1
|
Yokoyama A, Niida H, Kutateladze TG, Côté J. HBO1, a MYSTerious KAT and its links to cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195045. [PMID: 38851533 PMCID: PMC11330361 DOI: 10.1016/j.bbagrm.2024.195045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/27/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
The histone acetyltransferase HBO1, also known as KAT7, is a major chromatin modifying enzyme responsible for H3 and H4 acetylation. It is found within two distinct tetrameric complexes, the JADE subunit-containing complex and BRPF subunit-containing complex. The HBO1-JADE complex acetylates lysine 5, 8 and 12 of histone H4, and the HBO1-BRPF complex acetylates lysine 14 of histone H3. HBO1 regulates gene transcription, DNA replication, DNA damage repair, and centromere function. It is involved in diverse signaling pathways and plays crucial roles in development and stem cell biology. Recent work has established a strong relationship of HBO1 with the histone methyltransferase MLL/KMT2A in acute myeloid leukemia. Here, we discuss functional and pathological links of HBO1 to cancer, highlighting the underlying mechanisms that may pave the way to the development of novel anti-cancer therapies.
Collapse
Affiliation(s)
- Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata 997-0052, Japan.
| | - Hiroyuki Niida
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, United States of America.
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Oncology Division-CHU de Québec-UL Research Center, Laval University Cancer Research Center, Quebec City, QC G1R 3S3, Canada.
| |
Collapse
|
2
|
Ahn JY, Kim S, Rok Kim C, Lee JH, Kim JM, Klompstra TM, Ha Choi Y, Jeon Y, Na Y, Kim JS, Okada Y, Lee H, Kim IS, Kim JK, Koo BK, Baek SH. Dual function of PHF16 in reinstating homeostasis of murine intestinal epithelium after crypt regeneration. Dev Cell 2024:S1534-5807(24)00492-1. [PMID: 39232563 DOI: 10.1016/j.devcel.2024.08.009] [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: 06/11/2023] [Revised: 10/24/2023] [Accepted: 08/08/2024] [Indexed: 09/06/2024]
Abstract
Intestinal stem cells (ISCs) are highly vulnerable to damage, being in a constant state of proliferation. Reserve stem cells repair the intestinal epithelium following damage-induced ablation of ISCs. Here, we report that the epigenetic regulator plant homology domain (PHD) finger protein 16 (PHF16) restores homeostasis of the intestinal epithelium after initial damage-induced repair. In Phf16-/Y mice, revival stem cells (revSCs) showed defects in exiting the regenerative state, and intestinal crypt regeneration failed even though revSCs were still induced in response to tissue damage, as observed by single-cell RNA sequencing (scRNA-seq). Analysis of Phf16-/Y intestinal organoids by RNA sequencing (RNA-seq) and ATAC sequencing identified that PHF16 restores homeostasis of the intestinal epithelium by inducing retinoic acid receptor (RAR)/retinoic X receptor (RXR) target genes through HBO1-mediated histone H3K14 acetylation, while at the same time counteracting YAP/TAZ activity by ubiquitination of CDC73. Together, our findings demonstrate the importance of timely suppression of regenerative activity by PHF16 for the restoration of gut homeostasis after acute tissue injury.
Collapse
Affiliation(s)
- Jun-Yeong Ahn
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Seoul National University, Seoul 08826, South Korea; School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Somi Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Chang Rok Kim
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Seoul National University, Seoul 08826, South Korea; School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Ji-Hyun Lee
- Center for Genome Engineering, Institute for Basic Science, 55, Expo-ro, Yuseong-gu, Daejeon 34126, South Korea
| | - Jong Min Kim
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Seoul National University, Seoul 08826, South Korea; School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Thomas M Klompstra
- Center for Genome Engineering, Institute for Basic Science, 55, Expo-ro, Yuseong-gu, Daejeon 34126, South Korea
| | - Yoon Ha Choi
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Yoon Jeon
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, South Korea
| | - Yongwoo Na
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea; Center for RNA Research, Institute for Basic Science, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Yuki Okada
- Laboratory of Pathology and Development, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Ho Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, South Korea
| | - Ik Soo Kim
- Department of Microbiology, Gachon University College of Medicine, Incheon 21999, South Korea.
| | - Jong Kyoung Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea; Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Seoul 03722, South Korea.
| | - Bon-Kyoung Koo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea; Center for Genome Engineering, Institute for Basic Science, 55, Expo-ro, Yuseong-gu, Daejeon 34126, South Korea.
| | - Sung Hee Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Seoul National University, Seoul 08826, South Korea; School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
| |
Collapse
|
3
|
Lee K, Barone M, Waterbury AL, Jiang H, Nam E, DuBois-Coyne SE, Whedon SD, Wang ZA, Caroli J, Neal K, Ibeabuchi B, Dhoondia Z, Kuroda MI, Liau BB, Beck S, Mattevi A, Cole PA. Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1. Nat Chem Biol 2024:10.1038/s41589-024-01671-9. [PMID: 38965385 DOI: 10.1038/s41589-024-01671-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 06/07/2024] [Indexed: 07/06/2024]
Abstract
Biochemical crosstalk between two or more histone modifications is often observed in epigenetic enzyme regulation, but its functional significance in cells has been difficult to discern. Previous enzymatic studies revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine-specific demethylase 1 (LSD1). In the present study, we engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation. K562 cells with the Y391K LSD1 CRISPR knockin show decreased expression of a set of genes associated with cellular adhesion and myeloid leukocyte activation. Chromatin profiling revealed that the cis-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation, and edited K562 cells show diminished H3 mono-methyl Lys4 near these silenced genes, consistent with a role for enhanced LSD1 demethylase activity. These findings illuminate the functional consequences of disconnecting histone modification crosstalk for a key epigenetic enzyme.
Collapse
Affiliation(s)
- Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Marco Barone
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy
| | - Amanda L Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hanjie Jiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eunju Nam
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sarah E DuBois-Coyne
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Samuel D Whedon
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jonatan Caroli
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy
| | - Katherine Neal
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Brian Ibeabuchi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zuzer Dhoondia
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Samuel Beck
- Department of Dermatology, Boston University School of Medicine & Boston Medical Center, Boston, MA, USA.
| | - Andrea Mattevi
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy.
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
4
|
Gaurav N, Kanai A, Lachance C, Cox KL, Liu J, Grzybowski AT, Saksouk N, Klein BJ, Komata Y, Asada S, Ruthenburg AJ, Poirier MG, Côté J, Yokoyama A, Kutateladze TG. Guiding the HBO1 complex function through the JADE subunit. Nat Struct Mol Biol 2024; 31:1039-1049. [PMID: 38448574 PMCID: PMC11320721 DOI: 10.1038/s41594-024-01245-2] [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: 04/13/2023] [Accepted: 02/12/2024] [Indexed: 03/08/2024]
Abstract
JADE is a core subunit of the HBO1 acetyltransferase complex that regulates developmental and epigenetic programs and promotes gene transcription. Here we describe the mechanism by which JADE facilitates recruitment of the HBO1 complex to chromatin and mediates its enzymatic activity. Structural, genomic and complex assembly in vivo studies show that the PZP (PHD1-zinc-knuckle-PHD2) domain of JADE engages the nucleosome through binding to histone H3 and DNA and is necessary for the association with chromatin targets. Recognition of unmethylated H3K4 by PZP directs enzymatic activity of the complex toward histone H4 acetylation, whereas H3K4 hypermethylation alters histone substrate selectivity. We demonstrate that PZP contributes to leukemogenesis, augmenting transforming activity of the NUP98-JADE2 fusion. Our findings highlight biological consequences and the impact of the intact JADE subunit on genomic recruitment, enzymatic function and pathological activity of the HBO1 complex.
Collapse
Affiliation(s)
- Nitika Gaurav
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Akinori Kanai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Catherine Lachance
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, Québec, Canada
| | - Khan L Cox
- Department of Physics, Ohio State University, Columbus, OH, USA
| | - Jiuyang Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Adrian T Grzybowski
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Nehmé Saksouk
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, Québec, Canada
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Yosuke Komata
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Japan
| | - Shuhei Asada
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alexander J Ruthenburg
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | | | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, Québec, Canada.
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Japan.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.
| |
Collapse
|
5
|
Almalki WH, Almujri SS. The dual roles of circRNAs in Wnt/β-Catenin signaling and cancer progression. Pathol Res Pract 2024; 255:155132. [PMID: 38335783 DOI: 10.1016/j.prp.2024.155132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
Cancer, a complex pathophysiological condition, arises from the abnormal proliferation and survival of cells due to genetic mutations. Dysregulation of cell cycle control, apoptosis, and genomic stability contribute to uncontrolled growth and metastasis. Tumor heterogeneity, microenvironmental influences, and immune evasion further complicate cancer dynamics. The intricate interplay between circular RNAs (circRNAs) and the Wnt/β-Catenin signalling pathway has emerged as a pivotal axis in the landscape of cancer biology. The Wnt/β-Catenin pathway, a critical regulator of cell fate and proliferation, is frequently dysregulated in various cancers. CircRNAs, a class of non-coding RNAs with closed-loop structures, have garnered increasing attention for their diverse regulatory functions. This review systematically explores the intricate crosstalk between circRNAs and the Wnt/β-Catenin pathway, shedding light on their collective impact on cancer initiation and progression. The review explores the diverse mechanisms through which circRNAs modulate the Wnt/β-Catenin pathway, including sponging microRNAs, interacting with RNA-binding proteins, and influencing the expression of key components in the pathway. Furthermore, the review highlights specific circRNAs implicated in various cancer types, elucidating their roles as either oncogenic or tumour-suppressive players in the context of Wnt/β-Catenin signaling. The intricate regulatory networks formed by circRNAs in conjunction with the Wnt/β-Catenin pathway are discussed, providing insights into potential therapeutic targets and diagnostic biomarkers. This comprehensive review delves into the multifaceted roles of circRNAs in orchestrating tumorigenesis through their regulatory influence on the Wnt/β-Catenin pathway.
Collapse
Affiliation(s)
- Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Salem Salman Almujri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha 61421, Aseer, Saudi Arabia
| |
Collapse
|
6
|
White J, Derheimer FA, Jensen-Pergakes K, O'Connell S, Sharma S, Spiegel N, Paul TA. Histone lysine acetyltransferase inhibitors: an emerging class of drugs for cancer therapy. Trends Pharmacol Sci 2024; 45:243-254. [PMID: 38383216 DOI: 10.1016/j.tips.2024.01.010] [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: 01/05/2024] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/23/2024]
Abstract
Lysine acetyltransferases (KATs) are a family of epigenetic enzymes involved in the regulation of gene expression; they represent a promising class of emerging drug targets. The frequent molecular dysregulation of these enzymes, as well as their mechanistic links to biological functions that are crucial to cancer, have led to exploration around the development of small-molecule inhibitors against KATs. Despite early challenges, recent advances have led to the development of potent and selective enzymatic and bromodomain (BRD) KAT inhibitors. In this review we discuss the discovery and development of new KAT inhibitors and their application as oncology therapeutics. Additionally, new chemically induced proximity approaches are presented, offering opportunities for unique target selectivity profiles and tissue-specific targeting of KATs. Emerging clinical data for CREB binding protein (CREBBP)/EP300 BRD inhibitors and KAT6 catalytic inhibitors indicate the promise of this target class in cancer therapeutics.
Collapse
Affiliation(s)
- Jeffrey White
- Pfizer Inc., Oncology Research Unit, San Diego, CA 92121, USA
| | | | | | - Shawn O'Connell
- Pfizer Inc., Oncology Research Unit, San Diego, CA 92121, USA
| | - Shikhar Sharma
- Pfizer Inc., Oncology Research Unit, San Diego, CA 92121, USA
| | - Noah Spiegel
- Pfizer Inc., Oncology Research Unit, San Diego, CA 92121, USA
| | - Thomas A Paul
- Pfizer Inc., Oncology Research Unit, San Diego, CA 92121, USA.
| |
Collapse
|
7
|
Barbosa K, Deshpande A, Perales M, Xiang P, Murad R, Pramod AB, Minkina A, Robertson N, Schischlik F, Lei X, Sun Y, Brown A, Amend D, Jeremias I, Doench JG, Humphries RK, Ruppin E, Shendure J, Mali P, Adams PD, Deshpande AJ. Transcriptional control of leukemogenesis by the chromatin reader SGF29. Blood 2024; 143:697-712. [PMID: 38048593 PMCID: PMC10900139 DOI: 10.1182/blood.2023021234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023] Open
Abstract
ABSTRACT Aberrant expression of stem cell-associated genes is a common feature in acute myeloid leukemia (AML) and is linked to leukemic self-renewal and therapy resistance. Using AF10-rearranged leukemia as a prototypical example of the recurrently activated "stemness" network in AML, we screened for chromatin regulators that sustain its expression. We deployed a CRISPR-Cas9 screen with a bespoke domain-focused library and identified several novel chromatin-modifying complexes as regulators of the TALE domain transcription factor MEIS1, a key leukemia stem cell (LSC)-associated gene. CRISPR droplet sequencing revealed that many of these MEIS1 regulators coordinately controlled the transcription of several AML oncogenes. In particular, we identified a novel role for the Tudor-domain-containing chromatin reader protein SGF29 in the transcription of AML oncogenes. Furthermore, SGF29 deletion impaired leukemogenesis in models representative of multiple AML subtypes in multiple AML subtype models. Our studies reveal a novel role for SGF29 as a nononcogenic dependency in AML and identify the SGF29 Tudor domain as an attractive target for drug discovery.
Collapse
Affiliation(s)
- Karina Barbosa
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Anagha Deshpande
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Marlenne Perales
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Ping Xiang
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Rabi Murad
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Akula Bala Pramod
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Anna Minkina
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Neil Robertson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Fiorella Schischlik
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Xue Lei
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Younguk Sun
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Adam Brown
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Diana Amend
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, Munich, Germany
| | | | | | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, San Diego, CA
| | - Peter D. Adams
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| | - Aniruddha J. Deshpande
- Cancer Genome and Epigenetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA
| |
Collapse
|
8
|
Voutsadakis IA. Molecular Characteristics and Therapeutic Vulnerabilities of Claudin-low Breast Cancers Derived from Cell Line Models. Cancer Genomics Proteomics 2023; 20:539-555. [PMID: 37889067 PMCID: PMC10614063 DOI: 10.21873/cgp.20404] [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: 06/25/2023] [Revised: 08/16/2023] [Accepted: 08/28/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND/AIM Breast cancers constitute heterogeneous tumor groups and their categorization in subtypes based on the expression of the estrogen (ER), progesterone (PR) and HER2 receptors has advanced therapeutics. Claudin-low breast cancer has been proposed as an additional subtype which is mostly ER, PR and HER2 negative, but its identification has not led to corresponding specific treatments yet. MATERIALS AND METHODS Breast cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) were assessed for mRNA suppression of claudins and mRNA expression of ER and ERBB2 (the gene encoding HER2). The set of identified claudin-low cell lines were compared with representative ER-/ERBB2- cell lines for associated molecular alterations, gene dependencies through CRISPR and microRNA arrays and in vitro drug sensitivities using the Genomics of Drug Sensitivity in Cancer (GDSC) project. RESULTS Claudin-low cell lines display up-regulation of mRNA expression of epithelial to mesenchymal transition (EMT) regulators. Methylation sensitive genes are down-regulated in claudin-low lines compared with other cell lines, without associated up-regulation of DNA methyltransferases. Dependency screen microarrays reveal dependencies of claudin-low cell lines on components of the cytoskeleton but no consistent dependencies in known oncogenes or tumor suppressors. Potential drug sensitivities revealed in the drug screens included sensitivities to WNT pathway modulators, tyrosine kinase cascade inhibitors and BET inhibitors. On the other hand, claudin-low cell lines showed resistance to deacetylase inhibitors. CONCLUSION Claudin-low cell line models duplicate features of claudin-low breast cancers and may serve as guides for identification of drugs worth exploring for further development.
Collapse
Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste Marie, ON, Canada;
- Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, ON, Canada
| |
Collapse
|
9
|
Hu H, Muntean AG. The YEATS domain epigenetic reader proteins ENL and AF9 and their therapeutic value in leukemia. Exp Hematol 2023; 124:15-21. [PMID: 37295550 PMCID: PMC10527611 DOI: 10.1016/j.exphem.2023.06.001] [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: 04/07/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Recent studies have uncovered similarities and differences between 2 highly homologous epigenetic reading proteins, namely, ENL (MLLT1) and AF9 (MLLT3) with therapeutic implications. The importance of these proteins has traditionally been exemplified by their involvement in chromosomal translocations with the mixed-lineage leukemia gene (MLL; aka KMT2a). MLL rearrangements occur in a subset of acute leukemias and generate potent oncogenic MLL-fusion proteins that impact epigenetic and transcriptional regulation. Leukemic patients with MLL rearrangements display intermediate-to-poor prognoses, necessitating further mechanistic research. Several protein complexes involved in regulating RNA polymerase II transcription and the epigenetic landscape are hijacked in MLL-r leukemia, which include ENL and AF9. Recent biochemical studies have defined a highly homologous YEATS domain in ENL and AF9 that binds acylated histones, which aids in the localization and retention of these proteins to transcriptional targets. In addition, detailed characterization of the homologous ANC-1 homology domain (AHD) on ENL and AF9 revealed differential association with transcriptional activating and repressing complexes. Importantly, CRISPR knockout screens have demonstrated a unique role for wild-type ENL in leukemic stem cell function, whereas AF9 appears important for normal hematopoietic stem cells. In this perspective, we examine the ENL and AF9 proteins with attention to recent work characterizing the epigenetic reading YEATS domains and AHD on both wild-type proteins and when fused to MLL. We summarized the drug development efforts and their therapeutic potential and assess ongoing research that has refined our understanding of how these proteins function, which continues to reveal new therapeutic avenues.
Collapse
Affiliation(s)
- Hsiangyu Hu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Andrew G Muntean
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI.
| |
Collapse
|
10
|
Komata Y, Kanai A, Maeda T, Inaba T, Yokoyama A. MOZ/ENL complex is a recruiting factor of leukemic AF10 fusion proteins. Nat Commun 2023; 14:1979. [PMID: 37031220 PMCID: PMC10082848 DOI: 10.1038/s41467-023-37712-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 03/22/2023] [Indexed: 04/10/2023] Open
Abstract
Changes in the transcriptional machinery cause aberrant self-renewal of non-stem hematopoietic progenitors. AF10 fusions, such as CALM-AF10, are generated via chromosomal translocations, causing malignant leukemia. In this study, we demonstrate that AF10 fusion proteins cause aberrant self-renewal via ENL, which binds to MOZ/MORF lysine acetyltransferases (KATs). The interaction of ENL with MOZ, via its YEATS domain, is critical for CALM-AF10-mediated leukemic transformation. The MOZ/ENL complex recruits DOT1L/AF10 fusion complexes and maintains their chromatin retention via KAT activity. Therefore, inhibitors of MOZ/MORF KATs directly suppress the functions of AF10 fusion proteins, thereby exhibiting strong antitumor effects on AF10 translocation-induced leukemia. Combinatorial inhibition of MOZ/MORF and DOT1L cooperatively induces differentiation of CALM-AF10-leukemia cells. These results reveal roles for the MOZ/ENL complex as an essential recruiting factor of the AF10 fusion/DOT1L complex, providing a rationale for using MOZ/MORF KAT inhibitors in AF10 translocation-induced leukemia.
Collapse
Affiliation(s)
- Yosuke Komata
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata, 997-0052, Japan
| | - Akinori Kanai
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Hiroshima, 734-8553, Japan
| | - Takahiro Maeda
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, 812-8582, Japan
| | - Toshiya Inaba
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Hiroshima, 734-8553, Japan
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata, 997-0052, Japan.
| |
Collapse
|
11
|
Chromatin complex dependencies reveal targeting opportunities in leukemia. Nat Commun 2023; 14:448. [PMID: 36707513 PMCID: PMC9883437 DOI: 10.1038/s41467-023-36150-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Chromatin regulators are frequently mutated in human cancer and are attractive drug targets. They include diverse proteins that share functional domains and assemble into related multi-subunit complexes. To investigate functional relationships among these regulators, here we apply combinatorial CRISPR knockouts (KOs) to test over 35,000 gene-gene pairings in leukemia cells, using a library of over 300,000 constructs. Top pairs that demonstrate either compensatory non-lethal interactions or synergistic lethality enrich for paralogs and targets that occupy the same protein complex. The screen highlights protein complex dependencies not apparent in single KO screens, for example MCM histone exchange, the nucleosome remodeling and deacetylase (NuRD) complex, and HBO1 (KAT7) complex. We explore two approaches to NuRD complex inactivation. Paralog and non-paralog combinations of the KAT7 complex emerge as synergistic lethal and specifically nominate the ING5 PHD domain as a potential therapeutic target when paired with other KAT7 complex member losses. These findings highlight the power of combinatorial screening to provide mechanistic insight and identify therapeutic targets within redundant networks.
Collapse
|
12
|
Okuda H, Miyamoto R, Takahashi S, Kawamura T, Ichikawa J, Harada I, Tamura T, Yokoyama A. RNA-binding proteins of KHDRBS and IGF2BP families control the oncogenic activity of MLL-AF4. Nat Commun 2022; 13:6688. [PMID: 36335100 PMCID: PMC9637093 DOI: 10.1038/s41467-022-34558-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 10/27/2022] [Indexed: 11/08/2022] Open
Abstract
Chromosomal translocation generates the MLL-AF4 fusion gene, which causes acute leukemia of multiple lineages. MLL-AF4 is a strong oncogenic driver that induces leukemia without additional mutations and is the most common cause of pediatric leukemia. However, establishment of a murine disease model via retroviral transduction has been difficult owning to a lack of understanding of its regulatory mechanisms. Here, we show that MLL-AF4 protein is post-transcriptionally regulated by RNA-binding proteins, including those of KHDRBS and IGF2BP families. MLL-AF4 translation is inhibited by ribosomal stalling, which occurs at regulatory sites containing AU-rich sequences recognized by KHDRBSs. Synonymous mutations disrupting the association of KHDRBSs result in proper translation of MLL-AF4 and leukemic transformation. Consequently, the synonymous MLL-AF4 mutant induces leukemia in vivo. Our results reveal that post-transcriptional regulation critically controls the oncogenic activity of MLL-AF4; these findings might be valuable in developing novel therapies via modulation of the activity of RNA-binding proteins.
Collapse
Affiliation(s)
- Hiroshi Okuda
- grid.272242.30000 0001 2168 5385Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata Japan ,grid.268441.d0000 0001 1033 6139Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa Japan
| | - Ryo Miyamoto
- grid.272242.30000 0001 2168 5385Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata Japan
| | - Satoshi Takahashi
- grid.272242.30000 0001 2168 5385Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata Japan ,grid.258799.80000 0004 0372 2033Department of Hematology and Oncology, Kyoto University Graduate School of Medicine, Kyoto, Kyoto Japan
| | - Takeshi Kawamura
- grid.26999.3d0000 0001 2151 536XResearch Center for Advanced Science and Technology (RCAST), The University of Tokyo, Bunkyo, Tokyo Japan
| | - Juri Ichikawa
- grid.268441.d0000 0001 1033 6139Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa Japan
| | - Ibuki Harada
- grid.268441.d0000 0001 1033 6139Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa Japan
| | - Tomohiko Tamura
- grid.268441.d0000 0001 1033 6139Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa Japan ,grid.268441.d0000 0001 1033 6139Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa Japan
| | - Akihiko Yokoyama
- grid.272242.30000 0001 2168 5385Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata Japan ,grid.272242.30000 0001 2168 5385National Cancer Center Research Institute, Chuo, Tokyo Japan
| |
Collapse
|
13
|
Koyauchi T, Niida H, Motegi A, Sakai S, Uchida C, Ohhata T, Iijima K, Yokoyama A, Suda T, Kitagawa M. Chromatin-remodeling factor BAZ1A/ACF1 targets UV damage sites in an MLL1-dependent manner to facilitate nucleotide excision repair. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119332. [PMID: 35940372 DOI: 10.1016/j.bbamcr.2022.119332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Ultraviolet (UV) light irradiation generates pyrimidine dimers on DNA, such as cyclobutane pyrimidine dimers (CPDs) and (6-4) photoproducts. Such dimers distort the high-order DNA structure and prevent transcription and replication. The nucleotide excision repair (NER) system contributes to resolving this type of DNA lesion. There are two pathways that recognize pyrimidine dimers. One acts on transcribed strands of DNA (transcription-coupled NER), and the other acts on the whole genome (global genome-NER; GG-NER). In the latter case, DNA damage-binding protein 2 (DDB2) senses pyrimidine dimers with several histone modification enzymes. We previously reported that histone acetyltransferase binding to ORC1 (HBO1) interacts with DDB2 and facilitates recruitment of the imitation switch chromatin remodeler at UV-irradiated sites via an unknown methyltransferase. Here, we found that the phosphorylated histone methyltransferase mixed lineage leukemia 1 (MLL1) was maintained at UV-irradiated sites in an HBO1-dependent manner. Furthermore, MLL1 catalyzed histone H3K4 methylation and recruited the chromatin remodeler bromodomain adjacent to zinc finger domain 1A (BAZ1A)/ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1). Depletion of MLL1 suppressed BAZ1A accumulation at UV-irradiated sites and inhibited the removal of CPDs. These data indicate that the DDB2-HBO1-MLL1 axis is essential for the recruitment of BAZ1A to facilitate GG-NER.
Collapse
Affiliation(s)
- Takafumi Koyauchi
- Department of Molecular Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Hiroyuki Niida
- Department of Molecular Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan.
| | - Akira Motegi
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Satoshi Sakai
- Department of Molecular Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Chiharu Uchida
- Advanced Research Facilities and Services, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Tatsuya Ohhata
- Department of Molecular Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Kenta Iijima
- Laboratory Animal Facilities and Services, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata 997-0052, Japan
| | - Takafumi Suda
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Masatoshi Kitagawa
- Department of Molecular Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| |
Collapse
|
14
|
Fioretti T, Zanobio M, Raia M, Errichiello S, Izzo B, Cattaneo F, Ammendola R, Cevenini A, Esposito G. MiR-27a downregulates 14-3-3θ, RUNX1, AF4, and MLL-AF4, crucial drivers of blast transformation in t(4;11) leukemia cells. Cell Biochem Funct 2022; 40:706-717. [PMID: 35981137 PMCID: PMC9804920 DOI: 10.1002/cbf.3736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/01/2022] [Accepted: 07/28/2022] [Indexed: 01/09/2023]
Abstract
The chromosomal translocation t(4;11)(q21;q23), a hallmark of an aggressive form of acute lymphoblastic leukemia (ALL), encodes mixed-lineage leukemia (MLL)-AF4 oncogenic chimera that triggers aberrant transcription of genes involved in lymphocyte differentiation, including HOXA9 and MEIS1. The scaffold protein 14-3-3θ, which promotes the binding of MLL-AF4 to the HOXA9 promoter, is a target of MiR-27a, a tumor suppressor in different human leukemia cell types. We herein study the role of MiR-27a in the pathogenesis of t(4;11) ALL. Reverse transcription quantitative PCR (qPCR) reveals that MiR-27a and 14-3-3θ expression is inversely correlated in t(4;11) ALL cell lines; interestingly, MiR-27a relative expression is significantly lower in patients affected by t(4;11) ALL than in patients affected by the less severe t(12;21) leukemia. In t(4;11) leukemia cells, ectopic expression of MiR-27a decreases protein level of 14-3-3θ and of the key transcription factor RUNX1. We show for the first time that MiR-27a also targets AF4 and MLL-AF4; in agreement, MiR-27a overexpression strongly reduces AF4 and MLL-AF4 protein levels in RS4;11 cells. Consequent to AF4 and MLL-AF4 downregulation, MiR-27a overexpression negatively affects transcription of HOXA9 and MEIS1 in different t(4;11) leukemia cell lines. In agreement, we show through chromatin immunoprecipitation experiments that MiR-27a overexpression impairs the binding of MLL-AF4 to the HOXA9 promoter. Lastly, we found that MiR-27a overexpression decreases viability, proliferation, and clonogenicity of t(4;11) cells, whereas it enhances their apoptotic rate. Overall, our study identifies the first microRNAthat strikes in one hit four crucial drivers of blast transformation in t(4;11) leukemia. Therefore, MiR-27a emerges as a new promising therapeutic target for this aggressive and poorly curable form of leukemia.
Collapse
Affiliation(s)
- Tiziana Fioretti
- CEINGE Advanced Biotechnologies Franco Salvatore s.c. a r.l.NaplesItaly
| | - Mariateresa Zanobio
- Department of Molecular Medicine and Medical Biotechnology, School of MedicineUniversity of Naples Federico IINaplesItaly,Precision MedicineUniversity of Campania “Luigi Vanvitelli”Naples, Italy
| | - Maddalena Raia
- CEINGE Advanced Biotechnologies Franco Salvatore s.c. a r.l.NaplesItaly
| | - Santa Errichiello
- CEINGE Advanced Biotechnologies Franco Salvatore s.c. a r.l.NaplesItaly
| | - Barbara Izzo
- CEINGE Advanced Biotechnologies Franco Salvatore s.c. a r.l.NaplesItaly,Department of Molecular Medicine and Medical Biotechnology, School of MedicineUniversity of Naples Federico IINaplesItaly
| | - Fabio Cattaneo
- Department of Molecular Medicine and Medical Biotechnology, School of MedicineUniversity of Naples Federico IINaplesItaly
| | - Rosario Ammendola
- Department of Molecular Medicine and Medical Biotechnology, School of MedicineUniversity of Naples Federico IINaplesItaly
| | - Armando Cevenini
- CEINGE Advanced Biotechnologies Franco Salvatore s.c. a r.l.NaplesItaly,Department of Molecular Medicine and Medical Biotechnology, School of MedicineUniversity of Naples Federico IINaplesItaly
| | - Gabriella Esposito
- CEINGE Advanced Biotechnologies Franco Salvatore s.c. a r.l.NaplesItaly,Department of Molecular Medicine and Medical Biotechnology, School of MedicineUniversity of Naples Federico IINaplesItaly
| |
Collapse
|