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Zakharia Y, Singer EA, Acharyya S, Garje R, Joshi M, Peace D, Baladandayuthapani V, Majumdar A, Li X, Lalancette C, Kryczek I, Zou W, Alva A. Durvalumab and guadecitabine in advanced clear cell renal cell carcinoma: results from the phase Ib/II study BTCRC-GU16-043. Nat Commun 2024; 15:972. [PMID: 38302476 PMCID: PMC10834488 DOI: 10.1038/s41467-024-45216-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/18/2024] [Indexed: 02/03/2024] Open
Abstract
Epigenetic modulation is well established in hematologic malignancies but to a lesser degree in solid tumors. Here we report the results of a phase Ib/II study of guadecitabine and durvalumab in advanced clear cell renal cell carcinoma (ccRCC; NCT03308396). Patients received guadecitabine (starting at 60 mg/m2 subcutaneously on days 1-5 with de-escalation to 45 mg/m2 in case of dose limiting toxicity) with durvalumab (1500 mg intravenously on day 8). The study enrolled 57 patients, 6 in phase Ib with safety being the primary objective and 51in phase II, comprising 2 cohorts: 36 patients in Cohort 1 were treatment naive to checkpoint inhibitors (CPI) with 0-1 prior therapies and 15 patients in Cohort 2 were treated with up to two prior systemic therapies including one CPI. The combination of guadecitabine 45 mg/m2 with durvalumab 1500 mg was deemed safe. The primary objective of overall response rate (ORR) in cohort 1 was 22%. Sixteen patients (44%) experienced stable disease (SD). Secondary objectives included overall survival (OS), duration of response, progression-free survival (PFS), clinical benefit rate, and safety as well as ORR for Cohort 2. Median PFS for cohort 1 and cohort 2 were 14.26 and 3.91 months respectively. Median OS was not reached. In cohort 2, one patient achieved a partial response and 60% achieved SD. Asymptomatic neutropenia was the most common adverse event. Even though the trial did not meet the primary objective in cohort 1, the tolerability and PFS signal in CPI naive patients are worth further investigation.
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Affiliation(s)
- Yousef Zakharia
- University of Iowa Holden Comprehensive Cancer Center, Iowa City, IA, USA.
| | - Eric A Singer
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | | | - Rohan Garje
- University of Iowa Holden Comprehensive Cancer Center, Iowa City, IA, USA
| | | | - David Peace
- University of Illinois at Chicago, Chicago, IL, USA
| | | | | | - Xiong Li
- University of Michigan, Ann Arbor, MI, USA
| | | | | | | | - Ajjai Alva
- University of Michigan, Ann Arbor, MI, USA
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2
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Morgan RK, Wang K, Svoboda LK, Rygiel CA, Lalancette C, Cavalcante R, Bartolomei MS, Prasasya R, Neier K, Perera BP, Jones TR, Colacino JA, Sartor MA, Dolinoy DC. Effects of Developmental Lead and Phthalate Exposures on DNA Methylation in Adult Mouse Blood, Brain, and Liver Identifies Tissue- and Sex-Specific Changes with Implications for Genomic Imprinting. bioRxiv 2023:2023.09.29.560131. [PMID: 37873115 PMCID: PMC10592650 DOI: 10.1101/2023.09.29.560131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background Maternal exposure to environmental chemicals can cause adverse health effects in offspring. Mounting evidence supports that these effects are influenced, at least in part, by epigenetic modifications. Objective We examined tissue- and sex-specific changes in DNA methylation (DNAm) associated with human-relevant lead (Pb) and di(2-ethylhexyl) phthalate (DEHP) exposure during perinatal development in cerebral cortex, blood, and liver. Methods Female mice were exposed to human relevant doses of either Pb (32ppm) via drinking water or DEHP (5 mg/kg-day) via chow for two weeks prior to mating through offspring weaning. Whole genome bisulfite sequencing (WGBS) was utilized to examine DNAm changes in offspring cortex, blood, and liver at 5 months of age. Metilene and methylSig were used to identify differentially methylated regions (DMRs). Annotatr and Chipenrich were used for genomic annotations and geneset enrichment tests of DMRs, respectively. Results The cortex contained the majority of DMRs associated with Pb (69%) and DEHP (58%) exposure. The cortex also contained the greatest degree of overlap in DMR signatures between sexes (n = 17 and 14 DMRs with Pb and DEHP exposure, respectively) and exposure types (n = 79 and 47 DMRs in males and females, respectively). In all tissues, detected DMRs were preferentially found at genomic regions associated with gene expression regulation (e.g., CpG islands and shores, 5' UTRs, promoters, and exons). An analysis of GO terms associated with DMR-containing genes identified imprinted genes to be impacted by both Pb and DEHP exposure. Of these, Gnas and Grb10 contained DMRs across tissues, sexes, and exposures. DMRs were enriched in the imprinting control regions (ICRs) of Gnas and Grb10, with 15 and 17 ICR-located DMRs across cortex, blood, and liver in each gene, respectively. The ICRs were also the location of DMRs replicated across target and surrogate tissues, suggesting epigenetic changes these regions may be potentially viable biomarkers. Conclusions We observed Pb- and DEHP-specific DNAm changes in cortex, blood, and liver, and the greatest degree of overlap in DMR signatures was seen between exposures followed by sex and tissue type. DNAm at imprinted control regions was altered by both Pb and DEHP, highlighting the susceptibility of genomic imprinting to these exposures during the perinatal window of development.
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Affiliation(s)
- Rachel K. Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christine A. Rygiel
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Claudia Lalancette
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raymond Cavalcante
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rexxi Prasasya
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kari Neier
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bambarendage P.U. Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tamara R Jones
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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Petroff RL, Cavalcante RG, Colacino JA, Goodrich JM, Jones TR, Lalancette C, Morgan RK, Neier K, Perera BPU, Rygiel CA, Svoboda LK, Wang K, Sartor MA, Dolinoy DC. Developmental exposures to common environmental contaminants, DEHP and lead, alter adult brain and blood hydroxymethylation in mice. Front Cell Dev Biol 2023; 11:1198148. [PMID: 37384255 PMCID: PMC10294071 DOI: 10.3389/fcell.2023.1198148] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/25/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction: The developing epigenome changes rapidly, potentially making it more sensitive to toxicant exposures. DNA modifications, including methylation and hydroxymethylation, are important parts of the epigenome that may be affected by environmental exposures. However, most studies do not differentiate between these two DNA modifications, possibly masking significant effects. Methods: To investigate the relationship between DNA hydroxymethylation and developmental exposure to common contaminants, a collaborative, NIEHS-sponsored consortium, TaRGET II, initiated longitudinal mouse studies of developmental exposure to human-relevant levels of the phthalate plasticizer di(2-ethylhexyl) phthalate (DEHP), and the metal lead (Pb). Exposures to 25 mg DEHP/kg of food (approximately 5 mg DEHP/kg body weight) or 32 ppm Pb-acetate in drinking water were administered to nulliparous adult female mice. Exposure began 2 weeks before breeding and continued throughout pregnancy and lactation, until offspring were 21 days old. At 5 months, perinatally exposed offspring blood and cortex tissue were collected, for a total of 25 male mice and 17 female mice (n = 5-7 per tissue and exposure). DNA was extracted and hydroxymethylation was measured using hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq). Differential peak and pathway analysis was conducted comparing across exposure groups, tissue types, and animal sex, using an FDR cutoff of 0.15. Results: DEHP-exposed females had two genomic regions with lower hydroxymethylation in blood and no differences in cortex hydroxymethylation. For DEHP-exposed males, ten regions in blood (six higher and four lower) and 246 regions (242 higher and four lower) and four pathways in cortex were identified. Pb-exposed females had no statistically significant differences in blood or cortex hydroxymethylation compared to controls. Pb-exposed males, however, had 385 regions (all higher) and six pathways altered in cortex, but no differential hydroxymethylation was identified in blood. Discussion: Overall, perinatal exposure to human-relevant levels of two common toxicants showed differences in adult DNA hydroxymethylation that was specific to sex, exposure type, and tissue, but male cortex was most susceptible to hydroxymethylation differences by exposure. Future assessments should focus on understanding if these findings indicate potential biomarkers of exposure or are related to functional long-term health effects.
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Affiliation(s)
- Rebekah L. Petroff
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Raymond G. Cavalcante
- Epigenomics Core, Biomedical Research Core Facilities, Michigan Medicine, Ann Arbor, MI, United States
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Tamara R. Jones
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Claudia Lalancette
- Epigenomics Core, Biomedical Research Core Facilities, Michigan Medicine, Ann Arbor, MI, United States
| | - Rachel K. Morgan
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Kari Neier
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Bambarendage P. U. Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Christine A. Rygiel
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, Ann Arbor, MI, United States
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, Ann Arbor, MI, United States
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
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Straight B, Qiao X, Ngo D, Hilton CE, Olungah CO, Naugle A, Lalancette C, Needham BL. Epigenetic mechanisms underlying the association between maternal climate stress and child growth: characterizing severe drought and its impact on a Kenyan community engaging in a climate change-sensitive livelihood. Epigenetics 2022; 17:2421-2433. [PMID: 36242778 PMCID: PMC9665148 DOI: 10.1080/15592294.2022.2135213] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/04/2022] [Indexed: 11/03/2022] Open
Abstract
Pastoralists in East Africa are among the world's most vulnerable communities to climate change, already living near their upper thermal limits and engaging in a climate-sensitive livelihood in a climate change global hot spot. Pregnant women and children are even more at risk. Here, we report the findings of a study characterizing Samburu pastoralist women's experiences of severe drought and outcomes in their children (N = 213, 1.8-9.6 y). First, we examined potential DNA methylation (DNAm) differences between children exposed to severe drought in utero and same-sex unexposed siblings. Next, we performed a high-dimensional mediation analysis to test whether DNAm mediated associations of exposure to severe drought with body weight and adiposity. DNAm was measured using the Infinium MethylationEPIC BeadChip array. After quality control; batch, chip, and genomic inflation corrections; covariate adjustment; and multiple testing correction, 16 CpG sites were differentially methylated between exposed and unexposed children, predominantly in metabolism and immune function pathways. We found a significant indirect effect of drought exposure on child body weight through cg03771070. Our results are the first to identify biological mediators linking severe drought to child growth in a low-income global hot spot for climate change. A better understanding of the mechanisms underlying the association between drought exposure and child growth is important to increasing climate change resilience by identifying targets for intervention.
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Affiliation(s)
- Bilinda Straight
- Gender & Women’s Studies, Western Michigan University, Kalamazoo, Michigan, USA
| | - Xi Qiao
- Statistics, Western Michigan University, Kalamazoo, Michigan, USA
| | - Duy Ngo
- Statistics, Western Michigan University, Kalamazoo, Michigan, USA
| | - Charles E. Hilton
- Anthropology, University of North Carolina Chapel Hill, Carolina, USA
| | - Charles Owuor Olungah
- Institute of Anthropology, Gender, and African Studies, University of Nairobi, Nairobi, Kenya
| | - Amy Naugle
- Psychology, Western Michigan University, Kalamazoo, Michigan, USA
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5
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Foox J, Nordlund J, Lalancette C, Gong T, Lacey M, Lent S, Langhorst BW, Ponnaluri VKC, Williams L, Padmanabhan KR, Cavalcante R, Lundmark A, Butler D, Mozsary C, Gurvitch J, Greally JM, Suzuki M, Menor M, Nasu M, Alonso A, Sheridan C, Scherer A, Bruinsma S, Golda G, Muszynska A, Łabaj PP, Campbell MA, Wos F, Raine A, Liljedahl U, Axelsson T, Wang C, Chen Z, Yang Z, Li J, Yang X, Wang H, Melnick A, Guo S, Blume A, Franke V, Ibanez de Caceres I, Rodriguez-Antolin C, Rosas R, Davis JW, Ishii J, Megherbi DB, Xiao W, Liao W, Xu J, Hong H, Ning B, Tong W, Akalin A, Wang Y, Deng Y, Mason CE. The SEQC2 epigenomics quality control (EpiQC) study. Genome Biol 2021; 22:332. [PMID: 34872606 PMCID: PMC8650396 DOI: 10.1186/s13059-021-02529-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA's Epigenomics Quality Control Group. RESULTS Each sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms. CONCLUSIONS The data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.
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Affiliation(s)
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Jessica Nordlund
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Claudia Lalancette
- BRCF Epigenomics Core, University of Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Ting Gong
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | | | - Samantha Lent
- AbbVie Genomics Research Center, 1 N. Waukegan Rd, North Chicago, IL, 60036, USA
| | | | | | | | | | - Raymond Cavalcante
- BRCF Epigenomics Core, University of Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Anders Lundmark
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Justin Gurvitch
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - John M Greally
- Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Masako Suzuki
- Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Mark Menor
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Masaki Nasu
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Alicia Alonso
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Caroline Sheridan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Andreas Scherer
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Gosia Golda
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agata Muszynska
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Paweł P Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Frank Wos
- New York Genome Center, New York, NY, 10013, USA
| | - Amanda Raine
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Ulrika Liljedahl
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Tomas Axelsson
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Zhong Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Zhaowei Yang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing Li
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaopeng Yang
- Department of Neurology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
| | - Hongwei Wang
- Development of Medicine, the University of Chicago, Chicago, IL, 60637, USA
| | - Ari Melnick
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Shang Guo
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
| | - Alexander Blume
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Inmaculada Ibanez de Caceres
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Carlos Rodriguez-Antolin
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Rocio Rosas
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Justin Wade Davis
- AbbVie Genomics Research Center, 1 N. Waukegan Rd, North Chicago, IL, 60036, USA
| | | | - Dalila B Megherbi
- CMINDS Research Center, Francis College of Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Wenming Xiao
- Center for Devices and Radiological Health, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Will Liao
- New York Genome Center, New York, NY, 10013, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Baitang Ning
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Yunliang Wang
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China.
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA.
- The Feil Family Brain and Mind Research Institute, New York, New York, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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6
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Orchard P, Manickam N, Ventresca C, Vadlamudi S, Varshney A, Rai V, Kaplan J, Lalancette C, Mohlke KL, Gallagher K, Burant CF, Parker SCJ. Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits. Genome Res 2021; 31:2258-2275. [PMID: 34815310 PMCID: PMC8647829 DOI: 10.1101/gr.268482.120] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/16/2021] [Indexed: 12/12/2022]
Abstract
Skeletal muscle accounts for the largest proportion of human body mass, on average, and is a key tissue in complex diseases and mobility. It is composed of several different cell and muscle fiber types. Here, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell-specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We additionally perform multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33,862 nuclei and identify seven cell types ranging in abundance from 59.6% to 1.0% of all nuclei. We introduce a regression-based approach to infer cell types by comparing transcription start site-distal ATAC-seq peaks to reference enhancer maps and show consistency with RNA-based marker gene cell type assignments. We find heterogeneity in enrichment of genetic variants linked to complex phenotypes from the UK Biobank and diabetes genome-wide association studies in cell-specific ATAC-seq peaks, with the most striking enrichment patterns in muscle mesenchymal stem cells (∼3.5% of nuclei). Finally, we overlay these chromatin accessibility maps on GWAS data to nominate causal cell types, SNPs, transcription factor motifs, and target genes for type 2 diabetes signals. These chromatin accessibility profiles for human and rat skeletal muscle cell types are a useful resource for nominating causal GWAS SNPs and cell types.
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Affiliation(s)
- Peter Orchard
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nandini Manickam
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Christa Ventresca
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Swarooparani Vadlamudi
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Arushi Varshney
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Vivek Rai
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jeremy Kaplan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Claudia Lalancette
- Epigenomics Core, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Katherine Gallagher
- Department of Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
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7
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Laubach ZM, Greenberg JR, Turner JW, Montgomery TM, Pioon MO, Sawdy MA, Smale L, Cavalcante RG, Padmanabhan KR, Lalancette C, vonHoldt B, Faulk CD, Dolinoy DC, Holekamp KE, Perng W. Early-life social experience affects offspring DNA methylation and later life stress phenotype. Nat Commun 2021; 12:4398. [PMID: 34285226 PMCID: PMC8292380 DOI: 10.1038/s41467-021-24583-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 07/20/2020] [Accepted: 06/24/2021] [Indexed: 02/06/2023] Open
Abstract
Studies in rodents and captive primates suggest that the early-life social environment affects future phenotype, potentially through alterations to DNA methylation. Little is known of these associations in wild animals. In a wild population of spotted hyenas, we test the hypothesis that maternal care during the first year of life and social connectedness during two periods of early development leads to differences in DNA methylation and fecal glucocorticoid metabolites (fGCMs) later in life. Here we report that although maternal care and social connectedness during the den-dependent life stage are not associated with fGCMs, greater social connectedness during the subadult den-independent life stage is associated with lower adult fGCMs. Additionally, more maternal care and social connectedness after den independence correspond with higher global (%CCGG) DNA methylation. We also note differential DNA methylation near 5 genes involved in inflammation, immune response, and aging that may link maternal care with stress phenotype.
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Affiliation(s)
- Zachary M Laubach
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA.
- BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| | - Julia R Greenberg
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
| | - Julie W Turner
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
- BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
| | - Tracy M Montgomery
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
- Max Planck Institute of Animal Behavior, Department for the Ecology of Animal Societies, Konstanz, Germany
| | - Malit O Pioon
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
| | - Maggie A Sawdy
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
| | - Laura Smale
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Department of Psychology, Michigan State University, East Lansing, MI, USA
| | | | | | | | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | - Dana C Dolinoy
- Epigenomics Core, University of Michigan, Ann Arbor, MI, USA
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kay E Holekamp
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
- BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
| | - Wei Perng
- Department of Epidemiology and Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Denver, Aurora, CO, USA
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8
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Svoboda LK, Neier K, Wang K, Cavalcante RG, Rygiel CA, Tsai Z, Jones TR, Liu S, Goodrich JM, Lalancette C, Colacino JA, Sartor MA, Dolinoy DC. Tissue and sex-specific programming of DNA methylation by perinatal lead exposure: implications for environmental epigenetics studies. Epigenetics 2020; 16:1102-1122. [PMID: 33164632 DOI: 10.1080/15592294.2020.1841872] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Early developmental environment can influence long-term health through reprogramming of the epigenome. Human environmental epigenetics studies rely on surrogate tissues, such as blood, to assess the effects of environment on disease-relevant but inaccessible target tissues. However, the extent to which environment-induced epigenetic changes are conserved between these tissues is unclear. A better understanding of this conservation is imperative for effective design and interpretation of human environmental epigenetics studies. The Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription (TaRGET II) consortium was established by the National Institute of Environmental Health Sciences to address the utility of surrogate tissues as proxies for toxicant-induced epigenetic changes in target tissues. We and others have recently reported that perinatal exposure to lead (Pb) is associated with adverse metabolic outcomes. Here, we investigated the sex-specific effects of perinatal exposure to a human environmentally relevant level of Pb on DNA methylation in paired liver and blood samples from adult mice using enhanced reduced-representation bisulphite sequencing. Although Pb exposure ceased at 3 weeks of age, we observed thousands of sex-specific differentially methylated cytosines in the blood and liver of Pb-exposed animals at 5 months of age, including 44 genomically imprinted loci. We observed significant tissue overlap in the genes mapping to differentially methylated cytosines. A small but significant subset of Pb-altered genes exhibit basal sex differences in gene expression in the mouse liver. Collectively, these data identify potential molecular targets for Pb-induced metabolic diseases, and inform the design of more robust human environmental epigenomics studies.
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Affiliation(s)
- Laurie K Svoboda
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kari Neier
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA
| | | | - Christine A Rygiel
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Zing Tsai
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA
| | - Tamara R Jones
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Siyu Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Claudia Lalancette
- Epigenomics Core, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Justin A Colacino
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan, School of Public Health, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
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9
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Straight B, Fisher G, Needham BL, Naugle A, Olungah C, Wanitjirattikal P, Root C, Farman J, Barkman T, Lalancette C. Lifetime stress and war exposure timing may predict methylation changes at NR3C1 based on a pilot study in a warrior cohort in a small-scale society in Kenya. Am J Hum Biol 2020; 33:e23515. [PMID: 33058324 DOI: 10.1002/ajhb.23515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Candidate gene methylation studies of NR3C1 have identified associations with psychosocial adversity, including war trauma. This pilot study (sample sizes from 22 to 45 for primary analyses) examined NR3C1 methylation in a group of Kenyan pastoralist young men in relation to culturally relevant traumatic experiences, including participation in coalitional lethal gun violence. METHODS Adolescent and young adult Samburu men ("warriors") were recruited for participation. DNA was obtained from whole saliva and methylation analyses performed using mass spectrometry. We performed a data reduction of variables from a standardized instrument of lifetime stress using a factor analysis and we assessed the association between the extracted factors with culturally relevant and cross-culturally comparative experiences. RESULTS Cumulative lifetime trauma exposure and forms of violence to which warriors are particularly susceptible were associated with DNA methylation changes in the NR3C1 1F promoter region but not in the NR3C1 1D promoter region. However, sensitivity analyses revealed significant associations between individual CpG sites in both regions and cumulative stress exposures, war exposure timing, and war fatalities. CONCLUSIONS This study supports the importance of NR3C1 methylation changes in response to challenging life circumstances, including in a global south cultural context that contrasts in notable ways from global north contexts and from the starkly tragic examples of the Rwandan genocide and war-associated rape explored in recent studies. Timing of traumatic exposure and culturally salient means to measure enduring symptoms of trauma remain important considerations for DNA methylation studies.
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Affiliation(s)
- Bilinda Straight
- Department of Anthropology, Western Michigan University, Kalamazoo, Michigan, USA
| | - Georgiana Fisher
- Department of Statistics, Western Michigan University, Kalamazoo, Michigan, USA
| | - Belinda L Needham
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Amy Naugle
- Department of Psychology, Western Michigan University, Kalamazoo, Michigan, USA
| | - Charles Olungah
- University of Nairobi Institute of Anthropology, Gender & African Studies, Nairobi, Nairobi, Kenya
| | | | - Cecilia Root
- Unaffiliated (Western Michigan University Department of Anthropology Alum), Kalamazoo, Michigan, USA
| | - Jen Farman
- Unaffiliated (Western Michigan University Department of Anthropology Alum), Kalamazoo, Michigan, USA
| | - Todd Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
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10
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Albert O, Nardelli TC, Lalancette C, Hales BF, Robaire B. Effects of In Utero and Lactational Exposure to New Generation Green Plasticizers on Adult Male Rats: A Comparative Study With Di(2-Ethylhexyl) Phthalate. Toxicol Sci 2018; 164:129-141. [PMID: 29945229 PMCID: PMC6016686 DOI: 10.1093/toxsci/kfy072] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Di(2-ethylhexyl) phthalate (DEHP), a widely used plasticizer, is a ubiquitous environmental contaminant and may act as an endocrine disruptor. Early life exposures to DEHP may result in anti-androgenic effects, impairing the development of the male reproductive tract. However, data on the long-lasting consequences of such DEHP exposures on adult male reproductive function are still rare and discrepant. Previously, we identified 2 novel plasticizers, 1,4-butanediol dibenzoate (BDB) and dioctyl succinate (DOS), as potential substitutes for DEHP that did not reproduce classically described endocrine disrupting phenotypes in prepubertal male offspring after maternal exposure. Here, we investigated the consequences of in utero and lactational exposure to BDB and DOS on adult male rat reproductive function in a comparative study with DEHP and a commercially available alternative plasticizer, 1,2-cyclohexane dicarboxylic acid diisononyl ester (DINCH). Timed pregnant Sprague Dawley rats were gavaged with vehicle or a test chemical (30 or 300 mg/kg/day) from gestation day 8 to postnatal day 21. While DEHP exposure (300 mg/kg/day) significantly increased epididymal weight in the adult, exposure to DINCH, BDB, or DOS did not affect reproductive organ weights, steroid levels, or sperm quality. Using a toxicogenomic microarray approach, we found that adult testicular gene expression was affected by exposure to the higher dose of DEHP; transcripts such as Nr5a2, Ltf, or Runx2 were significantly downregulated, suggesting that DEHP was targeting estrogen signaling. Lesser effects were observed after treatment with either DINCH or BDB. DOS exposure did not produce such effects, confirming its potential as a responsible substitute for DEHP.
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Affiliation(s)
- Océane Albert
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC H3G1Y6, Canada
| | - Thomas C Nardelli
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC H3G1Y6, Canada
| | - Claudia Lalancette
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC H3G1Y6, Canada
| | - Barbara F Hales
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC H3G1Y6, Canada
| | - Bernard Robaire
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC H3G1Y6, Canada
- Department of Obstetrics & Gynecology, McGill University, Montreal, QC, H4A3J1, Canada
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11
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Bogaty C, Lévesque S, Garenc C, Frenette C, Bolduc D, Galarneau LA, Lalancette C, Loo V, Tremblay C, Trudeau M, Vachon J, Dionne M, Villeneuve J, Longtin J, Longtin Y. Trends in the use of laboratory tests for the diagnosis of Clostridium difficile infection and association with incidence rates in Quebec, Canada, 2010-2014. Am J Infect Control 2017; 45:964-968. [PMID: 28549882 DOI: 10.1016/j.ajic.2017.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 02/08/2017] [Revised: 04/01/2017] [Accepted: 04/03/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND Several Clostridium difficile infection (CDI) surveillance programs do not specify laboratory strategies to use. We investigated the evolution in testing strategies used across Quebec, Canada, and its association with incidence rates. METHODS Cross-sectional study of 95 hospitals by surveys conducted in 2010 and in 2013-2014. The association between testing strategies and institutional CDI incidence rates was analyzed via multivariate Poisson regressions. RESULTS The most common assays in 2014 were toxin A/B enzyme immunoassays (EIAs) (61 institutions, 64%), glutamate dehydrogenase (GDH) EIAs (51 institutions, 53.7%), and nucleic acid amplification tests (NAATs) (34 institutions, 35.8%). The most frequent algorithm was a single-step NAAT (20 institutions, 21%). Between 2010 and 2014, 35 institutions (37%) modified their algorithm. Institutions detecting toxigenic C difficile instead of C difficile toxin increased from 14 to 37 (P < .001). Institutions detecting toxigenic C difficile had higher CDI rates (7.9 vs 6.6 per 10,000 patient days; P = .01). Institutions using single-step NAATs, GDH plus toxigenic cultures, and GDH plus cytotoxicity assays had higher CDI rates than those using an EIA-based algorithm (P < .05). CONCLUSIONS Laboratory detection of CDI has changed since 2010. There is an association between diagnostic algorithms and CDI incidence. Mitigation strategies are warranted.
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Affiliation(s)
- C Bogaty
- McGill University Faculty of Medicine, Montréal, QC, Canada
| | - S Lévesque
- Laboratoire de Santé Publique du Québec, Institute National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec (QC), Canada
| | - C Garenc
- Institut National de Santé Publique du Québec, Quebec City, QC, Canada; Centre Hospitalier Universitaire de Québec, Québec City, QC, Canada
| | - C Frenette
- McGill University Faculty of Medicine, Montréal, QC, Canada; McGill University Health Centre, Montréal, QC, Canada
| | - D Bolduc
- Centre intégré de santé et de services sociaux du Bas-Saint-Laurent, Rimouski, Quebec (QC), Canada
| | - L-A Galarneau
- Centre intégré universitaire de santé et de services sociaux de la Mauricie-et-du-Centre-du-Québec, Trois-Rivières, Quebec (QC), Canada
| | - C Lalancette
- Laboratoire de Santé Publique du Québec, Institute National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec (QC), Canada
| | - V Loo
- McGill University Faculty of Medicine, Montréal, QC, Canada; McGill University Health Centre, Montréal, QC, Canada
| | - C Tremblay
- Centre Hospitalier Universitaire de Québec, Québec City, QC, Canada; Laval University Faculty of Medicine, Quebec City, QC, Canada
| | - M Trudeau
- Laboratoire de Santé Publique du Québec, Institute National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec (QC), Canada
| | - J Vachon
- Centre intégré de santé et de services sociaux de Chaudière-Appalaches, Thetford Mines, Quebec (QC), Canada
| | - M Dionne
- Institut National de Santé Publique du Québec, Quebec City, QC, Canada
| | - J Villeneuve
- Institut National de Santé Publique du Québec, Quebec City, QC, Canada
| | - J Longtin
- Laboratoire de Santé Publique du Québec, Institute National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec (QC), Canada; Laval University Faculty of Medicine, Quebec City, QC, Canada.
| | - Y Longtin
- McGill University Faculty of Medicine, Montréal, QC, Canada
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12
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Boyd DA, Lalancette C, Lévesque S, Golding GR. Characterization of a genomic island harbouring a new vanD allele from Enterococcus faecium N15-508 isolated in Canada. J Antimicrob Chemother 2016; 71:2052-4. [PMID: 27084917 DOI: 10.1093/jac/dkw063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D A Boyd
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - C Lalancette
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - S Lévesque
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - G R Golding
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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13
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Poon S, Wade MG, Aleksa K, Rawn DFK, Carnevale A, Gaertner DW, Sadler A, Breton F, Koren G, Ernest SR, Lalancette C, Robaire B, Hales BF, Goodyer CG. Hair as a biomarker of systemic exposure to polybrominated diphenyl ethers. Environ Sci Technol 2014; 48:14650-14658. [PMID: 25387207 DOI: 10.1021/es502789h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The efficacy of using hair as a biomarker for exposure to polybrominated diphenyl ether (PBDE) flame retardants was assessed in humans and an animal model. Paired human hair and serum samples were obtained from adult men and women (n = 50). In parallel, hair, serum, liver, and fat were collected from adult male Sprague-Dawley rats exposed to increasing doses of the PBDE mixture found in house dust for 70 days via the diet. All samples were analyzed by GC-MS for eight common PBDEs: BDE-28, -47, -99, -100, -153, -154, -183, and -209. Paired human hair and serum samples had five congeners (BDE-28, -47, -99, -100, and -154) with significant individual correlations (0.345-0.566). In rat samples, BDE-28 and BDE-183 were frequently below the level of detection. Significant correlations were observed for BDE-47, -99, -100, -153, -154, and -209 in rat hair, serum, liver, and fat across doses, with r values ranging from 0.803 to 0.988; weaker correlations were observed between hair and other tissues when data from the lowest dose group or for BDE-209 were analyzed. Thus, human and rat hair PBDE measurements correlate strongly with those in alternative matrices, validating the use of hair as a noninvasive biomarker of long-term PBDE exposure.
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Affiliation(s)
- Shirley Poon
- Hospital for Sick Children , 555 University Avenue , Toronto, Ontario M5G 1X8, Canada
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14
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Harvey AJ, Mao S, Lalancette C, Krawetz SA, Brenner CA. Transcriptional differences between rhesus embryonic stem cells generated from in vitro and in vivo derived embryos. PLoS One 2012; 7:e43239. [PMID: 23028448 PMCID: PMC3445581 DOI: 10.1371/journal.pone.0043239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 07/18/2012] [Indexed: 01/16/2023] Open
Abstract
Numerous studies have focused on the transcriptional signatures that underlie the maintenance of embryonic stem cell (ESC) pluripotency. However, it remains unclear whether ESC retain transcriptional aberrations seen in in vitro cultured embryos. Here we report the first global transcriptional profile comparison between ESC generated from either in vitro cultured or in vivo derived primate embryos by microarray analysis. Genes involved in pluripotency, oxygen regulation and the cell cycle were downregulated in rhesus ESC generated from in vitro cultured embryos (in vitro ESC). Significantly, several gene differences are similarly downregulated in preimplantation embryos cultured in vitro, which have been associated with long term developmental consequences and disease predisposition. This data indicates that prior to derivation, embryo quality may influence the molecular signature of ESC lines, and may differentially impact the physiology of cells prior to or following differentiation.
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Affiliation(s)
- Alexandra J Harvey
- Department of Physiology, Wayne State University, Detroit, Michigan, United States of America.
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15
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Ernest SR, Wade MG, Lalancette C, Ma YQ, Berger RG, Robaire B, Hales BF. Effects of chronic exposure to an environmentally relevant mixture of brominated flame retardants on the reproductive and thyroid system in adult male rats. Toxicol Sci 2012; 127:496-507. [PMID: 22387749 PMCID: PMC3355309 DOI: 10.1093/toxsci/kfs098] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [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] [Indexed: 11/13/2022] Open
Abstract
Brominated flame retardants (BFRs) are incorporated into a wide variety of consumer products, are readily released into home and work environments, and are present in house dust. Studies using animal models have revealed that exposure to polybrominated diphenyl ethers (PBDEs) may impair adult male reproductive function and thyroid hormone physiology. Such studies have generally characterized the outcome of acute or chronic exposure to a single BFR technical mixture or congener but not the impact of environmentally relevant BFR mixtures. We tested whether exposure to the BFRs found in house dust would have an adverse impact on the adult male rat reproductive system and thyroid function. Adult male Sprague Dawley rats were exposed to a complex BFR mixture composed of three commercial brominated diphenyl ethers (52.1% DE-71, 0.4% DE-79, and 44.2% decaBDE-209) and hexabromocyclododecane (3.3%), formulated to mimic the relative congener levels in house dust. BFRs were delivered in the diet at target doses of 0, 0.02, 0.2, 2, or 20 mg/kg/day for 70 days. Compared with controls, males exposed to the highest dose of BFRs displayed a significant increase in the weights of the kidneys and liver, which was accompanied by induction of CYP1A and CYP2B P450 hepatic drug–metabolizing enzymes. BFR exposure did not affect reproductive organ weights, serum testosterone levels, testicular function, or sperm DNA integrity. The highest dose caused thyroid toxicity as indicated by decreased serum thyroxine (T4) and hypertrophy of the thyroid gland epithelium. At lower doses, the thickness of the thyroid gland epithelium was reduced, but no changes in hormone levels (T4 and thyroid-stimulating hormone) were observed. Thus, exposure to BFRs affected liver and thyroid physiology but not male reproductive parameters.
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Affiliation(s)
- Sheila R Ernest
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada H3G 1Y6
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16
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Abstract
BACKGROUND There has been substantial interest in assessing whether RNAs (mRNAs and sncRNAs, i.e. small non-coding) delivered from mammalian spermatozoa play a functional role in early embryo development. While the cadre of spermatozoal mRNAs has been characterized, comparatively little is known about the distribution or function of the estimated 24,000 sncRNAs within each normal human spermatozoon. METHODS RNAs of <200 bases in length were isolated from the ejaculates from three donors of proved fertility. RNAs of 18-30 nucleotides in length were then used to construct small RNA Digital Gene Expression libraries for Next Generation Sequencing. Known sncRNAs that uniquely mapped to a single location in the human genome were identified. RESULTS Bioinformatic analysis revealed the presence of multiple classes of small RNAs in human spermatozoa. The primary classes resolved included microRNA (miRNAs) (≈ 7%), Piwi-interacting piRNAs (≈ 17%), repeat-associated small RNAs (≈ 65%). A minor subset of short RNAs within the transcription start site/promoter fraction (≈ 11%) frames the histone promoter-associated regions enriched in genes of early embryonic development. These have been termed quiescent RNAs. CONCLUSIONS A complex population of male derived sncRNAs that are available for delivery upon fertilization was revealed. Sperm miRNA-targeted enrichment in the human oocyte is consistent with their role as modifiers of early post-fertilization. The relative abundance of piRNAs and repeat-associated RNAs suggests that they may assume a role in confrontation and consolidation. This may ensure the compatibility of the genomes at fertilization.
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Affiliation(s)
- Stephen A Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA.
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17
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Johnson GD, Sendler E, Lalancette C, Hauser R, Diamond MP, Krawetz SA. Cleavage of rRNA ensures translational cessation in sperm at fertilization. Mol Hum Reprod 2011; 17:721-6. [PMID: 21831882 DOI: 10.1093/molehr/gar054] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Intact ribosomal RNAs (rRNAs) comprise the majority of somatic transcripts, yet appear conspicuously absent in spermatozoa, perhaps reflecting cytoplasmic expulsion during spermatogenesis. To discern their fate, total RNA retained in mature spermatozoa from three fertile donors was characterized by Next Generation Sequencing. In all samples, >75% of total sequence reads aligned to rRNAs. The distribution of reads along the length of these transcripts exhibited a high degree of non-uniformity that was reiterated between donors. The coverage of sequencing reads was inversely correlated with guanine-cytosine (GC)-richness such that sequences greater than ∼70% GC were virtually absent in all sperm RNA samples. To confirm the loss of sequence, the relative abundance of specific regions of the 28S transcripts in sperm was established by 7-Deaza-2'-deoxy-guanosine-5'-triphosphate RT-PCR. The inability to amplify specific regions of the 28S sequence from sperm despite the abundant representation of this transcript in the sequencing libraries demonstrates that approximately three-quarters of RNA retained in the mature male gamete are products of rRNA fragmentation. Hence, cleavage (not expulsion of the RNA component of the translational machinery) is responsible for preventing spurious translation following spermiogenesis. These results highlight the potential importance of those transcripts, including many mRNAs, which evade fragmentation and remain intact when sperm are delivered at fertilization. Sequencing data are deposited in GEO as: GSE29160.
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Affiliation(s)
- G D Johnson
- Center for Molecular Medicine and Genetics, C. S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Johnson GD, Lalancette C, Sendler E, Diamond MP, Hauser R, Krawetz SA. The Case of the Missing Ribosomal RNAs. Biol Reprod 2011. [DOI: 10.1093/biolreprod/85.s1.521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Hales BF, Grenier L, Lalancette C, Robaire B. Epigenetic programming: From gametes to blastocyst. ACTA ACUST UNITED AC 2011; 91:652-65. [DOI: 10.1002/bdra.20781] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/01/2010] [Accepted: 12/07/2010] [Indexed: 01/16/2023]
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Johnson GD, Platts AE, Lalancette C, Goodrich R, Heng HH, Krawetz SA. Interrogating the transgenic genome: development of an interspecies tiling array. Syst Biol Reprod Med 2011; 57:54-62. [PMID: 21214491 DOI: 10.3109/19396368.2010.506000] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A single expressing copy of the human protamine domain was randomly inserted into an intron of Cyp2c38. The transgenic locus was shown to recapitulate the level of expression observed in normal human testis while not perturbing endogenous protamine expression. The development of an interspecies tiling array was pursued to enable direct comparison of the orthologous protamine domains in a single experiment. Probe design was adapted to generate species-specific high resolution probe sets that would tolerate repetitive elements. Results from competitive hybridizations demonstrate that interspecies tiling arrays are a valuable tool for parallel analysis of highly similar DNA sequences. This approach provides a rapid and reliable means of interrogating samples prior to deep sequencing analysis. These arrays should readily compliment most DNA isolation and analysis techniques such as ChIP, nuclease sensitivity and nuclear matrix association assays.
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Affiliation(s)
- Graham D Johnson
- The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Abstract
Within the sperm nucleus, the paternal genome remains functionally inert and protected following protamination. This is marked by a structural morphogenesis that is heralded by a striking reduction in nuclear volume. Despite these changes, both human and mouse spermatozoa maintain low levels of nucleosomes that appear non-randomly distributed throughout the genome. These regions may be necessary for organizing higher order genomic structure through interactions with the nuclear matrix. The promoters of this transcriptionally quiescent genome are differentially marked by modified histones that may poise downstream epigenetic effects. This notion is supported by increasing evidence that the embryo inherits these differing levels of chromatin organization. In concert with the suite of RNAs retained in the mature sperm, they may synergistically interact to direct early embryonic gene expression. Irrespective, these features reflect the transcriptional history of spermatogenic differentiation. As such, they may soon be utilized as clinical markers of male fertility. In this review, we explore and discuss how this may be orchestrated.
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Affiliation(s)
- Graham D. Johnson
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
| | - Claudia Lalancette
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
- Department of Obstetrics and Gynecology, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
| | - Amelia K. Linnemann
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
| | - Frédéric Leduc
- Department of Biochemistry, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - Guylain Boissonneault
- Department of Biochemistry, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - Stephen A. Krawetz
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
- Department of Obstetrics and Gynecology, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
- Institute for Scientific Computing, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
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Platts AE, Lalancette C, Emery BR, Carrell DT, Krawetz SA. Disease progression and solid tumor survival: a transcriptome decoherence model. Mol Cell Probes 2009; 24:53-60. [PMID: 19835949 DOI: 10.1016/j.mcp.2009.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 09/28/2009] [Accepted: 09/29/2009] [Indexed: 11/19/2022]
Abstract
Networks of genes are typically generated from expression changes observed between control and test conditions. Nevertheless, within a single control state many genes show expression variance across biological replicates. These transcripts, typically termed unstable, are usually excluded from analyses because their behavior cannot be reconciled with biological constraints. Grouped as pairs of covariant genes they can however show a consistent response to the progression of a disease. We present a model of coherence arising from sets of covariant genes that was developed in-vitro then tested against a range of solid tumors. DGPMs, Decoherence Gene Pair Models, showed changes in network topology reflective of the metastatic transition. Across a range of solid tumor studies the model generalizes to reveal a richly connected topology of networks in healthy tissues that becomes sparser as the disease progresses reaching a minimum size in the advanced tumors with minim survivability.
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Affiliation(s)
- Adrian E Platts
- The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Johnson GD, Lalancette C, Platts AE, Krawetz SA. Interspecies CGH Array Comparison of Genomic Elements and Epigenetic Modifications. Biol Reprod 2009. [DOI: 10.1093/biolreprod/81.s1.362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Lalancette C, Platts AE, Diamond MP, Krawetz SA. Human Sperm RNA Getting More Complex: Identification of Small RNAs Carried by Human Spermatozoa Using Deep Sequencing. Biol Reprod 2009. [DOI: 10.1093/biolreprod/81.s1.361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Lalancette C, Platts AE, Johnson GD, Emery BR, Carrell DT, Krawetz SA. Identification of human sperm transcripts as candidate markers of male fertility. J Mol Med (Berl) 2009; 87:735-48. [DOI: 10.1007/s00109-009-0485-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2009] [Revised: 04/18/2009] [Accepted: 05/08/2009] [Indexed: 12/20/2022]
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Abstract
Whereas the presence of RNA in mature ejaculate spermatozoa is now established, its functional significance, if any, is still a matter of debate. This reflects the accepted description that spermatozoa are highly differentiated, specialized cells of minimal cytoplasm and compacted nucleus that are transcriptionally inactive. A significant proportion of the RNA required for the later, haploid stages of terminal spermatogenic differentiation (spermiogenesis) is synthesized prior to transcriptional arrest then stably stored until its translation during spermiogenesis. Spermatozoal RNAs, including messenger RNAs (mRNAs) are therefore considered to be stored remnants. Any role in fertilization and early development has, until recently, seemed unlikely, since the oocyte contains large stores of maternal mRNAs known to be required for early embryonic development prior to zygotic genome activation. Although the spermatozoon can deliver its RNA to the oocyte at fertilization, it has been generally assumed that compared to the oocyte RNA reserve, the spermatozoan payload is too small to be functional in embryo development. However, the debate continues as recent studies suggest that in specific instances sperm RNA is functional. This review presents and discusses the functional significance of spermatozoal RNA in relation to some recent advances in the field.
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Affiliation(s)
- Claudia Lalancette
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine
| | - David Miller
- Leeds Institute of Genetics and Therapeutics, University of Leeds
| | - Yan Li
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine
| | - Stephen A. Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine
- Institute for Scientific Computing, Wayne State University
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Lalancette C, Platts AE, Lu Y, Lu S, Krawetz SA. Computational identification of transcription frameworks of early committed spermatogenic cells. Mol Genet Genomics 2008; 280:263-74. [PMID: 18615256 DOI: 10.1007/s00438-008-0361-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Accepted: 06/17/2008] [Indexed: 11/28/2022]
Abstract
It is known that transcription factors (TFs) work in cooperation with each other to govern gene expression and thus single TF studies may not always reflect the underlying biology. Using microarray data obtained from two independent studies of the first wave of spermatogenesis, we tested the hypothesis that co-expressed spermatogenic genes in cells committed to differentiation are regulated by a set of distinct combinations of TF modules. A computational approach was designed to identify over-represented module combinations in the promoter regions of genes associated with transcripts that either increase or decrease in abundance between the first two major spermatogenic cell types: spermatogonia and spermatocytes. We identified five TFs constituting four module combinations that were correlated with expression and repression of similarly regulated genes. These modules were biologically assessed in the context that they represent the key transcriptional mediators in the developmental transition from the spermatogonia to spermatocyte.
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Affiliation(s)
- Claudia Lalancette
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 275 East Hancock, Detroit, MI 48201, USA.
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Abstract
Systems biology presents a new paradigm for elucidating the processes required to organize and sustain life. We now have access to whole genome sequences, gene expression data for multiple cell types, and databases for regulatory elements governing these genes. These resources make it feasible to identify conserved genomic sequences across multiple species, transcription factors regulating the expression of genes with similar expression patterns within a given cell type and to compare expression levels of specific genes between normal and diseased cellular states. In order to utilize this wealth of information, new computational tools that integrate these datasets in a genome-wide context are required. Using the protamine cluster as an example, we present a series of in-house applications that we have developed to integrate, contextualize and visualize datasets across multiple hierarchies.
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Affiliation(s)
- Laura Naismith
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
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Abstract
AIM To simultaneously determine the localization of histones and protamines within human sperm nuclei. METHODS Immunofluorescence of the core histones and protamines and fluorescence in situ hybridization of the telomere region of chromosome 16 was assessed in decondensed human sperm nuclei. RESULTS Immunofluorescent localization of histones, protamine 1 (PRM1) and protamine 2 (PRM2) along with fluorescence in situ hybridization localization of chromosome 16 telomeric sequences revealed a discrete distribution in sperm nuclei. Histones localized to the posterior ring region (i.e. the sperm nuclear annulus), whereas PRM1 and PRM2 appeared to be dispersed throughout the entire nucleus. CONCLUSION The co-localization of the human core sperm histones with the telomeric regions of chromosome 16 is consistent with the reorganization of specific non-protamine regions into a less compacted state.
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Affiliation(s)
- Yan Li
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne 48201, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Wayne 48201, MI, USA
| | - Claudia Lalancette
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne 48201, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Wayne 48201, MI, USA
| | - David Miller
- Reproduction and Early Development Group, University of Leeds, Institute of Genetics, Health and Therapeutics, Leeds LS29JT, UK
| | - Stephen A. Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne 48201, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Wayne 48201, MI, USA
- Institute for Scientific Computing, Wayne State University, Wayne 48201, MI, USA
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Lalancette C, Thibault C, Bachand I, Caron N, Bissonnette N. Transcriptome Analysis of Bull Semen with Extreme Nonreturn Rate: Use of Suppression-Subtractive Hybridization to Identify Functional Markers for Fertility1. Biol Reprod 2008; 78:618-35. [PMID: 18003951 DOI: 10.1095/biolreprod.106.059030] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Affiliation(s)
- C Lalancette
- Dairy and Swine Research and Development Center, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada J1M 1Z3
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Lalancette C, Faure RL, Leclerc P. Identification of the proteins present in the bull sperm cytosolic fraction enriched in tyrosine kinase activity: a proteomic approach. Proteomics 2006; 6:4523-40. [PMID: 16847872 DOI: 10.1002/pmic.200500578] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Numerous sperm proteins have been identified on the basis of their increase in tyrosine phosphorylation during capacitation. However, the tyrosine kinases present in spermatozoa that are responsible for this phosphorylation remain unknown. As spermatozoa are devoid of transcriptional and translational activities, molecular biology approaches might not reflect the transcriptional pattern in mature spermatozoa. Working directly with the proteins present in ejaculated spermatozoa is the most reliable approach to identify the tyrosine kinases potentially involved in the capacitation-associated increase in protein tyrosine phosphorylation. A combination of tyrosine kinase assays and proteomic identification tools were used as an approach to identify sperm protein tyrosine kinases. Fractionation by nitrogen cavitation showed that the majority of tyrosine kinase activity is present in the cytosolic fraction of bovine spermatozoa. By the use of Poly-Glu:Tyr(4:1)-agarose affinity chromatography, we isolated a fraction enriched in tyrosine kinase activity. Proteomics approaches permitted the identification of tyrosine kinases from three families: Src (Lyn), Csk, and Tec (Bmx, Btk). We also identified proteins implicated in different cellular events associated with sperm capacitation and acrosome reaction. These results confirm the implication of tyrosine phosphorylation in some aspects of capacitation/acrosome reaction and reveal the identity of new players potentially involved in these processes.
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Affiliation(s)
- Claudia Lalancette
- Département d'Obstétrique/Gynécologie, Centre de Recherche en Biologie de la Reproduction, Université Laval and Ontogénie et Reproduction, Centre de recherche du CHUQ, Ste-Foy, QC, Canada
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Lalancette C, Bordeleau LJ, Faure RL, Leclerc P. Bull testicular haploid germ cells express a messenger encoding for a truncated form of the protein tyrosine kinase HCK. Mol Reprod Dev 2006; 73:520-30. [PMID: 16432821 DOI: 10.1002/mrd.20422] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein tyrosine phosphorylation is a process that has been studied worldwide during sperm capacitation and acrosomal exocytosis events. Although few capacitation-induced phosphotyrosine-containing proteins have been identified, little is known about the tyrosine kinases directly involved in this post-translational modification. Different studies from our and other groups using tyrosine kinase inhibitors suggest the involvement of members of the family of src-related tyrosine kinases in the sperm capacitation associated increase in protein tyrosine phosphorylation. Using a molecular biology approach, we report for the first time messengers encoding for members from the src-related tyrosine kinase family in bovine spermatogenic cells. Degenerated primers were designed within a highly homologous region specific to the family of src tyrosine kinases, and RNAs coding for c-src, c-yes, lyn, lck, and hck were identified in bull testis and haploid germ cells by RT-PCR. We also report the presence of a messenger in haploid bull germ cells that could encode for a truncated isoform of the hck tyrosine kinase. This messenger was detected by screening of a haploid germ cells cDNA library using the RT-PCR product homologous to hck as a probe. The presence of this transcript in haploid germ cell RNA preparations was validated by RT-PCR, 3'RACE, 5'RACE as well as Northern blot. Such a truncated protein could function as an adaptor protein or as a competitive inhibitor in spermiogenesis or mature sperm functions.
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Affiliation(s)
- Claudia Lalancette
- Département d'Obstétrique/Gynécologie, Centre de Recherche en Biologie de la Reproduction, Université Laval and Endocrinologie de la Reproduction, Centre de recherche du CHUQ, Québec, Canada
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Samokhvalov IM, Thomson AM, Lalancette C, Liakhovitskaia A, Ure J, Medvinsky A. Multifunctional reversible knockout/reporter system enabling fully functional reconstitution of the AML1/Runx1 locus and rescue of hematopoiesis. Genesis 2006; 44:115-21. [PMID: 16496309 DOI: 10.1002/gene.20190] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [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] [Indexed: 11/06/2022]
Abstract
Mice deficient in the runt homology domain transcription factor Runx1 die of severe anemia in utero by embryonic day (E)12.5. A reactivatable Runx1 knockout embryonic stem cell (ESC) and mouse systems were generated by the targeted insertion of a loxP-flanked multipartite gene stop/trap cassette designed to simultaneously ablate the expression of Runx1 and report on the activity of its promoters. The cassette's in-frame LacZ reporter enabled activities of the proximal and the distal promoters to be differentially monitored. Although Runx1-null ESCs were capable of primitive erythroid differentiation in vitro, their capacity to generate granulocyte/macrophage or mixed myelo-erythroid embryoid bodies was lost. Cre-mediated reactivation restored Runx1 structural integrity and rescued the hematopoietic differentiation potential of ESCs. Mice with the reactivated allele survived, showed no hematopoietic deficit, and expressed all major splice isoforms of Runx1 appropriately. This multipurpose mouse model will be useful for the analysis of the critical Runx1-dependent check-point(s) in hematopoietic development.
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Affiliation(s)
- Igor M Samokhvalov
- Developmental Haematopoiesis Laboratory, Institute for Stem Cell Research, University of Edinburgh, Edinburgh EH9 3JQ, Scotland, United Kingdom
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Morin G, Lalancette C, Sullivan R, Leclerc P. Identification of the bull sperm p80 protein as a PH-20 ortholog and its modification during the epididymal transit. Mol Reprod Dev 2005; 71:523-34. [PMID: 15892045 DOI: 10.1002/mrd.20308] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We have identified an 80 kDa protein in ejaculated bull spermatozoa (p80) which is found in acrosomal and post-acrosomal areas of the head. It has a hyaluronidase activity and shares homologies with PH-20, a sperm surface glycoprotein involved in sperm-egg interaction. The aim of the present study was to characterize bull sperm p80 protein at the nucleic and amino acid levels to determine whether it is the bovine PH-20 ortholog. The complete nucleotide sequence determined by RT-PCR, 3' and 5' RACE show that bull p80, displays identity with the PH-20 nucleotide and amino acid sequences. Messenger RNA and protein expressions determined by Northern blot and immunohistochemistry revealed that the protein is testicular (expressed in spermatocytes and spermatids). The localization of p80 on spermatozoa, determined by indirect immunofluorescence using a monoclonal antibody, shows the protein in acrosomal and post acrosomal areas of the head with an increase in the signal intensity as sperm progress through the epididymis. Post-translational modifications of the protein were investigated during the epididymal maturation by Western blot on protein extracts from sperm collected in the caput, corpus and cauda portions of bull epididymis. Glycolysation status of sperm p80 protein on proteins from ejaculated and epididymidal sperm was investigated. Result show that the glycosylation status is modified as spermatozoa migrate through the epididymis. Hyaluronidase activity evaluated in protein extracts from spermatozoa of the three different epididymal sections revealed that the activity is higher at pH 7 than 4 and is not affected by epididymal maturation. These data strongly suggest that p80 is the bovine PH-20.
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Affiliation(s)
- Guillaume Morin
- Département d'Obstétrique/Gynécologie, Université Laval, Centre de recherche du CHUQ, Québec, Canada
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Abstract
This paper presents the partial characterization and the identification of an 80-kDa protein detected in bull spermatozoa using a monoclonal antibody directed against a 16-amino acid long peptide from the N-terminal domain of the protooncogene p60(src) from the Rous Sarcoma Virus When subjected to two-dimensional electrophoresis, this 80-kDa protein migrated as several isoforms, with an isoelectric point ranging from 7.4 to 8.2. Amino acid sequence analysis of a peptide obtained following trypsin digestion of the bull sperm protein showed homology to the PH-20/hyaluronidase precursor sperm protein. As for PH-20, this bull sperm 80-kDa protein is located at the plasma membrane surface in the postacrosomal region of the head. An increased immunolabeling in the anterior head region of fixed/permeabilized spermatozoa was observed when these cells were incubated under capacitating conditions, whereas most sperm cells challenged with the calcium ionophore A23187 to acrosome react lost their labeling almost completely. As for the PH-20 protein, the 80-kDa bull sperm protein possesses a hyaluronidase activity that is higher at pH 7.0 than at pH 4.0 in an in-gel assay. Unlike what has been observed in the guinea pig, mouse, and human PH-20, this 80-kDa protein was not released from the surface of bull spermatozoa by treatment with phosphatidylinositol-specific phospholipase C or with trypsin. However, this protein was not sedimented by a 100,000 x g centrifugation after nitrogen cavitation, which suggests that the 80-kDa protein is loosely attached to the sperm membrane by a yet-unknown mechanism. These results suggest that the 80-kDa bull sperm protein shares many homologies with the sperm PH-20 protein reported in the literature and, most likely, is the bull sperm homologue of the PH-20.
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Affiliation(s)
- C Lalancette
- Département d'Obstétrique/Gynécologie, Université Laval, Centre de Recherche du CHUQ and Centre de Recherche en Biologie de la Reproduction, Quebec, Canada G1L 3L5
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