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Gourisankar S, Krokhotin A, Wenderski W, Crabtree GR. Context-specific functions of chromatin remodellers in development and disease. Nat Rev Genet 2024; 25:340-361. [PMID: 38001317 DOI: 10.1038/s41576-023-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 11/26/2023]
Abstract
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.
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Affiliation(s)
- Sai Gourisankar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Andrey Krokhotin
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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Li Y, Yang X, Geng C, Liu Y, Tang T, Zhang L, Liu F, Zhang M, Hao J, Ma L. Identification of molecular subtypes based on chromatin regulator-related genes and experimental verification of the role of ASCL1 in conferring chemotherapy resistance to breast cancer. Front Immunol 2024; 15:1390261. [PMID: 38726001 PMCID: PMC11079216 DOI: 10.3389/fimmu.2024.1390261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Objective The aim of this study was to identify the molecular subtypes of breast cancer based on chromatin regulator-related genes. Methods The RNA sequencing data of The Cancer Genome Atlas-Breast Cancer cohort were obtained from the official website, while the single-cell data were downloaded from the Gene Expression Omnibus database (GSE176078). Validation was performed using the Molecular Taxonomy of Breast Cancer International Consortium dataset. Furthermore, the immune characteristics, tumor stemness, heterogeneity, and clinical characteristics of these molecular subtypes were analyzed. The correlation between chromatin regulators and chemotherapy resistance was examined in vitro using the quantitative real-time polymerase chain reaction (qRT-PCR) and Cell Counting Kit-8 (CCK8) assays. Results This study identified three stable molecular subtypes with different prognostic and pathological features. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and protein-protein interaction analyses revealed that the differentially expressed genes were associated with disease processes, such as mitotic nuclear division, chromosome segregation, condensed chromosome, and specific chromosome region. The T stage and subtypes were correlated with the clinical features. Tumor heterogeneity (mutant-allele tumor heterogeneity, tumor mutational burden, purity, and homologous recombination deficiency) and tumor stemness (RNA expression-based stemness score, epigenetically regulated RNA expression-based stemness score, DNA methylation-based stemness score, and epigenetically regulated DNA methylation-based stemness score) significantly varied between the three subtypes. Furthermore, Western blotting, qRT-PCR, and CCK8 assays demonstrated that the expression of ASCL1 was positively correlated with chemotherapy resistance in breast cancer. Conclusion This study identified the subtypes of breast cancer based on chromatin regulators and analyzed their clinical features, gene mutation status, immunophenotype, and drug sensitivity. The results of this study provide effective strategies for assessing clinical prognosis and developing personalized treatment strategies.
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Affiliation(s)
- Yilun Li
- Department of Breast Disease Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Pathology, Hebei Medical University, Shijiazhuang, China
| | - Xiaolu Yang
- Department of Breast Disease Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Pathology, Hebei Medical University, Shijiazhuang, China
| | - Cuizhi Geng
- Department of Breast Disease Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yunjiang Liu
- Department of Breast Disease Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Tiantian Tang
- Department of Breast Disease Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lina Zhang
- Department of Breast Disease Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Fei Liu
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Meng Zhang
- Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jun Hao
- Department of Pathology, Hebei Medical University, Shijiazhuang, China
| | - Li Ma
- Department of Breast Disease Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
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Sabnis N, Raut S, Nagarajan B, Kapic A, Dossou AS, Lothstein L, Fudala R, Bunnell BA, Lacko AG. A Spontaneous Assembling Lipopeptide Nanoconjugate Transporting the Anthracycline Drug N-Benzyladriamycin-14-valerate for Personalized Therapy of Ewing Sarcoma. Bioconjug Chem 2024; 35:187-202. [PMID: 38318778 DOI: 10.1021/acs.bioconjchem.3c00429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
To meet the current need for a tumor-selective, targeted therapy regimen associated with reduced toxicity, our laboratory has developed a spontaneously assembled nanostructure that resembles high-density lipoproteins (HDLs). These myristoyl-5A (MYR-5A) nanotransporters are designed to safely transport lipophilic pharmaceuticals, including a novel anthracycline drug (N-benzyladriamycin-14-valerate (AD198)). This formulation has been found to enhance the therapeutic efficacy and reduced toxicity of drugs in preclinical studies of 2D and 3D models of Ewing sarcoma (EWS) and cardiomyocytes. Our findings indicate that the MYR-5A/AD198 nanocomplex delivers its payload selectively to cancer cells via the scavenger receptor type B1 (SR-B1), thus providing a solid proof of concept for the development of an improved and highly effective, potentially personalized therapy for EWS while protecting against treatment-associated cardiotoxicity.
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Affiliation(s)
- Nirupama Sabnis
- Lipoprotein Drug Delivery Research Laboratory, Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Sangram Raut
- Department of Physiology and Anatomy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Bhavani Nagarajan
- North Texas Research Eye Institute, Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Ammar Kapic
- Lipoprotein Drug Delivery Research Laboratory, Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Akpedje Serena Dossou
- Lipoprotein Drug Delivery Research Laboratory, Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Leonard Lothstein
- Department of Pathology and Laboratory Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee 38103, United States
| | - Rafal Fudala
- Lipoprotein Drug Delivery Research Laboratory, Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Bruce A Bunnell
- Lipoprotein Drug Delivery Research Laboratory, Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Andras G Lacko
- Lipoprotein Drug Delivery Research Laboratory, Department of Microbiology, Immunology & Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
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Matthews ER, Johnson OD, Horn KJ, Gutiérrez JA, Powell SR, Ward MC. Anthracyclines induce cardiotoxicity through a shared gene expression response signature. PLoS Genet 2024; 20:e1011164. [PMID: 38416769 PMCID: PMC10927150 DOI: 10.1371/journal.pgen.1011164] [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: 09/30/2023] [Revised: 03/11/2024] [Accepted: 01/31/2024] [Indexed: 03/01/2024] Open
Abstract
TOP2 inhibitors (TOP2i) are effective drugs for breast cancer treatment. However, they can cause cardiotoxicity in some women. The most widely used TOP2i include anthracyclines (AC) Doxorubicin (DOX), Daunorubicin (DNR), Epirubicin (EPI), and the anthraquinone Mitoxantrone (MTX). It is unclear whether women would experience the same adverse effects from all drugs in this class, or if specific drugs would be preferable for certain individuals based on their cardiotoxicity risk profile. To investigate this, we studied the effects of treatment of DOX, DNR, EPI, MTX, and an unrelated monoclonal antibody Trastuzumab (TRZ) on iPSC-derived cardiomyocytes (iPSC-CMs) from six healthy females. All TOP2i induce cell death at concentrations observed in cancer patient serum, while TRZ does not. A sub-lethal dose of all TOP2i induces limited cellular stress but affects calcium handling, a function critical for cardiomyocyte contraction. TOP2i induce thousands of gene expression changes over time, giving rise to four distinct gene expression response signatures, denoted as TOP2i early-acute, early-sustained, and late response genes, and non-response genes. There is no drug- or AC-specific signature. TOP2i early response genes are enriched in chromatin regulators, which mediate AC sensitivity across breast cancer patients. However, there is increased transcriptional variability between individuals following AC treatments. To investigate potential genetic effects on response variability, we first identified a reported set of expression quantitative trait loci (eQTLs) uncovered following DOX treatment in iPSC-CMs. Indeed, DOX response eQTLs are enriched in genes that respond to all TOP2i. Next, we identified 38 genes in loci associated with AC toxicity by GWAS or TWAS. Two thirds of the genes that respond to at least one TOP2i, respond to all ACs with the same direction of effect. Our data demonstrate that TOP2i induce thousands of shared gene expression changes in cardiomyocytes, including genes near SNPs associated with inter-individual variation in response to DOX treatment and AC-induced cardiotoxicity.
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Affiliation(s)
- E. Renee Matthews
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Omar D. Johnson
- Biochemistry, Cellular and Molecular Biology Graduate Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kandace J. Horn
- John Sealy School of Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - José A. Gutiérrez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Simon R. Powell
- Neuroscience Graduate Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Michelle C. Ward
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
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Wang Y, Khalil A, Kamar A, Du M, Dinh T, McFarland C, Wang Z. Unveiling immune checkpoint regulation: exploring the power of in vivo CRISPR screenings in cancer immunotherapy. Front Genet 2023; 14:1304425. [PMID: 38162677 PMCID: PMC10755878 DOI: 10.3389/fgene.2023.1304425] [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: 09/29/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Immune checkpoint inhibitors (ICIs) have revolutionized cancer immunotherapy by reinvigorating antitumor immune responses, but their efficacy remains limited in most patients. To address this challenge and optimize Immune check inhibitor treatment, understanding the underlying molecular intricacies involved is crucial. The emergence of CRISPR-Cas9 technology has empowered researchers to precisely investigate gene function and has introduced transformative shifts in identifying key genes for various physiological and pathological processes. CRISPR screenings, particularly in vivo CRISPR screenings, have become invaluable tools in deciphering molecular networks and signaling pathways governing suppressive immune checkpoint molecules. In this review, we provide a comprehensive overview of in vivo CRISPR screenings in cancer immunotherapy, exploring how this cutting-edge technology has unraveled potential novel therapeutic targets and combination strategies. We delve into the latest findings and advancements, shedding light on immune checkpoint regulation and offering exciting prospects for the development of innovative and effective treatments for cancer patients.
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Affiliation(s)
- Yuxiang Wang
- Department of Genetics and Genome Sciences and Case Comprehesive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
| | - Athar Khalil
- Department of Genetics and Genome Sciences and Case Comprehesive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
| | - Amina Kamar
- Centre for Digital Transformation, Imperial College, London, United Kingdom
| | - Mengyan Du
- Department of Genetics and Genome Sciences and Case Comprehesive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
| | - Trang Dinh
- Department of Genetics and Genome Sciences and Case Comprehesive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
| | - Christopher McFarland
- Department of Genetics and Genome Sciences and Case Comprehesive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
| | - Zhenghe Wang
- Department of Genetics and Genome Sciences and Case Comprehesive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
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Song YQ, Yang GJ, Ma DL, Wang W, Leung CH. The role and prospect of lysine-specific demethylases in cancer chemoresistance. Med Res Rev 2023; 43:1438-1469. [PMID: 37012609 DOI: 10.1002/med.21955] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 02/08/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023]
Abstract
Histone methylation plays a key function in modulating gene expression, and preserving genome integrity and epigenetic inheritance. However, aberrations of histone methylation are commonly observed in human diseases, especially cancer. Lysine methylation mediated by histone methyltransferases can be reversed by lysine demethylases (KDMs), which remove methyl marks from histone lysine residues. Currently, drug resistance is a main impediment for cancer therapy. KDMs have been found to mediate drug tolerance of many cancers via altering the metabolic profile of cancer cells, upregulating the ratio of cancer stem cells and drug-tolerant genes, and promoting the epithelial-mesenchymal transition and metastatic ability. Moreover, different cancers show distinct oncogenic addictions for KDMs. The abnormal activation or overexpression of KDMs can alter gene expression signatures to enhance cell survival and drug resistance in cancer cells. In this review, we describe the structural features and functions of KDMs, the KDMs preferences of different cancers, and the mechanisms of drug resistance resulting from KDMs. We then survey KDM inhibitors that have been used for combating drug resistance in cancer, and discuss the opportunities and challenges of KDMs as therapeutic targets for cancer drug resistance.
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Affiliation(s)
- Ying-Qi Song
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Guan-Jun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao, China
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Wooten M, Takushi B, Ahmad K, Henikoff S. Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters. SCIENCE ADVANCES 2023; 9:eadg3257. [PMID: 37315134 DOI: 10.1126/sciadv.adg3257] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/08/2023] [Indexed: 06/16/2023]
Abstract
Anthracyclines are a class of widely prescribed anticancer drugs that disrupt chromatin by intercalating into DNA and enhancing nucleosome turnover. To understand the molecular consequences of anthracycline-mediated chromatin disruption, we used Cleavage Under Targets and Tagmentation (CUT&Tag) to profile RNA polymerase II during anthracycline treatment in Drosophila cells. We observed that treatment with the anthracycline aclarubicin leads to elevated levels of RNA polymerase II and changes in chromatin accessibility. We found that promoter proximity and orientation affect chromatin changes during aclarubicin treatment, as closely spaced divergent promoter pairs show greater chromatin changes when compared to codirectionally oriented tandem promoters. We also found that aclarubicin treatment changes the distribution of noncanonical DNA G-quadruplex structures both at promoters and at G-rich pericentromeric repeats. Our work suggests that the cancer-killing activity of aclarubicin is driven by the disruption of nucleosomes and RNA polymerase II.
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Affiliation(s)
| | | | - Kami Ahmad
- Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Steven Henikoff
- Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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8
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Tang ZN, Bi XF, Chen WL, Zhang CL. RANKL Promotes Chemotherapy Resistance in Breast Cancer Cells Through STAT3 Mediated Autophagy Induction. Clin Breast Cancer 2023; 23:388-396. [PMID: 36872108 DOI: 10.1016/j.clbc.2023.01.014] [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: 08/03/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023]
Abstract
BACKGROUND This study was to investigate the functional role and mechanism of receptor activator of nuclear factor-kappa B ligand (RANKL) associated autophagy and chemoresistance in breast cancer. MATERIALS AND METHODS Cell Counting Kit-8 (CCK-8) assay was used to detect the cell viability. Real-time polymerase chain reaction (PCR) was used for determining the relative mRNA levels of key genes and protein expression was assessed by Western blotting. Immunofluorescence was performed to evaluate the changes in the autophagy flux. Short hairpin (shRNA) was used to knockdown the expression of the target genes in breast cancer cells. Based on The Cancer Genome Atlas (TCGA) database, we explored the expression of receptor activator of nuclear factor-kappa B (RANK), autophagy and signal transducer and activator of transcription 3 (STAT3) signaling associated genes and analyzed their correlation with the prognosis of breast cancer patients. RESULTS The findings showed that receptor activator of nuclear factor-kappa B ligand (RANKL), the ligand of RANK, could effectively enhance the chemoresistance potential of breast cancer cells. Our results showed that RANKL induced autophagy and enhanced the expression of autophagy associated genes in breast cancer cells. The knockdown of RANK suppressed RANKL mediated autophagy induction in these cells. Furthermore, the inhibition of autophagy suppressed RANKL mediated chemoresistance in breast cancer cells. We found STAT3 signaling pathway was involved in RANKL-induced autophagy. Analysis of the expression of RANK, and autophagy and STAT3 signaling associated genes in breast cancer tissues showed that the expression of autophagy and STAT3 signaling associated genes was correlated with the prognosis of breast cancer patients. CONCLUSION The present study suggests that the RANKL/RANK axis may potentially mediate chemoresistance in breast cancer cells by inducing autophagy through the STAT3 signaling pathway.
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Affiliation(s)
- Zhen-Ning Tang
- Department of Surgical Oncology, General Hospital of Ningxia Medical University, 750004 Yinchuan, Ningxia, China
| | - Xiao-Fang Bi
- Department of Pathology, The First People's Hospital of Yinchuan, 750001 Yinchuan, Ningxia, China
| | - Wei-Liang Chen
- Department of Breast Surgery, Herbei Province Cangzhou Hospital of Integrated Traditional and Western Medicine, 061001 Cangzhou, Hebei, China
| | - Chao-Lin Zhang
- Department of Surgical Oncology, General Hospital of Ningxia Medical University, 750004 Yinchuan, Ningxia, China.
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Wooten M, Takushi B, Ahmad K, Henikoff S. Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523323. [PMID: 36712130 PMCID: PMC9882078 DOI: 10.1101/2023.01.09.523323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Anthracyclines are a class of widely prescribed anti-cancer drugs that disrupt chromatin by intercalating into DNA and enhancing nucleosome turnover. To understand the molecular consequences of anthracycline-mediated chromatin disruption, we utilized CUT&Tag to profile RNA polymerase II during anthracycline treatment in Drosophila cells. We observed that treatment with the anthracycline aclarubicin leads to elevated levels of elongating RNA polymerase II and changes in chromatin accessibility. We found that promoter proximity and orientation impacts chromatin changes during aclarubicin treatment, as closely spaced divergent promoter pairs show greater chromatin changes when compared to codirectionally-oriented tandem promoters. We also found that aclarubicin treatment changes the distribution of non-canonical DNA G-quadruplex structures both at promoters and at G-rich pericentromeric repeats. Our work suggests that the anti-cancer activity of aclarubicin is driven by the effects of nucleosome disruption on RNA polymerase II, chromatin accessibility and DNA structures.
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Affiliation(s)
- Matthew Wooten
- Fred Hutchinson Cancer Center, Seattle, WA 98109-1024, USA
| | | | - Kami Ahmad
- Fred Hutchinson Cancer Center, Seattle, WA 98109-1024, USA
| | - Steven Henikoff
- Fred Hutchinson Cancer Center, Seattle, WA 98109-1024, USA
- Howard Hughes Medical Institute
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Identification of a five genes prognosis signature for triple-negative breast cancer using multi-omics methods and bioinformatics analysis. Cancer Gene Ther 2022; 29:1578-1589. [PMID: 35474355 DOI: 10.1038/s41417-022-00473-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/26/2022] [Accepted: 04/08/2022] [Indexed: 02/04/2023]
Abstract
Triple-negative breast cancer (TNBC) has a high degree of malignancy, lack of effective diagnosis and treatment, and poor prognosis. Bioinformatics methods are used to screen the hub genes and signal pathways involved in the progress of TNBC to provide reliable biomarkers for the diagnosis and treatment of TNBC. Download the raw data of four TNBC-related datasets from the Gene Expression Omnibus (GEO) database and use them for bioinformatics analysis. GEO2R tool was used to analyze and identify differentially expressed (DE) mRNAs. DAVID database was used to carry out gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genome Pathways (KEGG) signal pathway enrichment analysis for DE mRNAs. STRING database and Cytoscape were used to build DE mRNAs protein-protein interaction (PPI) network diagram and visualize PPI network, respectively. Through cytoHubba, cBioPortal database, Kaplan-Meier mapper database, Gene Expression Profiling Interactive Analysis (GEPIA) Database, UALCAN Database, The Cancer Genome Atlas (TCGA) database, Tumor Immunity Estimation Resource identify hub genes. Perform qRT-PCR, Human Protein Atlas analysis, mutation analysis, survival analysis, clinical-pathological characteristics, and infiltrating immune cell analysis. 22 DE mRNAs were identified from the four datasets, including 16 upregulated DE mRNAs and six downregulated DE mRNAs. Enrichment analysis of the KEGG showed that DE mRNAs were principally enriched in pathways in cancer, mismatch repair, cell cycle, platinum drug resistance, breast cancer. Six hub genes were screened based on the PPI network diagram of DE mRNAs. Survival analysis found that TOP2A, CCNA2, PCNA, MSH2, CDK6 are related to the prognosis of TNBC. In addition, mutations, clinical indicators, and immune infiltration analysis show that these five hub genes play an important role in the progress of TNBC and immune monitoring. Compared with MCF-10A, MCF-7, and SKBR-3 cells, TOP2A, PCNA, MSH2, and CDK6 were significantly upregulated in MDA-MB-321 cells. Compared with normal, luminal, and Her-2 positive tissues, CCNA2, MSH2, and CDK6 were significantly upregulated in TNBC. Through comparative analysis of GEO datasets related to colorectal cancer and lung adenocarcinoma, it was determined that these five hub genes were unique differentially expressed genes of TNBC. At last, the hub genes related to the progression, prognosis, and immunity of TNBC have been successfully screened. They are indeed specific to TNBC as prognostic features. They can be used as potential markers for the prognosis of TNBC and provide potential therapeutic targets.
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Li F, Yin J, Lu M, Mou M, Li Z, Zeng Z, Tan Y, Wang S, Chu X, Dai H, Hou T, Zeng S, Chen Y, Zhu F. DrugMAP: molecular atlas and pharma-information of all drugs. Nucleic Acids Res 2022; 51:D1288-D1299. [PMID: 36243961 PMCID: PMC9825453 DOI: 10.1093/nar/gkac813] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/30/2022] [Accepted: 10/12/2022] [Indexed: 02/06/2023] Open
Abstract
The efficacy and safety of drugs are widely known to be determined by their interactions with multiple molecules of pharmacological importance, and it is therefore essential to systematically depict the molecular atlas and pharma-information of studied drugs. However, our understanding of such information is neither comprehensive nor precise, which necessitates the construction of a new database providing a network containing a large number of drugs and their interacting molecules. Here, a new database describing the molecular atlas and pharma-information of drugs (DrugMAP) was therefore constructed. It provides a comprehensive list of interacting molecules for >30 000 drugs/drug candidates, gives the differential expression patterns for >5000 interacting molecules among different disease sites, ADME (absorption, distribution, metabolism and excretion)-relevant organs and physiological tissues, and weaves a comprehensive and precise network containing >200 000 interactions among drugs and molecules. With the great efforts made to clarify the complex mechanism underlying drug pharmacokinetics and pharmacodynamics and rapidly emerging interests in artificial intelligence (AI)-based network analyses, DrugMAP is expected to become an indispensable supplement to existing databases to facilitate drug discovery. It is now fully and freely accessible at: https://idrblab.org/drugmap/.
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Affiliation(s)
| | | | - Mingkun Lu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba–Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhenyu Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba–Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Ying Tan
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Shanshan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Xinyi Chu
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Haibin Dai
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Su Zeng
- Correspondence may also be addressed to Su Zeng.
| | - Yuzong Chen
- Correspondence may also be addressed to Yuzong Chen.
| | - Feng Zhu
- To whom correspondence should be addressed.
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Wang Z, Zhu Q, Li X, Ren X, Li J, Zhang Y, Zeng S, Xu L, Dong X, Zhai B. TOP2A inhibition reverses drug resistance of hepatocellular carcinoma to regorafenib. Am J Cancer Res 2022; 12:4343-4360. [PMID: 36225636 PMCID: PMC9548008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death attributed to high frequency of metastasis and multiple drug resistance. We aim to examine the underlying molecular mechanism and to seek potential strategies to reverse primary/acquired resistance to regorafenib. Topoisomerase IIα (TOP2A) is critical for tumorigenesis and carcinogenesis. Clinically, high-TOP2A expression was correlated to shorter overall survival (OS) of patients, but its role in drug resistance of HCC remains unknown. Here, we screened the expression profiling of TOP2A in HCC and identified TOP2A as an upregulated gene involved in the resistance to regorafenib. Sustained exposure of HCC cells to regorafenib could upregulate the expression of TOP2A. Silencing TOP2A enhanced HCC cells' sensitivity to regorafenib. TOP2A inhibition by doxorubicin or epirubicin synergized with regorafenib to suppress the growth of sorafenib-resistant HCC tumors that possessed the sorafenib-resistant features both in vitro and in vivo. Thus, targeting TOP2A may be a promising therapeutic strategy to alleviate resistance to regorafenib and thus improving the efficacy of HCC treatment.
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Affiliation(s)
- Zongwen Wang
- Department of Surgical Oncology and Hepatobiliary Surgery, The Fourth Affiliated Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
| | - Qiankun Zhu
- Department of Surgical Oncology and Hepatobiliary Surgery, The Fourth Affiliated Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
| | - Xiaodong Li
- Department of Surgical Oncology and Hepatobiliary Surgery, The Fourth Affiliated Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
| | - Xiaohang Ren
- Department of Surgical Oncology and Hepatobiliary Surgery, The Fourth Affiliated Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
| | - Jingtao Li
- Department of Surgical Oncology and Hepatobiliary Surgery, The Fourth Affiliated Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
| | - Yao Zhang
- Department of Surgical Oncology and Hepatobiliary Surgery, The Fourth Affiliated Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
| | - Shicong Zeng
- Department of Surgical Oncology and Hepatobiliary Surgery, The Fourth Affiliated Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
| | - Lishan Xu
- Department of Surgical Oncology and Hepatobiliary Surgery, The Fourth Affiliated Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
| | - Xiaoqun Dong
- The Liver Research Center of Rhode Island Hospital/Lifespan; Department of Medicine, The Warren Alpert Medical School of Brown UniversityProvidence, RI 02903, USA
| | - Bo Zhai
- Department of Surgical Oncology and Hepatobiliary Surgery, The Fourth Affiliated Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
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13
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So JY, Ohm J, Lipkowitz S, Yang L. Triple negative breast cancer (TNBC): Non-genetic tumor heterogeneity and immune microenvironment: Emerging treatment options. Pharmacol Ther 2022; 237:108253. [PMID: 35872332 PMCID: PMC9378710 DOI: 10.1016/j.pharmthera.2022.108253] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/01/2022] [Accepted: 07/18/2022] [Indexed: 12/17/2022]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by extensive intra-tumoral heterogeneity, and frequently develops resistance to therapies. Tumor heterogeneity and lack of biomarkers are thought to be some of the most difficult challenges driving therapeutic resistance and relapse. This review will summarize current therapy for TNBC, studies in treatment resistance and relapse, including data from recent single cell sequencing. We will discuss changes in both the transcriptome and epigenome of TNBC, and we will review mechanisms regulating the immune microenvironment. Lastly, we will provide new perspective in patient stratification, and treatment options targeting transcriptome dysregulation and the immune microenvironment of TNBC patients.
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Affiliation(s)
- Jae Young So
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joyce Ohm
- Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Stan Lipkowitz
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Yang
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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14
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Huang KS, Wang YT, Byadgi O, Huang TY, Tai MH, Shaw JF, Yang CH. Screening of Specific and Common Pathways in Breast Cancer Cell Lines MCF-7 and MDA-MB-231 Treated with Chlorophyllides Composites. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123950. [PMID: 35745070 PMCID: PMC9229827 DOI: 10.3390/molecules27123950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/06/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022]
Abstract
Our previous findings have shown that the chlorophyllides composites have anticancer activities to breast cancer cell lines (MCF-7 and MDA-MB-231). In the present study, microarray gene expression profiling was utilized to investigate the chlorophyllides anticancer mechanism on the breast cancer cells lines. Results showed that chlorophyllides composites induced upregulation of 43 and 56 differentially expressed genes (DEG) in MCF-7 and MDA-MB-231 cells, respectively. In both cell lines, chlorophyllides composites modulated the expression of annexin A4 (ANXA4), chemokine C-C motif receptor 1 (CCR1), stromal interaction molecule 2 (STIM2), ethanolamine kinase 1 (ETNK1) and member of RAS oncogene family (RAP2B). Further, the KEGG annotation revealed that chlorophyllides composites modulated DEGs that are associated with the endocrine system in MCF-7 cells and with the nervous system in MDA-MB-231 cells, respectively. The expression levels of 9 genes were validated by quantitative reverse transcription PCR (RT-qPCR). The expression of CCR1, STIM2, ETNK1, MAGl1 and TOP2A were upregulated in both chlorophyllides composites treated-MCF-7 and MDA-MB-231 cells. The different expression of NLRC5, SLC7A7 and PKN1 provided valuable information for future investigation and development of novel cancer therapy.
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Affiliation(s)
- Keng-Shiang Huang
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, No. 8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan;
| | - Yi-Ting Wang
- Department of Biological Science and Technology, I-Shou University, No. 8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan; (Y.-T.W.); (T.-Y.H.); (M.-H.T.)
| | - Omkar Byadgi
- International College, International Program in Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan;
| | - Ting-Yu Huang
- Department of Biological Science and Technology, I-Shou University, No. 8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan; (Y.-T.W.); (T.-Y.H.); (M.-H.T.)
| | - Mi-Hsueh Tai
- Department of Biological Science and Technology, I-Shou University, No. 8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan; (Y.-T.W.); (T.-Y.H.); (M.-H.T.)
| | - Jei-Fu Shaw
- Department of Biological Science and Technology, I-Shou University, No. 8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan; (Y.-T.W.); (T.-Y.H.); (M.-H.T.)
- Correspondence: (J.-F.S.); (C.-H.Y.); Tel.: +886-7-6151100 (ext. 7310) (J.-F.S.); +886-7-6151100 (ext. 7312) (C.-H.Y.); Fax: +886-7-6151959 (J.-F.S. & C.-H.Y.)
| | - Chih-Hui Yang
- Department of Biological Science and Technology, I-Shou University, No. 8, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan; (Y.-T.W.); (T.-Y.H.); (M.-H.T.)
- Pharmacy Department, E-Da Hospital, No. 1, Yida Rd., Jiaosu Village Yanchao District, Kaohsiung City 82445, Taiwan
- Taiwan Instrument Research Institute, National Applied Research Laboratories, Taipei City 106214, Taiwan
- Correspondence: (J.-F.S.); (C.-H.Y.); Tel.: +886-7-6151100 (ext. 7310) (J.-F.S.); +886-7-6151100 (ext. 7312) (C.-H.Y.); Fax: +886-7-6151959 (J.-F.S. & C.-H.Y.)
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15
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Hu Y, Xue Z, Qiu C, Feng Z, Qi Q, Wang J, Jin W, Zhong Z, Liu X, Li W, Zhang Q, Huang B, Chen A, Wang J, Yang N, Zhou W. Knockdown of NUSAP1 inhibits cell proliferation and invasion through downregulation of TOP2A in human glioblastoma. Cell Cycle 2022; 21:1842-1855. [PMID: 35532155 PMCID: PMC9359390 DOI: 10.1080/15384101.2022.2074199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Nucleolar and spindle associated protein 1 (NUSAP1), an indispensable mitotic regulator, has been reported to be involved in the development, progression, and metastasis of several types of cancer. Here, we investigated the expression and biological function of NUSAP1 in human glioblastoma (GBM), an aggressive brain tumor type with largely ineffective treatment options. Analysis of the molecular data in CGGA, TCGA and Rembrandt datasets demonstrated that NUSAP1 was significantly upregulated in GBM relative to low grade gliomas and non-neoplastic brain tissue samples. Kaplan-Meier analysis indicated that patients with tumors showing high NUSAP1 expression exhibited significantly poorer survival in both CGGA (P = 0.002) and Rembrandt cohorts (P = 0.017). Analysis of RNA sequencing data from P3-cells with stable knockdown of NUSAP1 revealed topoisomerase 2A (TOP2A) as a possible molecule downregulated by the loss of NUSAP1. Molecular analysis of the CGGA data revealed a strong correlation between NUSAP1 and TOP2A expression in primary gliomas and recurrent gliomas samples. SiRNA knockdown of either NUSAP1 or TOP2A in U251, T98 and GBM derived patient P3 cells inhibited GBM cell proliferation and invasion, and induced cell apoptosis. Finally, stable knockdown of NUSAP1 with shRNA led to decreased tumor growth in an orthotopic xenograft model of GBM in mice. Taken together, NUSAP1 gene silencing induced apoptosis possibly through the downregulation of the candidate downstream molecule TOP2A. Interference with the expression of NUSAP1 might therefore inhibit malignant progression in GBM, and NUSAP1 might thus serve as a promising molecular target for GBM treatment.
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Affiliation(s)
- Yaotian Hu
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Zhiyi Xue
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Chen Qiu
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China.,Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Zichao Feng
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Qichao Qi
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jiwei Wang
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Wenxing Jin
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Zhaoyang Zhong
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Xiaofei Liu
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Wenjie Li
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Qing Zhang
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Bin Huang
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Anjing Chen
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Jian Wang
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China.,Department of Biomedicine, University of Bergen, Norway
| | - Ning Yang
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong, China
| | - Wenjing Zhou
- Department of Blood Transfusion, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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16
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Chalumeau C, Carton M, Eeckhoutte A, Ballet S, Vincent-Salomon A, Vuagnat P, Bellesoeur A, Pierga JY, Stern MH, Bidard FC, Lerebours F. Oral Etoposide and Trastuzumab Use for HER2-Positive Metastatic Breast Cancer: A Retrospective Study from the Institut Curie Hospitals. Cancers (Basel) 2022; 14:2114. [PMID: 35565244 PMCID: PMC9101021 DOI: 10.3390/cancers14092114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The TOP2A and ERBB2 genes are co-amplified in about 40% of HER2 positive (HER2+) breast cancers. Oral etoposide (VP16), an inhibitor of topoisomerase-II (encoded by TOP2A), has demonstrated clinical activity in metastatic breast cancer (MBC). The benefit of oral VP16 combined with trastuzumab (VP16-T) in HER2+ MBC has not yet been evaluated. METHODS Patients treated at the Institut Curie Hospitals with VP16-T for HER2+ MBC were retrieved by an in silico search. Progression-free survival (PFS), overall survival (OS), response rate, prolonged PFS (defined as at least 6 months), clinical benefit, and toxicity were assessed. The co-amplification of ERBB2 and TOP2A was assessed by shallow whole genome sequencing on tumor tissue whenever available. RESULTS Forty-three patients received VP16-T after a median number of six prior treatment lines for HER2+ MBC. Median PFS and OS were 2.9 months (95% CI [2.4-4.7]) and 11.3 months (95% CI [8.3-25.0]), respectively. Three patients had a complete response, while 12/40 (30%) experienced clinical benefit. Only three patients stopped treatment for toxicity. Seven (35%) patients displayed a TOP2A/ERBB2 co-amplification. No statistically significant correlation was found between outcome and TOP2A/ERBB2 co-amplification. CONCLUSION Our analysis suggests a favorable efficacy and toxicity profile for VP16-T in patients with heavily pretreated HER2+ MBC.
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Affiliation(s)
- Clelia Chalumeau
- Department of Medical Oncology, Institut Curie, 92210 St Cloud, France; (P.V.); (F.-C.B.); (F.L.)
| | | | - Alexandre Eeckhoutte
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Institut Curie, 75248 Paris, France; (A.E.); (M.-H.S.)
- Institut Curie, PSL Research University, 75005 Paris, France
| | - Stelly Ballet
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75005 Paris, France; (S.B.); (A.V.-S.)
| | - Anne Vincent-Salomon
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75005 Paris, France; (S.B.); (A.V.-S.)
| | - Perrine Vuagnat
- Department of Medical Oncology, Institut Curie, 92210 St Cloud, France; (P.V.); (F.-C.B.); (F.L.)
| | - Audrey Bellesoeur
- Department of Medical Oncology, Institut Curie, 75005 Paris, France; (A.B.); (J.-Y.P.)
| | - Jean-Yves Pierga
- Department of Medical Oncology, Institut Curie, 75005 Paris, France; (A.B.); (J.-Y.P.)
- Health Faculty, University of Paris, 75005 Paris, France
| | - Marc-Henri Stern
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Institut Curie, 75248 Paris, France; (A.E.); (M.-H.S.)
- Institut Curie, PSL Research University, 75005 Paris, France
| | - Francois-Clement Bidard
- Department of Medical Oncology, Institut Curie, 92210 St Cloud, France; (P.V.); (F.-C.B.); (F.L.)
- UVSQ/Paris Saclay University, 78000 Versailles, France
| | - Florence Lerebours
- Department of Medical Oncology, Institut Curie, 92210 St Cloud, France; (P.V.); (F.-C.B.); (F.L.)
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17
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Yang SX, Hewitt SM, Yu J. Locoregional tumor burden and risk of mortality in metastatic breast cancer. NPJ Precis Oncol 2022; 6:22. [PMID: 35383277 PMCID: PMC8983737 DOI: 10.1038/s41698-022-00265-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/24/2022] [Indexed: 11/09/2022] Open
Abstract
The role of lymph node involvement and tumor size in metastatic disease including breast cancer is unclear. Here, nodal metastasis and T stage on the risk of mortality were investigated in de novo metastatic breast cancer population (35812 patients) in the Surveillance, Epidemiology, and End Results (SEER) Program database in the United States. We found an association between all-cause mortality and regional node involvement (adjusted hazard ratio [HR] = 1.45, 95% confidence interval [CI] 1.36–1.55, p < 0.0001) or T stage (HR = 1.20, 95% CI 1.14–1.25, p < 0.0001), independent of known clinicopathologic measurements. Number of positive nodes, and size and chest wall involvement of the breast tumors exhibited similar significance for breast cancer-specific mortality in the population (p < 0.0001 each), and all-cause mortality in hormone receptor (HR)-positive/HER2-negative (HR+/HER2–), HR+/HER2+, HR–/HER2+ and triple-negative metastatic breast cancer subtypes. Thus, nodal involvement and T stage are independent risk factors for mortality in the population of de novo metastatic breast cancer.
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Affiliation(s)
- Sherry X Yang
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - John Yu
- ELIASSEN Group, Reston, VA, USA
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18
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Wang Z, Cai H, Zhao E, Cui H. The Diverse Roles of Histone Demethylase KDM4B in Normal and Cancer Development and Progression. Front Cell Dev Biol 2022; 9:790129. [PMID: 35186950 PMCID: PMC8849108 DOI: 10.3389/fcell.2021.790129] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/31/2021] [Indexed: 01/05/2023] Open
Abstract
Histone methylation status is an important process associated with cell growth, survival, differentiation and gene expression in human diseases. As a member of the KDM4 family, KDM4B specifically targets H1.4K26, H3K9, H3K36, and H4K20, which affects both histone methylation and gene expression. Therefore, KDM4B is often regarded as a key intermediate protein in cellular pathways that plays an important role in growth and development as well as organ differentiation. However, KDM4B is broadly defined as an oncoprotein that plays key roles in processes related to tumorigenesis, including cell proliferation, cell survival, metastasis and so on. In this review, we discuss the diverse roles of KDM4B in contributing to cancer progression and normal developmental processes. Furthermore, we focus on recent studies highlighting the oncogenic functions of KDM4B in various kinds of cancers, which may be a novel therapeutic target for cancer treatment. We also provide a relatively complete report of the progress of research related to KDM4B inhibitors and discuss their potential as therapeutic agents for overcoming cancer.
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Affiliation(s)
- Zhongze Wang
- State Key Laboratory of Silkworm Genome Biology, Medical Research Institute, Southwest University, Chongqing, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China
| | - Huarui Cai
- State Key Laboratory of Silkworm Genome Biology, Medical Research Institute, Southwest University, Chongqing, China
| | - Erhu Zhao
- State Key Laboratory of Silkworm Genome Biology, Medical Research Institute, Southwest University, Chongqing, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China
- *Correspondence: Erhu Zhao, ; Hongjuan Cui,
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Medical Research Institute, Southwest University, Chongqing, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China
- *Correspondence: Erhu Zhao, ; Hongjuan Cui,
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19
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Porazzi P, Petruk S, Pagliaroli L, De Dominici M, Deming D, Puccetti MV, Kushinsky S, Kumar G, Minieri V, Barbieri E, Deliard S, Grande A, Trizzino M, Gardini A, Canaani E, Palmisiano N, Porcu P, Ertel A, Fortina PM, Eischen CM, Mazo A, Calabretta B. Targeting chemotherapy to de-condensed H3K27me3-marked chromatin of AML cells enhances leukemia suppression. Cancer Res 2021; 82:458-471. [PMID: 34903608 DOI: 10.1158/0008-5472.can-21-1297] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 09/15/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022]
Abstract
Despite treatment with intensive chemotherapy, acute myeloid leukemia (AML) remains an aggressive malignancy with a dismal outcome in most patients. We found that AML cells exhibit an unusually rapid accumulation of the repressive histone mark H3K27me3 on nascent DNA. In cell lines, primary cells and xenograft mouse models, inhibition of the H3K27 histone methyltransferase EZH2 to de-condense the H3K27me3-marked chromatin of AML cells enhanced chromatin accessibility and chemotherapy-induced DNA damage, apoptosis, and leukemia suppression. These effects were further promoted when chromatin de-condensation of AML cells was induced upon S-phase entry after release from a transient G1 arrest mediated by CDK4/6 inhibition. In the p53-null KG-1 and THP-1 AML cell lines, EZH2 inhibitor and doxorubicin co-treatment induced transcriptional reprogramming that was, in part, dependent on de-repression of H3K27me3-marked gene promoters and led to increased expression of cell death-promoting and growth-inhibitory genes. In conclusion, decondensing H3K27me3-marked chromatin by EZH2 inhibition represents a promising approach to improve the efficacy of DNA-damaging cytotoxic agents in AML patients. This strategy might allow for a lowering of chemotherapy doses with a consequent reduction of treatment-related side effects in elderly AML patients or those with significant comorbidities.
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Affiliation(s)
- Patrizia Porazzi
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center,, Thomas Jefferson University
| | - Luca Pagliaroli
- Department of Biochemistry and Molecular Biology and Sidney Kimmel Cancer Center,, Thomas Jefferson University
| | | | - David Deming
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center,, Thomas Jefferson University
| | - Matthew V Puccetti
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
| | - Saul Kushinsky
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
| | - Gaurav Kumar
- Department of Cancer Biology, Thomas Jefferson University
| | - Valentina Minieri
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
| | - Elisa Barbieri
- Gene Expression and Regulation Program, The Wistar Institute
| | - Sandra Deliard
- Gene Expression and Regulation Program, The Wistar Institute
| | - Alexis Grande
- Department of Life Sciences, University of Modena and Reggio Emilia
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center,, Thomas Jefferson University
| | | | - Eli Canaani
- The Department of Molecular Cell Biology, Weizmann Institute of Science
| | | | | | - Adam Ertel
- Department of Cancer Biology, Thomas Jefferson University
| | | | | | - Alexander Mazo
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center,, Thomas Jefferson University
| | - Bruno Calabretta
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
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20
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Batra RN, Lifshitz A, Vidakovic AT, Chin SF, Sati-Batra A, Sammut SJ, Provenzano E, Ali HR, Dariush A, Bruna A, Murphy L, Purushotham A, Ellis I, Green A, Garrett-Bakelman FE, Mason C, Melnick A, Aparicio SAJR, Rueda OM, Tanay A, Caldas C. DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation. Nat Commun 2021; 12:5406. [PMID: 34518533 PMCID: PMC8437946 DOI: 10.1038/s41467-021-25661-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/18/2021] [Indexed: 11/08/2022] Open
Abstract
DNA methylation is aberrant in cancer, but the dynamics, regulatory role and clinical implications of such epigenetic changes are still poorly understood. Here, reduced representation bisulfite sequencing (RRBS) profiles of 1538 breast tumors and 244 normal breast tissues from the METABRIC cohort are reported, facilitating detailed analysis of DNA methylation within a rich context of genomic, transcriptional, and clinical data. Tumor methylation from immune and stromal signatures are deconvoluted leading to the discovery of a tumor replication-linked clock with genome-wide methylation loss in non-CpG island sites. Unexpectedly, methylation in most tumor CpG islands follows two replication-independent processes of gain (MG) or loss (ML) that we term epigenomic instability. Epigenomic instability is correlated with tumor grade and stage, TP53 mutations and poorer prognosis. After controlling for these global trans-acting trends, as well as for X-linked dosage compensation effects, cis-specific methylation and expression correlations are uncovered at hundreds of promoters and over a thousand distal elements. Some of these targeted known tumor suppressors and oncogenes. In conclusion, this study demonstrates that global epigenetic instability can erode cancer methylomes and expose them to localized methylation aberrations in-cis resulting in transcriptional changes seen in tumors.
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Affiliation(s)
- Rajbir Nath Batra
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Aviezer Lifshitz
- Department of Computer Science and Applied Mathematics, and Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | | | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Ankita Sati-Batra
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Stephen-John Sammut
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Elena Provenzano
- Cancer Research UK Cambridge Centre, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - H Raza Ali
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Centre, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ali Dariush
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alejandra Bruna
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Leigh Murphy
- Research Institute in Oncology and Hematology, Winnipeg, Manitoba, Canada
| | - Arnie Purushotham
- School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Ian Ellis
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK
| | - Andrew Green
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK
| | - Francine E Garrett-Bakelman
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Chris Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ari Melnick
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Samuel A J R Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Oscar M Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, and Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
- Cancer Research UK Cambridge Centre, Cambridge, UK.
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
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21
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Lai J, Lin X, Cao F, Mok H, Chen B, Liao N. CDKN1C as a prognostic biomarker correlated with immune infiltrates and therapeutic responses in breast cancer patients. J Cell Mol Med 2021; 25:9390-9401. [PMID: 34464504 PMCID: PMC8500970 DOI: 10.1111/jcmm.16880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/01/2021] [Accepted: 08/09/2021] [Indexed: 12/14/2022] Open
Abstract
Breast cancer (BC) prognosis and therapeutic sensitivity could not be predicted efficiently. Previous evidence have shown the vital roles of CDKN1C in BC. Therefore, we aimed to construct a CDKN1C‐based model to accurately predicting overall survival (OS) and treatment responses in BC patients. In this study, 995 BC patients from The Cancer Genome Atlas database were selected. Kaplan‐Meier curve, Gene set enrichment and immune infiltrates analyses were executed. We developed a novel CDKN1C‐based nomogram to predict the OS, verified by the time‐dependent receiver operating characteristic curve, calibration curve and decision curve. Therapeutic response prediction was followed based on the low‐ and high‐nomogram score groups. Our results indicated that low‐CDKN1C expression was associated with shorter OS and lower proportion of naïve B cells, CD8 T cells, activated NK cells. The predictive accuracy of the nomogram for 5‐year OS was superior to the tumour‐node‐metastasis stage (area under the curve: 0.746 vs. 0.634, p < 0.001). The nomogram exhibited excellent predictive performance, calibration ability and clinical utility. Moreover, low‐risk patients were identified with stronger sensitivity to therapeutic agents. This tool can improve BC prognosis and therapeutic responses prediction, thus guiding individualized treatment decisions.
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Affiliation(s)
- Jianguo Lai
- Department of Breast Cancer, Guangdong Provincial People's Hospital,Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiaoyi Lin
- Department of Breast Cancer, Guangdong Provincial People's Hospital,Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Fangrong Cao
- Department of Breast Cancer, Guangdong Provincial People's Hospital,Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hsiaopei Mok
- Department of Breast Cancer, Guangdong Provincial People's Hospital,Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Bo Chen
- Department of Breast Cancer, Guangdong Provincial People's Hospital,Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ning Liao
- Department of Breast Cancer, Guangdong Provincial People's Hospital,Guangdong Academy of Medical Sciences, Guangzhou, China
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22
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Sterling J, Menezes SV, Abbassi RH, Munoz L. Histone lysine demethylases and their functions in cancer. Int J Cancer 2021; 148:2375-2388. [PMID: 33128779 DOI: 10.1002/ijc.33375] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 12/29/2022]
Abstract
Histone lysine demethylases (KDMs) are enzymes that remove the methylation marks on lysines in nucleosomes' histone tails. These changes in methylation marks regulate gene transcription during both development and malignant transformation. Depending on which lysine residue is targeted, the effect of a given KDM on gene transcription can be either activating or repressing, and KDMs can regulate the expression of both oncogenes and tumour suppressors. Thus, the functions of KDMs can be regarded as both oncogenic and tumour suppressive, contingent on cell context and the enzyme isoform. Finally, KDMs also demethylate nonhistone proteins and have a variety of demethylase-independent functions. These epigenetic and other mechanisms that KDMs control make them important regulators of malignant tumours. Here, we present an overview of eight KDM subfamilies, their most-studied lysine targets and selected recent data on their roles in cancer stem cells, tumour aggressiveness and drug tolerance.
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Affiliation(s)
- Jayden Sterling
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Sharleen V Menezes
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Ramzi H Abbassi
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Lenka Munoz
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
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23
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Caswell-Jin JL, Lorenz C, Curtis C. Molecular Heterogeneity and Evolution in Breast Cancer. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2021. [DOI: 10.1146/annurev-cancerbio-060220-014137] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Breast cancer comprises a heterogeneous group of tumor subtypes, whether defined by immunohistochemistry of key proteins, RNA expression profiles, or genetic alterations, and each of these subtypes may benefit from a distinct treatment approach. However, there can be striking heterogeneity within tumors, which may pose challenges to the development of personalized approaches to therapy. Intratumor heterogeneity can be divided into three main categories: genetic, phenotypic, and microenvironmental. Here, we review technologies to interrogate these three categories of heterogeneity in patient samples, as well as the current state of understanding of these categories in breast cancer, from cell to cell, across different regions of the same tumor mass, across treatment, and across metastasis. Efforts to characterize tumor heterogeneity longitudinally will be crucial to the development of personalized oncology for breast cancer.
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Affiliation(s)
- Jennifer L. Caswell-Jin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Carina Lorenz
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Christina Curtis
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
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24
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Singh S, Abu-Zaid A, Lin W, Low J, Abdolvahabi A, Jin H, Wu Q, Cooke B, Fang J, Bowling J, Vaithiyalingam S, Currier D, Yun MK, Fernando DM, Maier J, Tillman H, Bulsara P, Lu Z, Das S, Shelat A, Li Z, Young B, Lee R, Rankovic Z, Murphy AJ, White SW, Davidoff AM, Chen T, Yang J. 17-DMAG dually inhibits Hsp90 and histone lysine demethylases in alveolar rhabdomyosarcoma. iScience 2020; 24:101996. [PMID: 33490904 PMCID: PMC7811140 DOI: 10.1016/j.isci.2020.101996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/09/2020] [Accepted: 12/23/2020] [Indexed: 12/15/2022] Open
Abstract
Histone lysine demethylases (KDMs) play critical roles in oncogenesis and therefore may be effective targets for anticancer therapy. Using a time-resolved fluorescence resonance energy transfer demethylation screen assay, in combination with multiple orthogonal validation approaches, we identified geldanamycin and its analog 17-DMAG as KDM inhibitors. In addition, we found that these Hsp90 inhibitors increase degradation of the alveolar rhabdomyosarcoma (aRMS) driver oncoprotein PAX3-FOXO1 and induce the repressive epigenetic mark H3K9me3 and H3K36me3 at genomic loci of PAX3-FOXO1 targets. We found that as monotherapy 17-DMAG significantly inhibits expression of PAX3-FOXO1 target genes and multiple oncogenic pathways, induces a muscle differentiation signature, delays tumor growth and extends survival in aRMS xenograft mouse models. The combination of 17-DMAG with conventional chemotherapy significantly enhances therapeutic efficacy, indicating that targeting KDM in combination with chemotherapy may serve as a therapeutic approach to PAX3-FOXO1-positive aRMS. Identification of geldanamycin/17-DMAG as histone lysine demethylase inhibitors Geldanamycin/17-DMAG causes degradation of PAX3-FOXO1, an Hsp90 client Geldanamycin/17-DMAG induces epigenetic changes and targets PAX3-FOXO1 pathway 17-DMAG alone or combined with chemotherapy show potency to PAX3-FOXO1 xenografts
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Affiliation(s)
- Shivendra Singh
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis TN 38105, USA
| | - Ahmed Abu-Zaid
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis TN 38105, USA
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jonathan Low
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Alireza Abdolvahabi
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Qiong Wu
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis TN 38105, USA
| | - Bailey Cooke
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis TN 38105, USA
| | - Jie Fang
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis TN 38105, USA
| | - John Bowling
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Sivaraja Vaithiyalingam
- Protein Technologies Center, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Duane Currier
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mi-Kyung Yun
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Dinesh M Fernando
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Julie Maier
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Heather Tillman
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Purva Bulsara
- Department of Biostatistics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zhaohua Lu
- Department of Biostatistics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Anang Shelat
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zhenmei Li
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Brandon Young
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Richard Lee
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Andrew J Murphy
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis TN 38105, USA
| | - Stephen W White
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Andrew M Davidoff
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jun Yang
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis TN 38105, USA
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25
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Martin CJ, Moorehead RA. Polycomb repressor complex 2 function in breast cancer (Review). Int J Oncol 2020; 57:1085-1094. [PMID: 33491744 PMCID: PMC7549536 DOI: 10.3892/ijo.2020.5122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/07/2020] [Indexed: 11/24/2022] Open
Abstract
Epigenetic modifications are important contributors to the regulation of genes within the chromatin. The polycomb repressive complex 2 (PRC2) is a multi‑subunit protein complex that is involved in silencing gene expression through the trimethylation of lysine 27 at histone 3 (H3K27me3). The dysregulation of this modification has been associated with tumorigenicity through the increased repression of tumour suppressor genes via condensing DNA to reduce access to the transcription start site (TSS) within tumor suppressor gene promoters. In the present review, the core proteins of PRC2, as well as key accessory proteins, will be described. In addition, mechanisms controlling the recruitment of the PRC2 complex to H3K27 will be outlined. Finally, literature identifying the role of PRC2 in breast cancer proliferation, apoptosis and migration, including the potential roles of long non‑coding RNAs and the miR‑200 family will be summarized as will the potential use of the PRC2 complex as a therapeutic target.
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Affiliation(s)
- Courtney J. Martin
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Roger A. Moorehead
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G2W1, Canada
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26
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Jiang YZ, Liu Y, Xiao Y, Hu X, Jiang L, Zuo WJ, Ma D, Ding J, Zhu X, Zou J, Verschraegen C, Stover DG, Kaklamani V, Wang ZH, Shao ZM. Molecular subtyping and genomic profiling expand precision medicine in refractory metastatic triple-negative breast cancer: the FUTURE trial. Cell Res 2020; 31:178-186. [PMID: 32719455 PMCID: PMC8027015 DOI: 10.1038/s41422-020-0375-9] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 06/30/2020] [Indexed: 01/20/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly heterogeneous disease, and molecular subtyping may result in improved diagnostic precision and targeted therapies. Our previous study classified TNBCs into four subtypes with putative therapeutic targets. Here, we conducted the FUTURE trial (ClinicalTrials.gov identifier: NCT03805399), a phase Ib/II subtyping-based and genomic biomarker-guided umbrella trial, to evaluate the efficacy of these targets. Patients with refractory metastatic TNBC were enrolled and stratified by TNBC subtypes and genomic biomarkers, and assigned to one of these seven arms: (A) pyrotinib with capecitabine, (B) androgen receptor inhibitor with CDK4/6 inhibitor, (C) anti PD-1 with nab-paclitaxel, (D) PARP inhibitor included, (E) and (F) anti-VEGFR included, or (G) mTOR inhibitor with nab-paclitaxel. The primary end point was the objective response rate (ORR). We enrolled 69 refractory metastatic TNBC patients with a median of three previous lines of therapy (range, 1–8). Objective response was achieved in 20 (29.0%, 95% confidence interval (CI): 18.7%–41.2%) of the 69 intention-to-treat (ITT) patients. Our results showed that immunotherapy (arm C), in particular, achieved the highest ORR (52.6%, 95% CI: 28.9%–75.6%) in the ITT population. Arm E demonstrated favorable ORR (26.1%, 95% CI: 10.2%–48.4% in the ITT population) but with more high grade (≥ 3) adverse events. Somatic mutations of TOP2A and CD8 immunohistochemical score may have the potential to predict immunotherapy response in the immunomodulatory subtype of TNBC. In conclusion, the phase Ib/II FUTURE trial suggested a new concept for TNBC treatment, demonstrating the clinical benefit of subtyping-based targeted therapy for refractory metastatic TNBC.
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Affiliation(s)
- Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Key Laboratory of Breast Cancer in Shanghai, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yin Liu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Key Laboratory of Breast Cancer in Shanghai, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yi Xiao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Key Laboratory of Breast Cancer in Shanghai, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xin Hu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Key Laboratory of Breast Cancer in Shanghai, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Lin Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Key Laboratory of Breast Cancer in Shanghai, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wen-Jia Zuo
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Key Laboratory of Breast Cancer in Shanghai, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ding Ma
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Key Laboratory of Breast Cancer in Shanghai, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jiahan Ding
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Key Laboratory of Breast Cancer in Shanghai, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xiaoyu Zhu
- Jiangsu Hengrui Medicine Co Ltd, Lianyungang, Jiangsu, 222002, China
| | - Jianjun Zou
- Jiangsu Hengrui Medicine Co Ltd, Lianyungang, Jiangsu, 222002, China
| | - Claire Verschraegen
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Daniel G Stover
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Virginia Kaklamani
- Division of Hematology/Oncology, University of Texas Health Science Center San Antonio, San Antonio, TX, 78284, USA
| | - Zhong-Hua Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Key Laboratory of Breast Cancer in Shanghai, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Zhi-Ming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Key Laboratory of Breast Cancer in Shanghai, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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