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Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, Hosseini N, Song X, Petralia F, Calinawan A, Savage SR, Berry AB, Reva B, Ozbek U, Krek A, Ma W, da Veiga Leprevost F, Ji J, Yoo S, Lin C, Voytovich UJ, Huang Y, Lee SH, Bergan L, Lorentzen TD, Mesri M, Rodriguez H, Hoofnagle AN, Herbert ZT, Nesvizhskii AI, Zhang B, Whiteaker JR, Fenyo D, McKerrow W, Wang J, Schürer SC, Stathias V, Chen XS, Barcellos-Hoff MH, Starr TK, Winterhoff BJ, Nelson AC, Mok SC, Kaufmann SH, Drescher C, Cieslik M, Wang P, Birrer MJ, Paulovich AG. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer. Cell 2024; 187:1016. [PMID: 38364782 DOI: 10.1016/j.cell.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
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Zhu S, Xu J, Shi RR, Wang XK, Sun MM, Li SN, Gao LL, Li YY, Wen HM, Zhao CL, Li S, Ji J, Yang CH, Yu YH. [Association between congenital hypothyroidism and in-hospital adverse outcomes in very low birth weight infants]. Zhonghua Er Ke Za Zhi 2024; 62:29-35. [PMID: 38154974 DOI: 10.3760/cma.j.cn112140-20231012-00281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Objective: To investigate the association between congenital hypothyroidism (CH) and the adverse outcomes during hospitalization in very low birth weight infants (VLBWI). Methods: This prospective, multicenter observational cohort study was conducted based on the data from the Sino-northern Neonatal Network (SNN). Data of 5 818 VLBWI with birth weight <1 500 g and gestational age between 24-<37 weeks that were admitted to the 37 neonatal intensive care units from January 1st, 2019 to December 31st, 2022 were collected and analyzed. Thyroid function was first screened at 7 to 10 days after birth, followed by weekly tests within the first 4 weeks, and retested at 36 weeks of corrected gestational age or before discharge. The VLBWI were assigned to the CH group or non-CH group. Chi-square test, Fisher exact probability method, Wilcoxon rank sum test, univariate and multivariate Logistic regression were used to analyze the relationship between CH and poor prognosis during hospitalization in VLBWI. Results: A total of 5 818 eligible VLBWI were enrolled, with 2 982 (51.3%) males and the gestational age of 30 (29, 31) weeks. The incidence of CH was 5.5% (319 VLBWI). Among the CH group, only 121 VLBWI (37.9%) were diagnosed at the first screening. Univariate Logistic regression analysis showed that CH was associated with increased incidence of extrauterine growth retardation (EUGR) (OR=1.31(1.04-1.64), P<0.05) and retinopathy of prematurity (ROP) of stage Ⅲ and above (OR=1.74(1.11-2.75), P<0.05). However, multivariate Logistic regression analysis showed no significant correlation between CH and EUGR, moderate to severe bronchopulmonary dysplasia, grade Ⅲ to Ⅳ intraventricular hemorrhage, neonatal necrotizing enterocolitis in stage Ⅱ or above, and ROP in stage Ⅲ or above (OR=1.04 (0.81-1.33), 0.79 (0.54-1.15), 1.15 (0.58-2.26), 1.43 (0.81-2.53), 1.12 (0.70-1.80), all P>0.05). Conclusion: There is no significant correlation between CH and in-hospital adverse outcomes, possibly due to timely diagnosis and active replacement therapy.
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Affiliation(s)
- S Zhu
- Department of Neonatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250014, China
| | - J Xu
- Department of Neonatology, Affiliated Hospital of Jining Medical University, Jining 272000, China
| | - R R Shi
- Department of Neonatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250014, China
| | - X K Wang
- Department of Neonatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250014, China
| | - M M Sun
- Department of Neonatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250014, China
| | - S N Li
- Department of Neonatology, Yantai Yuhuangding Hospital, Yantai 264000, China
| | - L L Gao
- Department of Neonatology, Liaocheng People's Hospital, Liaocheng 252000, China
| | - Y Y Li
- Department of Neonatology, W.F. Maternal and Child Health Hospital, Weifang 261000, China
| | - H M Wen
- Department of Neonatology, Hebei PetroChina Central Hospital, Langfang 065000, China
| | - C L Zhao
- Department of Neonatology, the Third Hospital of Baogang Group, Baotou 014010, China
| | - S Li
- Department of Neonatology, the First Affiliated Hospital of Shandong First Medical University, Jinan 250014, China
| | - J Ji
- Department of Neonatology, Feixian People's Hospital, Linyi 273400, China
| | - C H Yang
- Department of Neonatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250014, China
| | - Y H Yu
- Department of Neonatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250014, China
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Hu Y, Ji J, Cheng H, Luo R, Zhang J, Li W, Wang X, Zhang J, Yao Y. The miR408a-BBP-LAC3/CSD1 module regulates anthocyanin biosynthesis mediated by crosstalk between copper homeostasis and ROS homeostasis during light induction in Malus plants. J Adv Res 2023; 51:27-44. [PMID: 36371057 PMCID: PMC10491975 DOI: 10.1016/j.jare.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/19/2022] [Accepted: 11/06/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION The expression of miR408 is affected by copper (Cu) conditions and positively regulates anthocyanin biosynthesis in Arabidopsis. However, the underlying mechanisms by which miR408 regulates anthocyanin biosynthesis mediated by Cu homeostasis and reactive oxygen species (ROS) homeostasis remain unclear in Malus plants. OBJECTIVES Our study aims to elucidate how miR408a and its target, basic blue protein (BBP) regulate Cu homeostasis and ROS homeostasis, and anthocyanin biosynthesis in Malus plants. METHODS The roles of miR408a and its target BBP in regulating anthocyanin biosynthesis, Cu homeostasis, and ROS homeostasis were mainly identified in Malus plants. RESULTS We found that the BBP protein interacted with the copper-binding proteins LAC3 (laccase) and CSD1 (Cu/Zn SOD superoxide dismutase), indicating a potential crosstalk between Cu homeostasis and ROS homeostasis might be mediated by miR408 to regulate the anthocyanin accumulation. Further studies showed that overexpressing miR408a or suppressing BBP transiently significantly increased the expression of genes related to Cu binding and Cu transport, leading to anthocyanin accumulation under light induction in apple fruit and Malus plantlets. Consistently, opposite results were obtained when repressing miR408a or overexpressing BBP. Moreover, light induction significantly increased the expression of miR408a, CSD1, and LAC3, but significantly reduced the BBP expression, resulting in increased Cu content and anthocyanin accumulation. Furthermore, excessive Cu significantly increased the anthocyanin accumulation, accompanied by reduced expression of miR408a and Cu transport genes, and upregulated expression of Cu binding proteins including BBP, LAC3, and CSD1 to maintain the Cu homeostasis and ROS homeostasis in Malus plantlets. CONCLUSION Our findings provide new insights into the mechanism by which the miR408a-BBP-LAC3/CSD1 module perceives light and Cu signals regulating Cu and ROS homeostasis, ultimately affecting anthocyanin biosynthesis in Malus plants.
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Affiliation(s)
- Yujing Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Jiayi Ji
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China; Beijing Forestry University, China
| | - Hao Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Rongli Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Wenjing Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Xingsui Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China.
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China; College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China; Beijing Key Laboratory for Agricultural Application and New Technique, Beijing 102206, China.
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Li Y, Dou Y, Da Veiga Leprevost F, Geffen Y, Calinawan AP, Aguet F, Akiyama Y, Anand S, Birger C, Cao S, Chaudhary R, Chilappagari P, Cieslik M, Colaprico A, Zhou DC, Day C, Domagalski MJ, Esai Selvan M, Fenyö D, Foltz SM, Francis A, Gonzalez-Robles T, Gümüş ZH, Heiman D, Holck M, Hong R, Hu Y, Jaehnig EJ, Ji J, Jiang W, Katsnelson L, Ketchum KA, Klein RJ, Lei JT, Liang WW, Liao Y, Lindgren CM, Ma W, Ma L, MacCoss MJ, Martins Rodrigues F, McKerrow W, Nguyen N, Oldroyd R, Pilozzi A, Pugliese P, Reva B, Rudnick P, Ruggles KV, Rykunov D, Savage SR, Schnaubelt M, Schraink T, Shi Z, Singhal D, Song X, Storrs E, Terekhanova NV, Thangudu RR, Thiagarajan M, Wang LB, Wang JM, Wang Y, Wen B, Wu Y, Wyczalkowski MA, Xin Y, Yao L, Yi X, Zhang H, Zhang Q, Zuhl M, Getz G, Ding L, Nesvizhskii AI, Wang P, Robles AI, Zhang B, Payne SH. Proteogenomic data and resources for pan-cancer analysis. Cancer Cell 2023; 41:1397-1406. [PMID: 37582339 PMCID: PMC10506762 DOI: 10.1016/j.ccell.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/15/2022] [Accepted: 06/27/2023] [Indexed: 08/17/2023]
Abstract
The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and computational resources for aiding biological discoveries. We also discuss challenges for multi-omics data integration and analysis, specifically the unique challenges of working with both nucleotide sequencing and mass spectrometry proteomics data.
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Affiliation(s)
- Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Yifat Geffen
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Anna P Calinawan
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Yo Akiyama
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Shankara Anand
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Chet Birger
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | | | - Marcin Cieslik
- Department of Computational Medicine & Bioinformatics, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Antonio Colaprico
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Daniel Cui Zhou
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Corbin Day
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | | | - Myvizhi Esai Selvan
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Steven M Foltz
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Tania Gonzalez-Robles
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Zeynep H Gümüş
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David Heiman
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | - Runyu Hong
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiayi Ji
- Tisch Cancer Institute and Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wen Jiang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lizabeth Katsnelson
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Robert J Klein
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Caleb M Lindgren
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Weiping Ma
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lei Ma
- ICF, Rockville, MD 20850, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Fernanda Martins Rodrigues
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Robert Oldroyd
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | | | - Pietro Pugliese
- Department of Sciences and Technologies, University of Sannio, Benevento 82100, Italy
| | - Boris Reva
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paul Rudnick
- Spectragen Informatics, Bainbridge Island, WA 98110, USA
| | - Kelly V Ruggles
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Dmitry Rykunov
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Tobias Schraink
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Xiaoyu Song
- Tisch Cancer Institute and Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erik Storrs
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nadezhda V Terekhanova
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | | | - Liang-Bo Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Joshua M Wang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ying Wang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yige Wu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yi Xin
- ICF, Rockville, MD 20850, USA
| | - Lijun Yao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Qing Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Cancer Center and Department of Pathology, Mass. General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Pei Wang
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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Hu L, Ji J, Joshi H, Scott ER, Li F. Estimating the causal effects of multiple intermittent treatments with application to COVID-19. ArXiv 2023:arXiv:2109.13368v4. [PMID: 34981032 PMCID: PMC8722604] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 05/06/2022] [Indexed: 11/21/2022]
Abstract
To draw real-world evidence about the comparative effectiveness of multiple time-varying treatments on patient survival, we develop a joint marginal structural survival model and a novel weighting strategy to account for time-varying confounding and censoring. Our methods formulate complex longitudinal treatments with multiple start/stop switches as the recurrent events with discontinuous intervals of treatment eligibility. We derive the weights in continuous time to handle a complex longitudinal dataset without the need to discretize or artificially align the measurement times. We further use machine learning models designed for censored survival data with time-varying covariates and the kernel function estimator of the baseline intensity to efficiently estimate the continuous-time weights. Our simulations demonstrate that the proposed methods provide better bias reduction and nominal coverage probability when analyzing observational longitudinal survival data with irregularly spaced time intervals, compared to conventional methods that require aligned measurement time points. We apply the proposed methods to a large-scale COVID-19 dataset to estimate the causal effects of several COVID-19 treatments on the composite of in-hospital mortality and ICU admission.
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Affiliation(s)
- Liangyuan Hu
- Department of Biostatistics and Epidemiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Jiayi Ji
- Department of Biostatistics and Epidemiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Himanshu Joshi
- Institute for Health Care Delivery Science, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Erick R. Scott
- Kaiser Permanente Hospital Foundation, Oakland, CA 94611, USA
| | - Fan Li
- Department of Biostatitics, Yale University, New Haven, Connecticut 06510, USA
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6
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Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, Hosseini N, Song X, Petralia F, Calinawan A, Savage SR, Berry AB, Reva B, Ozbek U, Krek A, Ma W, da Veiga Leprevost F, Ji J, Yoo S, Lin C, Voytovich UJ, Huang Y, Lee SH, Bergan L, Lorentzen TD, Mesri M, Rodriguez H, Hoofnagle AN, Herbert ZT, Nesvizhskii AI, Zhang B, Whiteaker JR, Fenyo D, McKerrow W, Wang J, Schürer SC, Stathias V, Chen XS, Barcellos-Hoff MH, Starr TK, Winterhoff BJ, Nelson AC, Mok SC, Kaufmann SH, Drescher C, Cieslik M, Wang P, Birrer MJ, Paulovich AG. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer. Cell 2023; 186:3476-3498.e35. [PMID: 37541199 PMCID: PMC10414761 DOI: 10.1016/j.cell.2023.07.004] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
To improve the understanding of chemo-refractory high-grade serous ovarian cancers (HGSOCs), we characterized the proteogenomic landscape of 242 (refractory and sensitive) HGSOCs, representing one discovery and two validation cohorts across two biospecimen types (formalin-fixed paraffin-embedded and frozen). We identified a 64-protein signature that predicts with high specificity a subset of HGSOCs refractory to initial platinum-based therapy and is validated in two independent patient cohorts. We detected significant association between lack of Ch17 loss of heterozygosity (LOH) and chemo-refractoriness. Based on pathway protein expression, we identified 5 clusters of HGSOC, which validated across two independent patient cohorts and patient-derived xenograft (PDX) models. These clusters may represent different mechanisms of refractoriness and implicate putative therapeutic vulnerabilities.
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Affiliation(s)
- Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Oscar D Murillo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Noshad Hosseini
- Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Xiaoyu Song
- Tisch Cancer Institute, Department of Population Health Science and Policy, Institute for Health Care Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Umut Ozbek
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Jiayi Ji
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Chenwei Lin
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Uliana J Voytovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Yajue Huang
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Sun-Hee Lee
- Departments of Oncology and Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Lindsay Bergan
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Travis D Lorentzen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David Fenyo
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Joshua Wang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, and Institute for Data Science & Computing, University of Miami, Miami, FL 33136, USA
| | - Vasileios Stathias
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, and Institute for Data Science & Computing, University of Miami, Miami, FL 33136, USA
| | - X Steven Chen
- Department of Public Health Sciences, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Mary Helen Barcellos-Hoff
- Helen Diller Family Comprehensive Cancer Center, Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Timothy K Starr
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Boris J Winterhoff
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samuel C Mok
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott H Kaufmann
- Departments of Oncology and Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Charles Drescher
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Marcin Cieslik
- Department of Pathology, Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Michael J Birrer
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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7
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Ji J, Jackson DJ, Leaché AD, Yang Z. Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks. Syst Biol 2023; 72:446-465. [PMID: 36504374 PMCID: PMC10275556 DOI: 10.1093/sysbio/syac077] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 12/07/2021] [Revised: 11/15/2022] [Accepted: 12/01/2022] [Indexed: 10/25/2023] Open
Abstract
In the past two decades, genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HYDE to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program BPP to re-analyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HYDE and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid-speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data. [Bayesian test; BPP; chipmunks; introgression; MSci; multispecies coalescent; Savage-Dickey density ratio.].
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Affiliation(s)
- Jiayi Ji
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Donavan J Jackson
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - Adam D Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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8
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Zheng P, Ge J, Ji J, Zhong J, Chen H, Luo D, Li W, Bi B, Ma Y, Tong W, Han L, Ma S, Zhang Y, Wu J, Zhao Y, Pan R, Fan P, Lu M, Du H. Metabolic engineering and mechanical investigation of enhanced plant autoluminescence. Plant Biotechnol J 2023. [PMID: 37155328 PMCID: PMC10363767 DOI: 10.1111/pbi.14068] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
The fungal bioluminescence pathway (FBP) was identified from glowing fungi, which releases self-sustained visible green luminescence. However, weak bioluminescence limits the potential application of the bioluminescence system. Here, we screened and characterized a C3'H1 (4-coumaroyl shikimate/quinate 3'-hydroxylase) gene from Brassica napus, which efficiently converts p-coumaroyl shikimate to caffeic acid and hispidin. Simultaneous expression of BnC3'H1 and NPGA (null-pigment mutant in A. nidulans) produces more caffeic acid and hispidin as the natural precursor of luciferin and significantly intensifies the original fungal bioluminescence pathway (oFBP). Thus, we successfully created enhanced FBP (eFBP) plants emitting 3 × 1011 photons/min/cm2 , sufficient to illuminate its surroundings and visualize words clearly in the dark. The glowing plants provide sustainable and bio-renewable illumination for the naked eyes, and manifest distinct responses to diverse environmental conditions via caffeic acid biosynthesis pathway. Importantly, we revealed that the biosynthesis of caffeic acid and hispidin in eFBP plants derived from the sugar pathway, and the inhibitors of the energy production system significantly reduced the luminescence signal rapidly from eFBP plants, suggesting that the FBP system coupled with the luciferin metabolic flux functions in an energy-driven way. These findings lay the groundwork for genetically creating stronger eFBP plants and developing more powerful biological tools with the FBP system.
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Affiliation(s)
- Peng Zheng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Jieyu Ge
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiayi Ji
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jingling Zhong
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Hongyu Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Daren Luo
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wei Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Bo Bi
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Yongjun Ma
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wanghui Tong
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Leiqin Han
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Siqi Ma
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yuqi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Westlake Laboratory of Life Sciences and Biomedicine, Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Jianping Wu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Westlake Laboratory of Life Sciences and Biomedicine, Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yanqiu Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Ronghui Pan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Pengxiang Fan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Hao Du
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
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9
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Tang FT, Ji J, Ding J, Ke F, Xu H. [Cervical gastric-type adenocarcinomas with enteroblastoid characteristic: report of a case]. Zhonghua Bing Li Xue Za Zhi 2023; 52:417-420. [PMID: 36973210 DOI: 10.3760/cma.j.cn112151-20221104-00919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Affiliation(s)
- F T Tang
- Department of Pathology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nɑnjinɡ 210029, China
| | - J Ji
- Department of Pathology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, China
| | - J Ding
- Department of Pathology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nɑnjinɡ 210029, China
| | - F Ke
- Department of Pathology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nɑnjinɡ 210029, China
| | - H Xu
- Department of Pathology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nɑnjinɡ 210029, China
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10
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Song X, Ji J, Rothstein JH, Alexeeff SE, Sakoda LC, Sistig A, Achacoso N, Jorgenson E, Whittemore AS, Klein RJ, Habel LA, Wang P, Sieh W. MiXcan: a framework for cell-type-aware transcriptome-wide association studies with an application to breast cancer. Nat Commun 2023; 14:377. [PMID: 36690614 PMCID: PMC9871010 DOI: 10.1038/s41467-023-35888-4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 01/05/2023] [Indexed: 01/25/2023] Open
Abstract
Human bulk tissue samples comprise multiple cell types with diverse roles in disease etiology. Conventional transcriptome-wide association study approaches predict genetically regulated gene expression at the tissue level, without considering cell-type heterogeneity, and test associations of predicted tissue-level expression with disease. Here we develop MiXcan, a cell-type-aware transcriptome-wide association study approach that predicts cell-type-level expression, identifies disease-associated genes via combination of cell-type-level association signals for multiple cell types, and provides insight into the disease-critical cell type. As a proof of concept, we conducted cell-type-aware analyses of breast cancer in 58,648 women and identified 12 transcriptome-wide significant genes using MiXcan compared with only eight genes using conventional approaches. Importantly, MiXcan identified genes with distinct associations in mammary epithelial versus stromal cells, including three new breast cancer susceptibility genes. These findings demonstrate that cell-type-aware transcriptome-wide analyses can reveal new insights into the genetic and cellular etiology of breast cancer and other diseases.
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Affiliation(s)
- Xiaoyu Song
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Jiayi Ji
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph H Rothstein
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stacey E Alexeeff
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Adriana Sistig
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ninah Achacoso
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Alice S Whittemore
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert J Klein
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Pei Wang
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Weiva Sieh
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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11
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Ji J, Li H, Liu C, Chen Y, Li R, Zhang Z. Synthesis, Crystal Structure, and Activity of Cu(II) and Zn(II) Complexes of 2-Mercaptoquinoline N-Oxide. RUSS J GEN CHEM+ 2023. [DOI: 10.1134/s1070363223010243] [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: 03/11/2023]
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12
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Hu L, Ji J. CIMTx: An R Package for Causal Inference with Multiple Treatments using Observational Data. The R Journal 2022. [DOI: 10.32614/rj-2022-058] [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] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | - Jiayi Ji
- Rutgers University School of Public Health
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13
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He L, Yang H, Sun J, Zhai L, Ji J, Ma X, Tang D, Mu Y, Wang L, Iqbal Z, Yang Z. Synthesis and β-Lactamase Inhibition Activity of Diazabicyclooctane Derivatives in Combination with Imipenem. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363222120428] [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: 02/11/2023]
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14
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Hu L, Ji J, Liu H, Ennis R. A Flexible Approach for Assessing Heterogeneity of Causal Treatment Effects on Patient Survival Using Large Datasets with Clustered Observations. Int J Environ Res Public Health 2022; 19:14903. [PMID: 36429621 PMCID: PMC9690785 DOI: 10.3390/ijerph192214903] [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] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Personalized medicine requires an understanding of treatment effect heterogeneity. Evolving toward causal evidence for scenarios not studied in randomized trials necessitates a methodology using real-world evidence. Herein, we demonstrate a methodology that generates causal effects, assesses the heterogeneity of the effects and adjusts for the clustered nature of the data. This study uses a state-of-the-art machine learning survival model, riAFT-BART, to draw causal inferences about individual survival treatment effects, while accounting for the variability in institutional effects; further, it proposes a data-driven approach to agnostically (as opposed to a priori hypotheses) ascertain which subgroups exhibit an enhanced treatment effect from which intervention, relative to global evidence-average treatment effects measured at the population level. Comprehensive simulations show the advantages of the proposed method in terms of bias, efficiency and precision in estimating heterogeneous causal effects. The empirically validated method was then used to analyze the National Cancer Database.
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Affiliation(s)
- Liangyuan Hu
- Department of Biostatistics and Epidemiology, Rutgers University, New Brunswick, NJ 07102, USA
| | - Jiayi Ji
- Department of Biostatistics and Epidemiology, Rutgers University, New Brunswick, NJ 07102, USA
| | - Hao Liu
- Department of Biostatistics and Epidemiology, Rutgers University, New Brunswick, NJ 07102, USA
- Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 07102, USA
| | - Ronald Ennis
- Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 07102, USA
- Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 07102, USA
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15
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Hu L, Ji J, Ennis RD, Hogan JW. A flexible approach for causal inference with multiple treatments and clustered survival outcomes. Stat Med 2022; 41:4982-4999. [PMID: 35948011 PMCID: PMC9588538 DOI: 10.1002/sim.9548] [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] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 01/07/2023]
Abstract
When drawing causal inferences about the effects of multiple treatments on clustered survival outcomes using observational data, we need to address implications of the multilevel data structure, multiple treatments, censoring, and unmeasured confounding for causal analyses. Few off-the-shelf causal inference tools are available to simultaneously tackle these issues. We develop a flexible random-intercept accelerated failure time model, in which we use Bayesian additive regression trees to capture arbitrarily complex relationships between censored survival times and pre-treatment covariates and use the random intercepts to capture cluster-specific main effects. We develop an efficient Markov chain Monte Carlo algorithm to draw posterior inferences about the population survival effects of multiple treatments and examine the variability in cluster-level effects. We further propose an interpretable sensitivity analysis approach to evaluate the sensitivity of drawn causal inferences about treatment effect to the potential magnitude of departure from the causal assumption of no unmeasured confounding. Expansive simulations empirically validate and demonstrate good practical operating characteristics of our proposed methods. Applying the proposed methods to a dataset on older high-risk localized prostate cancer patients drawn from the National Cancer Database, we evaluate the comparative effects of three treatment approaches on patient survival, and assess the ramifications of potential unmeasured confounding. The methods developed in this work are readily available in the R $$ \mathsf{R}\kern.15em $$ package riAFTBART $$ \mathsf{riAFTBART} $$ .
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Affiliation(s)
- Liangyuan Hu
- Department of Biostatistics and EpidemiologyRutgers UniversityPiscatawayNew JerseyUSA
| | - Jiayi Ji
- Department of Biostatistics and EpidemiologyRutgers UniversityPiscatawayNew JerseyUSA
| | - Ronald D. Ennis
- Department of Radiation OncologyCancer Institute of New Jersey of Rutgers UniversityNew BrunswickNew JerseyUSA
| | - Joseph W. Hogan
- Department of BiostatisticsBrown UniversityProvidenceRhode IslandUSA
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16
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Affiliation(s)
- Y H Zhou
- Department of Pathology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China
| | - S Qin
- Department of Pathology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China
| | - J X Yan
- Department of Pathology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China
| | - J Ji
- Department of Pathology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China
| | - T Lan
- Department of Pathology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China
| | - Y Liu
- Department of Pathology, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610042, China
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17
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Du R, Ming J, Geng J, Sui X, Li S, Liu Z, Zhu X, Cai Y, Wang Z, L. Tang, Zhang X, Peng Z, Yan Y, Li Z, Peng Y, Wu A, Li Y, Li Z, Wang W, Ji J. 1215P Neoadjuvant concurrent chemoradiotherapy combined with immunotherapy in the treatment of adenocarcinoma of the oesophagogastric junction: A phase II study. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1333] [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: 11/29/2022] Open
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18
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Rabinowitz LG, Zylberberg HM, Yang J, Gold SL, Chesner J, Ji J, Hu L, Dubinsky M. De Novo Ostomy Placement Is Associated with Increased Outpatient Opioid Use In Patients with Inflammatory Bowel Disease. Dig Dis Sci 2022; 67:4033-4042. [PMID: 34613501 DOI: 10.1007/s10620-021-07257-y] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/13/2021] [Indexed: 12/09/2022]
Abstract
BACKGROUND/AIMS Opioid use is associated with poor outcomes in patients with inflammatory bowel disease (IBD). We aimed to identify novel factors associated with increased outpatient opioid (OPRx) use following IBD-related hospitalization. METHODS This was a retrospective cohort study of IBD patients ≥ 18 years old, hospitalized during 2018. The primary outcome was receiving ≥ 1(OPRx) in the year following index hospitalization (IH), excluding prescriptions written within 2 weeks of discharge. Secondary outcomes included having 1-2 vs ≥ 3 OPRx and rates of healthcare utilization. Univariate and multivariate analyses tested associations with OPRx. RESULTS Of 526 patients analyzed, 209 (40%) received at least 1 OPRx; with a median of 2 [1-3] OPRx. Presence or placement of ostomy at IH, exposure to opioids during IH, ulcerative colitis (UC), mental health comorbidities, admission for surgery and managed on the surgical service, and IBD surgery within 1 year prior to IH were associated with ≥ 1 OPRx on univariate analysis. On multivariable analysis, UC, ostomy placement during IH, anxiety, and inpatient opioid exposure were independently associated with ≥ 1 OPRx. A majority (> 70%) of both inpatient and outpatient opioid prescriptions were written by surgeons. Patients requiring ≥ 3 OPRx had the highest rates of unplanned IBD surgery (56% p = 0.04), all-cause repeat hospitalization (81%, p = 0.003), and IBD-related repeat hospitalization (77%, p = 0.007) in the year following IH. CONCLUSIONS A multimodal approach to pain management for IBD patients, as well as increased recognition that any patient with a de novo ostomy is at particular risk of opioid use, is needed.
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Affiliation(s)
- Loren G Rabinowitz
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA.
| | - Haley M Zylberberg
- Division of Gastroenterology, Department of Medicine, New York Presbyterian Hospital-Columbia University, New York, NY, USA
| | - Jeong Yang
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephanie Lauren Gold
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jaclyn Chesner
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jiayi Ji
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liangyuan Hu
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla Dubinsky
- Department of Pediatrics, Susan and Leonard Feinstein Inflammatory Bowel Disease Clinical Center, Icahn School of Medicine Mount Sinai, New York, NY, USA
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Li L, Ji J, Li Y, Huang YJ, Moon JY, Kim RS. Gestational Diabetes, Subsequent Type 2 Diabetes, and Food Security Status: National Health and Nutrition Examination Survey, 2007-2018. Prev Chronic Dis 2022; 19:E42. [PMID: 35834736 PMCID: PMC9336195 DOI: 10.5888/pcd19.220052] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Introduction Despite many studies linking various risk factors to the association between gestational diabetes and subsequent type 2 diabetes, little is known about how food insecurity affects their association. We aimed to assess how the association between gestational diabetes and subsequent type 2 diabetes varies by food security status among women in the US. Methods This study is a secondary data analysis of 9,505 US women aged 20 years or older who had at least 1 live birth; we used cross-sectional data from the National Health and Nutrition Examination Survey (NHANES) from 2007 through 2018. The main outcome was a diagnosis of type 2 diabetes in the subsequent years after the first live birth. We used multivariable survey-weighted negative binomial regressions to examine whether the association between gestational diabetes and subsequent type 2 diabetes differed by food security status, with and without adjusting for health behavior factors. Results Gestational diabetes was significantly associated with subsequent type 2 diabetes (incidence rate ratio [IRR], 2.57; 95% CI, 2.45–2.69). The association between gestational diabetes and subsequent type 2 diabetes was significantly different by food security status (IRR, 2.34; 95% CI, 2.23–2.45 among food-secure women; IRR, 2.99; 95% CI, 2.70–3.28 among food-insecure women). Conclusion The association between gestational diabetes and subsequent type 2 diabetes differs significantly by food security status. Public health and health care practitioners should consider food security status when designing and implementing diabetes prevention interventions for women with a history of gestational diabetes.
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Affiliation(s)
- Lihua Li
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1077, New York, NY 10029. .,Institute for Healthcare Delivery Science, Icahn School of Medicine at Mount Sinai, New York, New York.,Tisch Cancer Institute, New York, New York
| | - Jiayi Ji
- Department of Biostatistics & Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey
| | - Yan Li
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yuanhui Jasmine Huang
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Ryung S Kim
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
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20
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Cohen BL, Fleshner P, Kane SV, Herfarth HH, Palekar N, Farraye FA, Leighton JA, Katz JA, Cohen RD, Gerich ME, Cross RK, Higgins PDR, Tinsley A, Glover S, Siegel CA, Bohl JL, Iskandar H, Ji J, Hu L, Sands BE. Prospective Cohort Study to Investigate the Safety of Preoperative Tumor Necrosis Factor Inhibitor Exposure in Patients With Inflammatory Bowel Disease Undergoing Intra-abdominal Surgery. Gastroenterology 2022; 163:204-221. [PMID: 35413359 DOI: 10.1053/j.gastro.2022.03.057] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/24/2022] [Accepted: 03/31/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Whether preoperative treatment of inflammatory bowel disease (IBD) with tumor necrosis factor inhibitors (TNFis) increases the risk of postoperative infectious complications remains controversial. The primary aim of this study was to determine whether preoperative exposure to TNFis is an independent risk factor for postoperative infectious complications within 30 days of surgery. METHODS We conducted a multicenter prospective observational study of patients with IBD undergoing intra-abdominal surgery across 17 sites from the Crohn's & Colitis Foundation Clinical Research Alliance. Infectious complications were categorized as surgical site infections (SSIs) or non-SSIs. Current TNFi exposure was defined as use within 12 weeks of surgery, and serum was collected for drug-level analyses. Multivariable models for occurrence of the primary outcome, any infection, or SSI were adjusted by predefined covariates (age, sex, preoperative steroid use, and disease type), baseline variables significantly associated (P < .05) with any infection or SSI separately, and TNFi exposure status. Exploratory models used TNFi exposure based on serum drug concentration. RESULTS A total of 947 patients were enrolled from September 2014 through June 2017. Current TNFi exposure was reported by 382 patients. Any infection (18.1% vs 20.2%, P = .469) and SSI (12.0% vs 12.6%, P = .889) rates were similar in patients currently exposed to TNFis and those unexposed. In multivariable analysis, current TNFi exposure was not associated with any infection (odds ratio, 1.050; 95% confidence interval, 0.716-1.535) or SSI (odds ratio, 1.249; 95% confidence interval, 0.793-1.960). Detectable TNFi drug concentration was not associated with any infection or SSI. CONCLUSIONS Preoperative TNFi exposure was not associated with postoperative infectious complications in a large prospective multicenter cohort.
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Affiliation(s)
- Benjamin L Cohen
- Dr Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Gastroenterology, Hepatology, and Nutrition, Cleveland Clinic Foundation, Cleveland, Ohio.
| | - Phillip Fleshner
- Division of Colorectal Surgery, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California
| | - Sunanda V Kane
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Hans H Herfarth
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, North Carolina
| | - Nicole Palekar
- Department of Gastroenterology, Cleveland Clinic Florida, Weston, Florida
| | - Francis A Farraye
- Department of Medicine and Section of Gastroenterology, Boston Medical Center, Boston University School of Medicine, Boston, Massachusetts; Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida
| | - Jonathan A Leighton
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, Arizona
| | - Jeffry A Katz
- Division of Gastroenterology, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Russell D Cohen
- University of Chicago Medicine Inflammatory Bowel Disease Center, Chicago, Illinois
| | - Mark E Gerich
- Division of Gastroenterology and Hepatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Raymond K Cross
- Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Peter D R Higgins
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Andrew Tinsley
- Department of Medicine, Division of Gastroenterology & Hepatology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Sarah Glover
- Division of Gastroenterology, Hepatology and Nutrition, University of Florida, Gainesville, Florida
| | - Corey A Siegel
- Section of Gastroenterology and Hepatology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Jaime L Bohl
- Department of General Surgery, Wake Forest School of Medicine, Winston-Salem, North Carolina; Department of Surgery, Division of Colon and Rectal Surgery, Virginia Commonwealth University Medical Center, Richmond, Virginia
| | - Heba Iskandar
- Department of Medicine, Division of Digestive Diseases, Emory University, Atlanta, Georgia
| | - Jiayi Ji
- Dr Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Liangyuan Hu
- Dr Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bruce E Sands
- Dr Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York
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Ji J, Ma Y, Sun X, Zhou Y, Wu Y, Ji R. Knowing What to Learn: A Metric-Oriented Focal Mechanism for Image Captioning. IEEE Trans Image Process 2022; 31:4321-4335. [PMID: 35727782 DOI: 10.1109/tip.2022.3183434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Despite considerable progress, image captioning still suffers from the huge difference in quality between easy and hard examples, which is left unexploited in existing methods. To address this issue, we explore the hard example mining in image captioning, and propose a simple yet effective mechanism to instruct the model to pay more attention to hard examples, thereby improving the performance in both general and complex scenarios. We first propose a novel learning strategy, termed Metric-oriented Focal Mechanism (MFM), for hard example mining in image captioning. Differing from the existing strategies for classification tasks, MFM can adopt the generative metrics of image captioning to measure the difficulties of examples, and then up-weight the rewards of hard examples during training. To make MFM applicable to different datasets without tedious parameter tuning, we further introduce an adaptive reward metric called Effective CIDEr (ECIDEr), which considers the data distribution of easy and hard examples during reward estimation. Extensive experiments are conducted on the MS COCO benchmark, and the results show that while maintaining the performance on simple examples, MFM can significantly improve the quality of captions for hard examples. The ECIDEr-based MFM is equipped on the current SOTA method, e.g., DLCT (Luo et al., 2021), which outperforms all existing methods and achieves new state-of-the-art performance on both the off-line and on- line testing, i.e., 134.3 CIDEr for the off-line testing and 136.1 for the on- line testing of MSCOCO. To validate the generalization ability of ECIDEr-based MFM, we also apply it to another dataset, namely Flickr30k, and superior performance gains can also be obtained.
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22
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Hu L, Zou J, Gu C, Ji J, Lopez M, Kale M. A FLEXIBLE SENSITIVITY ANALYSIS APPROACH FOR UNMEASURED CONFOUNDING WITH MULTIPLE TREATMENTS AND A BINARY OUTCOME WITH APPLICATION TO SEER-MEDICARE LUNG CANCER DATA. Ann Appl Stat 2022; 16:1014-1037. [PMID: 36644682 PMCID: PMC9835106 DOI: 10.1214/21-aoas1530] [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] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In the absence of a randomized experiment, a key assumption for drawing causal inference about treatment effects is the ignorable treatment assignment. Violations of the ignorability assumption may lead to biased treatment effect estimates. Sensitivity analysis helps gauge how causal conclusions will be altered in response to the potential magnitude of departure from the ignorability assumption. However, sensitivity analysis approaches for unmeasured confounding in the context of multiple treatments and binary outcomes are scarce. We propose a flexible Monte Carlo sensitivity analysis approach for causal inference in such settings. We first derive the general form of the bias introduced by unmeasured confounding, with emphasis on theoretical properties uniquely relevant to multiple treatments. We then propose methods to encode the impact of unmeasured confounding on potential outcomes and adjust the estimates of causal effects in which the presumed unmeasured confounding is removed. Our proposed methods embed nested multiple imputation within the Bayesian framework, which allow for seamless integration of the uncertainty about the values of the sensitivity parameters and the sampling variability, as well as use of the Bayesian Additive Regression Trees for modeling flexibility. Expansive simulations validate our methods and gain insight into sensitivity analysis with multiple treatments. We use the SEER-Medicare data to demonstrate sensitivity analysis using three treatments for early stage non-small cell lung cancer. The methods developed in this work are readily available in the R package SAMTx.
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Affiliation(s)
- Liangyuan Hu
- Department of Biostatistics and Epidemiology, Rutgers University
| | - Jungang Zou
- Department of Biostatistics, Columbia University
| | | | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai
| | | | - Minal Kale
- Department of Medicine, Icahn School of Medicine at Mount Sinai
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23
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Costable NJ, Borman ZA, Ji J, Dubinsky MC, Ungaro RC. Prior Immunogenicity to Anti-TNF Biologics Is Not Associated with Increased Anti-drug Antibodies to Vedolizumab or Ustekinumab. Dig Dis Sci 2022; 67:2480-2484. [PMID: 34021427 PMCID: PMC8609532 DOI: 10.1007/s10620-021-07046-7] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/08/2021] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Patients with inflammatory bowel disease (IBD) on biologic therapy may lose response to anti-tumor necrosis factor agents (anti-TNFs) due to the development of anti-drug antibodies (ADAs). A history of anti-TNF ADA increases the risk of developing ADA to subsequent anti-TNFs; however, it is not known whether ADA to anti-TNFs increases the risk of ADA development to vedolizumab (VDZ) or ustekinumab (UST). We aimed to investigate whether prior history of ADA to anti-TNF increases the risk of ADA to VDZ and UST. METHODS We conducted a retrospective cohort study of patients at a tertiary care IBD center over the course of four years who had previous anti-TNF drug and ADA level data during maintenance treatment and subsequent VDZ or UST drug and antibody levels, all collected as standard of care. The primary outcome was the rate of ADA development to VDZ and UST in patients with and without prior anti-TNF immunogenicity. Descriptive statistics summarized the data and univariate tested associations. RESULTS Of the 152 IBD patients analyzed, 41 (27%) had a history of previous anti-TNF ADA with 22 (53.7%) having simultaneously undetectable anti-TNF drug levels. There was no significant difference in the rates of ustekinumab and vedolizumab ADA development between patients with prior ADA and patients without prior ADA (1/41 [2.7%] vs 1/111 [0.9%]; p = 0.54). There was also no difference in concomitant immunomodulator use with ustekinumab or vedolizumab initiation in patients with or without prior ADA (13/41 [31.7%] vs 31/111 [27.9%], p = 0.84). Neither patient who developed ADA to VDZ or UST was on concomitant immunomodulator at drug initiation, and both patients had detectable drug levels at the time of antibody detection. CONCLUSIONS We observed that prior immunogenicity to anti-TNF agents does not confer an increased risk of immunogenicity to ustekinumab or vedolizumab. Our data support the use of vedolizumab or ustekinumab as monotherapy for the treatment of IBD.
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Affiliation(s)
| | - Zachary A. Borman
- Department of Medicine, Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Marla C. Dubinsky
- Department of Medicine, Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Ryan C. Ungaro
- Department of Medicine, Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, USA
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Li L, Hu L, Ji J, Mckendrick K, Moreno J, Kelley AS, Mazumdar M, Aldridge M. Determinants of Total End-of-Life Health Care Costs of Medicare Beneficiaries: A Quantile Regression Forests Analysis. J Gerontol A Biol Sci Med Sci 2022; 77:1065-1071. [PMID: 34153101 PMCID: PMC9071433 DOI: 10.1093/gerona/glab176] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND To identify and rank the importance of key determinants of end-of-life (EOL) health care costs, and to understand how the key factors impact different percentiles of the distribution of health care costs. METHOD We applied a principled, machine learning-based variable selection algorithm, using Quantile Regression Forests, to identify key determinants for predicting the 10th (low), 50th (median), and 90th (high) quantiles of EOL health care costs, including costs paid for by Medicare, Medicaid, Medicare Health Maintenance Organizations (HMOs), private HMOs, and patient's out-of-pocket expenditures. RESULTS Our sample included 7 539 Medicare beneficiaries who died between 2002 and 2017. The 10th, 50th, and 90th quantiles of EOL health care cost are $5 244, $35 466, and $87 241, respectively. Regional characteristics, specifically, the EOL-Expenditure Index, a measure for regional variation in Medicare spending driven by physician practice, and the number of total specialists in the hospital referral region were the top 2 influential determinants for predicting the 50th and 90th quantiles of EOL costs but were not determinants of the 10th quantile. Black race and Hispanic ethnicity were associated with lower EOL health care costs among decedents with lower total EOL health care costs but were associated with higher costs among decedents with the highest total EOL health care costs. CONCLUSIONS Factors associated with EOL health care costs varied across different percentiles of the cost distribution. Regional characteristics and decedent race/ethnicity exemplified factors that did not impact EOL costs uniformly across its distribution, suggesting the need to use a "higher-resolution" analysis for examining the association between risk factors and health care costs.
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Affiliation(s)
- Lihua Li
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Healthcare Delivery Science, Mount Sinai Health System, New York, New York, USA
- Tisch Cancer Institute, New York, New York, USA
| | - Liangyuan Hu
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Healthcare Delivery Science, Mount Sinai Health System, New York, New York, USA
- Tisch Cancer Institute, New York, New York, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Healthcare Delivery Science, Mount Sinai Health System, New York, New York, USA
- Tisch Cancer Institute, New York, New York, USA
| | - Karen Mckendrick
- Brookdale Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jaison Moreno
- Brookdale Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Amy S Kelley
- Brookdale Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Madhu Mazumdar
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Institute for Healthcare Delivery Science, Mount Sinai Health System, New York, New York, USA
- Tisch Cancer Institute, New York, New York, USA
| | - Melissa Aldridge
- Brookdale Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Rodriguez-Tirado C, Kale N, Carlini MJ, Shrivastava N, Rodrigues AA, Khalil B, Bravo-Cordero JJ, Alexander M, Ji J, Hong Y, Behbod F, Sosa MS. NR2F1 is a barrier to dissemination of early stage breast cancer cells. Cancer Res 2022; 82:2313-2326. [PMID: 35471456 PMCID: PMC9203932 DOI: 10.1158/0008-5472.can-21-4145] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/09/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]
Abstract
Cancer cells can disseminate during very early and sometimes asymptomatic stages of tumor progression. Though biological barriers to tumorigenesis have been identified and characterized, the mechanisms that limit early dissemination remain largely unknown. We report here that the orphan nuclear receptor NR2F1/COUP-TF1 serves as a barrier to early dissemination. NR2F1 expression was decreased in patient ductal carcinoma in situ (DCIS) samples. High-resolution intravital imaging of HER2+ early stage cancer cells revealed that loss of function of NR2F1 increased in vivo dissemination and was accompanied by decreased E-cadherin expression, activation of WNT-dependent β-catenin signaling, disorganized laminin 5 deposition, and increased expression of EMT genes such as TWIST1, ZEB1, and PRRX1. Furthermore, downregulation of NR2F1 promoted a hybrid luminal/basal phenotype. NR2F1 expression was positively regulated by p38α signaling and repressed by HER2 and WNT4 pathways. Lastly, early cancer cells with NR2F1LOW/PRRX1HIGH staining were observed in DCIS samples. Together, these findings reveal the existence of an inhibitory mechanism of dissemination regulated by NR2F1 in early stage breast cancer cells.
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Affiliation(s)
| | - Nupura Kale
- University of California, San Francisco, San Francisco, CA, United States
| | | | | | | | - Bassem Khalil
- Western Atlantic University School of Medicine, Plantation, FL, United States
| | - Jose J Bravo-Cordero
- Icahn School of Medicine, Tisch Cancer Institute at Mount Sinai, New York, United States
| | - Melissa Alexander
- Icahn School of Medicine at Mount Sinai, New York,, NY, United States
| | - Jiayi Ji
- Icahn School of Medicine at Mount Sinai, New York,, NY, United States
| | - Yan Hong
- University of Kansas Medical Center, Kansas City, KS, United States
| | - Fariba Behbod
- Kansas University Medical Center, Kansas City, KS, United States
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Xie X, Ji J, Chen X, Xu W, Chen H, Zhu S, Wu J, Wu Y, Sun Y, Sai W, Liu Z, Xiao M, Bao B. Human umbilical cord mesenchymal stem cell-derived exosomes carrying hsa-miRNA-128-3p suppress pancreatic ductal cell carcinoma by inhibiting Galectin-3. Clin Transl Oncol 2022; 24:517-531. [PMID: 34811696 DOI: 10.1007/s12094-021-02705-7] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/31/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is one of the most fatal malignant tumors of the digestive system. Many patients are diagnosed at an advanced stage and lose eligibility for surgery. Moreover, there are few effective methods for treating pancreatic ductal cell carcinoma. Increasing attention has been given to microRNAs (miRNAs) and their regulatory roles in tumor progression. In this study, we investigated the effects of exosomes extracted from human umbilical cord mesenchymal stem cells (HUCMSCs) carrying hsa-miRNA-128-3p on pancreatic cancer cells. METHODS Based on existing experimental and database information, we selected Galectin-3, which is associated with pancreatic cancer, and the corresponding upstream hsa-miRNA-128-3p. We extracted HUCMSCs from a fresh umbilical cord, hsa-miRNA-128-3p was transfected into HUCMSCs, and exosomes containing hsa-miRNA-128-3p were extracted and collected. The effect of exosomes rich in hsa-miRNA-128-3p on pancreatic cancer cells was analyzed. RESULTS The expression of Galectin-3 in normal pancreatic duct epithelial cells was significantly lower than that in PDAC cell lines. We successfully extracted HUCMSCs from the umbilical cord and transfected hsa-miRNA-128-3p into HUCMSCs. Then we demonstrated that HUCMSC-derived exosomes with hsa-miRNA-128-3p could suppress the proliferation, invasion, and migration of PANC-1 cells in vitro by targeting Galectin-3. CONCLUSION Hsa-miRNA-128-3p could be considered as a potential therapy for pancreatic cancer. We provided a new idea for targeted therapy of PDAC.
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Affiliation(s)
- X Xie
- Department of Gastroenterology, Affiliated Hospital and Medical School of Nantong University, Nantong, 226001, Jiangsu, China
| | - J Ji
- Department of Gastroenterology, Affiliated Hospital and Medical School of Nantong University, Nantong, 226001, Jiangsu, China
| | - X Chen
- Office of Infection Management, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - W Xu
- Department of Gastroenterology, Second People's Hospital of Nantong, Nantong, 226001, China
| | - H Chen
- Office of Infection Management, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - S Zhu
- Medical School of Nantong University Oral Medicine, Nantong, 226001, Jiangsu, China
| | - J Wu
- Department of Gastroenterology, Affiliated Hospital and Medical School of Nantong University, Nantong, 226001, Jiangsu, China
| | - Y Wu
- Department of Gastroenterology, Affiliated Hospital and Medical School of Nantong University, Nantong, 226001, Jiangsu, China
| | - Y Sun
- Blood Center of Jiangsu Province, Nanjing, 210000, Jiangsu, China
| | - W Sai
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Z Liu
- Department of Gastroenterology, Affiliated Hospital and Medical School of Nantong University, Nantong, 226001, Jiangsu, China
| | - M Xiao
- Department of Gastroenterology, Affiliated Hospital and Medical School of Nantong University, Nantong, 226001, Jiangsu, China.
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.
| | - B Bao
- Department of Gastroenterology, Affiliated Hospital and Medical School of Nantong University, Nantong, 226001, Jiangsu, China.
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Veluswamy R, Hu L, Smith C, Ji J, Wang X, Wisnivesky J, Morillo J, Kale MS. Immunotherapy Outcomes in Individuals with Non-Small Cell Lung Cancer and Poor Performance Status. JNCI Cancer Spectr 2022; 6:6534340. [PMID: 35603847 PMCID: PMC8921740 DOI: 10.1093/jncics/pkac013] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/17/2021] [Accepted: 12/28/2021] [Indexed: 11/24/2022] Open
Abstract
Background Patients with non–small cell lung cancer (NSCLC) treated in real-world practice typically have worse performance status (PS) compared with clinical trial patients, and the effectiveness of immunotherapy in this population in unknown. In this study, we assessed the effectiveness of standard of care immunotherapy for the first-line treatment of stage IV patients with NSCLC with Eastern Cooperative Oncology Group (ECOG) PS greater than or equal to 2. Methods We selected ECOG PS greater than or equal to 2 patients from real-world oncology data from a deidentified database and included them if they were diagnosed with stage IV NSCLC and had documented Programmed death-ligand 1 [PD-(L)1] expression greater than 0. Patients with tumor PD-(L)1 expression of at least 50% treated with pembrolizumab monotherapy were compared with those who did not have any documented treatment. Patients with tumor PD-(L)1 expression less than 50% treated with pembrolizumab and chemotherapy were compared with those treated with pembrolizumab monotherapy and those without documented treatment. Results In our propensity score–adjusted analysis, patients with ECOG PS of at least 2 and tumor PD-(L)1 expression of at least 50% treated with pembrolizumab monotherapy had statistically significantly better real-world overall survival compared with those without documented treatment (adjusted hazard ratio [HR] = 0.39, 95% confidence internal [CI] = 0.32 to 0.47). For patients with tumor PD-(L)1 expression less than 50%, there was also a statistically significant real-world overall survival benefit for those who received treatment either with combination pembrolizumab plus chemotherapy (adjusted HR = 0.39, 95% CI = 0.32 to 0.46) or pembrolizumab monotherapy (adjusted HR = 0.55, 95% CI = 0.41 to 0.70) compared with patients receiving no documented treatment. Conclusions Among a highly representative sample of patients with advanced NSCLC and poor PS, our findings suggest that immunotherapy may provide an important survival benefit in individuals with high PD-(L)1–expressing tumors and in conjunction with chemotherapy in tumors with low PD-(L)1 expression.
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Affiliation(s)
- Rajwanth Veluswamy
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, NY, NY, USA
| | - Liangyuan Hu
- Department of Biostatistics and Epidemiology, Rutgers University, NJ, USA
| | - Cardinale Smith
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, NY, NY, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Institute for Translational Epidemiology at Mount Sinai, NY, NY, USA
| | | | - Juan Wisnivesky
- Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, NY, NY, USA
| | - Jose Morillo
- Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, NY, NY, USA
| | - Minal S Kale
- Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, NY, NY, USA
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Rodriguez-Tirado C, Kale N, Carlini MJ, Shrivastava N, Rodrigues A, Khalil B, Bravo-Cordero JJ, Alexander M, Ji J, Sosa MS. Abstract P3-06-03: NR2F1 is a barrier to dissemination of early-evolved mammary cancer cells. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p3-06-03] [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
Pre-malignant cells disseminate during very early and sometimes asymptomatic stages of tumor progression. Once settled in permissive environments at secondary organs, they can act as a source for metastasis (e.g. in breast, pancreatic, colon, melanoma and lung carcinomas), thus emerging as important players in future prognosis. Granted that biological barriers to tumorigenesis exist, there must also be limiting steps to early dissemination in pre-malignant cells, all of which remain largely unknown. We report that the orphan nuclear receptor NR2F1/COUP-TF1, downstream of Her2 signaling via p38alpha serves as a barrier to early dissemination in pre-malignant breast cells. Our work shows that NR2F1 expression is positively regulated by p38α-MAPK pathway and inhibited by HER2 oncogenic signaling pathway. Furthermore, NR2F1 downregulation in human and murine pre-malignant cell lines led to a partial epithelial-to-mesenchymal transition characterized by decreased E-cadherin expression and β-catenin membrane localization, disorganized laminin 5 deposition, and increased expression of CK14, TWIST1, ZEB1 and PRRX1, thus explaining an increased motility and dissemination of early cells upon loss of NR2F1. Interestingly, NR2F1 lost also maintained epithelial markers (like CK18), suggesting an hybrid luminal-mesenchymal phenotype that could favor cellular plasticity to adapt to distant sites. We also showed that NR2F1 blocked b-catenin nuclear localization via a WNT-dependent pathway. Significantly, downregulation of NR2F1 increased the in vivo dissemination potential of pre-malignant cells to lungs in a HER2-dependent manner. Lastly, Nr2f1 expression was downregulated in non-invasive DCIS biopsies when compared to benign adjacent tissue, and its expression was inversely correlated to Prrx1 levels. The inverse correlation between Nr2f1 and Prrx1 levels was lost in genetically evolved primary tumors, which suggests that a unique inhibitory mechanism of dissemination dominates at early stages of tumor progression. Overall, our data suggest the existence of an inhibitory mechanism of dissemination regulated by NR2F1 downstream of HER2 signaling in premalignant breast cells and propose that therapeutic strategies that aim to maintain NR2F1 expression could reduce dissemination of premalignant cells and delay relapses.
Citation Format: Carolina Rodriguez-Tirado, Nupura Kale, Maria Jose Carlini, Nitisha Shrivastava, Alcina Rodrigues, Bassem Khalil, Jose Javier Bravo-Cordero, Melissa Alexander, Jiayi Ji, Maria Soledad Sosa. NR2F1 is a barrier to dissemination of early-evolved mammary cancer cells [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 P3-06-03.
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Affiliation(s)
| | - Nupura Kale
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | | | - Bassem Khalil
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | - Jiayi Ji
- Icahn School of Medicine at Mount Sinai, New York, NY
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Zhao Y, Li F, Li S, Ji J, Qiao W, Fang J. Aluminum chloride induces G0/G1 phase arrest via regulating the reactive oxygen species-depended non-canonical STAT1 pathway in hFOB1.19 cells. Hum Exp Toxicol 2022; 41:9603271221129846. [PMID: 36154299 DOI: 10.1177/09603271221129846] [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] [Indexed: 11/16/2022]
Abstract
Treatment with aluminum chloride (AlCl3) suppresses the growth of osteoblastic cells; however, the molecular mechanisms underlying the impact of AlCl3 on cell growth have not been fully characterized. In this study, we observed that exposure of hFOB1.19 cells to AlCl3 arrested cells at G0/G1 phase by inducing p21 expression. Further studies indicated that AlCl3 upregulated the phosphorylation level of signal transducer and activator of transcription 1 (STAT1) at serine 727 site (Ser727). By chromatin immunoprecipitation and electrophoretic mobility shift assay, we found that AlCl3 promoted STAT1/DNA binding activity to p21 promoter, thus resulting in the upregulation of p21. Moreover, siRNA-mediated knockdown of STAT1 attenuated p21 level induced by AlCl3. Notably, using hFOB1.19 cells stably expressing dominant-negative STAT1 (Ser727Ala), we demonstrated that phosphorylation of STAT1 at Ser727 site is required for p21-mediated cycle arrest induced by AlCl3. Mechanism investigation indicated that AlCl3 stimulated the phosphorylation of JNK, and administration of JNK inhibitor SP600125 prevented AlCl3-induced G0/G1 arrest through suppressing the phosphorylation of STAT1. Notably, pretreatment with N-acetyl-cysteine, a reactive oxygen species scavenger, conferred a significantly inhibitory effect on AlCl3-mediated activation of JNK/STAT1 signaling pathway. Taken together, our findings provide the molecular mechanism for G0/G1 arrest induced by AlCl3 in osteoblastic cells.
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Affiliation(s)
- Y Zhao
- Department of Orthopaedics, 12561The First Affiliated Hospital of Henan Polytechnic University. The Second People's Hospital of Jiaozuo City, Jiaozuo, P.R. China
| | - F Li
- Otolaryngology Head and Neck Surgery, 12561The First Affiliated Hospital of Henan Polytechnic University. The Second People's Hospital of Jiaozuo City, Jiaozuo, P.R. China
| | - S Li
- Department of Orthopaedics, 12561The First Affiliated Hospital of Henan Polytechnic University. The Second People's Hospital of Jiaozuo City, Jiaozuo, P.R. China
| | - J Ji
- Department of Orthopaedics, 618971The Central Hospital of Kaifeng City, Kaifeng, P.R. China
| | - W Qiao
- Department of Orthopaedics, 12561The First Affiliated Hospital of Henan Polytechnic University. The Second People's Hospital of Jiaozuo City, Jiaozuo, P.R. China
| | - J Fang
- Department of Orthopaedics, 12561The First Affiliated Hospital of Henan Polytechnic University. The Second People's Hospital of Jiaozuo City, Jiaozuo, P.R. China
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Wu XH, Yao ZQ, Zhao QQ, Chen S, Hu ZZ, Xie Z, Chen LY, Ji J, Chen F, Zhang XH, Xie QM. Development and Application of a Reverse-transcription Recombinase-Aided Amplification Assay for Subgroup J Avian Leukosis Virus. Poult Sci 2022; 101:101743. [PMID: 35240352 PMCID: PMC8889409 DOI: 10.1016/j.psj.2022.101743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/15/2022] [Accepted: 01/17/2022] [Indexed: 11/29/2022] Open
Abstract
Subgroup J Avian leukosis virus (ALV-J) is an important pathogen of poultry tumor diseases. Since its discovery, it has caused significant economic losses to the poultry industry. Thus, the rapid detection of molecular level with strong specificity is particularly important whether poultry are infected with ALV-J. In this study, we designed primers and probe for real-time fluorescent reverse-transcription recombinase-aided amplification assay (RT-RAA) based on the ALV-J gp85 sequence. We had established a real-time fluorescent RT-RAA method and confirmed this system by verifying the specificity and sensitivity of the primers and probe. In addition, repeatability tests and clinical sample regression tests were used for preliminary evaluation of this detection method. The sensitivity of established method was about 101 copies/μL, and the repeatability of the CV of the CT value is 4%, indicating repeatability is good. Moreover, there was no cross-reactivity with NDV, IBV, IBDV, H9N2, MDV, and REV, and other avian leukosis virus subgroups, such as subgroups A, B, C, D, K and E. Importantly, the real-time fluorescent RT-RAA completed the test within 30 min at a constant temperature of 41°C. Forty-two clinical samples with known background were tested, and the test results were coincided with 100%. Overall, these results suggested that the real-time fluorescent RT-RAA developed in this study had strong specificity, high sensitivity, and good feasibility. The method is simple, easy, and portable, that is suitable for clinical and laboratory diagnosis, and provides technical support for the prevention and control of ALV-J.
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Affiliation(s)
- X H Wu
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, P. R. China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, P. R. China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, P. R. China
| | - Z Q Yao
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, P. R. China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, P. R. China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, P. R. China
| | - Q Q Zhao
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, P. R. China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, P. R. China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, P. R. China
| | - S Chen
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, P. R. China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, P. R. China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, P. R. China
| | - Z Z Hu
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, P. R. China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, P. R. China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, P. R. China
| | - Z Xie
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, P. R. China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, P. R. China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, P. R. China
| | - L Y Chen
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, P. R. China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, P. R. China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, P. R. China
| | - J Ji
- Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, P. R. China
| | - F Chen
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, P. R. China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, P. R. China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, P. R. China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642, P. R. China
| | - X H Zhang
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, P. R. China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, P. R. China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, P. R. China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642, P. R. China
| | - Q M Xie
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, P. R. China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, P. R. China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, P. R. China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642, P. R. China.
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Chen KB, Ji J, Li H, Chen XW, Ding X. [Effect of daily average temperature on the incidence of allergic rhinitis in Lanzhou]. Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2021; 56:1300-1306. [PMID: 34963218 DOI: 10.3760/cma.j.cn115330-20210330-00158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Objective: To evaluate the effect of daily average temperature on the atteck of allergic rhinitis (AR) by analyzing the changes of the outpatient visits of AR in Lanzhou. Methods: The meteorological and air pollution data of Lanzhou City and the outpatient visits of AR in Departments of Otorhinolaryngology and head and neck surgery of The First Hospital of Lanzhou University, The Second Hospital of Lanzhou University and Gansu Provincial People's Hospital from 2013 to 2017 were collected to describe the meteorological factors, air pollutants and the outpatient visits of AR. The correlation among the three factors was then analyzed by Spearman rank correlation analysis. Using the distributed lag non-linear model, the relationship between daily average temperature and the number of daily outpatient visits of AR was studied and stratified by gender and age with the long-term trend, seasonal trend and other confounding factors controlled. Results: From 2013 to 2017, the outpatient visits of AR in the above three hospitals reached 20 008 person times. Daily average temperature in Lanzhou showed a non-linear correlation to the outpatient visits of AR, with a certain lag effect. When the daily average temperature was 22 ℃ and the cumulative lag was 21 days (lag 0-21 d), the relative risk (RR) peaked at 4.851 (95%CI: 3.986-5.904). The effect of relatively low temperature (2.3 ℃, P25), relatively high temperature (19.8 ℃, P75) and high temperature (25.5 ℃, P95) on lag 0-21 d were the highest, which were 1.761 (95%CI: 1.375-2.255), 4.299 (95%CI: 3.574-5.171) and 3.656 (95%CI: 3.046-4.389), respectively. According to the stratified analysis, low and relatively low temperature had more significant effect on the outpatient visits of AR among women and people aged 0-14 years. When lag was 0-21 days, the RR value of low temperature for female outpatient visits of AR was 1.433 (95%CI: 1.105-1.860); the RR value of relatively low temperature for female outpatient visits of AR was 1.879 (95%CI: 1.460-2.419); the RR value of low temperature for AR outpatient visits for people aged 0-14 years was 1.511 (95%CI: 0.999-2.287), the RR value of relatively low temperature for AR outpatient visits for people aged 0-14 years was 2.051 (95%CI: 1.383-3.042). Relatively high temperature, on the other hand, had a more significant effect on men and people aged 15-59 years. High temperature had a greater impact on the number of AR outpatients in men and people aged 0-14 years. Conclusions: Temperature may be an important influencing factor of AR onset in Lanzhou. At relatively high temperature (19.8 ℃), the risk of AR outpatient visits is significantly increased, and the cumulative lagged effects are observed. The sensitivity of AR patients to temperature is different in different genders and ages.
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Affiliation(s)
- K B Chen
- Department of Otorhinolaryngology Head and Neck Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - J Ji
- Department of Otorhinolaryngology Head and Neck Surgery, The First People's Hospital of Lanzhou, Lanzhou 730000, China
| | - H Li
- Department of Otorhinolaryngology Head and Neck Surgery, Gansu Provincial People's Hospital, Lanzhou 730000, China
| | - X W Chen
- Department of Otorhinolaryngology Head and Neck Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - X Ding
- Department of Pediatrics, The Second Hospital of Lanzhou University, Lanzhou 730000, China
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Walshe M, Nayeri S, Ji J, Hernandez-Rocha C, Sabic K, Hu L, Giri M, Nayar S, Brant S, McGovern DPB, Rioux JD, Duerr RH, Cho JH, Schumm PL, Lazarev M, Silverberg MS. A Role for CXCR3 Ligands as Biomarkers of Post-Operative Crohn's Disease Recurrence. J Crohns Colitis 2021; 16:900-910. [PMID: 34698823 PMCID: PMC9282882 DOI: 10.1093/ecco-jcc/jjab186] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Crohn's disease [CD] recurrence following ileocolic resection [ICR] is common. We sought to identify blood-based biomarkers associated with CD recurrence. METHODS CD patients undergoing ICR were recruited across six centres. Serum samples were obtained at post-operative colonoscopy. A multiplex immunoassay was used to analyse 92 inflammation-related proteins [Olink Proteomics]. Bayesian analysis was used to identify proteins associated with increasing Rutgeerts score. Identified proteins were used in receiver operating characteristic [ROC] analysis to examine the ability to identify CD recurrence [Rutgeerts score ≥i2]. Existing single cell data were interrogated to further elucidate the role of the identified proteins. RESULTS Data from 276 colonoscopies in 213 patients were available. Median time from surgery to first and second colonoscopy was 7 (interquartile range [IQR] 6-9) and 19 [IQR 16-23] months, respectively. Disease recurrence was evident at 60 [30%] first and 36 [49%] second colonoscopies. Of 14 proteins significantly associated with Rutgeerts score, the strongest signal was seen for CXCL9 and MMP1. Among patients on anti-tumour necrosis factor drugs, CXCL9 and CXCL11 were most strongly associated with Rutgeerts score. Both are CXCR3 ligands. Incorporation of identified proteins into ROC analysis improved the ability to identify disease recurrence as compared to C-reactive protein alone: area under the curve [AUC] 0.75 (95% confidence interval [CI]: 0.66-0.82] vs 0.64 [95% CI 0.56-0.72], p = 0.012. Single cell transcriptomic data provide evidence that innate immune cells are the primary source of the identified proteins. CONCLUSIONS CXCR3 ligands are associated with CD recurrence following ICR. Incorporation of novel blood-based candidate biomarkers may aid in identification of CD recurrence.
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Affiliation(s)
- Margaret Walshe
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada,Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Shadi Nayeri
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cristian Hernandez-Rocha
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada,Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Ksenija Sabic
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liangyuan Hu
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shikha Nayar
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven Brant
- Crohn’s and Colitis Center of New Jersey, Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - John D Rioux
- Research Centre, Montreal Heart Institute, Montréal, QC, Canada,Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA,USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Phil L Schumm
- Department of Health Sciences, University of Chicago, Chicago, IL, USA
| | | | - Mark S Silverberg
- Corresponding author: Dr Mark Silverberg, MD, PhD, FRCPC, University of Toronto, Division of Gastroenterology, Mount Sinai Hospital Inflammatory Bowel Disease Centre, 441–600 University Avenue, Toronto, Ontario, M5G1X5, Canada. Tel: +1-416-586-4800 ext 8236; Fax: +1-416-619-5524;
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Abstract
Variable selection in the presence of both missing covariates and outcomes is an important statistical research topic. Parametric regression are susceptible to misspecification, and as a result are sub-optimal for variable selection. Flexible machine learning methods mitigate the reliance on the parametric assumptions, but do not provide as naturally defined variable importance measure as the covariate effect native to parametric models. We investigate a general variable selection approach when both the covariates and outcomes can be missing at random and have general missing data patterns. This approach exploits the flexibility of machine learning models and bootstrap imputation, which is amenable to nonparametric methods in which the covariate effects are not directly available. We conduct expansive simulations investigating the practical operating characteristics of the proposed variable selection approach, when combined with four tree-based machine learning methods, extreme gradient boosting, random forests, Bayesian additive regression trees, and conditional random forests, and two commonly used parametric methods, lasso and backward stepwise selection. Numeric results suggest that, extreme gradient boosting and Bayesian additive regression trees have the overall best variable selection performance with respect to the F1 score and Type I error, while the lasso and backward stepwise selection have subpar performance across various settings. There is no significant difference in the variable selection performance due to imputation methods. We further demonstrate the methods via a case study of risk factors for 3-year incidence of metabolic syndrome with data from the Study of Women's Health Across the Nation.
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Affiliation(s)
- Liangyuan Hu
- Department of Biostatistics and Epidemiology, 242612Rutgers University School of Public Health, USA
| | - Jung-Yi Joyce Lin
- Department of Population Health Science & Policy, 5925Icahn School of Medicine at Mount Sinai, USA
| | - Jiayi Ji
- Department of Population Health Science & Policy, 5925Icahn School of Medicine at Mount Sinai, USA
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Hirten RP, Danieletto M, Scheel R, Shervey M, Ji J, Hu L, Sauk J, Chang L, Arnrich B, Bӧttinger E, Dudley J, Keefer L, Sands BE. Longitudinal Autonomic Nervous System Measures Correlate With Stress and Ulcerative Colitis Disease Activity and Predict Flare. Inflamm Bowel Dis 2021; 27:1576-1584. [PMID: 33382065 DOI: 10.1093/ibd/izaa323] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND Differences in autonomic nervous system function, measured by heart rate variability (HRV), have been observed between patients with inflammatory bowel disease and healthy control patients and have been associated in cross-sectional studies with systemic inflammation. High HRV has been associated with low stress. METHODS Patients with ulcerative colitis (UC) were followed for 9 months. Their HRV was measured every 4 weeks using the VitalPatch, and blood was collected at baseline and every 12 weeks assessing cortisol, adrenocorticotropin hormone, interleukin-1β, interleukin-6, tumor necrosis factor-α, and C-reactive protein (CRP). Stool was collected at enrollment and every 6 weeks for fecal calprotectin. Surveys assessing symptoms, stress, resilience, quality of life, anxiety, and depression were longitudinally collected. RESULTS Longitudinally evaluated perceived stress was significantly associated with systemic inflammation (CRP, P = 0.03) and UC symptoms (P = 0.02). There was a significant association between HRV and stress (low-frequency to high-frequency power [LFHF], P = 0.04; root mean square of successive differences [RMSSD], P = 0.04). The HRV was associated with UC symptoms (LFHF, P = 0.03), CRP (high frequency, P < 0.001; low frequency, P < 0.001; RMSSD, P < 0.001), and fecal calprotectin (high frequency, P < 0.001; low frequency, P < 0.001; RMSSD, P < 0.001; LFHF, P < 0.001). Significant changes in HRV indices from baseline developed before the identification of a symptomatic or inflammatory flare (P < 0.001). CONCLUSIONS Longitudinally evaluated HRV was associated with UC symptoms, inflammation, and perceived and physiological measures of stress. Significant changes in HRV were observed before the development of symptomatic or inflammatory flare.
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Affiliation(s)
- Robert P Hirten
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Matteo Danieletto
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert Scheel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mark Shervey
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Liangyuan Hu
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jenny Sauk
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Lin Chang
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Bert Arnrich
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Erwin Bӧttinger
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joel Dudley
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Laurie Keefer
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bruce E Sands
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Ji J, Chen L, Zhao W, Wang Y, Wang J. 151 A Method for in vitro assessment of Pollutant Removal Based on a Tailor-made Pollution Chamber. J Invest Dermatol 2021. [DOI: 10.1016/j.jid.2021.08.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Hu L, Ji J, Li F. Estimating heterogeneous survival treatment effect in observational data using machine learning. Stat Med 2021; 40:4691-4713. [PMID: 34114252 PMCID: PMC9827499 DOI: 10.1002/sim.9090] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 01/12/2023]
Abstract
Methods for estimating heterogeneous treatment effect in observational data have largely focused on continuous or binary outcomes, and have been relatively less vetted with survival outcomes. Using flexible machine learning methods in the counterfactual framework is a promising approach to address challenges due to complex individual characteristics, to which treatments need to be tailored. To evaluate the operating characteristics of recent survival machine learning methods for the estimation of treatment effect heterogeneity and inform better practice, we carry out a comprehensive simulation study presenting a wide range of settings describing confounded heterogeneous survival treatment effects and varying degrees of covariate overlap. Our results suggest that the nonparametric Bayesian Additive Regression Trees within the framework of accelerated failure time model (AFT-BART-NP) consistently yields the best performance, in terms of bias, precision, and expected regret. Moreover, the credible interval estimators from AFT-BART-NP provide close to nominal frequentist coverage for the individual survival treatment effect when the covariate overlap is at least moderate. Including a nonparametrically estimated propensity score as an additional fixed covariate in the AFT-BART-NP model formulation can further improve its efficiency and frequentist coverage. Finally, we demonstrate the application of flexible causal machine learning estimators through a comprehensive case study examining the heterogeneous survival effects of two radiotherapy approaches for localized high-risk prostate cancer.
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Affiliation(s)
- Liangyuan Hu
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Fan Li
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
- Center for Methods in Implementation and Prevention Science, Yale University School of Public Health, New Haven, Connecticut
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37
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Zhang J, Wang A, Li Z, Su X, Wu A, Li H, Ji J. 334TiP A phase I trial of niraparib plus anlotinib in advanced solid tumors with homologous recombination repair (HRR) gene mutations. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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38
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Wu Z, Wang Q, Li Z, Ji J. Use of transanal drainage tube to prevent anastomotic leakage: intangible differences between the East and the West. Br J Surg 2021; 108:e121-e122. [PMID: 33793729 DOI: 10.1093/bjs/znaa144] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 11/12/2022]
Abstract
Trans-anal drainage tube is used to reduce the rectal pressure, especially at the anastomotic site and thus to protect the anastomosis. Ideally it serves as and even may replace a diverting stoma. When compared to no treatment, the effectiveness of TDT seems confirmed based on the literature, but it remains uncertain whether TDT can replace the diverting stoma. Despite the insignificant tangible costs of TDT, it seems different cultures put varied weight on the intangible costs such as discomfort and pain to patients after surgery.
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Affiliation(s)
- Z Wu
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Q Wang
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Z Li
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - J Ji
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
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39
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Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gümüş ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur Ö, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyö D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA, Zhang B, Mani DR, Gillette MA. A proteogenomic portrait of lung squamous cell carcinoma. Cell 2021; 184:4348-4371.e40. [PMID: 34358469 PMCID: PMC8475722 DOI: 10.1016/j.cell.2021.07.016] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/26/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such as LSD1 and EZH2 to target SOX2-overexpressing tumors. Our data support complex regulation of metabolic pathways by crosstalk between post-translational modifications including ubiquitylation. Numerous immune-related proteogenomic observations suggest directions for further investigation. Proteogenomic dissection of CDKN2A mutations argue for more nuanced assessment of RB1 protein expression and phosphorylation before declaring CDK4/6 inhibition unsuccessful. Finally, triangulation between LSCC, LUAD, and HNSCC identified both unique and common therapeutic vulnerabilities. These observations and proteogenomics data resources may guide research into the biology and treatment of LSCC.
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Affiliation(s)
- Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Pierre M Jean Beltran
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Yongchao Dou
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - M Harry Kane
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Shayan C Avanessian
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Suhas V Vasaikar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Erik J Bergstrom
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Vasileios Stathias
- Sylvester Comprehensive Cancer Center and Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Karen E Christianson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David I Heiman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Marcin P Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Song Cao
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Xiaoyu Song
- Department of Population Health Science and Policy, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wenke Liu
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yize Li
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myvizhi Esai Selvan
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rama Soundararajan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tanvi H Visal
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria G Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Özgün Babur
- Computer Science Department, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Pankaj Vats
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Tobias Schraink
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - MacIntosh Cornwell
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Houxiang Zhu
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Chia-Kuei Mo
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Chen Huang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Stephan Schurer
- Sylvester Comprehensive Cancer Center and Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Kelly V Ruggles
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Namrata D Udeshi
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - James Suh
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Qing Kay Li
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD 21224, USA
| | | | - Paul K Paik
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Ramaswamy Govindan
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Li Ding
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02115, USA.
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40
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Ji J, Zhou L, Xu Z, Ma L, Lu Z. Two atypical gram-negative bacteria-binding proteins are involved in the antibacterial response in the pea aphid (Acyrthosiphon pisum). Insect Mol Biol 2021; 30:427-435. [PMID: 33928689 DOI: 10.1111/imb.12708] [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] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/26/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
The activation of immune pathways is triggered by the recognition of pathogens by pattern recognition receptors (PRRs). Gram-negative bacteria-binding proteins (GNBPs)/β-1,3-glucan recognition proteins (βGRPs) are a conserved family of PRRs in insects. Two GNBPs are predicted in the genome database of pea aphids; however, little is known about their functions in the aphid immune system. Here, we show that pea aphid GNBPs possess domain architectures and sequence features distinct from those of typical GNBPs/βGRPs and that their expression is induced by bacterial infection. Knockdown of their expression by dsRNA resulted in lower phenoloxidase activity, higher bacterial loads and higher mortality in aphids after infection. Our data suggest that these two atypical GNBPs are involved in the antibacterial response in the pea aphid, likely acting as PRRs in the prophenoloxidase pathway.
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Affiliation(s)
- J Ji
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, China
| | - L Zhou
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Z Xu
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, China
| | - L Ma
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Z Lu
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
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41
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He Y, Luo Y, Huang L, Zhang D, Wang X, Ji J, Liang S. New frontiers against sorafenib resistance in renal cell carcinoma: From molecular mechanisms to predictive biomarkers. Pharmacol Res 2021; 170:105732. [PMID: 34139345 DOI: 10.1016/j.phrs.2021.105732] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 02/08/2023]
Abstract
Renal cell carcinoma (RCC) is a highly vascularized tumor and prone to distant metastasis. Sorafenib is the first targeted multikinase inhibitor and first-line chemical drug approved for RCC therapy. In fact, only a small number of RCC patients benefit significantly from sorafenib treatment, while the growing prevalence of sorafenib resistance has become a major obstacle for drug therapy effectivity of sorafenib. The molecular mechanisms of sorafenib resistance in RCC are not completely understood by now. Herein, we comprehensively summarize the underlying mechanisms of sorafenib resistance and molecular biomarkers for predicting sorafenib responsiveness. Moreover, we outline strategies suitable for overcoming sorafenib resistance and prospect potential approaches for identifying biomarkers associated with sorafenib resistance in RCC, which contributes to guide individualized and precision drug therapy.
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Affiliation(s)
- Yu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China.
| | - Yang Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China.
| | - Lan Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China.
| | - Dan Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China.
| | - Xixi Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China.
| | - Jiayi Ji
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China.
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China.
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42
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Shen L, Wu T, Chen P, Qin S, Ji J, Wu Y, Chen Y, Chen Y, Wang J, Wu Y. P-144 A comparative analysis of secondary data from the ToGA and EVIDENCE studies on the effectiveness of trastuzumab plus chemotherapy in Asian patients with HER2+ metastatic gastric cancer. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.05.199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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43
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Song X, Ji J, Reva B, Joshi H, Calinawan AP, Mazumdar M, Wisnivesky JP, Taioli E, Wang P, Veluswamy RR. Post-anticoagulant D-dimer is a highly prognostic biomarker of COVID-19 mortality. ERJ Open Res 2021; 7:00018-2021. [PMID: 34230883 PMCID: PMC7942219 DOI: 10.1183/23120541.00018-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/08/2021] [Indexed: 01/08/2023] Open
Abstract
Clinical biomarkers that accurately predict mortality are needed for the effective management of patients with severe coronavirus disease 2019 (COVID-19) illness. In this study, we determine whether changes in D-dimer levels after anticoagulation are independently predictive of in-hospital mortality. Adult patients hospitalised for severe COVID-19 who received therapeutic anticoagulation for thromboprophylaxis were identified from a large COVID-19 database of the Mount Sinai Health System in New York City (NY, USA). We studied the ability of post-anticoagulant D-dimer levels to predict in-hospital mortality, while taking into consideration 65 other clinically important covariates including patient demographics, comorbidities, vital signs and several laboratory tests. 1835 adult patients with PCR-confirmed COVID-19 who received therapeutic anticoagulation during hospitalisation were included. Overall, 26% of patients died in the hospital. Significantly different in-hospital mortality rates were observed in patient groups based on mean D-dimer levels and trend following anticoagulation: 49% for the high mean-increase trend group; 27% for the high-decrease group; 21% for the low-increase group; and 9% for the low-decrease group (p<0.001). Using penalised logistic regression models to simultaneously analyse 67 clinical variables, the high increase (adjusted odds ratios (ORadj): 6.58, 95% CI 3.81-11.16), low increase (ORadj: 4.06, 95% CI 2.23-7.38) and high decrease (ORadj: 2.37; 95% CI 1.37-4.09) D-dimer groups (reference: low decrease group) had the highest odds for in-hospital mortality among all clinical features. Changes in D-dimer levels and trend following anticoagulation are highly predictive of in-hospital mortality and may help guide resource allocation and future studies of emerging treatments for severe COVID-19.
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Affiliation(s)
- Xiaoyu Song
- Institute for Healthcare Delivery Science, Dept of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jiayi Ji
- Institute for Healthcare Delivery Science, Dept of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Boris Reva
- Dept of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Himanshu Joshi
- Institute for Healthcare Delivery Science, Dept of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anna Pamela Calinawan
- Dept of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Madhu Mazumdar
- Institute for Healthcare Delivery Science, Dept of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juan P. Wisnivesky
- Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emanuela Taioli
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Translational Epidemiology, Dept of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pei Wang
- Dept of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rajwanth R. Veluswamy
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Translational Epidemiology, Dept of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Dept of Medicine, Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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44
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Sosa MS, Rodriguez-Tirado C, Kale N, Carlini M, Shrivastava N, Khalil B, Bravo-Cordero J, Alexander M, Ji J. Abstract 2837: NR2F1 is a barrier to early dissemination of pre-malignant mammary cells. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2837] [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
Cancer cells disseminate during very early and sometimes asymptomatic stages of tumor progression. Granted that biological barriers to tumorigenesis exist, there must also be limiting steps to early dissemination, all of which remain largely unknown. We report that the orphan nuclear receptor NR2F1/COUP-TF1 serves as a barrier to early dissemination. High-resolution intravital imaging revealed that loss of function of NR2F1 in HER2+ early cancer cells increased in vivo dissemination without accelerating mammary tumor formation. NR2F1 expression was positively regulated by the tumor suppressive MMK3/6-p38-MAPK pathway and downregulated by HER2 and Wnt4 oncogenic signaling. NR2F1 downregulation by HER2 in early cancer cells led to decreased E-cadherin expression and β-catenin membrane localization, disorganized laminin 5 deposition, and increased expression of CK14, TWIST1, ZEB1 and PRRX1. Our findings reveal the existence of an inhibitory mechanism of dissemination regulated by NR2F1 downstream of HER2 signaling.
Citation Format: Maria Soledad Sosa, Carolina Rodriguez-Tirado, Nupura Kale, Maria Carlini, Nitisha Shrivastava, Bassem Khalil, Javier Bravo-Cordero, Melissa Alexander, Jiayi Ji. NR2F1 is a barrier to early dissemination of pre-malignant mammary cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2837.
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Affiliation(s)
| | | | - Nupura Kale
- 2UCSF Helen Diller Comprehensive Family Cancer Center, University of California, San Francisco, CA
| | - Maria Carlini
- 1Icahn School of Medicine at Mount Sinai Hospital, New York, NY
| | | | - Bassem Khalil
- 1Icahn School of Medicine at Mount Sinai Hospital, New York, NY
| | | | | | - Jiayi Ji
- 1Icahn School of Medicine at Mount Sinai Hospital, New York, NY
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45
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Gao J, Liu Y, Ji J, Liu Z. [Heat stress induces neuronal apoptosis by up-regulating endoplasmic reticulum stress pathway]. Nan Fang Yi Ke Da Xue Xue Bao 2021; 41:702-709. [PMID: 34134957 DOI: 10.12122/j.issn.1673-4254.2021.05.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To explore the role of endoplasmic reticulum stress in heat stress-induced apoptosis of human neuroblastoma SH-SY5Y cells. OBJECTIVE SH-SY5Y cells were incubated at 43 ℃ for 2 h followed by further culture at 37 ℃ for 0, 3 h, or 6 h. With the cells cultured at 37 ℃ as the control, the cells exposed to heat stress were examined for morphological changes under optical microscope and changes in cell viability using CCK-8 assay. Flow cytometry was performed for detecting apoptosis of the cells following heat stress, and intracellular Ca2+ level in the cells was determined using flow cytometry and immunofluorescence confocal microscopy. The mRNA expression levels of caspase-12, BIP and XBP-1 in the cells were detected using qRT-PCR, and the protein expressions of caspase-12, BIP, P-JNK, JNK and XBP-1 were examined using Western blotting. The effect of pretreatment with 4-PBA on cell apoptosis following heat stress was analyzed with Western blotting. OBJECTIVE SH-SY5Y cells showed obvious cell shrinkage immediately after the exposure to heat stress, followed then by gradual cell stretching over time. The cell viability decreased significantly after heat stress (P=0.001), and the intracellular Ca2+ level increased significantly at 0 h and gradually recovered the normal level at 3 and 6 h. Heat stress induced significant increase in the protein expression of cleaved caspase-3 and time-dependent increase of caspase-12 (P=0.002) and BIP (P=0.008) expression at both the protein and mRNA levels. The expression of P-JNK/JNK protein increased significantly at 0 h (P=0.003) followed by gradual decrease; the expression levels of XBP-1 protein and mRNA gradually decreased after heat stress (P=0.005, P=0.002). Pretreatment with 4-PBA significantly reduced the expression level of cleaved caspase-3 in SH-SY5Y cells following heat stress. OBJECTIVE Heat stress induces apoptosis of SH-SY5Y cells by triggering endoplasmic reticulum stress and the imbalance of intracellular calcium ion homeostasis.
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Affiliation(s)
- J Gao
- First College of Clinical Medicine, Southern Medical University, Guangzhou 510515, China.,Department of Critical Care Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China
| | - Y Liu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - J Ji
- Department of Critical Care Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China
| | - Z Liu
- First College of Clinical Medicine, Southern Medical University, Guangzhou 510515, China.,Department of Critical Care Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China
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Sha X, Ge X, Jin Y, Chen T, Ni X, Zheng W, Ji J, Gu Z. POS0788 CIRCULATING EXOSOMES PROMOTE LUPUS NEPHRITIS IN MRL-LPR MICE. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.3904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:Systemic Lupus Erythematosus (SLE) is a prototypic autoimmune disease that characterized by the loss of self-tolerance and the production of autoantibodies (autoAbs) [1, 2]. Lupus nephritis (LN), the severe organ-threatening manifestations of SLE, could cause massive damage to patients[3, 4]. Currently, some exosomal microRNAs (miRNAs) are considered as potential biomarkers in SLE. However, the role of exosomal miRNAs in Lupus Nephritis (LN) remains unclear.Objectives:The purpose of this study was to investigate molecular mechanism of plasma exosomal miRNAs in the development of Lupus Nephritis.Methods:Circulating exosomes were isolated from plasma of patients with LN, SLE without LN (NLN). Plasma exosomes were authenticated by Western Blot, Nanosight Tracking Analysis (NTA) and transmission electron microscopy (TEM). Fluorescence microscopy of co-cultured plasma exosomes and podocytes demonstrated that exosomes were uptaken into podocytes. Moreover, cell apoptosis and the inflammation factors was assessed using Western Blot. We analyzed the expression profiles of miRNAs in LN and NLN exosomes and the expression profiles of mRNAs of podocytes stimulated with LN and NLN exosomes with the help of next generation sequencing (NGS).Results:We demonstrate that exosomes derived from LN plasma could be taken by neighboring podocytes and promote the apoptosis of podocytes and the expression of inflammation factors. In addition, the sequencing found that miRNAs were differentially expressed in LN and NLN exosomes and mRNAs were differentially expressed in podocytes stimulated with LN and NLN exosomes.Conclusion:LN plasma exosomes have a potency to stimulate the apoptosis of podocytes and the expression of inflammation factors. Moreover, differentially expressed miRNAs in exosomes play a potential role in the development of LN.References:[1]T. Colasanti, A. Maselli, F. Conti, M. Sanchez, C. Alessandri, C. Barbati, D. Vacirca, A. Tinari, F. Chiarotti, A. Giovannetti, F. Franconi, G. Valesini, W. Malorni, M. Pierdominici, E. Ortona, Autoantibodies to estrogen receptor α interfere with T lymphocyte homeostasis and are associated with disease activity in systemic lupus erythematosus, Arthritis and rheumatism, 64 (2012) 778-787.[2]H.A. Al-Shobaili, A.A. Al Robaee, A.A. Alzolibani, Z. Rasheed, Antibodies against 4-hydroxy-2-nonenal modified epitopes recognized chromatin and its oxidized forms: role of chromatin, oxidized forms of chromatin and 4-hydroxy-2-nonenal modified epitopes in the etiopathogenesis of SLE, Disease markers, 33 (2012) 19-34.[3]A. Kaul, C. Gordon, M.K. Crow, Z. Touma, M.B. Urowitz, R. van Vollenhoven, G. Ruiz-Irastorza, G. Hughes, Systemic lupus erythematosus, Nat Rev Dis Primers, 2 (2016) 16039.[4]M.G. Tektonidou, A. Dasgupta, M.M. Ward, Risk of End-Stage Renal Disease in Patients With Lupus Nephritis, 1971-2015: A Systematic Review and Bayesian Meta-Analysis, Arthritis & rheumatology (Hoboken, N.J.), 68 (2016) 1432-1441.Disclosure of Interests:None declared
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Dong C, Gu X, Ji J, Zhang X, Gu Z. OP0073 SINGLE-CELL TRANSCRIPTOMICS UNCOVERS DEFECTIVE BONE MARROW EARLY B CELL DEVELOPMENT IN A SUBSET OF LUPUS PATIENTS ASSOCIATED WITH AGGRAVATED INFLAMMATION. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.3061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that occurs when the body’s immune system attacks own tissues and organs. B cells play a central role in SLE pathogenesis by producing autoantibodies as well as antibody-independent functions. Peripheral B cell abnormality is well known in lupus patients such as expansions of plasmablasts and atypical memory B cells, which are associated with active diseases. However, little is known about the B cell development in the bone marrow of lupus patients.Objectives:We conduct this survey to explore the disorder of the B cell development in the bone marrow of lupus patients.Methods:In this study, we have performed the scRNASeq to profile the bone marrow B cell compartment in lupus patients and healthy donors.Results:We identified that in a subset of lupus patients, the early B cells (proB and preB cells) were strongly decreased, which were confirmed by flow cytometry in an expanded cohort. Furthermore, bone marrow B cells from these patients showed a strong proinflammatory signature revealed by pathway analysis. Interestingly, BCR repertoire analysis showed that the IGHV-4-34 was highly enriched in these patients, indicating an enhanced B cell tolerance defect. Finally, a panel of proinflammatory cytokines (TNF-a, IL-1a, IL-12p70, IFN-g, et al.) were strongly increased in the bone marrow plasma of these patients compared with early B normal patients and healthy donors, confirming a localized proinflammatory microenvironment.Conclusion:Altogether, the current study has revealed that a defective early B cell development in lupus patients is associated with a more severe B cell tolerance defect and aggravated inflammation, which may shed new light on developing novel therapies by targeting relevant pathways.References:[1]Min Wang, Hua Chen, Jia Qiu, et al. Antagonizing miR-7 suppresses B cell hyperresponsiveness and inhibits lupus development. J Autoimmun 2020.[2]A M Jacobi, D M Goldenberg, F Hiepe, et al. Differential effects of epratuzumab on peripheral blood B cells of patients with systemic lupus erythematosus versus normal controls. Ann Rheum Dis, 2008.Acknowledgements:This work was funded by Special project of clinical medicine of Nantong University (Grant/Award number: 2019LQ001), National Natural Science Foundation of China (Grant/Award number: 81671616, 81871278 and 82071838).Disclosure of Interests:None declared
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Bao Y, Ji J, Xue Z, Gu Z. POS0787 BERBERINE MODULATE LUPUS SYNDROME VIA THE REGULATION OF GUT MICROBIOTA IN MRL/LPR MICE. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.3838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:Intestinal flora disorder and immune abnormalities have been reported in systemic lupus erythematosus (SLE) patients1,2. Berberine (BBR) showed significant effects in regulating the intestinal flora, repairing gut barriers and regulating immune cells3,4. While few reports mentioned the abnormal gut microbiota and metabolites in Chinese SLE patients.Objectives:Our investigation tried to illustrate the relationship between gut microbiota, intestinal metabolites and disease activity in Chinese SLE patients. And the effect of BBR to intestinal dysbacteriosis, multiple organ damages and over-activated immune system in MRL/Lpr mice.Methods:16S high-throughput (16S rRNA) sequence, qRT-PCR and gas chromatography technology were used to determine the gut microbiota and metabolites in 104 SLE patients from Affiliated Hospital of Nantong University, China. BBR was orally treated to the MRL/Lpr mice in low, medium and high doses. After 6 weeks treatment, mice were sacrificed. Serum, faeces and organs were collected for further studies.Results:Chinese SLE patients showed higher abundance of Bacteroidetes and lower abundance of Firmcutes. The results of qRT-PCR showed high Firmcutes/Bacteroidetes (F/B) ratio of SLE patients. The F/B ratio was negative correlated with SLE disease activity index (SLEDA) score. Almost all the tested short-chain fatty acids (SCFAs) found statistically significant results in SLE and LN (lupus nephritis) patients, especially the propanoic acid and butyric. BBR altered the relative abundance of Bacteroides and Verrucomicrobia and the butyric acid content in colon of MRL/Lpr mice. The increase of tight junction protein also indicated the gut barrier was repaired by BBR. Treg and Tfr cells in spleen and mesenteric lymph node (MLN) were increased. These results revealed a positive therapeutic effect of berberine on SLE from gut microbiota to immune status.Conclusion:Our study highlights current status of intestinal dysbacteriosis in Chinese patients with SLE and differences in intestinal metabolites among patients with different disease states. The regulation of intestinal flora and the repairment of gut barrier by intestinal metabolites in BBR treated mice seemed to be the factor that directed the immune responses and disease outcomes. The ultimate goal of our study was to determine the beneficial effects of regulating the gut microbiota on the treatment of SLE. The application of berberine is a relatively safe and convenient way. In the coming investigations, we plan to focus on the study of berberine and its metabolites on intestinal function and systemic immunity.References:[1]Guo, M. et al. Alteration in gut microbiota is associated with dysregulation of cytokines and glucocorticoid therapy in systemic lupus erythematosus. Gut microbes11, 1758-1773, doi:10.1080/19490976.2020.1768644 (2020).[2]Mu, Q. et al. Control of lupus nephritis by changes of gut microbiota. Microbiome5, 73, doi:10.1186/s40168-017-0300-8 (2017).[3]Habtemariam, S. Berberine pharmacology and the gut microbiota: A hidden therapeutic link. Pharmacological research155, 104722, doi:10.1016/j.phrs.2020.104722 (2020).[4]Cui, H. et al. Berberine Regulates Treg/Th17 Balance to Treat Ulcerative Colitis Through Modulating the Gut Microbiota in the Colon. Frontiers in pharmacology9, 571, doi:10.3389/fphar.2018.00571 (2018).Figure 1.Disclosure of Interests:None declared
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Fu T, Yang Y, Gu X, Dong C, Zhao R, Ji J, Xue Z, Zhang X, Gu Z. POS0761 INVESTIGATION ON THE EFFECT AND MECHANISM OF ABNORMALLY ACTIVATED CD8+ T CELLS FROM BONE MARROW ON HEMATOPOIETIC STEM CELLS IN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.3060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:SLE is an autoimmune disease characterized by the abnormal function of lymphocytes. The impairment of hematopoietic function of bone marrow participates in its pathogenesis, in which T cells play an important role. However, study on bone marrow T cells in SLE patients is very limited.Objectives:This study aims to characterize the phenotype and molecular characteristics of abnormally activated CD8+T cells in bone marrow of SLE patients and explore the mechanism of hematopoietic stem cells (HSCs) reduction caused by the abnormally activated CD8+T cells in bone marrow of patients with SLE.Methods:A total of 8 SLE patients and 5 age- and sex-matched controls were recruited in our study. Among them, 3 SLE patients and 4 donors were collected bone marrow and peripheral blood samples for Single-cell RNA sequencing (scRNA-seq) and functional studies. BM and peripheral T cell subsets were measured by flow cytometry. Plasma cytokines and secreted immunoglobulins were detected by Luminex. Disease activity of SLE patients was measured using the SLE Disease Activity Index (SLEDAI). All analyses were performed using R language and Flowjo 9.Results:In the present study, SLE patients had increased CD8+T%αβT cells and decreased CD4+T%αβT cells in bone marrow of SLE, compared to healthy controls. A large number of CD38+HLADR+CD8+T cells existed in the bone marrow and peripheral blood of SLE patients. Those patients also showed reduced number of HSCs, and with a downward trend of the numbers of peripheral red blood cells, white blood cells, neutrophils, hemoglobin, and platelets. By scRNA-seq, the CD38+HLADR+CD8+T cells contained high levels of GZMK, GZMA, PRF1, IFNG, and TNF in the bone marrow of SLE patients. the CD38+HLADR+CD8+T cells exhibited significant relationship with HSCs, white blood cells, neutrophils, and platelets.Conclusion:These findings demonstrated that the abnormally activated CD8+T cells in bone marrow can reduce the number of HSCs by the expression of killer molecules, which contributes to the impairment of hematopoietic function and the development of SLE. This project focuses on the specific bone marrow T cell subset in SLE. The completement of this project provides information for exploring the mechanism of hematopoiesis involvement.References:[1]Anderson E, Shah B, Davidson A, Furie R. Lessons learned from bone marrow failure in systemic lupus erythematosus: Case reports and review of the literature. Semin Arthritis Rheum. 2018;48(1):90-104.[2]Sun LY, Zhou KX, Feng XB, Zhang HY, Ding XQ, Jin O, Lu LW, Lau CS, Hou YY, Fan LM. Abnormal surface markers expression on bone marrow CD34+cells and correlation with disease activity in patients with systemic lupus erythematosus. Clin Rheumatol. 2007;26(12):2073-2079.Acknowledgements:We want to thank Lu Meng, Teng Li, Wei Zhou, and Jiaxin Guo for their assistance with this study.Disclosure of Interests:None declared
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Feng Z, Guo X, Ji J, Hou X, Luo Y, Fu X. AB0066 MECHANISMS OF TOTAL SAPONINS OF PANAX JAPONICUS MITIGATES COLLAGEN-INDUCED ARTHRITIS. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.3496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:Total saponins of Panax japonicus (TSPJ) are extracted from Panax japonicus (T.Nees) C.A.Mey and have achieved a good therapeutic effect in the treatment of rheumatoid arthritis (RA). Unfortunately, the mechanism of TSPJ acting on RA is not clear.Objectives:To investigate the potential mechanisms and key targets of TSPJ on RA.Methods:The raw data were downloaded from the Gene Expression Omnibus (GEO) database, and the RStudio3.6.1 software was used to identify differentially expressed genes (DEGs). The potential targets of active compounds from TSPJ were predicted by the Pharmmapper and SwissTargetPrediction databases. Based on the overlapping genes, we used Cytoscape 3.7.2 software to construct a protein-protein interactions (PPI) network and to determine the mechanisms of the treatment by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Collagen-induced arthritis (CIA) model was established and treated with different doses of TSPJ. Arthritis index (AI) and histology score were used to evaluate the symptoms of CIA. The levels of vascular endothelial growth factor (VEGF), hypoxia-inducible factor 1 (HIF-1), IL-1β, and IL-17A tested by enzyme linked immunosorbent assay and real time-quantitative Polymerase Chain Reaction.Results:A total of 2670 DEGs and 371 TSPJ targets were obtained, including 52 overlapping genes. 41 genes had protein interactions that are used to build the PPI network. The results of the KEGG enrichment analysis included VEGF and HIF-1 signaling pathway. Seven negative correlation genes and 16 positive correlation genes were obtained by correlational analysis of DEGs in VEGF and HIF-1 signaling pathway. SRC proto-oncogene, nonreceptor tyrosine kinase (SRC), and the signal transducer and the activator of transcription 3 (STAT 3) had a higher value of degree in PPI and showed a significant correlation in the pathways; they were regarded as key targets. Compared with the CIA model group, TSPJ significantly decreased the AI and histology scores. Moreover, the expression of VEGF-A, HIF-1α, IL-1β, and IL-17A in serum or spleens significantly reduced in a dose-dependent.Conclusion:Present study show that SRC and STAT 3 may be the key targets of TSPJ acting on the VEGF and HIF-1 signaling pathways, thus inhibiting angiogenesis and improving RA.Disclosure of Interests:None declared
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