1
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Huang G, Cierpicki T, Grembecka J. Thioamides in medicinal chemistry and as small molecule therapeutic agents. Eur J Med Chem 2024; 277:116732. [PMID: 39106658 DOI: 10.1016/j.ejmech.2024.116732] [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: 06/18/2024] [Revised: 07/18/2024] [Accepted: 07/30/2024] [Indexed: 08/09/2024]
Abstract
Thioamides, which are fascinating isosteres of amides, have garnered significant attention in drug discovery and medicinal chemistry programs, spanning peptides and small molecule compounds. This review provides an overview of the various applications of thioamides in small molecule therapeutic agents targeting a range of human diseases, including cancer, microbial infections (e.g., tuberculosis, bacteria, and fungi), viral infections, neurodegenerative conditions, analgesia, and others. Particular focus is given to design strategies of biologically active thioamide-containing compounds and their biological targets, such as kinases and histone methyltransferase ASH1L. Additionally, the review discusses the impact of the thioamide moiety on key properties, including potency, target interactions, physicochemical characteristics, and pharmacokinetics profiles. We hope that this work will offer valuable insights to inspire the future development of novel bioactive thioamide-containing compounds, facilitating their effective use in combating a wide array of human diseases.
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Affiliation(s)
- Guang Huang
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
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2
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Shipman GA, Padilla R, Horth C, Hu B, Bareke E, Vitorino FN, Gongora JM, Garcia BA, Lu C, Majewski J. Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation. Genome Biol 2024; 25:263. [PMID: 39390582 PMCID: PMC11465688 DOI: 10.1186/s13059-024-03415-3] [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: 09/22/2023] [Accepted: 10/01/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Methylation of histone 3 lysine 36 (H3K36me) has emerged as an essential epigenetic component for the faithful regulation of gene expression. Despite its importance in development and disease, how the molecular agents collectively shape the H3K36me landscape is unclear. RESULTS We use mouse mesenchymal stem cells to perturb the H3K36me methyltransferases (K36MTs) and infer the activities of the five most prominent enzymes: SETD2, NSD1, NSD2, NSD3, and ASH1L. We find that H3K36me2 is the most abundant of the three methylation states and is predominantly deposited at intergenic regions by NSD1, and partly by NSD2. In contrast, H3K36me1/3 are most abundant within exons and are positively correlated with gene expression. We demonstrate that while SETD2 deposits most H3K36me3, it may also deposit H3K36me2 within transcribed genes. Additionally, loss of SETD2 results in an increase of exonic H3K36me1, suggesting other (K36MTs) prime gene bodies with lower methylation states ahead of transcription. While NSD1/2 establish broad intergenic H3K36me2 domains, NSD3 deposits H3K36me2 peaks on active promoters and enhancers. Meanwhile, the activity of ASH1L is restricted to the regulatory elements of developmentally relevant genes, and our analyses implicate PBX2 as a potential recruitment factor. CONCLUSIONS Within genes, SETD2 primarily deposits H3K36me3, while the other K36MTs deposit H3K36me1/2 independently of SETD2 activity. For the deposition of H3K36me1/2, we find a hierarchy of K36MT activities where NSD1 > NSD2 > NSD3 > ASH1L. While NSD1 and NSD2 are responsible for most genome-wide propagation of H3K36me2, the activities of NSD3 and ASH1L are confined to active regulatory elements.
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Affiliation(s)
- Gerry A Shipman
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Reinnier Padilla
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Cynthia Horth
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Bo Hu
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Eric Bareke
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Francisca N Vitorino
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joanna M Gongora
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Benjamin A Garcia
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada.
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada.
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3
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Mellis IA, Melzer ME, Bodkin N, Goyal Y. Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells. Genome Biol 2024; 25:217. [PMID: 39135102 PMCID: PMC11320884 DOI: 10.1186/s13059-024-03351-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Cells and tissues have a remarkable ability to adapt to genetic perturbations via a variety of molecular mechanisms. Nonsense-induced transcriptional compensation, a form of transcriptional adaptation, has recently emerged as one such mechanism, in which nonsense mutations in a gene trigger upregulation of related genes, possibly conferring robustness at cellular and organismal levels. However, beyond a handful of developmental contexts and curated sets of genes, no comprehensive genome-wide investigation of this behavior has been undertaken for mammalian cell types and conditions. How the regulatory-level effects of inherently stochastic compensatory gene networks contribute to phenotypic penetrance in single cells remains unclear. RESULTS We analyze existing bulk and single-cell transcriptomic datasets to uncover the prevalence of transcriptional adaptation in mammalian systems across diverse contexts and cell types. We perform regulon gene expression analyses of transcription factor target sets in both bulk and pooled single-cell genetic perturbation datasets. Our results reveal greater robustness in expression of regulons of transcription factors exhibiting transcriptional adaptation compared to those of transcription factors that do not. Stochastic mathematical modeling of minimal compensatory gene networks qualitatively recapitulates several aspects of transcriptional adaptation, including paralog upregulation and robustness to mutation. Combined with machine learning analysis of network features of interest, our framework offers potential explanations for which regulatory steps are most important for transcriptional adaptation. CONCLUSIONS Our integrative approach identifies several putative hits-genes demonstrating possible transcriptional adaptation-to follow-up on experimentally and provides a formal quantitative framework to test and refine models of transcriptional adaptation.
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Affiliation(s)
- Ian A Mellis
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| | - Madeline E Melzer
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Nicholas Bodkin
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- CZ Biohub Chicago, LLC, Chicago, IL, USA.
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4
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Ma S, Long G, Jiang Z, Zhang Y, Sun L, Pan Y, You Q, Guo X. Recent advances in targeting histone H3 lysine 36 methyltransferases for cancer therapy. Eur J Med Chem 2024; 274:116532. [PMID: 38805937 DOI: 10.1016/j.ejmech.2024.116532] [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: 04/09/2024] [Revised: 05/14/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024]
Abstract
Histone H3 lysine 36 (H3K36) methylation is a typical epigenetic histone modification that is involved in various biological processes such as DNA transcription, repair and recombination in vivo. Mutations, translocations, and aberrant gene expression associated with H3K36 methyltransferases have been implicated in different malignancies such as acute myeloid leukemia, lung cancer, multiple myeloma, and others. Herein, we provided a comprehensive overview of the latest advances in small molecule inhibitors targeting H3K36 methyltransferases. We analyzed the structures and biological functions of the H3K36 methyltransferases family members. Additionally, we discussed the potential directions for future development of inhibitors targeting H3K36 methyltransferases.
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Affiliation(s)
- Sai Ma
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Guanlu Long
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Zheng Jiang
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Yan Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Liangkui Sun
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Yun Pan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Xiaoke Guo
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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5
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Mabe NW, Perry JA, Malone CF, Stegmaier K. Pharmacological targeting of the cancer epigenome. NATURE CANCER 2024; 5:844-865. [PMID: 38937652 DOI: 10.1038/s43018-024-00777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
Epigenetic dysregulation is increasingly appreciated as a hallmark of cancer, including disease initiation, maintenance and therapy resistance. As a result, there have been advances in the development and evaluation of epigenetic therapies for cancer, revealing substantial promise but also challenges. Three epigenetic inhibitor classes are approved in the USA, and many more are currently undergoing clinical investigation. In this Review, we discuss recent developments for each epigenetic drug class and their implications for therapy, as well as highlight new insights into the role of epigenetics in cancer.
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Affiliation(s)
- Nathaniel W Mabe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jennifer A Perry
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Clare F Malone
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
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6
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Mellis IA, Bodkin N, Melzer ME, Goyal Y. Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553318. [PMID: 37645989 PMCID: PMC10462021 DOI: 10.1101/2023.08.14.553318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Cells and tissues have a remarkable ability to adapt to genetic perturbations via a variety of molecular mechanisms. Nonsense-induced transcriptional compensation, a form of transcriptional adaptation, has recently emerged as one such mechanism, in which nonsense mutations in a gene can trigger upregulation of related genes, possibly conferring robustness at cellular and organismal levels. However, beyond a handful of developmental contexts and curated sets of genes, to date, no comprehensive genome-wide investigation of this behavior has been undertaken for mammalian cell types and contexts. Moreover, how the regulatory-level effects of inherently stochastic compensatory gene networks contribute to phenotypic penetrance in single cells remains unclear. Here we combine computational analysis of existing datasets with stochastic mathematical modeling and machine learning to uncover the widespread prevalence of transcriptional adaptation in mammalian systems and the diverse single-cell manifestations of minimal compensatory gene networks. Regulon gene expression analysis of a pooled single-cell genetic perturbation dataset recapitulates important model predictions. Our integrative approach uncovers several putative hits-genes demonstrating possible transcriptional adaptation-to follow up on experimentally, and provides a formal quantitative framework to test and refine models of transcriptional adaptation.
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Affiliation(s)
- Ian A. Mellis
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Nicholas Bodkin
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madeline E. Melzer
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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7
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Shipman GA, Padilla R, Horth C, Hu B, Bareke E, Vitorino FN, Gongora JM, Garcia BA, Lu C, Majewski J. Systematic perturbations of SETD2, NSD1, NSD2, NSD3 and ASH1L reveals their distinct contributions to H3K36 methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559313. [PMID: 37905045 PMCID: PMC10614729 DOI: 10.1101/2023.09.27.559313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Background Methylation of histone 3 lysine 36 (H3K36me) has emerged as an essential epigenetic component for the faithful regulation of gene expression. Despite its importance in development, disease, and cancer, how the molecular agents collectively shape the H3K36me landscape is unclear. Results We use a mouse mesenchymal stem cell model to perturb the H3K36me deposition machinery and infer the activities of the five most prominent players: SETD2, NSD1, NSD2, NSD3, and ASH1L. We find that H3K36me2 is the most abundant of the three methylation states and is predominantly deposited at intergenic regions by NSD1, and partly by NSD2. In contrast, H3K36me1/3 are most abundant within exons and are positively correlated with gene expression. We demonstrate that while SETD2 deposits most H3K36me3, it also deposits H3K36me2 within transcribed genes. Additionally, loss of SETD2 results in an increase of exonic H3K36me1, suggesting other H3K36 methyltransferases (K36MTs) prime gene bodies with lower methylation states ahead of transcription. Through a reductive approach, we uncover the distribution patterns of NSD3- and ASH1L-catalyzed H3K36me2. While NSD1/2 establish broad intergenic H3K36me2 domains, NSD3 deposits H3K36me2 peaks on active promoters and enhancers. Meanwhile, the activity of ASH1L is restricted to the regulatory elements of developmentally relevant genes, and our analyses implicate PBX2 as a potential recruitment factor. Conclusions Within genes, SETD2 deposits both H3K36me2/3, while the other K36MTs are capable of depositing H3K36me1/2 independently of SETD2 activity. For the deposition of H3K36me1/2, we find a hierarchy of K36MT activities where NSD1>NSD2>NSD3>ASH1L. While NSD1 and NSD2 are responsible for most genome-wide propagation of H3K36me2, the activities of NSD3 and ASH1L are confined to active regulatory elements.
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8
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Al-Harthi S, Li H, Winkler A, Szczepski K, Deng J, Grembecka J, Cierpicki T, Jaremko Ł. MRG15 activates histone methyltransferase activity of ASH1L by recruiting it to the nucleosomes. Structure 2023; 31:1200-1207.e5. [PMID: 37527654 DOI: 10.1016/j.str.2023.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/16/2023] [Accepted: 07/05/2023] [Indexed: 08/03/2023]
Abstract
ASH1L is a histone methyltransferase that regulates gene expression through methylation of histone H3 on lysine K36. While the catalytic SET domain of ASH1L has low intrinsic activity, several studies found that it can be vastly enhanced by the interaction with MRG15 protein and proposed allosteric mechanism of releasing its autoinhibited conformation. Here, we found that full-length MRG15, but not the MRG domain alone, can enhance the activity of the ASH1L SET domain. In addition, we showed that catalytic activity of MRG15-ASH1L depends on nucleosome binding mediated by MRG15 chromodomain. We found that in solution MRG15 binds to ASH1L, but has no impact on the conformation of the SET domain autoinhibitory loop or the S-adenosylmethionine cofactor binding site. Moreover, MRG15 binding did not impair the potency of small molecule inhibitors of ASH1L. These findings suggest that MRG15 functions as an adapter that enhances ASH1L catalytic activity by recruiting nucleosome substrate.
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Affiliation(s)
- Samah Al-Harthi
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Bioscience Program, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Hao Li
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Alyssa Winkler
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Kacper Szczepski
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Bioscience Program, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Jing Deng
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA.
| | - Łukasz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Bioscience Program, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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Batista MDP, Roffé M, Romero I, López-Guerrero JA, Illueca C, Lopez R, Balieiro Anastácio da Costa AA, De Brot L, Molina JP, Barboza L, Peria FM, Chaud F, Gouvêa Yamada AS, Poveda A, Rego EM. Genomic landscapes of ovarian clear cell carcinoma from latin countries reveal aberrations linked to survival and progression. BMC Cancer 2023; 23:613. [PMID: 37400764 DOI: 10.1186/s12885-023-11095-8] [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: 11/22/2022] [Accepted: 06/21/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Ovarian clear cell carcinomas (OCCCs) are rare, aggressive and chemoresistant tumors. Geographical and ethnic differences in the incidence of OCCC have been reported with a higher incidence in Asiatic countries. There is a paucity of information regarding OCCC in Latin America (LA) and other countries. METHODS Here, we characterized two cohorts of 33 patients with OCCC from LA (24 from Brazil and 9 from Costa Rica) and a cohort of 27 patients from Spain. Genomic analysis was performed for 26 OCCC using the OncoScan platform. Tumors were classified according to their genomic landscapes into subgroups. Clinical parameters were related to the frequency of genomic aberrations. RESULTS The median overall survival (OS) was not significantly different between the cohorts. Genomic landscapes were characterized by different homologous recombination deficiency (HRD) levels. No difference in the distribution of genomic landscapes profiles was detected between patients from the different cohorts. OCCCs with MYC-amplified tumors harboring a concomitant loss of a region in chromosome 13q12-q13 that includes the BRCA2 gene had the longest OS. In contrast, patients carrying a high number (> 30) of total copy number (CN) aberrations with no concomitant alterations in MYC and BRCA2 genes presented the shortest OS. Furthermore, amplification of the ASH1L gene was also associated with a shorter OS. Initial-stage OCCCs with early progression were characterized by gains in the JNK1 and MKL1 genes. CONCLUSIONS Our results provide new data from understudied OCCC populations and reveal new potential markers for OCCCs.
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Affiliation(s)
- Mariana de Paiva Batista
- Department of Internal Medicine, Medical School of Ribeirão Preto and Center for Cell Based Therapy, University of São Paulo, 14051-140, Tenente Catao Roxo, 2501, Ribeirão Preto, Brazil.
| | - Martín Roffé
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Ignacio Romero
- Gynecological Oncology Area, Valencian Institute of Oncology Foundation, Valencia, Spain
| | | | - Carmen Illueca
- Gynecological Oncology Area, Valencian Institute of Oncology Foundation, Valencia, Spain
| | - Raquel Lopez
- Gynecological Oncology Area, Valencian Institute of Oncology Foundation, Valencia, Spain
| | | | - Louise De Brot
- Department of Pathology, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Juan Pablo Molina
- Medical Oncology Service, México Hospital, CCSS, San José, Costa Rica
| | - Laura Barboza
- Pathological Anatomy Service, San Juan de Dios Hospital, San José, Costa Rica
| | - Fernanda Maris Peria
- Department of Internal Medicine, Medical School of Ribeirão Preto and Center for Cell Based Therapy, University of São Paulo, 14051-140, Tenente Catao Roxo, 2501, Ribeirão Preto, Brazil
| | - Fernando Chaud
- Department of Internal Medicine, Medical School of Ribeirão Preto and Center for Cell Based Therapy, University of São Paulo, 14051-140, Tenente Catao Roxo, 2501, Ribeirão Preto, Brazil
| | - Ana Silvia Gouvêa Yamada
- Department of Internal Medicine, Medical School of Ribeirão Preto and Center for Cell Based Therapy, University of São Paulo, 14051-140, Tenente Catao Roxo, 2501, Ribeirão Preto, Brazil
| | - Andres Poveda
- Oncogynecologic Department, Quironsalud Hospital, Valencia, Spain
| | - Eduardo Magalhães Rego
- Department of Internal Medicine, Medical School of Ribeirão Preto and Center for Cell Based Therapy, University of São Paulo, 14051-140, Tenente Catao Roxo, 2501, Ribeirão Preto, Brazil
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10
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Czerwinska P, Mackiewicz AA. Bromodomain (BrD) Family Members as Regulators of Cancer Stemness-A Comprehensive Review. Int J Mol Sci 2023; 24:995. [PMID: 36674511 PMCID: PMC9861003 DOI: 10.3390/ijms24020995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Epigenetic mechanisms involving DNA methylation and chromatin modifications have emerged as critical facilitators of cancer heterogeneity, substantially affecting cancer development and progression, modulating cell phenotypes, and enhancing or inhibiting cancer cell malignant properties. Not surprisingly, considering the importance of epigenetic regulators in normal stem cell maintenance, many chromatin-related proteins are essential to maintaining the cancer stem cell (CSC)-like state. With increased tumor-initiating capacities and self-renewal potential, CSCs promote tumor growth, provide therapy resistance, spread tumors, and facilitate tumor relapse after treatment. In this review, we characterized the epigenetic mechanisms that regulate the acquisition and maintenance of cancer stemness concerning selected epigenetic factors belonging to the Bromodomain (BrD) family of proteins. An increasing number of BrD proteins reinforce cancer stemness, supporting the maintenance of the cancer stem cell population in vitro and in vivo via the utilization of distinct mechanisms. As bromodomain possesses high druggable potential, specific BrD proteins might become novel therapeutic targets in cancers exhibiting de-differentiated tumor characteristics.
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Affiliation(s)
- Patrycja Czerwinska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Andrzej Adam Mackiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
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11
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Yu M, Jia Y, Ma Z, Ji D, Wang C, Liang Y, Zhang Q, Yi H, Zeng L. Structural insight into ASH1L PHD finger recognizing methylated histone H3K4 and promoting cell growth in prostate cancer. Front Oncol 2022; 12:906807. [PMID: 36033518 PMCID: PMC9399681 DOI: 10.3389/fonc.2022.906807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
ASH1L is a member of the Trithorax-group protein and acts as a histone methyltransferase for gene transcription activation. It is known that ASH1L modulates H3K4me3 and H3K36me2/3 at its gene targets, but its specific mechanism of histone recognition is insufficiently understood. In this study, we found that the ASH1L plant homeodomain (PHD) finger interacts with mono-, di-, and trimethylated states of H3K4 peptides with comparable affinities, indicating that ASH1L PHD non-selectively binds to all three methylation states of H3K4. We solved nuclear magnetic resonance structures picturing the ASH1L PHD finger binding to the dimethylated H3K4 peptide and found that a narrow binding groove and residue composition in the methylated-lysine binding pocket restricts the necessary interaction with the dimethyl-ammonium moiety of K4. In addition, we found that the ASH1L protein is overexpressed in castrate-resistant prostate cancer (PCa) PC3 and DU145 cells in comparison to PCa LNCaP cells. The knockdown of ASH1L modulated gene expression and cellular pathways involved in apoptosis and cell cycle regulation and consequently induced cell cycle arrest, cell apoptosis, and reduced colony-forming abilities in PC3 and DU145 cells. The overexpression of the C-terminal core of ASH1L but not the PHD deletion mutant increased the overall H3K36me2 level but had no effect on the H3K4me2/3 level. Overall, our study identifies the ASH1L PHD finger as the first native reader that non-selectively recognizes the three methylation states of H3K4. Additionally, ASH1L is required for the deregulation of cell cycle and survival in PCas.
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Affiliation(s)
- Miaomiao Yu
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, China
- International Center of Future Science, Jilin University, Changchun, China
| | - Yanjie Jia
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, China
| | - Zhanchuan Ma
- Central Laboratory, The First Hospital, Jilin University, Changchun, China
| | - Donglei Ji
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, China
- International Center of Future Science, Jilin University, Changchun, China
| | - Chunyu Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, China
| | - Yingying Liang
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, China
- International Center of Future Science, Jilin University, Changchun, China
| | - Qiang Zhang
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, China
| | - Huanfa Yi
- Central Laboratory, The First Hospital, Jilin University, Changchun, China
- *Correspondence: Huanfa Yi, ; Lei Zeng,
| | - Lei Zeng
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, China
- International Center of Future Science, Jilin University, Changchun, China
- *Correspondence: Huanfa Yi, ; Lei Zeng,
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12
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Feoli A, Viviano M, Cipriano A, Milite C, Castellano S, Sbardella G. Lysine methyltransferase inhibitors: where we are now. RSC Chem Biol 2022; 3:359-406. [PMID: 35441141 PMCID: PMC8985178 DOI: 10.1039/d1cb00196e] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/10/2021] [Indexed: 12/14/2022] Open
Abstract
Protein lysine methyltransferases constitute a large family of epigenetic writers that catalyse the transfer of a methyl group from the cofactor S-adenosyl-l-methionine to histone- and non-histone-specific substrates. Alterations in the expression and activity of these proteins have been linked to the genesis and progress of several diseases, including cancer, neurological disorders, and growing defects, hence they represent interesting targets for new therapeutic approaches. Over the past two decades, the identification of modulators of lysine methyltransferases has increased tremendously, clarifying the role of these proteins in different physio-pathological states. The aim of this review is to furnish an updated outlook about the protein lysine methyltransferases disclosed modulators, reporting their potency, their mechanism of action and their eventual use in clinical and preclinical studies.
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Affiliation(s)
- Alessandra Feoli
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Monica Viviano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Alessandra Cipriano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Ciro Milite
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Sabrina Castellano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Gianluca Sbardella
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
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13
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Chen S, Tu Y, Yuan H, Shi Z, Guo Y, Gong W, Tu S. Regulatory functions of miR‑200b‑3p in tumor development (Review). Oncol Rep 2022; 47:96. [PMID: 35322861 PMCID: PMC8968761 DOI: 10.3892/or.2022.8307] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/11/2022] [Indexed: 01/01/2023] Open
Abstract
MicroRNAs (miRNAs/miRs), non‑coding single‑stranded RNAs of length 18‑24 nucleotides, can modulate gene expression through post‑transcriptional control. As such, they can influence tumor proliferation, apoptosis, invasion, metastasis as well as chemotherapy resistance by regulating certain downstream genes. In this context, miR‑200b‑3p, one particular member of the miR‑200 family, possesses the ability to suppress tumor progression. However, many studies have suggested that, in certain cases, this miRNA may also promote the development of some tumors due to differences in the microenvironments and molecular backgrounds of different cancers. This review summarizes previous studies on the involvement of miR‑200b‑3p in tumors, including the underlying mechanism.
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Affiliation(s)
- Sheng Chen
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang 310014, P.R. China
| | - Yifeng Tu
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Hang Yuan
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang 310014, P.R. China
| | - Zhan Shi
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Yang Guo
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang 310014, P.R. China
| | - Wenjing Gong
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang 310014, P.R. China
| | - Shiliang Tu
- General Surgery, Cancer Center, Department of Colorectal Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, Zhejiang 310014, P.R. China
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14
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Fuziwara CS, de Mello DC, Kimura ET. Gene Editing with CRISPR/Cas Methodology and Thyroid Cancer: Where Are We? Cancers (Basel) 2022; 14:cancers14030844. [PMID: 35159110 PMCID: PMC8834610 DOI: 10.3390/cancers14030844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary The advent of genomic editing with CRISPR/Cas9 has transformed the way we manipulate the genome, and has facilitated the investigation of tumor cell biology in vitro and in vivo. Not only we can modify genome sequence to blunt an overactivated gene or correct a mutation, but also we may modulate gene expression using CRISPR/Cas system. In this review, we present the basics of CRISPR/Cas methodology, its components and how to start a CRISPR/Cas experiment; Moreover, we present how CRISPR/Cas methodology has been applied to study the function of coding and noncoding genes in thyroid cancer and provided insights into cancer biology. Abstract Important advances on the role of genetic alterations in thyroid cancer have been achieved in the last two decades. One key reason is linked to the development of technical approaches that allowed for the mimicking of genetic alterations in vitro and in vivo and, more recently, the gene editing methodology. The CRISPR/Cas methodology has emerged as a tangible tool for editing virtually any DNA sequence in the genome. To induce a double-strand break and programmable gene editing, Cas9 endonuclease is guided by a single-guide RNA (sgRNA) that is complementary to the target sequence in DNA. The gene editing per se occurs as the cells repair the broken DNA and may erroneously change the original DNA sequence. In this review, we explore the principles of the CRISPR/Cas system to facilitate an understanding of the mainstream technique and its applications in gene editing. Furthermore, we explored new applications of CRISPR/Cas for gene modulation without changing the DNA sequence and provided a Dry Lab experience for those who are interested in starting “CRISPRing” any given gene. In the last section, we will discuss the progress in the knowledge of thyroid cancer biology fostered by the CRISPR/Cas gene editing tools.
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Affiliation(s)
- Cesar Seigi Fuziwara
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Diego Claro de Mello
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
| | - Edna Teruko Kimura
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil
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A Pan-Cancer Study of KMT2 Family as Therapeutic Targets in Cancer. JOURNAL OF ONCOLOGY 2022; 2022:3982226. [PMID: 35058979 PMCID: PMC8766195 DOI: 10.1155/2022/3982226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022]
Abstract
Objective Exome sequencing studies have shown that the histone-lysine N-methyltransferase 2 (KMT2) gene is one of the most commonly mutated genes in a range of human malignancies and is linked to some of the most common and deadly solid tumors. However, the connection between this gene family's function and tumor type, immunological subtype, and molecular subtype dependency is still unknown. Methods We examine the expression patterns of the histone-lysine N-methyltransferase 2 (KMT2) gene, as well as their relationship to patient survival. We also used a pan-cancer analysis to link their function to immunological subtypes, the tumor microenvironment, and treatment sensitivity. Results Using the TCGA pan-cancer data, researchers looked at and examined KMT2 expression patterns and their links to patient survival and the tumor microenvironment in 33 cancer types. The expression of the KMT2 family changes significantly across and within cancer types, indicating significant inter- and intracancer heterogeneity. Patients' overall survival was often linked to the expression of KMT2 family members. However, the direction of the link differed depending on the KMT2 isoform and cancer type studied. Notably, in all cancer types examined, nearly all KMT2 family members were substantially linked with overall survival in patients with renal clear cell carcinoma (KIRC). Furthermore, all KMT2 genes have a strong relationship with immune infiltrate subtypes, as well as varying degrees of stromal cell infiltration and tumor cell stemness. Finally, we discovered that higher expression of KMT2s, particularly KMT2F and KMT2G, was linked to greater chemotherapeutic sensitivity in several cell lines. Conclusions The necessity to investigate each KMT2 member as a distinct entity inside each particular cancer type is highlighted by our comprehensive investigation of KMT2 gene expression and its relationship with immune infiltrates, tumor microenvironment, and cancer patient outcomes. Our research also confirmed the identification of KMT2 as a potential therapeutic target in cancer, but further laboratory testing is required.
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16
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Paulsson JO, Zedenius J, Juhlin CC. TERT Promoter Mutated Follicular Thyroid Carcinomas Exhibit a Distinct microRNA Expressional Profile with Potential Implications for Tumor Progression. Endocr Pathol 2021; 32:513-516. [PMID: 34676499 PMCID: PMC8608760 DOI: 10.1007/s12022-021-09695-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 12/23/2022]
Affiliation(s)
- Johan O Paulsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Zedenius
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Breast, Endocrine Tumors and Sarcoma, Karolinska University Hospital, Stockholm, Sweden
| | - C Christofer Juhlin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden.
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17
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Chen W, Zhong M, Yu J, Xie R, Zhou T, Zhang S, Xiong C, Huang D. KMT2B promotes SHPRH expression to regulate 131I sensitivity in thyroid carcinoma cells by affecting FYN protein stability. Cell Signal 2021; 88:110165. [PMID: 34606908 DOI: 10.1016/j.cellsig.2021.110165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022]
Abstract
Radioiodine (131I) is one of the most well-known and widely used targeted therapies. In thyroid carcinoma (THCA), it has been applied for more than eight decades and is still being utilized to eliminate remnants after resection and to reduce tumor metastases. Here, we aimed to investigate if lysine methyltransferase 2B (KMT2B) silencing could confer 131I resistance to THCA cells and the epigenetic mechanism behind. RT-qPCR, immunohistochemistry and western blot revealed that KMT2B was poorly expressed in THCA cells, and 131I resistance of cells led to a further decrease in KMT2B expression. EdU, colony formation, TUNEL, and tumor growth and metastasis assays showed that overexpression of KMT2B sensitized THCA cell to 131I and inhibited cell growth and metastasis. Further bioinformatics prediction and functional assay validation revealed that KMT2B elevated SHPRH expression via H3K4me3 modification in the SHPRH promoter, and that SHPRH modulated FYN ubiquitination, thereby promoting its protein degradation. We finally proved that the 131I-resistant cells regained resistance to 131I by FYN overexpression in the presence of KMT2B overexpression in vitro and in vivo. Therefore, we conclude that the overexpression of KMT2B represents a potential target for THCA therapy.
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Affiliation(s)
- Wanzhi Chen
- Department of Thyroid Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, PR China.
| | - Meijun Zhong
- Department of Thyroid Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, PR China
| | - Jichun Yu
- Department of Thyroid Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, PR China
| | - Rong Xie
- Department of Thyroid Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, PR China
| | - Tao Zhou
- Department of Thyroid Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, PR China
| | - Shuyong Zhang
- Department of Thyroid Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, PR China
| | - Chengfeng Xiong
- Department of Thyroid Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, PR China
| | - Da Huang
- Department of Thyroid Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, PR China
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18
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Zhu J, Liu C, Wang D, Cao X, Wang S, Liu Y, Wang J, Li P, He Q. The Emerging Landscapes of Long Noncoding RNA in Thyroid Carcinoma: Biological Functions and Clinical Significance. Front Oncol 2021; 11:706011. [PMID: 34447696 PMCID: PMC8383148 DOI: 10.3389/fonc.2021.706011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022] Open
Abstract
Thyroid carcinoma (TC) is one of the most prevalent primary endocrine tumors, and its incidence is steadily and gradually increasing worldwide. Accumulating evidence has revealed the critical functions of long noncoding RNAs (lncRNAs) in the tumorigenesis and development of TC. Many TC-associated lncRNAs have been documented to be implicated in TC malignant behaviors, including abnormal cell proliferation, enhanced stem cell properties and aggressiveness, and resistance to therapeutics, through interaction with proteins, DNA, or RNA or encoding small peptides. Therefore, further elucidating the lncRNA dysregulation sheds additional insights into TC tumorigenesis and progression and opens new avenues for the early diagnosis and clinical therapy of TC. In this review, we summarize the abnormal expression of lncRNA in TC and the fundamental characteristics in TC tumorigenesis and development. Additionally, we introduce the potential prognostic and therapeutic significance of lncRNAs in TC.
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Affiliation(s)
- Jian Zhu
- The First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
- Department of Thyroid and Breast Surgery, The 960th Hospital of the Chinese People’s Liberation Army, Jinan, China
| | - Changrui Liu
- Department of Thyroid and Breast Surgery, The 960th Hospital of the Chinese People’s Liberation Army, Jinan, China
| | - Dan Wang
- Department of Thyroid and Breast Surgery, The 960th Hospital of the Chinese People’s Liberation Army, Jinan, China
| | - Xianjiao Cao
- The First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shuai Wang
- The First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yixin Liu
- The First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jun Wang
- The First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Peifeng Li
- Department of Pathology, The 960th Hospital of the Chinese People’s Liberation Army, Jinan, China
| | - Qingqing He
- Department of Thyroid and Breast Surgery, The 960th Hospital of the Chinese People’s Liberation Army, Jinan, China
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Poorly Differentiated and Anaplastic Thyroid Cancer: Insights into Genomics, Microenvironment and New Drugs. Cancers (Basel) 2021; 13:cancers13133200. [PMID: 34206867 PMCID: PMC8267688 DOI: 10.3390/cancers13133200] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary In the last decades, many researchers produced promising data concerning genetics and tumor microenvironment of poorly differentiated thyroid cancer (PDTC) and anaplastic thyroid cancer (ATC). They are trying to tear the veil covering these orphan cancers, suggesting new therapeutic weapons as single or combined therapies. Abstract PDTC and ATC present median overall survival of 6 years and 6 months, respectively. In spite of their rarity, patients with PDTC and ATC represent a significant clinical problem, because of their poor survival and the substantial inefficacy of classical therapies. We reviewed the newest findings about genetic features of PDTC and ATC, from mutations occurring in DNA to alterations in RNA. Therefore, we describe their tumor microenvironments (both immune and not-immune) and the interactions between tumor and neighboring cells. Finally, we recapitulate how this upcoming evidence are changing the treatment of PDTC and ATC.
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20
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Zhao H, De Souza C, Kumar VE, Nambiar R, Hao D, Zhu X, Luo Y, Liu S, Zhang L, Zhu J. Long non-coding RNA signatures as predictors of prognosis in thyroid cancer: a narrative review. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:359. [PMID: 33708986 PMCID: PMC7944284 DOI: 10.21037/atm-20-8191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/26/2021] [Indexed: 02/05/2023]
Abstract
Thyroid cancer (TC) is the most common endocrine malignancy, with high incidence rates in recent decades. Most TC cases have good prognoses, but a high risk of recurrence and metastases poses challenges, especially for patients with high-risk factors. Currently used prognostic markers for TC involve a combination of genetic factors and overexpressed proteins. Long non-coding RNAs (lncRNAs) regulate several integral biologic processes by playing key roles in the transcription of several downstream targets maintaining cellular behavior. Prior studies have revealed that lncRNAs promote tumor cell proliferation, invasion, metastasis, and angiogenesis, making them important targets for therapeutic intervention in cancer. While the exact molecular mechanisms underlying the role of lncRNAs in modulating TC progression and recurrence is still unclear, it is important to note that some lncRNAs are upregulated in certain cancers, while others are downregulated. In the present study, we review several key lncRNAs, their association with cancer progression, and the important roles they may play as tumor suppressors or tumor promoters in tumorigenesis. We discuss the potential mechanisms of lncRNA-mediated pathogenesis that can be targeted for the treatment of TC, the existing and potential benefits of using lncRNAs as diagnostic and prognostic measures for cancer detection, and tumor burden in patients.
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Affiliation(s)
- Hongyuan Zhao
- Department of Thyroid and Parathyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Cristabelle De Souza
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Sacramento, CA, USA
- Institute for Regenerative Medicine and Stem Cell Research, Stanford University, Stanford, CA, USA
| | - Vigneshwari Easwar Kumar
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Sacramento, CA, USA
| | - Roshni Nambiar
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Sacramento, CA, USA
| | - Dake Hao
- Department of Surgery, School of Medicine, University of California, Sacramento, CA, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, Sacramento, CA, USA
| | - Xiaofeng Zhu
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yi Luo
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Shengshan Liu
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Lingyun Zhang
- Department of Thyroid and Parathyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiang Zhu
- Department of Thyroid and Parathyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
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21
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Na K, Kim M, Kim CY, Lim JS, Cho JY, Shin H, Lee HJ, Kang BJ, Han DH, Kim H, Baik JH, Swiatek-de Lange M, Karl J, Paik YK. Potential Regulatory Role of Human-Carboxylesterase-1 Glycosylation in Liver Cancer Cell Growth. J Proteome Res 2020; 19:4867-4883. [PMID: 33206527 DOI: 10.1021/acs.jproteome.0c00787] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We previously reported that human carboxylesterase 1 (CES1), a serine esterase containing a unique N-linked glycosyl group at Asn79 (N79 CES1), is a candidate serological marker of hepatocellular carcinoma (HCC). CES1 is normally present at low-to-undetectable levels in normal human plasma, HCC tumors, and major liver cancer cell lines. To investigate the potential mechanism underlying the suppression of CES1 expression in liver cancer cells, we took advantage of the low detectability of this marker in tumors by overexpressing CES1 in multiple HCC cell lines, including stable Hep3B cells. We found that the population of CES1-overexpressing (OE) cells decreased and that their doubling time was longer compared with mock control liver cancer cells. Using interactive transcriptome, proteome, and subsequent Gene Ontology enrichment analysis of CES1-OE cells, we found substantial decreases in the expression levels of genes involved in cell cycle regulation and proliferation. This antiproliferative function of the N79 glycan of CES1 was further supported by quantitative real-time polymerase chain reaction, flow cytometry, and an apoptosis protein array assay. An analysis of the levels of key signaling target proteins via Western blotting suggested that CES1 overexpression exerted an antiproliferative effect via the PKD1/PKCμ signaling pathway. Similar results were also seen in another HCC cell line (PLC/RFP/5) after transient transfection with CES1 but not in similarly treated non-HCC cell lines (e.g., HeLa and Tera-1 cells), suggesting that CES1 likely exerts a liver cell-type-specific suppressive effect. Given that the N-linked glycosyl group at Asn79 (N79 glycan) of CES1 is known to influence CES1 enzyme activity, we hypothesized that the post-translational modification of CES1 at N79 may be linked to its antiproliferative activity. To investigate the regulatory effect of the N79 glycan on cellular growth, we mutated the single N-glycosylation site in CES1 from Asn to Gln (CES1-N79Q) via site-directed mutagenesis. Fluorescence 2-D difference gel electrophoresis protein expression analysis of cell lysates revealed an increase in cell growth and a decrease in doubling time in cells carrying the N79Q mutation. Thus our results suggest that CES1 exerts an antiproliferative effect in liver cancer cells and that the single N-linked glycosylation at Asn79 plays a potential regulatory role. These functions may underlie the undetectability of CES1 in human HCC tumors and liver cancer cell lines. Mass spectrometry data are available via ProteomeXchange under the identifier PXD021573.
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Affiliation(s)
- Keun Na
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
| | - Minjoo Kim
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
| | - Chae-Yeon Kim
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
| | - Jong-Sun Lim
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
| | - Jin-Young Cho
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
| | - Heon Shin
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
| | - Hyo Jin Lee
- Department of Life Sciences, Korea University, 145 Anamro, Seongbuk-ku, Seoul 02841, South Korea
| | - Byeong Jun Kang
- Department of Life Sciences, Korea University, 145 Anamro, Seongbuk-ku, Seoul 02841, South Korea
| | | | | | - Ja-Hyun Baik
- Department of Life Sciences, Korea University, 145 Anamro, Seongbuk-ku, Seoul 02841, South Korea
| | | | - Johann Karl
- Roche Diagnostics, GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University, 50 Yonsei-ro, Seodaemoon-ku, Seoul 03722, South Korea
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Cui LX, Tian YQ, Hao HS, Zou HY, Pang YW, Zhao SJ, Zhao XM, Zhu HB, Du WH. Knockdown of ASH1L methyltransferase induced apoptosis inhibiting proliferation and H3K36 methylation in bovine cumulus cells. Theriogenology 2020; 161:65-73. [PMID: 33296745 DOI: 10.1016/j.theriogenology.2020.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/11/2020] [Accepted: 11/14/2020] [Indexed: 12/19/2022]
Abstract
This study aims to investigate the expression and function of absent, small, or homeotic 1-like (ASH1L) methyltransferase in bovine cumulus cells in order to reveal by which mechanisms ASH1L regulates epigenetic modification and apoptosis in cumulus cells. The location of ASH1L and the methylation pattern of H3K36 were detected using immunofluorescence staining in cumulus cells. Quantitative PCR (qPCR) and western blotting were used to screen for effective siRNA targeting the ASH1L gene. Also, the mRNA expression levels of apoptosis-related genes and polycomb inhibitory complex genes were estimated by qPCR after knocking down the ASH1L gene in bovine cumulus cells. Cell proliferation and apoptosis were measured with the CCK-8 method and Annexin V-FITC by flow cytometry, respectively. The results of immunofluorescence analysis showed that ASH1L is located in the nucleus of bovine cumulus cells and is distributed in a dotted pattern. ASH1L knockdown in cumulus cells induced a decrease in the levels of H3K36me1/2/3 methylation (P < 0.05). Additionally, ASH1L knockdown inhibited cell proliferation, increased the apoptosis rate, and upregulated the expression of apoptosis genes CASPASE-3, BAX and BAX/BCL-2 ratio (P < 0.05). Meanwhile, the mRNA expression levels of EZH2 and SUZ12, two subunits of PRC2 protein, were increased in cells with ASH1L knockdown (P < 0.05). Therefore, the expression of ASH1L methyltransferase and its function in on the apoptosis of bovine cumulus cells were first studied. The mechanism by which ASH1L regulates the histone methylation and apoptosis in cumulus cells was also revealed.
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Affiliation(s)
- Li-Xin Cui
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ya-Qing Tian
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hai-Sheng Hao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui-Ying Zou
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yun-Wei Pang
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan-Jiang Zhao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue-Ming Zhao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hua-Bin Zhu
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei-Hua Du
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
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