1
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Nguyen ED, Ding CKC, Umetsu SE, Choi WT, Ferrell LD, Wen KW. Use of orcein as an adjunct stain in the evaluation of advanced liver fibrosis. Histopathology 2023; 83:538-545. [PMID: 37222207 DOI: 10.1111/his.14962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/24/2023] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
AIMS Advanced liver fibrosis can regress following the elimination of causative injuries. Trichrome (TC) stain has traditionally been used to evaluate the degree of fibrosis in liver, although it is rarely helpful in assessing quality of fibrosis (i.e. progression and regression). Orcein (OR) stain highlights established elastic fibres, but its use in examining fibrosis is not well recognised. This study assessed the potential utility of comparing OR and TC staining patterns to evaluate the quality of fibrosis in various settings of advanced fibrosis. METHODS AND RESULTS The haematoxylin and eosin and TC stains of 65 liver resection/explant specimens with advanced fibrosis caused by different elements were reviewed. Twenty-two cases were scored as progressive (P), 16 as indeterminate (I) and 27 as regressive (R) using TC stain based on the Beijing criteria. The OR stains confirmed 18 of 22 P cases. The remaining P cases showed either stable fibrosis or mixed P and R. Of the 27 R cases, 26 were supported by OR stain, with many showing thin perforated septa typically seen in adequately treated viral hepatitis cases. The 16 I cases showed a variety of OR staining patterns, which allowed for further subclassification than using TC stain alone. Viral hepatitis cases were enriched for regressive features (17 of 27). CONCLUSIONS Our data demonstrated the utility of OR as an adjunctive stain to evaluate the changes in fibrosis in cases of cirrhosis.
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Affiliation(s)
- Eric D Nguyen
- Department of Pathology, University of California, San Francisco, CA, USA
| | | | - Sarah E Umetsu
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Won-Tak Choi
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Linda D Ferrell
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Kwun Wah Wen
- Department of Pathology, University of California, San Francisco, CA, USA
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2
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Nguyen ED, Wang D, Lauwers GY, Choi WT. Increased Histologic Inflammation is an Independent Risk Factor for Non-Conventional Dysplasia in Ulcerative Colitis. Histopathology 2022; 81:644-652. [PMID: 35942654 DOI: 10.1111/his.14765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/18/2022] [Accepted: 08/05/2022] [Indexed: 11/28/2022]
Abstract
AIMS Several types of non-conventional dysplasia have been described in inflammatory bowel disease. Hypermucinous, goblet cell deficient, and crypt cell dysplasias are considered high-risk subtypes, as they often have molecular features of advanced neoplasia (e.g., aneuploidy) and are more frequently associated with advanced neoplasia than conventional dysplasia. This study investigated if increased colonic inflammation is a risk factor for non-conventional dysplasia. METHODS AND RESULTS A cohort of 125 patients with ulcerative colitis (UC)-associated dysplasia were analyzed and compared with 50 control UC patients without a history of neoplasia. For each patient, all biopsies prior to the initial detection of dysplasia were scored using a 4-point inflammatory activity score. Both mean and maximum scores from all biopsies taken during each colonoscopy were derived. Inflammation burden was calculated by multiplying average maximum score between each pair of surveillance episodes by length of surveillance interval in years. The average scores of all colonoscopies were used to calculate overall mean, maximum, and inflammation burden scores. In multivariate analyses, higher maximum (odds ratio [OR] 3.4) and inflammation burden (OR 4.2) scores were significantly associated with the detection of dysplasia (p < 0.05). Similarly, higher mean and maximum scores increased the odds of non-conventional dysplasia by 2.7 and 4.9, respectively (p < 0.05). There was a stronger association between these two scores and high-risk subtypes (ORs 4.0 and 7.5, respectively, p < 0.05). CONCLUSIONS The risk of non-conventional dysplasia is significantly associated with increased inflammation, which may contribute to its higher rates of aneuploidy and malignancy.
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Affiliation(s)
- Eric D Nguyen
- University of California at San Francisco, Department of Pathology, San Francisco, CA, 94143, USA
| | - Dongliang Wang
- SUNY Upstate Medical University, Department of Public Health and Preventive Medicine, Syracuse, NY, 13210, USA
| | - Gregory Y Lauwers
- H. Lee Moffitt Cancer Center and Research Institute, Department of Pathology, Tampa, FL, 33612, USA
| | - Won-Tak Choi
- University of California at San Francisco, Department of Pathology, San Francisco, CA, 94143, USA
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3
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Wheeler JR, Whitney ON, Vogler TO, Nguyen ED, Pawlikowski B, Lester E, Cutler A, Elston T, Dalla Betta N, Parker KR, Yost KE, Vogel H, Rando TA, Chang HY, Johnson AM, Parker R, Olwin BB. RNA-binding proteins direct myogenic cell fate decisions. eLife 2022; 11:e75844. [PMID: 35695839 PMCID: PMC9191894 DOI: 10.7554/elife.75844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
RNA-binding proteins (RBPs), essential for skeletal muscle regeneration, cause muscle degeneration and neuromuscular disease when mutated. Why mutations in these ubiquitously expressed RBPs orchestrate complex tissue regeneration and direct cell fate decisions in skeletal muscle remains poorly understood. Single-cell RNA-sequencing of regenerating Mus musculus skeletal muscle reveals that RBP expression, including the expression of many neuromuscular disease-associated RBPs, is temporally regulated in skeletal muscle stem cells and correlates with specific stages of myogenic differentiation. By combining machine learning with RBP engagement scoring, we discovered that the neuromuscular disease-associated RBP Hnrnpa2b1 is a differentiation-specifying regulator of myogenesis that controls myogenic cell fate transitions during terminal differentiation in mice. The timing of RBP expression specifies cell fate transitions by providing post-transcriptional regulation of messenger RNAs that coordinate stem cell fate decisions during tissue regeneration.
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Affiliation(s)
- Joshua R Wheeler
- Department of Biochemistry, University of ColoradoBoulderUnited States
- Medical Scientist Training Program, University of Colorado Anschutz Medical CampusAuroraUnited States
- Howard Hughes Medical Institute, University of ColoradoBoulderUnited States
- Department of Pathology, Stanford UniversityStanfordUnited States
- Department of Neuropathology, Stanford UniversityStanfordUnited States
| | - Oscar N Whitney
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Thomas O Vogler
- Medical Scientist Training Program, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Molecular, Cellular and Developmental Biology, University of ColoradoBoulderUnited States
- Department of Surgery, University of ColoradoAuroraUnited States
| | - Eric D Nguyen
- Medical Scientist Training Program, University of Colorado Anschutz Medical CampusAuroraUnited States
- Molecular Biology Program and Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Bradley Pawlikowski
- Department of Molecular, Cellular and Developmental Biology, University of ColoradoBoulderUnited States
| | - Evan Lester
- Department of Biochemistry, University of ColoradoBoulderUnited States
- Medical Scientist Training Program, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Alicia Cutler
- Department of Molecular, Cellular and Developmental Biology, University of ColoradoBoulderUnited States
| | - Tiffany Elston
- Department of Molecular, Cellular and Developmental Biology, University of ColoradoBoulderUnited States
| | - Nicole Dalla Betta
- Department of Molecular, Cellular and Developmental Biology, University of ColoradoBoulderUnited States
| | - Kevin R Parker
- Center for Personal and Dynamic Regulomes, Stanford UniversityPalo AltoUnited States
| | - Kathryn E Yost
- Center for Personal and Dynamic Regulomes, Stanford UniversityPalo AltoUnited States
| | - Hannes Vogel
- Department of Pathology, Stanford UniversityStanfordUnited States
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of MedicineStanfordUnited States
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of MedicineStanfordUnited States
- Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Health Care SystemPalo AltoUnited States
| | - Howard Y Chang
- Center for Personal and Dynamic Regulomes, Stanford UniversityPalo AltoUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Aaron M Johnson
- Molecular Biology Program and Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
- University of Colorado School of Medicine, RNA Bioscience Initiative, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Roy Parker
- Howard Hughes Medical Institute, University of ColoradoBoulderUnited States
| | - Bradley B Olwin
- Department of Molecular, Cellular and Developmental Biology, University of ColoradoBoulderUnited States
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4
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Wu AHB, Nguyen ED, Ong CM, Yun C, Lynch KL. Rate of Serum SARS-CoV-2 Antibody Decline for Two mRNA Vaccines. J Appl Lab Med 2022; 7:625-627. [PMID: 34648027 PMCID: PMC8524641 DOI: 10.1093/jalm/jfab137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/17/2021] [Indexed: 11/14/2022]
Affiliation(s)
- Alan H B Wu
- University of California, San Francisco, San Francisco, CA, 94110
| | - Eric D Nguyen
- University of California, San Francisco, San Francisco, CA, 94110
| | - Chui Mei Ong
- University of California, San Francisco, San Francisco, CA, 94110
| | - Cassandra Yun
- University of California, San Francisco, San Francisco, CA, 94110
| | - Kara L Lynch
- University of California, San Francisco, San Francisco, CA, 94110
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5
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Gu W, Rauschecker AM, Hsu E, Zorn KC, Sucu Y, Federman S, Gopez A, Arevalo S, Sample HA, Talevich E, Nguyen ED, Gottschall M, Nourbakhsh B, Gold CA, Cree BAC, Douglas VC, Richie MB, Shah MP, Josephson SA, Gelfand JM, Miller S, Wang L, Tihan T, DeRisi JL, Chiu CY, Wilson MR. Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid. JAMA Neurol 2021; 78:1355-1366. [PMID: 34515766 DOI: 10.1001/jamaneurol.2021.3088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Importance Cerebrospinal fluid (CSF) cytologic testing and flow cytometry are insensitive for diagnosing neoplasms of the central nervous system (CNS). Such clinical phenotypes can mimic infectious and autoimmune causes of meningoencephalitis. Objective To ascertain whether CSF metagenomic next-generation sequencing (mNGS) can identify aneuploidy, a hallmark of malignant neoplasms, in difficult-to-diagnose cases of CNS malignant neoplasm. Design, Setting, and Participants Two case-control studies were performed at the University of California, San Francisco (UCSF). The first study used CSF specimens collected at the UCSF Clinical Laboratories between July 1, 2017, and December 31, 2019, and evaluated test performance in specimens from patients with a CNS malignant neoplasm (positive controls) or without (negative controls). The results were compared with those from CSF cytologic testing and/or flow cytometry. The second study evaluated patients who were enrolled in an ongoing prospective study between April 1, 2014, and July 31, 2019, with presentations that were suggestive of neuroinflammatory disease but who were ultimately diagnosed with a CNS malignant neoplasm. Cases of individuals whose tumors could have been detected earlier without additional invasive testing are discussed. Main Outcomes and Measures The primary outcome measures were the sensitivity and specificity of aneuploidy detection by CSF mNGS. Secondary subset analyses included a comparison of CSF and tumor tissue chromosomal abnormalities and the identification of neuroimaging characteristics that were associated with test performance. Results Across both studies, 130 participants were included (median [interquartile range] age, 57.5 [43.3-68.0] years; 72 men [55.4%]). The test performance study used 125 residual laboratory CSF specimens from 47 patients with a CNS malignant neoplasm and 56 patients with other neurological diseases. The neuroinflammatory disease study enrolled 12 patients and 17 matched control participants. The sensitivity of the CSF mNGS assay was 75% (95% CI, 63%-85%), and the specificity was 100% (95% CI, 96%-100%). Aneuploidy was detected in 64% (95% CI, 41%-83%) of the patients in the test performance study with nondiagnostic cytologic testing and/or flow cytometry, and in 55% (95% CI, 23%-83%) of patients in the neuroinflammatory disease study who were ultimately diagnosed with a CNS malignant neoplasm. Of the patients in whom aneuploidy was detected, 38 (90.5%) had multiple copy number variations with tumor fractions ranging from 31% to 49%. Conclusions and Relevance This case-control study showed that CSF mNGS, which has low specimen volume requirements, does not require the preservation of cell integrity, and was orginally developed to diagnose neurologic infections, can also detect genetic evidence of a CNS malignant neoplasm in patients in whom CSF cytologic testing and/or flow cytometry yielded negative results with a low risk of false-positive results.
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Affiliation(s)
- Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco.,Department of Pathology, Stanford University, Stanford, California
| | - Andreas M Rauschecker
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco
| | - Yasemin Sucu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Allan Gopez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Shaun Arevalo
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Hannah A Sample
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco
| | | | - Eric D Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Marc Gottschall
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Bardia Nourbakhsh
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland
| | - Carl A Gold
- Department of Neurology, Stanford University, Stanford, California
| | - Bruce A C Cree
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco
| | - Vanja C Douglas
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco
| | - Megan B Richie
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco
| | - Maulik P Shah
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco
| | - S Andrew Josephson
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco.,Editor in Chief, JAMA Neurology
| | - Jeffrey M Gelfand
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Linlin Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Tarik Tihan
- Department of Pathology, University of California, San Francisco, San Francisco
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco.,Chan Zuckerberg Biohub, San Francisco, California
| | - Charles Y Chiu
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California.,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco
| | - Michael R Wilson
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco
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6
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Nguyen ED, Balas MM, Griffin AM, Roberts JT, Johnson AM. Global profiling of hnRNP A2/B1-RNA binding on chromatin highlights LncRNA interactions. RNA Biol 2018; 15:901-913. [PMID: 29938567 PMCID: PMC6161681 DOI: 10.1080/15476286.2018.1474072] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/02/2018] [Indexed: 01/03/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) often carry out their functions through associations with adaptor proteins. We recently identified heterogeneous ribonucleoprotein (hnRNP) A2/B1 as an adaptor of the human HOTAIR lncRNA. hnRNP A2 and B1 are splice isoforms of the same gene. The spliced version of HOTAIR preferentially associates with the B1 isoform, which we hypothesize contributes to RNA-RNA matching between HOTAIR and transcripts of target genes in breast cancer. Here we used enhanced cross-linking immunoprecipitation (eCLIP) to map the direct interactions between A2/B1 and RNA in breast cancer cells. Despite differing by only twelve amino acids, the A2 and B1 splice isoforms associate preferentially with distinct populations of RNA in vivo. Through cellular fractionation experiments we characterize the pattern of RNA association in chromatin, nucleoplasm, and cytoplasm. We find that a majority of interactions occur on chromatin, even those that do not contribute to co-transcriptional splicing. A2/B1 binding site locations on multiple RNAs hint at a contribution to the regulation and function of lncRNAs. Surprisingly, the strongest A2/B1 binding site occurs in a retained intron of HOTAIR, which interrupts an RNA-RNA interaction hotspot. In vitro eCLIP experiments highlight additional exonic B1 binding sites in HOTAIR which also surround the RNA-RNA interaction hotspot. Interestingly, a version of HOTAIR with the intron retained is still capable of making RNA-RNA interactions in vitro through the hotspot region. Our data further characterize the multiple functions of a repurposed splicing factor with isoform-biased interactions, and highlight that the majority of these functions occur on chromatin-associated RNA.
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Affiliation(s)
- Eric D. Nguyen
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
- Department of Biochemistry and Molecular Genetics, Aurora, University of Colorado School of Medicine, CO, USA
- Medical Scientist Training Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Maggie M. Balas
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
- Department of Biochemistry and Molecular Genetics, Aurora, University of Colorado School of Medicine, CO, USA
- University of Colorado School of Medicine RNA Bioscience Initiative, Aurora, CO, USA
| | - April M. Griffin
- Department of Biochemistry and Molecular Genetics, Aurora, University of Colorado School of Medicine, CO, USA
| | - Justin T. Roberts
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
- Department of Biochemistry and Molecular Genetics, Aurora, University of Colorado School of Medicine, CO, USA
| | - Aaron M. Johnson
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
- Department of Biochemistry and Molecular Genetics, Aurora, University of Colorado School of Medicine, CO, USA
- University of Colorado School of Medicine RNA Bioscience Initiative, Aurora, CO, USA
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7
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Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, Sandstrom R, Bates D, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Harding L, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome. Nature 2012; 489:75-82. [PMID: 22955617 PMCID: PMC3721348 DOI: 10.1038/nature11232] [Citation(s) in RCA: 1898] [Impact Index Per Article: 158.2] [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: 12/15/2011] [Accepted: 05/15/2012] [Indexed: 02/07/2023]
Abstract
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect ∼580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation.
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Affiliation(s)
- Robert E. Thurman
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Eric Rynes
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Richard Humbert
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | | | - Hao Wang
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Benjamin Vernot
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Kavita Garg
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Daniel Bates
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Douglas Dunn
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Abigail K. Ebersol
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Tristan Frum
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Erika Giste
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Lisa Harding
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Audra K. Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Ericka M. Johnson
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Tanya Kutyavin
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Bryan Lajoie
- Program in Gene Function, University of Massachusetts Medical School, Worcester, MA
| | - Bum-Kyu Lee
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX
| | - Kristen Lee
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Darin London
- Institute for Genome Sciences and Policy, Duke University, Durham, NC
| | - Dimitra Lotakis
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Fidencio Neri
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Eric D. Nguyen
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Alex P. Reynolds
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Vaughn Roach
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alexias Safi
- Institute for Genome Sciences and Policy, Duke University, Durham, NC
| | - Minerva E. Sanchez
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Amartya Sanyal
- Program in Gene Function, University of Massachusetts Medical School, Worcester, MA
| | - Anthony Shafer
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Jeremy M. Simon
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Lingyun Song
- Institute for Genome Sciences and Policy, Duke University, Durham, NC
| | - Shinny Vong
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Molly Weaver
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Zhancheng Zhang
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Zhuzhu Zhang
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Boris Lenhard
- Bergen Center for Computational Science, University of Bergen, Bergen, Norway
| | - Muneesh Tewari
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Michael O. Dorschner
- Dept. of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA
| | - R. Scott Hansen
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Patrick A. Navas
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | | | - Vishwanath R. Iyer
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX
| | - Jason D. Lieb
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Shamil R. Sunyaev
- Dept. of Medicine, Division of Genetics, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Peter J. Sabo
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Rajinder Kaul
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Terrence S. Furey
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Job Dekker
- Program in Gene Function, University of Massachusetts Medical School, Worcester, MA
| | | | - John A. Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Medicine, Division of Oncology, University of Washington, Seattle, WA
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8
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Abstract
Proteins involved in reproductive fitness have evolved unusually rapidly across diverse groups of organisms. These reproductive proteins show unusually high rates of amino acid substitutions, suggesting that the proteins have been subject to positive selection. We sought to identify seminal fluid proteins experiencing adaptive evolution because such proteins are often involved in sperm competition, host immunity to pathogens, and manipulation of female reproductive physiology and behavior. We performed an evolutionary screen of the mouse prostate transcriptome for genes with elevated evolutionary rates between mouse and rat. We observed that secreted rodent prostate proteins evolve approximately twice as fast as nonsecreted proteins, remarkably similar to findings in the primate prostate and in the Drosophila male accessory gland. Our screen led us to identify and characterize a group of seminal vesicle secretion (Svs) proteins and to show that the gene Svs7 is evolving very rapidly, with many amino acid sites under positive selection. Another gene in this group, Svs5, showed evidence of branch-specific selection in the rat. We also found that Svs7 is under selection in primates and, by using three-dimensional models, demonstrated that the same regions have been under selection in both groups. Svs7 has been identified as mouse caltrin, a protein involved in sperm capacitation, the process responsible for the timing of changes in sperm activity and behavior, following ejaculation. We propose that the most likely explanation of the adaptive evolution of Svs7 that we have observed in rodents and primates stems from an important function in sperm competition.
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Affiliation(s)
- Robert C Karn
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
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