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Jin K, McCoy BM, Goldman EA, Usova V, Tkachev V, Chitsazan AD, Kakebeen A, Jeffery U, Creevy KE, Wills A, Snyder‐Mackler N, Promislow DEL. DNA methylation and chromatin accessibility predict age in the domestic dog. Aging Cell 2024; 23:e14079. [PMID: 38263575 PMCID: PMC11019125 DOI: 10.1111/acel.14079] [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: 11/10/2021] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Across mammals, the epigenome is highly predictive of chronological age. These "epigenetic clocks," most of which have been built using DNA methylation (DNAm) profiles, have gained traction as biomarkers of aging and organismal health. While the ability of DNAm to predict chronological age has been repeatedly demonstrated, the ability of other epigenetic features to predict age remains unclear. Here, we use two types of epigenetic information-DNAm, and chromatin accessibility as measured by ATAC-seq-to develop age predictors in peripheral blood mononuclear cells sampled from a population of domesticated dogs. We measured DNAm and ATAC-seq profiles for 71 dogs, building separate predictive clocks from each, as well as the combined dataset. We also use fluorescence-assisted cell sorting to quantify major lymphoid populations for each sample. We found that chromatin accessibility can accurately predict chronological age (R2 ATAC = 26%), though less accurately than the DNAm clock (R2 DNAm = 33%), and the clock built from the combined datasets was comparable to both (R2 combined = 29%). We also observed various populations of CD62L+ T cells significantly correlated with dog age. Finally, we found that all three clocks selected features that were in or near at least two protein-coding genes: BAIAP2 and SCARF2, both previously implicated in processes related to cognitive or neurological impairment. Taken together, these results highlight the potential of chromatin accessibility as a complementary epigenetic resource for modeling and investigating biologic age.
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Affiliation(s)
- Kelly Jin
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Brianah M. McCoy
- Center for Evolution and MedicineArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | | | - Viktoria Usova
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Victor Tkachev
- Division of Pediatric Hematology/OncologyBoston Children's HospitalBostonMassachusettsUSA
- Dana Farber Cancer InstituteBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Alex D. Chitsazan
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Anneke Kakebeen
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Unity Jeffery
- College of Veterinary MedicineTexas A & M UniversityCollege StationTexasUSA
| | - Kate E. Creevy
- College of Veterinary MedicineTexas A & M UniversityCollege StationTexasUSA
| | - Andrea Wills
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Noah Snyder‐Mackler
- Center for Evolution and MedicineArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Daniel E. L. Promislow
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
- Department of BiologyUniversity of WashingtonSeattleWashingtonUSA
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Pang AWC, Kosco K, Sahajpal NS, Sridhar A, Hauenstein J, Clifford B, Estabrook J, Chitsazan AD, Sahoo T, Iqbal A, Kolhe R, Raca G, Hastie AR, Chaubey A. Analytic Validation of Optical Genome Mapping in Hematological Malignancies. Biomedicines 2023; 11:3263. [PMID: 38137484 PMCID: PMC10741484 DOI: 10.3390/biomedicines11123263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/23/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Standard-of-care (SOC) methods such as karyotyping and fluorescence in situ hybridization (FISH), which have been employed globally for the past three decades, have significant limitations in terms of resolution and the number of recurrent aberrations that can be simultaneously assessed, respectively. Next-generation sequencing (NGS)-based technologies are now widely used to detect clinically significant sequence variants but are limited in their ability to accurately detect SVs. Optical genome mapping (OGM) is an emerging technology enabling the genome-wide detection of all classes of SVs at a significantly higher resolution than karyotyping and FISH. OGM requires neither cultured cells nor amplification of DNA, addressing the limitations of culture and amplification biases. This study reports the clinical validation of OGM as a laboratory-developed test (LDT) according to stringent regulatory (CAP/CLIA) guidelines for genome-wide SV detection in different hematological malignancies. In total, 60 cases with hematological malignancies (of various subtypes), 18 controls, and 2 cancer cell lines were used for this study. Ultra-high-molecular-weight DNA was extracted from the samples, fluorescently labeled, and run on the Bionano Saphyr system. A total of 215 datasets, Inc.luding replicates, were generated, and analyzed successfully. Sample data were then analyzed using either disease-specific or pan-cancer-specific BED files to prioritize calls that are known to be diagnostically or prognostically relevant. Sensitivity, specificity, and reproducibility were 100%, 100%, and 96%, respectively. Following the validation, 14 cases and 10 controls were run and analyzed using OGM at three outside laboratories showing reproducibility of 96.4%. OGM found more clinically relevant SVs compared to SOC testing due to its ability to detect all classes of SVs at higher resolution. The results of this validation study demonstrate the superiority of OGM over traditional SOC methods for the detection of SVs for the accurate diagnosis of various hematological malignancies.
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Affiliation(s)
| | | | - Nikhil S. Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | | | | | | | | | | | | | - Anwar Iqbal
- DNA Microarray CGH Laboratory, Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA
| | - Alex R. Hastie
- Bionano, San Diego, CA 92121, USA; (A.W.C.P.)
- Bionano Laboratories, San Diego, CA 92121, USA
| | - Alka Chaubey
- Bionano, San Diego, CA 92121, USA; (A.W.C.P.)
- Bionano Laboratories, San Diego, CA 92121, USA
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Wilkerson BA, Zebroski HL, Finkbeiner CR, Chitsazan AD, Beach KE, Sen N, Zhang RC, Bermingham-McDonogh O. Novel cell types and developmental lineages revealed by single-cell RNA-seq analysis of the mouse crista ampullaris. eLife 2021; 10:e60108. [PMID: 34003106 PMCID: PMC8189719 DOI: 10.7554/elife.60108] [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: 06/16/2020] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
This study provides transcriptomic characterization of the cells of the crista ampullaris, sensory structures at the base of the semicircular canals that are critical for vestibular function. We performed single-cell RNA-seq on ampullae microdissected from E16, E18, P3, and P7 mice. Cluster analysis identified the hair cells, support cells and glia of the crista as well as dark cells and other nonsensory epithelial cells of the ampulla, mesenchymal cells, vascular cells, macrophages, and melanocytes. Cluster-specific expression of genes predicted their spatially restricted domains of gene expression in the crista and ampulla. Analysis of cellular proportions across developmental time showed dynamics in cellular composition. The new cell types revealed by single-cell RNA-seq could be important for understanding crista function and the markers identified in this study will enable the examination of their dynamics during development and disease.
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Affiliation(s)
- Brent A Wilkerson
- Department of Biological Structure, University of WashingtonSeattleUnited States
- Institute for Stem Cells and Regenerative Medicine, University of WashingtonSeattleUnited States
| | - Heather L Zebroski
- Department of Biological Structure, University of WashingtonSeattleUnited States
- Institute for Stem Cells and Regenerative Medicine, University of WashingtonSeattleUnited States
| | - Connor R Finkbeiner
- Department of Biological Structure, University of WashingtonSeattleUnited States
- Institute for Stem Cells and Regenerative Medicine, University of WashingtonSeattleUnited States
| | - Alex D Chitsazan
- Department of Biological Structure, University of WashingtonSeattleUnited States
- Institute for Stem Cells and Regenerative Medicine, University of WashingtonSeattleUnited States
- Department of Biochemistry, University of WashingtonSeattleUnited States
| | - Kylie E Beach
- Department of Biological Structure, University of WashingtonSeattleUnited States
- Institute for Stem Cells and Regenerative Medicine, University of WashingtonSeattleUnited States
| | - Nilasha Sen
- Department of Biological Structure, University of WashingtonSeattleUnited States
| | - Renee C Zhang
- Department of Biological Structure, University of WashingtonSeattleUnited States
| | - Olivia Bermingham-McDonogh
- Department of Biological Structure, University of WashingtonSeattleUnited States
- Institute for Stem Cells and Regenerative Medicine, University of WashingtonSeattleUnited States
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Tettey TT, Gao X, Shao W, Li H, Story BA, Chitsazan AD, Glaser RL, Goode ZH, Seidel CW, Conaway RC, Zeitlinger J, Blanchette M, Conaway JW. A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing. Cell Rep 2020; 27:3770-3779.e7. [PMID: 31242411 DOI: 10.1016/j.celrep.2019.05.099] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 04/22/2019] [Accepted: 05/24/2019] [Indexed: 01/06/2023] Open
Abstract
FACT (facilitates chromatin transcription) is an evolutionarily conserved histone chaperone that was initially identified as an activity capable of promoting RNA polymerase II (Pol II) transcription through nucleosomes in vitro. In this report, we describe a global analysis of FACT function in Pol II transcription in Drosophila. We present evidence that loss of FACT has a dramatic impact on Pol II elongation-coupled processes including histone H3 lysine 4 (H3K4) and H3K36 methylation, consistent with a role for FACT in coordinating histone modification and chromatin architecture during Pol II transcription. Importantly, we identify a role for FACT in the maintenance of promoter-proximal Pol II pausing, a key step in transcription activation in higher eukaryotes. These findings bring to light a broader role for FACT in the regulation of Pol II transcription.
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Affiliation(s)
- Theophilus T Tettey
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; The Open University, Walton Hall, Milton Keynes, Buckinghamshire MK7 6AA, UK
| | - Xin Gao
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Wanqing Shao
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Benjamin A Story
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Alex D Chitsazan
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Robert L Glaser
- Wadsworth Center, New York State Department of Health, PO Box 509, Albany, NY 12201, USA
| | - Zach H Goode
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Christopher W Seidel
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Marco Blanchette
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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Affiliation(s)
| | - Alex D Chitsazan
- Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Chris W Seidel
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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