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Feng SS, Wang SJ, Guo L, Ma PP, Ye XL, Pan ML, Hang B, Mao JH, Snijders AM, Lu YB, Ding DF. Serum bile acid and unsaturated fatty acid profiles of non-alcoholic fatty liver disease in type 2 diabetic patients. World J Diabetes 2024; 15:898-913. [DOI: 10.4239/wjd.v15.i5.898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/29/2024] [Accepted: 03/14/2024] [Indexed: 05/10/2024] Open
Abstract
BACKGROUND The understanding of bile acid (BA) and unsaturated fatty acid (UFA) profiles, as well as their dysregulation, remains elusive in individuals with type 2 diabetes mellitus (T2DM) coexisting with non-alcoholic fatty liver disease (NAFLD). Investigating these metabolites could offer valuable insights into the pathophy-siology of NAFLD in T2DM.
AIM To identify potential metabolite biomarkers capable of distinguishing between NAFLD and T2DM.
METHODS A training model was developed involving 399 participants, comprising 113 healthy controls (HCs), 134 individuals with T2DM without NAFLD, and 152 individuals with T2DM and NAFLD. External validation encompassed 172 participants. NAFLD patients were divided based on liver fibrosis scores. The analytical approach employed univariate testing, orthogonal partial least squares-discriminant analysis, logistic regression, receiver operating characteristic curve analysis, and decision curve analysis to pinpoint and assess the diagnostic value of serum biomarkers.
RESULTS Compared to HCs, both T2DM and NAFLD groups exhibited diminished levels of specific BAs. In UFAs, particular acids exhibited a positive correlation with NAFLD risk in T2DM, while the ω-6:ω-3 UFA ratio demonstrated a negative correlation. Levels of α-linolenic acid and γ-linolenic acid were linked to significant liver fibrosis in NAFLD. The validation cohort substantiated the predictive efficacy of these biomarkers for assessing NAFLD risk in T2DM patients.
CONCLUSION This study underscores the connection between altered BA and UFA profiles and the presence of NAFLD in individuals with T2DM, proposing their potential as biomarkers in the pathogenesis of NAFLD.
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Affiliation(s)
- Su-Su Feng
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
| | - Si-Jing Wang
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
| | - Lin Guo
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
| | - Pan-Pan Ma
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
| | - Xiao-Long Ye
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
| | - Ming-Lin Pan
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Yi-Bing Lu
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
| | - Da-Fa Ding
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
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Wei H, Yu Q, Chen D, Zhang M, Guan Q, Hang B, Snijders AM, Covaci A, Xia Y. Residential energy transition and chronic respiratory diseases. Innovation (N Y) 2024; 5:100597. [PMID: 38510068 PMCID: PMC10951461 DOI: 10.1016/j.xinn.2024.100597] [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: 10/07/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
Obtaining clean energy is of prime importance for planetary health and sustainable development. We aimed to assess the association between residential energy transition and the risk of chronic respiratory diseases. Using data from the Global Health Observatory and Global Burden of Diseases, Injuries, and Risk Factors Study, we delineated the spatial distribution and temporal trends of the population using clean fuels for cooking at a global scale. In the China Health and Retirement Longitudinal Study, we performed rigorous and well-structured multistage analyses incorporating both cross-sectional and prospective data analyses to examine the associations between solid fuel use, residential energy transition, duration of solid fuel use, and the risk of chronic respiratory diseases. Despite great progress, huge disparities in access to clean energy persist globally. Residential energy transition was associated with a lower risk of chronic respiratory diseases. In the period of 2011-2013, compared with persistent solid fuel users, both participants who switched from solid to clean fuels (adjusted risk ratio [RR] 0.78, 95% confidence interval [CI] 0.62-0.98) and persistent clean fuel users (adjusted RR 0.71, 95% CI 0.57-0.89) had significantly lower risk of chronic respiratory diseases (p < 0.001 for trend). Consistent associations were observed in the period of 2011-2015 and 2011-2018. Household energy transition from solid to clean fuels could reduce the risk of chronic respiratory diseases. This is a valuable lesson for policy-makers and the general public to accelerate energy switching to alleviate the burden of chronic respiratory diseases and achieve health benefits, particularly in low- and middle-income countries.
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Affiliation(s)
- Hongcheng Wei
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Qiurun Yu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Danrong Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Mingzhi Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Quanquan Guan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Adrian Covaci
- Toxicological Centre, University of Antwerp, 2610 Wilrijk, Belgium
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi 214023, China
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3
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Inman JL, Wu Y, Chen L, Brydon E, Ghosh D, Wan KH, De Chant J, Obst-Huebl L, Nakamura K, Ralston CY, Celniker SE, Mao JH, Zwart PH, Holman HYN, Chang H, Brown JB, Snijders AM. Long-term, non-invasive FTIR detection of low-dose ionizing radiation exposure. Sci Rep 2024; 14:6119. [PMID: 38480827 PMCID: PMC10937999 DOI: 10.1038/s41598-024-56491-7] [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: 11/24/2023] [Accepted: 03/07/2024] [Indexed: 03/17/2024] Open
Abstract
Non-invasive methods of detecting radiation exposure show promise to improve upon current approaches to biological dosimetry in ease, speed, and accuracy. Here we developed a pipeline that employs Fourier transform infrared (FTIR) spectroscopy in the mid-infrared spectrum to identify a signature of low dose ionizing radiation exposure in mouse ear pinnae over time. Mice exposed to 0.1 to 2 Gy total body irradiation were repeatedly measured by FTIR at the stratum corneum of the ear pinnae. We found significant discriminative power for all doses and time-points out to 90 days after exposure. Classification accuracy was maximized when testing 14 days after exposure (specificity > 0.9 with a sensitivity threshold of 0.9) and dropped by roughly 30% sensitivity at 90 days. Infrared frequencies point towards biological changes in DNA conformation, lipid oxidation and accumulation and shifts in protein secondary structure. Since only hundreds of samples were used to learn the highly discriminative signature, developing human-relevant diagnostic capabilities is likely feasible and this non-invasive procedure points toward rapid, non-invasive, and reagent-free biodosimetry applications at population scales.
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Affiliation(s)
- Jamie L Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Yulun Wu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- Department of Statistics, University of California, Berkeley, CA, 94720, USA
| | - Liang Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Ella Brydon
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Dhruba Ghosh
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA
| | - Kenneth H Wan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Jared De Chant
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Lieselotte Obst-Huebl
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Kei Nakamura
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Corie Y Ralston
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Peter H Zwart
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Hoi-Ying N Holman
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA.
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA.
| | - James B Brown
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA.
- Department of Statistics, University of California, Berkeley, CA, 94720, USA.
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA.
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4
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Li D, Zhong C, Yang M, He L, Chang H, Zhu N, Celniker SE, Threadgill DW, Snijders AM, Mao JH, Yuan Y. Genetic and microbial determinants of azoxymethane-induced colorectal tumor susceptibility in Collaborative Cross mice and their implication in human cancer. Gut Microbes 2024; 16:2341647. [PMID: 38659246 PMCID: PMC11057575 DOI: 10.1080/19490976.2024.2341647] [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: 01/03/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
The insights into interactions between host genetics and gut microbiome (GM) in colorectal tumor susceptibility (CTS) remains lacking. We used Collaborative Cross mouse population model to identify genetic and microbial determinants of Azoxymethane-induced CTS. We identified 4417 CTS-associated single nucleotide polymorphisms (SNPs) containing 334 genes that were transcriptionally altered in human colorectal cancers (CRCs) and consistently clustered independent human CRC cohorts into two subgroups with different prognosis. We discovered a set of genera in early-life associated with CTS and defined a 16-genus signature that accurately predicted CTS, the majority of which were correlated with human CRCs. We identified 547 SNPs associated with abundances of these genera. Mediation analysis revealed GM as mediators partially exerting the effect of SNP UNC3869242 within Duox2 on CTS. Intestine cell-specific depletion of Duox2 altered GM composition and contribution of Duox2 depletion to CTS was significantly influenced by GM. Our findings provide potential novel targets for personalized CRC prevention and treatment.
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Affiliation(s)
- Dan Li
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ZJ, China
| | - Chenhan Zhong
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mengyuan Yang
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
| | - Li He
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ning Zhu
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David W Threadgill
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, USA
- Department of Molecular and Cellular Medicine and Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ying Yuan
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Zhejiang Provincial Clinical Research Center for CANCER, Hangzhou, ZJ, China
- Cancer Center, Zhejiang University, Hangzhou, ZJ, China
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5
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Gupta S, Inman JL, De Chant J, Obst-Huebl L, Nakamura K, Costello SM, Marqusee S, Mao JH, Kunz L, Paisley R, Vozenin MC, Snijders AM, Ralston CY. A Novel Platform for Evaluating Dose Rate Effects on Oxidative Damage to Peptides: Toward a High-Throughput Method to Characterize the Mechanisms Underlying the FLASH Effect. Radiat Res 2023; 200:523-530. [PMID: 38014573 PMCID: PMC10754258 DOI: 10.1667/rade-23-00131.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/05/2023] [Indexed: 11/29/2023]
Abstract
High dose rate radiation has gained considerable interest recently as a possible avenue for increasing the therapeutic window in cancer radiation treatment. The sparing of healthy tissue at high dose rates relative to conventional dose rates, while maintaining tumor control, has been termed the FLASH effect. Although the effect has been validated in animal models using multiple radiation sources, it is not yet well understood. Here, we demonstrate a new experimental platform for quantifying oxidative damage to protein sidechains in solution as a function of radiation dose rate and oxygen availability using liquid chromatography mass spectrometry. Using this reductionist approach, we show that for both X-ray and electron sources, isolated peptides in solution are oxidatively modified to different extents as a function of both dose rate and oxygen availability. Our method provides an experimental platform for exploring the parameter space of the dose rate effect on oxidative changes to proteins in solution.
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Affiliation(s)
- Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Jamie L. Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Jared De Chant
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Lieselotte Obst-Huebl
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Kei Nakamura
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Shawn M. Costello
- Biophysics Graduate Program, Department of Chemistry; California Institute for Quantitative Biosciences, University of California, Berkeley, Califormia; Chan Zuckerberg Biohub, San Francisco, California
| | - Susan Marqusee
- Department of Molecular and Cell Biology, Department of Chemistry; California Institute for Quantitative Biosciences, University of California, Berkeley, Califormia; Chan Zuckerberg Biohub, San Francisco, California
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Louis Kunz
- University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Ryan Paisley
- University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Corie Y. Ralston
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
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6
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He L, Zhong C, Chang H, Inman JL, Celniker SE, Ioakeim-Ioannidou M, Liu KX, Haas-Kogan D, MacDonald SM, Threadgill DW, Kogan SC, Mao JH, Snijders AM. Genetic architecture of the acute and persistent immune cell response after radiation exposure. Cell Genom 2023; 3:100422. [PMID: 38020972 PMCID: PMC10667298 DOI: 10.1016/j.xgen.2023.100422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/19/2023] [Accepted: 09/12/2023] [Indexed: 12/01/2023]
Abstract
Hematologic toxicity is a common side effect of multimodal cancer therapy. Nearly all animal studies investigating the causes of radiotherapy-induced hematologic toxicity use inbred strains with limited genetic diversity and do not reflect the diverse responses observed in humans. We used the population-based Collaborative Cross (CC) mouse resource to investigate the genetic architecture of the acute and persistent immune response after radiation exposure by measuring 22 immune parameters in 1,720 CC mice representing 35 strains. We determined relative acute and persistent radiation resistance scores at the individual strain level considering contributions from all immune parameters. Genome-wide association analysis identified quantitative trait loci associated with baseline and radiation responses. A cross-species radiation resistance score predicted recurrence-free survival in medulloblastoma patients. We present a community resource of immune parameters and genome-wide association analyses before and after radiation exposure for future investigations of the contributions of host genetics on radiosensitivity.
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Affiliation(s)
- Li He
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430079, China
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chenhan Zhong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jamie L. Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Susan E. Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Kevin X. Liu
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daphne Haas-Kogan
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shannon M. MacDonald
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David W. Threadgill
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX 77843, USA
- Departments of Nutrition and Cell Biology and Genetics, Texas A&M University, College Station, TX 77843, USA
| | - Scott C. Kogan
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California Berkeley, Berkeley, CA 94720, USA
| | - Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California Berkeley, Berkeley, CA 94720, USA
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7
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Wan KH, Park S, Booth BW, Brydon EC, Eichenberger J, Inman JL, Mao JH, Snijders AM, Celniker SE. Complete genome sequence of the Microbacterium sp. strain BDGP8. Microbiol Resour Announc 2023; 12:e0038423. [PMID: 37607064 PMCID: PMC10508165 DOI: 10.1128/mra.00384-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/16/2023] [Indexed: 08/24/2023] Open
Abstract
Microbacterium sp. BDGP8 is a species of facultative anaerobic gram-positive bacterium of the family Microbacteriaceae. The complete genome consists of a single circular chromosome of 3,293,567 bp with a G + C content of 69.84% and two plasmids of 49,365 bp and 32,884 bp.
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Affiliation(s)
- Kenneth H. Wan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Soo Park
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Benjamin W. Booth
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ella C. Brydon
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Joanne Eichenberger
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jamie L. Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Susan E. Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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8
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Feng S, Guo L, Wang S, Chen L, Chang H, Hang B, Mao J, Snijders AM, Lu Y, Ding D. Association of Serum Bile Acid and Unsaturated Fatty Acid Profiles with the Risk of Diabetic Retinopathy in Type 2 Diabetic Patients. Diabetes Metab Syndr Obes 2023; 16:2117-2128. [PMID: 37465650 PMCID: PMC10351529 DOI: 10.2147/dmso.s411522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/10/2023] [Indexed: 07/20/2023] Open
Abstract
Aim We aimed to identify the ability of serum bile acids (BAs) and unsaturated fatty acids (UFAs) profiles to predict the development of diabetic retinopathy (DR) in type 2 diabetes mellitus (T2DM) patients. Methods We first used univariate and multivariate analysis to compare 15 serum BA and 11 UFA levels in healthy control (HC) group (n = 82), T2DM patients with DR (n = 58) and T2DM patients without DR (n = 60). Forty T2DM patients were considered for validation. Then, the receiver operating characteristic curve (ROC) and decision curve analysis were used to assess the diagnostic value and clinical benefit of serum biomarkers alone, clinical variables alone or in combination, and the area under the curve (AUC), integrated discrimination improvement (IDI), and net reclassification improvement (NRI) were used to further assess whether the addition of biomarkers significantly improved the predictive ability of the model. Results Orthogonal partial least squares-discriminant analysis (OPLS-DA) of serum BAs and UFAs separated the three cohorts including HC, T2DM patients with or without DR. The difference in serum BA and UFA profiles of T2DM patients with or without DR was mainly manifested in the three metabolites of taurolithocholic acid (TLCA), tauroursodeoxycholic acid (TUDCA) and arachidonic acid (AA). Together, they had an AUC of 0.785 (0.918 for validation cohort) for predicting DR in T2DM patients. After adjusting for numerous confounding factors, TLCA, TUDCA, and AA were independent predictors that differentiated T2DM with or without DR. The results of AUC, IDI, and NRI demonstrated that adding these three biomarkers to a model with clinical variables statistically increased their predictive value and were replicated in our independent validation cohort. Conclusion These findings highlight the association of three metabolites, TLCA, TUDCA and AA, with DR and may indicate their potential value in the pathogenesis of DR.
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Affiliation(s)
- Susu Feng
- Department of Endocrinology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Lin Guo
- Department of Endocrinology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Sijing Wang
- Department of Endocrinology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Lijuan Chen
- Department of Endocrinology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Biomaterials, Berkeley-Nanjing Research Center, Nanjing, People's Republic of China
| | - Jianhua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yibing Lu
- Department of Endocrinology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Dafa Ding
- Department of Endocrinology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
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9
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Matt GE, Greiner L, Record RA, Wipfli H, Long J, Dodder NG, Hoh E, Lopez Galvez N, Novotny TE, Quintana PJE, Destaillats H, Tang X, Snijders AM, Mao JH, Hang B, Schick S, Jacob P, Talbot P, Mahabee-Gittens EM, Merianos AL, Northrup TF, Gundel L, Benowitz NL. Policy-relevant differences between secondhand and thirdhand smoke: strengthening protections from involuntary exposure to tobacco smoke pollutants. Tob Control 2023:tc-2023-057971. [PMID: 37263783 DOI: 10.1136/tc-2023-057971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023]
Abstract
Starting in the 1970s, individuals, businesses and the public have increasingly benefited from policies prohibiting smoking indoors, saving thousands of lives and billions of dollars in healthcare expenditures. Smokefree policies to protect against secondhand smoke exposure, however, do not fully protect the public from the persistent and toxic chemical residues from tobacco smoke (also known as thirdhand smoke) that linger in indoor environments for years after smoking stops. Nor do these policies address the economic costs that individuals, businesses and the public bear in their attempts to remediate this toxic residue. We discuss policy-relevant differences between secondhand smoke and thirdhand smoke exposure: persistent pollutant reservoirs, pollutant transport, routes of exposure, the time gap between initial cause and effect, and remediation and disposal. We examine four policy considerations to better protect the public from involuntary exposure to tobacco smoke pollutants from all sources. We call for (a) redefining smokefree as free of tobacco smoke pollutants from secondhand and thirdhand smoke; (b) eliminating exemptions to comprehensive smoking bans; (c) identifying indoor environments with significant thirdhand smoke reservoirs; and (d) remediating thirdhand smoke. We use the case of California as an example of how secondhand smoke-protective laws may be strengthened to encompass thirdhand smoke protections. The health risks and economic costs of thirdhand smoke require that smokefree policies, environmental protections, real estate and rental disclosure policies, tenant protections, and consumer protection laws be strengthened to ensure that the public is fully protected from and informed about the risks of thirdhand smoke exposure.
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Affiliation(s)
- Georg E Matt
- Department of Psychology, San Diego State University, San Diego, CA, USA
| | - Lydia Greiner
- Department of Psychology, San Diego State University, San Diego, CA, USA
| | - Rachael A Record
- School of Communication, San Diego State University, San Diego, CA, USA
| | - Heather Wipfli
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jamie Long
- Public Health Law Center, Mitchell Hamline School of Law, University of Minnesota, St Paul, MN, USA
| | - Nathan G Dodder
- School of Public Health, San Diego State University, San Diego, CA, USA
| | - Eunha Hoh
- School of Public Health, San Diego State University, San Diego, CA, USA
| | | | - Thomas E Novotny
- School of Public Health, San Diego State University, San Diego, CA, USA
| | | | - Hugo Destaillats
- Indoor Environment Group, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xiaochen Tang
- Indoor Environment Group, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Suzaynn Schick
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Peyton Jacob
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Prue Talbot
- Department of Molecular, Cell, and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - E Melinda Mahabee-Gittens
- Department of Pediatrics, Division of Emergency Medicine Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ashley L Merianos
- School of Human Services, University of Cincinnati, Cincinnati, OH, USA
| | - Thomas F Northrup
- Department of Family & Community Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Lara Gundel
- Indoor Environment Group, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Neal L Benowitz
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
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10
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Chen L, Guo L, Feng S, Wang C, Cui Z, Wang S, Lu Q, Chang H, Hang B, Snijders AM, Mao JH, Lu Y, Ding D. Fecal microbiota transplantation ameliorates type 2 diabetes via metabolic remodeling of the gut microbiota in db/db mice. BMJ Open Diabetes Res Care 2023; 11:11/3/e003282. [PMID: 37253485 DOI: 10.1136/bmjdrc-2022-003282] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/30/2023] [Indexed: 06/01/2023] Open
Abstract
INTRODUCTION Gut microbiome (GM) deregulation has been implicated in major conditions such as obesity and type 2 diabetes (T2DM). Our previous prospective study indicated that fecal microbiota transplantation (FMT) successfully improved patients with T2DM. We hypothesized that FMT may be a potential therapeutic method for T2DM, but its precise mechanisms in T2DM remains to be elucidated. RESEARCH DESIGN AND METHODS Eight db/m mice were FMT donors and control mice, and 16 genetically diabetic db/db mice were equally divided into two groups (db/db+phosphate-buffered saline (PBS) group, db/db+FMT group). The db/db+FMT group was administered fresh fecal suspension (0.2 mL/mice) daily for 4 weeks. Analysis of the GM and serum metabolome was carried out by 16S ribosomal RNA sequencing and liquid chromatogram-mass spectrometry, respectively. Effects of FMT on the gut barrier and pancreas were assessed using protein assays, messenger RNA, immunohistology and clinical indicators testing. RESULTS Our results showed that FMT treatment of db/db mice relieves a series of clinical indicators, including fasting plasma glucose, serum insulin and oral glucose tolerance test among others. Compared with non-diabetic control mice, db/db+PBS mice exhibited decreased abundance of Ruminococaceae, Porphyromonadaceae and increased abundance of Rikenellaceae and Lactobacillaceae. FMT treatment reversed this effect on the microbiome. Eleven metabolites were changed between the db/db+PBS and db/db+FMT groups. Correlation analysis showed that the structural changes of the GM were correlated with host metabolite levels. We further showed that FMT treatment of db/db mice improved intestinal barrier function, reduced inflammation and caused an alteration in the number of circulating immune cells. CONCLUSIONS FMT-mediated changes in the GM, serum metabolites, intestinal epithelial barrier, inflammation and circulating immune cells play an important role in the efficacy of FMT on T2DM disease progression.
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Affiliation(s)
- Lijuan Chen
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing Medical University Second Affiliated Hospital, Nanjing, Jiangsu, China
| | - Lin Guo
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing Medical University Second Affiliated Hospital, Nanjing, Jiangsu, China
| | - Susu Feng
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing Medical University Second Affiliated Hospital, Nanjing, Jiangsu, China
| | - Congcong Wang
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing Medical University Second Affiliated Hospital, Nanjing, Jiangsu, China
| | - Zhicheng Cui
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing Medical University Second Affiliated Hospital, Nanjing, Jiangsu, China
| | - Sijing Wang
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing Medical University Second Affiliated Hospital, Nanjing, Jiangsu, China
| | - Qingmiao Lu
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing Medical University Second Affiliated Hospital, Nanjing, Jiangsu, China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Biomaterials, Berkeley-Nanjing Research Center, Nanjing, Jiangsu, China
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yibing Lu
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing Medical University Second Affiliated Hospital, Nanjing, Jiangsu, China
| | - Dafa Ding
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing Medical University Second Affiliated Hospital, Nanjing, Jiangsu, China
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11
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Schulte R, Johnstone C, Boucher S, Esarey E, Geddes CGR, Kravchenko M, Kutsaev S, Loo BW, Méot F, Mustapha B, Nakamura K, Nanni EA, Obst-Huebl L, Sampayan SE, Schroeder CB, Sheng K, Snijders AM, Snively E, Tantawi SG, Van Tilborg J. Transformative Technology for FLASH Radiation Therapy. Appl Sci (Basel) 2023; 13:5021. [PMID: 38240007 PMCID: PMC10795821 DOI: 10.3390/app13085021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
The general concept of radiation therapy used in conventional cancer treatment is to increase the therapeutic index by creating a physical dose differential between tumors and normal tissues through precision dose targeting, image guidance, and radiation beams that deliver a radiation dose with high conformality, e.g., protons and ions. However, the treatment and cure are still limited by normal tissue radiation toxicity, with the corresponding side effects. A fundamentally different paradigm for increasing the therapeutic index of radiation therapy has emerged recently, supported by preclinical research, and based on the FLASH radiation effect. FLASH radiation therapy (FLASH-RT) is an ultra-high-dose-rate delivery of a therapeutic radiation dose within a fraction of a second. Experimental studies have shown that normal tissues seem to be universally spared at these high dose rates, whereas tumors are not. While dose delivery conditions to achieve a FLASH effect are not yet fully characterized, it is currently estimated that doses delivered in less than 200 ms produce normal-tissue-sparing effects, yet effectively kill tumor cells. Despite a great opportunity, there are many technical challenges for the accelerator community to create the required dose rates with novel compact accelerators to ensure the safe delivery of FLASH radiation beams.
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Affiliation(s)
- Reinhard Schulte
- Division of Biomedical Engineering Sciences, Loma Linda University, Loma Linda, CA 92350, USA
| | - Carol Johnstone
- Fermi National Accelerator Laboratory, Batavia, IL 60510, USA
| | - Salime Boucher
- RadiaBeam Technologies, LLC, Santa Monica, CA 90404, USA
| | - Eric Esarey
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | - Sergey Kutsaev
- RadiaBeam Technologies, LLC, Santa Monica, CA 90404, USA
| | - Billy W. Loo
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - François Méot
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | - Kei Nakamura
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emilio A. Nanni
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Stephen E. Sampayan
- Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
- Opcondys, Inc., Manteca, CA 95336, USA
| | | | - Ke Sheng
- Department of Radiation Oncology, University of California, San Francisco, CA 94115, USA
| | | | - Emma Snively
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sami G. Tantawi
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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12
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Yang H, Wang X, Wang P, He L, Schick SF, Jacob P, Benowitz N, Gundel LA, Zhu C, Xia Y, Inman JL, Chang H, Snijders AM, Mao JH, Hang B. Thirdhand tobacco smoke exposure increases the genetic background-dependent risk of pan-tumor development in Collaborative Cross mice. Environ Int 2023; 174:107876. [PMID: 36940581 DOI: 10.1016/j.envint.2023.107876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/15/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Increasing evidence has shown that thirdhand smoke (THS) exposure is likely to induce adverse health effects. An important knowledge gap remains in our understanding of THS exposure related to cancer risk in the human population. Population-based animal models are useful and powerful in investigating the interplay between host genetics and THS exposure on cancer risk. Here, we used the Collaborative Cross (CC) mouse population-based model system, which recapitulates the genetic and phenotypic diversity observed in the human population, to assess cancer risk after a short period of exposure, between 4 and 9 weeks of age. Eight CC strains (CC001, CC019, CC026, CC036, CC037, CC041, CC042 and CC051) were included in our study. We quantified pan-tumor incidence, tumor burden per mouse, organ tumor spectrum and tumor-free survival until 18 months of age. At the population level, we observed a significantly increased pan-tumor incidence and tumor burden per mouse in THS-treated mice as compared to the control (p = 3.04E-06). Lung and liver tissues exhibited the largest risk of undergoing tumorigenesis after THS exposure. Tumor-free survival was significantly reduced in THS-treated mice compared to control (p = 0.044). At the individual strain level, we observed a large variation in tumor incidence across the 8 CC strains. CC036 and CC041 exhibited a significant increase in pan-tumor incidence (p = 0.0084 and p = 0.000066, respectively) after THS exposure compared to control. We conclude that early-life THS exposure increases tumor development in CC mice and that host genetic background plays an important role in individual susceptibility to THS-induced tumorigenesis. Genetic background is an important factor that should be taken into account when determining human cancer risk of THS exposure.
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Affiliation(s)
- Hui Yang
- Department of Radiation and Medical Oncology, Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Xinzhi Wang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China
| | - Pin Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Li He
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Suzyann F Schick
- Department of Medicine, Division of Occupational and Environmental Medicine, University of California, San Francisco, CA 94143, USA
| | - Peyton Jacob
- Department of Medicine, Division of Cardiology, Clinical Pharmacology Program, University of California, San Francisco, CA 94143, USA
| | - Neal Benowitz
- Department of Medicine, Division of Cardiology, Clinical Pharmacology Program, University of California, San Francisco, CA 94143, USA
| | - Lara A Gundel
- Indoor Environment Group, Energy Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chi Zhu
- Hanszen College, Rice University, Houston, TX 77005, USA
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jamie L Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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13
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Yu S, Zhang M, Zhu J, Yang X, Bigambo FM, Snijders AM, Wang X, Hu W, Lv W, Xia Y. The effect of ambient ozone exposure on three types of diabetes: a meta-analysis. Environ Health 2023; 22:32. [PMID: 36998068 PMCID: PMC10061724 DOI: 10.1186/s12940-023-00981-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Ozone as an air pollutant is gradually becoming a threat to people's health. However, the effect of ozone exposure on risk of developing diabetes, a fast-growing global metabolic disease, remains controversial. OBJECTIVE To evaluate the impact of ambient ozone exposure on the incidence rate of type 1, type 2 and gestational diabetes mellitus. METHOD We systematically searched PubMed, Web of Science, and Cochrane Library databases before July 9, 2022, to determine relevant literature. Data were extracted after quality evaluation according to the Newcastle Ottawa Scale (NOS) and the agency for healthcare research and quality (AHRQ) standards, and a meta-analysis was used to evaluate the correlation between ozone exposure and type 1 diabetes mellitus (T1D), type 2 diabetes mellitus (T2D), and gestational diabetes mellitus (GDM). The heterogeneity test, sensitivity analysis, and publication bias were performed using Stata 16.0. RESULTS Our search identified 667 studies from three databases, 19 of which were included in our analysis after removing duplicate and ineligible studies. Among the remaining studies, three were on T1D, five were on T2D, and eleven were on GDM. The result showed that ozone exposure was positively correlated with T2D [effect size (ES) = 1.06, 95% CI: 1.02, 1.11] and GDM [pooled odds ratio (OR) = 1.01, 95% CI: 1.00, 1.03]. Subgroup analysis demonstrated that ozone exposure in the first trimester of pregnancy might raise the risk of GDM. However, no significant association was observed between ozone exposure and T1D. CONCLUSION Long-term exposure to ozone may increase the risk of T2D, and daily ozone exposure during pregnancy was a hazard factor for developing GDM. Decreasing ambient ozone pollution may reduce the burden of both diseases.
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Affiliation(s)
- Sirui Yu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Institute of Toxicology, School of Public Health, Nanjing Medical University, No.101 Longmian Road, Nanjing, 211166, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mingzhi Zhang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Institute of Toxicology, School of Public Health, Nanjing Medical University, No.101 Longmian Road, Nanjing, 211166, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiamin Zhu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Institute of Toxicology, School of Public Health, Nanjing Medical University, No.101 Longmian Road, Nanjing, 211166, China
| | - Xu Yang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Institute of Toxicology, School of Public Health, Nanjing Medical University, No.101 Longmian Road, Nanjing, 211166, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Francis Manyori Bigambo
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Institute of Toxicology, School of Public Health, Nanjing Medical University, No.101 Longmian Road, Nanjing, 211166, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xu Wang
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weiyue Hu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Institute of Toxicology, School of Public Health, Nanjing Medical University, No.101 Longmian Road, Nanjing, 211166, China.
- Department of Nutrition and Food Safety, School of Public Health, Nanjing Medical University, No.101 Longmian Road, Nanjing, 211166, China.
| | - Wei Lv
- Healthcare Management Program, School of Business, Nanjing University, 22 Hankou Rd, Nanjing, 210093, China.
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Institute of Toxicology, School of Public Health, Nanjing Medical University, No.101 Longmian Road, Nanjing, 211166, China.
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
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14
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Xu Y, Yang X, Chen D, Xu Y, Lan L, Zhao S, Liu Q, Snijders AM, Xia Y. Maternal exposure to pesticides and autism or attention-deficit/hyperactivity disorders in offspring: A meta-analysis. Chemosphere 2023; 313:137459. [PMID: 36470360 PMCID: PMC9839607 DOI: 10.1016/j.chemosphere.2022.137459] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
OBJECTIVE To analyze the association between maternal pesticide exposure and autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorders (ADHD) in offspring. METHOD Five databases including PubMed, Embase, Web of Science, Medline, as well as PsycINFO were systematically retrieved for the records related to pesticide exposure during pregnancy and ASD and ADHD in offspring before August 30, 2022. The pesticide category, maternal age and window of exposure as the main subgroups were presented. RESULTS 949 studies were initially identified, and 19 studies were eventually included. Eleven were on ASD, seven were on ADHD, and one was on both disorders. Maternal pesticide exposure was positively related to ASD (pooled OR = 1.19 (95%CI: 1.04 to 1.36)) and ADHD (pooled OR = 1.20 (95%CI: 1.04 to 1.38)) in offspring. In the subgroup analysis, organophosphorus pesticides (OPs) (pooled OR = 1.14 (95%CI: 1.04 to 1.24)), pyrethroid (pooled OR = 1.40 (95%CI: 1.09 to 1.80)), and maternal age ≥30 years old (pooled OR = 1.24 (95%CI: 1.10 to 1.40)) increased the risk of ASD in offspring. Maternal organochlorine pesticides (OCPs) exposure was a risk factor for ADHD in offspring (pooled OR = 1.22 (95%CI: 1.03 to 1.45)). CONCLUSION Maternal pesticide exposure increased the risk of ASD and ADHD in offspring. Moreover, OPs, pyrethroid, and maternal age ≥30 years old were found to be risk factors affecting children's ASD. Maternal exposure to OCPs increased the risk of ADHD in offspring. Our findings contribute to our understanding of health risks related to maternal pesticide exposure and indicate that the in utero developmental period is a vulnerable window-of-susceptibility for ASD and ADHD risk in offspring. These findings should guide policies that limit maternal exposure to pesticides, especially for pregnant women living in agricultural areas.
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Affiliation(s)
- Yifan Xu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xu Yang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Danrong Chen
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yadan Xu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Linchen Lan
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuangshuang Zhao
- Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Qianqi Liu
- Children's Hospital of Nanjing Medical University, Nanjing, China.
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.
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15
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Roman LJ, Snijders AM, Chang H, Mao JH, Jones KJA, Lawson GW. Effect of Husbandry Practices on the Fecal Microbiota of C57BL/6J Breeding Colonies Housed in 2 Different Barrier Facilities in the Same Institution. J Am Assoc Lab Anim Sci 2023; 62:26-37. [PMID: 36755206 PMCID: PMC9936858 DOI: 10.30802/aalas-jaalas-22-000068] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Evidence showing a relationship between the mouse gut microbiome and properties such as phenotype and reaction to therapeutic agents and other treatments has increased significantly over the past 20 to 30 y. Recent concerns regarding the reproducibility of animal experiments have underscored the importance of understanding this relationship and how differences in husbandry practices can affect the gut microbiome. The current study focuses on effects of different barrier practices in 2 barrier facilities at the same institution on the fecal microbiome of breeding C57Bl/6J mice. Ten female and 10 male C57Bl/6J mice were obtained in one shipment from Jackson Laboratories and were housed under different barrier conditions upon arrival. Fecal samples were collected on arrival and periodically thereafter and were sent to TransnetYX for microbiome analysis. Mice used for collection of feces were housed as breeding pairs, with a total of 5 breeding pairs per barrier. An additional fecal sample was collected from these mice at 8 wk after arrival. One F1 female and one F1 male from each breeding cage were housed as brother-sister breeding pairs and a fecal sample was collected from them at 8 wk of age. Brother-sister breeding colonies were continued through F3, with fecal samples for microbiome analysis were collected from each generation at 8 wk of age. Breeding colonies in the 2 barriers showed differences in relative abundance, α -diversity, and β -diversity. Our data indicate that differences in barrier husbandry practices, including the use of autoclaved cages, the degree of restricted access, feed treatment practices, and water provision practices, can affect fecal microbiome divergence in both the parental and filial generations of different breeding colonies. To our knowledge, this is the first study to examine the effect of barrier husbandry practices on the microbiome of breeding colonies through the F3 generation.
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Affiliation(s)
- Libette J Roman
- Office of Laboratory Animal Care, University of California Berkeley, Berkeley, California,,Corresponding author.
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Kristina JA Jones
- Office of Laboratory Animal Care, University of California Berkeley, Berkeley, California
| | - Gregory W Lawson
- Office of Laboratory Animal Care, University of California Berkeley, Berkeley, California
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16
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Zhang Y, Wang X, Yang X, Hu Q, Chawla K, Hang B, Mao JH, Snijders AM, Chang H, Xia Y. Chemical mixture exposure patterns and obesity among U.S. adults in NHANES 2005-2012. Ecotoxicol Environ Saf 2022; 248:114309. [PMID: 36427371 PMCID: PMC10012331 DOI: 10.1016/j.ecoenv.2022.114309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND The effect of chemical exposure on obesity has raised great concerns. Real-world chemical exposure always imposes mixture impacts, however their exposure patterns and the corresponding associations with obesity have not been fully evaluated. OBJECTIVES To discover obesity-related mixed chemical exposure patterns in the general U.S. METHODS Sparse Decompositional Regression (SDR), a model adapted from sparse representation learning technique, was developed to identify exposure patterns of chemical mixtures with exclusion (non-targeted model) and inclusion (targeted model) of health outcomes. We assessed the relationships between the identified chemical mixture patterns and obesity-related indexes. We also conducted a comprehensive evaluation of this SDR model by comparing to the existing models, including generalized linear regression model (GLM), principal component analysis (PCA), and Bayesian kernel machine regression (BKMR). RESULTS Eight core exposure patterns were identified using the non-targeted SDR model. Patterns of high levels of MEP, high levels of naphthalene metabolites (ΣOH-Nap), and a pattern of high exposure levels of MCOP, MCNP, and MCPP were positively associated with obesity. Patterns of high levels of BP3, and a pattern of higher mixed levels of MPB, PPB, and MEP were found to have negative associations. Associations were strengthened using the targeted SDR model. In the single chemical analysis by GLM, BP3, MBP, PPB, MCOP, and MCNP showed significant associations with obesity or body indexes. The SDR model exceeded the performance of PCA in pattern identification. Both SDR and BKMR identified a positive contribution of ΣOH-Nap and MCOP, as well as a negative contribution of BP3 and PPB to obesity. CONCLUSION Our study identified five core exposure patterns of chemical mixtures significantly associated with obesity using the newly developed SDR model. The SDR model could open a new avenue for assessing health effects of environmental mixture contaminants.
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Affiliation(s)
- Yuqing Zhang
- Department of Obstetrics and Gynecology, Women's Hospital of Nanjing Medical University,Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, China
| | - Xu Wang
- Department of endocrinology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Xu Yang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Qi Hu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Kuldeep Chawla
- Scientific Computing Group, Information Technology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian-Hua Mao
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Antoine M Snijders
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hang Chang
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
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17
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Kenneally R, Lawrence Q, Brydon E, Wan KH, Mao JH, Verma SC, Khazaieli A, Celniker SE, Snijders AM. Inactivation of multiple human pathogens by Fathhome's dry sanitizer device: Rapid and eco-friendly ozone-based disinfection. Medicine in Microecology 2022; 14:100059. [PMID: 35945946 PMCID: PMC9354387 DOI: 10.1016/j.medmic.2022.100059] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/30/2022] [Accepted: 07/24/2022] [Indexed: 11/25/2022] Open
Abstract
SARS-CoV-2 spread rapidly, causing millions of deaths across the globe. As a result, demand for medical supplies and personal protective equipment (PPE) surged and supplies dwindled. Separate entirely, hospital-acquired infections have become commonplace and challenging to treat. To explore the potential of novel sterilization techniques, this study evaluated the disinfection efficacy of Fathhome's ozone-based, dry-sanitizing device by dose and time response. Inactivation of human pathogens was tested on non-porous (plastic) surfaces. 95.42–100% inactivation was observed across all types of vegetative microorganisms and 27.36% inactivation of bacterial endospores tested, with no residual ozone detectable after completion. These results strongly support the hypothesis that Fathhome's commercial implementation of gas-based disinfection is suitable for rapid decontamination of a wide variety of pathogens on PPE and other industrially relevant materials.
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18
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Geulig LD, Obst-Huebl L, Nakamura K, Bin J, Ji Q, Steinke S, Snijders AM, Mao JH, Blakely EA, Gonsalves AJ, Bulanov S, van Tilborg J, Schroeder CB, Geddes CGR, Esarey E, Roth M, Schenkel T. Online charge measurement for petawatt laser-driven ion acceleration. Rev Sci Instrum 2022; 93:103301. [PMID: 36319346 DOI: 10.1063/5.0096423] [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] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Laser-driven ion beams have gained considerable attention for their potential use in multidisciplinary research and technology. Preclinical studies into their radiobiological effectiveness have established the prospect of using laser-driven ion beams for radiotherapy. In particular, research into the beneficial effects of ultrahigh instantaneous dose rates is enabled by the high ion bunch charge and uniquely short bunch lengths present for laser-driven ion beams. Such studies require reliable, online dosimetry methods to monitor the bunch charge for every laser shot to ensure that the prescribed dose is accurately applied to the biological sample. In this paper, we present the first successful use of an Integrating Current Transformer (ICT) for laser-driven ion accelerators. This is a noninvasive diagnostic to measure the charge of the accelerated ion bunch. It enables online estimates of the applied dose in radiobiological experiments and facilitates ion beam tuning, in particular, optimization of the laser ion source, and alignment of the proton transport beamline. We present the ICT implementation and the correlation with other diagnostics, such as radiochromic films, a Thomson parabola spectrometer, and a scintillator.
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Affiliation(s)
- Laura D Geulig
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Lieselotte Obst-Huebl
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kei Nakamura
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jianhui Bin
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Qing Ji
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Sven Steinke
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Eleanor A Blakely
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Anthony J Gonsalves
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Stepan Bulanov
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jeroen van Tilborg
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Carl B Schroeder
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Cameron G R Geddes
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Eric Esarey
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Markus Roth
- Institut für Kernphysik, Technische Universität Darmstadt, Schlossgartenstraße 9, 64289 Darmstadt, Germany
| | - Thomas Schenkel
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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19
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Tang X, Benowitz N, Gundel L, Hang B, Havel CM, Hoh E, Jacob Iii P, Mao JH, Martins-Green M, Matt GE, Quintana PJE, Russell ML, Sarker A, Schick SF, Snijders AM, Destaillats H. Thirdhand Exposures to Tobacco-Specific Nitrosamines through Inhalation, Dust Ingestion, Dermal Uptake, and Epidermal Chemistry. Environ Sci Technol 2022; 56:12506-12516. [PMID: 35900278 DOI: 10.1021/acs.est.2c02559] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Tobacco-specific nitrosamines (TSNAs) are emitted during smoking and form indoors by nitrosation of nicotine. Two of them, N'-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), are human carcinogens with No Significant Risk Levels (NSRLs) of 500 and 14 ng day-1, respectively. Another TSNA, 4-(methylnitrosamino)-4-(3-pyridyl) butanal (NNA), shows genotoxic and mutagenic activity in vitro. Here, we present additional evidence of genotoxicity of NNA, an assessment of TSNA dermal uptake, and predicted exposure risks through different pathways. Dermal uptake was investigated by evaluating the penetration of NNK and nicotine through mice skin. Comparable mouse urine metabolite profiles suggested that both compounds were absorbed and metabolized via similar mechanisms. We then investigated the effects of skin constituents on the reaction of adsorbed nicotine with nitrous acid (epidermal chemistry). Higher TSNA concentrations were formed on cellulose and cotton substrates that were precoated with human skin oils and sweat compared to clean substrates. These results were combined with reported air, dust, and surface concentrations to assess NNK intake. Five different exposure pathways exceeded the NSRL under realistic scenarios, including inhalation, dust ingestion, direct dermal contact, gas-to-skin deposition, and epidermal nitrosation of nicotine. These results illustrate potential long-term health risks for nonsmokers in homes contaminated with thirdhand tobacco smoke.
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Affiliation(s)
- Xiaochen Tang
- Indoor Environment Group, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Neal Benowitz
- Clinical Pharmacology Program, Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California 94143, United States
| | - Lara Gundel
- Indoor Environment Group, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Bo Hang
- Bioengineering & Biomedical Sciences Department, Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher M Havel
- Clinical Pharmacology Program, Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California 94143, United States
| | - Eunha Hoh
- School of Public Health, San Diego State University, San Diego, California 92182, United States
| | - Peyton Jacob Iii
- Clinical Pharmacology Program, Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California 94143, United States
| | - Jian-Hua Mao
- Bioengineering & Biomedical Sciences Department, Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Manuela Martins-Green
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California 92506, United States
| | - Georg E Matt
- Department of Psychology, San Diego State University, San Diego, California 92182, United States
| | - Penelope J E Quintana
- School of Public Health, San Diego State University, San Diego, California 92182, United States
| | - Marion L Russell
- Indoor Environment Group, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Altaf Sarker
- Bioengineering & Biomedical Sciences Department, Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Suzaynn F Schick
- Clinical Pharmacology Program, Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California 94143, United States
| | - Antoine M Snijders
- Bioengineering & Biomedical Sciences Department, Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hugo Destaillats
- Indoor Environment Group, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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20
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Liu XP, Jin X, Seyed Ahmadian S, Yang X, Tian SF, Cai YX, Chawla K, Snijders AM, Xia Y, van Diest PJ, Weiss WA, Mao JH, Li ZQ, Vogel H, Chang H. Clinical significance and molecular annotation of cellular morphometric subtypes in lower-grade gliomas discovered by machine learning. Neuro Oncol 2022; 25:68-81. [PMID: 35716369 PMCID: PMC9825346 DOI: 10.1093/neuonc/noac154] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Lower-grade gliomas (LGG) are heterogeneous diseases by clinical, histological, and molecular criteria. We aimed to personalize the diagnosis and therapy of LGG patients by developing and validating robust cellular morphometric subtypes (CMS) and to uncover the molecular signatures underlying these subtypes. METHODS Cellular morphometric biomarkers (CMBs) were identified with artificial intelligence technique from TCGA-LGG cohort. Consensus clustering was used to define CMS. Survival analysis was performed to assess the clinical impact of CMBs and CMS. A nomogram was constructed to predict 3- and 5-year overall survival (OS) of LGG patients. Tumor mutational burden (TMB) and immune cell infiltration between subtypes were analyzed using the Mann-Whitney U test. The double-blinded validation for important immunotherapy-related biomarkers was executed using immunohistochemistry (IHC). RESULTS We developed a machine learning (ML) pipeline to extract CMBs from whole-slide images of tissue histology; identifying and externally validating robust CMS of LGGs in multicenter cohorts. The subtypes had independent predicted OS across all three independent cohorts. In the TCGA-LGG cohort, patients within the poor-prognosis subtype responded poorly to primary and follow-up therapies. LGGs within the poor-prognosis subtype were characterized by high mutational burden, high frequencies of copy number alterations, and high levels of tumor-infiltrating lymphocytes and immune checkpoint genes. Higher levels of PD-1/PD-L1/CTLA-4 were confirmed by IHC staining. In addition, the subtypes learned from LGG demonstrate translational impact on glioblastoma (GBM). CONCLUSIONS We developed and validated a framework (CMS-ML) for CMS discovery in LGG associated with specific molecular alterations, immune microenvironment, prognosis, and treatment response.
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Affiliation(s)
| | | | - Saman Seyed Ahmadian
- Department of Pathology, Stanford University Medical Center, Stanford, California, USA
| | - Xu Yang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Su-Fang Tian
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yu-Xiang Cai
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Kuldeep Chawla
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yankai Xia
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - William A Weiss
- Departments of Neurology, Neurological Surgery, and Pediatrics, University of California, San Francisco, San Francisco, California, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Zhi-Qiang Li
- Corresponding Authors: Zhi-Qiang Li, MD, PhD, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 169 East Lake Road, Wuchang District, Wuhan, Hubei 430071 China (); Hang Chang, PhD, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA ()
| | | | - Hang Chang
- Corresponding Authors: Zhi-Qiang Li, MD, PhD, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 169 East Lake Road, Wuchang District, Wuhan, Hubei 430071 China (); Hang Chang, PhD, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA ()
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21
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Chang H, Yang X, Moore J, Liu XP, Jen KY, Snijders AM, Ma L, Chou W, Corchado-Cobos R, García-Sancha N, Mendiburu-Eliçabe M, Pérez-Losada J, Barcellos-Hoff MH, Mao JH. From Mouse to Human: Cellular Morphometric Subtype Learned From Mouse Mammary Tumors Provides Prognostic Value in Human Breast Cancer. Front Oncol 2022; 11:819565. [PMID: 35242697 PMCID: PMC8886672 DOI: 10.3389/fonc.2021.819565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 12/30/2021] [Indexed: 12/17/2022] Open
Abstract
Mouse models of cancer provide a powerful tool for investigating all aspects of cancer biology. In this study, we used our recently developed machine learning approach to identify the cellular morphometric biomarkers (CMB) from digital images of hematoxylin and eosin (H&E) micrographs of orthotopic Trp53-null mammary tumors (n = 154) and to discover the corresponding cellular morphometric subtypes (CMS). Of the two CMS identified, CMS-2 was significantly associated with shorter survival (p = 0.0084). We then evaluated the learned CMB and corresponding CMS model in MMTV-Erbb2 transgenic mouse mammary tumors (n = 53) in which CMS-2 was significantly correlated with the presence of metastasis (p = 0.004). We next evaluated the mouse CMB and CMS model on The Cancer Genome Atlas breast cancer (TCGA-BRCA) cohort (n = 1017). Kaplan–Meier analysis showed significantly shorter overall survival (OS) of CMS-2 patients compared to CMS-1 patients (p = 0.024) and added significant prognostic value in multi-variable analysis of clinical and molecular factors, namely, age, pathological stage, and PAM50 molecular subtype. Thus, application of CMS to digital images of routine workflow H&E preparations can provide unbiased biological stratification to inform patient care.
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Affiliation(s)
- Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Xu Yang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jade Moore
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Xiao-Ping Liu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kuang-Yu Jen
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Lin Ma
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - William Chou
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Roberto Corchado-Cobos
- Instituto de Biología Molecular y Celular del Cáncer, Universidad de Salamanca/Consejo Superior de Investigaciones Científicas (CSIC), Salamanca, Spain.,Instituto de Investigación Biosanitaria de Salamanca, Salamanca, Spain
| | - Natalia García-Sancha
- Instituto de Biología Molecular y Celular del Cáncer, Universidad de Salamanca/Consejo Superior de Investigaciones Científicas (CSIC), Salamanca, Spain.,Instituto de Investigación Biosanitaria de Salamanca, Salamanca, Spain
| | - Marina Mendiburu-Eliçabe
- Instituto de Biología Molecular y Celular del Cáncer, Universidad de Salamanca/Consejo Superior de Investigaciones Científicas (CSIC), Salamanca, Spain.,Instituto de Investigación Biosanitaria de Salamanca, Salamanca, Spain
| | - Jesus Pérez-Losada
- Instituto de Biología Molecular y Celular del Cáncer, Universidad de Salamanca/Consejo Superior de Investigaciones Científicas (CSIC), Salamanca, Spain.,Instituto de Investigación Biosanitaria de Salamanca, Salamanca, Spain
| | - Mary Helen Barcellos-Hoff
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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22
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Abstract
Live cells acquire different fates including apoptosis, necrosis, and senescence in response to stress and stimuli. Rapid and label-free enrichment of live cells from a mixture of cells adopting various cell fates remains a challenge. We developed a ViaChip for high-throughput enrichment of Viable cells via size-based separation on a multi-stage microfluidic Chip. Our chip takes advantage of the characteristic increase in cell size during cellular senescence and decreases during apoptosis and necrosis, in comparison to their viable and healthy counterparts. The core component of our ViaChip is a slanted and tunable 3D filter array in the vertical direction (z-gap) for rapid and continuous cell sieving. The shape of the 3D filter array is optimized for target cells to prevent clogging during continuous separation. We demonstrated enrichment of live human and mouse mesenchymal stem cells in culture and from live animals, as well as the removal of senescent and necrotic MSCs, respectively, achieving an enrichment efficiency of ~67% with the continuous flow at 1.5 mL/hour. With further improvements in throughput and separation efficiency, our ViaChip could find applications in cell-based drug screening for anti-cancer and anti-aging cell therapies.
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23
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Zhang Y, Chen T, Zhang Y, Hu Q, Wang X, Chang H, Mao JH, Snijders AM, Xia Y. Contribution of trace element exposure to gestational diabetes mellitus through disturbing the gut microbiome. Environ Int 2021; 153:106520. [PMID: 33774496 PMCID: PMC8638703 DOI: 10.1016/j.envint.2021.106520] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND A healthy gut microbiome is critical for glucose metabolism during pregnancy. In vivo studies indicate that trace element affects the composition and function of the gut microbiome and potentially leads to metabolic disorders but their relationships are largely unknown. We aimed to investigate whether the gut microbiome plays a role in the relationship between trace element exposure and gestational diabetes mellitus (GDM). METHODS In a prospective cohort study, serum levels of 22 trace elements and the fecal gut microbiome composition were assessed in 837 pregnant women in the second trimester between 22 and 24 weeks of pregnancy prior to GDM diagnosis. Regression and mediation analysis were used to explore the link between element exposure, the gut microbiome, and GDM. RESULTS 128 pregnant women (15.3%) were diagnosed with GDM. No individual trace elements were found significantly associated with GDM. In contrast, the composition of the gut microbiome was dramatically altered in women later diagnosed with GDM and characterized by lower alpha diversity and lower abundance of co-abundance groups (CAGs) composed of genera belonging to Ruminococcaceae, Coriobacteriales, and Lachnospiraceae. Rubidium (Rb) was positively associated with alpha diversity indices while mercury (Hg) and vanadium (V) showed negative associations. Elements including rubidium (Rb), thallium (Tl), arsenic (As), and antimony (Sb) were significantly correlated with GDM-related CAGs and mediation analysis revealed that Rb and Sb were inversely related to GDM risk by altering abundance levels of CAGs enriched for Lachnospiraceae, Coriobacteriales, and Ruminococcaceae. CONCLUSION Our study indicates that trace element exposure is associated with specific gut microbiome features that may contribute to GDM development, which could provide a new avenue for intervening in environmental exposure-related GDM.
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Affiliation(s)
- Yuqing Zhang
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Hospital, Nanjing, China; State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ting Chen
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Hospital, Nanjing, China; State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yiyun Zhang
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qi Hu
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xu Wang
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.
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24
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He L, Wang P, Schick SF, Huang A, Jacob P, Yang X, Xia Y, Snijders AM, Mao JH, Chang H, Hang B. Genetic background influences the effect of thirdhand smoke exposure on anxiety and memory in Collaborative Cross mice. Sci Rep 2021; 11:13285. [PMID: 34168244 PMCID: PMC8225773 DOI: 10.1038/s41598-021-92702-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/08/2021] [Indexed: 01/18/2023] Open
Abstract
Growing evidence indicates that thirdhand smoke (THS) exposure induces many adverse health effects. However, it is unclear how THS exposure affects behavior and how host genetic background modulates phenotypic changes. Here we used the Collaborative Cross (CC) mouse population-based model to assess behavioral alterations immediately after THS exposure from 4 to 9 weeks of age. We first measured anxiety-like behavior in six strains using light/dark box combined with a custom multivariate mouse tracking system. We developed an anxiety risk scoring system based on anxiety-related traits and then evaluated the THS impact on them. THS exposure significantly decreased anxiety risk in CC019 (P = 0.002) and CC051 (P = 0.009), but increased anxiety risk in CC036 (P < 0.001), while the other three strains did not show significant changes in anxiety-related traits. Such differences were driven by female mice for the six measures of anxiety-like behavior. Memory potential was measured in the same cohort of mice using the passive avoidance assay. Both THS-exposed male and female CC019 mice displayed significant memory loss compared to controls while no significant changes were found in the other five strains. This study provides strong evidence that THS exposure leads to strain-dependent changes in anxiety-like behavior and memory, suggesting that host genetic variations play a critical role in individual susceptibility to THS-induced effects.
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Affiliation(s)
- Li He
- Department of Internal Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Pin Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
| | - Suzyann F Schick
- Division of Occupational and Environmental Medicine, Department of Medicine, University of California, San Francisco, CA, 94143, USA
| | - Abel Huang
- Division of Occupational and Environmental Medicine, Department of Medicine, University of California, San Francisco, CA, 94143, USA
| | - Peyton Jacob
- Division of Cardiology, Department of Medicine, Clinical Pharmacology Program, University of California, San Francisco, CA, 94143, USA
| | - Xu Yang
- School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Yankai Xia
- School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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25
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He L, Zhou Y, Zhang Y, Hang B, Chang H, Schick SF, Celniker SE, Xia Y, Snijders AM, Mao J. Thirdhand cigarette smoke leads to age-dependent and persistent alterations in the cecal microbiome of mice. Microbiologyopen 2021; 10:e1198. [PMID: 34180593 PMCID: PMC8123915 DOI: 10.1002/mbo3.1198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 01/11/2023] Open
Abstract
The gut microbiome composition is influenced by many factors including environmental exposures. Here, we investigated the effect of thirdhand cigarette smoke (THS) and exposure age on gut microbiome diversity. C57BL/6 mice were exposed to THS at human exposure relevant levels for three weeks during three different life stages: postnatal (0-3 weeks of age), pubescent (4-7 weeks of age), and adult (9-12 weeks of age), respectively. Cecal microbiome profiles were assessed at 17 weeks of age by 16S rRNA gene sequencing. We found that age at THS exposure strongly influenced the cecal microbiome composition. Although postnatal THS exposure significantly influenced the microbial composition, pubescent and adulthood exposures only had minor effects. The microbiome of postnatally THS-exposed mice significantly increased several degradation pathways that regulate glycolysis and pyruvate decarboxylation, and significantly decreased coenzyme A biosynthesis and pyrimidine deoxyribonucleoside salvage. Our results indicate that mouse postnatal development is particularly susceptible to persistent THS exposure effects on the gut microbiome.
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Affiliation(s)
- Li He
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
- Department of HematologyZhongnan HospitalWuhan UniversityWuhanChina
| | - Yan‐Xia Zhou
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
- Marine CollegeShandong UniversityWeihaiChina
| | - Yuqing Zhang
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
- State Key Laboratory of Reproductive MedicineInstitute of ToxicologyNanjing Medical UniversityNanjingChina
| | - Bo Hang
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Hang Chang
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Suzaynn F. Schick
- Department of MedicineDivision of Occupational and Environmental MedicineUniversity of CaliforniaSan FranciscoCAUSA
| | - Susan E. Celniker
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Yankai Xia
- State Key Laboratory of Reproductive MedicineInstitute of ToxicologyNanjing Medical UniversityNanjingChina
| | - Antoine M. Snijders
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Jian‐Hua Mao
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
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26
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Uppal T, Khazaieli A, Snijders AM, Verma SC. Inactivation of Human Coronavirus by FATHHOME's Dry Sanitizer Device: Rapid and Eco-Friendly Ozone-Based Disinfection of SARS-CoV-2. Pathogens 2021; 10:339. [PMID: 33799334 PMCID: PMC8002133 DOI: 10.3390/pathogens10030339] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/20/2022] Open
Abstract
The pandemic of SARS-CoV-2/COVID-19 was reported in December 2019 in Wuhan, China. Pertaining to its high transmissibility and wide host adaptability, this unique human coronavirus spread across the planet inflicting 115 million people and causing 2.5 million deaths (as of March 3rd, 2021). Limited or negligible pre-existing immunity to multiple SARS-CoV-2 variants has resulted in severe morbidity and mortality worldwide, as well as a record-breaking surge in the use of medical-surgical supplies and personal protective equipment. In response to the global need for effective sterilization techniques, this study evaluated the virucidal efficacy of FATHHOME's self-contained, ozone-based dry-sanitizing device, by dose and time response assessment. We tested inactivation of human coronavirus, HCoV-OC43, a close genetic model of SARS-CoV-2, on porous (N95 filtering facepiece respirator/FFR) and nonporous (glass) surfaces. We started our assays with 20 ppm-10 min ozone exposure, and effectively reduced 99.8% and 99.9% of virus from glass and N95 FFR surfaces, respectively. Importantly, the virus was completely inactivated, below the detection limit (over 6-log10 reduction) with 25 ppm-15 min ozone exposure on both tested surfaces. As expected, a higher ozone exposure (50 ppm-10 min) resulted in faster inactivation of HCoV-OC43 with 100% inactivation from both the surfaces, with no residual ozone present after completion of the 5-min post exposure recapture cycle and no measurable increase in ambient ozone levels. These results confirmed that FATHHOME's device is suitable for rapid decontamination of SARS-CoV-2- from worn items, frequently touched items, and PPE including N95 FFRs, face shields, and other personal items.
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Affiliation(s)
- Timsy Uppal
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, 1664 N Virginia Street, Reno, NV 89557, USA;
| | - Amir Khazaieli
- FATHHOME, INC., 8000 Edgewater Drive Suite #200, Oakland, CA 94621, USA;
| | - Antoine M. Snijders
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, 1 Cyclotron Road, Berkeley, CA 94720, USA;
| | - Subhash C. Verma
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, 1664 N Virginia Street, Reno, NV 89557, USA;
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27
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Kim YM, Snijders AM, Brislawn CJ, Stratton KG, Zink EM, Fansler SJ, Metz TO, Mao JH, Jansson JK. Corrigendum: Light-Stress Influences the Composition of the Murine Gut Microbiome, Memory Function, and Plasma Metabolome. Front Mol Biosci 2021; 7:619718. [PMID: 33732731 PMCID: PMC7959737 DOI: 10.3389/fmolb.2020.619718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/23/2020] [Indexed: 11/14/2022] Open
Affiliation(s)
- Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Colin J Brislawn
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kelly G Stratton
- Computing and Analytics Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erika M Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
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28
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Jiang C, Zhao Y, Yuan B, Chang H, Hang B, Snijders AM, Mao JH, Zou X, Wang P. Identification of a novel 15-gene expression signature predicting overall survival of human colorectal cancer. Clin Transl Med 2020; 10:e258. [PMID: 33377636 PMCID: PMC7759535 DOI: 10.1002/ctm2.258] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 11/30/2020] [Accepted: 12/06/2020] [Indexed: 11/29/2022] Open
Affiliation(s)
- Chengfei Jiang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Yue Zhao
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Binbin Yuan
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Xiaoping Zou
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Pin Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
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29
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Pariset E, Penninckx S, Kerbaul CD, Guiet E, Macha AL, Cekanaviciute E, Snijders AM, Mao JH, Paris F, Costes SV. 53BP1 Repair Kinetics for Prediction of In Vivo Radiation Susceptibility in 15 Mouse Strains. Radiat Res 2020; 194:485-499. [PMID: 32991727 DOI: 10.1667/rade-20-00122.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/05/2020] [Indexed: 11/03/2022]
Abstract
We present a novel mathematical formalism to predict the kinetics of DNA damage repair after exposure to both low- and high-LET radiation (X rays; 350 MeV/n 40Ar; 600 MeV/n 56Fe). Our method is based on monitoring DNA damage repair protein 53BP1 that forms radiation-induced foci (RIF) at locations of DNA double-strand breaks (DSB) in the nucleus and comparing its expression in primary skin fibroblasts isolated from 15 mice strains. We previously reported strong evidence for clustering of nearby DSB into single repair units as opposed to the classic "contact-first" model where DSB are considered immobile. Here we apply this clustering model to evaluate the number of remaining RIF over time. We also show that the newly introduced kinetic metrics can be used as surrogate biomarkers for in vivo radiation toxicity, with potential applications in radiotherapy and human space exploration. In particular, we observed an association between the characteristic time constant of RIF repair measured in vitro and survival levels of immune cells collected from irradiated mice. Moreover, the speed of DNA damage repair correlated not only with radiation-induced cellular survival in vivo, but also with spontaneous cancer incidence data collected from the Mouse Tumor Biology database, suggesting a relationship between the efficiency of DSB repair after irradiation and cancer risk.
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Affiliation(s)
- Eloise Pariset
- Universities Space Research Association (USRA), Columbia, Maryland 21046.,Space Biosciences Division, NASA Ames Research Center, Mountain View, California 94035
| | - Sébastien Penninckx
- Namur Research Institute for Life Science, University of Namur, 5000 Namur, Belgium.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | | | - Elodie Guiet
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | | | - Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Mountain View, California 94035
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - François Paris
- Université de Nantes, INSERM, CNRS, CRCINA, Nantes, France 44007
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Mountain View, California 94035
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30
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Liu KX, Ioakeim-Ioannidou M, Susko MS, Rao AD, Yeap BY, Snijders AM, Ladra MM, Vogel J, Zaslowe-Dude C, Marcus KJ, Yock TI, Grassberger C, Braunstein SE, Haas-Kogan DA, Terezakis SA, MacDonald SM. A Multi-institutional Comparative Analysis of Proton and Photon Therapy-Induced Hematologic Toxicity in Patients With Medulloblastoma. Int J Radiat Oncol Biol Phys 2020; 109:726-735. [PMID: 33243479 DOI: 10.1016/j.ijrobp.2020.09.049] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 09/11/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE This multi-institutional retrospective study sought to examine the hematologic effects of craniospinal irradiation (CSI) in pediatric patients with medulloblastoma using proton or photon therapy. METHODS AND MATERIALS Clinical and treatment characteristics were recorded for 97 pediatric patients with medulloblastoma who received CSI without concurrent chemotherapy or with concurrent single-agent vincristine from 2000 to 2017. Groups of 60 and 37 patients underwent treatment with proton-based and photon-based therapy, respectively. Overall survival was determined by Kaplan-Meier curves with log-rank test. Comparisons of blood counts at each timepoint were conducted using multiple t tests with Bonferroni corrections. Univariate and multivariate analyses of time to grade ≥3 hematologic toxicity were performed with Cox regression analyses. RESULTS Median age of patients receiving proton and photon CSI was 7.5 years (range, 3.5-22.7 years) and 9.9 years (range, 3.6-19.5 years), respectively. Most patients had a diagnosis of standard risk medulloblastoma, with 86.7% and 89.2% for the proton and photon cohorts, respectively. Median total dose to involved field or whole posterior fossa was 54.0 Gy/Gy relative biological effectiveness (RBE) and median CSI dose was 23.4 Gy/Gy(RBE) (range, 18-36 Gy/Gy[RBE]) for both cohorts. Counts were significantly higher in the proton cohort compared with the photon cohort in weeks 3 to 6 of radiation therapy (RT). Although white blood cell counts did not differ between the 2 cohorts, patients receiving proton RT had significantly higher lymphocyte counts throughout the RT course. Similar results were observed when excluding patients who received vertebral body sparing proton RT or limiting to those receiving 23.4 Gy. Only photon therapy was associated with decreased time to grade ≥3 hematologic toxicity on univariate and multivariable analyses. No difference in overall survival was observed, and lymphopenia did not predict survival. CONCLUSIONS Patients who receive CSI using proton therapy experience significantly decreased hematologic toxicity compared with those receiving photon therapy.
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Affiliation(s)
- Kevin X Liu
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Myrsini Ioakeim-Ioannidou
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Department of Radiation and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Matthew S Susko
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Avani D Rao
- Department of Radiation and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Beow Y Yeap
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Matthew M Ladra
- Department of Radiation and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jennifer Vogel
- Department of Radiation and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Cierra Zaslowe-Dude
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Karen J Marcus
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Torunn I Yock
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Clemens Grassberger
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Steve E Braunstein
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Daphne A Haas-Kogan
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stephanie A Terezakis
- Department of Radiation and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center Johns Hopkins School of Medicine, Baltimore, Maryland; Department of Radiation Oncology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Shannon M MacDonald
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
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31
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Cai TT, Ye XL, Li RR, Chen H, Wang YY, Yong HJ, Pan ML, Lu W, Tang Y, Miao H, Snijders AM, Mao JH, Liu XY, Lu YB, Ding DF. Resveratrol Modulates the Gut Microbiota and Inflammation to Protect Against Diabetic Nephropathy in Mice. Front Pharmacol 2020; 11:1249. [PMID: 32973502 PMCID: PMC7466761 DOI: 10.3389/fphar.2020.01249] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/29/2020] [Indexed: 12/18/2022] Open
Abstract
Oral administration of resveratrol is able to ameliorate the progression of diabetic nephropathy (DN); however, its mechanisms of action remain unclear. Recent evidence suggested that the gut microbiota is involved in the metabolism therapeutics. In the current study, we sought to determine whether the anti-DN effects of resveratrol are mediated through modulation of the gut microbiota using the genetic db/db mouse model of DN. We demonstrate that resveratrol treatment of db/db mice relieves a series of clinical indicators of DN. We then show that resveratrol improves intestinal barrier function and ameliorates intestinal permeability and inflammation. The composition of the gut microbiome was significantly altered in db/db mice compared to control db/m mice. Dysbiosis in db/db mice characterized by low abundance levels of Bacteroides, Alistipes, Rikenella, Odoribacter, Parabacteroides, and Alloprevotella genera were reversed by resveratrol treatment, suggesting a potential role for the microbiome in DN progression. Furthermore, fecal microbiota transplantation, derived from healthy resveratrol-treated db/m mice, was sufficient to antagonize the renal dysfunction, rebalance the gut microbiome and improve intestinal permeability and inflammation in recipient db/db mice. These results indicate that resveratrol-mediated changes in the gut microbiome may play an important role in the mechanism of action of resveratrol, which provides supporting evidence for the gut–kidney axis in DN.
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Affiliation(s)
- Ting-Ting Cai
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiao-Long Ye
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ru-Run Li
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hui Chen
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ya-Yun Wang
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hui-Juan Yong
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ming-Lin Pan
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Lu
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ying Tang
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Heng Miao
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Xing-Yin Liu
- Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, Nanjing Medical University, Nanjing, China
| | - Yi-Bing Lu
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Da-Fa Ding
- Department of Endocrinology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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32
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Tang W, Su Y, Yuan C, Zhang Y, Zhou L, Peng L, Wang P, Chen G, Li Y, Li H, Zhi Z, Chang H, Hang B, Mao JH, Snijders AM, Xia Y. Prospective study reveals a microbiome signature that predicts the occurrence of post-operative enterocolitis in Hirschsprung disease (HSCR) patients. Gut Microbes 2020; 11:842-854. [PMID: 31944159 PMCID: PMC7524399 DOI: 10.1080/19490976.2020.1711685] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Hirschsprung disease (HSCR) is a birth defect with an approximate incidence of 1/5,000 live births, and up to one-third of HSCR patients develop Hirschsprung-associated enterocolitis (HAEC), the leading cause of HSCR-related death. Very little is known about the pathogenesis, prevention, and early diagnosis of HAEC. Here, we used a prospective study to investigate the enteric microbiome composition at the time of surgery as a predictor for developing postoperative HAEC. We identified a microbiome signature containing 21 operational taxonomic units (OTUs) that can potentially predict postoperative HAEC with ~85% accuracy. Furthermore, we identified exclusive breastfeeding as a novel protective factor for total HAEC (i.e., preoperative and postoperative HAEC combined). In addition, we discovered that breastfeeding was associated with a lowered risk for HAEC potentially mediated by modulating the gut microbiome composition characterized by a lower abundance of Gram-negative bacteria and lower LPS concentrations. In conclusion, modulating the gut microbiome by encouraging breastfeeding might prevent HAEC progression in HSCR patients.
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Affiliation(s)
- Weibing Tang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China,Department of Pediatric Surgery, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yang Su
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China,Department of Surgery, The Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University, Huaian, Jiangsu, China
| | - Chen Yuan
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yuqing Zhang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lingling Zhou
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China,Department of Pediatric Surgery, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Peng
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Pin Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Guanglin Chen
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China,Department of Pediatric Surgery, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yang Li
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China,Department of Pediatric Surgery, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongxing Li
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China,Department of Pediatric Surgery, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhengke Zhi
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China,Department of Pediatric Surgery, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA,Antoine M. Snijders Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA94720, USA
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China,CONTACT Yankai Xia Nanjing Medical University, 101 Longmian Ave, Jiangning District, Nanjing211166, China
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Mao JH, Kim YM, Zhou YX, Hu D, Zhong C, Chang H, Brislawn CJ, Fansler S, Langley S, Wang Y, Peisl BYL, Celniker SE, Threadgill DW, Wilmes P, Orr G, Metz TO, Jansson JK, Snijders AM. Correction to: Genetic and metabolic links between the murine microbiome and memory. Microbiome 2020; 8:73. [PMID: 32466793 PMCID: PMC7257159 DOI: 10.1186/s40168-020-00870-5] [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] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
An amendment to this paper has been published and can be accessed via the original article.
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Affiliation(s)
- Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yan-Xia Zhou
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Marine College, Shandong University, Weihai, 264209, China
| | - Dehong Hu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chenhan Zhong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarah Fansler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sasha Langley
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yunshan Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - B Y Loulou Peisl
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - David W Threadgill
- Department of Veterinary Pathobiology, A&M University, College Station, Texas, USA
- Department of Molecular and Cellular Medicine Texas, A&M University, College Station, Texas, USA
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Galya Orr
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas O Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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Lu C, Zhang Y, Qin Y, Xu Q, Zhou R, Cui Y, Zhu Y, Zhang X, Zhang J, Wei X, Wang M, Hang B, Mao JH, Snijders AM, Liu M, Hu Z, Shen H, Zhou Z, Guo X, Wu X, Wang X, Xia Y. Human X chromosome exome sequencing identifies BCORL1 as contributor to spermatogenesis. J Med Genet 2020; 58:56-65. [PMID: 32376790 DOI: 10.1136/jmedgenet-2019-106598] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 09/24/2019] [Revised: 03/16/2020] [Accepted: 03/21/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND Infertility affects approximately 15% of couples worldwide with male infertility being responsible for approximately 50% of cases. Although accumulating evidence demonstrates the critical role of the X chromosome in spermatogenesis during the last few decades, the expression patterns and potential impact of the X chromosome, together with X linked genes, on male infertility are less well understood. METHODS We performed X chromosome exome sequencing followed by a two-stage independent population validation in 1333 non-obstructive azoospermia cases and 1141 healthy controls to identify variant classes with high likelihood of pathogenicity. To explore the functions of these candidate genes in spermatogenesis, we first knocked down these candidate genes individually in mouse spermatogonial stem cells (SSCs) using short interfering RNA oligonucleotides and then generated candidate genes knockout mice by CRISPR-Cas9 system. RESULTS Four low-frequency variants were identified in four genes (BCORL1, MAP7D3, ARMCX4 and H2BFWT) associated with male infertility. Functional studies of the mouse SSCs revealed that knocking down Bcorl1 or Mtap7d3 could inhibit SSCs self-renewal and knocking down Armcx4 could repress SSCs differentiation in vitro. Using CRISPR-Cas9 system, Bcorl1 and Mtap7d3 knockout mice were generated. Excitingly, Bcorl1 knockout mice were infertile with impaired spermatogenesis. Moreover, Bcorl1 knockout mice exhibited impaired sperm motility and sperm cells displayed abnormal mitochondrial structure. CONCLUSION Our data indicate that the X-linked genes are associated with male infertility and involved in regulating SSCs, which provides a new insight into the role of X-linked genes in spermatogenesis.
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Affiliation(s)
- Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yan Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yufeng Qin
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Qiaoqiao Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ran Zhou
- Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Yiqiang Cui
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yunfei Zhu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xin Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jintao Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiang Wei
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Min Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Bo Hang
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jian-Hua Mao
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Antoine M Snijders
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mingxi Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zuomin Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xin Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
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Hang B, Mao JH, Snijders AM. Genetic Susceptibility to Thirdhand-Smoke-Induced Lung Cancer Development. Nicotine Tob Res 2020; 21:1294-1296. [PMID: 29917126 DOI: 10.1093/ntr/nty127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/15/2018] [Indexed: 11/14/2022]
Abstract
Recently, potential health concerns have been raised about thirdhand smoke (THS), a much less well-understood type of smoke exposure defined as residual tobacco smoke sorbed onto indoor surfaces after active smoking has ceased. THS exposure is derived from the involuntary inhalation, ingestion, or dermal uptake of indoor pollutants. The timescale for exposure to THS pollution is generally much longer than secondhand smoke, and could stretch to days, months, or years (long-term, low-level exposure). Recent studies showed that exposure to THS at early age in mice can affect body weight, immunity, and lung cancer development. However, adverse health effects of THS in human populations remain poorly understood and many questions remain unanswered. One major question is how genetic factors influence susceptibility to THS-induced health effects, especially tumor development and whether there is an age-specific window of susceptibility for these effects. By addressing these questions, we will provide a better understanding of the effects of THS on human health and disease. This information would address critical knowledge gaps that are required for the formulation of policies related to indoor air quality. IMPLICATIONS THS, the residual tobacco smoke remaining in the environment after tobacco has been smoked, represents an underestimated public health hazard. Evidence supports its widespread presence in indoor environments. Vulnerable populations are believed to include infants and children living in a smoking household exposed to THS and/or secondhand smoke, and exposure has been identified as a risk factor for lung cancer later in life. These and future studies will provide novel and important evidence of how early-life exposure to THS affects cancer development and other diseases, which should be useful for framing and enforcing new policies against passive smoking in the world.
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Affiliation(s)
- Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA.,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA.,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA
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Mao JH, Kim YM, Zhou YX, Hu D, Zhong C, Chang H, Brislawn CJ, Fansler S, Langley S, Wang Y, Peisl BYL, Celniker SE, Threadgill DW, Wilmes P, Orr G, Metz TO, Jansson JK, Snijders AM. Genetic and metabolic links between the murine microbiome and memory. Microbiome 2020; 8:53. [PMID: 32299497 PMCID: PMC7164142 DOI: 10.1186/s40168-020-00817-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/02/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Recent evidence has linked the gut microbiome to host behavior via the gut-brain axis [1-3]; however, the underlying mechanisms remain unexplored. Here, we determined the links between host genetics, the gut microbiome and memory using the genetically defined Collaborative Cross (CC) mouse cohort, complemented with microbiome and metabolomic analyses in conventional and germ-free (GF) mice. RESULTS A genome-wide association analysis (GWAS) identified 715 of 76,080 single-nucleotide polymorphisms (SNPs) that were significantly associated with short-term memory using the passive avoidance model. The identified SNPs were enriched in genes known to be involved in learning and memory functions. By 16S rRNA gene sequencing of the gut microbial community in the same CC cohort, we identified specific microorganisms that were significantly correlated with longer latencies in our retention test, including a positive correlation with Lactobacillus. Inoculation of GF mice with individual species of Lactobacillus (L. reuteri F275, L. plantarum BDGP2 or L. brevis BDGP6) resulted in significantly improved memory compared to uninoculated or E. coli DH10B inoculated controls. Untargeted metabolomics analysis revealed significantly higher levels of several metabolites, including lactate, in the stools of Lactobacillus-colonized mice, when compared to GF control mice. Moreover, we demonstrate that dietary lactate treatment alone boosted memory in conventional mice. Mechanistically, we show that both inoculation with Lactobacillus or lactate treatment significantly increased the levels of the neurotransmitter, gamma-aminobutyric acid (GABA), in the hippocampus of the mice. CONCLUSION Together, this study provides new evidence for a link between Lactobacillus and memory and our results open possible new avenues for treating memory impairment disorders using specific gut microbial inoculants and/or metabolites. Video Abstract.
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Affiliation(s)
- Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Yan-Xia Zhou
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Marine College, Shandong University, Weihai, 264209 China
| | - Dehong Hu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Chenhan Zhong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Colin J. Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Sarah Fansler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Sasha Langley
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Yunshan Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033 Shandong China
| | - B. Y. Loulou Peisl
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Susan E. Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - David W. Threadgill
- Department of Veterinary Pathobiology, A&M University, College Station, Texas, USA
- Department of Molecular and Cellular Medicine Texas, A&M University, College Station, Texas, USA
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Galya Orr
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Thomas O. Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Janet K. Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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Yin C, Lin X, Wang Y, Liu X, Xiao Y, Liu J, Snijders AM, Wei G, Mao JH, Zhang P. FAM83D promotes epithelial-mesenchymal transition, invasion and cisplatin resistance through regulating the AKT/mTOR pathway in non-small-cell lung cancer. Cell Oncol (Dordr) 2020; 43:395-407. [PMID: 32006253 DOI: 10.1007/s13402-020-00494-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2020] [Indexed: 12/14/2022] Open
Abstract
PURPOSE FAM83D has been proposed to act as an oncoprotein in several types of human cancer. Its role and mode of action in human non-small cell lung cancer (NSCLC) metastasis and its impact on chemotherapy are as yet, however, poorly understood. METHODS FAM83D expression was measured in NSCLC cells and normal lung epithelial cells, as well as in primary NSCLC tissues and corresponding adjacent non-cancerous tissues, using qRT-PCR, Western blotting and immunohistochemistry. FAM83D was stably overexpressed in BEAS2B cells or silenced in A549 and H1299 cells using retroviral or lentiviral vectors. The growth capacity of NSCLC cells was evaluated using MTT and colony formation assays. Epithelial-mesenchymal transition (EMT) was assessed using Western blotting and immunofluorescence. NSCLC cell invasive capacities were assessed using scratch wound healing and Boyden chamber assays. NSCLC cell viability in response to cisplatin treatment was assessed using MTT assays in vitro and a xenograft model in vivo. RESULTS We found that FAM83D expression levels were significantly elevated in NSCLC cells and tissues, and positively correlated with tumor progression and a poor prognosis. Exogenous FAM83D overexpression promoted, while FAM83D silencing inhibited NSCLC cell proliferation, EMT and invasion. FAM83D silencing also reduced cisplatin resistance. Concordantly, we found that NSCLC patients with a low FAM83D expression benefited most from chemotherapy. Mechanistically, we found that FAM83D activated the protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway. Pharmacological treatment with either AKT or mTOR inhibitors reverted FAM83D-induced tumorigenic phenotypes. CONCLUSIONS Our results suggest a role of FAM83D in NSCLC development. In addition, our results indicate that NSCLC patients exhibiting FAM83D overexpression are likely to benefit from AKT and/or mTOR inhibitor treatment.
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Affiliation(s)
- Chunli Yin
- Key Laboratory Experimental, Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China.,Shandong Medical College, Linyi, China
| | - Xiaoyan Lin
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250021, Shandong, China
| | - Yige Wang
- Key Laboratory Experimental, Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
| | - Xianqiang Liu
- Department of Breast and thyroid Surgery, Jinan Central Hospital Affiliated to Shandong University, Jinan, 250013, Shandong, China
| | - Yi Xiao
- Key Laboratory Experimental, Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
| | - Jingchao Liu
- Department of Urology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guangwei Wei
- Key Laboratory Experimental, Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Pengju Zhang
- Key Laboratory Experimental, Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China.
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38
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Zargar A, Chang S, Kothari A, Snijders AM, Mao JH, Wang J, Hernández AC, Keasling JD, Bivona TG. Overcoming the challenges of cancer drug resistance through bacterial-mediated therapy. Chronic Dis Transl Med 2019; 5:258-266. [PMID: 32055785 PMCID: PMC7004931 DOI: 10.1016/j.cdtm.2019.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Indexed: 12/23/2022] Open
Abstract
Despite tremendous efforts to fight cancer, it remains a major public health problem and a leading cause of death worldwide. With increased knowledge of cancer pathways and improved technological platforms, precision therapeutics that specifically target aberrant cancer pathways have improved patient outcomes. Nevertheless, a primary cause of unsuccessful cancer therapy remains cancer drug resistance. In this review, we summarize the broad classes of resistance to cancer therapy, particularly pharmacokinetics, the tumor microenvironment, and drug resistance mechanisms. Furthermore, we describe how bacterial-mediated cancer therapy, a bygone mode of treatment, has been revitalized by synthetic biology and is uniquely suited to address the primary resistance mechanisms that confound traditional therapies. Through genetic engineering, we discuss how bacteria can be potent anticancer agents given their tumor targeting potential, anti-tumor activity, safety, and coordinated delivery of anti-cancer drugs.
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Affiliation(s)
- Amin Zargar
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
- QB3 Institute, University of California-Berkeley, 174 Stanley Hall, Berkeley, CA 94720, USA
| | - Samantha Chang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
| | - Ankita Kothari
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Antoine M. Snijders
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jessica Wang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
| | - Amanda C. Hernández
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
- QB3 Institute, University of California-Berkeley, 174 Stanley Hall, Berkeley, CA 94720, USA
| | - Trever G. Bivona
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94143, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA
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Wang P, Wang Y, Langley SA, Zhou YX, Jen KY, Sun Q, Brislawn C, Rojas CM, Wahl KL, Wang T, Fan X, Jansson JK, Celniker SE, Zou X, Threadgill DW, Snijders AM, Mao JH. Diverse tumour susceptibility in Collaborative Cross mice: identification of a new mouse model for human gastric tumourigenesis. Gut 2019; 68:1942-1952. [PMID: 30842212 PMCID: PMC6839736 DOI: 10.1136/gutjnl-2018-316691] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The Collaborative Cross (CC) is a mouse population model with diverse and reproducible genetic backgrounds used to identify novel disease models and genes that contribute to human disease. Since spontaneous tumour susceptibility in CC mice remains unexplored, we assessed tumour incidence and spectrum. DESIGN We monitored 293 mice from 18 CC strains for tumour development. Genetic association analysis and RNA sequencing were used to identify susceptibility loci and candidate genes. We analysed genomes of patients with gastric cancer to evaluate the relevance of genes identified in the CC mouse model and measured the expression levels of ISG15 by immunohistochemical staining using a gastric adenocarcinoma tissue microarray. Association of gene expression with overall survival (OS) was assessed by Kaplan-Meier analysis. RESULTS CC mice displayed a wide range in the incidence and types of spontaneous tumours. More than 40% of CC036 mice developed gastric tumours within 1 year. Genetic association analysis identified Nfκb1 as a candidate susceptibility gene, while RNA sequencing analysis of non-tumour gastric tissues from CC036 mice showed significantly higher expression of inflammatory response genes. In human gastric cancers, the majority of human orthologues of the 166 mouse genes were preferentially altered by amplification or deletion and were significantly associated with OS. Higher expression of the CC036 inflammatory response gene signature is associated with poor OS. Finally, ISG15 protein is elevated in gastric adenocarcinomas and correlated with shortened patient OS. CONCLUSIONS CC strains exhibit tremendous variation in tumour susceptibility, and we present CC036 as a spontaneous laboratory mouse model for studying human gastric tumourigenesis.
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Affiliation(s)
- Pin Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yunshan Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA,Clinical Laboratory, Second Hospital of Shandong University, Jinan, China
| | - Sasha A Langley
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yan-Xia Zhou
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA,College of Marine Science, Shandong University, Weihai, China
| | - Kuang-Yu Jen
- Department of Pathology, University of California Davis Medical Center, Sacramento, California, USA
| | - Qi Sun
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Colin Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carolina M Rojas
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA,Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas, USA
| | - Kimberly L Wahl
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA,Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas, USA
| | - Ting Wang
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiangshan Fan
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Xiaoping Zou
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - David W Threadgill
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA,Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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40
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Kim YM, Snijders AM, Brislawn CJ, Stratton KG, Zink EM, Fansler SJ, Metz TO, Mao JH, Jansson JK. Light-Stress Influences the Composition of the Murine Gut Microbiome, Memory Function, and Plasma Metabolome. Front Mol Biosci 2019; 6:108. [PMID: 31681796 PMCID: PMC6813214 DOI: 10.3389/fmolb.2019.00108] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome plays an important role in the mammalian host and when in proper balance helps protect health and prevent disease. Host environmental stress and its influence on the gut microbiome, health, and disease is an emerging area of research. Exposures to unnatural light cycles are becoming increasingly common due to travel and shift work. However, much remains unknown about how these changes influence the microbiome and host health. This information is needed to understand and predict the relationship between the microbiome and host response to altered sleep cycles. In the present study, we exposed three cohorts of mice to different light cycle regimens for 12 consecutive weeks; including continuous light, continuous dark, and a standard light dark regimen consisting of 12 h light followed by 12 h of dark. After exposure, motor and memory behavior, and the composition of the fecal microbiome and plasma metabolome were measured. Memory potential was significantly reduced in mice exposed to continuous light, whereas rotarod performance was minimally affected. The overall composition of the microbiome was relatively constant over time. However, Bacteroidales Rikenellaceae was relatively more abundant in mice exposed to continuous dark, while Bacteroidales S24-7 was relatively more abundant in mice exposed to continuous light. The plasma metabolome after the continuous dark exposure differed from the other exposure conditions. Several plasma metabolites, including glycolic acid, tryptophan, pyruvate, and several unidentified metabolites, were correlated to continuous dark and light exposure conditions. Networking analyses showed that serotonin was positively correlated with three microbial families (Rikenellaceae, Ruminococcaceae, and Turicibacteraceae), while tryptophan was negatively correlated with abundance of Bacteroidales S24-7 based on light exposure. This study provides the foundation for future studies into the mechanisms underlying the role of the gut microbiome on the murine host during light-dark stress.
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Affiliation(s)
- Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Colin J Brislawn
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kelly G Stratton
- Computing and Analytics Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erika M Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
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41
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Chen K, Luan X, Liu Q, Wang J, Chang X, Snijders AM, Mao JH, Secombe J, Dan Z, Chen JH, Wang Z, Dong X, Qiu C, Chang X, Zhang D, Celniker SE, Liu X. Drosophila Histone Demethylase KDM5 Regulates Social Behavior through Immune Control and Gut Microbiota Maintenance. Cell Host Microbe 2019; 25:537-552.e8. [PMID: 30902578 DOI: 10.1016/j.chom.2019.02.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 12/05/2018] [Accepted: 02/15/2019] [Indexed: 12/20/2022]
Abstract
Loss-of-function mutations in the histone demethylases KDM5A, KDM5B, or KDM5C are found in intellectual disability (ID) and autism spectrum disorders (ASD) patients. Here, we use the model organism Drosophila melanogaster to delineate how KDM5 contributes to ID and ASD. We show that reducing KDM5 causes intestinal barrier dysfunction and changes in social behavior that correlates with compositional changes in the gut microbiota. Therapeutic alteration of the dysbiotic microbiota through antibiotic administration or feeding with a probiotic Lactobacillus strain partially rescues the behavioral, lifespan, and cellular phenotypes observed in kdm5-deficient flies. Mechanistically, KDM5 was found to transcriptionally regulate component genes of the immune deficiency (IMD) signaling pathway and subsequent maintenance of host-commensal bacteria homeostasis in a demethylase-dependent manner. Together, our study uses a genetic approach to dissect the role of KDM5 in the gut-microbiome-brain axis and suggests that modifying the gut microbiome may provide therapeutic benefits for ID and ASD patients.
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Affiliation(s)
- Kun Chen
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Holistic Integrative Enterology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Xiaoting Luan
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Qisha Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Jianwei Wang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Xinxia Chang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Julie Secombe
- Departments of Genetics and Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Zhou Dan
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Jian-Huan Chen
- Genomic and Precision Medicine Laboratory, Department of Public Health, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China
| | - Zibin Wang
- Center for Analysis and Testing, Nanjing Medical University, Nanjing 211166, China
| | - Xiao Dong
- Departments of Genetics and Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Chen Qiu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Xiaoai Chang
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing 211166, China
| | - Dong Zhang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Xingyin Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Holistic Integrative Enterology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China.
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42
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Zhou YX, Fuentes-Creollo G, Ponce F, Langley SA, Jen KY, Celniker SE, Mao JH, Snijders AM. No difference in 4-nitroquinoline induced tumorigenesis between germ-free and colonized mice. Mol Carcinog 2019; 58:627-632. [PMID: 30632250 DOI: 10.1002/mc.22972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/14/2018] [Accepted: 01/03/2019] [Indexed: 12/24/2022]
Abstract
Variations in oral bacterial communities have been linked to oral cancer suggesting that the oral microbiome is an etiological factor that can influence oral cancer development. The 4-nitroquinoline 1-oxide (4-NQO)-induced murine oral and esophageal cancer model is frequently used to assess the effects of preventive and/or therapeutic agents. We used this model to assess the impact of the microbiome on tumorigenesis using axenic (germ-free) and conventionally housed mice. Increased toxicity was observed in germ-free mice, however, no difference in tumor incidence, multiplicity, and size was observed. Transcriptional profiling of liver tissue from germ-free and conventionally housed mice identified 254 differentially expressed genes including ten cytochrome p450 enzymes, the largest family of phase-1 drug metabolizing enzymes in the liver. Gene ontology revealed that differentially expressed genes were enriched for liver steatosis, inflammation, and oxidative stress in livers of germ-free mice. Our observations emphasize the importance of the microbiome in mediating chemical toxicity at least in part by altering host gene expression. Studies on the role of the microbiome in chemical-induced cancer using germ-free animal models should consider the potential difference in dose due to the microbiome-mediated changes in host metabolizing capacity, which might influence the ability to draw conclusions especially for tumor induction models that are dose dependent.
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Affiliation(s)
- Yan-Xia Zhou
- College of Marine Science, Shandong University at Weihai, Weihai, China.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Gabriela Fuentes-Creollo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Frank Ponce
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Sasha A Langley
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Kuang-Yu Jen
- Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, California
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, California.,School of BioEngineering and BioInformatics, Nanjing Medical University, Nanjing, China
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, California.,School of BioEngineering and BioInformatics, Nanjing Medical University, Nanjing, China
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43
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Xiao Y, Yin C, Wang Y, Lv H, Wang W, Huang Y, Perez-Losada J, Snijders AM, Mao JH, Zhang P. FBXW7 deletion contributes to lung tumor development and confers resistance to gefitinib therapy. Mol Oncol 2018; 12:883-895. [PMID: 29633504 PMCID: PMC5983212 DOI: 10.1002/1878-0261.12200] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 11/26/2022] Open
Abstract
Gefitinib, an epidermal growth factor receptor–tyrosine kinase inhibitor (EGFR‐TKI), is an effective treatment for non‐small‐cell lung cancer (NSCLC) with EGFR activating mutations, but inevitably, the clinical efficacy is impeded by the emergence of acquired resistance. The tumor suppressor gene FBXW7 modulates chemosensitivity in various human cancers. However, its role in EGFR‐TKI therapy in NSCLC has not been well studied. Here, we demonstrate that the mice with deficient Fbxw7 have greater susceptibility to urethane‐induced lung tumor development. Through analysis of The Cancer Genome Atlas data, we show that deletion of FBXW7 occurs in 30.9% of lung adenocarcinomas and 63.5% of lung squamous cell carcinomas, which significantly leads to decrease in FBXW7 mRNA expression. The reduction in FBXW7 mRNA level is associated with poor overall survival in lung cancer patients. FBXW7 knockdown dramatically promotes epithelial–mesenchymal transition, migration, and invasion in NSCLC cells. Moreover, with silenced FBXW7, EGFR‐TKI‐sensitive cells become resistant to gefitinib, which is reversed by the mammalian target of rapamycin inhibitor, rapamycin. Furthermore, xenograft mouse model studies show that FBXW7 knockdown enhances tumorigenesis and resistance to gefitinib. Combination of gefitinib with rapamycin treatment suppresses tumor formation of gefitinib‐resistant (GR) FBXW7‐knockdown cells. In conclusion, our findings suggest that loss of FBXW7 promotes NSCLC progression as well as gefitinib resistance and combination of gefitinib and rapamycin may provide an effective therapy for GR NSCLC.
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Affiliation(s)
- Yi Xiao
- Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, Jinan, China
| | - Chunli Yin
- Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, Jinan, China
| | - Yuli Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Hanlin Lv
- Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, Jinan, China
| | - Wenqing Wang
- Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, Jinan, China
| | - Yurong Huang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, CA, USA
| | - Jesus Perez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Instituto Mixto Universidad de Salamanca/CSIC, IBSAL, Salamanca, Spain
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, CA, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, CA, USA
| | - Pengju Zhang
- Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, Jinan, China
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44
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Chang H, Han J, Zhong C, Snijders AM, Mao JH. Unsupervised Transfer Learning via Multi-Scale Convolutional Sparse Coding for Biomedical Applications. IEEE Trans Pattern Anal Mach Intell 2018; 40:1182-1194. [PMID: 28129148 PMCID: PMC5522776 DOI: 10.1109/tpami.2017.2656884] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The capabilities of (I) learning transferable knowledge across domains; and (II) fine-tuning the pre-learned base knowledge towards tasks with considerably smaller data scale are extremely important. Many of the existing transfer learning techniques are supervised approaches, among which deep learning has the demonstrated power of learning domain transferrable knowledge with large scale network trained on massive amounts of labeled data. However, in many biomedical tasks, both the data and the corresponding label can be very limited, where the unsupervised transfer learning capability is urgently needed. In this paper, we proposed a novel multi-scale convolutional sparse coding (MSCSC) method, that (I) automatically learns filter banks at different scales in a joint fashion with enforced scale-specificity of learned patterns; and (II) provides an unsupervised solution for learning transferable base knowledge and fine-tuning it towards target tasks. Extensive experimental evaluation of MSCSC demonstrates the effectiveness of the proposed MSCSC in both regular and transfer learning tasks in various biomedical domains.
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Affiliation(s)
- Hang Chang
- Correspondence should be addressed to Hang Chang ()
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45
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Abstract
Cellular senescence plays an important role in organismal aging and age-related diseases. However, it is challenging to isolate low numbers of senescent cells from small volumes of biofluids for downstream analysis. Furthermore, there is no technology that could selectively remove senescent cells in a high-throughput manner. In this work, we developed a novel microfluidic chip platform, termed senescence chip, for ultrahigh-throughput isolation and removal of senescent cells. The core component of our senescence chip is a slanted and tunable 3D micropillar array with a variety of shutters in the vertical direction for rapid cell sieving, taking advantage of the characteristic cell size increase during cellular senescence. The 3D configuration achieves high throughput, high recovery rate, and device robustness with minimum clogging. We demonstrated proof-of-principle applications in isolation and enumeration of senescent mesenchymal stem cells (MSCs) from undiluted human whole blood, and senescent cells from mouse bone marrow after total body irradiation, with the single-cell resolution. After scale-up to a multilayer and multichannel structure, our senescence chip achieved ultrahigh-throughput removal of senescent cells from human whole blood with an efficiency of over 70% at a flow rate of 300 ml/hr. Sensitivity and specificity of our senescence chips could be augmented with implementation of multiscale size separation, and identification of background white blood cells using their cell surface markers such as CD45. With the advantages of high throughput, robustness, and simplicity, our senescence chips may find wide applications and contribute to diagnosis and therapeutic targeting of cellular senescence.
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Affiliation(s)
| | - Pan Mao
- Newomics Inc.EmeryvilleCAUSA
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46
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Hang B, Wang Y, Huang Y, Wang P, Langley SA, Bi L, Sarker AH, Schick SF, Havel C, Jacob P, Benowitz N, Destaillats H, Tang X, Xia Y, Jen KY, Gundel LA, Mao JH, Snijders AM. Short-term early exposure to thirdhand cigarette smoke increases lung cancer incidence in mice. Clin Sci (Lond) 2018; 132:475-488. [PMID: 29440622 PMCID: PMC6365648 DOI: 10.1042/cs20171521] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/02/2018] [Accepted: 02/09/2018] [Indexed: 02/01/2023]
Abstract
Exposure to thirdhand smoke (THS) is a recently described health concern that arises in many indoor environments. However, the carcinogenic potential of THS, a critical consideration in risk assessment, remains untested. Here we investigated the effects of short-term early exposure to THS on lung carcinogenesis in A/J mice. Forty weeks after THS exposure from 4 to 7 weeks of age, the mice had increased incidence of lung adenocarcinoma, tumor size and, multiplicity, compared with controls. In vitro studies using cultured human lung cancer cells showed that THS exposure induced DNA double-strand breaks and increased cell proliferation and colony formation. RNA sequencing analysis revealed that THS exposure induced endoplasmic reticulum stress and activated p53 signaling. Activation of the p53 pathway was confirmed by an increase in its targets p21 and BAX. These data indicate that early exposure to THS is associated with increased lung cancer risk.
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Affiliation(s)
- Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
| | - Yunshan Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
- International Biotechnology R&D Center, Shandong University School of Ocean, Weihai, Shandong 264209, China
| | - Yurong Huang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
| | - Pin Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu 210008, China
| | - Sasha A Langley
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
| | - Lei Bi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
| | - Altaf H Sarker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
| | - Suzaynn F Schick
- Department of Medicine, Division of Occupational and Environmental Medicine, University of California, San Francisco, Box 0843, San Francisco, CA 94143, U.S.A
| | - Christopher Havel
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine University of California, San Francisco, Box 0843, San Francisco, CA 94143, U.S.A
| | - Peyton Jacob
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine University of California, San Francisco, Box 0843, San Francisco, CA 94143, U.S.A
| | - Neal Benowitz
- Division of Clinical Pharmacology and Experimental Therapeutics, Medical Services, Department of Medicine, and Bioengineering & Therapeutic Sciences, University of California, San Francisco, Box 0843, San Francisco, CA 94143, U.S.A
| | - Hugo Destaillats
- Indoor Environment Group, Energy Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
| | - Xiaochen Tang
- Indoor Environment Group, Energy Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 211166, China
| | - Kuang-Yu Jen
- Department of Pathology and Laboratory Medicine, University of California Davis Medical Center, Sacramento, CA 95817, U.S.A
| | - Lara A Gundel
- Indoor Environment Group, Energy Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A.
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A.
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
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47
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Chen EG, Wang P, Lou H, Wang Y, Yan H, Bi L, Liu L, Li B, Snijders AM, Mao JH, Hang B. A robust gene expression-based prognostic risk score predicts overall survival of lung adenocarcinoma patients. Oncotarget 2017; 9:6862-6871. [PMID: 29467935 PMCID: PMC5805521 DOI: 10.18632/oncotarget.23490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/05/2017] [Indexed: 12/24/2022] Open
Abstract
Identification of reliable predictive biomarkers and new therapeutic targets is a critical step for significant improvement in patient outcomes. Here, we developed a multi-step bioinformatics analytic strategy to mine large omics and clinical data to build a prognostic scoring system for predicting the overall survival (OS) of lung adenocarcinoma (LuADC) patients. In latter we first identified 1327 significantly and robustly deregulated genes, 600 of which were significantly associated with the OS of LuADC patients. Gene co-expression network analysis revealed the biological functions of these 600 genes in normal lung and LuADCs, which were found to be enriched for cell cycle-related processes, blood vessel development, cell-matrix adhesion and metabolic processes. Finally, we implemented a multiple resampling method combined with Cox regression analysis to identify a 27-gene signature associated with OS, and then created a prognostic scoring system based on this signature. This scoring system robustly predicted OS of LuADC patients in 100 sampling test sets and was further validated in four independent LuADC cohorts. In addition, in comparison to other existing prognostic gene signatures published in the literature, our signature was significantly superior in predicting OS of LuADC patients. In summary, our multi-omics and clinical data integration study created a 27-gene prognostic risk score that can predict OS of LuADC patients independent of age, gender and clinical stage. This score could guide therapeutic selection and allow stratification in clinical trials.
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Affiliation(s)
- En-Guo Chen
- Department of Pulmonary Medicine, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Pin Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Gastroenterology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Haizhou Lou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yunshan Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hong Yan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Lei Bi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Liang Liu
- Department of Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Bin Li
- Nanjing KDRB Biotech Inc., Ltd, Jiangning District, Nanjing, Jiangsu, China
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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48
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Mao JH, Diest PJV, Perez-Losada J, Snijders AM. Revisiting the impact of age and molecular subtype on overall survival after radiotherapy in breast cancer patients. Sci Rep 2017; 7:12587. [PMID: 28974723 PMCID: PMC5626767 DOI: 10.1038/s41598-017-12949-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 05/31/2017] [Accepted: 09/12/2017] [Indexed: 01/07/2023] Open
Abstract
Adjuvant radiotherapy (RT) in breast cancer (BC) is often used to eradicate remaining tumor cells following surgery with the goal of maximizing local control and increasing overall survival. The current study investigated the impact of age and BC molecular subtype on overall survival after RT using a meta-analysis of the METABRIC and TCGA BC patient cohorts. We found that RT significantly prolonged survival across the whole BC patient population. The survival benefit of RT was predominantly observed in stage II BC patients treated with breast conserving surgery. Patients were then stratified by age and molecular subtype to investigate survival rate associated with RT. An increase in survival for the luminal-A and basal BC molecular subtypes was observed after RT. Stratifying patients based on age revealed that increased survival was restricted to younger patients (≤60 years of age at diagnosis). There was a significant survival benefit of radiotherapy for younger patients with tumors of the luminal A and basal molecular subtypes. Patients with other breast tumor subtypes or older breast cancer patients did not seem to benefit effects of RT. Therefore, alternate local treatment strategies should be considered for older, luminal B, and HER2 driven BC patients.
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Affiliation(s)
- Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jesus Perez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca/CSIC, Salamanca, 37007, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, 37007, Spain
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
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49
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Mao XY, Lee MJ, Zhu J, Zhu C, Law SM, Snijders AM. Genome-wide screen identifies a novel prognostic signature for breast cancer survival. Oncotarget 2017; 8:14003-14016. [PMID: 28122328 PMCID: PMC5355157 DOI: 10.18632/oncotarget.14776] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/31/2016] [Indexed: 12/17/2022] Open
Abstract
Large genomic datasets in combination with clinical data can be used as an unbiased tool to identify genes important in patient survival and discover potential therapeutic targets. We used a genome-wide screen to identify 587 genes significantly and robustly deregulated across four independent breast cancer (BC) datasets compared to normal breast tissue. Gene expression of 381 genes was significantly associated with relapse-free survival (RFS) in BC patients. We used a gene co-expression network approach to visualize the genetic architecture in normal breast and BCs. In normal breast tissue, co-expression cliques were identified enriched for cell cycle, gene transcription, cell adhesion, cytoskeletal organization and metabolism. In contrast, in BC, only two major co-expression cliques were identified enriched for cell cycle-related processes or blood vessel development, cell adhesion and mammary gland development processes. Interestingly, gene expression levels of 7 genes were found to be negatively correlated with many cell cycle related genes, highlighting these genes as potential tumor suppressors and novel therapeutic targets. A forward-conditional Cox regression analysis was used to identify a 12-gene signature associated with RFS. A prognostic scoring system was created based on the 12-gene signature. This scoring system robustly predicted BC patient RFS in 60 sampling test sets and was further validated in TCGA and METABRIC BC data. Our integrated study identified a 12-gene prognostic signature that could guide adjuvant therapy for BC patients and includes novel potential molecular targets for therapy.
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Affiliation(s)
- Xuan Y Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew J Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jeffrey Zhu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Carissa Zhu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sindy M Law
- Department of Psychiatry, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Hang B, Wang P, Zhao Y, Sarker A, Chenna A, Xia Y, Snijders AM, Mao JH. Adverse Health Effects of Thirdhand Smoke: From Cell to Animal Models. Int J Mol Sci 2017; 18:ijms18050932. [PMID: 28452951 PMCID: PMC5454845 DOI: 10.3390/ijms18050932] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 11/12/2022] Open
Abstract
The newly identified smoke hazard, thirdhand smoke (THS), has gained public attention in recent years but its health impact and biological effects are largely unknown. THS may be defined by “the four Rs”: tobacco chemicals that remain, react, re-emit, and/or are resuspended long after active smoking has ceased. This review summarizes recent research progress in the effects of THS on genotoxicity, metabolism and early life development using cellular and animal models. We first reported that THS generated in laboratory systems caused significant DNA damage in human cell lines. Our finding that THS significantly induces oxidative base lesions has been confirmed in skin wounds of mice models exposed to THS. THS also induced metabolomic changes in human reproductive cell lines. Furthermore, we demonstrated that early exposure to THS not only negatively impacts body weight in both male and female mice, but also induces persistent changes to immunological parameters in peripheral blood in these mice. These results indicate that THS is genotoxic at realistic experimental doses and that there may be a window of susceptibility for some forms of cellular damage induced by THS.
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Affiliation(s)
- Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Pin Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
- Department of Gastroenterology, Drum Tower Clinical Medical School of Nanjing Medical University, Nanjing 210008, China.
| | - Yue Zhao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Altaf Sarker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Ahmed Chenna
- LabCorp Specialty Testing Group, Monogram Biosciences Inc., South San Francisco, CA 94080, USA.
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 211166, China.
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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