials in cancer treatment. However, the possible adverse effects of either direct inhibition of Mcl-1 or upregulation of Mcl-1S, proapoptotic isoform resulting from alternative splicing of Mcl-1, remain unclear. Here, we investigated changes in Mcl-1S levels during cell cycle and the cell cycle-related functions of Mcl-1 isoforms to address the above-mentioned concerns. It was shown that an anti-mitotic agent monastrol caused accumulation of Mcl-1S mRNA, although without increasing the protein level. In contrast, both mRNA and protein levels of Mcl-1S accrued during the premitotic stages of the normal cell cycle progression. Importantly, Mcl-1S was observed in the nuclear compartment and an overexpression of Mcl-1S, as well as knockdown of Mcl-1, accelerated the progression of cells into mitosis and resulted in DNA damage accumulation. Surprisingly, a small molecule inhibitor of Mcl-1, BH3-mimetic S63845, did not affect the cell cycle progression or the amount of DNA damage. In general, upregulated Mcl-1S protein or genetically inhibited Mcl-1L were associated with the cell cycle perturbations and DNA damage accumulation in normal and cancer cells. At the same time, BH3-mimetic to Mcl-1 did not affect the cell cycle progression, suggesting that direct inhibition of Mcl-1 is devoid of cell-cycle related undesired effects.
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Affiliation(s)
| | | | | | - Timofei S Zatsepin
- Faculty of Medicine, MV Lomonosov Moscow State University, Moscow, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Boris Zhivotovsky
- Faculty of Medicine, MV Lomonosov Moscow State University, Moscow, Russia.,Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gelina S Kopeina
- Faculty of Medicine, MV Lomonosov Moscow State University, Moscow, Russia
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Sulkshane P, Duek I, Ram J, Thakur A, Reis N, Ziv T, Glickman MH. Inhibition of proteasome reveals basal mitochondrial ubiquitination. J Proteomics 2020; 229:103949. [PMID: 32882436 DOI: 10.1016/j.jprot.2020.103949] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 02/06/2023]
Abstract
Strict quality control for mitochondrial proteins is necessary to ensure cell homeostasis. Two cellular pathways-Ubiquitin Proteasome System (UPS) and autophagy-contribute to mitochondrial homeostasis under stressful conditions. Here, we investigate changes to the mitochondria proteome and to the ubiquitin landscape at mitochondria in response to proteasome inhibition. Treatment of HeLa cells devoid of Parkin, the primary E3 ligase responsible for mitophagy, with proteasome inhibitor MG132 for a few hours caused mitochondrial oxidative stress and fragmentation, reduced energy output, and increased mitochondrial ubiquitination without inducing mitophagy. Overexpression of Parkin did not show any induction of mitophagy in response to MG132 treatment. Analysis of ubiquitin chains on isolated mitochondria revealed predominance of K48, K29 and K63-linked polyubiquitin. Interestingly, of all ubiquitinated mitochondrial proteins detected in response to MG132 treatment, a majority (≥90%) were intramitochondrial irrespective of Parkin expression. However, overall levels of these ubiquitinated mitochondrial proteins did not change significantly upon proteasome inhibition when evaluated by quantitative proteomics (LFQ and SILAC), suggesting that only a small portion are ubiquitinated under basal conditions. Another aspect of proteasome inhibition is significant enrichment of UPS, lysosomal and phagosomal components, and other heat shock proteins associated with isolated mitochondria. Taken together, our study highlights a critical role of UPS for ubiquitinating and removing imported proteins as part of a basal mitochondrial quality control system independent of Parkin. SIGNIFICANCE: As centers of cellular bioenergetics, numerous metabolic pathways and signaling cascades, the health of mitochondria is of utmost importance for ensuring cell survival. Due to their unique physiology, mitochondria are constantly subjected to damaging oxidative radicals (ROS) and protein import-related stress due to buildup of unfolded aggregate-prone proteins. Thus, for quality control purposes, mitochondria are constantly under surveillance by Autophagy and the Ubiquitin Proteasome System (UPS), both of which share ubiquitin as a common signal. The ubiquitin landscape of mitochondria has been studied in detail under stressful conditions, however, little is known about basal mitochondrial ubiquitination. Our study reveals that the extent of ubiquitination at mitochondria greatly increases upon proteasome inhibition, pointing to a large number of potential substrates for proteasomal degradation. Interestingly, most of the ubiquitination occurs on intramitochondrial proteins, components of the electron transport chain (ETC) and matrix-resident metabolic enzymes in particular. Moreover, numerous cytosolic UPS components, chaperones and autophagy-lysosomal proteins were recruited to mitochondria upon proteasome inhibition. Taken together, this suggests that the levels and functions of mitochondrial proteins are constantly regulated through ubiquitin-dependent proteasomal degradation even under basal conditions. Unclogging mitochondrial import channels may provide a mechanism to alleviate stress associated with mitochondrial protein import or to adapt cells according to their metabolic needs. Therefore, targeting the mitochondrial ubiquitination/deubiquitination machinery, such as improving the therapeutic potency of proteasome inhibitors, may provide an additional therapeutic arsenal against tumors.
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Affiliation(s)
- Prasad Sulkshane
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Inbar Duek
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Jonathan Ram
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Anita Thakur
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Noa Reis
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Tamar Ziv
- The Smoler Protein Research Center, Technion Israel Institute of Technology, Haifa 32000, Israel.
| | - Michael H Glickman
- The Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel.
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11
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Senichkin VV, Streletskaia AY, Zhivotovsky B, Kopeina GS. Molecular Comprehension of Mcl-1: From Gene Structure to Cancer Therapy. Trends Cell Biol 2019; 29:549-562. [DOI: 10.1016/j.tcb.2019.03.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 01/19/2023]
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12
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Zhu M, Xu Y, Wang H, Shen Z, Xie Z, Chen F, Gao Y, Chen X, Zhang Y, Wu Q, Li X, Yu J, Luo H, Wang K. Heroin Abuse Results in Shifted RNA Expression to Neurodegenerative Diseases and Attenuation of TNFα Signaling Pathway. Sci Rep 2018; 8:9231. [PMID: 29915338 PMCID: PMC6006288 DOI: 10.1038/s41598-018-27419-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/31/2018] [Indexed: 12/18/2022] Open
Abstract
Repeated administration of heroin results in the induction of physical dependence, which is characterized as a behavioral state of compulsive drug seeking and a high rate of relapse even after periods of abstinence. However, few studies have been dedicated to characterization of the long-term alterations in heroin-dependent patients (HDPs). Herein, we examined the peripheral blood from 810 HDPs versus 500 healthy controls (HCs) according to the inclusion criteria. Compared with the control group, significant decreases of albumin, triglyceride, and total cholesterol levels were identified in HDPs (P < 0.001) versus HCs coupled with an insignificant decrease in BMI. Meanwhile, RNA-sequencing analyses were performed on blood of 16 long-term HDPs and 25 HCs. The results showed that the TNFα signaling pathway and hematopoiesis related genes were inhibited in HDPs. We further compared the transcriptome data to those of SCA2 and posttraumatic stress disorder patients, identified neurodegenerative diseases related genes were commonly up-regulated in coupled with biological processes "vesicle transport", "mitochondria" and "splicing". Genes in the categories of "protein ubiquitination" were down-regulated indicating potential biochemical alterations shared by all three comparative to their controls. In summary, this is a leading study performing a series of through investigations and using delicate approaches. Results from this study would benefit the study of drug addiction overall and link long-term heroin abuse to neurodegenerative diseases.
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Affiliation(s)
- Mei Zhu
- Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Yu Xu
- Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Huawei Wang
- Department of Gastrointestinal surgery, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Zongwen Shen
- Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
- Kunming Engineering Technology Center of Diagnosis and Treatment of Digestive Diseases, Kunming, 650032, Yunnan, China
| | - Zhenrong Xie
- Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
- Department of reproduction and genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Fengrong Chen
- Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
- Department of reproduction and genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Yunhong Gao
- Yunnan Drug Enforcement Commission Office, Kunming, 650032, Yunnan, China
- Yunnan Drug Enforcement Administration, Kunming, 650032, Yunnan, China
| | - Xin Chen
- Yunnan Drug Enforcement Commission Office, Kunming, 650032, Yunnan, China
- Yunnan Drug Enforcement Administration, Kunming, 650032, Yunnan, China
| | - Ying Zhang
- Yunnan Drug Enforcement Commission Office, Kunming, 650032, Yunnan, China
- Yunnan Drug Enforcement Administration, Kunming, 650032, Yunnan, China
| | - Qiang Wu
- Yunnan Drug Enforcement Commission Office, Kunming, 650032, Yunnan, China
- Yunnan Drug Enforcement Administration, Kunming, 650032, Yunnan, China
| | - Xuejun Li
- Yunnan Drug Enforcement Commission Office, Kunming, 650032, Yunnan, China
- Yunnan Drug Enforcement Administration, Kunming, 650032, Yunnan, China
| | - Juehua Yu
- Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Huayou Luo
- Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China.
| | - Kunhua Wang
- Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China.
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13
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Targeting the spliceosome for cutaneous squamous cell carcinoma therapy: a role for c-MYC and wild-type p53 in determining the degree of tumour selectivity. Oncotarget 2018; 9:23029-23046. [PMID: 29796170 PMCID: PMC5955416 DOI: 10.18632/oncotarget.25196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/04/2018] [Indexed: 12/25/2022] Open
Abstract
We show that suppression of the spliceosome has potential for the treatment of cutaneous squamous cell carcinoma (cSCC). The small-molecule inhibitors of the spliceosome at the most advanced stage of development target the splicing factor SF3B1/SF3b155. The majority of cSCC cell lines are more sensitive than normal skin cells to death induced by the SF3B1 inhibitor pladienolide B. Knockdown of SF3B1 and a range of other splicing factors with diverse roles in the spliceosome can also selectively kill cSCC cells. We demonstrate that endogenous c-MYC participates in conferring sensitivity to spliceosome inhibition. c-MYC expression is elevated in cSCC lines and its knockdown reduces alterations in mRNA splicing and attenuates cell death caused by interference with the spliceosome. In addition, this study provides further support for a key role of the p53 pathway in the response to spliceosome disruption. SF3B1 inhibition causes wild-type p53 upregulation associated with altered mRNA splicing and reduced protein expression of both principal p53 negative regulators MDMX/MDM4 and MDM2. We observed that wild-type p53 can promote pladienolide B-induced death in tumour cells. However, p53 is commonly inactivated by mutation in cSCCs and p53 participates in killing normal skin cells at high concentrations of pladienolide B. This may limit the therapeutic window of SF3B1 inhibitors for cSCC. We provide evidence that, while suppression of SF3B1 has promise for treating cSCCs with mutant p53, inhibitors which target the spliceosome through SF3B1-independent mechanisms could have greater cSCC selectivity as a consequence of reduced p53 upregulation in normal cells.
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14
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Ivanova H, Ritaine A, Wagner L, Luyten T, Shapovalov G, Welkenhuyzen K, Seitaj B, Monaco G, De Smedt H, Prevarskaya N, Yule DI, Parys JB, Bultynck G. The trans-membrane domain of Bcl-2α, but not its hydrophobic cleft, is a critical determinant for efficient IP3 receptor inhibition. Oncotarget 2018; 7:55704-55720. [PMID: 27494888 PMCID: PMC5342447 DOI: 10.18632/oncotarget.11005] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/18/2016] [Indexed: 12/29/2022] Open
Abstract
The anti-apoptotic Bcl-2 protein is emerging as an efficient inhibitor of IP3R function, contributing to its oncogenic properties. Yet, the underlying molecular mechanisms remain not fully understood. Using mutations or pharmacological inhibition to antagonize Bcl-2's hydrophobic cleft, we excluded this functional domain as responsible for Bcl-2-mediated IP3Rs inhibition. In contrast, the deletion of the C-terminus, containing the trans-membrane domain, which is only present in Bcl-2α, but not in Bcl-2β, led to impaired inhibition of IP3R-mediated Ca2+ release and staurosporine-induced apoptosis. Strikingly, the trans-membrane domain was sufficient for IP3R binding and inhibition. We therefore propose a novel model, in which the Bcl-2's C-terminus serves as a functional anchor, which beyond mere ER-membrane targeting, underlies efficient IP3R inhibition by (i) positioning the BH4 domain in the close proximity of its binding site on IP3R, thus facilitating their interaction; (ii) inhibiting IP3R-channel openings through a direct interaction with the C-terminal region of the channel downstream of the channel-pore. Finally, since the hydrophobic cleft of Bcl-2 was not involved in IP3R suppression, our findings indicate that ABT-199 does not interfere with IP3R regulation by Bcl-2 and its mechanism of action as a cell-death therapeutic in cancer cells likely does not involve Ca2+ signaling.
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Affiliation(s)
- Hristina Ivanova
- Katholieke Universiteit Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine and Leuven Cancer Institute (LKI), BE-3000 Leuven, Belgium
| | - Abigael Ritaine
- Inserm U-1003, Equipe Labellisée par la Ligue Nationale Contre le Cancer et LABEX (Laboratoire d'excellence), Université Lille1, 59655 Villeneuve d'Ascq, France
| | - Larry Wagner
- University of Rochester Medical Center School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Tomas Luyten
- Katholieke Universiteit Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine and Leuven Cancer Institute (LKI), BE-3000 Leuven, Belgium
| | - George Shapovalov
- Inserm U-1003, Equipe Labellisée par la Ligue Nationale Contre le Cancer et LABEX (Laboratoire d'excellence), Université Lille1, 59655 Villeneuve d'Ascq, France
| | - Kirsten Welkenhuyzen
- Katholieke Universiteit Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine and Leuven Cancer Institute (LKI), BE-3000 Leuven, Belgium
| | - Bruno Seitaj
- Katholieke Universiteit Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine and Leuven Cancer Institute (LKI), BE-3000 Leuven, Belgium
| | - Giovanni Monaco
- Katholieke Universiteit Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine and Leuven Cancer Institute (LKI), BE-3000 Leuven, Belgium
| | - Humbert De Smedt
- Katholieke Universiteit Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine and Leuven Cancer Institute (LKI), BE-3000 Leuven, Belgium
| | - Natalia Prevarskaya
- Inserm U-1003, Equipe Labellisée par la Ligue Nationale Contre le Cancer et LABEX (Laboratoire d'excellence), Université Lille1, 59655 Villeneuve d'Ascq, France
| | - David I Yule
- University of Rochester Medical Center School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Jan B Parys
- Katholieke Universiteit Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine and Leuven Cancer Institute (LKI), BE-3000 Leuven, Belgium
| | - Geert Bultynck
- Katholieke Universiteit Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine and Leuven Cancer Institute (LKI), BE-3000 Leuven, Belgium
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15
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Post-Transcriptional Regulation of Anti-Apoptotic BCL2 Family Members. Int J Mol Sci 2018; 19:ijms19010308. [PMID: 29361709 PMCID: PMC5796252 DOI: 10.3390/ijms19010308] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/05/2018] [Accepted: 01/16/2018] [Indexed: 12/20/2022] Open
Abstract
Anti-apoptotic B cell lymphoma 2 (BCL2) family members (BCL2, MCL1, BCLxL, BCLW, and BFL1) are key players in the regulation of intrinsic apoptosis. Dysregulation of these proteins not only impairs normal development, but also contributes to tumor progression and resistance to various anti-cancer therapies. Therefore, cells maintain strict control over the expression of anti-apoptotic BCL2 family members using multiple mechanisms. Over the past two decades, the importance of post-transcriptional regulation of mRNA in controlling gene expression and its impact on normal homeostasis and disease have begun to be appreciated. In this review, we discuss the RNA binding proteins (RBPs) and microRNAs (miRNAs) that mediate post-transcriptional regulation of the anti-apoptotic BCL2 family members. We describe their roles and impact on alternative splicing, mRNA turnover, and mRNA subcellular localization. We also point out the importance of future studies in characterizing the crosstalk between RBPs and miRNAs in regulating anti-apoptotic BCL2 family member expression and ultimately apoptosis.
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16
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Bo L, Wei B, Wang Z, Kong D, Gao Z, Miao Z. Bioinformatics analysis of the CDK2 functions in neuroblastoma. Mol Med Rep 2018; 17:3951-3959. [PMID: 29328425 DOI: 10.3892/mmr.2017.8368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 11/14/2017] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to elucidate the potential mechanism of cyclin-dependent kinase 2 (CDK2) in neuroblastoma progression and to identify the candidate genes associated with neuroblastoma with CDK2 silencing. The microarray data of GSE16480 were obtained from the gene expression omnibus database. This dataset contained 15 samples: Neuroblastoma cell line IMR32 transfected with CDK2 shRNA at 0, 8, 24, 48 and 72 h (n=3 per group; total=15). Significant clusters associated with differentially expressed genes (DEGs) were identified using fuzzy C‑Means algorithm in the Mfuzz package. Gene ontology and pathway enrichment analysis of DEGs in each cluster were performed, and a protein‑protein interaction (PPI) network was constructed. Additionally, functional annotation of DEGs in clusters was performed for the detection of transcription factors and tumor‑associated genes. A total of 4 clusters with significant change tendency and 1,683 DEGs were identified. The hub nodes of the PPI network constructed by DEGs in Cluster 1, Cluster 2, Cluster 3 and Cluster 4 were MDM2 oncogene, E3 ubiquitin protein ligase (MDM2), cyclin‑dependent kinase 1 (CDK1), proteasome (prosome, macropain) 26S subunit, non‑ATPase, 14 (PSMD14) and translocator protein (18 kDa) (TSPO) respectively. These genes were significantly enriched in the p53 signaling pathway, cell cycle, proteasome and systemic lupus erythematosus pathways. MDM2, CDK1, PSMD14 and TSPO may be key target genes of CDK2. CDK2 may have key functions in neuroblastoma progression by regulating the expression of these genes.
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Affiliation(s)
- Lijuan Bo
- Department of Infections, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Bo Wei
- Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zhanfeng Wang
- Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Daliang Kong
- Department of Orthopaedics, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zheng Gao
- Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zhuang Miao
- Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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17
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Baumann J, Ignashkova TI, Chirasani SR, Ramírez-Peinado S, Alborzinia H, Gendarme M, Kuhnigk K, Kramer V, Lindemann RK, Reiling JH. Golgi stress-induced transcriptional changes mediated by MAPK signaling and three ETS transcription factors regulate MCL1 splicing. Mol Biol Cell 2018; 29:42-52. [PMID: 29118074 PMCID: PMC5746065 DOI: 10.1091/mbc.e17-06-0418] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/11/2017] [Accepted: 10/31/2017] [Indexed: 12/14/2022] Open
Abstract
The secretory pathway is a major determinant of cellular homoeostasis. While research into secretory stress signaling has so far mostly focused on the endoplasmic reticulum (ER), emerging data suggest that the Golgi itself serves as an important signaling hub capable of initiating stress responses. To systematically identify novel Golgi stress mediators, we performed a transcriptomic analysis of cells exposed to three different pharmacological compounds known to elicit Golgi fragmentation: brefeldin A, golgicide A, and monensin. Subsequent gene-set enrichment analysis revealed a significant contribution of the ETS family transcription factors ELK1, GABPA/B, and ETS1 to the control of gene expression following compound treatment. Induction of Golgi stress leads to a late activation of the ETS upstream kinases MEK1/2 and ERK1/2, resulting in enhanced ETS factor activity and the transcription of ETS family target genes related to spliceosome function and cell death induction via alternate MCL1 splicing. Further genetic analyses using loss-of-function and gain-of-function experiments suggest that these transcription factors operate in parallel.
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Affiliation(s)
- Jan Baumann
- BioMed X Innovation Center, 69120 Heidelberg, Germany
| | | | | | | | | | | | - Kyra Kuhnigk
- BioMed X Innovation Center, 69120 Heidelberg, Germany
| | | | - Ralph K Lindemann
- Translational Innovation Platform Oncology, Merck Biopharma, Merck KGaA, 64293 Darmstadt, Germany
| | - Jan H Reiling
- BioMed X Innovation Center, 69120 Heidelberg, Germany
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18
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Chan S, Sridhar P, Kirchner R, Lock YJ, Herbert Z, Buonamici S, Smith P, Lieberman J, Petrocca F. Basal-A Triple-Negative Breast Cancer Cells Selectively Rely on RNA Splicing for Survival. Mol Cancer Ther 2017; 16:2849-2861. [PMID: 28878028 PMCID: PMC5997774 DOI: 10.1158/1535-7163.mct-17-0461] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/21/2017] [Accepted: 08/30/2017] [Indexed: 12/25/2022]
Abstract
Prognosis of triple-negative breast cancer (TNBC) remains poor. To identify shared and selective vulnerabilities of basal-like TNBC, the most common TNBC subtype, a directed siRNA lethality screen was performed in 7 human breast cancer cell lines, focusing on 154 previously identified dependency genes of 1 TNBC line. Thirty common dependency genes were identified, including multiple proteasome and RNA splicing genes, especially those associated with the U4/U6.U5 tri-snRNP complex (e.g., PRPF8, PRPF38A). PRPF8 or PRPF38A knockdown or the splicing modulator E7107 led to widespread intronic retention and altered splicing of transcripts involved in multiple basal-like TNBC dependencies, including protein homeostasis, mitosis, and apoptosis. E7107 treatment suppressed the growth of basal-A TNBC cell line and patient-derived basal-like TNBC xenografts at a well-tolerated dose. The antitumor response was enhanced by adding the proteasome inhibitor bortezomib. Thus, inhibiting both splicing and the proteasome might be an effective approach for treating basal-like TNBC. Mol Cancer Ther; 16(12); 2849-61. ©2017 AACR.
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Affiliation(s)
- Stefanie Chan
- Division of Computational Biomedicine, Department of Surgery, Boston University School of Medicine, Boston, Massachusetts
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Praveen Sridhar
- Division of Computational Biomedicine, Department of Surgery, Boston University School of Medicine, Boston, Massachusetts
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Rory Kirchner
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Ying Jie Lock
- Division of Computational Biomedicine, Department of Surgery, Boston University School of Medicine, Boston, Massachusetts
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Zach Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Peter Smith
- H3 Biomedicine Inc., Cambridge, Massachusetts
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.
| | - Fabio Petrocca
- Division of Computational Biomedicine, Department of Surgery, Boston University School of Medicine, Boston, Massachusetts.
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
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19
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WITHDRAWN: Bioinformatic analysis of the roles of CDK2 in neuroblastoma. Clin Neurol Neurosurg 2017. [DOI: 10.1016/j.clineuro.2017.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Pham D, Koide K. Discoveries, target identifications, and biological applications of natural products that inhibit splicing factor 3B subunit 1. Nat Prod Rep 2017; 33:637-47. [PMID: 26812544 DOI: 10.1039/c5np00110b] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Covering: 1992 to 2015The natural products FR901464, pladienolide, and herboxidiene were discovered as activators of reporter gene systems. Unexpectedly, these compounds target neither transcription nor translation; rather, they target splicing factor 3B subunit 1 of the spliceosome, causing changes in splicing patterns. All of them showed anticancer activity in a low nanomolar range. Since their discovery, these molecules have been used in a variety of biological applications.
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Affiliation(s)
- Dianne Pham
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA.
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA.
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21
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Makowski K, Vigevani L, Albericio F, Valcárcel J, Álvarez M. Sudemycin K: A Synthetic Antitumor Splicing Inhibitor Variant with Improved Activity and Versatile Chemistry. ACS Chem Biol 2017; 12:163-173. [PMID: 28103691 DOI: 10.1021/acschembio.6b00562] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Important links exist between the process of pre-mRNA splicing and cancer, as illustrated by the frequent mutation of splicing factors in tumors and the emergence of various families of antitumor drugs that target components of the splicing machinery, notably SF3B1, a protein subunit of spliceosomal U2 small nuclear ribonucleoprotein particle (snRNP). Sudemycins are synthetic compounds that harbor a pharmacophore common to various classes of splicing inhibitors. Here, we describe the synthesis and functional characterization of novel sudemycin analogues that functionally probe key chemical groups within this pharmacophore. Our results confirm the importance of a conjugated diene group and in addition reveal significant spatial flexibility in this region of the molecule. Sudemycin K, a derivative that replaces the pharmacophore's oxycarbonyl by an amide group, displays improved potency as an inhibitor of cancer cell proliferation, as a regulator of alternative splicing in cultured cells and as an inhibitor of in vitro spliceosome assembly. Sudemycin K displays higher stability, likely related to the replacement of the oxycarbonyl group, which can be a substrate of esterases, by an amide group. The activity and special reactivity of sudemycin K can pave the way to the synthesis and evaluation of a variety of novel sudemycin derivatives.
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Affiliation(s)
- Kamil Makowski
- Centre
for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institute for Research in Biomedicine (IRB-Barcelona), Baldiri i Reixac 10, 08028, Barcelona, Spain
| | - Luisa Vigevani
- Centre
for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr.
Aiguader 88, 08003 Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine (IRB-Barcelona), Baldiri i Reixac 10, 08028, Barcelona, Spain
- Department
of Organic Chemistry, Faculty of Chemistry, University of Barcelona, Martí Franqués 1, 08028 Barcelona,Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
| | - Juan Valcárcel
- Centre
for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr.
Aiguader 88, 08003 Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Mercedes Álvarez
- Institute for Research in Biomedicine (IRB-Barcelona), Baldiri i Reixac 10, 08028, Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
- Laboratory
of Organic Chemistry, Faculty of Pharmacy, University of Barcelona, Joan XXIII s/n, 08028 Barcelona, Spain
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22
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Kumar D, Kashyap MK, La Clair JJ, Villa R, Spaanderman I, Chien S, Rassenti LZ, Kipps TJ, Burkart MD, Castro JE. Selectivity in Small Molecule Splicing Modulation. ACS Chem Biol 2016; 11:2716-2723. [PMID: 27499047 DOI: 10.1021/acschembio.6b00399] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The dysregulation of RNA splicing is a molecular hallmark of disease, including different and often complex cancers. While gaining recognition as a target for therapeutic discovery, understanding the complex mechanisms guiding RNA splicing remains a challenge for chemical biology. The discovery of small molecule splicing modulators has recently enabled an evaluation of the mechanisms of aberrant splicing. We now report on three unique features within the selectivity of splicing modulators. First, we provide evidence that structural modifications within a splicing modulator can alter the splicing of introns in specific genes differently. These studies indicate that structure activity relationships not only have an effect on splicing activity but also include specificity for specific introns within different genes. Second, we find that these splicing modulators also target the mRNAs encoding components of the spliceosome itself. Remarkably, this effect includes the genes for the SF3B complex, a target of pladienolide B and related splicing modulators. Finally, we report on the first observation of a temporal phenomenon associated with small molecule splicing modulation. Combined, these three observations provide an important new perspective for the exploration of splicing modulation in terms of both future medicinal chemistry programs as well as understanding the key facets underlying its timing.
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Affiliation(s)
- Deepak Kumar
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
| | - Manoj K Kashyap
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Reymundo Villa
- Department of Chemistry and Biochemistry, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Ide Spaanderman
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
| | - Stephen Chien
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
| | - Laura Z Rassenti
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
- CLL Research Consortium, and Department of Medicine, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Thomas J Kipps
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
- CLL Research Consortium, and Department of Medicine, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Januario E Castro
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
- CLL Research Consortium, and Department of Medicine, University of California , San Diego, La Jolla, California 92093-0358, United States
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23
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Xargay-Torrent S, López-Guerra M, Rosich L, Montraveta A, Roldán J, Rodríguez V, Villamor N, Aymerich M, Lagisetti C, Webb TR, López-Otín C, Campo E, Colomer D. The splicing modulator sudemycin induces a specific antitumor response and cooperates with ibrutinib in chronic lymphocytic leukemia. Oncotarget 2016; 6:22734-49. [PMID: 26068951 PMCID: PMC4673195 DOI: 10.18632/oncotarget.4212] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 05/26/2015] [Indexed: 12/20/2022] Open
Abstract
Mutations or deregulated expression of the components of the spliceosome can influence the splicing pattern of several genes and contribute to the development of tumors. In this context, we report that the spliceosome modulator sudemycin induces selective cytotoxicity in primary chronic lymphocytic leukemia (CLL) cells when compared with healthy lymphocytes and tumor cells from other B-lymphoid malignancies, with a slight bias for CLL cases with mutations in spliceosome-RNA processing machinery. Consistently, sudemycin exhibits considerable antitumor activity in NOD/SCID/IL2Rγ−/− (NSG) mice engrafted with primary cells from CLL patients. The antileukemic effect of sudemycin involves the splicing modulation of several target genes important for tumor survival, both in SF3B1-mutated and -unmutated cases. Thus, the apoptosis induced by this compound is related to the alternative splicing switch of MCL1 toward its proapoptotic isoform. Sudemycin also functionally disturbs NF-κB pathway in parallel with the induction of a spliced RELA variant that loses its DNA binding domain. Importantly, we show an enhanced antitumor effect of sudemycin in combination with ibrutinib that might be related to the modulation of the alternative splicing of the inhibitor of Btk (IBTK). In conclusion, we provide first evidence that the spliceosome is a relevant therapeutic target in CLL, supporting the use of splicing modulators alone or in combination with ibrutinib as a promising approach for the treatment of CLL patients.
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Affiliation(s)
- Sílvia Xargay-Torrent
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mónica López-Guerra
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematopathology Unit, Department of Pathology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Laia Rosich
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Arnau Montraveta
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Jocabed Roldán
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Vanina Rodríguez
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Neus Villamor
- Hematopathology Unit, Department of Pathology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Marta Aymerich
- Hematopathology Unit, Department of Pathology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Chandraiah Lagisetti
- Center for Chemical Biology, Biosciences Division, SRI International, Menlo Park, California, USA
| | - Thomas R Webb
- Center for Chemical Biology, Biosciences Division, SRI International, Menlo Park, California, USA
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo - IUOPA, Oviedo, Spain
| | - Elias Campo
- Hematopathology Unit, Department of Pathology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Dolors Colomer
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematopathology Unit, Department of Pathology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
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Effenberger KA, Urabe VK, Jurica MS. Modulating splicing with small molecular inhibitors of the spliceosome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27440103 DOI: 10.1002/wrna.1381] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 06/06/2016] [Accepted: 06/28/2016] [Indexed: 12/23/2022]
Abstract
Small molecule inhibitors that target components of the spliceosome have great potential as tools to probe splicing mechanism and dissect splicing regulatory networks in cells. These compounds also hold promise as drug leads for diseases in which splicing regulation plays a critical role, including many cancers. Because the spliceosome is a complicated and dynamic macromolecular machine comprised of many RNA and protein components, a variety of compounds that interfere with different aspects of spliceosome assembly is needed to probe its function. By screening chemical libraries with high-throughput splicing assays, several labs have added to the collection of splicing inhibitors, although the mechanistic insight into splicing yielded from the initial compound hits is somewhat limited so far. In contrast, SF3B1 inhibitors stand out as a great example of what can be accomplished with small molecule tools. This group of compounds were first discovered as natural products that are cytotoxic to cancer cells, and then later shown to target the core spliceosome protein SF3B1. The inhibitors have since been used to uncover details of SF3B1 mechanism in the spliceosome and its impact on gene expression in cells. Continuing structure activity relationship analysis of the compounds is also making progress in identifying chemical features key to their function, which is critical in understanding the mechanism of SF3B1 inhibition. The knowledge is also important for the design of analogs with new and useful features for both splicing researchers and clinicians hoping to exploit splicing as pressure point to target in cancer therapy. WIREs RNA 2017, 8:e1381. doi: 10.1002/wrna.1381 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Kerstin A Effenberger
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.,Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
| | - Veronica K Urabe
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.,Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
| | - Melissa S Jurica
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.,Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
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25
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Campagna D, Gasparini F, Franchi N, Vitulo N, Ballin F, Manni L, Valle G, Ballarin L. Transcriptome dynamics in the asexual cycle of the chordate Botryllus schlosseri. BMC Genomics 2016; 17:275. [PMID: 27038623 PMCID: PMC4818882 DOI: 10.1186/s12864-016-2598-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/16/2016] [Indexed: 12/15/2022] Open
Abstract
Background We performed an analysis of the transcriptome during the blastogenesis of the chordate Botryllus schlosseri, focusing in particular on genes involved in cell death by apoptosis. The tunicate B. schlosseri is an ascidian forming colonies characterized by the coexistence of three blastogenetic generations: filter-feeding adults, buds on adults, and budlets on buds. Cyclically, adult tissues undergo apoptosis and are progressively resorbed and replaced by their buds originated by asexual reproduction. This is a feature of colonial tunicates, the only known chordates that can reproduce asexually. Results Thanks to a newly developed web-based platform (http://botryllus.cribi.unipd.it), we compared the transcriptomes of the mid-cycle, the pre-take-over, and the take-over phases of the colonial blastogenetic cycle. The platform is equipped with programs for comparative analysis and allows to select the statistical stringency. We enriched the genome annotation with 11,337 new genes; 581 transcripts were resolved as complete open reading frames, translated in silico into amino acid sequences and then aligned onto the non-redundant sequence database. Significant differentially expressed genes were classified within the gene ontology categories. Among them, we recognized genes involved in apoptosis activation, de-activation, and regulation. Conclusions With the current work, we contributed to the improvement of the first released B. schlosseri genome assembly and offer an overview of the transcriptome changes during the blastogenetic cycle, showing up- and down-regulated genes. These results are important for the comprehension of the events underlying colony growth and regression, cell proliferation, colony homeostasis, and competition among different generations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2598-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Davide Campagna
- CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Fabio Gasparini
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Nicola Franchi
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Nicola Vitulo
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.,Department of Biotechnology, University of Verona, Verona, Italy
| | - Francesca Ballin
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Lucia Manni
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.
| | - Giorgio Valle
- CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.,Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Loriano Ballarin
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
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The SF3B1 inhibitor spliceostatin A (SSA) elicits apoptosis in chronic lymphocytic leukaemia cells through downregulation of Mcl-1. Leukemia 2015; 30:351-60. [PMID: 26488112 DOI: 10.1038/leu.2015.286] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 09/03/2015] [Accepted: 10/07/2015] [Indexed: 12/14/2022]
Abstract
The pro-survival Bcl-2 family member Mcl-1 is expressed in chronic lymphocytic leukaemia (CLL), with high expression correlated with progressive disease. The spliceosome inhibitor spliceostatin A (SSA) is known to regulate Mcl-1 and so here we assessed the ability of SSA to elicit apoptosis in CLL. SSA induced apoptosis of CLL cells at low nanomolar concentrations in a dose- and time-dependent manner, but independently of SF3B1 mutational status, IGHV status and CD38 or ZAP70 expression. However, normal B and T cells were less sensitive than CLL cells (P=0.006 and P<0.001, respectively). SSA altered the splicing of anti-apoptotic MCL-1(L) to MCL-1(s) in CLL cells coincident with induction of apoptosis. Overexpression studies in Ramos cells suggested that Mcl-1 was important for SSA-induced killing since its expression inversely correlated with apoptosis (P=0.001). IL4 and CD40L, present in patient lymph nodes, are known to protect tumour cells from apoptosis and significantly inhibited SSA, ABT-263 and ABT-199 induced killing following administration to CLL cells (P=0.008). However, by combining SSA with the Bcl-2/Bcl-x(L) antagonists ABT-263 or ABT-199, we were able to overcome this pro-survival effect. We conclude that SSA combined with Bcl-2/Bcl-x(L) antagonists may have therapeutic utility for CLL.
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Abstract
INTRODUCTION The significant challenge posed by cancer to human healthcare has led to the exploration of new approaches to combat it. Synthetic lethality (SL) is one such emerging area in the development of novel anticancer therapies. SL can be described as lethality (cell death) resulting from the combination of the two mutations, wherein the mutation in either of the two codependent genes in normal or cancer cells is viable. This concept is specifically being exploited in cancer research for selectively targeting specific tumor cells. AREAS COVERED In this review, the authors summarize studies of SL-based novel anticancer therapies. The review highlights some of the selected advances in DNA damage response pathway-related SL pairs, particularly poly (ADP-ribose) polymerase (PARP) and SL pairs involved in mitochondrial death signaling pathways published in the last 3 years. EXPERT OPINION Most of the currently used chemotherapeutic agents will destroy cells irrespective of whether they are cancer cells or fast growing normal cells; but SL is one of the approaches being developed with potential as a selective cancer therapy. PARP inhibitors, such as olaparib, are useful in BRCA mutated cancer cells and are also used in combination with other drug to enhance their efficacy. Research on PARP inhibitors is progressing at a good pace but there are still some significant challenges that must be addressed.
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Affiliation(s)
- Ahmed Kamal
- a 1 CSIR-Indian Institute of Chemical Technology, Medicinal Chemistry and Pharmacology , Hyderabad 500007, India +91 40 2719 3157 ; +91 40 2719 3189 ; .,b 2 National Institute of Pharmaceutical Education and Research , Balanagar, Hyderabad, 500037, India.,c 3 King Saud University, College of Science, Catalytic Chemistry Chair, Chemistry Department , Riyadh 11451, Saudi Arabia
| | - Thokhir Basha Shaik
- a 1 CSIR-Indian Institute of Chemical Technology, Medicinal Chemistry and Pharmacology , Hyderabad 500007, India +91 40 2719 3157 ; +91 40 2719 3189 ; .,d 4 Acharya Nagarjuna University , Nagarjuna Nagar, Guntur 522510, India
| | - Mohammed Shaheer Malik
- a 1 CSIR-Indian Institute of Chemical Technology, Medicinal Chemistry and Pharmacology , Hyderabad 500007, India +91 40 2719 3157 ; +91 40 2719 3189 ;
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Park SA, Platt J, Lee JW, López-Giráldez F, Herbst RS, Koo JS. E2F8 as a Novel Therapeutic Target for Lung Cancer. J Natl Cancer Inst 2015; 107:djv151. [PMID: 26089541 DOI: 10.1093/jnci/djv151] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/06/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The E2F members have been divided into transcription activators (E2F1-E2F3) and repressors (E2F4-E2F8). E2F8 with E2F7 has been known to play an important physiologic role in embryonic development and cell cycle regulation by repressing E2F1. However, the function of E2F8 in cancer cells is unknown. METHODS E2F8 expression was assessed by immunoblotting or immunofluorescence staining in human lung cancer (LC) cells and tissues from LC patients (n = 45). Cell proliferation, colony formation, and invasion analysis were performed to evaluate the role of E2F8 in LC. Microarray analysis was used to determine the target genes of E2F8. The regulation of E2F8 on the expression of ubiquitin-like PHD and RING domain-containing 1 (UHRF1), one of E2F8 target genes, was determined using chromatin immunoprecipitation and promoter activity assays. Human LC xenograft models were used to determine the effects of inhibiting E2F8 by siRNAs (n = 7 per group) or antisense morpholino (n = 8 per group) on tumor growth. Survival was analyzed using the Kaplan-Meier method and group differences by the Student's t test. All statistical tests were two-sided. RESULTS LC tumors overexpressed E2F8 compared with normal lung tissues. Depletion of E2F8 inhibited cell proliferation and tumor growth. E2F8 knockdown statistically significantly reduced the expression of UHRF1 (~60%-70%, P < .001), and the direct binding of E2F8 on the promoter of UHRF1 was identified. Kaplan-Meier analysis with a public database showed prognostic significance of aberrant E2F8 expression in LC (HR = 1.91 95% CI = 1.21 to 3.01 in chemo-naïve patients, P = .0047). CONCLUSIONS We demonstrated that E2F8 is overexpressed in LC and is required for the growth of LC cells. These findings implicate E2F8 as a novel therapeutic target for LC treatment.
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Affiliation(s)
- Sin-Aye Park
- Section of Medical Oncology, Department of Internal Medicine (SAP, JWL, RSH, JSK) and Translational Research Program (RSH, JSK), Yale Comprehensive Cancer Center, Departments of Pathology and Medical Oncology (JP), Yale School of Medicine, New Haven, CT; Yale Center for Genome Analysis, Yale University, Orange, CT (FLG)
| | - James Platt
- Section of Medical Oncology, Department of Internal Medicine (SAP, JWL, RSH, JSK) and Translational Research Program (RSH, JSK), Yale Comprehensive Cancer Center, Departments of Pathology and Medical Oncology (JP), Yale School of Medicine, New Haven, CT; Yale Center for Genome Analysis, Yale University, Orange, CT (FLG)
| | - Jong Woo Lee
- Section of Medical Oncology, Department of Internal Medicine (SAP, JWL, RSH, JSK) and Translational Research Program (RSH, JSK), Yale Comprehensive Cancer Center, Departments of Pathology and Medical Oncology (JP), Yale School of Medicine, New Haven, CT; Yale Center for Genome Analysis, Yale University, Orange, CT (FLG)
| | - Francesc López-Giráldez
- Section of Medical Oncology, Department of Internal Medicine (SAP, JWL, RSH, JSK) and Translational Research Program (RSH, JSK), Yale Comprehensive Cancer Center, Departments of Pathology and Medical Oncology (JP), Yale School of Medicine, New Haven, CT; Yale Center for Genome Analysis, Yale University, Orange, CT (FLG)
| | - Roy S Herbst
- Section of Medical Oncology, Department of Internal Medicine (SAP, JWL, RSH, JSK) and Translational Research Program (RSH, JSK), Yale Comprehensive Cancer Center, Departments of Pathology and Medical Oncology (JP), Yale School of Medicine, New Haven, CT; Yale Center for Genome Analysis, Yale University, Orange, CT (FLG)
| | - Ja Seok Koo
- Section of Medical Oncology, Department of Internal Medicine (SAP, JWL, RSH, JSK) and Translational Research Program (RSH, JSK), Yale Comprehensive Cancer Center, Departments of Pathology and Medical Oncology (JP), Yale School of Medicine, New Haven, CT; Yale Center for Genome Analysis, Yale University, Orange, CT (FLG).
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Shender VO, Pavlyukov MS, Ziganshin RH, Arapidi GP, Kovalchuk SI, Anikanov NA, Altukhov IA, Alexeev DG, Butenko IO, Shavarda AL, Khomyakova EB, Evtushenko E, Ashrafyan LA, Antonova IB, Kuznetcov IN, Gorbachev AY, Shakhparonov MI, Govorun VM. Proteome-metabolome profiling of ovarian cancer ascites reveals novel components involved in intercellular communication. Mol Cell Proteomics 2014; 13:3558-71. [PMID: 25271300 DOI: 10.1074/mcp.m114.041194] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Ovarian cancer ascites is a native medium for cancer cells that allows investigation of their secretome in a natural environment. This medium is of interest as a promising source of potential biomarkers, and also as a medium for cell-cell communication. The aim of this study was to elucidate specific features of the malignant ascites metabolome and proteome. In order to omit components of the systemic response to ascites formation, we compared malignant ascites with cirrhosis ascites. Metabolome analysis revealed 41 components that differed significantly between malignant and cirrhosis ascites. Most of the identified cancer-specific metabolites are known to be important signaling molecules. Proteomic analysis identified 2096 and 1855 proteins in the ovarian cancer and cirrhosis ascites, respectively; 424 proteins were specific for the malignant ascites. Functional analysis of the proteome demonstrated that the major differences between cirrhosis and malignant ascites were observed for the cluster of spliceosomal proteins. Additionally, we demonstrate that several splicing RNAs were exclusively detected in malignant ascites, where they probably existed within protein complexes. This result was confirmed in vitro using an ovarian cancer cell line. Identification of spliceosomal proteins and RNAs in an extracellular medium is of particular interest; the finding suggests that they might play a role in the communication between cancer cells. In addition, malignant ascites contains a high number of exosomes that are known to play an important role in signal transduction. Thus our study reveals the specific features of malignant ascites that are associated with its function as a medium of intercellular communication.
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Affiliation(s)
- Victoria O Shender
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str. 16/10, Moscow 117997, Russian Federation;
| | - Marat S Pavlyukov
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str. 16/10, Moscow 117997, Russian Federation
| | - Rustam H Ziganshin
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str. 16/10, Moscow 117997, Russian Federation
| | - Georgij P Arapidi
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str. 16/10, Moscow 117997, Russian Federation; ‖Moscow Institute of Physics and Technology, Institutskiy pereulok 9, Dolgoprudny 141700, Russian Federation
| | - Sergey I Kovalchuk
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str. 16/10, Moscow 117997, Russian Federation
| | - Nikolay A Anikanov
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str. 16/10, Moscow 117997, Russian Federation
| | - Ilya A Altukhov
- ‖Moscow Institute of Physics and Technology, Institutskiy pereulok 9, Dolgoprudny 141700, Russian Federation; **Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya str., 1a, Moscow 119435, Russian Federation
| | - Dmitry G Alexeev
- ‖Moscow Institute of Physics and Technology, Institutskiy pereulok 9, Dolgoprudny 141700, Russian Federation; **Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya str., 1a, Moscow 119435, Russian Federation
| | - Ivan O Butenko
- **Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya str., 1a, Moscow 119435, Russian Federation
| | - Alexey L Shavarda
- ‡‡Research Resource Center molecular and Cell Technologies, Saint-Petersburg State University, Universitetskaya nab. 7-9, Saint-Petersburg 199034, Russian Federation; §§Analytical Phytochemistry Laboratory, Komarov Botanical Institute, Prof. Popov Street 2, Saint-Petersburg 197376, Russia
| | - Elena B Khomyakova
- **Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya str., 1a, Moscow 119435, Russian Federation
| | - Evgeniy Evtushenko
- ¶¶Faculty of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, Moscow 119991, Russian Federation
| | - Lev A Ashrafyan
- ‖‖Russian Scientific Center of Roentgenoradiology, Profsoyuznaya str. 86, Moscow 117997, Russian Federation
| | - Irina B Antonova
- ‖‖Russian Scientific Center of Roentgenoradiology, Profsoyuznaya str. 86, Moscow 117997, Russian Federation
| | - Igor N Kuznetcov
- ‖‖Russian Scientific Center of Roentgenoradiology, Profsoyuznaya str. 86, Moscow 117997, Russian Federation
| | - Alexey Yu Gorbachev
- **Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya str., 1a, Moscow 119435, Russian Federation
| | - Mikhail I Shakhparonov
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str. 16/10, Moscow 117997, Russian Federation
| | - Vadim M Govorun
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str. 16/10, Moscow 117997, Russian Federation; **Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya str., 1a, Moscow 119435, Russian Federation; Kazan Federal University, Kremlyovskaya str. 18, Kazan 420008, Russian Federation
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Gao Y, Trivedi S, Ferris RL, Koide K. Regulation of HPV16 E6 and MCL1 by SF3B1 inhibitor in head and neck cancer cells. Sci Rep 2014; 4:6098. [PMID: 25139387 PMCID: PMC4138523 DOI: 10.1038/srep06098] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 07/22/2014] [Indexed: 11/16/2022] Open
Abstract
ABT-737 inhibits the anti-apoptotic proteins B-cell lymphoma 2 (BCL-2) and BCL-XL. Meayamycin B switches the splicing pattern of myeloid cell leukemia factor 1 (MCL1) pre-mRNA. Specifically, inhibition of splicing factor 3B subunit 1 (SF3B1) with meayamycin B promotes the generation of the proapoptotic, short splicing variant (MCL1-S) and diminishes the antiapoptotic, long variant (MCL1-L). This action was previously associated with the cytotoxicity of meayamycin B in non-small cell lung carcinoma cell lines. ABT-737 induced apoptosis in response to an ablation of MCL1-L by meayamycin B. In this study, we further exploited this synergistic combination in head and neck squamous cell carcinoma (HNSCC), up to 90% of which overexpress MCL1 and BCL-XL. In a panel of seven HNSCC cell lines, the combination of meayamycin B and ABT-737 rapidly triggered a Bax/Bak-mediated apoptosis that overcame the resistance from HPV16-positive HNSCC against each agent alone. Both RT-PCR and Western blotting showed that meayamycin B up-regulated MCL1-S and down-regulated MCL1-L. Significantly, we discovered that SF3B1 was involved in the splicing of oncogenic HPV16 E6 to produce non-oncogenic HPV16 E6*, indicating that SF3B1 may inhibit HPV16-induced tumorigenesis.
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Affiliation(s)
- Yang Gao
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Sumita Trivedi
- University of Pittsburgh Cancer institute, Pittsburgh, Pennsylvania 15213, USA
| | - Robert L Ferris
- University of Pittsburgh Cancer institute, Pittsburgh, Pennsylvania 15213, USA
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
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Ammon T, Mishra SK, Kowalska K, Popowicz GM, Holak TA, Jentsch S. The conserved ubiquitin-like protein Hub1 plays a critical role in splicing in human cells. J Mol Cell Biol 2014; 6:312-23. [PMID: 24872507 PMCID: PMC4141198 DOI: 10.1093/jmcb/mju026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Different from canonical ubiquitin-like proteins, Hub1 does not form covalent conjugates with substrates but binds proteins non-covalently. In Saccharomyces cerevisiae, Hub1 associates with spliceosomes and mediates alternative splicing of SRC1, without affecting pre-mRNA splicing generally. Human Hub1 is highly similar to its yeast homolog, but its cellular function remains largely unexplored. Here, we show that human Hub1 binds to the spliceosomal protein Snu66 as in yeast; however, unlike its S. cerevisiae homolog, human Hub1 is essential for viability. Prolonged in vivo depletion of human Hub1 leads to various cellular defects, including splicing speckle abnormalities, partial nuclear retention of mRNAs, mitotic catastrophe, and consequently cell death by apoptosis. Early consequences of Hub1 depletion are severe splicing defects, however, only for specific splice sites leading to exon skipping and intron retention. Thus, the ubiquitin-like protein Hub1 is not a canonical spliceosomal factor needed generally for splicing, but rather a modulator of spliceosome performance and facilitator of alternative splicing.
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Affiliation(s)
- Tim Ammon
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Shravan Kumar Mishra
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Present address: Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, 140306 Punjab, India
| | - Kaja Kowalska
- NMR Spectroscopy, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Grzegorz M Popowicz
- NMR Spectroscopy, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Present address: Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Tad A Holak
- NMR Spectroscopy, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Present address: Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Stefan Jentsch
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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