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Goyette MA, Stevens LE, DePinho CR, Seehawer M, Nishida J, Li Z, Wilde CM, Li R, Qiu X, Pyke AL, Zhao S, Lim K, Tender GS, Northey JJ, Riley NM, Long HW, Bertozzi CR, Weaver VM, Polyak K. Cancer-stromal cell interactions in breast cancer brain metastases induce glycocalyx-mediated resistance to HER2-targeting therapies. Proc Natl Acad Sci U S A 2024; 121:e2322688121. [PMID: 38709925 DOI: 10.1073/pnas.2322688121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/27/2024] [Indexed: 05/08/2024] Open
Abstract
Brain metastatic breast cancer is particularly lethal largely due to therapeutic resistance. Almost half of the patients with metastatic HER2-positive breast cancer develop brain metastases, representing a major clinical challenge. We previously described that cancer-associated fibroblasts are an important source of resistance in primary tumors. Here, we report that breast cancer brain metastasis stromal cell interactions in 3D cocultures induce therapeutic resistance to HER2-targeting agents, particularly to the small molecule inhibitor of HER2/EGFR neratinib. We investigated the underlying mechanisms using a synthetic Notch reporter system enabling the sorting of cancer cells that directly interact with stromal cells. We identified mucins and bulky glycoprotein synthesis as top-up-regulated genes and pathways by comparing the gene expression and chromatin profiles of stroma-contact and no-contact cancer cells before and after neratinib treatment. Glycoprotein gene signatures were also enriched in human brain metastases compared to primary tumors. We confirmed increased glycocalyx surrounding cocultures by immunofluorescence and showed that mucinase treatment increased sensitivity to neratinib by enabling a more efficient inhibition of EGFR/HER2 signaling in cancer cells. Overexpression of truncated MUC1 lacking the intracellular domain as a model of increased glycocalyx-induced resistance to neratinib both in cell culture and in experimental brain metastases in immunodeficient mice. Our results highlight the importance of glycoproteins as a resistance mechanism to HER2-targeting therapies in breast cancer brain metastases.
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Affiliation(s)
- Marie-Anne Goyette
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Harvard Medical School, Boston, MA 02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Harvard Medical School, Boston, MA 02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Carolyn R DePinho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Harvard Medical School, Boston, MA 02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Jun Nishida
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Harvard Medical School, Boston, MA 02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Harvard Medical School, Boston, MA 02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Callahan M Wilde
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Rong Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Alanna L Pyke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Stephanie Zhao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
| | | | - Jason J Northey
- Center for Bioengineering and Tissue Regeneration, University of California San Francisco, San Francisco, CA 94143
| | - Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305
| | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, University of California San Francisco, San Francisco, CA 94143
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94143
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94143
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Harvard Medical School, Boston, MA 02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
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Wang C, Wang Z, Fu L, Du J, Ji F, Qiu X. CircNRCAM up-regulates NRCAM to promote papillary thyroid carcinoma progression. J Endocrinol Invest 2024; 47:1215-1226. [PMID: 38485895 DOI: 10.1007/s40618-023-02241-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/04/2023] [Indexed: 04/23/2024]
Abstract
PURPOSE Papillary Thyroid Carcinoma (PTC) is the most prevalent subtype of Thyroid Carcinoma (THCA), a type of malignancy in the endocrine system. According to prior studies, Neural Cell Adhesion Molecule (NRCAM) has been found to be up-regulated in PTC and stimulates the proliferation and migration of PTC cells. However, the specific mechanism of NRCAM in PTC cells is not yet fully understood. Consequently, this study aimed to investigate the underlying mechanism of NRCAM in PTC cells, the findings of which could provide new insights for the development of potential treatment targets for PTC. METHODS AND RESULTS Bioinformatics tools were utilized and a series of experiments were conducted, including Western blot, colony formation, and dual-luciferase reporter assays. The data collected indicated that NRCAM was overexpressed in THCA tissues and PTC cells. Circular RNA NRCAM (circNRCAM) was found to be highly expressed in PTC cells and to positively regulate NRCAM expression. Through loss-of-function assays, both circNRCAM and NRCAM were shown to promote the proliferation, invasion, and migration of PTC cells. Mechanistically, this study confirmed that precursor microRNA-506 (pre-miR-506) could bind with m6A demethylase AlkB Homolog 5 (ALKBH5), leading to its m6A demethylation. It was also discovered that circNRCAM could competitively bind to ALKBH5, which restrained miR-506-3p expression and promoted NRCAM expression. CONCLUSION In summary, circNRCAM could up-regulate NRCAM by down-regulating miR-506-3p, thereby enhancing the biological behaviors of PTC cells.
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Affiliation(s)
- C Wang
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 East Jianshe Road, Zhengzhou, 450052, Henan, China
| | - Z Wang
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 East Jianshe Road, Zhengzhou, 450052, Henan, China
| | - L Fu
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 East Jianshe Road, Zhengzhou, 450052, Henan, China
| | - J Du
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 East Jianshe Road, Zhengzhou, 450052, Henan, China
| | - F Ji
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 East Jianshe Road, Zhengzhou, 450052, Henan, China
| | - X Qiu
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 East Jianshe Road, Zhengzhou, 450052, Henan, China.
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3
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Qiu X, Guo JJ, Jin CC, He J, Wang L, Yang BC, Zhang YH, Zhu BS, Tang XH. [Efficiency of CNV-seq in detecting fetal DMD gene deletion or duplication in prenatal diagnosis]. Zhonghua Fu Chan Ke Za Zhi 2024; 59:279-287. [PMID: 38644274 DOI: 10.3760/cma.j.cn112141-20230919-00107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Objective: To evaluate the diagnostic efficiency of copy number variation sequencing (CNV-seq) to detect the deletion or duplication of DMD gene in prenatal diagnosis. Methods: A retrospective analysis was carried out on the CNV-seq results of 34 544 fetuses diagnosed in the First People's Hospital of Yunnan Province from January 2018 to July 2023. A total of 156 cases of fetuses were collected, including Group 1:125 cases with family history of Duchenne muscular dystrophy or Becker muscular dystrophy (DMD/BMD), and Group 2:31 cases with no family history but a DMD gene deletion or duplication was detected unexpectedly by CNV-seq. Multiplex ligation-dependent probe amplification (MLPA) was used as a standard method to detect the deletion or duplication. Consistency test was carried out basing on the results of CNV-seq and MLPA of all 156 cases. Results: Comparing to MLPA, CNV-seq had a coincidence rate of 92.3% (144/156) for DMD gene deletion or duplication, with a sensitivity and positive predictive value of 88.2%, with a specificity and negative predictive value of 94.3%, a missed detection rate of 3.8%, and a Kappa value of 0.839. CNV-seq missed 4 cases with deletions and 2 with duplications due to involved fragments less than 100 Kb, among 20 cases of deletions and 6 cases of duplications detected by MLPA in Group 1. In Group 2, the deletions and duplications detected by CNV-seq were 42% (13/31) and 58% (18/31), respectively, in which the percentage of duplication was higher than that in Group 1. Among those 18 cases with duplications, 3 cases with duplication locating in exon 42~67 were likely pathogenic; while 9 cases with duplication covering the 5' or 3' end of the DMD gene, containing exon 1 or 79 and with only one breakpoint within the gene, along with the last 6 cases with duplications locating at chrX: 32650635_32910000 detected only by CNV-seq, which might be judged as variants of uncertain significance. Conclusions: CNV-seq has a good efficiency to detect fetal DMD gene deletion or duplication in prenatal diagnosis, while a further verification test by MLPA is recommended. The duplications on chrX: 32650635_32910000, 5' or 3' end of DMD gene detected by CNV-seq should be carefully verified and assessed because those variants appear to be nonpathogenic polymorphisms.
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Affiliation(s)
- X Qiu
- Department of Medical Genetics, NHC Key Laboratory of Health Birth and Birth Defect Prevention in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Affiliated Hospital of Kunming University of Science and Technology, the First People's Hospital of Yunnan Province, Kunming 650032, China
| | - J J Guo
- Department of Medical Genetics, NHC Key Laboratory of Health Birth and Birth Defect Prevention in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Affiliated Hospital of Kunming University of Science and Technology, the First People's Hospital of Yunnan Province, Kunming 650032, China
| | - C C Jin
- Department of Medical Genetics, NHC Key Laboratory of Health Birth and Birth Defect Prevention in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Affiliated Hospital of Kunming University of Science and Technology, the First People's Hospital of Yunnan Province, Kunming 650032, China
| | - J He
- Department of Medical Genetics, NHC Key Laboratory of Health Birth and Birth Defect Prevention in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Affiliated Hospital of Kunming University of Science and Technology, the First People's Hospital of Yunnan Province, Kunming 650032, China
| | - L Wang
- Department of Medical Genetics, NHC Key Laboratory of Health Birth and Birth Defect Prevention in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Affiliated Hospital of Kunming University of Science and Technology, the First People's Hospital of Yunnan Province, Kunming 650032, China
| | - B C Yang
- Department of Medical Genetics, NHC Key Laboratory of Health Birth and Birth Defect Prevention in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Affiliated Hospital of Kunming University of Science and Technology, the First People's Hospital of Yunnan Province, Kunming 650032, China
| | - Y H Zhang
- Department of Medical Genetics, NHC Key Laboratory of Health Birth and Birth Defect Prevention in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Affiliated Hospital of Kunming University of Science and Technology, the First People's Hospital of Yunnan Province, Kunming 650032, China
| | - B S Zhu
- Department of Medical Genetics, NHC Key Laboratory of Health Birth and Birth Defect Prevention in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Affiliated Hospital of Kunming University of Science and Technology, the First People's Hospital of Yunnan Province, Kunming 650032, China
| | - X H Tang
- Department of Medical Genetics, NHC Key Laboratory of Health Birth and Birth Defect Prevention in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Affiliated Hospital of Kunming University of Science and Technology, the First People's Hospital of Yunnan Province, Kunming 650032, China
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He Z, Sa R, Zhang K, Wang J, Qiu X, Chen L. Optimizing the indication of initial radioiodine oncolytic treatment for metastatic differentiated thyroid cancer by diagnostic 131I scan. Clin Radiol 2024:S0009-9260(24)00185-5. [PMID: 38641445 DOI: 10.1016/j.crad.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/27/2024] [Accepted: 03/25/2024] [Indexed: 04/21/2024]
Abstract
AIM As a classic theranostic radiopharmaceutical, radioiodine (131I) has been utilized in the management of differentiated thyroid cancer (DTC) for more than 8 decades, and the refinement of its clinical practice has been raised recently. This study was conducted to evaluate the efficiency of a diagnostic (Dx) 131I scan in optimizing the indication of initial radioiodine oncolytic treatment (ROT) for metastatic DTC by predicting therapeutic outcomes. RESULTS A total of 100 patients (Dx positive, n=29; Dx negative, n=71) were eligible for patient-based analysis. The matching rate was 83.0% between the Dx and the post-therapeutic scans (kappa = 0.648, P<0.001). The biochemical remission rate and structural shrinkage rate induced by the initial ROT in the Dx-positive group were, respectively, greater than those in the Dx-negative group (83.3% vs. 17.4%, P<0.001; 37.9% vs. 4.2%, P<0.001). Notably, the predictive values of positive Dx scans for ROT responsiveness and negative Dx scans for ROT nonresponsiveness reached up to 89.7% and 84.5%, respectively. CONCLUSION This Dx scan approach seems viable in characterizing the 131I-avidity of metastatic DTC and plays a pivotal role in optimizing the indication of initial ROT for metastatic DTC.
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Affiliation(s)
- Z He
- Department of Nuclear Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600(#) Yishan Rd, Shanghai 200233, People's Republic of China.
| | - R Sa
- Department of Nuclear Medicine, The First Hospital of Jilin University, 1(#) Xinmin St, Changchun 130021, People's Republic of China.
| | - K Zhang
- Department of Nuclear Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600(#) Yishan Rd, Shanghai 200233, People's Republic of China.
| | - J Wang
- Department of Nuclear Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600(#) Yishan Rd, Shanghai 200233, People's Republic of China.
| | - X Qiu
- Department of Nuclear Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600(#) Yishan Rd, Shanghai 200233, People's Republic of China.
| | - L Chen
- Department of Nuclear Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600(#) Yishan Rd, Shanghai 200233, People's Republic of China.
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5
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Baca SC, Seo JH, Davidsohn MP, Fortunato B, Semaan K, Sotudian S, Lakshminarayanan G, Diossy M, Qiu X, El Zarif T, Savignano H, Canniff J, Madueke I, Saliby RM, Zhang Z, Li R, Jiang Y, Taing L, Awad M, Chau CH, DeCaprio JA, Figg WD, Greten TF, Hata AN, Hodi FS, Hughes ME, Ligon KL, Lin N, Ng K, Oser MG, Meador C, Parsons HA, Pomerantz MM, Rajan A, Ritz J, Thakuria M, Tolaney SM, Wen PY, Long H, Berchuck JE, Szallasi Z, Choueiri TK, Freedman ML. Author Correction: Liquid biopsy epigenomic profiling for cancer subtyping. Nat Med 2024; 30:907. [PMID: 38049623 PMCID: PMC10957463 DOI: 10.1038/s41591-023-02735-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Affiliation(s)
- Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew P Davidsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brad Fortunato
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Karl Semaan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Shahabbedin Sotudian
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Gitanjali Lakshminarayanan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Miklos Diossy
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Talal El Zarif
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hunter Savignano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John Canniff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ikenna Madueke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Renee Maria Saliby
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ziwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Rong Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yijia Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cindy H Chau
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - William D Figg
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tim F Greten
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Melissa E Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keith L Ligon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nancy Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine Meador
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Arun Rajan
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Manisha Thakuria
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cutaneous Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zoltan Szallasi
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Bioinformatics and Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
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6
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Neeb A, Figueiredo I, Bogdan D, Cato L, Stober J, Jiménez-Vacas JM, Gourain V, Lee II, Seeger R, Muhle-Goll C, Gurel B, Welti J, Nava Rodrigues D, Rekowski J, Qiu X, Jiang Y, Di Micco P, Mateos B, Bielskutė S, Riisnaes R, Ferreira A, Miranda S, Crespo M, Buroni L, Ning J, Carreira S, Bräse S, Jung N, Gräßle S, Swain A, Salvatella X, Plymate SR, Al-Lazikani B, Long HW, Yuan W, Brown M, Cato ACB, de Bono JS, Sharp A. Thio-2 inhibits key signaling pathways required for the development and progression of castration resistant prostate cancer. Mol Cancer Ther 2024:734951. [PMID: 38412481 DOI: 10.1158/1535-7163.mct-23-0354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/26/2023] [Accepted: 02/22/2024] [Indexed: 02/29/2024]
Abstract
Therapies that abrogate persistent androgen receptor (AR) signaling in castration resistant prostate cancer (CRPC) remain an unmet clinical need. The N-terminal domain (NTD) of the AR that drives transcriptional activity in CRPC remains a challenging therapeutic target. Herein we demonstrate that BAG-1 mRNA is highly expressed and associates with signaling pathways, including AR signaling, that are implicated in the development and progression of CRPC. In addition, interrogation of geometric and physiochemical properties of the BAG domain of BAG-1 isoforms identifies it to be a tractable but challenging drug target. Furthermore, through BAG-1 isoform mouse knockout studies we confirm that BAG-1 isoforms regulate hormone physiology and that therapies targeting the BAG domain will be associated with limited 'on-target' toxicity. Importantly, the postulated inhibitor of BAG-1 isoforms, Thio-2, suppressed AR signaling and other important pathways implicated in the development and progression of CRPC to reduce the growth of treatment resistant prostate cancer cell lines and patient derived models. However, the mechanism by which Thio-2 elicits the observed phenotype needs further elucidation since the genomic abrogation of BAG-1 isoforms was unable to recapitulate the Thio-2 mediated phenotype. Overall, these data support the interrogation of related compounds with improved drug-like properties as a novel therapeutic approach in CRPC, and further highlight the clinical potential of treatments that block persistent AR signaling which are currently undergoing clinical evaluation in CRPC.
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Affiliation(s)
- Antje Neeb
- Institute of Cancer Research, Surrey, United Kingdom
| | - Ines Figueiredo
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Denisa Bogdan
- Institute of Cancer Research, London, United Kingdom
| | - Laura Cato
- Dana-Farber Cancer Institute, Boston, MA, United States
| | | | | | | | - Irene I Lee
- AbbVie (United States), North Chicago, IL, United States
| | | | | | - Bora Gurel
- Institute of Cancer Research, London, United Kingdom
| | | | | | - Jan Rekowski
- Institute of Cancer Research, London, United Kingdom
| | - Xintao Qiu
- Dana-Farber Cancer Institute, Boston, MA, United States
| | - Yija Jiang
- Dana-Farber Cancer Institute, United States
| | | | - Borja Mateos
- Institute of Biomedical Research of Barcelona, Spain
| | | | - Ruth Riisnaes
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Ana Ferreira
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Susana Miranda
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Mateus Crespo
- Institute of Cancer Research, Sutton, United Kingdom
| | | | - Jian Ning
- Institute of Cancer Research, London, United Kingdom
| | | | - Stefan Bräse
- KIT Campus South, Institute of Organic Chemistry, Karlsruhe, Germany
| | - Nicole Jung
- Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Simone Gräßle
- Karlsruhe Institute of Technology (KIT), Karlsruhe, Eggenstein-Leopoldshafen, Germany
| | - Amanda Swain
- Institute of Cancer Research, London, United Kingdom
| | | | | | | | - Henry W Long
- Dana-Farber Cancer Institute, Boston, MA, United States
| | - Wei Yuan
- Institute of Cancer Research, Sutton, United Kingdom
| | - Myles Brown
- Dana-Farber Cancer Institute, Boston, MA, United States
| | - Andrew C B Cato
- Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Adam Sharp
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
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7
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Duplaquet L, So K, Ying AW, Li X, Li Y, Qiu X, Li R, Singh S, Wu XS, Liu Q, Qi J, Somerville TDD, Heiling H, Mazzola E, Lee Y, Zoller T, Vakoc CR, Doench JG, Forrester WC, Abrams T, Long HW, Niederst MJ, Kadoch C, Oser MG. Mammalian SWI/SNF complex activity regulates POU2F3 and constitutes a targetable dependency in small cell lung cancer. bioRxiv 2024:2024.01.21.576304. [PMID: 38328215 PMCID: PMC10849479 DOI: 10.1101/2024.01.21.576304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Small cell lung cancers (SCLC) are comprised of heterogeneous subtypes marked by lineage-specific transcription factors, including ASCL1, NEUROD1, and POU2F3. POU2F3-positive SCLC, ∼12% of all cases, are uniquely dependent on POU2F3 itself; as such, approaches to attenuate POU2F3 expression may represent new therapeutic opportunities. Here using genome-scale screens for regulators of POU2F3 expression and SCLC proliferation, we define mSWI/SNF complexes, including non-canonical BAF (ncBAF) complexes, as top dependencies specific to POU2F3-positive SCLC. Notably, clinical-grade pharmacologic mSWI/SNF inhibition attenuates proliferation of all POU2F3-positive SCLCs, while disruption of ncBAF via BRD9 degradation is uniquely effective in pure non-neuroendocrine POU2F3-SCLCs. mSWI/SNF maintains accessibility over gene loci central to POU2F3-mediated gene regulatory networks. Finally, chemical targeting of SMARCA4/2 mSWI/SNF ATPases and BRD9 decrease POU2F3-SCLC tumor growth and increase survival in vivo . Taken together, these results characterize mSWI/SNF-mediated global governance of the POU2F3 oncogenic program and suggest mSWI/SNF inhibition as a therapeutic strategy for SCLC.
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8
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Poluben L, Nouri M, Liang J, Varkaris A, Ersoy-Fazlioglu B, Voznesensky O, Lee II, Qiu X, Cato L, Seo JH, Freedman ML, Sowalsky AG, Lack NA, Corey E, Nelson PS, Brown M, Long HW, Balk SP, Russo JW. Increased chromatin accessibility drives transition to androgen receptor splice variant dependence in castration-resistant prostate cancer. bioRxiv 2024:2024.01.10.575110. [PMID: 38260576 PMCID: PMC10802579 DOI: 10.1101/2024.01.10.575110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Androgen receptor (AR) splice variants, of which ARv7 is the most common, are increased in prostate cancer (PC) that develops resistance to androgen signaling inhibitor drugs, but the extent to which these variants drive AR activity, and whether they have novel functions or dependencies, remain to be determined. We generated a subline of VCaP PC cells (VCaP16) that is resistant to the AR inhibitor enzalutamide (ENZ) and found that AR activity was independent of the full-length AR (ARfl), despite its continued high-level expression, and was instead driven by ARv7. The ARv7 cistrome and transcriptome in VCaP16 cells mirrored that of the ARfl in VCaP cells, although ARv7 chromatin binding was weaker, and strong ARv7 binding sites correlated with higher affinity ARfl binding sites across multiple models and clinical samples. Notably, although ARv7 expression in VCaP cells increased rapidly in response to ENZ, there was a long lag before it gained chromatin binding and transcriptional activity. This lag was associated with an increase in chromatin accessibility, with the AR and nuclear factor I (NFI) motifs being most enriched at these more accessible sites. Moreover, the transcriptional effects of combined NFIB and NFIX knockdown versus ARv7 knockdown were highly correlated. These findings indicate that ARv7 can drive the AR program, but that its activity is dependent on adaptations that increase chromatin accessibility to enhance its intrinsically weak chromatin binding.
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9
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Jiang Y, Hu Z, Lynch AW, Jiang J, Zhu A, Zhang Y, Xie Y, Li R, Zhou N, Meyer CA, Cejas P, Brown M, Long HW, Qiu X. scATAnno: Automated Cell Type Annotation for single-cell ATAC Sequencing Data. bioRxiv 2024:2023.06.01.543296. [PMID: 37333088 PMCID: PMC10274707 DOI: 10.1101/2023.06.01.543296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The recent advances in single-cell epigenomic techniques have created a growing demand for scATAC-seq analysis. One key task is to determine cell types based on epigenetic profiling. We introduce scATAnno, a workflow designed to automatically annotate scATAC-seq data using large-scale scATAC-seq reference atlases. This workflow can generate scATAC-seq reference atlases from publicly available datasets, and enable accurate cell type annotation by integrating query data with reference atlases, without the aid of scRNA-seq profiling. To enhance annotation accuracy, we have incorporated KNN-based and weighted distance-based uncertainty scores to effectively detect unknown cell populations within the query data. We showcase the utility of scATAnno across multiple datasets, including peripheral blood mononuclear cell (PBMC), basal cell carcinoma (BCC) and Triple Negative Breast Cancer (TNBC), and demonstrate that scATAnno accurately annotates cell types across conditions. Overall, scATAnno is a powerful tool for cell type annotation in scATAC-seq data and can aid in the interpretation of new scATAC-seq datasets in complex biological systems.
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10
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Chen Q, Fu C, Qiu X, He J, Zhao T, Zhang Q, Hu X, Hu H. Machine-learning-based performance comparison of two-dimensional (2D) and three-dimensional (3D) CT radiomics features for intracerebral haemorrhage expansion. Clin Radiol 2024; 79:e26-e33. [PMID: 37926647 DOI: 10.1016/j.crad.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/07/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023]
Abstract
AIM To investigate the value of non-contrast CT (NCCT)-based two-dimensional (2D) radiomics features in predicting haematoma expansion (HE) after spontaneous intracerebral haemorrhage (ICH) and compare its predictive ability with the three-dimensional (3D) signature. MATERIALS AND METHODS Three hundred and seven ICH patients who received baseline NCCT within 6 h of ictus from two stroke centres were analysed retrospectively. 2D and 3D radiomics features were extracted in the manner of one-to-one correspondence. The 2D and 3D models were generated by four different machine-learning algorithms (regularised L1 logistic regression, decision tree, support vector machine and AdaBoost), and the receiver operating characteristic (ROC) curve was used to compare their predictive performance. A robustness analysis was performed according to baseline haematoma volume. RESULTS Each feature type of 2D and 3D modalities used for subsequent analyses had excellent consistency (mean ICC >0.9). Among the different machine-learning algorithms, pairwise comparison showed no significant difference in both the training (mean area under the ROC curve [AUC] 0.858 versus 0.802, all p>0.05) and validation datasets (mean AUC 0.725 versus 0.678, all p>0.05), and the 10-fold cross-validation evaluation yielded similar results. The AUCs of the 2D and 3D models were comparable either in the binary or tertile volume analysis (all p>0.5). CONCLUSION NCCT-derived 2D radiomics features exhibited acceptable and similar performance to the 3D features in predicting HE, and this comparability seemed unaffected by initial haematoma volume. The 2D signature may be preferred in future HE-related radiomic works given its compatibility with emergency condition of ICH.
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Affiliation(s)
- Q Chen
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - C Fu
- Department of Radiology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - X Qiu
- Department of Radiology, Qian Tang District of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - J He
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - T Zhao
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Q Zhang
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - X Hu
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - H Hu
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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11
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Jovanović B, Temko D, Stevens LE, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper NW, Daniels VW, Xiao-Yun H, Ge JY, Alečković M, Pyrdol J, Hinohara K, Egri SB, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram MB, Subedee A, Herbert ZT, Wucherpfennig KW, Letai AG, Jaffe JD, Sicinski P, Brown M, Dillon D, Long HW, Michor F, Polyak K. Heterogeneity and transcriptional drivers of triple-negative breast cancer. Cell Rep 2023; 42:113564. [PMID: 38100350 PMCID: PMC10842760 DOI: 10.1016/j.celrep.2023.113564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/05/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous disease with limited treatment options. To characterize TNBC heterogeneity, we defined transcriptional, epigenetic, and metabolic subtypes and subtype-driving super-enhancers and transcription factors by combining functional and molecular profiling with computational analyses. Single-cell RNA sequencing revealed relative homogeneity of the major transcriptional subtypes (luminal, basal, and mesenchymal) within samples. We found that mesenchymal TNBCs share features with mesenchymal neuroblastoma and rhabdoid tumors and that the PRRX1 transcription factor is a key driver of these tumors. PRRX1 is sufficient for inducing mesenchymal features in basal but not in luminal TNBC cells via reprogramming super-enhancer landscapes, but it is not required for mesenchymal state maintenance or for cellular viability. Our comprehensive, large-scale, multiplatform, multiomics study of both experimental and clinical TNBC is an important resource for the scientific and clinical research communities and opens venues for future investigation.
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Affiliation(s)
- Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Temko
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine Murphy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jayati Anand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kodie Garza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Anushree Gulvady
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nicholas W Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Veerle W Daniels
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Huang Xiao-Yun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jennifer Y Ge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Pyrdol
- Departments of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shawn B Egri
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | | | - Raga Vadhi
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alba Font-Tello
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert Witwicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Guillermo Peluffo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Trinh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Benedetto Diciaccio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Muhammad B Ekram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ashim Subedee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zachary T Herbert
- Department of Molecular Biology Core Facility, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kai W Wucherpfennig
- Departments of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony G Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jacob D Jaffe
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| | - Deborah Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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12
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Tarantino P, Gupta H, Hughes ME, Files J, Strauss S, Kirkner G, Feeney AM, Li Y, Garrido-Castro AC, Barroso-Sousa R, Bychkovsky BL, DiLascio S, Sholl L, MacConaill L, Lindeman N, Johnson BE, Meyerson M, Jeselsohn R, Qiu X, Li R, Long H, Winer EP, Dillon D, Curigliano G, Cherniack AD, Tolaney SM, Lin NU. Author Correction: Comprehensive genomic characterization of HER2-low and HER2-0 breast cancer. Nat Commun 2023; 14:8321. [PMID: 38097580 PMCID: PMC10721787 DOI: 10.1038/s41467-023-44124-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Affiliation(s)
- Paolo Tarantino
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Oncology and Hematology-Oncology, University of Milano, Milano, Italy.
| | - Hersh Gupta
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Janet Files
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Strauss
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gregory Kirkner
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Yvonne Li
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ana C Garrido-Castro
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Romualdo Barroso-Sousa
- Dasa Institute for Education and Research (IEPD), Brasilia, Brazil
- Dasa Oncology/Hospital Brasilia, Brasilia, Brazil
| | - Brittany L Bychkovsky
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Simona DiLascio
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lynette Sholl
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Neal Lindeman
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Weill Cornell Medicine, New York, NY, USA
| | - Bruce E Johnson
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew Meyerson
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Rinath Jeselsohn
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Xintao Qiu
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rong Li
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Henry Long
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eric P Winer
- Yale Cancer Center, Yale School of Medicine, Smilow Cancer Hospital, New Haven, CT, USA
| | - Deborah Dillon
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Giuseppe Curigliano
- Division of Early Drug Development, European Institute of Oncology IRCCS, Milano, Italy
| | - Andrew D Cherniack
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sara M Tolaney
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nancy U Lin
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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13
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Tarantino P, Gupta H, Hughes ME, Files J, Strauss S, Kirkner G, Feeney AM, Li Y, Garrido-Castro AC, Barroso-Sousa R, Bychkovsky BL, DiLascio S, Sholl L, MacConaill L, Lindeman N, Johnson BE, Meyerson M, Jeselsohn R, Qiu X, Li R, Long H, Winer EP, Dillon D, Curigliano G, Cherniack AD, Tolaney SM, Lin NU. Comprehensive genomic characterization of HER2-low and HER2-0 breast cancer. Nat Commun 2023; 14:7496. [PMID: 37980405 PMCID: PMC10657399 DOI: 10.1038/s41467-023-43324-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023] Open
Abstract
The molecular underpinnings of HER2-low and HER2-0 (IHC 0) breast tumors remain poorly defined. Using genomic findings from 1039 patients with HER2-negative metastatic breast cancer undergoing next-generation sequencing from 7/2013-12/2020, we compare results between HER2-low (n = 487, 47%) and HER2-0 tumors (n = 552, 53%). A significantly higher number of ERBB2 alleles (median copy count: 2.05) are observed among HER2-low tumors compared to HER2-0 (median copy count: 1.79; P = 2.36e-6), with HER2-0 tumors harboring a higher rate of ERBB2 hemideletions (31.1% vs. 14.5%). No other genomic alteration reaches significance after accounting for multiple hypothesis testing, and no significant differences in tumor mutational burden are observed between HER2-low and HER2-0 tumors (median: 7.26 mutations/megabase vs. 7.60 mutations/megabase, p = 0.24). Here, we show that the genomic landscape of HER2-low and HER2-0 tumors does not differ significantly, apart from a higher ERBB2 copy count among HER2-low tumors, and a higher rate of ERBB2 hemideletions in HER2-0 tumors.
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Affiliation(s)
- Paolo Tarantino
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Oncology and Hematology-Oncology, University of Milano, Milano, Italy.
| | - Hersh Gupta
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Janet Files
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Strauss
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gregory Kirkner
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Yvonne Li
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ana C Garrido-Castro
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Romualdo Barroso-Sousa
- Dasa Institute for Education and Research (IEPD), Brasilia, Brazil
- Dasa Oncology/Hospital Brasilia, Brasilia, Brazil
| | - Brittany L Bychkovsky
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Simona DiLascio
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lynette Sholl
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Neal Lindeman
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Weill Cornell Medicine, New York, NY, USA
| | - Bruce E Johnson
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew Meyerson
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Rinath Jeselsohn
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Xintao Qiu
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rong Li
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Henry Long
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eric P Winer
- Yale Cancer Center, Yale School of Medicine, Smilow Cancer Hospital, New Haven, CT, USA
| | - Deborah Dillon
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Giuseppe Curigliano
- Division of Early Drug Development, European Institute of Oncology IRCCS, Milano, Italy
| | - Andrew D Cherniack
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sara M Tolaney
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nancy U Lin
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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14
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Alečković M, Li Z, Zhou N, Qiu X, Lulseged B, Foidart P, Huang XY, Garza K, Shu S, Kesten N, Li R, Lim K, Garrido-Castro AC, Guerriero JL, Qi J, Long HW, Polyak K. Combination Therapies to Improve the Efficacy of Immunotherapy in Triple-negative Breast Cancer. Mol Cancer Ther 2023; 22:1304-1318. [PMID: 37676980 PMCID: PMC10618734 DOI: 10.1158/1535-7163.mct-23-0303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/05/2023] [Accepted: 08/31/2023] [Indexed: 09/09/2023]
Abstract
Immune checkpoint inhibition combined with chemotherapy is currently approved as first-line treatment for patients with advanced PD-L1-positive triple-negative breast cancer (TNBC). However, a significant proportion of metastatic TNBC is PD-L1-negative and, in this population, chemotherapy alone largely remains the standard-of-care and novel therapeutic strategies are needed to improve clinical outcomes. Here, we describe a triple combination of anti-PD-L1 immune checkpoint blockade, epigenetic modulation thorough bromodomain and extra-terminal (BET) bromodomain inhibition (BBDI), and chemotherapy with paclitaxel that effectively inhibits both primary and metastatic tumor growth in two different syngeneic murine models of TNBC. Detailed cellular and molecular profiling of tumors from single and combination treatment arms revealed increased T- and B-cell infiltration and macrophage reprogramming from MHCIIlow to a MHCIIhigh phenotype in mice treated with triple combination. Triple combination also had a major impact on gene expression and chromatin profiles shifting cells to a more immunogenic and senescent state. Our results provide strong preclinical evidence to justify clinical testing of BBDI, paclitaxel, and immune checkpoint blockade combination.
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Affiliation(s)
- Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Ningxuan Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard University, Cambridge, Massachusetts
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard University, Cambridge, Massachusetts
| | - Bethlehem Lulseged
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Pierre Foidart
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Xiao-Yun Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kodie Garza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Nikolas Kesten
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard University, Cambridge, Massachusetts
| | - Rong Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard University, Cambridge, Massachusetts
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard University, Cambridge, Massachusetts
| | - Ana C. Garrido-Castro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jennifer L. Guerriero
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Surgery, Division of Breast Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Henry W. Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard University, Cambridge, Massachusetts
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
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15
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Baca SC, Seo JH, Davidsohn MP, Fortunato B, Semaan K, Sotudian S, Lakshminarayanan G, Diossy M, Qiu X, El Zarif T, Savignano H, Canniff J, Madueke I, Saliby RM, Zhang Z, Li R, Jiang Y, Taing L, Awad M, Chau CH, DeCaprio JA, Figg WD, Greten TF, Hata AN, Hodi FS, Hughes ME, Ligon KL, Lin N, Ng K, Oser MG, Meador C, Parsons HA, Pomerantz MM, Rajan A, Ritz J, Thakuria M, Tolaney SM, Wen PY, Long H, Berchuck JE, Szallasi Z, Choueiri TK, Freedman ML. Liquid biopsy epigenomic profiling for cancer subtyping. Nat Med 2023; 29:2737-2741. [PMID: 37865722 PMCID: PMC10695830 DOI: 10.1038/s41591-023-02605-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/21/2023] [Indexed: 10/23/2023]
Abstract
Although circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1 ml of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling has the potential to unlock clinically actionable information that is currently accessible only via direct tissue sampling.
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Affiliation(s)
- Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew P Davidsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brad Fortunato
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Karl Semaan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Shahabbedin Sotudian
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Gitanjali Lakshminarayanan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Miklos Diossy
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Talal El Zarif
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hunter Savignano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John Canniff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ikenna Madueke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Renee Maria Saliby
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ziwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Rong Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yijia Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cindy H Chau
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - William D Figg
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tim F Greten
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Melissa E Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keith L Ligon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nancy Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine Meador
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Arun Rajan
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Manisha Thakuria
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cutaneous Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zoltan Szallasi
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Bioinformatics and Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
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16
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Hermida-Prado F, Xie Y, Sherman S, Nagy Z, Russo D, Akhshi T, Chu Z, Feit A, Campisi M, Chen M, Nardone A, Guarducci C, Lim K, Font-Tello A, Lee I, García-Pedrero J, Cañadas I, Agudo J, Huang Y, Sella T, Jin Q, Tayob N, Mittendorf EA, Tolaney SM, Qiu X, Long H, Symmans WF, Lin JR, Santagata S, Bedrosian I, Yardley DA, Mayer IA, Richardson ET, Oliveira G, Wu CJ, Schuster EF, Dowsett M, Welm AL, Barbie D, Metzger O, Jeselsohn R. Endocrine Therapy Synergizes with SMAC Mimetics to Potentiate Antigen Presentation and Tumor Regression in Hormone Receptor-Positive Breast Cancer. Cancer Res 2023; 83:3284-3304. [PMID: 37450351 PMCID: PMC10543960 DOI: 10.1158/0008-5472.can-23-1711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Immunotherapies have yet to demonstrate significant efficacy in the treatment of hormone receptor-positive (HR+) breast cancer. Given that endocrine therapy (ET) is the primary approach for treating HR+ breast cancer, we investigated the effects of ET on the tumor immune microenvironment (TME) in HR+ breast cancer. Spatial proteomics of primary HR+ breast cancer samples obtained at baseline and after ET from patients enrolled in a neoadjuvant clinical trial (NCT02764541) indicated that ET upregulated β2-microglobulin and influenced the TME in a manner that promotes enhanced immunogenicity. To gain a deeper understanding of the underlying mechanisms, the intrinsic effects of ET on cancer cells were explored, which revealed that ET plays a crucial role in facilitating the chromatin binding of RelA, a key component of the NF-κB complex. Consequently, heightened NF-κB signaling enhanced the response to interferon-gamma, leading to the upregulation of β2-microglobulin and other antigen presentation-related genes. Further, modulation of NF-κB signaling using a SMAC mimetic in conjunction with ET augmented T-cell migration and enhanced MHC-I-specific T-cell-mediated cytotoxicity. Remarkably, the combination of ET and SMAC mimetics, which also blocks prosurvival effects of NF-κB signaling through the degradation of inhibitors of apoptosis proteins, elicited tumor regression through cell autonomous mechanisms, providing additional support for their combined use in HR+ breast cancer. SIGNIFICANCE Adding SMAC mimetics to endocrine therapy enhances tumor regression in a cell autonomous manner while increasing tumor immunogenicity, indicating that this combination could be an effective treatment for HR+ patients with breast cancer.
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Affiliation(s)
- Francisco Hermida-Prado
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- University of Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), IUOPA, Oviedo, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shira Sherman
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zsuzsanna Nagy
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Douglas Russo
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tara Akhshi
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zhengtao Chu
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
| | - Avery Feit
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marco Campisi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Minyue Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Agostina Nardone
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cristina Guarducci
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alba Font-Tello
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Irene Lee
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Juana García-Pedrero
- University of Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), IUOPA, Oviedo, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Israel Cañadas
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Judith Agudo
- Harvard Medical School, Boston, Massachusetts
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ying Huang
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tal Sella
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Qingchun Jin
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nabihah Tayob
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Elizabeth A. Mittendorf
- Harvard Medical School, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Sara M. Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Jia-Ren Lin
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Sandro Santagata
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Isabelle Bedrosian
- Department of Breast Surgical Oncology, Division of Surgery, MD Anderson Cancer Center, Houston, Texas
| | - Denise A. Yardley
- Department of Medical Oncology, Sarah Cannon Cancer Center, Nashville, Tennessee
- Tennessee Oncology, Nashville, Tennessee
| | - Ingrid A. Mayer
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Edward T. Richardson
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Catherine J. Wu
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Eugene F. Schuster
- The BC Now Toby Robins Research Centre at the Institute of Cancer Research, London, United Kingdom
- Ralph Lauren Centre for BC Research, Royal Marsden Hospital, London, United Kingdom
- The Royal Marsden Hospital, London, United Kingdom
| | - Mitch Dowsett
- The BC Now Toby Robins Research Centre at the Institute of Cancer Research, London, United Kingdom
- Ralph Lauren Centre for BC Research, Royal Marsden Hospital, London, United Kingdom
- The Royal Marsden Hospital, London, United Kingdom
| | - Alana L. Welm
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
| | - David Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Otto Metzger
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Rinath Jeselsohn
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
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17
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Xu Z, Liang J, Fu R, Yang L, Xin Chen Y, Ren W, Lu Y, Qiu X, Gu Q. Effect of PD-L1 Expression for the PD-1/L1 Inhibitors on Non-small Cell Lung Cancer: A Meta-analysis Based on Randomised Controlled Trials. Clin Oncol (R Coll Radiol) 2023; 35:640-651. [PMID: 37563075 DOI: 10.1016/j.clon.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/23/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023]
Abstract
AIMS As PD-L1 expression has been proposed as one of the cancer biomarkers for non-small cell lung cancer (NSCLC), the predictive value of tumour proportional score (TPS) in the effect of immunotherapy [programmed death protein-1/ligand 1 (PD-1/L1) inhibitors] for NSCLC is worth exploring further. Here, we aimed to summarise the outcomes of current NSCLC randomised controlled trials (RCTs) and explore the predictive value of TPS in clinical immunotherapy, including immune checkpoint inhibitors (ICIs) with or without chemotherapy. MATERIALS AND METHODS RCTs published by PubMed, Medline, Embase and Scopus before February 2023 comparing immunotherapy (PD-1/L1 with or without other therapy) versus a control group in advanced or metastatic NSCLC were included to assess the prognosis according to the patients' TPS with 1% and 50% as the thresholds. The primary endpoints were overall survival and progression-free survival. RESULTS In total, 28 RCTs containing 17 266 participants with advanced or metastatic NSCLC were included in this meta-analysis. Statistical results showed that compared with TPS <1%, ≥1% or within 1-49%, patients with TPS ≥50% benefited more significantly from the immunotherapy. A subgroup analysis showed that when TPS was <1%, ≥1% or within 1-49%, ICIs + chemotherapy had better efficacy than ICIs alone; PD-1 (such as pembrolizumab) inhibitors had better efficacy than PD-L1 inhibitors (such as atezolizumab). CONCLUSION The efficacy of immunotherapy (PD-1/L1 inhibitors) for advanced or metastatic NSCLC is influenced by TPS.
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Affiliation(s)
- Z Xu
- Department of Respiratory and Critical Care Medicine, Linhai Second People's Hospital, Taizhou, Zhejiang, China
| | - J Liang
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - R Fu
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - L Yang
- Emergency Medical Center, Ningbo Yinzhou No. 2 Hospital, Ningbo, Zhejiang, China
| | - Y Xin Chen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - W Ren
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Y Lu
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - X Qiu
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Q Gu
- Department of Respiratory and Critical Care Medicine, Linhai Second People's Hospital, Taizhou, Zhejiang, China.
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18
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Duplaquet L, Li Y, Booker MA, Xie Y, Olsen SN, Patel RA, Hong D, Hatton C, Denize T, Walton E, Laimon YN, Li R, Jiang Y, Bronson RT, Southard J, Li S, Signoretti S, Qiu X, Cejas P, Armstrong SA, Long HW, Tolstorukov MY, Haffner MC, Oser MG. KDM6A epigenetically regulates subtype plasticity in small cell lung cancer. Nat Cell Biol 2023; 25:1346-1358. [PMID: 37591951 PMCID: PMC10546329 DOI: 10.1038/s41556-023-01210-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Small cell lung cancer (SCLC) exists broadly in four molecular subtypes: ASCL1, NEUROD1, POU2F3 and Inflammatory. Initially, SCLC subtypes were thought to be mutually exclusive, but recent evidence shows intra-tumoural subtype heterogeneity and plasticity between subtypes. Here, using a CRISPR-based autochthonous SCLC genetically engineered mouse model to study the consequences of KDM6A/UTX inactivation, we show that KDM6A inactivation induced plasticity from ASCL1 to NEUROD1 resulting in SCLC tumours that express both ASCL1 and NEUROD1. Mechanistically, KDM6A normally maintains an active chromatin state that favours the ASCL1 subtype with its loss decreasing H3K4me1 and increasing H3K27me3 at enhancers of neuroendocrine genes leading to a cell state that is primed for ASCL1-to-NEUROD1 subtype switching. This work identifies KDM6A as an epigenetic regulator that controls ASCL1 to NEUROD1 subtype plasticity and provides an autochthonous SCLC genetically engineered mouse model to model ASCL1 and NEUROD1 subtype heterogeneity and plasticity, which is found in 35-40% of human SCLCs.
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Affiliation(s)
- Leslie Duplaquet
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yixiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew A Booker
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yingtian Xie
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Naomi Olsen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Radhika A Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Deli Hong
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Charlie Hatton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily Walton
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yasmin N Laimon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rong Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yijia Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Roderick T Bronson
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Jackson Southard
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shuqiang Li
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael Y Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, MA, USA.
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19
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Yang L, Wang J, Altreuter J, Jhaveri A, Wong CJ, Song L, Fu J, Taing L, Bodapati S, Sahu A, Tokheim C, Zhang Y, Zeng Z, Bai G, Tang M, Qiu X, Long HW, Michor F, Liu Y, Liu XS. Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA. Nat Protoc 2023; 18:2404-2414. [PMID: 37391666 DOI: 10.1038/s41596-023-00841-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/22/2023] [Indexed: 07/02/2023]
Abstract
RNA-sequencing (RNA-seq) has become an increasingly cost-effective technique for molecular profiling and immune characterization of tumors. In the past decade, many computational tools have been developed to characterize tumor immunity from gene expression data. However, the analysis of large-scale RNA-seq data requires bioinformatics proficiency, large computational resources and cancer genomics and immunology knowledge. In this tutorial, we provide an overview of computational analysis of bulk RNA-seq data for immune characterization of tumors and introduce commonly used computational tools with relevance to cancer immunology and immunotherapy. These tools have diverse functions such as evaluation of expression signatures, estimation of immune infiltration, inference of the immune repertoire, prediction of immunotherapy response, neoantigen detection and microbiome quantification. We describe the RNA-seq IMmune Analysis (RIMA) pipeline integrating many of these tools to streamline RNA-seq analysis. We also developed a comprehensive and user-friendly guide in the form of a GitBook with text and video demos to assist users in analyzing bulk RNA-seq data for immune characterization at both individual sample and cohort levels by using RIMA.
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Affiliation(s)
- Lin Yang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jin Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Jennifer Altreuter
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aashna Jhaveri
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cheryl J Wong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Li Song
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jingxin Fu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- School of Life Science and Technology, Tongji University, Shanghai, China
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sudheshna Bodapati
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Avinash Sahu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yi Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Gali Bai
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA
- The Ludwig Center at Harvard, Boston, MA, USA
| | - Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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20
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Liu Z, Qiu X, Yang H, Wu X, Ye W. [Inhibitor of growth protein-2 silencing alleviates angiotensin Ⅱ-induced cardiac remodeling in mice by reducing p53 acetylation]. Nan Fang Yi Ke Da Xue Xue Bao 2023; 43:1127-1135. [PMID: 37488795 PMCID: PMC10366506 DOI: 10.12122/j.issn.1673-4254.2023.07.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
OBJECTIVE To investigate the effect of inhibitor of growth protein-2 (Ing2) silencing on angiotensin Ⅱ (AngⅡ)-induced cardiac remodeling in mice and explore the underlying mechanism. METHODS An adenoviral vector carrying Ing2 shRNA or empty adenoviral vector was injected into the tail vein of mice, followed 48 h later by infusion of 1000 ng · kg-1 · min-1 Ang Ⅱ or saline using a mini-osmotic pump for 42 consecutive days. Transthoracic echocardiography was used to assess cardiac geometry and function and the level of cardiac hypertrophy in the mice. Masson and WGA staining were used to detect myocardial fibrosis and cross-sectional area of cardiomyocytes, and myocardial cell apoptosis was detected with TUNEL assay. Western blotting was performed to detect myocardial expressions of cleaved caspase 3, ING2, collagen Ⅰ, Ac-p53(Lys382) and p-p53 (Ser15); Ing2 mRNA expression was detected using real-time PCR. Mitochondrial biogenesis, as measured by mitochondrial ROS content, ATP content, citrate synthase activity and calcium storage, was determined using commercial assay kits. RESULTS The expression levels of Ing2 mRNA and protein were significantly higher in the mice with chronic Ang Ⅱ infusion than in saline-infused mice. Chronic infusion of AngⅡ significantly increased the left ventricular end-systolic diameter (LVESD) and left ventricular end-diastolic diameter (LVEDD) and reduced left ventricular ejection fraction (LVEF) and left ventricular fractional shortening (LVFS) in the mice. Ing2 silencing obviously alleviated AngⅡ-induced cardiac function decline, as shown by decreased LVEDD and LVESD and increased LVEF and LVFS, improved myocardial mitochondrial damage and myocardial hypertrophy and fibrosis, and inhibited cardiomyocyte apoptosis. Chronic AngⅡ infusion significantly increased myocardial expression levels of Ac-p53(Lys382) and p-p53(Ser15) in the mice, and Ing2 silencing prior to AngⅡ infusion lessened AngⅡ- induced increase of Ac-p53(Lys382) without affecting p53 (ser15) expression. CONCLUSION Ing2 silencing can inhibit AngⅡ-induced cardiac remodeling and dysfunction in mice by reducing p53 acetylation.
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Affiliation(s)
- Z Liu
- Department of Cardiovascular Medicine, Chinese Traditional Medicine Hospital of Hainan Province, Haikou 570203, China
| | - X Qiu
- Department of Endocrinology, Chinese Traditional Medicine Hospital of Hainan Province, Haikou 570203, China
| | - H Yang
- Department of Cardiovascular Medicine, Chinese Traditional Medicine Hospital of Hainan Province, Haikou 570203, China
| | - X Wu
- Department of Endocrinology, Chinese Traditional Medicine Hospital of Hainan Province, Haikou 570203, China
| | - W Ye
- Guangzhou University of Chinese Medicine, Guangzhou 510006, China
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21
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Erchick DJ, Hazel EA, Katz J, Lee ACC, Diaz M, Wu LSF, Yoshida S, Bahl R, Grandi C, Labrique AB, Rashid M, Ahmed S, Roy AD, Haque R, Shaikh S, Baqui AH, Saha SK, Khanam R, Rahman S, Shapiro R, Zash R, Silveira MF, Buffarini R, Kolsteren P, Lachat C, Huybregts L, Roberfroid D, Zeng L, Zhu Z, He J, Qiu X, Gebreyesus SH, Tesfamariam K, Bekele D, Chan G, Baye E, Workneh F, Asante KP, Kaali EB, Adu-Afarwuah S, Dewey KG, Gyaase S, Wylie BJ, Kirkwood BR, Manu A, Thulasiraj RD, Tielsch J, Chowdhury R, Taneja S, Babu GR, Shriyan P, Ashorn P, Maleta K, Ashorn U, Mangani C, Acevedo-Gallegos S, Rodriguez-Sibaja MJ, Khatry SK, LeClerq SC, Mullany LC, Jehan F, Ilyas M, Rogerson SJ, Unger HW, Ghosh R, Musange S, Ramokolo V, Zembe-Mkabile W, Lazzerini M, Rishard M, Wang D, Fawzi WW, Minja DTR, Schmiegelow C, Masanja H, Smith E, Lusingu JPA, Msemo OA, Kabole FM, Slim SN, Keentupthai P, Mongkolchati A, Kajubi R, Kakuru A, Waiswa P, Walker D, Hamer DH, Semrau KEA, Chaponda EB, Chico RM, Banda B, Musokotwane K, Manasyan A, Pry JM, Chasekwa B, Humphrey J, Black RE. Vulnerable newborn types: analysis of subnational, population-based birth cohorts for 541 285 live births in 23 countries, 2000-2021. BJOG 2023. [PMID: 37156239 DOI: 10.1111/1471-0528.17510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 05/10/2023]
Abstract
OBJECTIVE To examine prevalence of novel newborn types among 541 285 live births in 23 countries from 2000 to 2021. DESIGN Descriptive multi-country secondary data analysis. SETTING Subnational, population-based birth cohort studies (n = 45) in 23 low- and middle-income countries (LMICs) spanning 2000-2021. POPULATION Liveborn infants. METHODS Subnational, population-based studies with high-quality birth outcome data from LMICs were invited to join the Vulnerable Newborn Measurement Collaboration. We defined distinct newborn types using gestational age (preterm [PT], term [T]), birthweight for gestational age using INTERGROWTH-21st standards (small for gestational age [SGA], appropriate for gestational age [AGA] or large for gestational age [LGA]), and birthweight (low birthweight, LBW [<2500 g], nonLBW) as ten types (using all three outcomes), six types (by excluding the birthweight categorisation), and four types (by collapsing the AGA and LGA categories). We defined small types as those with at least one classification of LBW, PT or SGA. We presented study characteristics, participant characteristics, data missingness, and prevalence of newborn types by region and study. RESULTS Among 541 285 live births, 476 939 (88.1%) had non-missing and plausible values for gestational age, birthweight and sex required to construct the newborn types. The median prevalences of ten types across studies were T+AGA+nonLBW (58.0%), T+LGA+nonLBW (3.3%), T+AGA+LBW (0.5%), T+SGA+nonLBW (14.2%), T+SGA+LBW (7.1%), PT+LGA+nonLBW (1.6%), PT+LGA+LBW (0.2%), PT+AGA+nonLBW (3.7%), PT+AGA+LBW (3.6%) and PT+SGA+LBW (1.0%). The median prevalence of small types (six types, 37.6%) varied across studies and within regions and was higher in Southern Asia (52.4%) than in Sub-Saharan Africa (34.9%). CONCLUSIONS Further investigation is needed to describe the mortality risks associated with newborn types and understand the implications of this framework for local targeting of interventions to prevent adverse pregnancy outcomes in LMICs.
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Affiliation(s)
- D J Erchick
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - E A Hazel
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - J Katz
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - A C C Lee
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - M Diaz
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - L S F Wu
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - S Yoshida
- Department of Maternal, Newborn, Child and Adolescent Health and Ageing, World Health Organization, Geneva, Switzerland
| | - R Bahl
- Department of Maternal, Newborn, Child and Adolescent Health and Ageing, World Health Organization, Geneva, Switzerland
| | - C Grandi
- Argentine Society of Paediatrics, Ciudad Autónoma de Buenos Aires, Argentina
| | - A B Labrique
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - M Rashid
- IntraHealth International, Dhaka, Bangladesh
| | - S Ahmed
- Projahnmo Research Foundation, Dhaka, Bangladesh
| | - A D Roy
- Projahnmo Research Foundation, Dhaka, Bangladesh
| | - R Haque
- JiVitA Maternal and Child Health Research Project, Rangpur, Bangladesh
| | - S Shaikh
- JiVitA Maternal and Child Health Research Project, Rangpur, Bangladesh
| | - A H Baqui
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - S K Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | - R Khanam
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - S Rahman
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - R Shapiro
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - R Zash
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - M F Silveira
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - R Buffarini
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - P Kolsteren
- Department of Food Technology, Safety and Health, Ghent University, Ghent, Belgium
| | - C Lachat
- Department of Food Technology, Safety and Health, Ghent University, Ghent, Belgium
| | - L Huybregts
- Department of Food Technology, Safety and Health, Ghent University, Ghent, Belgium
- Poverty, Health and Nutrition Division, International Food Policy Research Institute, Washington, DC, USA
| | - D Roberfroid
- Medicine Department, Faculty of Medicine, University of Namur, Namur, Belgium
| | - L Zeng
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Z Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - J He
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - X Qiu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - S H Gebreyesus
- Department of Nutrition and Dietetics, School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - K Tesfamariam
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - D Bekele
- Department of Obstetrics and Gynecology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - G Chan
- Department of Obstetrics and Gynecology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - E Baye
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - F Workneh
- Addis Continental Institute of Public Health, Addis Ababa, Ethiopia
| | - K P Asante
- Kintampo Health Research Centre, Research and Development Division, Kintampo, Ghana
| | - E B Kaali
- Kintampo Health Research Centre, Research and Development Division, Kintampo, Ghana
| | - S Adu-Afarwuah
- Department of Nutrition and Food Science, University of Ghana, Accra, Ghana
| | - K G Dewey
- Institute for Global Nutrition, Department of Nutrition, University of California, Davis, California, USA
| | - S Gyaase
- Department of Statistics, Kintampo Health Research Centre, Kintampo, Ghana
| | - B J Wylie
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, New York, USA
| | - B R Kirkwood
- Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - A Manu
- Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- University of Ghana School of Public Health, Accra, Ghana
| | | | - J Tielsch
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - R Chowdhury
- Centre for Health Research and Development, Society for Applied Studies, Delhi, India
| | - S Taneja
- Centre for Health Research and Development, Society for Applied Studies, Delhi, India
| | - G R Babu
- Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - P Shriyan
- Indian Institute of Public Health, Public Health Foundation of India, Bengaluru, India
| | - P Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University and Tampere University Hospital, Tampere, Finland
| | - K Maleta
- School of Global and Public Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - U Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University and Tampere University Hospital, Tampere, Finland
| | - C Mangani
- School of Global and Public Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - S Acevedo-Gallegos
- National Institute of Perinatology, Maternal-Fetal Medicine Department, Mexico City, Mexico
| | - M J Rodriguez-Sibaja
- National Institute of Perinatology, Maternal-Fetal Medicine Department, Mexico City, Mexico
| | - S K Khatry
- Nepal Nutrition Intervention Project - Sarlahi (NNIPS), Kathmandu, Nepal
| | - S C LeClerq
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Nepal Nutrition Intervention Project - Sarlahi (NNIPS), Kathmandu, Nepal
| | - L C Mullany
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - F Jehan
- Department of Paediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - M Ilyas
- The Aga Khan University, Karachi, Pakistan
| | - S J Rogerson
- Department of Infectious Diseases, University of Melbourne, Doherty Institute, Melbourne, Victoria, Australia
| | - H W Unger
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - R Ghosh
- Institute for Global Health Sciences, Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - S Musange
- School of Public Health, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - V Ramokolo
- HIV and Other Infectious Diseases Research Unit, South African Medical Research Council, Cape Town, South Africa
- Gertrude H Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - W Zembe-Mkabile
- Health Systems Research Unit, South African Medical Research Council, Cape Town, South Africa
- College Graduate of Studies, University of South Africa, Johannesburg, South Africa
| | - M Lazzerini
- Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo', WHO Collaborating Centre for Maternal and Child Health, Trieste, Italy
| | - M Rishard
- University Obstetrics Unit, De Soysa Hospital for Women, Colombo, Sri Lanka
- Department of Obstetrics & Gynaecology, University of Colombo, Colombo, Sri Lanka
| | - D Wang
- Department of Global and Community Health, College of Public Health, George Mason University, Fairfax, Virginia, USA
| | - W W Fawzi
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - D T R Minja
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - C Schmiegelow
- Centre for Medical Parasitology, Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - H Masanja
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - E Smith
- Department of Global Health, Milken Institute School of Public Health, Washington, DC, USA
| | - J P A Lusingu
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - O A Msemo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - F M Kabole
- Ministry of Health Zanzibar, Zanzibar, Tanzania
| | - S N Slim
- Ministry of Health Zanzibar, Zanzibar, Tanzania
| | - P Keentupthai
- College of Medicine and Public Health, Ubon Ratchathani University, Ubon Ratchathani, Thailand
| | - A Mongkolchati
- ASEAN Institute for Health Development, Mahidol University, Salaya, Thailand
| | - R Kajubi
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - A Kakuru
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - P Waiswa
- Department of Health Policy Planning and Management, Makerere University School of Public Health, New Mulago Hospital Complex, Kampala, Uganda
- Division of Global Health, Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - D Walker
- Institute for Global Health Sciences and Department of Obstetrics and Gynecology, University of California San Francisco, San Francisco, California, USA
| | - D H Hamer
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
- Section of Infectious Diseases, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - K E A Semrau
- Ariadne Labs, Brigham and Women's Hospital and Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Division of Global Health Equity & Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - E B Chaponda
- Department of Biological Sciences, School of Natural Sciences, University of Zambia, Lusaka, Zambia
| | - R M Chico
- Department of Disease Control, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - B Banda
- Research Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - K Musokotwane
- Health Specialist PMTCT and Pediatric AIDS, UNICEF, Lusaka, Zambia
| | - A Manasyan
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - J M Pry
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - B Chasekwa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - J Humphrey
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - R E Black
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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22
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Friel DM, Sandusky Z, Jiang Y, Qiu X, Li R, Long H, Jeselsohn R, Brown M. Abstract 3875: Evaluation of resistance mechanisms to ARV471, an ER-targeted PROTAC. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Estrogen receptor alpha (ER) is a ligand activated transcription factor and a driver of ER+ breast cancer. The discovery of activating mutations in ER (gene name ESR1), in patients with advanced endocrine-resistant ER+ breast cancer, has ignited a large pharmaceutical effort to develop next-generation ER antagonists that also target the mutant protein. Here, we profiled the potency and selectivity of many next-generation ER antagonists currently in clinical trials, including ER-targeted proteolysis-targeting chimeras (PROTACs), selective ER modulators (SERMs), and selective ER degraders (SERDs). To contextualize these antagonists, we evaluated their activity against the only FDA-approved SERD, Fulvestrant, at the level of chromatin, transcriptome, proteome, and cell viability, using cells expressing wild-type ER as well as activating mutant ER (ERY537S and ERD538G). Overall, we find that many of the novel oral SERDs are potent ER antagonists, including against mutant ER. To anticipate resistance mechanisms to these next-generation ER antagonists, we developed a strategy initially focused on ARV471 (the most clinically advanced ER PROTAC), with two approaches. First, we performed whole-genome CRISPR/Cas9-knockout screening in ER+ breast cancer cell lines treated with ARV471. Among the enriched gRNAs were PTEN, NF2, and CRBN. Loss of PTEN and NF2 results in activation of the PI3K and MAPK pathways, respectively, and CRBN is the ubiquitin E3 ligase required for ER protein degradation by ARV471. PTEN and NF2 are known mechanisms of endocrine resistance but it is not yet known if CRBN loss in response to PROTACs is a predominant clinical resistance mechanism. Therefore, in a second approach we generated ARV471 resistant breast cancer cell lines through long term exposure (LTE-ARV471). These cells developed an ER-independent resistance mechanism, with decreased ER expression and increased expression of pathways associated with Ras/MAPK and EMT. Therefore, as more potent ER degraders enter the clinic, such as PROTACs and oral SERDs, it may be important to monitor resistance mechanisms that involve loss of ER. Currently, we are following up our findings with LTE-ARV471 cells and performing CRISPR screening to identify targetable dependencies and combination therapies for endocrine resistant breast cancer.
Citation Format: Delia Margaret Friel, Zachary Sandusky, Yijia Jiang, Xintao Qiu, Rong Li, Henry Long, Rinath Jeselsohn, Myles Brown. Evaluation of resistance mechanisms to ARV471, an ER-targeted PROTAC. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3875.
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Affiliation(s)
| | | | | | - Xintao Qiu
- 1DFCI/Harvard Medical School, Boston, MA
| | - Rong Li
- 1DFCI/Harvard Medical School, Boston, MA
| | - Henry Long
- 1DFCI/Harvard Medical School, Boston, MA
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23
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Tarantino P, Gupta HV, Hughes ME, Files JL, Strauss S, Kirkner G, Feeney AM, Li YY, Garrido-Castro AC, Barroso-Sousa R, Bychkovsky B, MacConaill L, Lindeman N, Johnson B, Meyerson M, Kabraji S, Jeselsohn R, Qiu X, Li R, Long HW, Winer E, Dillon DA, Curigliano G, Cherniack A, Tolaney S, Lin NU. Abstract HER2-05: HER2-05 Comprehensive genomic characterization of HER2-low breast cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-her2-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background: About half of all breast cancers exhibit low HER2 expression. Despite lack of ERBB2 amplification, HER2-low tumors respond to trastuzumab deruxtecan (T-DXd), leading to the NCCN recommendation of T-DXd both for patients with HER2+ and HER2-low metastatic breast cancer (MBC). It remains however unclear if HER2-low represents a distinct molecular entity, as compared to HER2-0 MBC. Here, we compare the genomic landscape of HER2-low versus HER2-0 breast cancers in a large, single institution cohort. Methods: We identified consecutive patients with MBC seen at Dana-Farber Cancer Institute between 07/2013 and 12/2020. Patients were included if they had HER2-negative MBC per ASCO/CAP Guidelines and had undergone next generation sequencing (NGS) testing with a targeted, tumor-only platform (OncoPanel). Based on the HER2 status of the specimen tested by NGS, patients were divided into 2 groups: (i) HER2-low if immunohistochemistry (IHC) 1+ or 2+ non-amplified, or (ii) HER2-0 if IHC 0. Mutations of interest detected on NGS were classified as oncogenic using the OncoKB tool and additional annotation. Genomic profiles of HER2-low and HER2-0 tumors were compared using Chi-Square and Kruskal-Wallis tests. To determine genomic event enrichment between the two HER2 groups, logistic regression models were used, accounting for background rate and estrogen receptor (ER) expression. ERBB2 copy counts were calculated for tumors with recorded histology-estimated purities and copy-number segmentation using a simple model of allelic gain/loss. Results: Among 1847 patients with HER2-negative MBC, 1043 underwent NGS testing on a HER2-low (n=489, 47%) or HER2-0 sample (n=554, 53%). Most samples were metastatic (71%, n=743) while 29% (n=300) were from primary tumors. 73% had ductal histology, 13% were lobular and 14% had mixed or other histology. ER expression was enriched among HER2-low vs. HER2-0 tumors (76% vs. 60%; p< 0.001). Focusing on the most commonly occurring genetic mutations, no major differences were observed in HER2-low vs. HER2-0 tumors, after correcting for ER status (Table 1). Among all mutational events, any mutation in MPL, CYLD, and MAP3K and oncogenic mutations in TP53 and NF1 were more common in HER2-0, while any mutation in MTOR, RAD21, DNMT3A, and PDGFRA were enriched in HER2-low patients, when controlling for ER status and background mutational rate (p< 0.05). However, no mutation reached significance after accounting for multiple hypothesis testing. Similarly, no deep deletion or high amplification CNV events reached significance for either group. Analysis of tumor mutational burden in HER2-low vs. HER-0 tumors revealed no significant differences (median: 7.26 muts/Mb vs. 7.60 muts/Mb, p=1.00), including when accounting for ER status. Finally, among tumors with sufficient tumor purity for ERBB2 copy count analysis (n=374 and 419 for HER2-low and HER2-0, respectively), HER2-low tumors had a significantly higher number of ERBB2 alleles as compared to HER2-0 (< 2 copies, 15.0% vs. 30.9%, 2 copies 67.4% vs. 60.5%, and >2 copies, 17.6% vs. 8.6%; p< 0.001 by Kruskal-Wallis). Conclusions: To our knowledge, this is the largest comprehensive genomic analysis of HER2-low MBC to date. In our cohort of patients with HER2-negative MBC, the genomic landscape of HER2-low and HER2-0 tumors did not differ significantly, apart from a higher number of ERBB2 alleles. These data further support the notion that HER2-low, as currently defined, is not a distinct molecular subtype of breast cancer.
Citation Format: Paolo Tarantino, Hersh V. Gupta, Melissa E. Hughes, Janet L. Files, Sarah Strauss, Gregory Kirkner, Anne-Marie Feeney, Yvonne Y. Li, Ana C. Garrido-Castro, Romualdo Barroso-Sousa, Brittany Bychkovsky, Laura MacConaill, Neal Lindeman, Bruce Johnson, Matthew Meyerson, Sheheryar Kabraji, Rinath Jeselsohn, Xintao Qiu, Rong Li, Henry W. Long, Eric Winer, Deborah A. Dillon, Giuseppe Curigliano, Andrew Cherniack, Sara Tolaney, Nancy U. Lin. HER2-05 Comprehensive genomic characterization of HER2-low breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr HER2-05.
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Affiliation(s)
- Paolo Tarantino
- 1Breast Oncology Program, Dana-Farber Cancer Institute; Harvard Medical School, Boston, Massachusetts
| | - Hersh V. Gupta
- 2Albert Einstein College of Medicine MSTP (previously: Medical Oncology, Dana-Farber Cancer Institute)
| | | | - Janet L. Files
- 4Medical Oncology, Dana-Farber Cancer Institute, Hull, Massachusetts
| | | | | | | | | | | | | | - Brittany Bychkovsky
- 11Comprehensive Breast Health Center, Brigham and Women’s Hospital; Breast Oncology Program, Dana-Farber Brigham Cancer Center Division of Cancer Genetics and Prevention; Dana-Farber Cancer Institute; Harvard Medical School
| | - Laura MacConaill
- 12Dana-Farber Cancer Institute; Harvard Medical School; Broad Institute of Harvard and MIT
| | - Neal Lindeman
- 13Brigham and Women’s Hospital; Harvard Medical School
| | - Bruce Johnson
- 14Medical Oncology, Dana-Farber Cancer Institute; Harvard Medical School
| | - Matthew Meyerson
- 15Medical Oncology, Dana-Farber Cancer Institute; Center for Cancer Genomics, Dana-Farber Cancer Institute; Harvard Medical School; Broad Institute
| | | | | | | | - Rong Li
- 19Dana-Farber Cancer Institute
| | | | | | - Deborah A. Dillon
- 22Brigham and Women’s Hospital, Breast Oncology Program, Susan F. Smith Center for Women’s Cancers, Dana-Farber Brigham Cancer Center; Harvard Medical School
| | | | - Andrew Cherniack
- 24Medical Oncology, Dana-Farber Cancer Institute; Broad Institute
| | | | - Nancy U. Lin
- 26Dana-Farber Cancer Institute, Boston, Massachusetts
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24
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Stevens LE, Peluffo G, Qiu X, Temko D, Fassl A, Li Z, Trinh A, Seehawer M, Jovanović B, Alečković M, Wilde CM, Geck RC, Shu S, Kingston NL, Harper NW, Almendro V, Pyke AL, Egri SB, Papanastasiou M, Clement K, Zhou N, Walker S, Salas J, Park SY, Frank DA, Meissner A, Jaffe JD, Sicinski P, Toker A, Michor F, Long HW, Overmoyer BA, Polyak K. JAK-STAT Signaling in Inflammatory Breast Cancer Enables Chemotherapy-Resistant Cell States. Cancer Res 2023; 83:264-284. [PMID: 36409824 PMCID: PMC9845989 DOI: 10.1158/0008-5472.can-22-0423] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/23/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022]
Abstract
Inflammatory breast cancer (IBC) is a difficult-to-treat disease with poor clinical outcomes due to high risk of metastasis and resistance to treatment. In breast cancer, CD44+CD24- cells possess stem cell-like features and contribute to disease progression, and we previously described a CD44+CD24-pSTAT3+ breast cancer cell subpopulation that is dependent on JAK2/STAT3 signaling. Here we report that CD44+CD24- cells are the most frequent cell type in IBC and are commonly pSTAT3+. Combination of JAK2/STAT3 inhibition with paclitaxel decreased IBC xenograft growth more than either agent alone. IBC cell lines resistant to paclitaxel and doxorubicin were developed and characterized to mimic therapeutic resistance in patients. Multi-omic profiling of parental and resistant cells revealed enrichment of genes associated with lineage identity and inflammation in chemotherapy-resistant derivatives. Integrated pSTAT3 chromatin immunoprecipitation sequencing and RNA sequencing (RNA-seq) analyses showed pSTAT3 regulates genes related to inflammation and epithelial-to-mesenchymal transition (EMT) in resistant cells, as well as PDE4A, a cAMP-specific phosphodiesterase. Metabolomic characterization identified elevated cAMP signaling and CREB as a candidate therapeutic target in IBC. Investigation of cellular dynamics and heterogeneity at the single cell level during chemotherapy and acquired resistance by CyTOF and single cell RNA-seq identified mechanisms of resistance including a shift from luminal to basal/mesenchymal cell states through selection for rare preexisting subpopulations or an acquired change. Finally, combination treatment with paclitaxel and JAK2/STAT3 inhibition prevented the emergence of the mesenchymal chemo-resistant subpopulation. These results provide mechanistic rational for combination of chemotherapy with inhibition of JAK2/STAT3 signaling as a more effective therapeutic strategy in IBC. SIGNIFICANCE Chemotherapy resistance in inflammatory breast cancer is driven by the JAK2/STAT3 pathway, in part via cAMP/PKA signaling and a cell state switch, which can be overcome using paclitaxel combined with JAK2 inhibitors.
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Affiliation(s)
- Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Guillermo Peluffo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Daniel Temko
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Anne Trinh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Callahan M Wilde
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Renee C Geck
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Natalie L Kingston
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nicholas W Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Vanessa Almendro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Alanna L Pyke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shawn B Egri
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | | | - Kendell Clement
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Ningxuan Zhou
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sarah Walker
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jacqueline Salas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - So Yeon Park
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - David A Frank
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Jacob D Jaffe
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Alex Toker
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts.,The Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts.,The Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts.,Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Beth A Overmoyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts.,The Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts.,Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, Massachusetts
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25
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Qiu X, Sun X, Li HO, Wang DH, Zhang SM. Maternal alcohol consumption and risk of postpartum depression: a meta-analysis of cohort studies. Public Health 2022; 213:163-170. [PMID: 36423494 DOI: 10.1016/j.puhe.2022.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/30/2022] [Accepted: 08/30/2022] [Indexed: 11/22/2022]
Abstract
OBJECTIVES The relationship between maternal alcohol consumption and postpartum depression (PPD) is still controversial. The objective of the present study was to assess the association between maternal alcohol consumption and the risk of developing PPD by means of a meta-analysis of cohort studies. STUDY DESIGN This was a meta-analysis. METHODS PubMed, Web of Science, Embase, Cochrane Library, China Biology Medicine disc, Chinese National Knowledge Infrastructure, Weipu, and Wanfang databases were searched up to February 4, 2021, to identify relevant studies that evaluated the association between maternal alcohol consumption and PPD. Meta-analysis was conducted using RevMan software and Stata software. Subgroup and sensitivity analyses were performed to explore the potential heterogeneity source, and Begg's funnel plots and Begg's linear regression test were conducted to assess the potential publication bias. RESULTS A total of 12 studies involving 50,377 participants were identified in our study. Overall, pregnant women who were exposed to alcohol were at a significantly greater risk of developing PPD compared with those who did not consume alcohol (odds ratio = 1.21; 95% confidence interval: 1.04-1.41; P = 0.020). CONCLUSIONS Maternal alcohol consumption is significantly associated with the risk of developing PPD. These results emphasize the necessity of enhancing health awareness, improving the public health policies and regulations concerning alcohol use, and strengthening the prevention and intervention of maternal alcohol consumption to promote maternal mental health.
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Affiliation(s)
- X Qiu
- Department of Nursing, Xiangya School of Nursing, Central South University, Changsha, Hunan, China
| | - X Sun
- Department of Humanistic Nursing, School of Nursing, Changsha Medical University, Changsha, Hunan, China
| | - H O Li
- Department of Humanistic Nursing, School of Nursing, Changsha Medical University, Changsha, Hunan, China
| | - D H Wang
- Department of Humanistic Nursing, School of Nursing, Changsha Medical University, Changsha, Hunan, China
| | - S M Zhang
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, Hunan, China.
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26
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Li R, Wang Z, Xu H, Jiang C, Wang N, Li X, Qiu X, Wang X. Genetic Diversity among Takifugu rubripes and Takifugu obscurus in Different Regions of China Based on Mitochondrial DNA Sequencing Data. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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27
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Zhuang J, Zhang S, Qiu X, Guo H. 175TiP A prospective phase II study to investigate the efficacy and safety of olaparib plus abiraterone and prednisone combination therapy in mHSPC patients with HRR gene mutation. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.10.502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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28
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Spohn S, Draulans C, Kishan A, Spratt D, Ross A, Maurer T, Tilki D, Berlin A, Blanchard P, Collins S, Bronsert P, Chen R, Dal Pra A, De Meerler G, Eade T, Haustermans K, Hölscher T, Höcht S, Ghadjar P, Davicioni E, Heck M, Kerkmeijer L, Kirste S, Tselis N, Tran P, Pinkawa M, Pommier P, Deltas C, Schmidt-Hegemann NS, Wiegel T, Zilli T, Tree A, Qiu X, Murthy V, Epstein J, Graztke C, Grosu A, Kamran S, Zamboglou C, Pinkawa. Genomic classifiers in personalized prostate cancer radiotherapy approaches – a systematic review and future perspectives based on international consensus. EUR UROL SUPPL 2022. [DOI: 10.1016/s2666-1683(22)02485-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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29
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Nardone A, Qiu X, Spisak S, Nagy Z, Feiglin A, Feit A, Cohen Feit G, Xie Y, Font-Tello A, Guarducci C, Hermida-Prado F, Syamala S, Lim K, Munoz Gomez M, Pun M, Cornwell M, Liu W, Ors A, Mohammed H, Cejas P, Brock JB, Freedman ML, Winer EP, Fu X, Schiff R, Long HW, Metzger Filho O, Jeselsohn R. A Distinct Chromatin State Drives Therapeutic Resistance in Invasive Lobular Breast Cancer. Cancer Res 2022; 82:3673-3686. [PMID: 35950920 PMCID: PMC9588703 DOI: 10.1158/0008-5472.can-21-3186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/04/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022]
Abstract
Most invasive lobular breast cancers (ILC) are of the luminal A subtype and are strongly hormone receptor-positive. Yet, ILC is relatively resistant to tamoxifen and associated with inferior long-term outcomes compared with invasive ductal cancers (IDC). In this study, we sought to gain mechanistic insights into these clinical findings that are not explained by the genetic landscape of ILC and to identify strategies to improve patient outcomes. A comprehensive analysis of the epigenome of ILC in preclinical models and clinical samples showed that, compared with IDC, ILC harbored a distinct chromatin state linked to gained recruitment of FOXA1, a lineage-defining pioneer transcription factor. This resulted in an ILC-unique FOXA1-estrogen receptor (ER) axis that promoted the transcription of genes associated with tumor progression and poor outcomes. The ILC-unique FOXA1-ER axis led to retained ER chromatin binding after tamoxifen treatment, which facilitated tamoxifen resistance while remaining strongly dependent on ER signaling. Mechanistically, gained FOXA1 binding was associated with the autoinduction of FOXA1 in ILC through an ILC-unique FOXA1 binding site. Targeted silencing of this regulatory site resulted in the disruption of the feed-forward loop and growth inhibition in ILC. In summary, ILC is characterized by a unique chromatin state and FOXA1-ER axis that is associated with tumor progression, offering a novel mechanism of tamoxifen resistance. These results underscore the importance of conducting clinical trials dedicated to patients with ILC in order to optimize treatments in this breast cancer subtype. SIGNIFICANCE A unique FOXA1-ER axis in invasive lobular breast cancer promotes disease progression and tamoxifen resistance, highlighting a potential therapeutic avenue for clinical investigations dedicated to this disease. See related commentary by Blawski and Toska, p. 3668.
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Affiliation(s)
- Agostina Nardone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.,Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zsuzsanna Nagy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ariel Feiglin
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Avery Feit
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gabriela Cohen Feit
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alba Font-Tello
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cristina Guarducci
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Francisco Hermida-Prado
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sudeepa Syamala
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Miguel Munoz Gomez
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew Pun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - MacIntosh Cornwell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Weihan Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Aysegul Ors
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, Oregon
| | - Hisham Mohammed
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, Oregon
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jane B Brock
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eric P Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Xiaoyong Fu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Rachel Schiff
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Otto Metzger Filho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.,Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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30
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Pan BY, Xu Y, Ni JM, Zhou SY, Hong XC, Qiu X, Li SY. Unambiguous Experimental Verification of Linear-in-Temperature Spinon Thermal Conductivity in an Antiferromagnetic Heisenberg Chain. Phys Rev Lett 2022; 129:167201. [PMID: 36306770 DOI: 10.1103/physrevlett.129.167201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/07/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
The everlasting interest in spin chains is mostly rooted in the fact that they generally allow for comparisons between theory and experiment with remarkable accuracy, especially for exactly solvable models. A notable example is the spin-1/2 antiferromagnetic Heisenberg chain (AFHC), which can be well described by the Tomonaga-Luttinger liquid theory and exhibits fractionalized spinon excitations with distinct thermodynamic and spectroscopic experimental signatures consistent with theoretical predictions. A missing piece, however, is the lack of a comprehensive understanding of the spinon heat transport in AFHC systems, due to difficulties in its experimental evaluation against the backdrop of other heat carriers and complex scattering processes. Here we address this situation by performing ultralow-temperature thermal conductivity measurements on a nearly ideal spin-1/2 AFHC system copper benzoate Cu(C_{6}H_{5}COO)_{2}·3H_{2}O, whose field-dependent spin excitation gap enables a reliable extraction of the spinon thermal conductivity κ_{s} at zero field. κ_{s} was found to exhibit a linear temperature dependence κ_{s}∼T at low temperatures, with κ_{s}/T as large as 1.70 mW cm^{-1} K^{-2}, followed by a precipitate decline below ∼0.3 K. The observed κ_{s}∼T clarifies the discrepancies between various spin chain systems and serves as a benchmark for one-dimensional spinon heat transport in the low-temperature limit. The abrupt loss of κ_{s} with no corresponding anomaly in the specific heat is discussed in the context of many-body localization.
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Affiliation(s)
- B Y Pan
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200438, China
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai, Shandong 264025, China
| | - Y Xu
- Key Laboratory of Polar Materials and Devices (MOE), School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - J M Ni
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200438, China
| | - S Y Zhou
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200438, China
| | - X C Hong
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200438, China
| | - X Qiu
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200438, China
| | - S Y Li
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200438, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, China
- Shanghai Research Center for Quantum Sciences, Shanghai, 201315, China
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31
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Zeng R, Wu H, Qiu X, Zhuo Z, Sha W, Chen H. Predicting survival and immune microenvironment in colorectal cancer: a STAT signaling-related signature. QJM 2022; 115:596-604. [PMID: 34978566 DOI: 10.1093/qjmed/hcab334] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/17/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Despite research advances, studies on predictive models of colorectal cancer (CRC) remain scarce and none have evaluated signal transducer and activator of transcription (STAT) signaling. AIM To develop an effective prognostic signature for and evaluate its association with immune microenvironment. DESIGN Comprehensive analysis based on The Cancer Genome Atlas and Gene Expression Omnibus databases with experimental validation. METHODS Gene expression and clinical profiles of CRC patients were extracted from the databases. Differentially expressed genes with prognostic values were used to construct a signature. Immune cell infiltration and composition were further evaluated by TIMER, single-sample gene set enrichment and CIBERSORT analyses. The impact of the hub gene Caveolin-1 (CAV1) on cell proliferation, apoptosis, senescence and tumor angiogenesis was experimentally validated. RESULTS The five-gene-based STAT signaling-related prognostic signature was significantly associated with CRC survival, and the nomogram was with improved prognostic efficacy than the conventional TNM stage. The STAT signaling-related signature was correlated with tumor immune microenvironment. CAV1 was further identified as the hub gene within the signature. CAV1 inhibits the proliferation and induces the apoptosis as well as senescence of CRC cells. In addition, the tumor angiogenesis of CRC can be suppressed by CAV1 overexpression. CONCLUSIONS The STAT signaling-related signature effectively predicts the prognosis and regulates tumor immune microenvironment in CRC. Our study underscores the role of STAT regulator, CAV1, as an important tumor suppressor in CRC carcinogenesis. Modulating STAT and its regulators could be a promising strategy for CRC in clinical practice.
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Affiliation(s)
- R Zeng
- From the Department of Gastroenterology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, Yuexiu District, Guangdong, China
- Shantou University Medical College, Shantou 515041, Jinping District, Guangdong, China
| | - H Wu
- From the Department of Gastroenterology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, Yuexiu District, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou 510006, Panyu District, Guangdong, China
| | - X Qiu
- Zhuguang Community Healthcare Center, Guangzhou 510080, Yuexiu District, Guangdong, China
| | - Z Zhuo
- From the Department of Gastroenterology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, Yuexiu District, Guangdong, China
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, Panyu District, Guangdong, China
| | - W Sha
- From the Department of Gastroenterology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, Yuexiu District, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, Baiyun District, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou 510006, Panyu District, Guangdong, China
| | - H Chen
- From the Department of Gastroenterology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, Yuexiu District, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, Baiyun District, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou 510006, Panyu District, Guangdong, China
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32
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He J, Wang B, Tao J, Liu Q, Peng M, Qiu X, Yang Y, Ye Z, Liu D, W. li, Chen Z, Zeng Q, Fan J, Liang W. 905MO Synergistic combination of clinical, imaging and DNA methylation biomarkers improves the classification of pulmonary nodules. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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33
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Shi XY, Zhang XL, Shi QY, Qiu X, Wu XB, Zheng BL, Jiang HX, Qin SY. IFN-γ affects pancreatic cancer properties by MACC1-AS1/MACC1 axis via AKT/mTOR signaling pathway. Clin Transl Oncol 2022; 24:1073-1085. [PMID: 35037236 DOI: 10.1007/s12094-021-02748-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/01/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Metastasis-related in colon cancer 1 (MACC1) is highly expressed in a variety of solid tumours, but its role in pancreatic cancer (PC) remains unknown. Interferon gamma (IFN-γ) affecting MACC1 expression was explored as the potential mechanism following its intervention. METHODS Expressions of MACC1 treated with IFN-γ gradient were confirmed by quantitative real-time PCR (qRT-PCR) and western blot (WB). Proliferation, migration, and invasion abilities of PC cells treated with IFN-γ were analysed by CCK8, EDU, colony formation, Transwell (with or without matrix gel) and wound-healing assays. Expression of antisense long non-coding RNA of MACC1, MACC1-AS1, and proteins of AKT/mTOR pathway, (pho-)AKT, and (pho-)mTOR was also assessed by qRT-PCR and WB. SiRNA kit and lentiviral fluid were conducted for transient expression of MACC1 and stable expression of MACC1-AS1, respectively. Rescue assays of cells overexpressing MACC1-AS1 and of cells silencing MACC1 were performed and cellular properties and proteins were assessed by the above-mentioned assays as well. RESULTS IFN-γ inhibited MACC1 expression in a time- and dose-dependent manner; 100 ng/mL IFN-γ generally caused downregulation of most significant (p ≤ 0.05). In vitro experiments revealed that IFN-γ decreased cellular proliferation, migration, and invasion abilities and downregulated the expression of pho-AKT and pho-mTOR (p ≤ 0.05). Conversely, overexpression of MACC1-AS1 upregulated pho-AKT and pho-mTOR proteins, and reversed cellular properties (p ≤ 0.05). Rescue assays alleviated the above changes of pho-AKT/ mTOR and cellular properties. CONCLUSION IFN-γ affected PC properties by MACC1-AS1/MACC1 axis via AKT/mTOR signaling pathway, which provides novel insight for candidate targets for treating PC.
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Affiliation(s)
- X-Y Shi
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - X-L Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Q-Y Shi
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - X Qiu
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - X-B Wu
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - B-L Zheng
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - H-X Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - S-Y Qin
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China.
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Qiu X, Brown LG, Conner JL, Nguyen HM, Boufaied N, Abou Alaiwi S, Seo JH, El Zarif T, Bell C, O’Connor E, Hanratty B, Pomerantz M, Freedman ML, Brown M, Haffner MC, Nelson PS, Feng FY, Labbé DP, Long HW, Corey E. Response to supraphysiological testosterone is predicted by a distinct androgen receptor cistrome. JCI Insight 2022; 7:157164. [PMID: 35603787 PMCID: PMC9220831 DOI: 10.1172/jci.insight.157164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The androgen receptor (AR) is a master transcription factor that regulates prostate cancer (PC) development and progression. Inhibition of AR signaling by androgen deprivation is the first-line therapy with initial efficacy for advanced and recurrent PC. Paradoxically, supraphysiological levels of testosterone (SPT) also inhibit PC progression. However, as with any therapy, not all patients show a therapeutic benefit, and responses differ widely in magnitude and duration. In this study, we evaluated whether differences in the AR cistrome before treatment can distinguish between SPT-responding (R) and -nonresponding (NR) tumors. We provide the first preclinical evidence to our knowledge that SPT-R tumors exhibit a distinct AR cistrome when compared with SPT-NR tumors, indicating a differential biological role of the AR. We applied an integrated analysis of ChIP-Seq and RNA-Seq to the pretreatment tumors and identified an SPT-R signature that distinguishes R and NR tumors. Because transcriptomes of SPT-treated clinical specimens are not available, we interrogated available castration-resistant PC (CRPC) transcriptomes and showed that the SPT-R signature is associated with improved survival and has the potential to identify patients who would respond to SPT. These findings provide an opportunity to identify the subset of patients with CRPC who would benefit from SPT therapy.
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Affiliation(s)
- Xintao Qiu
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Lisha G. Brown
- Department of Urology, University of Washington, Seattle, Washington, USA
| | - Jennifer L. Conner
- Department of Urology, University of Washington, Seattle, Washington, USA
| | - Holly M. Nguyen
- Department of Urology, University of Washington, Seattle, Washington, USA
| | - Nadia Boufaied
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Sarah Abou Alaiwi
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Ji-Heui Seo
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Talal El Zarif
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Connor Bell
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Edward O’Connor
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Brian Hanratty
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Mark Pomerantz
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew L. Freedman
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael C. Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Peter S. Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Felix Y. Feng
- University of California at San Francisco, San Francisco, California, USA
| | - David P. Labbé
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Department of Surgery, Division of Urology, McGill University, Montréal, Québec, Canada
| | - Henry W. Long
- Center for Functional Cancer Epigenetics, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington, USA
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35
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Qiu X, Boufaied N, Hallal T, Feit A, de Polo A, Luoma AM, Alahmadi W, Larocque J, Zadra G, Xie Y, Gu S, Tang Q, Zhang Y, Syamala S, Seo JH, Bell C, O'Connor E, Liu Y, Schaeffer EM, Jeffrey Karnes R, Weinmann S, Davicioni E, Morrissey C, Cejas P, Ellis L, Loda M, Wucherpfennig KW, Pomerantz MM, Spratt DE, Corey E, Freedman ML, Shirley Liu X, Brown M, Long HW, Labbé DP. MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets. Nat Commun 2022; 13:2559. [PMID: 35562350 PMCID: PMC9106722 DOI: 10.1038/s41467-022-30257-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 04/22/2022] [Indexed: 12/30/2022] Open
Abstract
c-MYC (MYC) is a major driver of prostate cancer tumorigenesis and progression. Although MYC is overexpressed in both early and metastatic disease and associated with poor survival, its impact on prostate transcriptional reprogramming remains elusive. We demonstrate that MYC overexpression significantly diminishes the androgen receptor (AR) transcriptional program (the set of genes directly targeted by the AR protein) in luminal prostate cells without altering AR expression. Analyses of clinical specimens reveal that concurrent low AR and high MYC transcriptional programs accelerate prostate cancer progression toward a metastatic, castration-resistant disease. Data integration of single-cell transcriptomics together with ChIP-seq uncover an increase in RNA polymerase II (Pol II) promoter-proximal pausing at AR-dependent genes following MYC overexpression without an accompanying deactivation of AR-bound enhancers. Altogether, our findings suggest that MYC overexpression antagonizes the canonical AR transcriptional program and contributes to prostate tumor initiation and progression by disrupting transcriptional pause release at AR-regulated genes.
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Affiliation(s)
- Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nadia Boufaied
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Tarek Hallal
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada
| | - Avery Feit
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Anna de Polo
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Division of Urology, Department of Surgery, McGill University, Montréal, QC, Canada
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Walaa Alahmadi
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC, Canada
| | - Janie Larocque
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC, Canada
| | - Giorgia Zadra
- Departments of Oncologic Pathology and Pathology, Dana-Farber Cancer Institute and Brigham's Women Hospital, Boston, MA, USA
- Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Shengqing Gu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Qin Tang
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yi Zhang
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sudeepa Syamala
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yang Liu
- Decipher Biosciences, San Diego, CA, USA
| | | | | | - Sheila Weinmann
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | | | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Leigh Ellis
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weil Cornell Medicine, New York Presbyterian-Weill Cornell Campus, New York, NY, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Matthew L Freedman
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - X Shirley Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - David P Labbé
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada.
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada.
- Division of Urology, Department of Surgery, McGill University, Montréal, QC, Canada.
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC, Canada.
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Severson T, Qiu X, Alshalalfa M, Sjöström M, Quigley D, Bergman A, Long H, Feng F, Freedman ML, Zwart W, Pomerantz MM. Androgen receptor reprogramming demarcates prognostic, context-dependent gene sets in primary and metastatic prostate cancer. Clin Epigenetics 2022; 14:60. [PMID: 35509021 PMCID: PMC9069737 DOI: 10.1186/s13148-022-01278-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/19/2022] [Indexed: 11/10/2022] Open
Abstract
The androgen receptor (AR) is a prostate master transcription factor. It binds to genetic enhancers, where it regulates gene activity and plays a fundamental role in prostate pathophysiology. Previous work has demonstrated that AR-DNA binding is systematically and consistently reprogrammed during prostate tumorigenesis and disease progression. We charted these reprogrammed AR sites and identified genes proximal to them. We were able to devise gene lists based on AR status within specific histological contexts: normal prostate epithelium, primary prostate tumor, and metastatic prostate cancer. We evaluated expression of the genes in these gene sets in subjects from two distinct clinical cohorts-men treated with surgery for localized prostate cancer and men with metastatic prostate cancer. Among men with localized prostate cancer, expression of genes proximal to AR sites lost in the transition from normal prostate to prostate tumor was associated with clinical outcome. Among men with metastatic disease, expression of genes proximal to AR sites gained in metastatic tumors was associated with clinical outcome. These results are consistent with the notion that AR is fundamental to both maintaining differentiation in normal prostate tissue and driving de-differentiation in advanced prostate cancer. More broadly, the study demonstrates the power of incorporating context-dependent epigenetic data into genetic analyses.
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Affiliation(s)
- Tesa Severson
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.,Division of Oncology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - David Quigley
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Andries Bergman
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Felix Feng
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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37
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Chen N, Qiu X, Wang D, Cui BQ, Chang XD. [Establishment and stress analysis of a finite element model of a marathon runner's hip joint based on material properties given by CT gray value]. Zhonghua Yi Xue Za Zhi 2022; 102:679-682. [PMID: 35249314 DOI: 10.3760/cma.j.cn112137-20210817-01854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this study, a finite element model of the hip joint of a marathon runner was established based on the method of assigning material properties by CT gray value, and the biomechanics of the hip joint were analyzed when standing on one foot. The results of the study demonstrated that the stress was concentrated in the arcuate line, the greater sciatic notch, the pubic comb, and the acetabular region in the pelvis model; in the femoral model, the stress was concentrated in the femoral head, medial side of femoral neck and femoral shaft. The stress is transmitted from the sacroiliac joint to the acetabular dome through the arcuate line, on one side of the femoral head, from the medial side of the femoral neck to the lower side of the lesser trochanter to the medial side of the femoral shaft, and on the other side from the upper side of the femoral neck to the lateral side of the femoral shaft. The maximum principal stress was distributed in the posterior superior of the acetabular roof (7.22 MPa) and the posterior superior of the femoral head (6.68 MPa). The displacement of the model was about 1 to 3 mm at the upper edge of the ilium, and gradually decreased along the femoral axis, and the displacement at the hip joint was about 0.1 to 0.3 mm.
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Affiliation(s)
- N Chen
- Department of Radiology, Zhongshan Hospital, Dalian University, Dalian 116000, China
| | - X Qiu
- Department of Orthopedics, Zhongshan Hospital, Dalian University, Dalian 116000, China
| | - D Wang
- Department of Radiology, Qiqihar First Hospital, Qiqihar 161000, China
| | - B Q Cui
- Zhongshan Clinical College of Dalian University, Dalian 116000, China
| | - X D Chang
- Department of Radiology, Zhongshan Hospital, Dalian University, Dalian 116000, China
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Li Y, Qiu X, Wang X, Liu H, Geck RG, Tewari A, Chow KH, Xiao T, Cejas P, Nguyen QD, Long H, Liu SX, Toker A, Brown M. Abstract P4-01-04: FGFR inhibitor mediated dismissal of SWI/SNF complexes from YAP-dependent enhancers induces therapeutic resistance in triple negative breast cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p4-01-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
How cancer cells adapt to evade the therapeutic effects of drugs targeting oncogenic drivers is poorly understood. Here we report an epigenetic mechanism leading to the adaptive resistance of triple-negative breast cancer (TNBC) to fibroblast growth factor receptor (FGFR) inhibitors. Prolonged FGFR inhibition suppresses the function of BRG1-dependent chromatin remodeling leading to an epigenetic state that derepresses YAP-associated enhancers. These chromatin changes induce the expression of several amino acid transporters resulting in increased intracellular levels of specific amino acids that reactivate mTORC1. Consistent with this mechanism, addition of mTORC1 or YAP inhibitors to FGFR blockade synergistically attenuated the growth of TNBC patient-derived xenografts (PDX) models. Collectively, these findings reveal a novel feedback loop involving an epigenetic state transition and metabolic reprogramming that leads to adaptive therapeutic resistance and provide new therapeutic strategies to overcome this mechanism of resistance.
Citation Format: Yihao Li, Xintao Qiu, Xiaoqing Wang, Hui Liu, Renee Geck Geck, Alok Tewari, Kin-Hoe Chow, Tengfei Xiao, Paloma Cejas, Quang-Dé Nguyen, Henry Long, Shirley X Liu, Alex Toker, Myles Brown. FGFR inhibitor mediated dismissal of SWI/SNF complexes from YAP-dependent enhancers induces therapeutic resistance in triple negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P4-01-04.
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Affiliation(s)
- Yihao Li
- Dana-Farber Cancer Institute, Boston, MA
| | - Xintao Qiu
- Dana-Farber Cancer Institute, Boston, MA
| | | | - Hui Liu
- Beth Israel Deaconess Medical Center, Boston, MA
| | | | | | | | | | | | | | - Henry Long
- Dana-Farber Cancer Institute, Boston, MA
| | | | - Alex Toker
- Beth Israel Deaconess Medical Center, Boston, MA
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Li Y, Qiu X, Wang X, Liu H, Geck RC, Tewari AK, Xiao T, Font-Tello A, Lim K, Jones KL, Morrow M, Vadhi R, Kao PL, Jaber A, Yerrum S, Xie Y, Chow KH, Cejas P, Nguyen QD, Long HW, Liu XS, Toker A, Brown M. FGFR-inhibitor-mediated dismissal of SWI/SNF complexes from YAP-dependent enhancers induces adaptive therapeutic resistance. Nat Cell Biol 2021; 23:1187-1198. [PMID: 34737445 DOI: 10.1038/s41556-021-00781-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/26/2021] [Indexed: 12/20/2022]
Abstract
How cancer cells adapt to evade the therapeutic effects of drugs targeting oncogenic drivers is poorly understood. Here we report an epigenetic mechanism leading to the adaptive resistance of triple-negative breast cancer (TNBC) to fibroblast growth factor receptor (FGFR) inhibitors. Prolonged FGFR inhibition suppresses the function of BRG1-dependent chromatin remodelling, leading to an epigenetic state that derepresses YAP-associated enhancers. These chromatin changes induce the expression of several amino acid transporters, resulting in increased intracellular levels of specific amino acids that reactivate mTORC1. Consistent with this mechanism, addition of mTORC1 or YAP inhibitors to FGFR blockade synergistically attenuated the growth of TNBC patient-derived xenograft models. Collectively, these findings reveal a feedback loop involving an epigenetic state transition and metabolic reprogramming that leads to adaptive therapeutic resistance and provides potential therapeutic strategies to overcome this mechanism of resistance.
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Affiliation(s)
- Yihao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xiaoqing Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hui Liu
- Department of Pathology, and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Renee C Geck
- Department of Pathology, and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Alok K Tewari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tengfei Xiao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alba Font-Tello
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristen L Jones
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, Boston, MA, USA
| | - Murry Morrow
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, Boston, MA, USA
| | - Raga Vadhi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pei-Lun Kao
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aliya Jaber
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Smitha Yerrum
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yingtian Xie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kin-Hoe Chow
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Quang-Dé Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - X Shirley Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alex Toker
- Department of Pathology, and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA. .,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
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40
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Qiu X, Chen H, Feng D, Dong W. [G-protein coupled receptor Smo positively regulates proliferation and migration of adult neural stem cells in vitro]. Nan Fang Yi Ke Da Xue Xue Bao 2021; 41:1588-1592. [PMID: 34755677 DOI: 10.12122/j.issn.1673-4254.2021.10.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the role of G-protein coupled receptor Smoothened (Smo) in regulating proliferation and migration of adult neural stem cells (ANSCs) and explore the underlying mechanism. METHODS Cultured ANSCs were treated with purmorphamine (PM, an agonist of Smo) or cyclopamine (CPM, an inhibitor of Smo), and the changes in cell proliferation migration abilities were assessed using cell counting kit-8 (CCK8) assay and wound healing assay, respectively. The mRNA expressions of membrane receptor Patched 1 (Ptch1), Smo, glioma-associated oncogene homolog 1 (Gli1), axon guidance cue slit1 (Slit1) and brain-derived neurotrophic factor (BDNF) in the treated cells were detected using real-time quantitative PCR (RT-PCR). RESULTS PM significantly promoted the proliferation (P < 0.01) and migration of ANSCs (P < 0.01), and up-regulated the mRNA expressions of Ptch1, Smo, Gli1, Slit1 and BDNF. Treatment with CPM significantly inhibited the proliferation and migration of ANSCs. CONCLUSION Modulating Smo activity can positively regulate the proliferation and migration of ANSCs possibly by regulating the expressions of BDNF and Slit1.
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Affiliation(s)
- X Qiu
- Experiment Teaching and Administration Center, Southern Medical University, Guangzhou 510515, China
| | - H Chen
- Department of Neurosurgery, Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - D Feng
- Institute of Oncology, Southern Medical University, Guangzhou 510515, China
| | - W Dong
- Experiment Teaching and Administration Center, Southern Medical University, Guangzhou 510515, China
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41
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Cejas P, Xie Y, Font-Tello A, Lim K, Syamala S, Qiu X, Tewari AK, Shah N, Nguyen HM, Patel RA, Brown L, Coleman I, Hackeng WM, Brosens L, Dreijerink KMA, Ellis L, Alaiwi SA, Seo JH, Baca S, Beltran H, Khani F, Pomerantz M, Dall'Agnese A, Crowdis J, Van Allen EM, Bellmunt J, Morrisey C, Nelson PS, DeCaprio J, Farago A, Dyson N, Drapkin B, Liu XS, Freedman M, Haffner MC, Corey E, Brown M, Long HW. Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer. Nat Commun 2021; 12:5775. [PMID: 34599169 PMCID: PMC8486778 DOI: 10.1038/s41467-021-26042-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 09/07/2021] [Indexed: 12/30/2022] Open
Abstract
Neuroendocrine carcinomas (NEC) are tumors expressing markers of neuronal differentiation that can arise at different anatomic sites but have strong histological and clinical similarities. Here we report the chromatin landscapes of a range of human NECs and show convergence to the activation of a common epigenetic program. With a particular focus on treatment emergent neuroendocrine prostate cancer (NEPC), we analyze cell lines, patient-derived xenograft (PDX) models and human clinical samples to show the existence of two distinct NEPC subtypes based on the expression of the neuronal transcription factors ASCL1 and NEUROD1. While in cell lines and PDX models these subtypes are mutually exclusive, single-cell analysis of human clinical samples exhibits a more complex tumor structure with subtypes coexisting as separate sub-populations within the same tumor. These tumor sub-populations differ genetically and epigenetically contributing to intra- and inter-tumoral heterogeneity in human metastases. Overall, our results provide a deeper understanding of the shared clinicopathological characteristics shown by NECs. Furthermore, the intratumoral heterogeneity of human NEPCs suggests the requirement of simultaneous targeting of coexisting tumor populations as a therapeutic strategy. Neuroendocrine carcinomas (NECs) arise from different anatomic sites, but have similar histological and clinical features. Here, the authors show that the epigenetic landscape of a range of NECs converges towards a common epigenetic state, while distinct subtypes occur within neuroendocrine prostate cancer contributing to intratumor heterogeneity in clinical samples.
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Affiliation(s)
- Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA. .,Translational Oncology Laboratory, Hospital La Paz Institute for Health Research (IdiPAZ) and CIBERONC, La Paz University Hospital, Madrid, Spain.
| | - Yingtian Xie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alba Font-Tello
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sudeepa Syamala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alok K Tewari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neel Shah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Holly M Nguyen
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Radhika A Patel
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lisha Brown
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wenzel M Hackeng
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Lodewijk Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Leigh Ellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Sarah Abou Alaiwi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Sylvan Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Francesca Khani
- Weill Cornell Medical Center, Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital, New York, NY, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | | | - Jett Crowdis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joaquim Bellmunt
- Beth Israel Deaconess Medical Center and PSMAR-IMIM Lab. Harvard Medical School, Boston, Massachusetts, USA
| | - Colm Morrisey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Anna Farago
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Nicholas Dyson
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Benjamin Drapkin
- Nancy B. and Jake L. Hamon Center for Therapeutic Oncology Research, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - X Shirley Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Matthew Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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Lu S, Huang D, Chen X, Wang B, Xue J, Wang J, Bao Y, Liang L, Qiu X, Zhang L. 1290P RATIONALE 304: Tislelizumab (TIS) plus chemotherapy (chemo) vs chemo alone as first-line (1L) treatment for non-squamous (non-sq) non-small cell lung cancer (NSCLC) in patients (pts) who are smokers vs non-smokers. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Li Y, Qiu X, Liu H, Wang X, Geck RC, Tewari A, Chow KH, Cejas P, Nguyen QD, Long H, Liu SX, Toker A, Brown M. Abstract 1400: SWI/SNF chromatin remodeling complex regulation of YAP-dependent enhancers drives therapeutic resistance in triple-negative breast cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-1400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Outcomes for patients with triple negative breast cancer (TNBC) remain poor despite significant advances in the treatment of other breast cancer subtypes. We report an epigenetic mechanism leading to the adaptive resistance of TNBC to fibroblast growth factor receptor (FGFR) inhibitors. Prolonged FGFR inhibition suppresses the function of BRG1-dependent chromatin remodeling leading to an epigenetic state that derepresses YAP-associated enhancers. These chromatin changes induce the expression of several amino acid transporters resulting in increased intracellular levels of specific amino acids that reactivate mTORC1. Consistent with this mechanism, addition of mTORC1 or YAP inhibitors to FGFR blockade synergistically attenuated the growth of TNBC patient-derived xenografts (PDX) models. Treatment-induced YAP/TEAD accessible chromatin was observed in a subpopulation of PDX cells by single cell analysis of accessible chromatin. Thus, combinatorial therapies based on the YAP and mTORC1 dependent feedback loop have the potential to improve the efficacy of FGFR inhibitors in TNBC.
Citation Format: Yihao Li, Xintao Qiu, Hui Liu, Xiaoqing Wang, Renee C. Geck, Alok Tewari, Kin-Hoe Chow, Paloma Cejas, Quang-Dé Nguyen, Henry Long, Shirley X. Liu, Alex Toker, Myles Brown. SWI/SNF chromatin remodeling complex regulation of YAP-dependent enhancers drives therapeutic resistance in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1400.
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Affiliation(s)
- Yihao Li
- 1Dana-Farber Cancer Institute, Boston, MA
| | - Xintao Qiu
- 1Dana-Farber Cancer Institute, Boston, MA
| | - Hui Liu
- 2Beth Israel Deaconess Medical Center, Boston, MA
| | | | | | | | | | | | | | - Henry Long
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | - Alex Toker
- 2Beth Israel Deaconess Medical Center, Boston, MA
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44
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Wu Z, Zhou J, Zhang X, Zhang Z, Xie Y, Liu JB, Ho ZV, Panda A, Qiu X, Cejas P, Cañadas I, Akarca FG, McFarland JM, Nagaraja AK, Goss LB, Kesten N, Si L, Lim K, Liu Y, Zhang Y, Baek JY, Liu Y, Patil DT, Katz JP, Hai J, Bao C, Stachler M, Qi J, Ishizuka JJ, Nakagawa H, Rustgi AK, Wong KK, Meyerson M, Barbie DA, Brown M, Long H, Bass AJ. Reprogramming of the esophageal squamous carcinoma epigenome by SOX2 promotes ADAR1 dependence. Nat Genet 2021; 53:881-894. [PMID: 33972779 PMCID: PMC9124436 DOI: 10.1038/s41588-021-00859-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 03/29/2021] [Indexed: 01/28/2023]
Abstract
Esophageal squamous cell carcinomas (ESCCs) harbor recurrent chromosome 3q amplifications that target the transcription factor SOX2. Beyond its role as an oncogene in ESCC, SOX2 acts in development of the squamous esophagus and maintenance of adult esophageal precursor cells. To compare Sox2 activity in normal and malignant tissue, we developed engineered murine esophageal organoids spanning normal esophagus to Sox2-induced squamous cell carcinoma and mapped Sox2 binding and the epigenetic and transcriptional landscape with evolution from normal to cancer. While oncogenic Sox2 largely maintains actions observed in normal tissue, Sox2 overexpression with p53 and p16 inactivation promotes chromatin remodeling and evolution of the Sox2 cistrome. With Klf5, oncogenic Sox2 acquires new binding sites and enhances activity of oncogenes such as Stat3. Moreover, oncogenic Sox2 activates endogenous retroviruses, inducing expression of double-stranded RNA and dependence on the RNA editing enzyme ADAR1. These data reveal SOX2 functions in ESCC, defining targetable vulnerabilities.
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Affiliation(s)
- Zhong Wu
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,These authors contributed equally: Zhong Wu, Jin Zhou, Xiaoyang Zhang
| | - Jin Zhou
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,These authors contributed equally: Zhong Wu, Jin Zhou, Xiaoyang Zhang
| | - Xiaoyang Zhang
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,These authors contributed equally: Zhong Wu, Jin Zhou, Xiaoyang Zhang
| | - Zhouwei Zhang
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jie bin Liu
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Zandra V. Ho
- Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Arpit Panda
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Committee on Immunology, The University of Chicago, Chicago, IL, USA
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Israel Cañadas
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Present address: Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Fahire Goknur Akarca
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - James M. McFarland
- Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Ankur K. Nagaraja
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Present address: Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Louisa B. Goss
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nikolas Kesten
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Longlong Si
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yanli Liu
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Yanxi Zhang
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ji Yeon Baek
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yang Liu
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Deepa T. Patil
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jonathan P. Katz
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Josephine Hai
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chunyang Bao
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Matthew Stachler
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jun Qi
- Cancer Biology Department, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jeffrey J. Ishizuka
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Hiroshi Nakagawa
- Herbert Irving Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Anil K. Rustgi
- Herbert Irving Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Kwok-Kin Wong
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Matthew Meyerson
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - David A. Barbie
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Myles Brown
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Adam J. Bass
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Herbert Irving Comprehensive Cancer Center, Division of Hematology and Oncology, Department of Medicine, Columbia University, New York, NY, USA
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45
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Yin H, Chen M, Qiu X, Qiu X, Guo H. Can 68Ga-PSMA-11 PET/CT predict pathological upgrading of prostate cancer from MRI-targeted biopsy to radical prostatectomy? Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)01286-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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46
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Zhang T, Li W, Qiu X, Liu B, Li G, Feng C, Liao J, Lin K. [CRISPR/Cas9-mediated TEAD1 knockout induces phenotypic modulation of corpus cavernosum smooth muscle cells in diabetic rats with erectile dysfunction]. Nan Fang Yi Ke Da Xue Xue Bao 2021; 41:567-573. [PMID: 33963717 DOI: 10.12122/j.issn.1673-4254.2021.04.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To construct a corpus cavemosum smooth muscle cell (CCSMCs) line with TEAD1 knockout from diabetic rats with erectile dysfunction (ED) using CRISPR/Cas9 technology and explore the role of TEAD1 in phenotypic modulation of CCSMCs in diabetic rats with ED. OBJECTIVE Models of diabetic ED were established in male Sprague-Dawley rats by intraperitoneal injection of streptozotocin. CCSMCs from the rat models were primarily cultured and identified with immunofluorescence assay. Three sgRNAs (sgRNA-1, sgRNA-2 and sgRNA-3) were transfected via lentiviral vectors into 293T cells to prepare the sgRNA-Cas9 lentivirus. CCSMCs from diabetic rats with ED were infected by the lentivirus, and the cellular expression of TEAD1 protein was detected using Western blotting. In CCSMCs infected with the sgRNA-Cas9 lentivirus (CCSMCs-sgRNA-2), or the empty lentiviral vector (CCSMCs-sgRNA-NC) and the blank control cells (CCSMCs-CK), the expressions of cellular phenotypic markers SMMHC, calponin and PCNA at the mRNA and protein levels were detected using real-time fluorescence quantitative RT-PCR (qRT-PCR) and Western blotting, respectively. OBJECTIVE The primarily cultured CCSMCs from diabetic rats with ED showed a high α-SMA-positive rate of over 95%. The recombinant lentivirus of TEAD1-sgRNA was successfully packaged, and stable TEAD1-deficient CCSMC lines derived from diabetic rat with ED were obtained. Western blotting confirmed that the protein expression of TEAD1 in TEAD1-sgRNA-2 group was the lowest (P < 0.05), and this cell line was used in subsequent experiment. The results of qRT-PCR and Western blotting showed significantly up-regulated expressions of SMMHC and calponin (all P < 0.05) and down-regulated expression of PCNA (all P < 0.05) at both the mRNA and protein levels in TEAD1-deficient CCSMCs from diabetic rats with ED. OBJECTIVE We successfully constructed a stable CCSMCs line with CRISPR/Cas9-mediated TEAD1 knockout from diabetic rats with ED. TEAD1 gene knockout can induce phenotype transformation of the CCSMCs from diabetic rats with ED from the synthetic to the contractile type.
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Affiliation(s)
- T Zhang
- Department of Urology, Second Guangdong Provincial People's Hospital, Guangzhou 510317, China
| | - W Li
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - X Qiu
- Department of Urology, Second Guangdong Provincial People's Hospital, Guangzhou 510317, China
| | - B Liu
- Department of Urology, Second Guangdong Provincial People's Hospital, Guangzhou 510317, China
| | - G Li
- Department of Urology, Second Guangdong Provincial People's Hospital, Guangzhou 510317, China
| | - C Feng
- Department of Urology, Second Guangdong Provincial People's Hospital, Guangzhou 510317, China
| | - J Liao
- Department of Urology, Second Guangdong Provincial People's Hospital, Guangzhou 510317, China
| | - K Lin
- Department of Urology, Second Guangdong Provincial People's Hospital, Guangzhou 510317, China
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47
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He JR, Ramakrishnan R, Wei XL, Lu JH, Lu MS, Xiao WQ, Tu S, Liu X, Zhou FJ, Zhang LF, Xia HM, Qiu X. Fetal growth at different gestational periods and risk of impaired childhood growth, low childhood weight and obesity: a prospective birth cohort study. BJOG 2021; 128:1615-1624. [PMID: 33690938 DOI: 10.1111/1471-0528.16698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To examine the longitudinal associations of fetal growth with adverse child growth outcomes and to assess whether maternal metabolic factors modify the associations. DESIGN Prospective cohort study. SETTING Born in Guangzhou Cohort Study, China. POPULATION A total of 4818 mother-child pairs. METHODS Fetal growth was assessed according to estimated fetal weight (EFW) from 22 weeks of gestation until birth and the measurement of the birthweight. Fetal growth Z-scores were computed from random effects in the multilevel linear spline models to represent fetal size in early pregnancy (22 weeks of gestation) and growth in mid-pregnancy (22-27 weeks of gestation), early third trimester (28-36 weeks of gestation) and late third trimester (≥37 weeks of gestation). MAIN OUTCOME MEASURES Z-scores for childhood stunting, low weight, overweight or obesity, length/height for age (LAZ/HAZ), weight for age (WAZ) and body mass index for age (BMIZ) at the age of 3 years. Adjusted associations were examined using multiple Poisson or linear regression models. RESULTS Increased Z-scores of fetal size in early pregnancy and growth in mid-pregnancy and early third trimester were associated with a higher risk of childhood overweight or obesity (risk ratios 1.25-1.45). Fetal growth in each period was negatively associated with stunting and low weight, with the strongest associations observed for fetal size in early pregnancy and growth in mid-pregnancy. The results for continuous outcomes (LAZ/HAZ, WAZ and BMIZ) were similar. The associations of fetal growth with overweight or obesity in childhood were stronger among mothers who were underweight and who were overweight or obese than among mothers of normal weight. CONCLUSIONS Accelerated fetal growth before 37 weeks of gestation is associated with children who are overweight or obese, whereas the critical period for stunting and low weight occurs before 28 weeks of gestation. TWEETABLE ABSTRACT Fetal growth during different periods is differentially associated with childhood stunting, underweight and overweight or obesity.
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Affiliation(s)
- J-R He
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK
| | - R Ramakrishnan
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK.,University of New South Wales, Sydney, NSW, Australia
| | - X-L Wei
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Woman and Child Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - J-H Lu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Woman and Child Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - M-S Lu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Woman and Child Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - W-Q Xiao
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Woman and Child Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - S Tu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Woman and Child Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - X Liu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Woman and Child Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - F-J Zhou
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Woman and Child Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - L-F Zhang
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Woman and Child Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - H-M Xia
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Neonatal Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - X Qiu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Woman and Child Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Obstetrics and Gynecology, Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, China
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48
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Baca SC, Takeda DY, Seo JH, Hwang J, Ku SY, Arafeh R, Arnoff T, Agarwal S, Bell C, O'Connor E, Qiu X, Alaiwi SA, Corona RI, Fonseca MAS, Giambartolomei C, Cejas P, Lim K, He M, Sheahan A, Nassar A, Berchuck JE, Brown L, Nguyen HM, Coleman IM, Kaipainen A, De Sarkar N, Nelson PS, Morrissey C, Korthauer K, Pomerantz MM, Ellis L, Pasaniuc B, Lawrenson K, Kelly K, Zoubeidi A, Hahn WC, Beltran H, Long HW, Brown M, Corey E, Freedman ML. Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer. Nat Commun 2021; 12:1979. [PMID: 33785741 PMCID: PMC8010057 DOI: 10.1038/s41467-021-22139-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
Lineage plasticity, the ability of a cell to alter its identity, is an increasingly common mechanism of adaptive resistance to targeted therapy in cancer. An archetypal example is the development of neuroendocrine prostate cancer (NEPC) after treatment of prostate adenocarcinoma (PRAD) with inhibitors of androgen signaling. NEPC is an aggressive variant of prostate cancer that aberrantly expresses genes characteristic of neuroendocrine (NE) tissues and no longer depends on androgens. Here, we investigate the epigenomic basis of this resistance mechanism by profiling histone modifications in NEPC and PRAD patient-derived xenografts (PDXs) using chromatin immunoprecipitation and sequencing (ChIP-seq). We identify a vast network of cis-regulatory elements (N~15,000) that are recurrently activated in NEPC. The FOXA1 transcription factor (TF), which pioneers androgen receptor (AR) chromatin binding in the prostate epithelium, is reprogrammed to NE-specific regulatory elements in NEPC. Despite loss of dependence upon AR, NEPC maintains FOXA1 expression and requires FOXA1 for proliferation and expression of NE lineage-defining genes. Ectopic expression of the NE lineage TFs ASCL1 and NKX2-1 in PRAD cells reprograms FOXA1 to bind to NE regulatory elements and induces enhancer activity as evidenced by histone modifications at these sites. Our data establish the importance of FOXA1 in NEPC and provide a principled approach to identifying cancer dependencies through epigenomic profiling.
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Affiliation(s)
- Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Y Takeda
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Justin Hwang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sheng Yu Ku
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rand Arafeh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Taylor Arnoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Supreet Agarwal
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Abou Alaiwi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rosario I Corona
- Department of Obstetrics and Gynecology and the Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marcos A S Fonseca
- Department of Obstetrics and Gynecology and the Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Claudia Giambartolomei
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Istituto Italiano di Tecnologia, Genova, Italy
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Monica He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anjali Sheahan
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amin Nassar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lisha Brown
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Holly M Nguyen
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Ilsa M Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Arja Kaipainen
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Navonil De Sarkar
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Keegan Korthauer
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Leigh Ellis
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kate Lawrenson
- Department of Obstetrics and Gynecology and the Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kathleen Kelly
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Vancouver, BC, Canada
- Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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49
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Wang KS, Yu G, Xu C, Meng XH, Zhou J, Zheng C, Deng Z, Shang L, Liu R, Su S, Zhou X, Li Q, Li J, Wang J, Ma K, Qi J, Hu Z, Tang P, Deng J, Qiu X, Li BY, Shen WD, Quan RP, Yang JT, Huang LY, Xiao Y, Yang ZC, Li Z, Wang SC, Ren H, Liang C, Guo W, Li Y, Xiao H, Gu Y, Yun JP, Huang D, Song Z, Fan X, Chen L, Yan X, Li Z, Huang ZC, Huang J, Luttrell J, Zhang CY, Zhou W, Zhang K, Yi C, Wu C, Shen H, Wang YP, Xiao HM, Deng HW. Accurate diagnosis of colorectal cancer based on histopathology images using artificial intelligence. BMC Med 2021; 19:76. [PMID: 33752648 PMCID: PMC7986569 DOI: 10.1186/s12916-021-01942-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Accurate and robust pathological image analysis for colorectal cancer (CRC) diagnosis is time-consuming and knowledge-intensive, but is essential for CRC patients' treatment. The current heavy workload of pathologists in clinics/hospitals may easily lead to unconscious misdiagnosis of CRC based on daily image analyses. METHODS Based on a state-of-the-art transfer-learned deep convolutional neural network in artificial intelligence (AI), we proposed a novel patch aggregation strategy for clinic CRC diagnosis using weakly labeled pathological whole-slide image (WSI) patches. This approach was trained and validated using an unprecedented and enormously large number of 170,099 patches, > 14,680 WSIs, from > 9631 subjects that covered diverse and representative clinical cases from multi-independent-sources across China, the USA, and Germany. RESULTS Our innovative AI tool consistently and nearly perfectly agreed with (average Kappa statistic 0.896) and even often better than most of the experienced expert pathologists when tested in diagnosing CRC WSIs from multicenters. The average area under the receiver operating characteristics curve (AUC) of AI was greater than that of the pathologists (0.988 vs 0.970) and achieved the best performance among the application of other AI methods to CRC diagnosis. Our AI-generated heatmap highlights the image regions of cancer tissue/cells. CONCLUSIONS This first-ever generalizable AI system can handle large amounts of WSIs consistently and robustly without potential bias due to fatigue commonly experienced by clinical pathologists. It will drastically alleviate the heavy clinical burden of daily pathology diagnosis and improve the treatment for CRC patients. This tool is generalizable to other cancer diagnosis based on image recognition.
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Affiliation(s)
- K S Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China
- Department of Pathology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - G Yu
- Department of Biomedical Engineering, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - C Xu
- Department of Biostatistics and Epidemiology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - X H Meng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - J Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China
- Department of Pathology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - C Zheng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China
- Department of Pathology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - Z Deng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China
- Department of Pathology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - L Shang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China
| | - R Liu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China
| | - S Su
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China
| | - X Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China
| | - Q Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China
| | - J Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China
| | - J Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China
| | - K Ma
- Department of Pathology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - J Qi
- Department of Pathology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - Z Hu
- Department of Pathology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - P Tang
- Department of Pathology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - J Deng
- Department of Deming Department of Medicine, Tulane Center of Biomedical Informatics and Genomics, Tulane University School of Medicine, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA
| | - X Qiu
- Centers of System Biology, Data Information and Reproductive Health, School of Basic Medical Science, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - B Y Li
- Centers of System Biology, Data Information and Reproductive Health, School of Basic Medical Science, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - W D Shen
- Centers of System Biology, Data Information and Reproductive Health, School of Basic Medical Science, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - R P Quan
- Centers of System Biology, Data Information and Reproductive Health, School of Basic Medical Science, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - J T Yang
- Centers of System Biology, Data Information and Reproductive Health, School of Basic Medical Science, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - L Y Huang
- Centers of System Biology, Data Information and Reproductive Health, School of Basic Medical Science, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - Y Xiao
- Centers of System Biology, Data Information and Reproductive Health, School of Basic Medical Science, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - Z C Yang
- Department of Pharmacology, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Z Li
- School of Life Sciences, Central South University, Changsha, 410013, Hunan, China
| | - S C Wang
- College of Information Science and Engineering, Hunan Normal University, Changsha, 410081, Hunan, China
| | - H Ren
- Department of Pathology, Gongli Hospital, Second Military Medical University, Shanghai, 200135, China
- Department of Pathology, the Peace Hospital Affiliated to Changzhi Medical College, Changzhi, 046000, China
| | - C Liang
- Pathological Laboratory of Adicon Medical Laboratory Co., Ltd, Hangzhou, 310023, Zhejiang, China
| | - W Guo
- Department of Pathology, First Affiliated Hospital of Hunan Normal University, The People's Hospital of Hunan Province, Changsha, 410005, Hunan, China
| | - Y Li
- Department of Pathology, First Affiliated Hospital of Hunan Normal University, The People's Hospital of Hunan Province, Changsha, 410005, Hunan, China
| | - H Xiao
- Department of Pathology, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Y Gu
- Department of Pathology, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - J P Yun
- Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - D Huang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Z Song
- Department of Pathology, Chinese PLA General Hospital, Beijing, 100853, China
| | - X Fan
- Department of Pathology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - L Chen
- Department of Pathology, The first affiliated hospital, Air Force Medical University, Xi'an, 710032, China
| | - X Yan
- Institute of Pathology and southwest cancer center, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Z Li
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Z C Huang
- Department of Biomedical Engineering, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - J Huang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - J Luttrell
- School of Computing Sciences and Computer Engineering, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - C Y Zhang
- School of Computing Sciences and Computer Engineering, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - W Zhou
- College of Computing, Michigan Technological University, Houghton, MI, 49931, USA
| | - K Zhang
- Department of Computer Science, Bioinformatics Facility of Xavier NIH RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA, 70125, USA
| | - C Yi
- Department of Pathology, Ochsner Medical Center, New Orleans, LA, 70121, USA
| | - C Wu
- Department of Statistics, Florida State University, Tallahassee, FL, 32306, USA
| | - H Shen
- Department of Deming Department of Medicine, Tulane Center of Biomedical Informatics and Genomics, Tulane University School of Medicine, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA
- Division of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Y P Wang
- Department of Deming Department of Medicine, Tulane Center of Biomedical Informatics and Genomics, Tulane University School of Medicine, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA
- Department of Biomedical Engineering, Tulane University, New Orleans, LA, 70118, USA
| | - H M Xiao
- Centers of System Biology, Data Information and Reproductive Health, School of Basic Medical Science, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China.
| | - H W Deng
- Department of Deming Department of Medicine, Tulane Center of Biomedical Informatics and Genomics, Tulane University School of Medicine, 1440 Canal Street, Suite 1610, New Orleans, LA, 70112, USA.
- Centers of System Biology, Data Information and Reproductive Health, School of Basic Medical Science, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China.
- Division of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
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Lu S, Yu Y, Barnes G, Qiu X, Bao Y, Li J, Tang B. MO01.43 Examining the Impact of Tislelizumab Added to Platinum Doublet Chemotherapy on Health-Related Quality of Life in Patients with Non-Squamous NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2020.10.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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