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Qing T, Xie TC, Zhu QY, Lu HP, Liu JX. Regulation of metal homoeostasis by two F-group bZIP transcription factors bZIP48 and bZIP50 in rice. Plant Cell Environ 2024; 47:1852-1864. [PMID: 38334305 DOI: 10.1111/pce.14852] [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] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 12/02/2023] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Zinc (Zn) deficiency not only impairs plant growth and development but also has negative effects on human health. Rice (Oryza Sativa L.) is a staple food for over half of the global population, yet the regulation of Zn deficiency response in rice remains largely unknown. In this study, we provide evidence that two F-group bZIP transcription factors, OsbZIP48/50, play a crucial role in Zn deficiency response. Mutations in OsbZIP48/50 result in impaired growth and reduced Zn/Fe/Cu content under Zn deficiency conditions. The N-terminus of OsbZIP48/OsbZIP50 contains two Zn sensor motifs (ZSMs), deletion or mutation of these ZSMs leads to increased nuclear localization. Both OsbZIP48 and OsbZIP50 exhibit transcriptional activation activity, and the upregulation of 1117 genes involved in metal uptake and other processes by Zn deficiency is diminished in the OsbZIP48/50 double mutant. Both OsbZIP48 and OsbZIP50 bind to the promoter of OsZIP10 and activate the ZDRE cis-element. Amino acid substitution mutation of the ZSM domain of OsbZIP48 in OsbZIP50 mutant background increases the content of Zn/Fe/Cu in brown rice seeds and leaves. Therefore, this study demonstrates that OsbZIP48/50 play a crucial role in regulating metal homoeostasis and identifies their downstream genes involved in the Zn deficiency response in rice.
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Affiliation(s)
- Tao Qing
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Tian-Ci Xie
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qiao-Yun Zhu
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hai-Ping Lu
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, China
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2
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Yu Y, Hou W, Liu Y, Wang H, Dong L, Mai Y, Chen Q, Li Z, Sun S, Yang J, Cao Z, Zhang P, Zi Y, Liu R, Gao J, Zhang N, Li J, Ren L, Jiang H, Shang J, Zhu S, Wang X, Qing T, Bao D, Li B, Li B, Suo C, Pi Y, Wang X, Dai F, Scherer A, Mattila P, Han J, Zhang L, Jiang H, Thierry-Mieg D, Thierry-Mieg J, Xiao W, Hong H, Tong W, Wang J, Li J, Fang X, Jin L, Xu J, Qian F, Zhang R, Shi L, Zheng Y. Author Correction: Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling. Nat Biotechnol 2023:10.1038/s41587-023-02008-y. [PMID: 37783850 DOI: 10.1038/s41587-023-02008-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Affiliation(s)
- Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | | | - Yuanbang Mai
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zhihui Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Shanyue Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, China
| | - Zehui Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yi Zi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ruimei Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jian Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
- Nextomics Biosciences Institute, Wuhan, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xiaolin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Tao Qing
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ding Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bingying Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bin Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Chen Suo
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yan Pi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xia Wang
- National Institute of Metrology, Beijing, China
| | | | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | - Pirkko Mattila
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | | | - Lijun Zhang
- Nanjing Vazyme Biotech Co. Ltd., Nanjing, China
| | | | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Wenming Xiao
- Office of Oncologic Diseases, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Jing Wang
- National Institute of Metrology, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China
- National Center of Gerontology, Beijing, China
| | - Xiang Fang
- National Institute of Metrology, Beijing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
| | - Feng Qian
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China.
- National Center of Gerontology, Beijing, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
- International Human Phenome Institutes, Shanghai, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
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3
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Yu Y, Hou W, Liu Y, Wang H, Dong L, Mai Y, Chen Q, Li Z, Sun S, Yang J, Cao Z, Zhang P, Zi Y, Liu R, Gao J, Zhang N, Li J, Ren L, Jiang H, Shang J, Zhu S, Wang X, Qing T, Bao D, Li B, Li B, Suo C, Pi Y, Wang X, Dai F, Scherer A, Mattila P, Han J, Zhang L, Jiang H, Thierry-Mieg D, Thierry-Mieg J, Xiao W, Hong H, Tong W, Wang J, Li J, Fang X, Jin L, Xu J, Qian F, Zhang R, Shi L, Zheng Y. Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling. Nat Biotechnol 2023:10.1038/s41587-023-01867-9. [PMID: 37679545 DOI: 10.1038/s41587-023-01867-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/15/2023] [Indexed: 09/09/2023]
Abstract
Certified RNA reference materials are indispensable for assessing the reliability of RNA sequencing to detect intrinsically small biological differences in clinical settings, such as molecular subtyping of diseases. As part of the Quartet Project for quality control and data integration of multi-omics profiling, we established four RNA reference materials derived from immortalized B-lymphoblastoid cell lines from four members of a monozygotic twin family. Additionally, we constructed ratio-based transcriptome-wide reference datasets between two samples, providing cross-platform and cross-laboratory 'ground truth'. Investigation of the intrinsically subtle biological differences among the Quartet samples enables sensitive assessment of cross-batch integration of transcriptomic measurements at the ratio level. The Quartet RNA reference materials, combined with the ratio-based reference datasets, can serve as unique resources for assessing and improving the quality of transcriptomic data in clinical and biological settings.
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Affiliation(s)
- Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | | | - Yuanbang Mai
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zhihui Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Shanyue Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, China
| | - Zehui Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yi Zi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ruimei Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jian Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
- Nextomics Biosciences Institute, Wuhan, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xiaolin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Tao Qing
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ding Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bingying Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bin Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Chen Suo
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yan Pi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xia Wang
- National Institute of Metrology, Beijing, China
| | | | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | - Pirkko Mattila
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | | | - Lijun Zhang
- Nanjing Vazyme Biotech Co. Ltd., Nanjing, China
| | | | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Wenming Xiao
- Office of Oncologic Diseases, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Jing Wang
- National Institute of Metrology, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China
- National Center of Gerontology, Beijing, China
| | - Xiang Fang
- National Institute of Metrology, Beijing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
| | - Feng Qian
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China.
- National Center of Gerontology, Beijing, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
- International Human Phenome Institutes, Shanghai, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.
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4
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Zheng Y, Liu Y, Yang J, Dong L, Zhang R, Tian S, Yu Y, Ren L, Hou W, Zhu F, Mai Y, Han J, Zhang L, Jiang H, Lin L, Lou J, Li R, Lin J, Liu H, Kong Z, Wang D, Dai F, Bao D, Cao Z, Chen Q, Chen Q, Chen X, Gao Y, Jiang H, Li B, Li B, Li J, Liu R, Qing T, Shang E, Shang J, Sun S, Wang H, Wang X, Zhang N, Zhang P, Zhang R, Zhu S, Scherer A, Wang J, Wang J, Huo Y, Liu G, Cao C, Shao L, Xu J, Hong H, Xiao W, Liang X, Lu D, Jin L, Tong W, Ding C, Li J, Fang X, Shi L. Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials. Nat Biotechnol 2023:10.1038/s41587-023-01934-1. [PMID: 37679543 DOI: 10.1038/s41587-023-01934-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/31/2023] [Indexed: 09/09/2023]
Abstract
Characterization and integration of the genome, epigenome, transcriptome, proteome and metabolome of different datasets is difficult owing to a lack of ground truth. Here we develop and characterize suites of publicly available multi-omics reference materials of matched DNA, RNA, protein and metabolites derived from immortalized cell lines from a family quartet of parents and monozygotic twin daughters. These references provide built-in truth defined by relationships among the family members and the information flow from DNA to RNA to protein. We demonstrate how using a ratio-based profiling approach that scales the absolute feature values of a study sample relative to those of a concurrently measured common reference sample produces reproducible and comparable data suitable for integration across batches, labs, platforms and omics types. Our study identifies reference-free 'absolute' feature quantification as the root cause of irreproducibility in multi-omics measurement and data integration and establishes the advantages of ratio-based multi-omics profiling with common reference materials.
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Affiliation(s)
- Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, China
| | | | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China
| | - Sha Tian
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Feng Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yuanbang Mai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | | | | | | | - Ling Lin
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Medical Diagnostics Co. Ltd., Shanghai, China
| | - Jingwei Lou
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Medical Diagnostics Co. Ltd., Shanghai, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Jingchao Lin
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | | | | | - Depeng Wang
- Nextomics Biosciences Institute, Wuhan, China
| | | | - Ding Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zehui Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qiaochu Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yuechen Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bin Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bingying Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
- Nextomics Biosciences Institute, Wuhan, China
| | - Ruimei Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Tao Qing
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Erfei Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Shanyue Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xiaolin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ruolan Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jing Wang
- National Institute of Metrology, Beijing, China
| | - Yinbo Huo
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Gang Liu
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Chengming Cao
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Li Shao
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Wenming Xiao
- Office of Oncologic Diseases, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Xiaozhen Liang
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Weida Tong
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China.
| | - Xiang Fang
- National Institute of Metrology, Beijing, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
- International Human Phenome Institutes (Shanghai), Shanghai, China.
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5
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Chen M, Li H, Xu X, Bao X, Xue L, Ai X, Xu J, Xu M, Shi Y, Zhen T, Li J, Yang Y, Ji Y, Fu Z, Xing K, Qing T, Wang Q, Zhong P, Zhu S. Identification of RAC1 in promoting brain metastasis of lung adenocarcinoma using single-cell transcriptome sequencing. Cell Death Dis 2023; 14:330. [PMID: 37202394 DOI: 10.1038/s41419-023-05823-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/20/2023]
Abstract
This study aims to give a new perspective to the biomarkers in the lung adenocarcinoma (LUAD) brain metastasis, pathways involved and potential therapeutics. We performed a comprehensive single-cell level transcriptomic analysis on one LUAD patient with circulating tumor cells (CTCs), primary tumor tissue and metastatic tumor tissue using scRNA-seq approach to identify metastasis related biomarkers. Further scRNA-seq were performed on 7 patients to validate the cancer metastatic hallmark. with single cells collected from either metastatic or primary LUAD tissues. Pathological and functional studies were also performed to evidence the critical role of RAC1 in the LUAD metastasis. Hallmark gene was verified based on immunohistochemistry staining, cytological experiment, survival information from The Cancer Genome Atlas (TCGA), and staining results from Human Protein Atlas (HPA) databases. PCA analysis revealed that CTCs were in the intermediate place between the metastatic group and primary group. In the unsupervised clustering analysis CTCs were closer to one of the metastatic tumor cells, implying heterogeneity of the metastatic tumor and origin of the CTCs were from metastatic site. Transitional phase related gene analysis identified RAC1 was enriched in metastatic tumor tissue (MTT) preferred gene set functioning as regulated cell death and apoptosis as well as promoted macromolecule organization. Compared with normal tissue, expression levels of RAC1 increased significantly in LUAD tissue based on HPA database. High expression of RAC1 predicts worse prognosis and higher-risk. EMT analysis identified the propensity of mesenchymal state in primary cells while epithelial signals were higher in the metastatic site. Functional clustering and pathway analyses suggested genes in RAC1 highly expressed cells played critical roles in adhesion, ECM and VEGF signaling pathways. Inhibition of RAC1 attenuates the proliferation, invasiveness and migration ability of lung cancer cells. Besides, through MRI T2WI results, we proved that RAC1 can promote brain metastasis in the RAC1-overexpressed H1975 cell burden nude mouse model. RAC1 and its mechanisms might promote drug design against LUAD brain metastasis.
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Affiliation(s)
- Mingyu Chen
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, 200040, Shanghai, China
- School of Life Sciences, Fudan University, 200438, Shanghai, China
- Research Unit of New Technologies of Micro-Endoscopy Combination in Skull Base Surgery (2018RU008), Chinese Academy of Medical Sciences, Beijing, China
- Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Hanyue Li
- Department of Lung Tumor Clinical Center, Shanghai Chest Hospital, Shanghai Jiaotong University, 200030, Shanghai, China
| | - Xiaolin Xu
- Department of Cardiothoracic Surgery, Third Affiliated Hospital of Naval Military Medical University, 200003, Shanghai, China
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, 507 Zhengmin Road, Shanghai, PR China
| | - Xunxia Bao
- School of Life Science, Anhui Medical University, 230032, Hefei, China
| | - Lei Xue
- Department of Thoracic Surgery, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Military Medical University, 200003, Shanghai, China
| | - Xinghao Ai
- Department of Lung Tumor Clinical Center, Shanghai Chest Hospital, Shanghai Jiaotong University, 200030, Shanghai, China
| | - Jian Xu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, 200040, Shanghai, China
- School of Life Sciences, Fudan University, 200438, Shanghai, China
- Research Unit of New Technologies of Micro-Endoscopy Combination in Skull Base Surgery (2018RU008), Chinese Academy of Medical Sciences, Beijing, China
- Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Ming Xu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, 200040, Shanghai, China
- School of Life Sciences, Fudan University, 200438, Shanghai, China
- Research Unit of New Technologies of Micro-Endoscopy Combination in Skull Base Surgery (2018RU008), Chinese Academy of Medical Sciences, Beijing, China
- Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Yong Shi
- Cinoasia Institute, 200438, Shanghai, China
| | | | - Jie Li
- Cinoasia Institute, 200438, Shanghai, China
| | - Yi Yang
- Cinoasia Institute, 200438, Shanghai, China
| | - Yang Ji
- Cinoasia Institute, 200438, Shanghai, China
| | | | | | - Tao Qing
- Cinoasia Institute, 200438, Shanghai, China
| | - Qiubo Wang
- Department of Clinical Laboratory, Wuxi 9th People's Hospital Affiliated to Soochow University, 214000, Wuxi, Jiangsu, China.
| | - Ping Zhong
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, 200040, Shanghai, China.
- School of Life Sciences, Fudan University, 200438, Shanghai, China.
- Research Unit of New Technologies of Micro-Endoscopy Combination in Skull Base Surgery (2018RU008), Chinese Academy of Medical Sciences, Beijing, China.
- Neurosurgical Institute of Fudan University, Shanghai, China.
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China.
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China.
| | - Sibo Zhu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, 200040, Shanghai, China.
- School of Life Sciences, Fudan University, 200438, Shanghai, China.
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Qing T, Karn T, Rozenblit M, Foldi J, Marczyk M, Shan NL, Blenman K, Holtrich U, Kalinsky K, Meric-Bernstam F, Pusztai L. Abstract PD9-09: Molecular differences between younger versus older estrogen receptor positive/human epidermal growth factor receptor-2 negative breast cancers. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-pd9-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background: The RxPONDER and TAILORx trials demonstrated benefit from adjuvant chemotherapy in patients < 50 years with node-positive breast cancer and Recurrence Score (RS) 0-25, and with node-negative disease and RS 16-25, respectively. Neither trial showed benefit in older women with RS < 26. It is unclear what explains the interaction between age and adjuvant chemotherapy benefit. Methods: We analyzed transcriptomic and genomic data from n=4,507 ER+/HER2- breast cancers to compare differences in estrogen receptor (ER), proliferation, and immune-related gene expressions, and somatic mutation patterns and mutation burden between younger (< 50 years of age) and older (>55 years) patients. We restricted our analysis to patients in the lower 80% range of in silico RS distribution to mimic the RxPONDER and TAILORx populations. Results: Five data sets were analyzed independently to assess consistency of results (TCGA n=530; microarray cohort A n=865; Cohort B n=609, METABRIC n=867, SCAN-B n=1636). Older patients had significantly higher somatic mutation burden and more frequent copy number gain in ESR1, LATS1, ARID1B, SGK1, and MYB genes (odds ratio [OR] > 8.5, FDR< 0.05), but lower frequency of GATA3 mutations (12% versus 26%, P< 0.0001). Younger patients had higher rate of ESR1 copy number loss (OR: 0.45, FDR: 0.03). There was no difference in proliferation-related gene expression. ESR1 mRNA expression was significantly lower in younger women in all cohorts (P < 0.001). A regression model of ESR1 mRNA expression using age and ER IHC positivity indicated that lower ER expression in younger patients is primarily driven by lower ESR1 mRNA per cancer cell and not by fewer ER positive cells. We also assessed four gene signatures associated with endocrine therapy sensitivity including a 4-gene ERS, a 7-gene ERS-Lum, a 106-gene ERS-Pos signature, and a 59-gene ERS-Neg signature associated with endocrine resistance. In the TCGA and METABRIC cohorts, the ERS, ERS-Lum, and ERS-Pos signatures were all lower (FDR< 0.03) while the ERS-Neg signature was higher (FDR< 0.001) in younger patients. Similarly, in both microarray cohorts, and in the SCAN-B-cohort, the ERS-Pos signature was lower and the ERS-Neg signature was higher in younger patients (FDR< 0.002). Next, we assessed 4 different immune cell signatures that have been associated with response to chemotherapy. In the TCGA, B-cell, T-cell, Mast-cell, and TIS signatures were significantly higher (FDR<.05). In the microarray Cohort-A, B cells and mast cells were significantly higher, and the T cell and TIS signatures showed a trend for higher expression. In Cohort-B, T cells, B cells, TIS, and dendritic cells signatures were significantly higher in younger patients. Significantly higher expression of immune gene signatures in younger patients were also seen in the METABRIC and SCAN-B data sets. The ER-related and immune-related gene signatures showed negative correlation and joint analysis defined three subpopulations in younger women: (i) immune-high/ER-low, (ii) immune-intermediate/ER-intermediate and (iii) immune-low/ER-intermediate, whereas in older women the dominant pattern was immune-low/ER-high. Conclusion: ESR1 mRNA and ER-associated gene expression is lower in ER positive cancers of younger compared to older patients, while immune infiltration is higher. The cytotoxic and endocrine effects of adjuvant chemotherapy could both contribute to the survival benefit seen in younger patients, but the relative contributions of these effects may vary by ER and immune phenotype. We hypothesize that in immune-high/ER-low cancers, the cytotoxic effect of chemotherapy may drive the benefit, whereas in immune-low/ER-intermediate cancers chemotherapy induced ovarian suppression may play a more important role.
Citation Format: Tao Qing, Thomas Karn, Mariya Rozenblit, Julia Foldi, Michal Marczyk, Naing Lin Shan, Kim Blenman, uwe Holtrich, Kevin Kalinsky, Funda Meric-Bernstam, Lajos Pusztai. Molecular differences between younger versus older estrogen receptor positive/human epidermal growth factor receptor-2 negative breast cancers [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 PD9-09.
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Affiliation(s)
| | - Thomas Karn
- 2Universitätsklinikum Frankfurt, Frankfurt am Main, Germany
| | | | | | - Michal Marczyk
- 5Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | | | | | - uwe Holtrich
- 8Universitätsklinikum Frankfurt, Frankfurt am Main, Germany
| | - Kevin Kalinsky
- 9Winship Cancer Institute at Emory University, Atlanta, GA
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7
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Yuan H, Qing T, Zhu S, Yang X, Wu W, Xu K, Chen H, Jiang Y, Zhu C, Yuan Z, Zhang T, Jin L, Suo C, Lu M, Chen X, Ye W. The effects of altered DNA damage repair genes on mutational processes and immune cell infiltration in esophageal squamous cell carcinoma. Cancer Med 2023; 12:10077-10090. [PMID: 36708047 PMCID: PMC10166979 DOI: 10.1002/cam4.5663] [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: 07/05/2022] [Revised: 01/01/2023] [Accepted: 01/18/2023] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Defects in DNA damage repair (DDR) pathways lead to genomic instability and oncogenesis. DDR deficiency is prevalent in esophageal squamous cell carcinoma (ESCC), but the effects of DDR alterations on mutational processes and tumor immune microenvironment in ECSS remain unclear. METHODS Whole-exome and transcriptome sequencing data of 45 ESCC samples from Taizhou, China, were used to identify genomic variations, gene expression modulation in DDR pathways, and the abundance of tumor-infiltrating immune cells. Ninety-six ESCC cases from The Cancer Genome Atlas (TCGA) project were used for validation. RESULTS A total of 57.8% (26/45) of the cases in the Taizhou data and 70.8% (68/96) of the cases in the TCGA data carried at least one functional impact DDR mutation. Mutations in the DDR pathways were associated with a high tumor mutation burden. Several DDR deficiency-related mutational signatures were discovered and were associated with immune cell infiltration, including T cells, monocytes, dendritic cells, and mast cells. The expression levels of two DDR genes, HFM1 and NEIL1, were downregulated in ESCC tumor tissues and had an independent effect on the infiltration of mast cells. In the Taizhou data, increased expression of HFM1 was associated with a poor prognosis, and the increased expression of NEIL1 was associated with a good outcome, but no reproducible correlation was observed in the TCGA data. CONCLUSION This research demonstrated that DDR alterations could impact mutational processes and immune cell infiltration in ESCC. The suppression of HFM1 and NEIL1 could play a crucial role in ESCC progression and may also serve as prognostic markers.
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Affiliation(s)
- Huangbo Yuan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China
| | - Tao Qing
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China.,Breast Medical Oncology, School of Medicine, Yale University, Connecticut, New Haven, USA
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaorong Yang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Weicheng Wu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China
| | - Kelin Xu
- Department of Biostatistics, School of Public Health, Fudan University, Shanghai, China
| | - Hui Chen
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Yanfeng Jiang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China.,Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Chengkai Zhu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China
| | - Ziyu Yuan
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Tiejun Zhang
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China.,Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China.,Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Chen Suo
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China.,Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Ming Lu
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China.,Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China.,Fudan University Taizhou Institute of Health Sciences, Taizhou, China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Yiwu Research Institute of Fudan University, Yiwu, China
| | - Weimin Ye
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China.,Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
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8
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Qing T, Karn T, Rozenblit M, Foldi J, Marczyk M, Shan NL, Blenman K, Holtrich U, Kalinsky K, Meric-Bernstam F, Pusztai L. Molecular differences between younger versus older ER-positive and HER2-negative breast cancers. NPJ Breast Cancer 2022; 8:119. [PMID: 36344517 PMCID: PMC9640562 DOI: 10.1038/s41523-022-00492-0] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
Abstract
The RxPONDER and TAILORx trials demonstrated benefit from adjuvant chemotherapy in patients age ≤ 50 with node-positive breast cancer and Recurrence Score (RS) 0-26, and in node-negative disease with RS 16-25, respectively, but no benefit in older women with the same clinical features. We analyzed transcriptomic and genomic data of ER+/HER2- breast cancers with in silico RS < 26 from TCGA (n = 530), two microarray cohorts (A: n = 865; B: n = 609), the METABRIC (n = 867), and the SCAN-B (n = 1636) datasets. There was no difference in proliferation-related gene expression between age groups. Older patients had higher mutation burden and more frequent ESR1 copy number gain, but lower frequency of GATA3 mutations. Younger patients had higher rate of ESR1 copy number loss. In all datasets, younger patients had significantly lower mRNA expression of ESR1 and ER-associated genes, and higher expression of immune-related genes. The ER- and immune-related gene signatures showed negative correlation and defined three subpopulations in younger women: immune-high/ER-low, immune-intermediate/ER-intermediate, and immune-low/ER-intermediate. We hypothesize that in immune-high cancers, the cytotoxic effect of chemotherapy may drive the benefit, whereas in immune-low/ER-intermediate cancers chemotherapy induced ovarian suppression may play important role.
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Affiliation(s)
- Tao Qing
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Thomas Karn
- Department of Gynecology and Obstetrics, Goethe-University Frankfurt, Frankfurt, Germany
| | - Mariya Rozenblit
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Julia Foldi
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Michal Marczyk
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Naing Lin Shan
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Kim Blenman
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Uwe Holtrich
- Department of Gynecology and Obstetrics, Goethe-University Frankfurt, Frankfurt, Germany
| | - Kevin Kalinsky
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lajos Pusztai
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA.
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9
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Mao R, Zheng Q, Mao JY, Qing T. Facilitating retail store clerks’ work-family balance: The roles of family-supportive supervisor behavior and store competitive climate. Curr Psychol 2022. [DOI: 10.1007/s12144-022-03687-7] [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: 11/28/2022]
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10
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Foldi J, Kahn A, Silber A, Qing T, Reisenbichler E, Fischbach N, Persico J, Adelson K, Katoch A, Chagpar A, Park T, Blanchard A, Blenman K, Rimm DL, Pusztai L. Clinical Outcomes and Immune Markers by Race in a Phase I/II Clinical Trial of Durvalumab Concomitant with Neoadjuvant Chemotherapy in Early-Stage TNBC. Clin Cancer Res 2022; 28:3720-3728. [PMID: 35903931 PMCID: PMC9444984 DOI: 10.1158/1078-0432.ccr-22-0862] [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: 03/17/2022] [Revised: 05/13/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE The incidence of triple-negative breast cancer (TNBC) is higher among Black or African American (AA) women, yet they are underrepresented in clinical trials. To evaluate safety and efficacy of durvalumab concurrent with neoadjuvant chemotherapy for stage I-III TNBC by race, we enrolled additional AA patients to a Phase I/II clinical trial. PATIENTS AND METHODS Our study population included 67 patients. The primary efficacy endpoint was pathologic complete response (pCR; ypT0/is, N0) rate. χ2 tests were used to evaluate associations between race and baseline characteristics. Cox proportional hazards models were used to assess association between race and overall survival (OS) and event-free survival (EFS). Multivariate logistic regression analyses were used to evaluate associations between race and pCR, immune-related adverse events (irAE) and recurrence. RESULTS Twenty-one patients (31%) self-identified as AA. No significant associations between race and baseline tumor stage (P = 0.40), PD-L1 status (0.92), and stromal tumor-infiltrating lymphocyte (sTIL) count (P = 0.57) were observed. pCR rates were similar between AA (43%) and non-AA patients (48%; P = 0.71). Three-year EFS rates were 78.3% and 71.4% in non-AA and AA patients, respectively [HR, 1.451; 95% confidence interval (CI), 0.524-4.017; P = 0.474]; 3-year OS was 87% and 81%, respectively (HR, 1.72; 95% CI, 0.481-6.136; P = 0.405). The incidence of irAEs was similar between AA and non-AA patients and no significant associations were found between irAEs and pathologic response. CONCLUSIONS pCR rates, 3-year OS and EFS after neoadjuvant immunotherapy and chemotherapy were similar in AA and non-AA patients. Toxicities, including the frequency of irAEs, were also similar.
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Affiliation(s)
- Julia Foldi
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Adriana Kahn
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Andrea Silber
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Tao Qing
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Neal Fischbach
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Justin Persico
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Kerin Adelson
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Anamika Katoch
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Anees Chagpar
- Department of Surgery, Yale School of Medicine, New Haven, CT 06510, USA
| | - Tristen Park
- Department of Surgery, Yale School of Medicine, New Haven, CT 06510, USA
| | - Adam Blanchard
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Kim Blenman
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT 06510, USA
| | - David L. Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Lajos Pusztai
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT 06510, USA
- Corresponding author: Dr. Lajos Pusztai, MD, DPhil, Breast Medical Oncology, Yale Cancer Center, Yale School of Medicine, 300 George St, Suite 120, Rm 133, New Haven, CT, 06520, USA. Tel: +1 203 737 8309.
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11
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Marczyk M, Qing T, O'Meara T, Yagahoobi V, Pelekanou V, Bai Y, Reisenbichler E, Cole KS, Li X, Gunasekharan V, Ibrahim E, Fanucci K, Wei W, Rimm DL, Pusztai L, Blenman KRM. Tumor immune microenvironment of self-identified African American and non-African American triple negative breast cancer. NPJ Breast Cancer 2022; 8:88. [PMID: 35869114 PMCID: PMC9307813 DOI: 10.1038/s41523-022-00449-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 06/20/2022] [Indexed: 02/06/2023] Open
Abstract
Differences in the tumor immune microenvironment may result in differences in prognosis and response to treatment in cancer patients. We hypothesized that differences in the tumor immune microenvironment may exist between African American (AA) and NonAA patients, due to ancestry-related or socioeconomic factors, that may partially explain differences in clinical outcomes. We analyzed clinically matched triple-negative breast cancer (TNBC) tissues from self-identified AA and NonAA patients and found that stromal TILs, PD-L1 IHC-positivity, mRNA expression of immune-related pathways, and immunotherapy response predictive signatures were significantly higher in AA samples (p < 0.05; Fisher's Exact Test, Mann-Whitney Test, Permutation Test). Cancer biology and metabolism pathways, TAM-M2, and Immune Exclusion were significantly higher in NonAA samples (p < 0.05; Permutation Test, Mann-Whitney Test). There were no differences in somatic tumor mutation burden. Overall, there is greater immune infiltration and inflammation in AA TNBC and these differences may impact response to immune checkpoint inhibitors and other therapeutic agents that modulate the immune microenvironment.
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Affiliation(s)
- Michal Marczyk
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
- Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Tao Qing
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
| | - Tess O'Meara
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Vesal Yagahoobi
- Department of Pathology, Yale University, New Haven, CT, USA
| | - Vasiliki Pelekanou
- Department of Pathology, Yale University, New Haven, CT, USA
- Precision Medicine - Oncology, Translational Medical Oncology, Translational Medicine Early Development, Sanofi, Cambridge, MA, USA
| | - Yalai Bai
- Department of Pathology, Yale University, New Haven, CT, USA
| | | | - Kimberly S Cole
- Department of Pathology, Yale University, New Haven, CT, USA
- Sema4 Genomics, Branford, CT, USA
| | - Xiaotong Li
- Department of Computational Biology & Bioinformatics, Biological & Biomedical Sciences, Yale University, New Haven, CT, USA
| | - Vignesh Gunasekharan
- Yale Cancer Center, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
| | - Eiman Ibrahim
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | | | - Wei Wei
- Yale Cancer Center, Yale University, New Haven, CT, USA
- Department of Biostatistics, Yale University, New Haven, CT, USA
| | - David L Rimm
- Yale Cancer Center, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
- Department of Pathology, Yale University, New Haven, CT, USA
| | - Lajos Pusztai
- Yale Cancer Center, Yale University, New Haven, CT, USA.
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA.
| | - Kim R M Blenman
- Yale Cancer Center, Yale University, New Haven, CT, USA.
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA.
- Department of Computer Science, Yale University, New Haven, CT, USA.
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12
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Qing T, Mohsen H, Cannataro VL, Marczyk M, Rozenblit M, Foldi J, Murray M, Townsend JP, Kluger Y, Gerstein M, Pusztai L. Cancer Relevance of Human Genes. J Natl Cancer Inst 2022; 114:988-995. [PMID: 35417011 PMCID: PMC9275765 DOI: 10.1093/jnci/djac068] [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: 09/03/2021] [Revised: 01/03/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND We hypothesize that genes that directly or indirectly interact with core cancer genes (CCGs) in a comprehensive gene-gene interaction network may have functional importance in cancer. METHODS We categorized 12 767 human genes into CCGs (n = 468), 1 (n = 5467), 2 (n = 5573), 3 (n = 915), and more than 3 steps (n = 416) removed from the nearest CCG in the Search Tool for the Retrieval of Interacting Genes/Proteins network. We estimated cancer-relevant functional importance in these neighborhood categories using 1) gene dependency score, which reflects the effect of a gene on cell viability after knockdown; 2) somatic mutation frequency in The Cancer Genome Atlas; 3) effect size that estimates to what extent a mutation in a gene enhances cell survival; and 4) negative selection pressure of germline protein-truncating variants in healthy populations. RESULTS Cancer biology-related functional importance of genes decreases as their distance from the CCGs increases. Genes closer to cancer genes show greater connectedness in the network, have greater importance in maintaining cancer cell viability, are under greater negative germline selection pressure, and have higher somatic mutation frequency in cancer. Based on these 4 metrics, we provide cancer relevance annotation to known human genes. CONCLUSIONS A large number of human genes are connected to CCGs and could influence cancer biology to various extent when dysregulated; any given mutation may be functionally important in one but not in another individual depending on genomic context.
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Affiliation(s)
- Tao Qing
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Hussein Mohsen
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | | | - Michal Marczyk
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Mariya Rozenblit
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Julia Foldi
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Michael Murray
- Department of Genetics, Yale Center for Genomic Health, New Haven, CT, USA
| | - Jeffrey P Townsend
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Yuval Kluger
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Pathology, School of Medicine, Yale University, New Haven, CT, USA
- Applied Mathematics Program, Yale University, New Haven, CT, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, USA
| | - Lajos Pusztai
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
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13
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Blenman KRM, Marczyk M, Karn T, Qing T, Li X, Gunasekharan V, Yaghoobi V, Bai Y, Ibrahim EY, Park T, Silber A, Wolf DM, Reisenbichler E, Denkert C, Sinn BV, Rozenblit M, Foldi J, Rimm DL, Loibl S, Pusztai L. Predictive Markers of Response to Neoadjuvant Durvalumab with Nab-Paclitaxel and Dose-Dense Doxorubicin/Cyclophosphamide in Basal-Like Triple-Negative Breast Cancer. Clin Cancer Res 2022; 28:2587-2597. [PMID: 35377948 PMCID: PMC9464605 DOI: 10.1158/1078-0432.ccr-21-3215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 09/06/2021] [Revised: 01/04/2022] [Accepted: 04/01/2022] [Indexed: 12/15/2022]
Abstract
PURPOSE We examined gene expression, germline variant, and somatic mutation features associated with pathologic response to neoadjuvant durvalumab plus chemotherapy in basal-like triple-negative breast cancer (bTNBC). EXPERIMENTAL DESIGN Germline and somatic whole-exome DNA and RNA sequencing, programmed death ligand 1 (PD-L1) IHC, and stromal tumor-infiltrating lymphocyte scoring were performed on 57 patients. We validated our results using 162 patients from the GeparNuevo randomized trial. RESULTS Gene set enrichment analysis showed that pathways involved in immunity (adaptive, humoral, innate), JAK-STAT signaling, cancer drivers, cell cycle, apoptosis, and DNA repair were enriched in cases with pathologic complete response (pCR), whereas epithelial-mesenchymal transition, extracellular matrix, and TGFβ pathways were enriched in cases with residual disease (RD). Immune-rich bTNBC with RD was enriched in CCL-3, -4, -5, -8, -23, CXCL-1, -3, -6, -10, and IL1, -23, -27, -34, and had higher expression of macrophage markers compared with immune-rich cancers with pCR that were enriched in IFNγ, IL2, -12, -21, chemokines CXCL-9, -13, CXCR5, and activated T- and B-cell markers (GZMB, CD79A). In the validation cohort, an immune-rich five-gene signature showed higher expression in pCR cases in the durvalumab arm (P = 0.040) but not in the placebo arm (P = 0.923) or in immune-poor cancers. Independent of immune markers, tumor mutation burden was higher, and PI3K, DNA damage repair, MAPK, and WNT/β-catenin signaling pathways were enriched in germline and somatic mutations in cases with pCR. CONCLUSIONS The TGFβ pathway is associated with immune-poor phenotype and RD in bTNBC. Among immune-rich bTNBC RD, macrophage/neutrophil chemoattractants dominate the cytokine milieu, and IFNγ and activated B cells and T cells dominate immune-rich cancers with pCR.
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Affiliation(s)
- Kim RM Blenman
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
- Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Michal Marczyk
- Yale Cancer Center, Yale University, New Haven, CT, USA
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | | | - Tao Qing
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
| | - Xiaotong Li
- Department of Computational Biology & Bioinformatics, Biological & Biomedical Sciences, Yale University, New Haven, CT, USA
| | - Vignesh Gunasekharan
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
- Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Vesal Yaghoobi
- Department of Pathology, Yale University, New Haven, CT, USA
| | - Yalai Bai
- Department of Pathology, Yale University, New Haven, CT, USA
| | - Eiman Y Ibrahim
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Tristen Park
- Department of Surgery, Yale University, New Haven, CT, USA
| | - Andrea Silber
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
- Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Denise M. Wolf
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | | | | | - Mariya Rozenblit
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
| | - Julia Foldi
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
| | - David L Rimm
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
- Yale Cancer Center, Yale University, New Haven, CT, USA
- Department of Pathology, Yale University, New Haven, CT, USA
| | | | - Lajos Pusztai
- Department of Internal Medicine, Section of Medical Oncology, Yale University, New Haven, CT, USA
- Yale Cancer Center, Yale University, New Haven, CT, USA
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14
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Foldi J, Kahn A, Silber A, Qing T, Reisenbichler E, Fischbach NA, Persico J, Adelson KB, Katoch A, Chagpar AB, Park T, Blanchard A, Blenman K, Rimm DL, Pusztai L. Clinical outcomes and immune markers by race in a phase I/II clinical trial of durvalumab concomitant with neoadjuvant chemotherapy in early-stage TNBC. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.516] [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: 11/20/2022] Open
Abstract
516 Background: The incidence of triple negative breast cancer (TNBC) is higher among Black or African American (AA) women, yet AA patients (pts) are underrepresented in clinical trials, exemplifying racial disparity in oncology. We conducted a phase I/II trial to assess the safety and efficacy of durvalumab concurrent with weekly nab-paclitaxel and dose dense doxorubicin/cyclophosphamide (ddAC) neoadjuvant therapy for stage I-III TNBC. The primary efficacy endpoint was pathologic complete response (pCR; ypT0/is,N0) rate. Given the unclear efficacy and safety of immunotherapy in AA pts with breast cancer, we extended our accrual to recruit AA pts, with the goal of evaluating the association between racial groups and PD-L1 expression, stromal tumor infiltrating lymphocytes (sTILs), toxicities, treatment response and survival. Methods: Our study population included 67 pts. PD-L1 immunohistochemistry results and sTIL counts were available on 59 and 60 pts, respectively. Chi-Squared test was used to evaluate associations between race and baseline characteristics. Cox proportional hazards model was used to assess association between AA race and overall survival (OS) and event free survival (EFS), adjusting for age, comorbidities and pCR status. Multivariate logistic regression analyses were used to evaluate the association between race and pCR, development of immune-related adverse events (irAEs) and breast cancer recurrence. Results: Twenty-one pts (31%) self-identified as AA. No significant associations between AA race and baseline body mass index (BMI; p=0.075), Charlson comorbidity index (p=0.32), tumor stage (p=0.40), grade (p=0.54), PD-L1 status (0.92) and sTIL count (p=0.57) were observed. pCR rates did not significantly differ between AA and non-AA pts: 9/21 (43%) AA vs. 22/48 (48%) non-AA (p=0.71). 3-yr OS was 87% in the non-AA versus 81% in the AA cohort (HR 1.72, 95% CI 0.481-6.136; p=0.405); 3 yr EFS were 78.3% and 71.4% in non-AA and AA pts respectively. (HR 1.451, 95% CI 0.524-4.017; p=0.474). Pts with pCR were more likely to remain event-free at 3 yrs, irrespective of race (HR 0.234, 95% CI 0.066-0.829; p=0.024). In multivariate logistic regression analyses, lack of pathologic response (OR for pCR 0.17, 95% CI 0.03-0.7; p=0.02) and node positive status (OR 4.13, 95% CI 1.05-19.88; p=0.05) were associated with recurrence. The incidence of irAEs was similar between AA and non-AA pts and no significant associations were found between irAEs and pathologic response. Conclusions: pCR rates after neoadjuvant immunotherapy and chemotherapy were similar in AA and non-AA pts. Stromal TILs, PD-L1 status, 3yr OS and EFS, and the frequency of irAEs were also similar. These results suggest that when patients receive identical treatment and are monitored closely, disparities in outcomes can be mitigated or abolished. Clinical trial information: NCT02489448.
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Affiliation(s)
| | | | | | - Tao Qing
- Yale School of Medicine, New Haven, CT
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15
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Polewko-Klim A, Zhu S, Wu W, Xie Y, Cai N, Zhang K, Zhu Z, Qing T, Yuan Z, Xu K, Zhang T, Lu M, Ye W, Chen X, Suo C, Rudnicki WR. Identification of Candidate Therapeutic Genes for More Precise Treatment of Esophageal Squamous Cell Carcinoma and Adenocarcinoma. Front Genet 2022; 13:844542. [PMID: 35664298 PMCID: PMC9161154 DOI: 10.3389/fgene.2022.844542] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/20/2022] [Indexed: 11/23/2022] Open
Abstract
The standard therapy administered to patients with advanced esophageal cancer remains uniform, despite its two main histological subtypes, namely esophageal squamous cell carcinoma (SCC) and esophageal adenocarcinoma (AC), are being increasingly considered to be different. The identification of potential drug target genes between SCC and AC is crucial for more effective treatment of these diseases, given the high toxicity of chemotherapy and resistance to administered medications. Herein we attempted to identify and rank differentially expressed genes (DEGs) in SCC vs. AC using ensemble feature selection methods. RNA-seq data from The Cancer Genome Atlas and the Fudan-Taizhou Institute of Health Sciences (China). Six feature filters algorithms were used to identify DEGs. We built robust predictive models for histological subtypes with the random forest (RF) classification algorithm. Pathway analysis also be performed to investigate the functional role of genes. 294 informative DEGs (87 of them are newly discovered) have been identified. The areas under receiver operator curve (AUC) were higher than 99.5% for all feature selection (FS) methods. Nine genes (i.e., ERBB3, ATP7B, ABCC3, GALNT14, CLDN18, GUCY2C, FGFR4, KCNQ5, and CACNA1B) may play a key role in the development of more directed anticancer therapy for SCC and AC patients. The first four of them are drug targets for chemotherapy and immunotherapy of esophageal cancer and involved in pharmacokinetics and pharmacodynamics pathways. Research identified novel DEGs in SCC and AC, and detected four potential drug targeted genes (ERBB3, ATP7B, ABCC3, and GALNT14) and five drug-related genes.
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Affiliation(s)
- Aneta Polewko-Klim
- Institute of Computer Science, University in Bialystok, Białystok, Poland
| | - Sibo Zhu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Weicheng Wu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
| | - Yijing Xie
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
| | - Ning Cai
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
| | - Kexun Zhang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
| | - Zhen Zhu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
| | - Tao Qing
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
| | - Ziyu Yuan
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
| | - Kelin Xu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
| | - Tiejun Zhang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
| | - Ming Lu
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Weimin Ye
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Xingdong Chen
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Chen Suo
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Fudan-Taizhou Institute of Health Sciences, Taizhou, China
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, China
| | - Witold R. Rudnicki
- Institute of Computer Science, University in Bialystok, Białystok, Poland
- Computational Centre, University of Bialystok, Białystok, Poland
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16
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Marczyk M, Gunasekharan V, Casadevall D, Qing T, Foldi J, Sehgal R, Shan NL, Blenman KRM, O'Meara TA, Umlauf S, Surovtseva YV, Muthusamy V, Rinehart J, Perry RJ, Kibbey R, Hatzis C, Pusztai L. Comprehensive Analysis of Metabolic Isozyme Targets in Cancer. Cancer Res 2022; 82:1698-1711. [PMID: 35247885 PMCID: PMC10883296 DOI: 10.1158/0008-5472.can-21-3983] [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: 12/29/2021] [Revised: 02/07/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022]
Abstract
Metabolic reprogramming is a hallmark of malignant transformation, and loss of isozyme diversity (LID) contributes to this process. Isozymes are distinct proteins that catalyze the same enzymatic reaction but can have different kinetic characteristics, subcellular localization, and tissue specificity. Cancer-dominant isozymes that catalyze rate-limiting reactions in critical metabolic processes represent potential therapeutic targets. Here, we examined the isozyme expression patterns of 1,319 enzymatic reactions in 14 cancer types and their matching normal tissues using The Cancer Genome Atlas mRNA expression data to identify isozymes that become cancer-dominant. Of the reactions analyzed, 357 demonstrated LID in at least one cancer type. Assessment of the expression patterns in over 600 cell lines in the Cancer Cell Line Encyclopedia showed that these reactions reflect cellular changes instead of differences in tissue composition; 50% of the LID-affected isozymes showed cancer-dominant expression in the corresponding cell lines. The functional importance of the cancer-dominant isozymes was assessed in genome-wide CRISPR and RNAi loss-of-function screens: 17% were critical for cell proliferation, indicating their potential as therapeutic targets. Lists of prioritized novel metabolic targets were developed for 14 cancer types; the most broadly shared and functionally validated target was acetyl-CoA carboxylase 1 (ACC1). Small molecule inhibition of ACC reduced breast cancer viability in vitro and suppressed tumor growth in cell line- and patient-derived xenografts in vivo. Evaluation of the effects of drug treatment revealed significant metabolic and transcriptional perturbations. Overall, this systematic analysis of isozyme expression patterns elucidates an important aspect of cancer metabolic plasticity and reveals putative metabolic vulnerabilities. SIGNIFICANCE This study exploits the loss of metabolic isozyme diversity common in cancer and reveals a rich pool of potential therapeutic targets that will allow the repurposing of existing inhibitors for anticancer therapy. See related commentary by Kehinde and Parker, p. 1695.
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Affiliation(s)
- Michal Marczyk
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | | | - David Casadevall
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Tao Qing
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Julia Foldi
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Raghav Sehgal
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Naing Lin Shan
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Kim R M Blenman
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Tess A O'Meara
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Sheila Umlauf
- Yale Center for Molecular Discovery, Yale University, West Haven, Connecticut
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, Connecticut
| | - Viswanathan Muthusamy
- Center for Precision Cancer Modeling, Yale School of Medicine, New Haven, Connecticut
| | - Jesse Rinehart
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Rachel J Perry
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Richard Kibbey
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Christos Hatzis
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Lajos Pusztai
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
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17
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Mao JY, Xiao J, Liu X, Qing T, Xu H. Emulating Coworkers: How and When Coworker Ideation Facilitates Employee Ideation. Creativity Research Journal 2022. [DOI: 10.1080/10400419.2022.2049533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Jih-Yu Mao
- School of Business Administration, Faculty of Business Administration, Southwestern University of Finance and Economics
| | | | - Xin Liu
- Renmin Business School, Renmin University of China
| | - Tao Qing
- School of Business Administration, Faculty of Business Administration, Southwestern University of Finance and Economics
| | - Hongling Xu
- School of Business Administration, Faculty of Business Administration, Southwestern University of Finance and Economics
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18
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Rozenblit M, Qing T, Ye Y, Zhao H, Hofstatter E, Singh V, Reisenbichler E, Murray M, Pusztai L. Abstract P3-07-01: Young women with breast cancer and high risk family history but no high penetrance germline mutations have a higher load of rare high functional impact germline variants in cancer relevant genes. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p3-07-01] [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
Background: There is an incomplete understanding of why some women develop breast cancer 20-25 years earlier than the majority of women. Only 30-40% of women with high risk family history are found to have known cancer predisposing mutations. This phenomenon is referred to as “missing heredity”. We hypothesize that women with high-risk cancer family history but no known high penetrance cancer predisposing mutations who develop breast cancer at a young age have a higher deleterious load of germline high functional impact (gHFI) single nucleotide variants in cancer relevant genes. Methods: 94 women diagnosed with breast cancer age <50 with high risk cancer family history who tested negative for germline cancer predisposing mutations were identified at Yale Cancer Prevention Clinic (YCPC). 149 controls, healthy Caucasian individuals age > 65 with no cancer family history were identified from Yale Generations project. Whole-exome sequencing (WES) was performed on peripheral blood from 94 cases, 149 controls, and 42 matched tumors. WES data was analyzed from 1,112 female breast cancer cases with first-degree breast cancer family history and 50,887 healthy women without breast cancer family history from UKBiobank. Rare gHFI variants were defined as nonsynonymous variants predicted as deleterious in MetaSVM, or loss-of-function in gnormAD, or pathogenic in ClinVar database with mutation frequency <0.01. Hallmark genes were 1,558 genes involved in 21 cancer pathways and 83 cancer predisposition genes (CPGs). 468 somatic cancer genes were used. Rare gHFI in cases vs controls were compared using SNP-set (Sequence) Kernel Association Test (SKAT). Somatic mutations in YCPC vs 652 ER+ breast cancer TCGA cases were compared using 13/468 cancer genes mutated >5% of cases using Fisher’s exact test. FDRs were calculated using Benjamini & Hochberg. Results: The majority of YCPC patients were Caucasian (78.7%), median age (43.5), with invasive ductal carcinoma (85.1%), ER+PR+HER2- (67.0%). YCPC patients had a higher average burden of rare gHFI variants in cancer hallmark genes (excluding CPGs) compared to controls (p=0.0075, adjusted for race), but did not show a higher germline burden in CPGs. Similarly, UKBiobank breast cancer patients with a family history had a higher germline variant burden in hallmark genes (excluding CPGs) compared to controls (p=0.0368). The main pathways affected by gHFI in the YCPC cohort were adaptive immunity (p=1.61 x 10-8) and extracellular matrix (p=0.0034). Thirty six (87.8%) YCPC matched tumors carried somatic mutations in known cancer related genes. Compared to TCGA, YCPC samples had fewer TP53 mutations (5% vs 17%, FDR = 0.27), but more mutations in CHEK2, GNAQ, APC, and SDHA (FDR<0.028). Conclusions: Our cohort of young women with breast cancer and high risk family history with no known germline high penetrance cancer gene mutations showed a higher burden of germline high functional impact variants in hallmark cancer genes. This higher germline variant burden suggests that the totality of gHFI variants in cancer related genes could explain why these women develop breast cancer at a younger age.
CohortRace (%)AgeCases (N)Control (N)GenesetAverage Case BurdenAverage Case BurdenSKAT testYaleCaucasian (78.7)439414983 CPGs0.27660.30200.56921508 Hallmark4.23404.18790.0075UK BiobankBritish (100)5611125088783 CPGs0.37410.28064.19x10-51508 Hallmark3.36423.33990.0368
Citation Format: Mariya Rozenblit, Tao Qing, Yixuan Ye, Hongyu Zhao, Erin Hofstatter, Vinit Singh, Emily Reisenbichler, Michael Murray, Lajos Pusztai. Young women with breast cancer and high risk family history but no high penetrance germline mutations have a higher load of rare high functional impact germline variants in cancer relevant genes [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 P3-07-01.
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Affiliation(s)
- Mariya Rozenblit
- contributed equally to this work, Yale University, New Haven, CT
| | - Tao Qing
- contributed equally to this work, Yale University, New Haven, CT
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Blenman KRM, Harigopal M, Huang R, Reisenbichler E, Qing T, Ibrahim E, Singh K, Ramkissoon S, Mustimbo R, Ross J, Pusztai L. Abstract P2-08-03: PD-L1 protein expression in relation to Recurrence Score values in early stage ER+HER2- breast cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p2-08-03] [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
Background: There is interest in exploring neoadjuvant chemotherapy + immune checkpoint inhibitor therapy in stage II-III ER+ breast cancer, but there is no information on correlation between PD-L1 expression and Oncotype DX Recurrence Score (RS) or histologic grade that currently inform patient selection for adjuvant/neoadjuvant chemotherapy. The goal of this study was to assess associations between PD-L1 protein expression, RS, tumor grade, and stromal tumor infiltrating lymphocyte (TIL) score in early stage ER+ cancers. Methods:. Formalin fixed surgical pathology blocks of 213 patients who had RS determination as routine care between 2012 and 2017 were retrieved from Yale Pathology. PD-L1 immunohistochemistry was performed with the SP142 assay by Foundation Medicine, cases with ≥1% tumor infiltrating immune cell positivity in the tumor area were considered PD-L1+. TIL scores were determined prospectively as part of this study by breast pathologists following the international TIL scoring guidelines. We compared PD-L1 expression positivity rates across RS (<11, 11-25, >25) and TIL categories (<10%, 10-29%, >30%), and tumor grade using Wilcoxon and Chi-square tests. Multivariate analysis was performed using logistic regression. Results: Patient characteristics are shown in the table below. PD-L1 results were available for 201, and TIL scores for 203 patients. Overall, 53% of cases were PD-L1+, but expression levels were low, among the positive cases only 14% had positivity ≥ 5%. PD-L1 expression was significantly higher among cases with RS>25 (78% PD-L1+, among these 19% had PD-L1+ ≥5%), compared to RS<11 and RS 11-25 which were similar to each other (overall 48% were PD-L1+, among these 10% had PD-L1 ≥ 5%). PD-L1 positivity also correlated significantly with TIL score, tumor grade and T stage (tumor size). Among cancers with TIL ≥ 30%, 92% were PD-L1+ and 59% of these had PD-L1 ≥5% compared to 42% PD-L1+ (4% with PD-L1 ≥5%) among TIL< 10%. Grade 3 cancers also had higher PD-L1 positivity (82%, among these 22% with PD-L1 > 5%) compared to grade 2 (49% PD-L1+) or 1 tumors (48% PD-L1+, all at 1% level). T2 and T3 tumors also had significantly more frequent PD-L1 expression (67% and 83%, respectively) compared to T1 cancers (48%). There was no correlation between PD-L1 expression and age, nodal status or histology. In multivariate analysis including age, grade, tumor size, histology, nodal status, TIL score and RS, only TIL and RS remained as independent predictors of PDL1 positivity.
Conclusions: Approximately half of early stage ER+ breast cancers were PD-L1+ using the SP142 assay, but expression levels are low with only 14% showing ≥ 5% immune cell staining. PD-L1 expression is significantly more frequent and higher in larger tumors (T2, T3), grade 3 cancers, and in cancers with RS >25. PD-L1 expression also correlates with TIL score but not with histologic type, nodal status or age. These findings suggest that the most chemotherapy sensitive (grade 3, RS> 25), larger ER+ cancers may benefit from immunotherapy added to chemotherapy, similar to triple negative cancers.
n (%)PD-L1 positivePD-L1 negativep-value (Chi-sq)Histology0.9IDC151 (71%)7567ILC53 (25%)2723other9 (4%)54Grade0.02174 (35%)33362110 (53%)5152329 (12%)236Tumor Size0.008T1145 (68%)6374T262 (29%)3919T3/T46 (3%)51Nodal Status0.9N0177 (84%)9077N135 (16%)1716Age (years)range 39-850.8≤5036 (17%)1815>50177 (83%)8979Recurrence Score0.003RS <1180 (37%)3443RS 12-2594 (45%)4543RS >2539 (18%)288TIL Count0.0000008<10%159 (78%)678610-29%30 (15%)263≥30%14 (7%)111PDL1positive (≥1%)107 (53%)negative94 (47%)
Citation Format: Kim RM Blenman, Malini Harigopal, Richard Huang, Emily Reisenbichler, Tao Qing, Eiman Ibrahim, Kamaljeet Singh, Shakti Ramkissoon, Roberts Mustimbo, Jeffrey Ross, Lajos Pusztai. PD-L1 protein expression in relation to Recurrence Score values in early stage ER+HER2- 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 P2-08-03.
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Foldi J, Marczyk M, Gunasekharan V, Qing T, Sehgal R, Shan NL, Muthusamy V, Umlau S, Surovtseva YV, Kibbey R, Pusztai L. Abstract P5-17-01: Targeting Acetyl-CoA carboxylase in pre-clinical breast cancer models. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p5-17-01] [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
Background: Cancer cells and normal cells of the same lineage differ in their metabolism. We previously described large scale shifts in isoenzyme distribution between matching cancer and normal tissues and identified Acetyl-coA carboxylase (ACC1/ACACA) as a cancer dominant enzyme that is overexpressed in multiple cancer types. ACC1 catalyzes the initial rate-limiting step in de novo fatty acid synthesis, the conversion of acetyl-CoA to malonyl-CoA. Gene knock-out experiments demonstrated that this enzyme is essential for cancer growth. In this study, we evaluated the in vitro and in vivo efficacy of a small molecule ACC inhibitor, PF05175157 as a potential anticancer drug. This drug has been tested in clinical trials for diabetes, but development was discontinued due to grade 2 thrombocytopenia.Methods: We performed in vitro cytotoxicity assays in 15 breast cancer cell lines and in normal mammary epithelial HMEC cells, examined effect on apoptosis and cell cycle progression, and tested for synergy with alpelisib, docetaxel, doxorubicin, everolimus, iniparib, neratinib and TEPP46 (PKM2 and PKLR activator). We next assessed in vivo single agent activity in a triple negative patient derived (PDX) model (J000102184) in NSGTM mice and in MDAMB468 xenografts implanted into Rag2/IL2RG double knockout mice. We performed RNA sequencing and metabolomic profiling of cells treated with PF05175157 to study metabolic and transcriptomic effects of the drug. Results: PF05175157 induced time and dose dependent growth inhibition in all but 1 of the 15 cancer cell lines. The estimated EC50 after 72h exposure ranged from 0.95 to 76 μg/mL in T47D and BT549 cells, respectively (Cmax of 20 μg/mL can be achieved in human serum). There was no significant inhibitory effect on HMEC cells. In cancer cell lines, the % of apoptotic cells increased from 4% to 8% in BT474 and from 7.7% to 17.8% in MDMBA468 cells upon treatment with the compound, and there was a trend towards G2/M cell cycle arrest in both cell lines after 72 hours of exposure (10μg/mL). In drug combination experiments, PF05175157 added to iniparib, or to the PKM2 activator, TEPP46, decreased cell viability compared to single agent therapies in several cell lines. PF05175157 significantly delayed tumor growth compared to vehicle, when administered orally (20mg/kg gavage BID) in a TNBC PDX model (median tumor volume after 33 days: 334.1 mm3 in PF05175157-treated vs. 490.5 mm3 in methylcellulose-treated mice; p=3.39e-7) and intraperitoneally (20 mg/kg in DMSO) in an MDAMB468 xenograft model (median tumor volume after 40 days: 244.5 mm3 in PF05175157-treated vs. 303.3 mm3 in DMSO-treated mice; p<0.05). Transcriptomic and metabolic profiling of MDAMB468 and BT474 cells treated with 10 ug/ml PF05175157 for 6 and 24 hours revealed activation of immune signaling, epigenetic regulation and DNA damage repair pathways along with down-regulation of a broad range of metabolic pathways. Conclusions: The small molecule ACC inhibitor, PF05175157, has significant single agent in vitro and in vivo growth inhibitory effect on a range of breast cancer cell lines at concentrations that can be achieved in human serum. It showed synergy with iniparib and another metabolic inhibitor (TEPP46). Targeting de novo fatty acid synthesis by inhibiting ACC is a promising therapeutic strategy.
Citation Format: Julia Foldi, Michal Marczyk, Vignesh Gunasekharan, Tao Qing, Raghav Sehgal, Naing Lin Shan, Viswanathan Muthusamy, Sheila Umlau, Yulia V. Surovtseva, Richard Kibbey, Lajos Pusztai. Targeting Acetyl-CoA carboxylase in pre-clinical breast cancer models [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 P5-17-01.
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Affiliation(s)
- Julia Foldi
- Yale University School of Medicine, New Haven, CT
| | - Michal Marczyk
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | | | - Tao Qing
- Yale University School of Medicine, New Haven, CT
| | | | | | | | - Sheila Umlau
- Yale Center for Molecular Discovery, Yale University, New Haven, CT
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Foldi J, Silber A, Reisenbichler E, Singh K, Fischbach N, Persico J, Adelson K, Katoch A, Horowitz N, Lannin D, Chagpar A, Park T, Marczyk M, Frederick C, Burrello T, Ibrahim E, Qing T, Bai Y, Blenman K, Rimm DL, Pusztai L. Author Correction: Neoadjuvant durvalumab plus weekly nab-paclitaxel and dose-dense doxorubicin/cyclophosphamide in triple-negative breast cancer. NPJ Breast Cancer 2022; 8:17. [PMID: 35115541 PMCID: PMC8814070 DOI: 10.1038/s41523-022-00392-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Julia Foldi
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Andrea Silber
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | | | - Kamaljeet Singh
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Neal Fischbach
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Justin Persico
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Kerin Adelson
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Anamika Katoch
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Nina Horowitz
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Donald Lannin
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Anees Chagpar
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Tristen Park
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Michal Marczyk
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA.,Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Courtney Frederick
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Trisha Burrello
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Eiman Ibrahim
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Tao Qing
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Yalai Bai
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Kim Blenman
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Lajos Pusztai
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA.
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Vathiotis IA, Moutafi MK, Divakar P, Aung TN, Qing T, Fernandez A, Yaghoobi V, El-Abed S, Wang Y, Guillaume S, Nuciforo P, Huober J, Di Cosimo S, Kim SB, Harbeck N, Gomez H, Shafi S, Syrigos KN, Fountzilas G, Sotiriou C, Pusztai L, Warren S, Rimm DL. Alpha-smooth Muscle Actin Expression in the Stroma Predicts Resistance to Trastuzumab in Patients with Early-stage HER2-positive Breast Cancer. Clin Cancer Res 2021; 27:6156-6163. [PMID: 34465600 PMCID: PMC8595766 DOI: 10.1158/1078-0432.ccr-21-2103] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 06/08/2021] [Revised: 07/28/2021] [Accepted: 08/25/2021] [Indexed: 12/28/2022]
Abstract
PURPOSE The companion diagnostic test for trastuzumab has not changed much in the last 25 years. We used high-plex digital spatial profiling to identify biomarkers besides HER2 that can help predict response to trastuzumab in HER2-positive breast cancer. EXPERIMENTAL DESIGN Fifty-eight protein targets were measured in three different molecularly defined compartments by the NanoString GeoMx Digital Spatial Profiler (DSP) in a tissue microarray containing 151 patients with breast cancer that received adjuvant trastuzumab as part of the Hellenic Cooperative Oncology Group 10/05 clinical trial. Promising candidate biomarkers were orthogonally validated with quantitative immunofluorescence (QIF). RNA-sequencing data from the Neoadjuvant Lapatinib and/or Trastuzumab Treatment Optimisation Study (NeoALTTO) were accessed to provide independent cohort validation. Disease-free survival (DFS) was the main outcome assessed. Statistical analyses were performed using a two-sided test (α = 0.05) and multiple testing correction (Benjamini-Hochberg method, FDR < 0.1). RESULTS By DSP, high expression of alpha-smooth muscle actin (α-SMA), both in the leukocyte and stromal compartments, was associated with shorter DFS in univariate analysis (P = 0.002 and P = 0.023, respectively). High α-SMA expression in the stroma was validated by QIF after controlling for estrogen receptor and progesterone receptor status [HR, 3.12; 95% confidence interval (CI), 1.12-8.68; P = 0.029] showing recurrence on trastuzumab in the same cohort. In the NeoALTTO cohort, elevated levels of ACTA2 were predictive for shorter DFS in the multivariate analysis (HR, 3.21; 95% CI, 1.14-9.05; P = 0.027). CONCLUSIONS This work identifies α-SMA as a novel, easy-to-implement biomarker of resistance to trastuzumab that may be valuable in settings where trastuzumab is combined with other therapies.
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Affiliation(s)
- Ioannis A Vathiotis
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Myrto K Moutafi
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | | | - Thazin Nwe Aung
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Tao Qing
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Aileen Fernandez
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Vesal Yaghoobi
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | | | | | - Sebastien Guillaume
- Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Paolo Nuciforo
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Jens Huober
- Department of Obstetrics and Gynaecology of the University of Ulm, Ulm, Germany
| | | | - Sung-Bae Kim
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of South Korea
| | - Nadia Harbeck
- Breast Center, Ludwig-Maximilians-University, University Hospital, Munich, Germany
| | - Henry Gomez
- Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru
| | - Saba Shafi
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Konstantinos N Syrigos
- Department of Medicine, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - George Fountzilas
- Aristotle University of Thessaloniki, Thessaloniki, Greece
- German Oncology Center, Limassol, Cyprus
| | - Christos Sotiriou
- Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Lajos Pusztai
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut
| | | | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut.
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
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Mohsen H, Gunasekharan V, Qing T, Seay M, Surovtseva Y, Negahban S, Szallasi Z, Pusztai L, Gerstein MB. Network propagation-based prioritization of long tail genes in 17 cancer types. Genome Biol 2021; 22:287. [PMID: 34620211 PMCID: PMC8496153 DOI: 10.1186/s13059-021-02504-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Received: 04/01/2021] [Accepted: 09/17/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The diversity of genomic alterations in cancer poses challenges to fully understanding the etiologies of the disease. Recent interest in infrequent mutations, in genes that reside in the "long tail" of the mutational distribution, uncovered new genes with significant implications in cancer development. The study of cancer-relevant genes often requires integrative approaches pooling together multiple types of biological data. Network propagation methods demonstrate high efficacy in achieving this integration. Yet, the majority of these methods focus their assessment on detecting known cancer genes or identifying altered subnetworks. In this paper, we introduce a network propagation approach that entirely focuses on prioritizing long tail genes with potential functional impact on cancer development. RESULTS We identify sets of often overlooked, rarely to moderately mutated genes whose biological interactions significantly propel their mutation-frequency-based rank upwards during propagation in 17 cancer types. We call these sets "upward mobility genes" and hypothesize that their significant rank improvement indicates functional importance. We report new cancer-pathway associations based on upward mobility genes that are not previously identified using driver genes alone, validate their role in cancer cell survival in vitro using extensive genome-wide RNAi and CRISPR data repositories, and further conduct in vitro functional screenings resulting in the validation of 18 previously unreported genes. CONCLUSION Our analysis extends the spectrum of cancer-relevant genes and identifies novel potential therapeutic targets.
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Affiliation(s)
- Hussein Mohsen
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT, 06511, USA.
| | | | - Tao Qing
- Breast Medical Oncology, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Montrell Seay
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, 06516, USA
| | - Yulia Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, 06516, USA
| | - Sahand Negahban
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06511, USA
| | - Zoltan Szallasi
- Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, 02115, USA
| | - Lajos Pusztai
- Breast Medical Oncology, Yale School of Medicine, New Haven, CT, 06511, USA.
| | - Mark B Gerstein
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT, 06511, USA.
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06511, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA.
- Department of Computer Science, Yale University, New Haven, CT, 06511, USA.
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Qing T, Wang X, Jun T, Ding L, Pusztai L, Huang KL. Genomic Determinants of Homologous Recombination Deficiency across Human Cancers. Cancers (Basel) 2021; 13:4572. [PMID: 34572800 PMCID: PMC8472123 DOI: 10.3390/cancers13184572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
Germline BRCA1/2 mutations associated with HRD are clinical biomarkers for sensitivity to poly-ADP ribose polymerase inhibitors (PARPi) treatment in breast, ovarian, pancreatic, and prostate cancers. However, it remains unclear whether other mutations may also lead to HRD and PARPi sensitivity across a broader range of cancer types. Our goal was to determine the germline or somatic alterations associated with the HRD phenotype that might therefore confer PARPi sensitivity. Using germline and somatic genomic data from over 9000 tumors representing 32 cancer types, we examined associations between HRD scores and pathogenic germline variants, somatic driver mutations, and copy number deletions in 30 candidate genes involved in homologous recombination. We identified several germline and somatic mutations (e.g., BRCA1/2, PALB2, ATM, and ATR mutations) associated with HRD phenotype in ovarian, breast, pancreatic, stomach, bladder, and lung cancer. The co-occurrence of germline BRCA1 variants and somatic TP53 mutations was significantly associated with increasing HRD in breast cancer. Notably, we also identified multiple somatic copy number deletions associated with HRD. Our study suggests that multiple cancer types include tumor subsets that show HRD phenotype and should be considered in the future clinical studies of PARPi and synthetic lethality strategies exploiting HRD, which can be caused by a large number of genomic alterations.
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Affiliation(s)
- Tao Qing
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT 06511, USA;
| | - Xinfeng Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China;
| | - Tomi Jun
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Li Ding
- Department of Medicine, McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63110, USA;
- Department of Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Lajos Pusztai
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT 06511, USA;
| | - Kuan-Lin Huang
- Department of Genetics and Genomic Sciences, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Qing T, Liu Z, Tang Y, Hu H, Zhang L, Chen S. Effects of Automation for Emergency Operating Procedures on Human Performance in a Nuclear Power Plant. Health Phys 2021; 121:261-270. [PMID: 34261893 PMCID: PMC8300853 DOI: 10.1097/hp.0000000000001445] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
ABSTRACT The digitization of the control systems in the main control room of a nuclear power plant has changed the operators' role in coping with accidents and has thus brought about new human factor problems. This article focuses on the procedures that are used for guiding the emergency operating procedures in a nuclear power plant, and experimentally investigates the effects of the digitization of procedures on operators' mental workload and situation awareness. In these experiments, the procedures at three different levels of automation, namely, paper-based procedures (PBPs), electronic procedures (EPs), and computer-based procedures (CBPs), are used as the independent variables. According to the experimental results, using these procedures at a high level of automation enables the operator to exhibit favorable operational performance with a decreased mental workload; however, the operator's situation awareness (SA) is decreased. The research results presented here can provide a reference level for optimally setting the level of automation of the emergency operating procedures in a nuclear power plant and provide support for the optimization of a corresponding HRA (Human Reliability Analysis) model.
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Affiliation(s)
| | - Zhaopeng Liu
- State Key Laboratory of Nuclear Power Safety Monitoring Technology and Equipment, China Nuclear Power Engineering Co., Ltd, Shenzhen of Guangdong Province, P.R. China
| | - Yaqin Tang
- Institute of Human Factors & Safety Engineering, Hunan Institute of Technology, Hengyang, P.R. China
| | - Hong Hu
- Institute of Human Factors & Safety Engineering, Hunan Institute of Technology, Hengyang, P.R. China
| | - Li Zhang
- Institute of Human Factors & Safety Engineering, Hunan Institute of Technology, Hengyang, P.R. China
| | - Shuai Chen
- School of Nuclear Science and Technology, University of South China, Hengyang, P.R. China
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Li F, Zhao D, Qing T, Kuang Y. Identification of occupational stress factors of commissioning workers in nuclear power plants based on a bottom-up survey design and factor analysis. J NUCL SCI TECHNOL 2021. [DOI: 10.1080/00223131.2020.1858988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Faquan Li
- State Key Laboratory of Nuclear Power Safety Monitoring Technology and Equipment, Shenzhen, Guangdong, People’s Republic of China
- Institute of Human Factors & Safety Engineering, Hunan Institute of Technology, Hengyang, Hunan, People’s Republic of China
| | - Dejun Zhao
- State Key Laboratory of Nuclear Power Safety Monitoring Technology and Equipment, Shenzhen, Guangdong, People’s Republic of China
- China Nuclear Power Engineering Co.,Ltd, Shenzhen, Guangdong, People’s Republic of China
| | - Tao Qing
- Institute of Human Factors & Safety Engineering, Hunan Institute of Technology, Hengyang, Hunan, People’s Republic of China
| | - Yuan Kuang
- School of Nuclear Science and Technology, University of South China, Hengyang, Hunan, People’s Republic of China
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Blenman K, Marczyk M, Qing T, O'Meara T, Yaghoobi V, Pelekanou V, Bai Y, Reisenbichler E, Li X, Gunasekharan V, Ibrahim EY, Rimm DL, Pusztai L, Cole K. Characterization of the tumor immune microenvironment of triple-negative breast cancer (TNBC) patients who self-identify as African American (AA) or non-African American (NonAA). J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.564] [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: 11/20/2022] Open
Abstract
564 Background: What tumor biological differences, if any, contribute to the higher incidence and worse prognosis of triple negative breast cancer (TNBC) in African American (AA) compared to NonAA patients are unknown. We hypothesized that differences in the tumor immune microenvironment may contribute to the outcome disparities. The purpose of this study was to characterize and compare the immune microenvironment of TNBC between patients self-identified as NonAA or AA. Methods: Formalin fixed paraffin embedded surgically resected cancer and paired normal tissues collected before any systemic therapy and the corresponding clinical data were collected for NonAA (n = 56) and AA (n = 54) stage I-III TNBC treated at Yale Cancer Center between 2000-2017. The two cohorts were matched for clinical stage, age of diagnosis, and year of diagnosis. We performed somatic and germline whole exome sequencing (WES), bulk RNA sequencing, and immunohistochemistry to assess PD-L1 expression (SP142). Stromal tumor infiltrating lymphocytes (sTILs) were assessed on H&E slides. Mutation load, mutation frequencies, and gene expression differences were compared at gene and pathway level. Immune cell composition was estimated through gene expression deconvolution analyses (TIDE). Results: Tumor mutational burden was similar between the two cohorts. At gene level, few genes had significantly different somatic mutation frequencies, or differential mRNA expression between AA and NonAA samples. Pathway level alterations showed inflammation, immunity (adaptive; innate), antigen presentation, and allograft rejection pathways were more affected by somatic mutations in AA samples. The affected genes differed from cancer to cancer and were not recurrent and therefore were missed at gene level analysis. Gene set enrichment and co-expression analysis also showed higher immune related pathway expression in AA samples. Unsupervised co-expression cluster analysis confirmed coordinated overexpression of genes involved in immunity, inflammation, and cytokine/chemokine signaling in AA patients. Two immunotherapy response predictive signatures, immune inflamed and the IFNG as well as sTILs score and PD-L1 positivity were also higher in AA samples. These findings raise the possibility that immune checkpoint inhibitors might be particularly effective in AA patients. In NonAA samples, the EMT transition, angiogenesis, adipogenesis, myogenesis, fatty acid metabolism, TGFβ signaling, UV-response, and hypoxia pathways were overexpressed. TIDE analysis suggested higher levels of TAM M2, overall TIDE score, and the Immune Exclusion score in NonAA samples. Conclusions: TNBC in AA patients more frequently harbor somatic mutations in genes involved with immune functions and overexpress immune and inflammatory genes compared to NonAA patients.
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Qing T, Jun T, Lindblad KE, Lujambio A, Marczyk M, Pusztai L, Huang KL. Diverse immune response of DNA damage repair-deficient tumors. Cell Rep Med 2021; 2:100276. [PMID: 34095878 PMCID: PMC8149377 DOI: 10.1016/j.xcrm.2021.100276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/26/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022]
Abstract
Tumors with DNA damage repair (DDR) deficiency accumulate genomic alterations that may serve as neoantigens and increase sensitivity to immune checkpoint inhibitor. However, over half of DDR-deficient tumors are refractory to immunotherapy, and it remains unclear which mutations may promote immunogenicity in which cancer types. We integrate deleterious somatic and germline mutations and methylation data of DDR genes in 10,080 cancers representing 32 cancer types and evaluate the associations of these alterations with tumor neoantigens and immune infiltrates. Our analyses identify DDR pathway mutations that are associated with higher neoantigen loads, adaptive immune markers, and survival outcomes of immune checkpoint inhibitor-treated animal models and patients. Different immune phenotypes are associated with distinct types of DDR deficiency, depending on the cancer type context. The comprehensive catalog of immune response-associated DDR deficiency may explain variations in immunotherapy outcomes across DDR-deficient cancers and facilitate the development of genomic biomarkers for immunotherapy. Tumor immunogenicity is associated with DNA damage repair deficiencies (DDR-ds) The immunogenicity of DDR alterations varies by pathways and cancer types DDR-d tumors with high immune infiltrates correlate with immunotherapy response
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Affiliation(s)
- Tao Qing
- Breast Medical Oncology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Tomi Jun
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Katherine E Lindblad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michal Marczyk
- Breast Medical Oncology, Yale School of Medicine, New Haven, CT 06511, USA.,Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Lajos Pusztai
- Breast Medical Oncology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Kuan-Lin Huang
- Department of Genetics and Genomic Sciences, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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29
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Zheng Y, Li B, Pan D, Cao J, Zhang J, Wang X, Li X, Hou W, Bao D, Ren L, Yang J, Wang S, Qiu Y, Zhou F, Liu Z, Zhu S, Zhang L, Qing T, Wang Y, Yu Y, Wu J, Hu X, Shi L. Functional consequences of a rare missense BARD1 c.403G>A germline mutation identified in a triple-negative breast cancer patient. Breast Cancer Res 2021; 23:53. [PMID: 33933153 PMCID: PMC8088670 DOI: 10.1186/s13058-021-01428-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/18/2020] [Accepted: 04/13/2021] [Indexed: 11/30/2022] Open
Abstract
We identified a rare missense germline mutation in BARD1 (c.403G>A or p.Asp135Asn) as pathogenic using integrated genomics and transcriptomics profiling of germline and tumor samples from an early-onset triple-negative breast cancer patient who later was administrated with a PARP inhibitor for 2 months. We demonstrated in cell and mouse models that, compared to the wild-type, (1) c.403G>A mutant cell lines were more sensitive to irradiation, a DNA damage agent, and a PARP inhibitor; (2) c.403G>A mutation inhibited interaction between BARD1 and RAD51 (but not BRCA1); and (3) c.403G>A mutant mice were hypersensitive to ionizing radiation. Our study shed lights on the clinical interpretation of rare germline mutations of BARD1.
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Affiliation(s)
- Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bingying Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Dejing Pan
- Cambridge-Suda Genomic Resource Center and Jiangsu Key Laboratory of Neuropsychiatric Diseases Research, Soochow University, Suzhou, China
| | - Jun Cao
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jian Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaolin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xiangnan Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ding Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Shangzi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yangyang Qiu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fei Zhou
- Cambridge-Suda Genomic Resource Center and Jiangsu Key Laboratory of Neuropsychiatric Diseases Research, Soochow University, Suzhou, China
| | - Zhiwei Liu
- Cambridge-Suda Genomic Resource Center and Jiangsu Key Laboratory of Neuropsychiatric Diseases Research, Soochow University, Suzhou, China
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Lei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Tao Qing
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China.
| | - Jiaxue Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Xichun Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China. .,Human Phenome Institute, Fudan University, Shanghai, China. .,Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai, China.
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30
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Chen S, Zhang L, Qing T, Liu X. Use of Bayesian networks and improved SPAR-H for quantitative analysis of human reliability during severe accidents mitigation process in nuclear power plant. J NUCL SCI TECHNOL 2021. [DOI: 10.1080/00223131.2021.1915893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Shuai Chen
- College of Nuclear Science and Technology, University of South China, Hengyang, Hunan, People's Republic of China
| | - Li Zhang
- College of Nuclear Science and Technology, University of South China, Hengyang, Hunan, People's Republic of China
- Institute of Human Factor Engineering&Safety Management, Hunan Institute of Technology, Hengyang, Hunan, People's Republic of China
| | - Tao Qing
- Institute of Human Factor Engineering&Safety Management, Hunan Institute of Technology, Hengyang, Hunan, People's Republic of China
| | - Xueyang Liu
- Institute of Human Factor Engineering&Safety Management, Hunan Institute of Technology, Hengyang, Hunan, People's Republic of China
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31
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Foldi J, Silber A, Reisenbichler E, Singh K, Fischbach N, Persico J, Adelson K, Katoch A, Horowitz N, Lannin D, Chagpar A, Park T, Marczyk M, Frederick C, Burrello T, Ibrahim E, Qing T, Bai Y, Blenman K, Rimm DL, Pusztai L. Neoadjuvant durvalumab plus weekly nab-paclitaxel and dose-dense doxorubicin/cyclophosphamide in triple-negative breast cancer. NPJ Breast Cancer 2021; 7:9. [PMID: 33558513 PMCID: PMC7870853 DOI: 10.1038/s41523-021-00219-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/23/2020] [Indexed: 12/31/2022] Open
Abstract
The goal of this Phase I/II trial is to assess the safety and efficacy of administering durvalumab concurrent with weekly nab-paclitaxel and dose-dense doxorubicin/cyclophosphamide (ddAC) neoadjuvant therapy for stages I-III triple-negative breast cancer. The primary endpoint is pathologic complete response (pCR:ypT0/is, ypN0). The response was correlated with PDL1 expression and stromal tumor-infiltrating lymphocytes (sTILs). Two dose levels of durvalumab (3 and 10 mg/kg) were assessed. PD-L1 was assessed using the SP263 antibody; ≥1% immune and tumor cell staining was considered positive; sTILs were calculated as the area occupied by mononuclear inflammatory cells over the total intratumoral stromal area. 59 patients were evaluable for toxicity and 55 for efficacy in the Phase II study (10 mg/kg dose). No dose-limiting toxicities were observed in Phase I. In Phase II, pCR rate was 44% (95% CI: 30-57%); 18 patients (31%) experienced grade 3/4 treatment-related adverse events (AE), most frequently neutropenia (n = 4) and anemia (n = 4). Immune-related grade 3/4 AEs included Guillain-Barre syndrome (n = 1), colitis (n = 2), and hyperglycemia (n = 2). Of the 50 evaluable patients for PD-L1, 31 (62%) were PD-L1 positive. pCR rates were 55% (95% CI: 0.38-0.71) and 32% (95% CI: 0.12-0.56) in the PD-L1 positive and negative groups (p = 0.15), respectively. sTIL counts were available on 52 patients and were significantly higher in the pCR group (p = 0.0167). Concomitant administration of durvalumab with sequential weekly nab-paclitaxel and ddAC neoadjuvant chemotherapy resulted in a pCR rate of 44%; pCR rates were higher in sTIL-high cancers.
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Affiliation(s)
- Julia Foldi
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Andrea Silber
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | | | - Kamaljeet Singh
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Neal Fischbach
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Justin Persico
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Kerin Adelson
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Anamika Katoch
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Nina Horowitz
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Donald Lannin
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Anees Chagpar
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Tristen Park
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Michal Marczyk
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Courtney Frederick
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Trisha Burrello
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Eiman Ibrahim
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Tao Qing
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Yalai Bai
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Kim Blenman
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Lajos Pusztai
- Section of Medical Oncology, Yale School of Medicine, New Haven, CT, USA.
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32
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Liu Y, Zhang X, Zhang G, Jiang J, Zhang L, Hu H, Qing T, Zou Y, Yang D, Xi L, Tang F, Jia M, Wu Y, Liu Z. Research on the Cognitive Reliability Model of DCS+SOP in the Ling’ao Phase II Nuclear Power Plant’s Main Control Room. NUCL TECHNOL 2021. [DOI: 10.1080/00295450.2020.1733376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Yanzi Liu
- China Nuclear Power Design Company LTD, State Key Laboratory of Nuclear Power Safety Monitoring Technology and Equipment, Shenzhen, Guangdong Province, China, 518045
| | - Xuegang Zhang
- China Nuclear Power Design Company LTD, State Key Laboratory of Nuclear Power Safety Monitoring Technology and Equipment, Shenzhen, Guangdong Province, China, 518045
| | - Gang Zhang
- China Nuclear Power Design Company LTD, State Key Laboratory of Nuclear Power Safety Monitoring Technology and Equipment, Shenzhen, Guangdong Province, China, 518045
| | - Jianjun Jiang
- Hunan Institute of Technology, School of Safety and Environment Engineering, Heng Yang, HuNan Province, China, 421002
| | - Li Zhang
- Hunan Institute of Technology, School of Safety and Environment Engineering, Heng Yang, HuNan Province, China, 421002
| | - Hong Hu
- Hunan Institute of Technology, School of Safety and Environment Engineering, Heng Yang, HuNan Province, China, 421002
| | - Tao Qing
- Hunan Institute of Technology, School of Safety and Environment Engineering, Heng Yang, HuNan Province, China, 421002
| | - Yanhua Zou
- Hunan Institute of Technology, School of Safety and Environment Engineering, Heng Yang, HuNan Province, China, 421002
| | - Dan Yang
- Hunan Institute of Technology, School of Safety and Environment Engineering, Heng Yang, HuNan Province, China, 421002
| | - Liaozi Xi
- Hunan Institute of Technology, School of Safety and Environment Engineering, Heng Yang, HuNan Province, China, 421002
| | - Fan Tang
- Hunan Institute of Technology, School of Safety and Environment Engineering, Heng Yang, HuNan Province, China, 421002
| | - Ming Jia
- China Nuclear Power Design Company LTD, State Key Laboratory of Nuclear Power Safety Monitoring Technology and Equipment, Shenzhen, Guangdong Province, China, 518045
| | - Yiqian Wu
- China Nuclear Power Design Company LTD, State Key Laboratory of Nuclear Power Safety Monitoring Technology and Equipment, Shenzhen, Guangdong Province, China, 518045
| | - Zhiyao Liu
- China Nuclear Power Design Company LTD, State Key Laboratory of Nuclear Power Safety Monitoring Technology and Equipment, Shenzhen, Guangdong Province, China, 518045
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Han L, Liu F, Li Q, Qing T, Zhai Z, Xia Z, Li J. The Efficacy of Beta-Blockers in Patients With Long QT Syndrome 1-3 According to Individuals' Gender, Age, and QTc Intervals: A Network Meta-analysis. Front Pharmacol 2021; 11:579525. [PMID: 33381033 PMCID: PMC7768040 DOI: 10.3389/fphar.2020.579525] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 07/02/2020] [Accepted: 11/13/2020] [Indexed: 02/02/2023] Open
Abstract
Long QT syndrome (LQTS) is an arrhythmic heart disease caused by congenital genetic mutations, and results in increased occurrence rates of polymorphic ventricular tachyarrhythmias and sudden cardiac death (SCD). Clinical evidence from numerous previous studies suggested that beta blockers (BBs), including atenolol, propranolol, metoprolol, and nadolol, exhibit different efficacies for reducing the risk of cardiac events (CEs), such as syncope, arrest cardiac arrest (ACA), and SCD, in patients with LQTS. In this study, we identified relevant studies in MEDLINE, PubMed, embase, and Cochrane databases and performed a meta-analysis to assess the relationship between the rate of CEs and LQTS individuals with confounding variables, including different gender, age, and QTc intervals. Moreover, a network meta-analysis was not only established to evaluate the effectiveness of different BBs, but also to provide the ranked efficacies of BBs treatment for preventing the recurrence of CEs in LQT1 and LQT2 patients. In conclusion, nadolol was recommended as a relatively effective strategy for LQT2 in order to improve the prognosis of patients during a long follow-up period.
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Affiliation(s)
- Lu Han
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Fuxiang Liu
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qing Li
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tao Qing
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhenyu Zhai
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zirong Xia
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Juxiang Li
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Xu S, Zhang Y, Zhang B, Qing T, Jin J. Does Inconsistent Social Support Matter? The Effects of Social Support on Work Absorption Through Relaxation at Work. Front Psychol 2020; 11:555501. [PMID: 33343441 PMCID: PMC7744690 DOI: 10.3389/fpsyg.2020.555501] [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: 04/25/2020] [Accepted: 11/02/2020] [Indexed: 11/25/2022] Open
Abstract
Drawing upon the conservation of resources theory and social exchange theory, we examined the effects of family supportive supervisor behavior (FSSB) and family support (FS) on work absorption at the within- and between-person levels. A 10-day study of 91 workers using 710 observations was employed. At the within-person level, the results suggested that daily relaxation at work mediated the relationships between daily FS, daily shifts in FS, and daily work absorption. However, at the between-person level, the results revealed that chronic relaxation at work mediated the relation between the average level of FSSB/FS and chronic work absorption. We conclude that FSSB/FS plays a vital role in relaxation at work and work absorption at the within- and between-person levels.
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Affiliation(s)
- Shan Xu
- School of Business Administration, Southwestern University of Finance and Economics, Chengdu, China
| | - Youxin Zhang
- School of Business Administration, Southwestern University of Finance and Economics, Chengdu, China
| | - Bingran Zhang
- School of Business Administration, Southwestern University of Finance and Economics, Chengdu, China
| | - Tao Qing
- School of Business Administration, Southwestern University of Finance and Economics, Chengdu, China
| | - Jiafei Jin
- School of Management, Harbin Institute of Technology, Harbin, China
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Qing T, Zheng-Ji J, Xiao-Jian L, Xiao-Yong R, Yan HE. [Study on endpoint determination and process analysis of tablet coating based on near infrared spectroscopy]. Zhongguo Zhong Yao Za Zhi 2020; 45:4625-4632. [PMID: 33164426 DOI: 10.19540/j.cnki.cjcmm.20200810.301] [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: 11/18/2022]
Abstract
To conduct endpoint determination of tablet coating and analyze coating process by near-infrared spectroscopy(NIRS). Firstly, the layered k-fold cross validation was used to discuss the optimal combination of spectral interval and preprocessing method, and the optimal result was used as the modeling condition. Secondly, in above condition, the qualitative model was proposed based on the throught of principal component analysis(PCA) and confidence interval, this model and the conformity test model were established respectively in this study, and the discrimination performance of coating eligibility was calculated. Then, the internal cross validation was used to obtain the coating end-point conforming rate as the threshold for determining the endpoint of tablet coating. Finally, the results of predicted conforming rate and discrimination parameters for the test samples of different batches were calculated with the above models, which were then further used for end-point detection and process analysis. As compared with the conformity test, this method proposed in this study was more accurate and stable in determining the coating conformity, and the coating endpoint can be accurately determined when 95% of the eligibility rate was used as the discriminant threshold. Meanwhile, in the process analysis, the change trend of the process parameters(model discrimination parameters, prediction conforming rate) was basically consistent with that in the conformity test. The results indicate that the method proposed in this study has a good and stable performance, which can be used to determine the endpoint of coating and analyze the process. It is of great significance to reduce the difference between batches and improve the product consistency. Meanwhile, this research method also lays a foundation for the future researches by online near infrared measurements.
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Affiliation(s)
- Tao Qing
- Jiangxi University of Traditional Chinese Medicine Nanchang 330004, China
| | - Jin Zheng-Ji
- Jiangxi University of Traditional Chinese Medicine Nanchang 330004, China
| | - Luo Xiao-Jian
- Jiangxi University of Traditional Chinese Medicine Nanchang 330004, China the National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine Nanchang 330006, China
| | - Rao Xiao-Yong
- Jiangxi University of Traditional Chinese Medicine Nanchang 330004, China the National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine Nanchang 330006, China
| | - H E Yan
- Jiangxi University of Traditional Chinese Medicine Nanchang 330004, China
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Rediti M, Venet D, Rothé F, Qing T, Maetens M, Bradbury I, Izquierdo MA, Cosimo SD, Hilbers F, Bajji M, Harbeck N, Untch M, Rimm DL, Chia S, Liu MC, Saura C, Huober J, Nuciforo P, Salgado R, Loi S, Pusztai L, Sotiriou C. Abstract 1998: Predictive and prognostic role of T- and B-cell receptor repertoire in HER2-positive breast cancer: An analysis of the NeoALTTO clinical trial. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1998] [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
Background: Disease relapse is observed in a significant proportion of HER2-positive breast cancer (BC) patients with residual disease (RD) after neoadjuvant treatment, as well as in a subgroup of those achieving pathological complete response (pCR). As the host immune response plays a key role in modulating the activity of anti-HER2 agents, we investigated the association of T- and B-cell receptor (TCR and BCR) repertoires with pCR and event-free survival (EFS) in the NeoALTTO phase 3 trial.
Methods: RNA sequencing (RNAseq) data from baseline tumor biopsies were available for 254 patients out of the 455 enrolled in the study. Among those, 166 did not achieve a pCR defined as ypT0/is. Matched RNAseq data from RD samples were available for 43 cases. TCR/BCR repertoires were extracted from RNAseq data using the MiXCR software. TCR and BCR read counts, number of clones, evenness, Shannon entropy, Gini index, length of the complementarity determining region 3, top and second top clone proportion were evaluated. Survival analysis was performed using univariate and multivariate (adjusted for tumor size, nodal status, grade, estrogen receptor [ER] status, age and treatment arm) Cox proportional hazard models, while logistic regressions were used for pCR. False discovery rate (FDR) was obtained using Benjamini & Hochberg method.
Results: Baseline TCR top (odds ratio [OR]=0.63 [95% CI 0.46-0.87], FDR=0.021) and second top (OR=0.57 [0.41-0.79], FDR=0.004) clone proportion were significantly associated with a lower probability of achieving pCR in the multivariate analysis. BCR evenness (hazard ratio [HR]=1.5 [1.2-2], FDR=0.015) and Gini index (HR=0.66 [0.52-0.85], FDR=0.015) were significantly associated with EFS in the multivariate analysis. In residual disease, BCR evenness and Gini index showed a similar trend in the EFS univariate analysis, while TCR read counts, number of clones, and entropy were associated with lower HR (P<0.05), although FDR were borderline significant (0.05<FDR<0.1). A model to predict EFS including baseline BCR evenness, ER status, stromal tumor-infiltrating lymphocyte level, and pCR was able to identify 3 groups with good, intermediate and poor prognosis (Kaplan-Meier 5-year EFS rates of 95%, 80% and 58%, respectively). Of note, about 63%, 45% and 12% of the patients achieved a pCR in the three prognostic groups, respectively.
Conclusions: In the NeoALTTO trial, the presence of an evenly distributed BCR repertoire was associated with worse EFS. A model integrating baseline immune-related and clinical features was able to identify patients with excellent prognosis despite RD or, conversely, with poor prognosis after pCR. We envision that our model has the potential to allow the personalization of post-operative treatment strategies after both pCR and RD in HER2-positive BC. Further validation of our findings is warranted.
Citation Format: Mattia Rediti, David Venet, Françoise Rothé, Tao Qing, Marion Maetens, Ian Bradbury, Miguel A. Izquierdo, Serena Di Cosimo, Florentine Hilbers, Mohammed Bajji, Nadia Harbeck, Michael Untch, David L. Rimm, Stephen Chia, Minetta C. Liu, Cristina Saura, Jens Huober, Paolo Nuciforo, Roberto Salgado, Sherene Loi, Lajos Pusztai, Christos Sotiriou. Predictive and prognostic role of T- and B-cell receptor repertoire in HER2-positive breast cancer: An analysis of the NeoALTTO clinical trial [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1998.
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Affiliation(s)
| | | | | | - Tao Qing
- 2Yale Cancer Center, New Haven, CT
| | | | - Ian Bradbury
- 4Frontier Science Scotland, Kingussie, United Kingdom
| | | | | | | | | | - Nadia Harbeck
- 8Ludwig-Maximilians-Universitat Munich, Munich, Germany
| | | | | | - Stephen Chia
- 11BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Cristina Saura
- 13Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Paolo Nuciforo
- 13Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Sherene Loi
- 15Peter MacCallum Cancer Centre, Melbourne, Australia
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Jun T, Qing T, Samstein R, Cordon-Cardo C, Pusztai L, Huang KL. Abstract 2226: Precise stratification of immunotherapy outcomes using response-associated somatic mutations. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-2226] [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
Background: Immune checkpoint inhibitors (ICIs) have demonstrated efficacy in a variety of cancer types. However, enhanced predictors of response are needed to identify patients who are likely to respond, while sparing others from unnecessary toxicity. Predictors of response have been identified, including tumor mutation burden (TMB), microsatellite instability (MSI) and PD-L1 expression. Studies looking for somatic mutations associated with ICI response have thus far been limited to single cancer types. Here, we used a clinical-genomic database combining ICI treatment outcomes with next-generation sequencing of tumors to identify somatic mutations associated with ICI response across 12 cancer types.
Methods and Results: The cohort consisted 1,525 patients with 12 cancer types, derived from the cohort published by Samstein et al. (Nature Genetics, 2019). All patients had received at least one dose of an ICI (anti-PD-1/PD-L1, anti-CTLA-4 or both) and had a next-generation sequencing panel performed on matched tumor and normal tissue to identify somatic mutations. Using multivariable Cox regression–stratified by cancer type and including age, sex, ICI type, and TMB as covariates–we identified 14 ICI-response associated genes (IRAGs) across 6 cancer types. We verified that these IRAGs were predictive rather than prognostic; they were not associated with overall survival in the non-ICI-treated TCGA cohort. In order to determine whether these IRAGs could be used in conjunction with TMB or MSI to more precisely predict ICI outcomes, we stratified the cohort by MSI and TMB status and repeated the regression analysis. MSI-H was defined as MSIsensor score ≥ 10, while TMB-H was defined as the top 20th percentile within each cancer type. When stratifying by MSI status, we found that RNF43 was independently associated with improved survival among MSI-H COADREAD patients, while 11 IRAGs were associated with worse outcomes in MSI-L tumors. When stratifying by both MSI and TMB status, we found that among TMB-L/MSI-L patients, 3 IRAGs in BLCA and 2 in LUAD were independently associated with worse outcomes.
Conclusions: Our results suggest that these IRAGs could be used in combination with MSI and/or TMB status to more precisely predict ICI treatment outcomes. Validation in other ICI-treated cohorts should be pursued.
Genes associated with immunotherapy response, stratified by MSI and/or TMB statusCancerGeneSubgroupPatientsMutated (%)HR (95% CI)PCOADREADRNF43MSI-H2919 (66%)0.11 (0.02-0.73)0.023BLCAELF3MSI-L20713 (6%)5.56 (2.03-15.2)<0.001BLCANOTCH1MSI-L20713 (6%)3.72 (1.82-7.61)<0.001BLCAPIK3CAMSI-L20743 (21%)1.99 (1.20-3.32)0.008BRCAKMT2DMSI-L445 (11%)5.33 (1.12-25.4)0.035BRCAPIK3CAMSI-L4414 (32%)3.04 (1.05-8.79)0.04COADREADNCOR1MSI-L815 (6%)8.66 (1.83-41.0)0.007HNSCROS1MSI-L1346 (4%)4.23 (1.35-13.2)0.003HNSCSMARCA4MSI-L1346 (4%)5.13 (1.74-15.1)0.003LUADBRAFMSI-L29322 (8%)2.1 (1.19-3.73)0.011LUADKEAP1MSI-L29364 (22%)1.53 (1.07-2.18)0.021LUADPBRM1MSI-L29316 (5%)2.8 (1.54-.511)<0.001BLCAELF3TMB-L/MSI-L16811 (7%)4.97 (1.63-15.2)0.005BLCANOTCH1TMB-L/MSI-L1686 (4%)5.21 (1.98-13.7)<0.001BLCAPIK3CATMB-L/MSI-L16827 (16%)2.15 (1.17-3.94)0.013LUADBRAFTMB-L/MSI-L23013 (6%)2.65 (1.35-5.18)0.004LUADPBRM1TMB-L/MSI-L2307 (3%)3.2 (1.45-7.08)0.004
Citation Format: Tomi Jun, Tao Qing, Robert Samstein, Carlos Cordon-Cardo, Lajos Pusztai, Kuan-Lin Huang. Precise stratification of immunotherapy outcomes using response-associated somatic mutations [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2226.
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Affiliation(s)
- Tomi Jun
- 1Icahn School of Medicine at Mount Sinai, New York, NY
| | - Tao Qing
- 2Yale School of Medicine, New Haven, CT
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O'Meara T, Marczyk M, Qing T, Yaghoobi V, Blenman K, Cole K, Pelekanou V, Rimm DL, Pusztai L. Immunological Differences Between Immune-Rich Estrogen Receptor-Positive and Immune-Rich Triple-Negative Breast Cancers. JCO Precis Oncol 2020; 4:1900350. [PMID: 32923897 PMCID: PMC7446500 DOI: 10.1200/po.19.00350] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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] [Accepted: 05/26/2020] [Indexed: 12/20/2022] Open
Abstract
PURPOSE A subset of estrogen receptor–positive (ER-positive) breast cancer (BC) contains high levels of tumor-infiltrating lymphocytes (TILs), similar to triple-negative BC (TNBC). The majority of immuno-oncology trials target TNBCs because of the greater proportion of TIL-rich TNBCs. The extent to which the immune microenvironments of immune-rich ER-positive BC and TNBC differ is unknown. PATIENTS AND METHODS RNA sequencing data from The Cancer Genome Atlas (TCGA; n = 697 ER-positive BCs; n = 191 TNBCs) were used for discovery; microarray expression data from Molecular Taxonomy of Breast Cancer International Consortium (METABRIC; n = 1,186 ER-positive BCs; n = 297 TNBCs) was used for validation. Patients in the top 25th percentile of a previously published total TIL metagene score distribution were considered immune rich. We compared expression of immune cell markers, immune function metagenes, and immuno-oncology therapeutic targets among immune-rich subtypes. RESULTS Relative fractions of resting mast cells (TCGA Padj = .009; METABRIC Padj = 4.09E-15), CD8+ T cells (TCGA Padj = .015; METABRIC Padj = 0.390), and M2-like macrophages (TCGA Padj= 4.68E-05; METABRIC Padj = .435) were higher in immune-rich ER-positive BCs, but M0-like macrophages (TCGA Padj = 0.015; METABRIC Padj = .004) and M1-like macrophages (TCGA Padj = 9.39E-08; METABRIC Padj = 6.24E-11) were higher in immune-rich TNBCs. Ninety-one immune-related genes (eg, CXCL14, CSF3R, TGF-B3, LRRC32/GARP, TGFB-R2) and a transforming growth factor β (TGF-β) response metagene were significantly overexpressed in immune-rich ER-positive BCs, whereas 41 immune-related genes (eg, IFNG, PD-L1, CTLA4, MAGEA4) were overexpressed in immune-rich TNBCs in both discovery and validation data sets. TGF-β pathway member genes correlated negatively with expression of immune activation markers (IFNG, granzyme-B, perforin) and positively with M2-like macrophages (IL4, IL10, and MMP9) and regulatory T-cell (FOXP3) markers in both subtypes. CONCLUSION Different immunotherapy strategies may be optimal in immune-rich ER-positive BC and TNBC. Drugs targeting the TGF-β pathway and M2-like macrophages are promising strategies in immune-rich ER-positive BCs to augment antitumor immunity.
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Affiliation(s)
- Tess O'Meara
- Department of Medical Oncology, Yale School of Medicine, New Haven, CT
| | - Michal Marczyk
- Department of Medical Oncology, Yale School of Medicine, New Haven, CT.,Data Mining Division, Silesian University of Technology, Gliwice, Poland
| | - Tao Qing
- Department of Medical Oncology, Yale School of Medicine, New Haven, CT
| | - Vesal Yaghoobi
- Department of Pathology, Yale School of Medicine, New Haven, CT
| | - Kim Blenman
- Department of Medical Oncology, Yale School of Medicine, New Haven, CT
| | - Kimberly Cole
- Department of Pathology, Yale School of Medicine, New Haven, CT
| | - Vasiliki Pelekanou
- Department of Pathology, Yale School of Medicine, New Haven, CT.,Sanofi, Oncology and Translational Medicine, Bridgewater Township, NJ
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT
| | - Lajos Pusztai
- Department of Medical Oncology, Yale School of Medicine, New Haven, CT
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Rediti M, Venet D, Rothe F, Qing T, Maetens M, Bradbury I, Izquierdo MA, Di Cosimo S, Hilbers F, Bajji M, Harbeck N, Untch M, Liu MC, Saura C, Huober JB, Nuciforo P, Salgado R, Loi S, Pusztai L, Sotiriou C. Association of T- and B-cell receptor repertoires with molecular subtypes and outcome in HER2+ breast cancer: An analysis of the NeoALTTO clinical trial. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.511] [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: 11/20/2022] Open
Abstract
511 Background: Clinicopathological and molecular features, including estrogen receptor (ER) status and PAM50 subtypes, have shown an association with immunogenicity and tumor-infiltrating lymphocyte (TIL) levels in breast cancer (BC). To investigate the complexity of the immune response in HER2+ BC, we explored the association of T- and B-cell receptor (TCR and BCR) repertoires with clinicopathological characteristics, PAM50 subtypes and outcome in the NeoALTTO phase III trial. Methods: RNA sequencing (RNAseq) data from baseline tumor biopsies were available for 254 out of the 455 patients enrolled. TCR and BCR repertoires were extracted from RNAseq data using the MiXCR software. Repertoire and diversity measures (read counts, number of clones, evenness, Gini index, Shannon entropy, length of the complementarity-determining region 3 [CDR3], top and second top clone proportions) were estimated. PAM50 subtypes were computed from RNAseq data. Univariate and multivariate (adjusted for clinicopathological characteristics, TIL levels dichotomized using the median value of 12.5% and treatment arm) Cox proportional hazard models were used for survival analysis, while logistic regressions were used for pathological complete response (pCR), defined as ypT0/is. All results reported had a false discovery rate (FDR) <0.05. Results: Higher BCR read counts, number of clones and Gini index were significantly associated with ER-negative as well as grade 3 tumors. Among the PAM50 subtypes, HER2-enriched (HER2-E) showed significantly higher BCR read counts, number of clones and Gini index along with lower evenness compared to luminal A and B, as well as higher length of CDR3 than luminal A. Of note, basal-like showed similar BCR diversity measures to HER2-E. No significant differences were noted for TCR diversity measures. In multivariate analyses, neither TCR nor BCR features were associated with pCR, while BCR evenness (HR 1.5; 95%CI 1.1-2.1) and Gini index (HR 0.66; 95%CI 0.5-0.88) were associated with event-free survival. Conclusions: BCR repertoire measures suggest a clonal expansion in HER2-E and basal-like PAM50 subtypes. Furthermore, the implementation of BCR-derived biomarkers can help to identify patients with an improved clinical outcome after neoadjuvant anti-HER2 treatment. Our findings highlight the heterogeneity of the immune response within HER2+ BC and provide support for biomarker-driven treatment strategies including immunotherapy in this BC subtype. Further validation is required. Clinical trial information: NCT00553358 .
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Affiliation(s)
- Mattia Rediti
- Breast Cancer Translational Research Laboratory J.-C. Heuson, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - David Venet
- Breast Cancer Translational Research Laboratory J.-C. Heuson, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Francoise Rothe
- Breast Cancer Translational Research Laboratory J.-C. Heuson, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Tao Qing
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT
| | | | | | | | - Serena Di Cosimo
- Biomarker Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Mohammed Bajji
- Institut Jules Bordet (Breast European Adjuvant Study Team), Brussels, Belgium
| | - Nadia Harbeck
- Breast Center, Dept. Obstetrics & Gynecology, University of Munich (LMU) and CCCLMU, Munich, Germany
| | | | | | - Cristina Saura
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Paolo Nuciforo
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Roberto Salgado
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Sherene Loi
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Lajos Pusztai
- Yale School of Medicine, Yale Cancer Center, New Haven, CT
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory J.-C. Heuson, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
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Yu Y, Wang Y, Xia Z, Zhang X, Jin K, Yang J, Ren L, Zhou Z, Yu D, Qing T, Zhang C, Jin L, Zheng Y, Guo L, Shi L. PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs. Nucleic Acids Res 2020; 47:D1090-D1101. [PMID: 30407536 PMCID: PMC6324052 DOI: 10.1093/nar/gky1042] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 08/15/2018] [Accepted: 10/19/2018] [Indexed: 01/01/2023] Open
Abstract
One important aspect of precision medicine aims to deliver the right medicine to the right patient at the right dose at the right time based on the unique ‘omics’ features of each individual patient, thus maximizing drug efficacy and minimizing adverse drug reactions. However, fragmentation and heterogeneity of available data makes it challenging to readily obtain first-hand information regarding some particular diseases, drugs, genes and variants of interest. Therefore, we developed the Precision Medicine Knowledgebase (PreMedKB) by seamlessly integrating the four fundamental components of precision medicine: diseases, genes, variants and drugs. PreMedKB allows for search of comprehensive information within each of the four components, the relationships between any two or more components, and importantly, the interpretation of the clinical meanings of a patient's genetic variants. PreMedKB is an efficient and user-friendly tool to assist researchers, clinicians or patients in interpreting a patient's genetic profile in terms of discovering potential pathogenic variants, recommending therapeutic regimens, designing panels for genetic testing kits, and matching patients for clinical trials. PreMedKB is freely accessible and available at http://www.fudan-pgx.org/premedkb/index.html#/home.
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Affiliation(s)
- Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai 200438, China
| | - Yunjin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai 200438, China
| | - Zhaojie Xia
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | | | | | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai 200438, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai 200438, China
| | - Zheng Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai 200438, China
| | - Dong Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai 200438, China
| | - Tao Qing
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai 200438, China
| | - Chengdong Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai 200438, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China.,Human Phenome Institute, Fudan University, Shanghai 201203, China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai 200438, China.,Human Phenome Institute, Fudan University, Shanghai 201203, China.,Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai 200438, China
| | - Li Guo
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai 200438, China.,Human Phenome Institute, Fudan University, Shanghai 201203, China.,Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai 200438, China
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Qing T, Mohsen H, Marczyk M, Ye Y, O'Meara T, Zhao H, Townsend JP, Gerstein M, Hatzis C, Kluger Y, Pusztai L. Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden. Nat Commun 2020; 11:2438. [PMID: 32415133 PMCID: PMC7228928 DOI: 10.1038/s41467-020-16293-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [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: 01/21/2020] [Accepted: 04/21/2020] [Indexed: 11/24/2022] Open
Abstract
Cancers harbor many somatic mutations and germline variants, we hypothesized that the combined effect of germline variants that alter the structure, expression, or function of protein-coding regions of cancer-biology related genes (gHFI) determines which and how many somatic mutations (sM) must occur for malignant transformation. We show that gHFI and sM affect overlapping genes and the average number of gHFI in cancer hallmark genes is higher in patients who develop cancer at a younger age (r = -0.77, P = 0.0051), while the average number of sM increases in increasing age groups (r = 0.92, P = 0.000073). A strong negative correlation exists between average gHFI and average sM burden in increasing age groups (r = -0.70, P = 0.017). In early-onset cancers, the larger gHFI burden in cancer genes suggests a greater contribution of germline alterations to the transformation process while late-onset cancers are more driven by somatic mutations.
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Affiliation(s)
- Tao Qing
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Hussein Mohsen
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Michal Marczyk
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
- Data Mining Division, Silesian University of Technology, Gliwice, Poland
| | - Yixuan Ye
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Tess O'Meara
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
| | - Hongyu Zhao
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA
| | - Jeffrey P Townsend
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, USA
| | - Christos Hatzis
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
- Bristol-Myers Squibb, New York, NY, USA
| | - Yuval Kluger
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Pathology, School of Medicine, Yale University, New Haven, CT, USA
- Program of Applied Mathematics, Yale University, New Haven, CT, USA
| | - Lajos Pusztai
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA.
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Xiao J, Mao JY, Quan J, Qing T. Relationally Charged: How and When Workplace Friendship Facilitates Employee Interpersonal Citizenship. Front Psychol 2020; 11:190. [PMID: 32153453 PMCID: PMC7045053 DOI: 10.3389/fpsyg.2020.00190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 09/26/2019] [Accepted: 01/27/2020] [Indexed: 11/13/2022] Open
Abstract
Having friends in the workplace not only provides an employee joy and meaning, but also facilitates one's positive behavior. In this study, we argue that workplace friendship has positive influence on an employee's interpersonal citizenship behavior. Drawing upon conservation of resources theory, the present study explores how and when workplace friendship fosters interpersonal citizenship. Using a time-lagged, multisource data of 620 employees from 83 workgroups, we found that workplace friendship increases an employee's relational energy, which subsequently, leads to greater interpersonal citizenship. Moreover, we discovered relational-interdependent self-construal as an important moderating influence that affects the saliency of this relationship. Specifically, for employee with a relational-interdependent self-construal, workplace friendship has a stronger positive influence on one's relational energy and hence interpersonal citizenship. Contributions to theory and practice are also discussed.
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Affiliation(s)
- Jincen Xiao
- School of Business Administration, Southwestern University of Finance and Economics, Chengdu, China
| | - Jih-Yu Mao
- School of Business Administration, Southwestern University of Finance and Economics, Chengdu, China
| | - Jing Quan
- School of Business Administration, Southwestern University of Finance and Economics, Chengdu, China
| | - Tao Qing
- School of Business Administration, Southwestern University of Finance and Economics, Chengdu, China
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Liu Y, Luan Y, Zhang G, Hu H, Jiang J, Zhang L, Qing T, Zou Y, Yang D, Xi L. Human reliability analysis for operators in the digital main control rooms of nuclear power plants. J NUCL SCI TECHNOL 2020. [DOI: 10.1080/00223131.2020.1720848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Yanzi Liu
- State Key Laboratory of Nuclear Power Safety Monitoring Technology and Equipment, China Nuclear Power Design Company LTD. (Shenzhen), Shenzhen, Guangdong Province, China
| | - Yu Luan
- State Key Laboratory of Nuclear Power Safety Monitoring Technology and Equipment, China Nuclear Power Design Company LTD. (Shenzhen), Shenzhen, Guangdong Province, China
| | - Gang Zhang
- State Key Laboratory of Nuclear Power Safety Monitoring Technology and Equipment, China Nuclear Power Design Company LTD. (Shenzhen), Shenzhen, Guangdong Province, China
| | - Hong Hu
- School of Safety and Environment Engineering, Hunan Institute Of Technology, HengYang, HuNan Province, China
| | - Jianjun Jiang
- School of Safety and Environment Engineering, Hunan Institute Of Technology, HengYang, HuNan Province, China
| | - Li Zhang
- School of Safety and Environment Engineering, Hunan Institute Of Technology, HengYang, HuNan Province, China
| | - Tao Qing
- School of Safety and Environment Engineering, Hunan Institute Of Technology, HengYang, HuNan Province, China
| | - Yanhua Zou
- School of Safety and Environment Engineering, Hunan Institute Of Technology, HengYang, HuNan Province, China
| | - Dang Yang
- School of Safety and Environment Engineering, Hunan Institute Of Technology, HengYang, HuNan Province, China
| | - Liaozi Xi
- School of Safety and Environment Engineering, Hunan Institute Of Technology, HengYang, HuNan Province, China
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Hong ZH, Qing T, Schubert D, Kleinmanns JA, Liu JX. BLISTER-regulated vegetative growth is dependent on the protein kinase domain of ER stress modulator IRE1A in Arabidopsis thaliana. PLoS Genet 2019; 15:e1008563. [PMID: 31869326 PMCID: PMC6946172 DOI: 10.1371/journal.pgen.1008563] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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] [Received: 06/12/2019] [Revised: 01/07/2020] [Accepted: 12/12/2019] [Indexed: 11/19/2022] Open
Abstract
The unfolded protein response (UPR) is required for protein homeostasis in the endoplasmic reticulum (ER) when plants are challenged by adverse environmental conditions. Inositol-requiring enzyme 1 (IRE1), the bifunctional protein kinase / ribonuclease, is an important UPR regulator in plants mediating cytoplasmic splicing of the mRNA encoding the transcription factor bZIP60. This activates the UPR signaling pathway and regulates canonical UPR genes. However, how the protein activity of IRE1 is controlled during plant growth and development is largely unknown. In the present study, we demonstrate that the nuclear and Golgi-localized protein BLISTER (BLI) negatively controls the activity of IRE1A/IRE1B under normal growth condition in Arabidopsis. Loss-of-function mutation of BLI results in chronic up-regulation of a set of both canonical UPR genes and non-canonical UPR downstream genes, leading to cell death and growth retardation. Genetic analysis indicates that BLI-regulated vegetative growth phenotype is dependent on IRE1A/IRE1B but not their canonical splicing target bZIP60. Genetic complementation with mutation analysis suggests that the D570/K572 residues in the ATP-binding pocket and N780 residue in the RNase domain of IRE1A are required for the activation of canonical UPR gene expression, in contrast, the D570/K572 residues and D590 residue in the protein kinase domain of IRE1A are important for the induction of non-canonical UPR downstream genes in the BLI mutant background, which correlates with the shoot growth phenotype. Hence, our results reveal the important role of IRE1A in plant growth and development, and BLI negatively controls IRE1A’s function under normal growth condition in plants. When unfolded or misfolded proteins are accumulated in the ER, a much conserved response, called the unfolded protein response (UPR), is elicited to lighten the load of unfolded proteins in the ER by bringing the protein-folding and degradation capacities into alignment with the protein folding demands. However, over-activation of the UPR pathways under normal growth conditions affects plant growth and development. The bifunctional protein kinase / ribonuclease protein IRE1 is important for UPR gene regulation, but how IRE1’ protein activity is tightly controlled in plants is currently unknown. Here we report that BLISTER (BLI) negatively controls the IRE1’s function under normal growth condition in Arabidopsis. Through genetic analysis, our results also provide novel insights into how the protein kinase domain and ribonuclease domain contribute to the function of IRE1A in downstream gene expression.
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Affiliation(s)
- Zheng-Hui Hong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Tao Qing
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Daniel Schubert
- Plant Developmental Epigenetics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Epigenetics of Plants, Freie Universität Berlin, Berlin, Germany
| | - Julia Anna Kleinmanns
- Plant Developmental Epigenetics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- * E-mail: (JAK); (JXL)
| | - Jian-Xiang Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
- * E-mail: (JAK); (JXL)
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Suo C, Qing T, Liu Z, Yang X, Yuan Z, Yang YJ, Fan M, Zhang T, Lu M, Jin L, Chen X, Ye W. Differential Cumulative Risk of Genetic Polymorphisms in Familial and Nonfamilial Esophageal Squamous Cell Carcinoma. Cancer Epidemiol Biomarkers Prev 2019; 28:2014-2021. [PMID: 31562207 DOI: 10.1158/1055-9965.epi-19-0484] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/31/2019] [Accepted: 09/23/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND To explore the relationship between family history of esophageal cancer, SNPs, and the risk of esophageal squamous cell carcinoma (ESCC), we performed a population-based case-control study and developed a genetic family history-related risk (GFR) score and non-family history-related risk (GnFR) score to quantify the cumulative number of risk genotypes carried by each individual. METHODS We used data of 700 patients with nonfamilial ESCC, 341 patients with familial ESCC, 1,445 controls without a family history of esophageal cancer, and 319 controls with a family history. We genotyped 87 genetic variants associated with the risk for ESCC, and constructed GFR and GnFR scores for cases and controls. RESULTS Our results show that ESCC risk increased with higher GFR score (P trend = 0.0096). Among the familial subgroup, we observed a nearly 7-fold [95% confidence interval (CI), 1.92-24.77] higher risk of ESCC in the highest GFR score group. The corresponding estimate was only 2-fold (95% CI, 1.41-3.93) higher risk of ESCC, in the stratum without a reported family history of esophageal cancer. Certain cell signaling pathways and immune-related pathways were enriched, specifically in familial ESCC. Results from a reconstructed cohort analysis demonstrated that cumulative risk to get esophageal cancer by age 75 years was 13.3%, 10.2%, 8.2%, and 5.1%, respectively, in four subgroups as defined by first-degree relatives of cases or controls with high or low genetic risk score. In particular, the cohort of relatives of ESCC cases with low genetic risk score exhibit a higher cumulative risk than the cohort of relatives of controls with high genetic risk score. It demonstrates that environmental factors play a major role in esophageal cancer. CONCLUSIONS Further studies are warranted to dissect the mechanisms of shared environmental and genetic susceptibility affecting the risk of getting ESCC. IMPACT Our study highlights that the need of preventive strategies to screen certain genetic polymorphisms, especially in individuals whose relatives had ESCC.
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Affiliation(s)
- Chen Suo
- Department of Epidemiology and Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Tao Qing
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Zhenqiu Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaorong Yang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Ziyu Yuan
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Ya-Jun Yang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Min Fan
- Taixing Disease Control and Prevention Center, Taizhou, China
| | - Tiejun Zhang
- Department of Epidemiology and Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Ming Lu
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China. .,Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Fudan University Taizhou Institute of Health Sciences, Taizhou, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China. .,Fudan University Taizhou Institute of Health Sciences, Taizhou, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Weimin Ye
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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46
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Ding R, Xu X, Qing T, Hu X. [The design of the software system for the interpretation and guidance of drug locus related to drug treatment]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2019; 36:657-663. [PMID: 31441268 PMCID: PMC10319505 DOI: 10.7507/1001-5515.201805001] [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] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Indexed: 06/10/2023]
Abstract
Based on the pharmacogenomics theory, this study developed a software system for interpretation of drug gene loci and guidance on clinical safe medication with the purpose of providing clinical guidance on the safety and effectiveness of drug use through accurate and efficient detection and interpretation of drug gene loci. The system infrastructure was built on a service-oriented architecture (SOA) design and Docker container virtualization approach to achieve a rapid and automatic interpretation of genetic results and best available drugs. The front end was established on HTML5 and JavaScript to realize visualization of analysis results and user interaction. The system was tested and validated to show robust performance which is reliable in clinical use. It will show high impact on the development of pharmacogenomics and clinical practice of patients with personalized medicine.
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Affiliation(s)
- Ruifeng Ding
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, P.R.China
| | - Xiulin Xu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, P.R.China
| | - Tao Qing
- School of Life Sciences, Fudan University, Shanghai 200438, P.R.China
| | - Xiufang Hu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093,
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Qing T, Marczyk M, Wali V, Gunasekharan V, Patwardhan G, Pusztai L, Hatzis C. Abstract P4-03-01: Pathway level complementarity of germline and somatic events in breast cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p4-03-01] [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
Background: Progression from a normal cell state to cancer requires multiple genomic hits in key regulatory pathways. In the case of hereditary cancer syndromes, some of these hits occur in the germline, but additional somatic mutations are required for malignant transformation. We hypothesize that this paradigm could be extended to sporadic cancers as well. What somatic mutation function as a cancer driver event may be determined by the constellation of germline variants a person is born with. We propose that even rare, non-recurrent, high functional impact germline variants in genes involved in cancer-related pathways could influence the biological impact of somatic mutations in other cancer-related genes. The goal of the current analysis was to examine associations between pathway alterations caused by high functional impact germline variants or somatic mutations in the “hallmarks of cancer” pathways in breast cancer.
Methods: We obtained germline DNA sequencing and copy number variation (CNV) data from the breast cancer TCGA cohort. After population clustering with the HapMap cohort, we selected a homogeneous group of 796 patients of Western European ancestry and downloaded the matching somatic mutations (SNVs and INDELs) that were available for 750 cases, that comprise the current study population. Germline CNVs were classified as recurrent or rare losses or gains. Potentially pathogenic germline variants (SNPs) were obtained from the PanCancer Altas project. All germline or somatic mutations were mapped at the gene level to the 50 Cancer Hallmarks pathway collection. We designated a pathway mutated if at least 1 gene had a germline or a somatic mutation. Complementarity between pathway alterations by germline and somatic events were evaluated using the Fisher exact test adjusted for multiple comparisons.
Results: At the germline level, 2,057 genes were affected by CNVs (mean 30, range 3-151 genes/patient), and a total of 43 genes carried germline pathogenic SNPs that affected 13.8% of the patients. At the somatic level, we detected 40,881 high functional impact mutations (mean 54.3, range 1-3889 mutations/patient) in 13,080 genes (mean 50.8, range 1-3166 genes/patient). The 50 Cancer Hallmark pathways contained 4386 genes (mean 146.5, range 32-200 genes/pathway), and were mutated in the majority of the patients (85% germline, 93% somatic). Several pathways, such as HEME_METABOLISM, INTERFERON_ALPHA_RESPONSE, and KRAS_SIGNALING, were frequently affected by germline alterations, while the somatic mutations were most frequently involved in the COMPLEMENT, E2F_TARGET, and UV_RESPONSE_UP. Interaction analysis revealed co-occurrence between MYC_TARGETS_V1 (germline) and UV_RESPONSE_DN (somatic) or MTORC1_SINGALING (somatic) (p<0.01), and TNFA_SIGNALING_VIA_NFKB (germline) and IL6_JAK_STAT3_SIGNALING (germline) with E2F_TARGETS (somatic) (p<0.01). We also observed an exclusive relationship between germline alterations in BILE_ACID_METABOLISM and somatic mutations in COMPLEMENT pathway (p<0.01).
Conclusions: Our results highlight the importance of pathway-level analysis of germline alterations in breast cancer, which might help to understand the interrelationship between germline and somatic alterations in breast cancer.
Citation Format: Qing T, Marczyk M, Wali V, Gunasekharan V, Patwardhan G, Pusztai L, Hatzis C. Pathway level complementarity of germline and somatic events in breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-03-01.
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Affiliation(s)
- T Qing
- Yale University, New Haven, CT
| | | | - V Wali
- Yale University, New Haven, CT
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Marczyk M, Gunasekharan V, Wali VB, Shi W, Patwardhan G, Qing T, Pusztai L, Hatzis C. Abstract P2-06-06: Targeting loss of isoenzyme diversity as a novel therapeutic strategy in breast cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p2-06-06] [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
Background: Several metabolic steps are mediated by distinct proteins or isoenzymes that catalyze the same reaction, providing redundancy of metabolic functions. Metabolic states are frequently altered in cancer to support survival and proliferation in hypoxic and otherwise hostile microenvironments, and metabolic re-wiring often involve loss of isoenzyme diversity. We hypothesize that targeting enzymes that have lost isoenzyme diversity in cancer, but not in normal cells, provides an opportunity to selectively target cancers. In this study, we assessed mRNA expression of all known human isoenzyme families in breast cancer and normal breast tissue and identified isoenzymes with loss of diversity within each breast cancer subtype.
Methods: We obtained RNAseq data from cancer and patient-matched normal breast tissues from the TCGA (N=66 HR+, N=24 HER2+, and N=15 TNBC tumors). We retrieved annotated human isoenzyme families from the ENZYME nomenclature database. We compared expression in cancer and matched normal samples from the same patient to identify isoenzymes that had i) same or increased expression of the target isoenzyme in cancer vs normal and ii) reduced expression of the complementary isoenzymes in cancer. We developed five scores that capture various elements of these characteristics and prioritized candidates as targets based on clustering and their combined ranking based on the five scores. We validated overexpression of the candidate isoenzymes relative to other isoforms in breast cancer microarray data from ArrayExpress (E-GEOD-76250: 33 TNBC, and E-GEOD-70951: 30 TNBC, 108 HR+, 10 HER2+).
Results: We identified 321 enzymes in the TCGA discovery cohort that correspond to 829 unique isoenzymes. Overall, 636, 483 and 429 isoenzymes were differentially expressed in HR+, HER2+ and TNBC cancers, respectively, compared to corresponding normal samples. Of these, 308 isoenzymes were differentially expressed relative to normal in all 3 subtypes. In all, 112 and 92, and 84 were selected as candidate isoenzyme therapeutic targets in HR+, HER2+ and TNBC, respectively. 23 isoenzymes prioritized in clustering step were further validated. Finally, 6 isoenzymes were validated in HR+ (ALDOA, GUSB, GYG1, MIF, P3H1, PCK2), 10 in HER2+ (ALDH1L2, ALDOA, GLYATL2, GUSB, GYG1, GYS1, MIF, P3H1, PCK2, PTGS1) and 12 in TNBC (ADSS, ALAS1, ALDH1L2, ALDOA, ART3, GLYATL2, GUSB, GYS1, HS3ST1, MIF, PCK2, SOAT1), as potential targets for breast cancer treatment. Of these, 5 potential isoenzyme targets (ALDH1L2, GUSB, GLYATL2, MIF, PCK2), which were mostly hydrolases and transferases, were further selected for ongoing experimental validation in the laboratory. Decreased expression of the complementary isoforms of these 5 targets were primarily due to DNA methylation of the genes in cancer.
Conclusions: We found that loss of isoenzyme diversity is a broad phenomenon in breast cancers that may be explored therapeutically. We identified several instances of “isoenzyme addiction” in which cancers depend exclusively on a single isoenzyme while downregulating via methylation the complementary isoenzymes, providing cancer-specific targeting opportunities. We are currently validating several of these targets in cell line models.
Citation Format: Marczyk M, Gunasekharan V, Wali VB, Shi W, Patwardhan G, Qing T, Pusztai L, Hatzis C. Targeting loss of isoenzyme diversity as a novel therapeutic strategy in breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-06-06.
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Affiliation(s)
- M Marczyk
- Yale School of Medicine, New Haven; OrigiMed, Shanghai, China; Silesian University of Technology, Gliwice, Poland
| | - V Gunasekharan
- Yale School of Medicine, New Haven; OrigiMed, Shanghai, China; Silesian University of Technology, Gliwice, Poland
| | - VB Wali
- Yale School of Medicine, New Haven; OrigiMed, Shanghai, China; Silesian University of Technology, Gliwice, Poland
| | - W Shi
- Yale School of Medicine, New Haven; OrigiMed, Shanghai, China; Silesian University of Technology, Gliwice, Poland
| | - G Patwardhan
- Yale School of Medicine, New Haven; OrigiMed, Shanghai, China; Silesian University of Technology, Gliwice, Poland
| | - T Qing
- Yale School of Medicine, New Haven; OrigiMed, Shanghai, China; Silesian University of Technology, Gliwice, Poland
| | - L Pusztai
- Yale School of Medicine, New Haven; OrigiMed, Shanghai, China; Silesian University of Technology, Gliwice, Poland
| | - C Hatzis
- Yale School of Medicine, New Haven; OrigiMed, Shanghai, China; Silesian University of Technology, Gliwice, Poland
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O'Meara T, Safonov A, Casadevall D, Qing T, Silber A, Killelea B, Hatzis C, Pusztai L. Immune microenvironment of triple-negative breast cancer in African-American and Caucasian women. Breast Cancer Res Treat 2019; 175:247-259. [PMID: 30725384 DOI: 10.1007/s10549-019-05156-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [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: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/31/2022]
Abstract
PURPOSE African-American (AA) patients with triple-negative breast cancer (TNBC) are less likely to achieve pathologic complete response from neoadjuvant chemotherapy and have poorer prognosis than Caucasian patients with TNBC, suggesting potential biological differences by race. Immune infiltration is the most consistent predictive marker for chemotherapy response and improved prognosis in TNBC. In this study, we test the hypothesis that the immune microenvironment differs between AA and Caucasian patients. METHODS RNA-seq expression data were obtained from The Cancer Genome Atlas (TCGA) database for 162 AA and 697 Caucasian breast cancers. Estrogen receptor (ER)-positive, human epidermal growth factor receptor-2 (HER2)-positive, and TNBC subtypes were included in the analyses. Tumor infiltrating lymphocyte (TIL) counts, immunomodulatory scores, and molecular subtypes were obtained from prior publications for a subset of the TNBC cases. Differences in immune cell distributions and immune functions, measured through gene expression and TIL counts, as well as neoantigen, somatic mutation, amplification, and deletion loads, were compared by race and tumor subtype. RESULTS Immune metagene analysis demonstrated marginal immune attenuation in AA TNBC relative to Caucasian TNBC that did not reach statistical significance. The distributions of immune cell populations, lymphocyte infiltration, molecular subtypes, and genomic aberrations between AA and Caucasian subtypes were also not significantly different. The MHC1 metagene demonstrated increased expression in AA ER-positive cancers relative to Caucasian ER-positive cancers. CONCLUSIONS This study suggests that the immunological differences between AA and Caucasian breast cancers represented by TCGA data are subtle, if they exist at all. We observed no consistent racial differences in immune gene expression or TIL counts in TNBC by race. However, this study cannot rule out small differences in immune cell subtype distribution and activity status that may not be apparent in bulk RNA analysis.
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Affiliation(s)
- Tess O'Meara
- Breast Medical Oncology, Yale School of Medicine, Yale Cancer Center, 300 George St, Suite 120, Rm 133, New Haven, CT, 06520, USA
| | - Anton Safonov
- University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - David Casadevall
- Breast Medical Oncology, Yale School of Medicine, Yale Cancer Center, 300 George St, Suite 120, Rm 133, New Haven, CT, 06520, USA.,Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Tao Qing
- Breast Medical Oncology, Yale School of Medicine, Yale Cancer Center, 300 George St, Suite 120, Rm 133, New Haven, CT, 06520, USA
| | - Andrea Silber
- Breast Medical Oncology, Yale School of Medicine, Yale Cancer Center, 300 George St, Suite 120, Rm 133, New Haven, CT, 06520, USA
| | - Brigid Killelea
- Breast Medical Oncology, Yale School of Medicine, Yale Cancer Center, 300 George St, Suite 120, Rm 133, New Haven, CT, 06520, USA
| | - Christos Hatzis
- Breast Medical Oncology, Yale School of Medicine, Yale Cancer Center, 300 George St, Suite 120, Rm 133, New Haven, CT, 06520, USA
| | - Lajos Pusztai
- Breast Medical Oncology, Yale School of Medicine, Yale Cancer Center, 300 George St, Suite 120, Rm 133, New Haven, CT, 06520, USA.
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50
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Wei Z, Qing T, Wei D. Clinical feasibility of pancreaticoduodenectomy in different ages. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy441.018] [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: 11/13/2022] Open
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