1
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Li Z, Chen F, Chen L, Liu J, Tseng D, Hadi F, Omarjee S, Kishore K, Kent J, Kirkpatrick J, D’Santos C, Lawson M, Gertz J, Sikora MJ, McDonnell DP, Carroll JS, Polyak K, Oesterreich S, Lee AV. EstroGene2.0: A multi-omic database of response to estrogens, ER-modulators, and resistance to endocrine therapies in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601163. [PMID: 39005294 PMCID: PMC11244912 DOI: 10.1101/2024.06.28.601163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Endocrine therapies targeting the estrogen receptor (ER/ESR1) are the cornerstone to treat ER-positive breast cancers patients, but resistance often limits their effectiveness. Understanding the molecular mechanisms is thus key to optimize the existing drugs and to develop new ER-modulators. Notable progress has been made although the fragmented way data is reported has reduced their potential impact. Here, we introduce EstroGene2.0, an expanded database of its precursor 1.0 version. EstroGene2.0 focusses on response and resistance to endocrine therapies in breast cancer models. Incorporating multi-omic profiling of 361 experiments from 212 studies across 28 cell lines, a user-friendly browser offers comprehensive data visualization and metadata mining capabilities (https://estrogeneii.web.app/). Taking advantage of the harmonized data collection, our follow-up meta-analysis revealed substantial diversity in response to different classes of ER-modulators including SERMs, SERDs, SERCA and LDD/PROTAC. Notably, endocrine resistant models exhibit a spectrum of transcriptomic alterations including a contra-directional shift in ER and interferon signaling, which is recapitulated clinically. Furthermore, dissecting multiple ESR1-mutant cell models revealed the different clinical relevance of genome-edited versus ectopic overexpression model engineering and identified high-confidence mutant-ER targets, such as NPY1R. These examples demonstrate how EstroGene2.0 helps investigate breast cancer's response to endocrine therapies and explore resistance mechanisms.
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Affiliation(s)
- Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Fangyuan Chen
- School of Medicine, Tsinghua University, Beijing, China
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Li Chen
- Computational Biology Department, Carnegie Mellon University, Pittsburgh PA, USA
| | - Jiebin Liu
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Danielle Tseng
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | | | - Soleilmane Omarjee
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kamal Kishore
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Joshua Kent
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Joanna Kirkpatrick
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Clive D’Santos
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Jason Gertz
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Matthew J. Sikora
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Donald P. McDonnell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Jason S. Carroll
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Steffi Oesterreich
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
| | - Adrian V. Lee
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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2
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Valentín López JC, Lange CA, Dehm SM. Androgen receptor and estrogen receptor variants in prostate and breast cancers. J Steroid Biochem Mol Biol 2024; 241:106522. [PMID: 38641298 PMCID: PMC11139604 DOI: 10.1016/j.jsbmb.2024.106522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/23/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
The androgen receptor (AR) and estrogen receptor alpha (ERα) are steroid receptor transcription factors with critical roles in the development and progression of prostate and breast cancers. Advances in the understanding of mechanisms underlying the ligand-dependent activation of these transcription factors have contributed to the development of small molecule inhibitors that block AR and ERα actions. These inhibitors include competitive antagonists and degraders that directly bind the ligand binding domains of these receptors, luteinizing hormone releasing hormone (LHRH) analogs that suppress gonadal synthesis of testosterone or estrogen, and drugs that block specific enzymes required for biosynthesis of testosterone or estrogen. However, resistance to these therapies is frequent, and is often driven by selection for tumor cells with alterations in the AR or ESR1 genes and/or alternatively spliced AR or ESR1 mRNAs that encode variant forms AR or ERα. While most investigations involving AR have been within the context of prostate cancer, and the majority of investigations involving ERα have been within the context of breast cancer, important roles for AR have been elucidated in breast cancer, and important roles for ERα have been elucidated in prostate cancer. Here, we will discuss the roles of AR and ERα in breast and prostate cancers, outline the effects of gene- and mRNA-level alterations in AR and ESR1 on progression of these diseases, and identify strategies that are being developed to target these alterations therapeutically.
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Affiliation(s)
| | - Carol A Lange
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Department of Medicine-Hematology, Oncology & Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA; Department of Urology, University of Minnesota, Minneapolis, MN, USA.
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3
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Young K, Hancock G, Fink E, Zigrossi A, Flowers B, Cooper D, Nguyen V, Martinez M, Mon K, Bosland M, Zak D, Runde A, Sharifi M, Kastrati I, Minh D, Kregel S, Fanning S. Targeting Unique Ligand Binding Domain Structural Features Downregulates DKK1 in Y537S ESR1 Mutant Breast Cancer Cells. RESEARCH SQUARE 2024:rs.3.rs-4542467. [PMID: 38978585 PMCID: PMC11230492 DOI: 10.21203/rs.3.rs-4542467/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Resistance to endocrine therapies remains a major clinical hurdle in breast cancer. Mutations to estrogen receptor alpha (ERα) arise after continued therapeutic pressure. Next generation selective estrogen receptor modulators and degraders/downregulators (SERMs and SERDs) show clinical efficacy, but responses are often non-durable. A tyrosine to serine point mutation at position 537 in the ERα ligand binding domain (LBD) is among the most common and most pathogenic alteration in this setting. It enables endocrine therapy resistance by superceding intrinsic structural-energetic gatekeepers of ER hormone-dependence, it enhances metastatic burden by enabling neomorphic ER-dependent transcriptional programs, and it resists SERM and SERD inhibiton by reducing their binding affinities and abilities to antagonize transcriptional coregulator binding. However, a subset of SERMs and SERDs can achieve efficacy by adopting poses that force the mutation to engage in a new interaction that favors the therapeutic receptor antagonist conformation. We previously described a chemically unconventional SERM, T6I-29, that demonstrates significant anti-proliferative activities in Y537S ERα breast cancer cells. Here, we use a comprehensive suite of structural-biochemical, in vitro, and in vivo approaches to better T6I-29's activities in breast cancer cells harboring Y537S ERα. RNA sequencing in cells treated with T6I-29 reveals a neomorphic downregulation of DKK1, a secreted glycoprotein known to play oncogenic roles in other cancers. Importantly, we find that DKK1 is significantly enriched in ER+ breast cancer plasma compared to healthy controls. This study shows how new SERMs and SERDs can identify new therapeutic pathways in endocrine-resistant ER+ breast cancers.
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Affiliation(s)
- K.S. Young
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - G.R. Hancock
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - E. Fink
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - A. Zigrossi
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - B. Flowers
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - D.A. Cooper
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616
| | - V.T. Nguyen
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616
| | - M. Martinez
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - K.S. Mon
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - M. Bosland
- Department of Pathology, University of Illinois Chicago, Chicago, IL 60607
| | - D. Zak
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - A. Runde
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - M.N. Sharifi
- Department of Medicine, University of Wisconsin, Madison, WI 53705
| | - I. Kastrati
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - D.D.L. Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616
| | - S. Kregel
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - S.W. Fanning
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
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4
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Young K, Hancock G, Fink E, Zigrossi A, Flowers B, Cooper D, Nguyen V, Martinez M, Mon K, Bosland M, Zak D, Runde A, Sharifi M, Kastrati I, Minh D, Kregel S, Fanning S. Targeting Unique Ligand Binding Domain Structural Features Downregulates DKK1 in Y537S ESR1 Mutant Breast Cancer Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596307. [PMID: 38854123 PMCID: PMC11160638 DOI: 10.1101/2024.05.28.596307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Resistance to endocrine therapies remains a major clinical hurdle in breast cancer. Mutations to estrogen receptor alpha (ERα) arise after continued therapeutic pressure. Next generation selective estrogen receptor modulators and degraders/downregulators (SERMs and SERDs) show clinical efficacy, but responses are often non-durable. A tyrosine to serine point mutation at position 537 in the ERα ligand binding domain (LBD) is among the most common and most pathogenic alteration in this setting. It enables endocrine therapy resistance by superceding intrinsic structural-energetic gatekeepers of ER hormone-dependence, it enhances metastatic burden by enabling neomorphic ER-dependent transcriptional programs, and it resists SERM and SERD inhibiton by reducing their binding affinities and abilities to antagonize transcriptional coregulator binding. However, a subset of SERMs and SERDs can achieve efficacy by adopting poses that force the mutation to engage in a new interaction that favors the therapeutic receptor antagonist conformation. We previously described a chemically unconventional SERM, T6I-29, that demonstrates significant anti-proliferative activities in Y537S ERα breast cancer cells. Here, we use a comprehensive suite of structural-biochemical, in vitro, and in vivo approaches to better T6I-29's activities in breast cancer cells harboring Y537S ERα. RNA sequencing in cells treated with T6I-29 reveals a neomorphic downregulation of DKK1, a secreted glycoprotein known to play oncogenic roles in other cancers. Importantly, we find that DKK1 is significantly enriched in ER+ breast cancer plasma compared to healthy controls. This study shows how new SERMs and SERDs can identify new therapeutic pathways in endocrine-resistant ER+ breast cancers.
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Affiliation(s)
- K.S. Young
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - G.R. Hancock
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - E. Fink
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - A. Zigrossi
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - B. Flowers
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - D.A. Cooper
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616
| | - V.T. Nguyen
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616
| | - M. Martinez
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - K.S. Mon
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - M. Bosland
- Department of Pathology, University of Illinois Chicago, Chicago, IL 60607
| | - D. Zak
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - A. Runde
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - M.N. Sharifi
- Department of Medicine, University of Wisconsin, Madison, WI 53705
| | - I. Kastrati
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - D.D.L. Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616
| | - S. Kregel
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
| | - S.W. Fanning
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 50153
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5
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Wu Y, Li Z, Lee AV, Oesterreich S, Luo B. Liver tropism of ER mutant breast cancer is characterized by unique molecular changes and immune infiltration. Breast Cancer Res Treat 2024; 205:371-386. [PMID: 38427312 DOI: 10.1007/s10549-024-07255-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/11/2024] [Indexed: 03/02/2024]
Abstract
PURPOSE Hotspot estrogen receptor alpha (ER/ESR1) mutations are recognized as the driver for both endocrine resistance and metastasis in advanced ER-positive (ER+) breast cancer, but their contributions to metastatic organ tropism remain insufficiently understood. In this study, we aim to comprehensively profile the organotropic metastatic pattern for ESR1 mutant breast cancer. METHODS The organ-specific metastatic pattern of ESR1 mutant breast cancer was delineated using multi-omics data from multiple publicly available cohorts of ER+ metastatic breast cancer patients. Gene mutation/copy number variation (CNV) and differential gene expression analyses were performed to identify the genomic and transcriptomic alterations uniquely associated with ESR1 mutant liver metastasis. Upstream regulator, downstream pathway, and immune infiltration analysis were conducted for subsequent mechanistic investigations. RESULTS ESR1 mutation-driven liver tropism was revealed by significant differences, encompassing a higher prevalence of liver metastasis in patients with ESR1 mutant breast cancer and an enrichment of mutations in liver metastatic samples. The significant enrichment of AGO2 copy number amplifications (CNAs) and multiple gene expression changes were revealed uniquely in ESR1 mutant liver metastasis. We also unveiled alterations in downstream signaling pathways and immune infiltration, particularly an enrichment of neutrophils, suggesting potential therapeutic vulnerabilities. CONCLUSION Our data provide a comprehensive characterization of the behaviors and mechanisms of ESR1 mutant liver metastasis, paving the way for the development of personalized therapy to target liver metastasis for patients with ESR1 mutant breast cancer.
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Affiliation(s)
- Yang Wu
- School of Medicine, Tsinghua University, Beijing, China
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, PA, USA
| | - Zheqi Li
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V Lee
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steffi Oesterreich
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bin Luo
- Department of General Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, China.
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6
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Hancock GR, Gertz J, Jeselsohn R, Fanning SW. Estrogen Receptor Alpha Mutations, Truncations, Heterodimers, and Therapies. Endocrinology 2024; 165:bqae051. [PMID: 38643482 PMCID: PMC11075793 DOI: 10.1210/endocr/bqae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/02/2024] [Accepted: 04/17/2024] [Indexed: 04/23/2024]
Abstract
Annual breast cancer (BCa) deaths have declined since its apex in 1989 concomitant with widespread adoption of hormone therapies that target estrogen receptor alpha (ERα), the prominent nuclear receptor expressed in ∼80% of BCa. However, up to ∼50% of patients who are ER+ with high-risk disease experience post endocrine therapy relapse and metastasis to distant organs. The vast majority of BCa mortality occurs in this setting, highlighting the inadequacy of current therapies. Genomic abnormalities to ESR1, the gene encoding ERα, emerge under prolonged selective pressure to enable endocrine therapy resistance. These genetic lesions include focal gene amplifications, hotspot missense mutations in the ligand binding domain, truncations, fusions, and complex interactions with other nuclear receptors. Tumor cells utilize aberrant ERα activity to proliferate, spread, and evade therapy in BCa as well as other cancers. Cutting edge studies on ERα structural and transcriptional relationships are being harnessed to produce new therapies that have shown benefits in patients with ESR1 hotspot mutations. In this review we discuss the history of ERα, current research unlocking unknown aspects of ERα signaling including the structural basis for receptor antagonism, and future directions of ESR1 investigation. In addition, we discuss the development of endocrine therapies from their inception to present day and survey new avenues of drug development to improve pharmaceutical profiles, targeting, and efficacy.
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Affiliation(s)
- Govinda R Hancock
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 60513, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Center, University of Utah, Salt Lake City, UT 84112, USA
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Sean W Fanning
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 60513, USA
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7
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Qin Q, Zhou Y, Guo J, Chen Q, Tang W, Li Y, You J, Li Q. Conserved methylation signatures associate with the tumor immune microenvironment and immunotherapy response. Genome Med 2024; 16:47. [PMID: 38566132 PMCID: PMC10985907 DOI: 10.1186/s13073-024-01318-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Aberrant DNA methylation is a major characteristic of cancer genomes. It remains unclear which biological processes determine epigenetic reprogramming and how these processes influence the variants in the cancer methylome, which can further impact cancer phenotypes. METHODS We performed pairwise permutations of 381,900 loci in 569 paired DNA methylation profiles of cancer tissue and matched normal tissue from The Cancer Genome Atlas (TCGA) and defined conserved differentially methylated positions (DMPs) based on the resulting null distribution. Then, we derived independent methylation signatures from 2,465 cancer-only methylation profiles from the TCGA and 241 cell line-based methylation profiles from the Genomics of Drug Sensitivity in Cancer (GDSC) cohort using nonnegative matrix factorization (NMF). We correlated DNA methylation signatures with various clinical and biological features, including age, survival, cancer stage, tumor immune microenvironment factors, and immunotherapy response. We inferred the determinant genes of these methylation signatures by integrating genomic and transcriptomic data and evaluated the impact of these signatures on cancer phenotypes in independent bulk and single-cell RNA/methylome cohorts. RESULTS We identified 7,364 differentially methylated positions (2,969 Hyper-DMPs and 4,395 Hypo-DMPs) in nine cancer types from the TCGA. We subsequently retrieved three highly conserved, independent methylation signatures (Hyper-MS1, Hypo-MS1, and Hypo-MS4) from cancer tissues and cell lines based on these Hyper and Hypo-DMPs. Our data suggested that Hypo-MS4 activity predicts poor survival and is associated with immunotherapy response and distant tumor metastasis, and Hypo-MS4 activity is related to TP53 mutation and FOXA1 binding specificity. In addition, we demonstrated a correlation between the activities of Hypo-MS4 in cancer cells and the fractions of regulatory CD4 + T cells with the expression levels of immunological genes in the tumor immune microenvironment. CONCLUSIONS Our findings demonstrated that the methylation signatures of distinct biological processes are associated with immune activity in the cancer microenvironment and predict immunotherapy response.
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Affiliation(s)
- Qingqing Qin
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Ying Zhou
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Jintao Guo
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Qinwei Chen
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
| | - Weiwei Tang
- Department of Medical Oncology, School of Medicine, The First Affiliated Hospital of Xiamen University and Institute of Hematology, Xiamen University, Xiamen, 361003, China
- Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, The School of Clinical Medicine of Fujian, Medical University, Xiamen, 361003, China
| | - Yuchen Li
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Jun You
- Department of Gastrointestinal Oncology Surgery, The First Affiliated Hospital of Xiamen University, Cancer Center, Xiamen, 361003, China
| | - Qiyuan Li
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China.
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China.
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China.
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8
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Xu X, Qiu S, Zeng B, Huang Y, Wang X, Li F, Yang Y, Cao L, Zhang X, Wang J, Ma L. N 6-methyladenosine demethyltransferase FTO mediated m 6A modification of estrogen receptor alpha in non-small cell lung cancer tumorigenesis. Oncogene 2024; 43:1288-1302. [PMID: 38443681 DOI: 10.1038/s41388-024-02992-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/07/2024]
Abstract
Fat mass and obesity-associated protein (FTO), which is closely linked with obesity and dietary intake, plays an important role in diet-related metabolic diseases. However, the underlying mechanism of the N6-methyladenosine (m6A) demethyltransferase FTO in tumor development and progression remains largely unexplored. Here, we demonstrated that FTO expression was largely lower in non-small cell lung cancer (NSCLC) samples than in adjacent healthy tissues, and its expression negatively correlated with poor prognosis. Gain- and loss-of-function assays revealed that FTO inhibited NSCLC tumor cell growth and metastasis in vitro and in vivo. Mechanistically, estrogen receptor alpha (ESR1) is a target of FTO, and increased FTO expression significantly impaired the m6A levels of ESR1 mRNA. There were two clear m6A modification sites (5247A and 5409A) in the 3' untranslated region (3'UTR) of ESR1, and FTO could decrease their methylation. Moreover, the m6A readers YTHDF1 and IGF2BP3 recognized and bound the m6A sites in ESR1 mRNA, thereby enhancing its stability and facilitating tumor growth. We also showed that ESR1 has good diagnostic value for NSCLC. In conclusion, we uncovered an important mechanism of epitranscriptomic regulation by the FTO-YTHDF1-IGF2BP3-ESR1 axis and identified the potential of m6A-dependent therapeutic strategies for NSCLC.
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Affiliation(s)
- Xin Xu
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Shiyu Qiu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Bingjie Zeng
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yiwen Huang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xianzhao Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Fusheng Li
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yiran Yang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Leiqun Cao
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xiao Zhang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Lifang Ma
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
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De Marchi T, Lai CF, Simmons GM, Goldsbrough I, Harrod A, Lam T, Buluwela L, Kjellström S, Brueffer C, Saal LH, Malmström J, Ali S, Niméus E. Proteomic profiling reveals that ESR1 mutations enhance cyclin-dependent kinase signaling. Sci Rep 2024; 14:6873. [PMID: 38519482 PMCID: PMC10959978 DOI: 10.1038/s41598-024-56412-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/06/2024] [Indexed: 03/25/2024] Open
Abstract
Three quarters of all breast cancers express the estrogen receptor (ER, ESR1 gene), which promotes tumor growth and constitutes a direct target for endocrine therapies. ESR1 mutations have been implicated in therapy resistance in metastatic breast cancer, in particular to aromatase inhibitors. ESR1 mutations promote constitutive ER activity and affect other signaling pathways, allowing cancer cells to proliferate by employing mechanisms within and without direct regulation by the ER. Although subjected to extensive genetic and transcriptomic analyses, understanding of protein alterations remains poorly investigated. Towards this, we employed an integrated mass spectrometry based proteomic approach to profile the protein and phosphoprotein differences in breast cancer cell lines expressing the frequent Y537N and Y537S ER mutations. Global proteome analysis revealed enrichment of mitotic and immune signaling pathways in ER mutant cells, while phosphoprotein analysis evidenced enriched activity of proliferation associated kinases, in particular CDKs and mTOR. Integration of protein expression and phosphorylation data revealed pathway-dependent discrepancies (motility vs proliferation) that were observed at varying degrees across mutant and wt ER cells. Additionally, protein expression and phosphorylation patterns, while under different regulation, still recapitulated the estrogen-independent phenotype of ER mutant cells. Our study is the first proteome-centric characterization of ESR1 mutant models, out of which we confirm estrogen independence of ER mutants and reveal the enrichment of immune signaling pathways at the proteomic level.
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Affiliation(s)
- Tommaso De Marchi
- Division of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, 22362, Lund, Sweden.
| | - Chun-Fui Lai
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Georgia M Simmons
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Isabella Goldsbrough
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Alison Harrod
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Thai Lam
- Division of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, 22362, Lund, Sweden
| | - Lakjaya Buluwela
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Sven Kjellström
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Solvegatan 19, 22362, Lund, Sweden
- Swedish National Infrastructure for Biological Mass Spectrometry - BioMS, Lund, Sweden
| | - Christian Brueffer
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, 22381, Lund, Sweden
| | - Lao H Saal
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, 22381, Lund, Sweden
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Klinikgatan 32, 22184, Lund, Sweden
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
| | - Emma Niméus
- Division of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, 22362, Lund, Sweden.
- Department of Surgery, Skåne University Hospital, Lund, Sweden.
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10
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Xie Q, Liu S, Zhang S, Liao L, Xiao Z, Wang S, Zhang P. Research progress on the multi-omics and survival status of circulating tumor cells. Clin Exp Med 2024; 24:49. [PMID: 38427120 PMCID: PMC10907490 DOI: 10.1007/s10238-024-01309-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
In the dynamic process of metastasis, circulating tumor cells (CTCs) emanate from the primary solid tumor and subsequently acquire the capacity to disengage from the basement membrane, facilitating their infiltration into the vascular system via the interstitial tissue. Given the pivotal role of CTCs in the intricate hematogenous metastasis, they have emerged as an essential resource for a deeper comprehension of cancer metastasis while also serving as a cornerstone for the development of new indicators for early cancer screening and new therapeutic targets. In the epoch of precision medicine, as CTC enrichment and separation technologies continually advance and reach full fruition, the domain of CTC research has transcended the mere straightforward detection and quantification. The rapid advancement of CTC analysis platforms has presented a compelling opportunity for in-depth exploration of CTCs within the bloodstream. Here, we provide an overview of the current status and research significance of multi-omics studies on CTCs, including genomics, transcriptomics, proteomics, and metabolomics. These studies have contributed to uncovering the unique heterogeneity of CTCs and identifying potential metastatic targets as well as specific recognition sites. We also review the impact of various states of CTCs in the bloodstream on their metastatic potential, such as clustered CTCs, interactions with other blood components, and the phenotypic states of CTCs after undergoing epithelial-mesenchymal transition (EMT). Within this context, we also discuss the therapeutic implications and potential of CTCs.
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Affiliation(s)
- Qingming Xie
- NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Shilei Liu
- NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Sai Zhang
- NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Liqiu Liao
- Department of Breast Surgery, Hunan Clinical Meditech Research Center for Breast Cancer, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Zhi Xiao
- Department of Breast Surgery, Hunan Clinical Meditech Research Center for Breast Cancer, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Shouman Wang
- Department of Breast Surgery, Hunan Clinical Meditech Research Center for Breast Cancer, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
| | - Pengfei Zhang
- NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
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11
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Lu J, Feng Y, Zhou Y, Xiao Z, Yang Z, Li J, Cai H, Wang J. DPM2 serve as novel oncogene and prognostic marker transactivated by ESR1 in breast cancer. ENVIRONMENTAL TOXICOLOGY 2024; 39:1737-1746. [PMID: 38050961 DOI: 10.1002/tox.24059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023]
Abstract
Breast cancer (BRCA) is the most common malignancies worldwide with increasing rate. Dolichol phosphate mannose synthase (DPMS) is a critical mannosyltransferase involved in the posttranslational modification of proteins. At present, there is limited knowledge regarding the function of DPMS in breast cancer. In this study, silica analysis in multiple datasets found that dolichyl-phosphate mannosyltransferase subunit 2 (DPM2) is an unfavorable prognostic marker, suggesting its oncogenic role. Cell counting kit-8 and apoptosis assays show that DPM2-silenced cancer cells exhibit decreased growth potential and enhanced cell death rate. Further, transwell and wound healing assays show reduced invasion and migration capabilities in DPM2 knockdown groups, xenograft nude mice model demonstrated smaller tumor volume in DPM2 silenced BC cells. Then, the underlying downstream mechanism of DPM2 in BC was predicted and analyzed, highlighting classical tumorigenic pathways like JAK/STAT signaling pathway and oxidative phosphorylation activated in the cancer group. Finally, ChIP-seq analysis, expression correlation analysis, inhibitor treatment, and dual luciferase assays show that DPM2 is transcriptionally activated by estrogen receptor1 (ESR1). The results show that high expression of DPM2 mRNA is significantly correlated with shorter overall survival (OS) and disease-free survival (DFS) in breast cancer patients, and in vitro knockdown of DPM2 can significantly inhibit the malignant phenotypes of cells, including proliferation, invasion, migration, and apoptosis. These results suggest that DPM2 may play an important role in breast cancer. Altogether, we first uncovered the tumorigenic and prognostic role of DPM2 in breast cancer, cellular assays, and bioinformatics analysis highlighted DPM2 as oncogene via inhibited cancer-related signaling pathways in breast cancer. Besides, DPM2 is transcriptionally activated by ESR1, the signaling axis of ESR1/DPM2 provides a new strategy for BC-targeted therapy.
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Affiliation(s)
- Jiahao Lu
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Shanghai, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Anhui, China
| | - Yuejiao Feng
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Shanghai, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Anhui, China
| | - Yiting Zhou
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Jiangsu, China
| | - Zengyou Xiao
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Shanghai, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Anhui, China
| | - Zean Yang
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Shanghai, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Anhui, China
| | - Jiaxian Li
- Department Surgery, Putuo Hospital, University of Traditional Chinese Medicine in Shanghai, Shanghai, China
| | - Han Cai
- Department Surgery, Putuo Hospital, University of Traditional Chinese Medicine in Shanghai, Shanghai, China
| | - Jie Wang
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Shanghai, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Anhui, China
- Department Surgery, Putuo Hospital, University of Traditional Chinese Medicine in Shanghai, Shanghai, China
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12
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Simanjuntak MV, Jauhar MM, Syaifie PH, Arda AG, Mardliyati E, Shalannanda W, Hermanto BR, Anshori I. Revealing Propolis Potential Activity on Inhibiting Estrogen Receptor and Heat Shock Protein 90 Overexpressed in Breast Cancer by Bioinformatics Approaches. Bioinform Biol Insights 2024; 18:11779322231224187. [PMID: 38274992 PMCID: PMC10809879 DOI: 10.1177/11779322231224187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Breast cancer is the most commonly diagnosed cancer globally, with the highest incidence of breast cancer occurring in Asian countries including Indonesia. Among the types of breast cancer, the estrogen receptor (ER)-positive subtype which is prominent with estrogen receptor alpha (ERα) and heat shock protein 90 (HSP90) overexpression genes becomes the most prevalent than the others, approximately 75% of all breast cancer cases. ERα and HSP90 play a role in breast cancer activities including breast tumor growth, invasion, and metastasis mechanism. Propolis, a natural bee product, has been explored for its anticancer activity. However, there is lack of studies that evaluated the potential inhibitor from propolis compounds to the ERα and HSP90 proteins. Therefore, this article focuses on examining the correlation between ERα and HSP90's role in breast cancer and investigating the potential of 93 unique propolis compositions in inhibiting these genes in breast cancer using in silico approaches. This study revealed the positive correlation between ERα and HSP90 genes in breast cancer disease development. Furthermore, we also found novel potential bioactive compounds of propolis against breast cancer through binding with ERα and HSP90; they were 3',4',7-trihydroxyisoflavone and baicalein-7-O-β-D glucopyranoside, respectively. Further research on these compounds is needed to elucidate deeper mechanisms and activity in the real biological system to develop new breast cancer drug treatments.
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Affiliation(s)
- Masriana Vivi Simanjuntak
- Biomedical Engineering Department, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia
| | - Muhammad Miftah Jauhar
- Center of Excellences Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
- Biomedical Engineering, The Graduate School of Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Putri Hawa Syaifie
- Center of Excellences Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | - Adzani Gaisani Arda
- Center of Excellences Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Etik Mardliyati
- Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Wervyan Shalannanda
- Biomedical Engineering Department, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia
| | - Beni Rio Hermanto
- Biomedical Engineering Department, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia
| | - Isa Anshori
- Biomedical Engineering Department, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia
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13
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Sun M, Lv F, Qin C, Du D, Li W, Liu S. The Potential Mechanism of Liujunzi Decoction in the Treatment of Breast Cancer based on Network Pharmacology and Molecular Docking Technology. Curr Pharm Des 2024; 30:702-726. [PMID: 38415453 DOI: 10.2174/0113816128289900240219104854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Liujunzi Decoction (LJZD) is a potential clinical treatment for Breast Cancer (BC), but the active ingredients and mechanisms underlying its effectiveness remain unclear. OBJECTIVE The study aimed to investigate the target gene of LJZD compatibility and the possible mechanism of action in the treatment of breast cancer by using network pharmacology and molecular docking. METHODS Based on TCMSP, ETCM, and BATMAN database searching and screening to obtain the ingredients of LJZD, the related targets were obtained. Breast cancer-related targets were collected through GEO, Geencards, OMIM, and other databases, and drug-disease Venn diagrams were drawn by R. The PPI network map was constructed by using Cytoscape. The intersecting targets were imported into the STRING database, and the core targets were analyzed and screened. The intersected targets were analyzed by the DAVID database for GO and KEGG enrichment. AutoDock Vina and Gromacs were used for molecular docking and simulation of the core targets and active ingredients. RESULTS 126 active ingredients of LJZD were obtained; 241 targets related to breast cancer were sought after screening, and 180 intersection targets were identified through Venn diagram analysis. The core targets were FOS and ESR1. KEGG enrichment analysis mainly involved PI3K/Akt, MAPK, and other signaling pathways. CONCLUSION This study has explored the possible targets and signaling pathways of LJZD in treating breast cancer through network pharmacology and bioinformatics analysis. Molecular docking and simulation have further validated the potential mechanism of action of LJZD in breast cancer treatment, providing essential experimental data for future studies.
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Affiliation(s)
- Mei Sun
- Department of Pharmacy, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Feng Lv
- Department of Pharmacy, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Chunmeng Qin
- Department of Pharmacy, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Dan Du
- Department of Pharmacy, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Wenjun Li
- Department of Pharmacy, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Songqing Liu
- Department of Pharmacy, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
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14
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Venetis K, Pepe F, Pescia C, Cursano G, Criscitiello C, Frascarelli C, Mane E, Russo G, Taurelli Salimbeni B, Troncone G, Guerini Rocco E, Curigliano G, Fusco N, Malapelle U. ESR1 mutations in HR+/HER2-metastatic breast cancer: Enhancing the accuracy of ctDNA testing. Cancer Treat Rev 2023; 121:102642. [PMID: 37864956 DOI: 10.1016/j.ctrv.2023.102642] [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: 08/19/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023]
Abstract
Activating mutations of the estrogen receptor alpha gene (ESR1) are common mechanisms of endocrine therapy (ET) resistance in hormone receptor-positive (HR + )/Human Epidermal Growth Factor Receptor 2 (HER2)-negative metastatic breast cancer (MBC). Recent clinical findings emphasize that both old and new generations of selective ER degraders (SERDs) demonstrate enhanced clinical effectiveness in patients with MBC who have detectable ESR1 mutations via liquid biopsy. This stands in contrast to individuals with MBC carrying these mutations and undergoing conventional endocrine monotherapies like aromatase inhibitors (AIs). Liquid biopsy, particularly the analysis of circulating tumor DNA (ctDNA), has emerged as a promising, minimally invasive alternative to conventional tissue-based testing for identifying ESR1 mutations. Within the context of the PADA-1 and EMERALD trials, distinct molecular methodologies and assays, specifically digital droplet PCR (ddPCR) and next-generation sequencing (NGS), have been employed to evaluate the mutational status of ESR1 within ctDNA. This manuscript critically examines the advantages and indications of various ctDNA testing methods on liquid biopsy for HR+/HER2-negative MBC. Specifically, we delve into the capabilities of ddPCR and NGS in identifying ESR1 mutations. Each methodology boasts unique strengths and limitations: ddPCR excels in its analytical sensitivity for pinpointing hotspot mutations, while NGS offers comprehensive coverage of the spectrum of ESR1 mutations. The significance of meticulous sample handling and timely analysis is emphasized, acknowledging the transient nature of cfDNA. Furthermore, we underscore the importance of detecting sub-clonal ESR1 mutations, as these variants can exert a pivotal influence on predicting both endocrine therapy resistance and responsiveness to SERDs. In essence, this work discusses the role of ctDNA analysis for detecting ESR1 mutations and their implications in tailoring effective therapeutic strategies for HR+/HER2- MBC.
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Affiliation(s)
| | - Francesco Pepe
- Department of Public Health, Federico II University of Naples, Naples, Italy
| | - Carlo Pescia
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy; School of Pathology, University of Milan, Milan, Italy
| | - Giulia Cursano
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Carmen Criscitiello
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Division of New Drugs and Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Frascarelli
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Eltjona Mane
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Gianluca Russo
- Department of Public Health, Federico II University of Naples, Naples, Italy
| | | | - Giancarlo Troncone
- Department of Public Health, Federico II University of Naples, Naples, Italy
| | - Elena Guerini Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Division of New Drugs and Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, Milan, Italy.
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Umberto Malapelle
- Department of Public Health, Federico II University of Naples, Naples, Italy
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15
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Betz M, Massard V, Gilson P, Witz A, Dardare J, Harlé A, Merlin JL. ESR1 Gene Mutations and Liquid Biopsy in ER-Positive Breast Cancers: A Small Step Forward, a Giant Leap for Personalization of Endocrine Therapy? Cancers (Basel) 2023; 15:5169. [PMID: 37958343 PMCID: PMC10649433 DOI: 10.3390/cancers15215169] [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: 10/03/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The predominant forms of breast cancer (BC) are hormone receptor-positive (HR+) tumors characterized by the expression of estrogen receptors (ERs) and/or progesterone receptors (PRs). Patients with HR+ tumors can benefit from endocrine therapy (ET). Three types of ET are approved for the treatment of HR+ BCs and include selective ER modulators, aromatase inhibitors, and selective ER downregulators. ET is the mainstay of adjuvant treatment in the early setting and the backbone of the first-line treatment in an advanced setting; however, the emergence of acquired resistance can lead to cancer recurrence or progression. The mechanisms of ET resistance are often related to the occurrence of mutations in the ESR1 gene, which encodes the ER-alpha protein. As ESR1 mutations are hardly detectable at diagnosis but are present in 30% to 40% of advanced BC (ABC) after treatment, the timeline of testing is crucial. To manage this resistance, ESR1 testing has recently been recommended; in ER+ HER2- ABC and circulating cell-free DNA, so-called liquid biopsy appears to be the most convenient way to detect the emergence of ESR1 mutations. Technically, several options exist, including Next Generation Sequencing and ultra-sensitive PCR-based techniques. In this context, personalization of ET through the surveillance of ESR1 mutations in the plasma of HR+ BC patients throughout the disease course represents an innovative way to improve the standard of care.
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Affiliation(s)
- Margaux Betz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN, Université de Lorraine, 54519 Vandœuvre-lès-Nancy, France
| | - Vincent Massard
- Département d’Oncologie Médicale, Institut de Cancérologie de Lorraine, 54519 Vandœuvre-lès-Nancy, France;
| | - Pauline Gilson
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN, Université de Lorraine, 54519 Vandœuvre-lès-Nancy, France
| | - Andréa Witz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN, Université de Lorraine, 54519 Vandœuvre-lès-Nancy, France
| | - Julie Dardare
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN, Université de Lorraine, 54519 Vandœuvre-lès-Nancy, France
| | - Alexandre Harlé
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN, Université de Lorraine, 54519 Vandœuvre-lès-Nancy, France
| | - Jean-Louis Merlin
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN, Université de Lorraine, 54519 Vandœuvre-lès-Nancy, France
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16
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Feng J, Yang K, Liu X, Song M, Zhan P, Zhang M, Chen J, Liu J. Machine learning: a powerful tool for identifying key microbial agents associated with specific cancer types. PeerJ 2023; 11:e16304. [PMID: 37901464 PMCID: PMC10601900 DOI: 10.7717/peerj.16304] [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: 02/08/2023] [Accepted: 09/26/2023] [Indexed: 10/31/2023] Open
Abstract
Machine learning (ML) includes a broad class of computer programs that improve with experience and shows unique strengths in performing tasks such as clustering, classification and regression. Over the past decade, microbial communities have been implicated in influencing the onset, progression, metastasis, and therapeutic response of multiple cancers. Host-microbe interaction may be a physiological pathway contributing to cancer development. With the accumulation of a large number of high-throughput data, ML has been successfully applied to the study of human cancer microbiomics in an attempt to reveal the complex mechanism behind cancer. In this review, we begin with a brief overview of the data sources included in cancer microbiomics studies. Then, the characteristics of the ML algorithm are briefly introduced. Secondly, the application progress of ML in cancer microbiomics is also reviewed. Finally, we highlight the challenges and future prospects facing ML in cancer microbiomics. On this basis, we conclude that the development of cancer microbiomics can not be achieved without ML, and that ML can be used to develop tumor-targeting microbial therapies, ultimately contributing to personalized and precision medicine.
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Affiliation(s)
- Jia Feng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Kailan Yang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Xuexue Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Min Song
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Ping Zhan
- Department of Obstetrics, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Mi Zhang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Jinsong Chen
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
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17
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Gerratana L, Davis AA, Velimirovic M, Clifton K, Hensing WL, Shah AN, Dai CS, Reduzzi C, D'Amico P, Wehbe F, Medford A, Wander SA, Gradishar WJ, Behdad A, Puglisi F, Ma CX, Bardia A, Cristofanilli M. Interplay between ESR1/PIK3CA codon variants, oncogenic pathway alterations and clinical phenotype in patients with metastatic breast cancer (MBC): comprehensive circulating tumor DNA (ctDNA) analysis. Breast Cancer Res 2023; 25:112. [PMID: 37784176 PMCID: PMC10546685 DOI: 10.1186/s13058-023-01718-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 09/24/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND although being central for the biology and druggability of hormone-receptor positive, HER2 negative metastatic breast cancer (MBC), ESR1 and PIK3CA mutations are simplistically dichotomized as mutated or wild type in current clinical practice. METHODS The study analyzed a multi-institutional cohort comprising 703 patients with luminal-like MBC characterized for circulating tumor DNA through next generation sequencing (NGS). Pathway classification was defined based on previous work (i.e., RTK, RAS, RAF, MEK, NRF2, ER, WNT, MYC, P53, cell cycle, notch, PI3K). Single nucleotide variations (SNVs) were annotated for their oncogenicity through OncoKB. Only pathogenic variants were included in the models. Associations among clinical characteristics, pathway classification, and ESR1/PIK3CA codon variants were explored. RESULTS The results showed a differential pattern of associations for ESR1 and PIK3CA codon variants in terms of co-occurring pathway alterations patterns of metastatic dissemination, and prognosis. ESR1 537 was associated with SNVs in the ER and RAF pathways, CNVs in the MYC pathway and bone metastases, while ESR1 538 with SNVs in the cell cycle pathway and liver metastases. PIK3CA 1047 and 542 were associated with CNVs in the PI3K pathway and with bone metastases. CONCLUSIONS The study demonstrated how ESR1 and PIK3CA codon variants, together with alterations in specific oncogenic pathways, can differentially impact the biology and clinical phenotype of luminal-like MBC. As novel endocrine therapy agents such as selective estrogen receptor degraders (SERDS) and PI3K inhibitors are being developed, these results highlight the pivotal role of ctDNA NGS to describe tumor evolution and optimize clinical decision making.
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Affiliation(s)
- Lorenzo Gerratana
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Andrew A Davis
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Marko Velimirovic
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Katherine Clifton
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Whitney L Hensing
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ami N Shah
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Charles S Dai
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Carolina Reduzzi
- Weill Cornell Medicine, 420 E 70th St, LH 204, New York, NY, 10021, USA
| | - Paolo D'Amico
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Firas Wehbe
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Arielle Medford
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Seth A Wander
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Amir Behdad
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Fabio Puglisi
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
- Department of Medicine, University of Udine, Udine, Italy
| | - Cynthia X Ma
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Aditya Bardia
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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18
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Will M, Liang J, Metcalfe C, Chandarlapaty S. Therapeutic resistance to anti-oestrogen therapy in breast cancer. Nat Rev Cancer 2023; 23:673-685. [PMID: 37500767 PMCID: PMC10529099 DOI: 10.1038/s41568-023-00604-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/29/2023] [Indexed: 07/29/2023]
Abstract
The hormone receptor oestrogen receptor-α (ER) orchestrates physiological mammary gland development, breast carcinogenesis and the progression of breast tumours into lethal, treatment-refractory systemic disease. Selective antagonism of ER signalling has been one of the most successful therapeutic approaches in oncology, benefiting patients as both a cancer preventative measure and a cancer treatment strategy. However, resistance to anti-oestrogen therapy is a major clinical challenge. Over the past decade, we have gained an understanding of how breast cancers evolve under the pressure of anti-oestrogen therapy. This is best depicted by the case of oestrogen-independent mutations in the gene encoding ER (ESR1), which are virtually absent in primary breast cancer but highly prevalent (20-40%) in anti-oestrogen-treated metastatic disease. These and other findings highlight the 'evolvability' of ER+ breast cancer and the need to understand molecular processes by which this evolution occurs. Recent development and approval of next-generation ER antagonists to target ESR1-mutant breast cancer underscores the clinical importance of this evolvability and sets a new paradigm for the treatment of ER+ breast cancers.
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Affiliation(s)
- Marie Will
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jackson Liang
- Department of Oncology Biomarker Development, Genentech, South San Francisco, CA, USA
| | - Ciara Metcalfe
- Department of Discovery Oncology, Genentech, South San Francisco, CA, USA.
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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19
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Yates ME, Li Z, Li Y, Guzolik H, Wang X, Liu T, Hooda J, Atkinson JM, Lee AV, Oesterreich S. ESR1 fusion proteins invoke breast cancer subtype-dependent enrichment of ligand independent pro-oncogenic signatures and phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558175. [PMID: 37790296 PMCID: PMC10542116 DOI: 10.1101/2023.09.18.558175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Breast cancer is a leading cause of female mortality and despite advancements in diagnostics and personalized therapeutics, metastatic disease largely remains incurable due to drug resistance. Fortunately, identification of mechanisms of therapeutic resistance have rapidly transformed our understanding of cancer evasion and is enabling targeted treatment regimens. When the druggable estrogen receptor (ER, ESR1 ), expressed in two-thirds of all breast cancer, is exposed to endocrine therapy, there is risk of somatic mutation development in approximately 30% of cases and subsequent treatment resistance. A more recently discovered mechanism of ER mediated endocrine resistance is the expression of ER fusion proteins. ER fusions, which retain the protein's DNA binding domain, harbor ESR1 exons 1-6 fused to an in-frame gene partner resulting in loss of the 3' ER ligand binding domain (LBD). In this report we demonstrate that in no-special type (NST) and invasive lobular carcinoma (ILC) cell line models, ER fusion proteins exhibit robust hyperactivation of canonical ER signaling pathways independent of the ligand estradiol or anti-endocrine therapies such as Fulvestrant and Tamoxifen. We employ cell line models stably overexpressing ER fusion proteins with concurrent endogenous ER knockdown to minimize the influence of endogenous wildtype ER. Cell lines exhibited shared transcriptomic enrichment in pathways known to be drivers of metastatic disease, notably the MYC pathway. The heterogeneous 3' fusion partners, particularly transcription factors SOX9 and YAP1 , evoked varying degrees of transcriptomic and cistromic activity that translated into unique phenotypic readouts. Herein we report that cell line activity is subtype-, fusion-, and assay-specific suggesting that the loss of the LBD, the 3' fusion partner, and the cellular landscape all influence fusion activity. Therefore, it will be critical to generate additional data on frequency of the ER fusions, in the context of the clinicopathological features of the tumor. Significance ER fusion proteins exhibit diverse mechanisms of endocrine resistance in breast cancer cell lines representing the no special type (NST) and invasive lobular cancer (ILC) subtypes. Our emphasize upon both the shared and unique cellular adaptations imparted by ER fusions offers the foundation for further translational research and clinical decision making.
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20
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Lee JE, Kim KT, Shin SJ, Cheong JH, Choi YY. Genomic and evolutionary characteristics of metastatic gastric cancer by routes. Br J Cancer 2023; 129:672-682. [PMID: 37422528 PMCID: PMC10421927 DOI: 10.1038/s41416-023-02338-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/07/2023] [Accepted: 06/19/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND In gastric cancer (GC) patients, metastatic progression through the lymphatic, hematogenous, peritoneal, and ovarian routes, is the ultimate cause of death. However, the genomic and evolutionary characteristics of metastatic GC have not been widely evaluated. METHODS Whole-exome sequencing data were analyzed for 99 primary and paired metastatic gastric cancers from 15 patients who underwent gastrectomy and metastasectomy. RESULTS Hematogenous metastatic tumors were associated with increased chromosomal instability and de novo gain/amplification in cancer driver genes, whereas peritoneal/ovarian metastasis was linked to sustained chromosomal stability and de novo somatic mutations in driver genes. The genomic distance of the hematogenous and peritoneal metastatic tumors was found to be closer to the primary tumors than lymph node (LN) metastasis, while ovarian metastasis was closer to LN and peritoneal metastasis than the primary tumor. Two migration patterns for metastatic GCs were identified; branched and diaspora. Both molecular subtypes of the metastatic tumors, rather than the primary tumor, and their migration patterns were related to patient survival. CONCLUSIONS Genomic characteristics of metastatic gastric cancer is distinctive by routes and associated with patients' prognosis along with genomic evolution pattenrs, indicating that both primary and metastatic gastric cancers require genomic evaluation.
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Affiliation(s)
- Jae Eun Lee
- Portrai Inc., Seoul, Korea
- Department of Surgery, Yonsei University Health System, Yonsei University College of Medicine, Seoul, South Korea
| | - Ki Tae Kim
- Department of Molecular Genetics & Dental Pharmacology, School of Dentistry, Seoul National University, Seoul, South Korea
- Dental Research Institute and Dental Multi-omics Center, Seoul National University, Seoul, South Korea
| | - Su-Jin Shin
- Department of Pathology, Yonsei University Health System, Yonsei University College of Medicine, Seoul, South Korea
| | - Jae-Ho Cheong
- Department of Surgery, Yonsei University Health System, Yonsei University College of Medicine, Seoul, South Korea.
| | - Yoon Young Choi
- Department of Surgery, Soonchunhyang Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, South Korea.
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21
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Li Z, Li T, Yates ME, Wu Y, Ferber A, Chen L, Brown DD, Carroll JS, Sikora MJ, Tseng GC, Oesterreich S, Lee AV. The EstroGene Database Reveals Diverse Temporal, Context-Dependent, and Bidirectional Estrogen Receptor Regulomes in Breast Cancer. Cancer Res 2023; 83:2656-2674. [PMID: 37272757 PMCID: PMC10527051 DOI: 10.1158/0008-5472.can-23-0539] [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: 02/16/2023] [Revised: 04/21/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
As one of the most successful cancer therapeutic targets, estrogen receptor-α (ER/ESR1) has been extensively studied over the past few decades. Sequencing technological advances have enabled genome-wide analysis of ER action. However, comparison of individual studies is limited by different experimental designs, and few meta-analyses are available. Here, we established the EstroGene database through unified processing of data from 246 experiments including 136 transcriptomic, cistromic, and epigenetic datasets focusing on estradiol (E2)-triggered ER activation across 19 breast cancer cell lines. A user-friendly browser (https://estrogene.org/) was generated for multiomic data visualization involving gene inquiry under user-defined experimental conditions and statistical thresholds. Notably, annotation of metadata associated with public datasets revealed a considerable lack of experimental details. Comparison of independent RNA-seq or ER ChIP-seq data with the same design showed large variability and only strong effects could be consistently detected. Temporal estrogen response metasignatures were defined, and the association of E2 response rate with temporal transcriptional factors, chromatin accessibility, and heterogeneity of ER expression was evaluated. Unexpectedly, harmonizing 146 E2-induced transcriptomic datasets uncovered a subset of genes harboring bidirectional E2 regulation, which was linked to unique transcriptional factors and highly associated with immune surveillance in the clinical setting. Furthermore, the context dependent E2 response programs were characterized in MCF7 and T47D cell lines, the two most frequently used models in the EstroGene database. Collectively, the EstroGene database provides an informative and practical resource to the cancer research community to uniformly evaluate key reproducible features of ER regulomes and unravels modes of ER signaling. SIGNIFICANCE A resource database integrating 246 publicly available ER profiling datasets facilitates meta-analyses and identifies estrogen response temporal signatures, a bidirectional program, and model-specific biases.
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Affiliation(s)
- Zheqi Li
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Tianqin Li
- School of Computer Science, Carnegie Mellon University, Pittsburgh PA, USA
| | - Megan E. Yates
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yang Wu
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Amanda Ferber
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Lyuqin Chen
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Daniel D. Brown
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jason S. Carroll
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Matthew J. Sikora
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh PA, USA
| | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V. Lee
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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22
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Zhou Y, Zhang T, Wang S, Yang R, Jiao Z, Lu K, Li H, Jiang W, Zhang X. Targeting of HBP1/TIMP3 axis as a novel strategy against breast cancer. Pharmacol Res 2023; 194:106846. [PMID: 37414199 DOI: 10.1016/j.phrs.2023.106846] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/08/2023]
Abstract
Malignant proliferation and metastasis are the main causes of breast cancer death. The transcription factor high mobility group (HMG) box-containing protein 1 (HBP1) is an important tumor suppressor whose deletion or mutation is closely related to the appearance of tumors. Here, we investigated the role of HBP1 in breast cancer suppression. HBP1 enhances the activity of the tissue inhibitors of metalloproteinases 3 (TIMP3) promoter, thereby increasing protein and mRNA levels of TIMP3. TIMP3 increases the phosphatase and tensin homolog (PTEN) protein level by inhibiting its degradation and acts as a metalloproteinase inhibitor to inhibit the protein levels of MMP2/9. In this study, we demonstrated that the HBP1/TIMP3 axis plays a crucial role in inhibiting the tumorigenesis of breast cancer. HBP1 deletion interferes with the regulation of the axis and induces the occurrence and malignant progression of breast cancer. In addition, the HBP1/TIMP3 axis promotes the sensitivity of breast cancer to radiation therapy and hormone therapy. Our study opens new perspectives on the treatment and prognosis of breast cancer.
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Affiliation(s)
- Yue Zhou
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Peking University Health Science Center, Beijing 100191, PR China
| | - Tongjia Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Peking University Health Science Center, Beijing 100191, PR China
| | - Shujie Wang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Peking University Health Science Center, Beijing 100191, PR China
| | - Ruixiang Yang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Peking University Health Science Center, Beijing 100191, PR China
| | - Zitao Jiao
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Peking University Health Science Center, Beijing 100191, PR China
| | - Kejia Lu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Peking University Health Science Center, Beijing 100191, PR China
| | - Hui Li
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Peking University Health Science Center, Beijing 100191, PR China
| | - Wei Jiang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Peking University Health Science Center, Beijing 100191, PR China
| | - Xiaowei Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Peking University Health Science Center, Beijing 100191, PR China.
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23
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Wu Y, Li Z, Wedn AM, Casey AN, Brown D, Rao SV, Omarjee S, Hooda J, Carroll JS, Gertz J, Atkinson JM, Lee AV, Oesterreich S. FOXA1 Reprogramming Dictates Retinoid X Receptor Response in ESR1-Mutant Breast Cancer. Mol Cancer Res 2023; 21:591-604. [PMID: 36930833 PMCID: PMC10239325 DOI: 10.1158/1541-7786.mcr-22-0516] [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: 06/29/2022] [Revised: 01/27/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023]
Abstract
Estrogen receptor alpha (ER/ESR1) mutations occur in 30% to 40% of endocrine resistant ER-positive (ER+) breast cancer. Forkhead box A1 (FOXA1) is a key pioneer factor mediating ER-chromatin interactions and endocrine response in ER+ breast cancer, but its role in ESR1-mutant breast cancer remains unclear. Our previous FOXA1 chromatin immunoprecipitation sequencing (ChIP-seq) identified a large portion of redistributed binding sites in T47D genome-edited Y537S and D538G ESR1-mutant cells. Here, we further integrated FOXA1 genomic binding profile with the isogenic ER cistrome, accessible genome, and transcriptome data of T47D cell model. FOXA1 redistribution was significantly associated with transcriptomic alterations caused by ESR1 mutations. Furthermore, in ESR1-mutant cells, FOXA1-binding sites less frequently overlapped with ER, and differential gene expression was less associated with the canonical FOXA1-ER axis. Motif analysis revealed a unique enrichment of retinoid X receptor (RXR) motifs in FOXA1-binding sites of ESR1-mutant cells. Consistently, ESR1-mutant cells were more sensitive to growth stimulation with the RXR agonist LG268. The mutant-specific response was dependent on two RXR isoforms, RXR-α and RXR-β, with a stronger dependency on the latter. In addition, T3, the agonist of thyroid receptor (TR) also showed a similar growth-promoting effect in ESR1-mutant cells. Importantly, RXR antagonist HX531 blocked growth of ESR1-mutant cells and a patient-derived xenograft (PDX)-derived organoid with an ESR1 D538G mutation. Collectively, our data support the evidence for a stronger RXR response associated with FOXA1 reprograming in ESR1-mutant cells, suggesting development of therapeutic strategies targeting RXR pathways in breast tumors with ESR1 mutation. IMPLICATIONS It provides comprehensive characterization of the role of FOXA1 in ESR1-mutant breast cancer and potential therapeutic strategy through blocking RXR activation.
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Affiliation(s)
- Yang Wu
- School of Medicine, Tsinghua University, Beijing, China
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
| | - Zheqi Li
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
| | - Abdalla M. Wedn
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
| | - Allison N. Casey
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
| | - Daniel Brown
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh PA, USA
| | - Shalini V. Rao
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Soleilmane Omarjee
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jagmohan Hooda
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
| | - Jason S. Carroll
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jason Gertz
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jennifer M. Atkinson
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh PA, USA
| | - Adrian V. Lee
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh PA, USA
| | - Steffi Oesterreich
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
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24
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Arnesen S, Polaski J, Blanchard Z, Osborne K, Welm A, O’Connell R, Gertz J. Estrogen receptor alpha mutations regulate gene expression and cell growth in breast cancer through microRNAs. NAR Cancer 2023; 5:zcad027. [PMID: 37275275 PMCID: PMC10233889 DOI: 10.1093/narcan/zcad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 04/18/2023] [Accepted: 05/18/2023] [Indexed: 06/07/2023] Open
Abstract
Estrogen receptor α (ER) mutations occur in up to 30% of metastatic ER-positive breast cancers. Recent data has shown that ER mutations impact the expression of thousands of genes not typically regulated by wildtype ER. While the majority of these altered genes can be explained by constant activity of mutant ER or genomic changes such as altered ER binding and chromatin accessibility, as much as 33% remain unexplained, indicating the potential for post-transcriptional effects. Here, we explored the role of microRNAs in mutant ER-driven gene regulation and identified several microRNAs that are dysregulated in ER mutant cells. These differentially regulated microRNAs target a significant portion of mutant-specific genes involved in key cellular processes. When the activity of microRNAs is altered using mimics or inhibitors, significant changes are observed in gene expression and cellular proliferation related to mutant ER. An in-depth evaluation of miR-301b led us to discover an important role for PRKD3 in the proliferation of ER mutant cells. Our findings show that microRNAs contribute to mutant ER gene regulation and cellular effects in breast cancer cells.
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Affiliation(s)
- Spencer Arnesen
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Jacob T Polaski
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Zannel Blanchard
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Kyle S Osborne
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Alana L Welm
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Ryan M O’Connell
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
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25
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Moreira-Dinzey J, Zhan H, Rozenblit M, Krishnamurti U, Harigopal M, Zhong M, Liang Y. The correlation of ESR1 genetic aberrations with estrogen receptor and progesterone receptor status in metastatic and primary estrogen receptor-positive breast carcinomas. Hum Pathol 2023; 137:56-62. [PMID: 37127079 DOI: 10.1016/j.humpath.2023.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/14/2023] [Accepted: 04/26/2023] [Indexed: 05/03/2023]
Abstract
INTRODUCTION Genetic aberrations in the Estrogen Receptor 1 (ESR1) gene have been identified as an important mechanism of resistance to endocrine therapy in metastatic breast carcinoma. In this study, we aimed to correlate ESR1 genetic aberrations with the ER and PR status in paired metastatic and primary breast carcinomas. METHODS Patients with ER-positive breast cancer were divided into two groups: ESR1 genetic aberration (n=26) and wild-type control (n=29) based on genetic profiling of their metastatic tumors. Clinicopathological features and ER/PR status were analyzed in paired primary and metastatic tumors. RESULTS Although there was no significant difference in ER expression between the ESR1 aberration and control groups in primary tumors, ER positivity rate in metastatic tumors was significantly higher in the ESR1 aberration group than in the control group (100% vs. 86%, p<0.05). ESR1 aberrated cases were associated with more liver metastases than control tumors (46% vs. 10%, p<0.01). The ER percentage and intensity slightly increased from primary to metastatic tumors in the ESR1 aberration group compared to a decrease in both in the wild-type group (percentage increase 2% vs. decrease 19%, p=0.0594; intensity increase 0.04 vs. decrease 0.8, p<0.05). Patients with ESR1 aberrated metastases were more likely than those with wild-type ESR1 metastases to have the following characteristics: 1) ER percentage ≥ 90% and intensity >2, as well as PR percentage ≥ 30% and intensity >1 in metastatic tumors; 2) ER percentage ≥ 90% and PR percentage ≥ 70% in primary tumors; and 3) slightly increase in ER percentage and intensity from primary to metastatic tumors. CONCLUSION Based on the ER/PR parameters of paired primary and metastatic breast cancer, ESR1 aberration in metastasis may be predicted.
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Affiliation(s)
| | - Haiying Zhan
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | - Mariya Rozenblit
- Department of Medical Oncology, Smilow Cancer Hospital at Yale New Haven, New Haven, CT
| | - Uma Krishnamurti
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | - Malini Harigopal
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | - Minghao Zhong
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | - Yuanxin Liang
- Department of Pathology, Yale University School of Medicine, New Haven, CT.
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Strati A, Markou A, Kyriakopoulou E, Lianidou E. Detection and Molecular Characterization of Circulating Tumour Cells: Challenges for the Clinical Setting. Cancers (Basel) 2023; 15:cancers15072185. [PMID: 37046848 PMCID: PMC10092977 DOI: 10.3390/cancers15072185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
Over the last decade, liquid biopsy has gained much attention as a powerful tool in personalized medicine since it enables monitoring cancer evolution and follow-up of cancer patients in real time. Through minimally invasive procedures, liquid biopsy provides important information through the analysis of circulating tumour cells (CTCs) and circulating tumour-derived material, such as circulating tumour DNA (ctDNA), circulating miRNAs (cfmiRNAs) and extracellular vehicles (EVs). CTC analysis has already had an important impact on the prognosis, detection of minimal residual disease (MRD), treatment selection and monitoring of cancer patients. Numerous clinical trials nowadays include a liquid biopsy arm. CTC analysis is now an exponentially expanding field in almost all types of solid cancers. Functional studies, mainly based on CTC-derived cell-lines and CTC-derived explants (CDx), provide important insights into the metastatic process. The purpose of this review is to summarize the latest findings on the clinical significance of CTCs for the management of cancer patients, covering the last four years. This review focuses on providing a comprehensive overview of CTC analysis in breast, prostate and non-small-cell lung cancer. The unique potential of CTC single-cell analysis for understanding metastasis biology, and the importance of quality control and standardization of methodologies used in this field, is also discussed.
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Affiliation(s)
- Areti Strati
- Analysis of Circulating Tumour Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Athina Markou
- Analysis of Circulating Tumour Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | | | - Evi Lianidou
- Analysis of Circulating Tumour Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
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Li Z, Li T, Yates ME, Wu Y, Ferber A, Chen L, Brown DD, Carroll JS, Sikora MJ, Tseng GC, Oesterreich S, Lee AV. EstroGene database reveals diverse temporal, context-dependent and directional estrogen receptor regulomes in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526388. [PMID: 36778377 PMCID: PMC9915613 DOI: 10.1101/2023.01.30.526388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
As one of the most successful cancer therapeutic targets, estrogen receptor-α (ER/ESR1) has been extensively studied in decade-long. Sequencing technological advances have enabled genome-wide analysis of ER action. However, reproducibility is limited by different experimental design. Here, we established the EstroGene database through centralizing 246 experiments from 136 transcriptomic, cistromic and epigenetic datasets focusing on estradiol-treated ER activation across 19 breast cancer cell lines. We generated a user-friendly browser ( https://estrogene.org/ ) for data visualization and gene inquiry under user-defined experimental conditions and statistical thresholds. Notably, documentation-based meta-analysis revealed a considerable lack of experimental details. Comparison of independent RNA-seq or ER ChIP-seq data with the same design showed large variability and only strong effects could be consistently detected. We defined temporal estrogen response metasignatures and showed the association with specific transcriptional factors, chromatin accessibility and ER heterogeneity. Unexpectedly, harmonizing 146 transcriptomic analyses uncovered a subset of E2-bidirectionally regulated genes, which linked to immune surveillance in the clinical setting. Furthermore, we defined context dependent E2 response programs in MCF7 and T47D cell lines, the two most frequently used models in the field. Collectively, the EstroGene database provides an informative resource to the cancer research community and reveals a diverse mode of ER signaling.
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Affiliation(s)
- Zheqi Li
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Tianqin Li
- School of Computer Science, Carnegie Mellon University, Pittsburgh PA, USA
| | - Megan E. Yates
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yang Wu
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Amanda Ferber
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Lyuqin Chen
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Daniel D. Brown
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jason S. Carroll
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Matthew J. Sikora
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh PA, USA
| | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V. Lee
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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Yamamoto A, Doak AE, Cheung KJ. Orchestration of Collective Migration and Metastasis by Tumor Cell Clusters. ANNUAL REVIEW OF PATHOLOGY 2023; 18:231-256. [PMID: 36207009 DOI: 10.1146/annurev-pathmechdis-031521-023557] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Metastatic dissemination has lethal consequences for cancer patients. Accruing evidence supports the hypothesis that tumor cells can migrate and metastasize as clusters of cells while maintaining contacts with one another. Collective metastasis enables tumor cells to colonize secondary sites more efficiently, resist cell death, and evade the immune system. On the other hand, tumor cell clusters face unique challenges for dissemination particularly during systemic dissemination. Here, we review recent progress toward understanding how tumor cell clusters overcome these disadvantages as well as mechanisms they utilize to gain advantages throughout the metastatic process. We consider useful models for studying collective metastasis and reflect on how the study of collective metastasis suggests new opportunities for eradicating and preventing metastatic disease.
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Affiliation(s)
- Ami Yamamoto
- Translational Research Program, Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA; , , .,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
| | - Andrea E Doak
- Translational Research Program, Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA; , , .,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
| | - Kevin J Cheung
- Translational Research Program, Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, USA; , ,
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Yadav N, Sunder R, Desai S, Dharavath B, Chandrani P, Godbole M, Dutt A. Progesterone modulates the DSCAM-AS1/miR-130a/ESR1 axis to suppress cell invasion and migration in breast cancer. Breast Cancer Res 2022; 24:97. [PMID: 36578092 PMCID: PMC9798554 DOI: 10.1186/s13058-022-01597-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND A preoperative-progesterone intervention increases disease-free survival in patients with breast cancer, with an unknown underlying mechanism. We elucidated the role of non-coding RNAs in response to progesterone in human breast cancer. METHODS Whole transcriptome sequencing dataset of 30 breast primary tumors (10 tumors exposed to hydroxyprogesterone and 20 tumors as control) were re-analyzed to identify differentially expressed non-coding RNAs followed by real-time PCR analyses to validate the expression of candidates. Functional analyses were performed by genetic knockdown, biochemical, and cell-based assays. RESULTS We identified a significant downregulation in the expression of a long non-coding RNA, Down syndrome cell adhesion molecule antisense DSCAM-AS1, in response to progesterone treatment in breast cancer. The progesterone-induced expression of DSCAM-AS1 could be effectively blocked by the knockdown of progesterone receptor (PR) or treatment of cells with mifepristone (PR-antagonist). We further show that knockdown of DSCAM-AS1 mimics the effect of progesterone in impeding cell migration and invasion in PR-positive breast cancer cells, while its overexpression shows an opposite effect. Additionally, DSCAM-AS1 sponges the activity of miR-130a that regulates the expression of ESR1 by binding to its 3'-UTR to mediate the effect of progesterone in breast cancer cells. Consistent with our findings, TCGA analysis suggests that high levels of miR-130a correlate with a tendency toward better overall survival in patients with breast cancer. CONCLUSION This study presents a mechanism involving the DSCAM-AS1/miR-130a/ESR1 genomic axis through which progesterone impedes breast cancer cell invasion and migration. The findings highlight the utility of progesterone treatment in impeding metastasis and improving survival outcomes in patients with breast cancer.
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Affiliation(s)
- Neelima Yadav
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Roma Sunder
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Bhasker Dharavath
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Pratik Chandrani
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Medical Oncology Molecular Lab & Centre for Computational Biology, Bioinformatics and Crosstalk Lab, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India
| | - Mukul Godbole
- School of Biosciences and Technology, Faculty of Sciences and Health Sciences, MIT World Peace University, Pune, Maharashtra, 411038, India
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
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30
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Metastatic Breast Cancer: Cytology Diagnosis with Implications for Treatment. JOURNAL OF MOLECULAR PATHOLOGY 2022. [DOI: 10.3390/jmp4010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Breast cancer is among the most frequent malignancies in women worldwide. While early detection and effective treatment provide many women with a cure and prevent their cancer from spreading, metastases to distant sites still occur in around 20% of women suffering from breast cancer. These relapses occur in many forms and locations and are as varied as the primary breast tumors. Metastatic spread makes a cancer incurable and potentially lethal, but new, targeted treatments can offer control of the cancer cells if the features of new targets are unlocked by advanced diagnostic testing. The article offers an overview of the pathomechanisms of metastatic progression and describes the types of metastases, such as hormone-receptor-positive and -negative breast cancers, and HER2-overexpressing or triple-negative types. Once distant metastatic spread occurs, cytology allows a precise diagnosis to confirm the breast origin. Other molecular targets include ESR1 and PIK3CA mutations, MSI, NTRK fusion, PD-L1 expression and others, which can be obtained also from cytology material and used to determine eligibility for emerging targeted therapeutic options. We outline the diagnostic features of metastatic breast cancer in cytology samples, together with validated and emergent biomarkers that may provide new, targeted treatment options.
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31
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Detection of circulating tumor cells: opportunities and challenges. Biomark Res 2022; 10:58. [PMID: 35962400 PMCID: PMC9375360 DOI: 10.1186/s40364-022-00403-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/26/2022] [Indexed: 11/25/2022] Open
Abstract
Circulating tumor cells (CTCs) are cells that shed from a primary tumor and travel through the bloodstream. Studying the functional and molecular characteristics of CTCs may provide in-depth knowledge regarding highly lethal tumor diseases. Researchers are working to design devices and develop analytical methods that can capture and detect CTCs in whole blood from cancer patients with improved sensitivity and specificity. Techniques using whole blood samples utilize physical prosperity, immunoaffinity or a combination of the above methods and positive and negative enrichment during separation. Further analysis of CTCs is helpful in cancer monitoring, efficacy evaluation and designing of targeted cancer treatment methods. Although many advances have been achieved in the detection and molecular characterization of CTCs, several challenges still exist that limit the current use of this burgeoning diagnostic approach. In this review, a brief summary of the biological characterization of CTCs is presented. We focus on the current existing CTC detection methods and the potential clinical implications and challenges of CTCs. We also put forward our own views regarding the future development direction of CTCs.
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32
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Li Z, Spoelstra NS, Sikora MJ, Sams SB, Elias A, Richer JK, Lee AV, Oesterreich S. Mutual exclusivity of ESR1 and TP53 mutations in endocrine resistant metastatic breast cancer. NPJ Breast Cancer 2022; 8:62. [PMID: 35538119 PMCID: PMC9090919 DOI: 10.1038/s41523-022-00426-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/31/2022] [Indexed: 12/12/2022] Open
Abstract
Both TP53 and ESR1 mutations occur frequently in estrogen receptor positive (ER+) metastatic breast cancers (MBC) and their distinct roles in breast cancer tumorigenesis and progression are well appreciated. Recent clinical studies discovered mutual exclusivity between TP53 and ESR1 mutations in metastatic breast cancers; however, mechanisms underlying this intriguing clinical observation remain largely understudied and unknown. Here, we explored the interplay between TP53 and ESR1 mutations using publicly available clinical and experimental data sets. We first confirmed the robust mutational exclusivity using six independent cohorts with 1,056 ER+ MBC samples and found that the exclusivity broadly applies to all ER+ breast tumors regardless of their clinical and distinct mutational features. ESR1 mutant tumors do not exhibit differential p53 pathway activity, whereas we identified attenuated ER activity and expression in TP53 mutant tumors, driven by a p53-associated E2 response gene signature. Further, 81% of these p53-associated E2 response genes are either direct targets of wild-type (WT) p53-regulated transactivation or are mutant p53-associated microRNAs, representing bimodal mechanisms of ER suppression. Lastly, we analyzed the very rare cases with co-occurrences of TP53 and ESR1 mutations and found that their simultaneous presence was also associated with reduced ER activity. In addition, tumors with dual mutations showed higher levels of total and PD-L1 positive macrophages. In summary, our study utilized multiple publicly available sources to explore the mechanism underlying the mutual exclusivity between ESR1 and TP53 mutations, providing further insights and testable hypotheses of the molecular interplay between these two pivotal genes in ER+ MBC.
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Affiliation(s)
- Zheqi Li
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Women's Cancer Research Center, Magee Women's Research Institute, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Nicole S Spoelstra
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew J Sikora
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sharon B Sams
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Anthony Elias
- School of Medicine, Division of Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jennifer K Richer
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Adrian V Lee
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Women's Cancer Research Center, Magee Women's Research Institute, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
- Women's Cancer Research Center, Magee Women's Research Institute, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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33
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Khan Z, Abubakar M, Arshed MJ, Aslam R, Sattar S, Shah NA, Javed S, Tariq A, Bostan N, Manzoor S. Molecular investigation of possible relationships concerning bovine leukemia virus and breast cancer. Sci Rep 2022; 12:4161. [PMID: 35264739 PMCID: PMC8907172 DOI: 10.1038/s41598-022-08181-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/25/2022] [Indexed: 11/17/2022] Open
Abstract
Worldwide, breast cancer has an eminent morbidity and mortality rate, as it is a neoplastic disease among females. The query of the prospective danger of bovine leukemia virus (BLV) to humans is an old but exceedingly topical focus of scientific debate. The objective of the current study was to determine the possible relationship between BLV and breast cancer. A total of 2710 formalin-fixed paraffin-embedded (FFPE) breast cancer samples were selected regardless of the age, ethnicity, or municipality origin of the subjects. The presence of BLV in human breast cancer was determined through nested PCR by amplifying tax and gag genes followed by partial sequencing. Homology was confirmed by using the online BLAST Tool. BLV genes were found to be positive in 26.8% (728/2710) of the samples from breast cancer patients and 10% (10/80) of the samples without cancer (negative control). The results indicated a correlation between the presence of the BLV gene and breast cancer (odds ratio = 0.3889; confidence interval = 1,18; p = 0.0029). The current findings suggest a possible link between BLV and human breast carcinoma. Therefore, screening cattle herds and milk products is suggested to reduce the viral transmission risk to humans.
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Affiliation(s)
- Zanib Khan
- Biosciences Department, COMSATS University, Islamabad, Pakistan
| | | | | | - Roohi Aslam
- NUTECH School of Applied Sciences and Humanities, National University of Technology, Islamabad, Pakistan
| | - Sadia Sattar
- Biosciences Department, COMSATS University, Islamabad, Pakistan
| | - Naseer Ali Shah
- Biosciences Department, COMSATS University, Islamabad, Pakistan
| | - Sundus Javed
- Biosciences Department, COMSATS University, Islamabad, Pakistan
| | - Aamira Tariq
- Biosciences Department, COMSATS University, Islamabad, Pakistan
| | - Nazish Bostan
- Biosciences Department, COMSATS University, Islamabad, Pakistan.
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Lloyd MR, Wander SA, Hamilton E, Razavi P, Bardia A. Next-generation selective estrogen receptor degraders and other novel endocrine therapies for management of metastatic hormone receptor-positive breast cancer: current and emerging role. Ther Adv Med Oncol 2022; 14:17588359221113694. [PMID: 35923930 PMCID: PMC9340905 DOI: 10.1177/17588359221113694] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Endocrine therapy (ET) is a pivotal strategy to manage early- and advanced-stage estrogen receptor-positive (ER+) breast cancer. In patients with metastatic breast cancer (MBC), progression of disease inevitably occurs due to the presence of acquired or intrinsic resistance mechanisms. ET resistance can be driven by ligand-independent, ER-mediated signaling that promotes tumor proliferation in the absence of hormone, or ER-independent oncogenic signaling that circumvents endocrine regulated transcription pathways. Estrogen receptor 1 (ESR1) mutations induce constitutive ER activity and upregulate ER-dependent gene transcription, provoking resistance to estrogen deprivation and aromatase inhibitor therapy. The role ESR1 mutations play in regulating response to other therapies, such as the selective estrogen receptor degrader (SERD) fulvestrant and the available CDK4/6 inhibitors, is less clear. Novel oral SERDs and other next-generation ETs are in clinical development for ER+ breast cancer as single agents and in combination with established targeted therapies. Recent results from the phase III EMERALD trial demonstrated improved outcomes with the oral SERD elacestrant compared to standard anti-estrogen therapies in ER+ MBC after prior progression on ET, and other agents have shown promise in both the laboratory and early-phase clinical trials. In this review, we will discuss the emerging data related to oral SERDs and other novel ET in managing ER+ breast cancer. As clinical data continue to mature on these next-generation ETs, important questions will emerge related to the optimal sequence of therapeutic options and the genomic and molecular landscape of resistance to these agents.
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Affiliation(s)
- Maxwell R. Lloyd
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Seth A. Wander
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Erika Hamilton
- Sarah Cannon Research Institute/Tennessee Oncology, Nashville, TN, USA
| | - Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, 10 North Grove Street, Harvard Medical School, Boston, MA 02114-2621, USA
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