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Kao TW, Chen HH, Lin J, Wang TL, Shen YA. PBX1 as a novel master regulator in cancer: Its regulation, molecular biology, and therapeutic applications. Biochim Biophys Acta Rev Cancer 2024; 1879:189085. [PMID: 38341110 DOI: 10.1016/j.bbcan.2024.189085] [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: 10/20/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
PBX1 is a critical transcription factor at the top of various cell fate-determining pathways. In cancer, PBX1 stands at the crossroads of multiple oncogenic signaling pathways and mediates responses by recruiting a broad repertoire of downstream targets. Research thus far has corroborated the involvement of PBX1 in cancer proliferation, resisting apoptosis, tumor-associated neoangiogenesis, epithelial-mesenchymal transition (EMT) and metastasis, immune evasion, genome instability, and dysregulating cellular metabolism. Recently, our understanding of the functional regulation of the PBX1 protein has advanced, as increasing evidence has depicted a regulatory network consisting of transcriptional, post-transcriptional, and post-translational levels of control mechanisms. Furthermore, accumulating studies have supported the clinical utilization of PBX1 as a prognostic or therapeutic target in cancer. Preliminary results showed that PBX1 entails vast potential as a targetable master regulator in the treatment of cancer, particularly in those with high-risk features and resistance to other therapeutic strategies. In this review, we will explore the regulation, protein-protein interactions, molecular pathways, clinical application, and future challenges of PBX1.
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Affiliation(s)
- Ting-Wan Kao
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Hsiao-Han Chen
- Department of General Medicine, National Taiwan University Hospital, Taipei 100224, Taiwan
| | - James Lin
- School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Tian-Li Wang
- Departments of Pathology, Oncology and Gynecology and Obstetrics, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB2, Room 306, Baltimore, MD 21231, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Yao-An Shen
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan; International Master/Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan.
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2
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Crisafulli L, Brindisi M, Liturri MG, Sobacchi C, Ficara F. PBX1: a TALE of two seasons-key roles during development and in cancer. Front Cell Dev Biol 2024; 12:1372873. [PMID: 38404687 PMCID: PMC10884236 DOI: 10.3389/fcell.2024.1372873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 01/29/2024] [Indexed: 02/27/2024] Open
Abstract
Pre-B cell leukemia factor 1 (PBX1) is a Three Aminoacid Loop Extension (TALE) homeodomain-containing transcription factor playing crucial roles in organ pattering during embryogenesis, through the formation of nuclear complexes with other TALE class and/or homeobox proteins to regulate target genes. Its contribution to the development of several organs has been elucidated mainly through the study of murine knockout models. A crucial role for human development has been recently highlighted through the discovery of different de novo pathogenic PBX1 variants in children affected by developmental defects. In the adult, PBX1 is expressed in selected tissues such as in the brain, in the gastro-intestinal and urinary systems, or in hematopoietic stem and progenitor cells, while in other organs is barely detectable. When involved in the t(1;19) chromosomal translocation it acts as an oncogene, since the resulting fusion protein drives pre-B cell leukemia, due to the induction of target genes not normally targeted by the native protein. Its aberrant expression has been associated to tumor development, progression, or therapy-resistance as in breast cancer, ovarian cancer or myeloproliferative neoplasm (MPN). On the other hand, in colorectal cancer PBX1 functions as a tumor suppressor, highlighting its context-dependent role. We here discuss differences and analogies of PBX1 roles during embryonic development and in cancer, focusing mainly on the most recent discoveries.
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Affiliation(s)
- Laura Crisafulli
- IRCCS Humanitas Research Hospital, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), National Research Council, Milan, Italy
| | - Matteo Brindisi
- IRCCS Humanitas Research Hospital, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), National Research Council, Milan, Italy
| | | | - Cristina Sobacchi
- IRCCS Humanitas Research Hospital, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), National Research Council, Milan, Italy
| | - Francesca Ficara
- IRCCS Humanitas Research Hospital, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), National Research Council, Milan, Italy
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3
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Mathes A, Duman MB, Neumann A, Dobreva G, Schmidt T. S-adenosylmethionine treatment affects histone methylation in prostate cancer cells. Gene 2024; 893:147915. [PMID: 37866662 DOI: 10.1016/j.gene.2023.147915] [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: 08/03/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
S-adenosylmethionine (SAM) represents a potent inhibitor of cancer cell proliferation, migration, and invasionin vitro.The underlying mechanisms remain elusive. Here, we examined, if treatment with SAM may cause alterations in the methylation of the histone marks H3K4me3 and H3K27me3, which are both known to play important roles in the initiation and progression of prostate cancer. We treated PC-3 cells with 200 µmol SAM, a concentration known to cause anticancerogenic effects, followed by ChIP-sequencing for H3K4me3 and H3K27me3. We detected 236 differentially methylated regions for H3K27me3 and 560 differentially methylated regions for H3K4me3. GO Term enrichment showed upregulation of anticancerogenic, as well as downregulation of cancerogenic related biological processes, molecular functions, and pathways. Furthermore, we compared specific methylation profiles of SAM treated samples to gene expression changes (RNA-Seq). 35 upregulated and 56 downregulated genes (total: 604 differentially expressed genes) could be related to hypomethylated and hypermethylated regions. 17 upregulated genes could be identified as tumor suppressor genes, 45 downregulated genes in contrast are considered as oncogenes. As a conclusion it can be stated that SAM treatment of prostate cancer cells resulted in alterations of H3K4me3 and H3K27me3 methylation profiles. Gene to peak annotation, alignment with results of a transcriptome study as well as GO-term analysis underpinned the biological relevance of methylation changes.
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Affiliation(s)
- Arthur Mathes
- Cardiovascular Genomics and Epigenomics, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | | | - Gergana Dobreva
- Cardiovascular Genomics and Epigenomics, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Schmidt
- Anatomy and Developmental Biology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
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Zeng Z, Fu M, Hu Y, Wei Y, Wei X, Luo M. Regulation and signaling pathways in cancer stem cells: implications for targeted therapy for cancer. Mol Cancer 2023; 22:172. [PMID: 37853437 PMCID: PMC10583419 DOI: 10.1186/s12943-023-01877-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023] Open
Abstract
Cancer stem cells (CSCs), initially identified in leukemia in 1994, constitute a distinct subset of tumor cells characterized by surface markers such as CD133, CD44, and ALDH. Their behavior is regulated through a complex interplay of networks, including transcriptional, post-transcriptional, epigenetic, tumor microenvironment (TME), and epithelial-mesenchymal transition (EMT) factors. Numerous signaling pathways were found to be involved in the regulatory network of CSCs. The maintenance of CSC characteristics plays a pivotal role in driving CSC-associated tumor metastasis and conferring resistance to therapy. Consequently, CSCs have emerged as promising targets in cancer treatment. To date, researchers have developed several anticancer agents tailored to specifically target CSCs, with some of these treatment strategies currently undergoing preclinical or clinical trials. In this review, we outline the origin and biological characteristics of CSCs, explore the regulatory networks governing CSCs, discuss the signaling pathways implicated in these networks, and investigate the influential factors contributing to therapy resistance in CSCs. Finally, we offer insights into preclinical and clinical agents designed to eliminate CSCs.
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Affiliation(s)
- Zhen Zeng
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Minyang Fu
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Yuan Hu
- Department of Pediatric Nephrology Nursing, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China
| | - Min Luo
- Laboratory of Aging Research and Cancer Agent Target, State Key Laboratory of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P.R. China.
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Park YP, Roach T, Soh S, Zeumer-Spataro L, Choi SC, Ostrov DA, Yang Y, Morel L. Molecular Mechanisms of Lupus Susceptibility Allele PBX1D. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:727-734. [PMID: 37486226 PMCID: PMC10530199 DOI: 10.4049/jimmunol.2300362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
Pre-B cell leukemia homeobox 1 (PBX1) controls chromatin accessibility to a large number of genes in various cell types. Its dominant negative splice isoform, PBX1D, which lacks the DNA and Hox-binding domains, is expressed more frequently in the CD4+ T cells from lupus-prone mice and patients with systemic lupus erythematosus than healthy control subjects. PBX1D overexpression in CD4+ T cells impaired regulatory T cell homeostasis and expanded inflammatory CD4+ T cells. In this study, we showed that PBX1 message expression is downregulated by activation in CD4+ T cells as well as in B cells. PBX1D protein was less stable than the normal isoform, PBX1B, and it is degraded through the ubiquitin-proteasome-dependent pathway. The DNA binding domain lacking in PBX1D has two putative ubiquitin binding sites, K292 and K293, that are predicted to be in direct contact with DNA. Mutation of K292-293 reduced PBX1B stability to a level similar to PBX1D and abrogated DNA binding. In addition, contrary to PBX1B, PBX1D is retained in the cytoplasm without the help of the cofactors MEIS or PREP1, indicating a different requirement for nuclear translocation. Overall, these findings suggest that multiple post-transcriptional mechanisms are responsible for PBX1D loss of function and induction of CD4+ T cell inflammatory phenotypes in systemic lupus erythematosus.
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Affiliation(s)
- Yuk Pheel Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health San Antonio, TX 78229-3900, USA
| | - Tracoyia Roach
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL32610, USA
| | - Sujung Soh
- Research Institute of Women’s Health, Sookmyung Women’s University, 100 Cheongparo 47-gil, Yongsan-Gu, Seoul 04310, South Korea, USA
| | - Leilani Zeumer-Spataro
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL32610, USA
| | - Seung-Chul Choi
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health San Antonio, TX 78229-3900, USA
| | - David A. Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL32610, USA
| | - Young Yang
- Research Institute of Women’s Health, Sookmyung Women’s University, 100 Cheongparo 47-gil, Yongsan-Gu, Seoul 04310, South Korea, USA
| | - Laurence Morel
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health San Antonio, TX 78229-3900, USA
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Bobbitt JR, Seachrist DD, Keri RA. Chromatin Organization and Transcriptional Programming of Breast Cancer Cell Identity. Endocrinology 2023; 164:bqad100. [PMID: 37394919 PMCID: PMC10370366 DOI: 10.1210/endocr/bqad100] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023]
Abstract
The advent of sequencing technologies for assessing chromosome conformations has provided a wealth of information on the organization of the 3-dimensional genome and its role in cancer progression. It is now known that changes in chromatin folding and accessibility can promote aberrant activation or repression of transcriptional programs that can drive tumorigenesis and progression in diverse cancers. This includes breast cancer, which comprises several distinct subtypes defined by their unique transcriptomes that dictate treatment response and patient outcomes. Of these, basal-like breast cancer is an aggressive subtype controlled by a pluripotency-enforcing transcriptome. Meanwhile, the more differentiated luminal subtype of breast cancer is driven by an estrogen receptor-dominated transcriptome that underlies its responsiveness to antihormone therapies and conveys improved patient outcomes. Despite the clear differences in molecular signatures, the genesis of each subtype from normal mammary epithelial cells remains unclear. Recent technical advances have revealed key distinctions in chromatin folding and organization between subtypes that could underlie their transcriptomic and, hence, phenotypic differences. These studies also suggest that proteins controlling particular chromatin states may be useful targets for treating aggressive disease. In this review, we explore the current state of understanding of chromatin architecture in breast cancer subtypes and its potential role in defining their phenotypic characteristics.
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Affiliation(s)
- Jessica R Bobbitt
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Darcie D Seachrist
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Ruth A Keri
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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7
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Guo L, Chen H, Chen J, Gao C, Fu X, Zhou S, Wu W, Li T, Lin J, Yang T, Chen Z, Cao L. PBX1-promoted SFRP4 transcription inhibits cell proliferation and epithelial-mesenchymal transition in endometrial carcinoma. Tissue Cell 2023; 82:102083. [PMID: 37054536 DOI: 10.1016/j.tice.2023.102083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023]
Abstract
OBJECTIVE To explore the effects and mechanisms of action of the PBX1/secreted frizzled-related protein 4 (SFRP4) axis in endometrial carcinoma (EC). METHODS The expression of PBX1 and SFRP4 was analyzed using bioinformatics prediction, followed by validation in EC cells using quantitative reverse transcription-polymerase chain reaction and western blotting. After transduction with overexpression vectors for PBX1 and SFRP4, migration, proliferation, and invasion of EC cells were measured, accompanied by the detection of E-cadherin, Snail, N-cadherin, Vimentin, β-catenin, GSK-3β, and C-myc expression. The association between PBX1 and SFRP4 was validated using dual luciferase reporter gene and chromatin immunoprecipitation assays. RESULTS PBX1 and SFRP4 were downregulated in EC cells. Overexpression of PBX1 or SFRP4 resulted in weakened cell proliferation, migration, and invasion, as well as decreased expression of Snail, N-cadherin, Vimentin, β-catenin, GSK-3β, and C-myc and increased expression of E-cadherin. PBX1 bound to the SFRP4 promoter and promoted its transcription. Knockdown of SFRP4 reversed the repression of overexpressed PBX1 in the malignant phenotypes and EMT of EC cells, and PBX1 repressed Wnt/β-catenin pathway activation by upregulating SFRP4 transcription. CONCLUSION PBX1 inhibited activation of the Wnt/β-catenin pathway by promoting SFRP4 transcription, thereby suppressing malignant phenotypes in EC cells and the EMT process.
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Sarker B, Rahaman MM, Islam MA, Alamin MH, Husain MM, Ferdousi F, Ahsan MA, Mollah MNH. Identification of host genomic biomarkers from multiple transcriptomics datasets for diagnosis and therapies of SARS-CoV-2 infections. PLoS One 2023; 18:e0281981. [PMID: 36913345 PMCID: PMC10010564 DOI: 10.1371/journal.pone.0281981] [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: 10/06/2022] [Accepted: 02/05/2023] [Indexed: 03/14/2023] Open
Abstract
The pandemic of COVID-19 is a severe threat to human life and the global economy. Despite the success of vaccination efforts in reducing the spread of the virus, the situation remains largely uncontrolled due to the random mutation in the RNA sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which demands different variants of effective drugs. Disease-causing gene-mediated proteins are usually used as receptors to explore effective drug molecules. In this study, we analyzed two different RNA-Seq and one microarray gene expression profile datasets by integrating EdgeR, LIMMA, weighted gene co-expression network and robust rank aggregation approaches, which revealed SARS-CoV-2 infection causing eight hub-genes (HubGs) including HubGs; REL, AURKA, AURKB, FBXL3, OAS1, STAT4, MMP2 and IL6 as the host genomic biomarkers. Gene Ontology and pathway enrichment analyses of HubGs significantly enriched some crucial biological processes, molecular functions, cellular components and signaling pathways that are associated with the mechanisms of SARS-CoV-2 infections. Regulatory network analysis identified top-ranked 5 TFs (SRF, PBX1, MEIS1, ESR1 and MYC) and 5 miRNAs (hsa-miR-106b-5p, hsa-miR-20b-5p, hsa-miR-93-5p, hsa-miR-106a-5p and hsa-miR-20a-5p) as the key transcriptional and post-transcriptional regulators of HubGs. Then, we conducted a molecular docking analysis to determine potential drug candidates that could interact with HubGs-mediated receptors. This analysis resulted in the identification of top-ranked ten drug agents, including Nilotinib, Tegobuvir, Digoxin, Proscillaridin, Olysio, Simeprevir, Hesperidin, Oleanolic Acid, Naltrindole and Danoprevir. Finally, we investigated the binding stability of the top-ranked three drug molecules Nilotinib, Tegobuvir and Proscillaridin with the three top-ranked proposed receptors (AURKA, AURKB, OAS1) by using 100 ns MD-based MM-PBSA simulations and observed their stable performance. Therefore, the findings of this study might be useful resources for diagnosis and therapies of SARS-CoV-2 infections.
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Affiliation(s)
- Bandhan Sarker
- Faculty of Science, Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
- Department of Statistics, Bioinformatics Laboratory (Dry), University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Matiur Rahaman
- Faculty of Science, Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md. Ariful Islam
- Department of Statistics, Bioinformatics Laboratory (Dry), University of Rajshahi, Rajshahi, Bangladesh
| | - Muhammad Habibulla Alamin
- Faculty of Science, Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md. Maidul Husain
- Faculty of Science, Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Farzana Ferdousi
- Faculty of Science, Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md. Asif Ahsan
- Department of Statistics, Bioinformatics Laboratory (Dry), University of Rajshahi, Rajshahi, Bangladesh
- Liangzhu Laboratory, Zhejiang University Medical Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Md. Nurul Haque Mollah
- Department of Statistics, Bioinformatics Laboratory (Dry), University of Rajshahi, Rajshahi, Bangladesh
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9
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Bahl S, Carroll JS, Lupien M. Chromatin Variants Reveal the Genetic Determinants of Oncogenesis in Breast Cancer. Cold Spring Harb Perspect Med 2022; 12:a041322. [PMID: 36041880 PMCID: PMC9524388 DOI: 10.1101/cshperspect.a041322] [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] [Indexed: 11/24/2022]
Abstract
Breast cancer presents as multiple distinct disease entities. Each tumor harbors diverse cell populations defining a phenotypic heterogeneity that impinges on our ability to treat patients. To date, efforts mainly focused on genetic variants to find drivers of inter- and intratumor phenotypic heterogeneity. However, these efforts have failed to fully capture the genetic basis of breast cancer. Through recent technological and analytical approaches, the genetic basis of phenotypes can now be decoded by characterizing chromatin variants. These variants correspond to polymorphisms in chromatin states at DNA sequences that serve a distinct role across cell populations. Here, we review the function and causes of chromatin variants as they relate to breast cancer inter- and intratumor heterogeneity and how they can guide the development of treatment alternatives to fulfill the goal of precision cancer medicine.
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Affiliation(s)
- Shalini Bahl
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
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10
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Trasanidis N, Katsarou A, Ponnusamy K, Shen YA, Kostopoulos IV, Bergonia B, Keren K, Reema P, Xiao X, Szydlo RM, Sabbattini PMR, Roberts IAG, Auner HW, Naresh KN, Chaidos A, Wang TL, Magnani L, Caputo VS, Karadimitris A. Systems medicine dissection of chr1q-amp reveals a novel PBX1-FOXM1 axis for targeted therapy in multiple myeloma. Blood 2022; 139:1939-1953. [PMID: 35015835 DOI: 10.1182/blood.2021014391] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/20/2021] [Indexed: 11/20/2022] Open
Abstract
Understanding the biological and clinical impact of copy number aberrations (CNAs) on the development of precision therapies in cancer remains an unmet challenge. Genetic amplification of chromosome 1q (chr1q-amp) is a major CNA conferring an adverse prognosis in several types of cancer, including in the blood cancer multiple myeloma (MM). Although several genes across chromosome 1 (chr1q) portend high-risk MM disease, the underpinning molecular etiology remains elusive. Here, with reference to the 3-dimensional (3D) chromatin structure, we integrate multi-omics data sets from patients with MM with genetic variables to obtain an associated clinical risk map across chr1q and to identify 103 adverse prognosis genes in chr1q-amp MM. Prominent among these genes, the transcription factor PBX1 is ectopically expressed by genetic amplification and epigenetic activation of its own preserved 3D regulatory domain. By binding to reprogrammed superenhancers, PBX1 directly regulates critical oncogenic pathways and a FOXM1-dependent transcriptional program. Together, PBX1 and FOXM1 activate a proliferative gene signature that predicts adverse prognosis across multiple types of cancer. Notably, pharmacological disruption of the PBX1-FOXM1 axis with existing agents (thiostrepton) and a novel PBX1 small molecule inhibitor (T417) is selectively toxic against chr1q-amp myeloma and solid tumor cells. Overall, our systems medicine approach successfully identifies CNA-driven oncogenic circuitries, links them to clinical phenotypes, and proposes novel CNA-targeted therapy strategies in MM and other types of cancer.
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Affiliation(s)
- Nikolaos Trasanidis
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Alexia Katsarou
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
| | - Kanagaraju Ponnusamy
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Yao-An Shen
- Department of Pathology
- Department of Oncology
- Department of Gynecology and Obstetrics, and
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ioannis V Kostopoulos
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Bien Bergonia
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Keren Keren
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Paudel Reema
- Imperial Experimental Cancer Medicine Centre and Cancer Research UK Imperial Centre, London, United Kingdom
| | - Xiaolin Xiao
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Richard M Szydlo
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Pierangela M R Sabbattini
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Irene A G Roberts
- Department of Paediatrics and Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
- Oxford Biomedical Research Centre Blood Theme, National Institute for Health Research Oxford Biomedical Centre, Oxford, United Kingdom
| | - Holger W Auner
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
| | - Kikkeri N Naresh
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
- Imperial Experimental Cancer Medicine Centre and Cancer Research UK Imperial Centre, London, United Kingdom
| | - Aristeidis Chaidos
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
| | - Tian-Li Wang
- Department of Pathology
- Department of Oncology
- Department of Gynecology and Obstetrics, and
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom; and
| | - Valentina S Caputo
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Cancer Biology and Therapy Laboratory, School of Applied Science, London South Bank University, London, United Kingdom
| | - Anastasios Karadimitris
- Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Foundation Trust, London, United Kingdom
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Agent myeloma has a new weapon from (ch1)Q. Blood 2022; 139:1927-1928. [PMID: 35357482 DOI: 10.1182/blood.2021015336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/12/2022] [Indexed: 11/20/2022] Open
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