1
|
Yu H, Khanshour AM, Ushiki A, Otomo N, Koike Y, Einarsdottir E, Fan Y, Antunes L, Kidane YH, Cornelia R, Sheng RR, Zhang Y, Pei J, Grishin NV, Evers BM, Cheung JPY, Herring JA, Terao C, Song YQ, Gurnett CA, Gerdhem P, Ikegawa S, Rios JJ, Ahituv N, Wise CA. Association of genetic variation in COL11A1 with adolescent idiopathic scoliosis. eLife 2024; 12:RP89762. [PMID: 38277211 PMCID: PMC10945706 DOI: 10.7554/elife.89762] [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] [Indexed: 01/27/2024] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is a common and progressive spinal deformity in children that exhibits striking sexual dimorphism, with girls at more than fivefold greater risk of severe disease compared to boys. Despite its medical impact, the molecular mechanisms that drive AIS are largely unknown. We previously defined a female-specific AIS genetic risk locus in an enhancer near the PAX1 gene. Here, we sought to define the roles of PAX1 and newly identified AIS-associated genes in the developmental mechanism of AIS. In a genetic study of 10,519 individuals with AIS and 93,238 unaffected controls, significant association was identified with a variant in COL11A1 encoding collagen (α1) XI (rs3753841; NM_080629.2_c.4004C>T; p.(Pro1335Leu); p=7.07E-11, OR = 1.118). Using CRISPR mutagenesis we generated Pax1 knockout mice (Pax1-/-). In postnatal spines we found that PAX1 and collagen (α1) XI protein both localize within the intervertebral disc-vertebral junction region encompassing the growth plate, with less collagen (α1) XI detected in Pax1-/- spines compared to wild-type. By genetic targeting we found that wild-type Col11a1 expression in costal chondrocytes suppresses expression of Pax1 and of Mmp3, encoding the matrix metalloproteinase 3 enzyme implicated in matrix remodeling. However, the latter suppression was abrogated in the presence of the AIS-associated COL11A1P1335L mutant. Further, we found that either knockdown of the estrogen receptor gene Esr2 or tamoxifen treatment significantly altered Col11a1 and Mmp3 expression in chondrocytes. We propose a new molecular model of AIS pathogenesis wherein genetic variation and estrogen signaling increase disease susceptibility by altering a PAX1-COL11a1-MMP3 signaling axis in spinal chondrocytes.
Collapse
Affiliation(s)
- Hao Yu
- Center for Translational Research, Scottish Rite for ChildrenDallasUnited States
| | - Anas M Khanshour
- Center for Translational Research, Scottish Rite for ChildrenDallasUnited States
| | - Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Institute for Human Genetics, University of California, San FranciscoSan FranciscoUnited States
| | - Nao Otomo
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical SciencesTokyoJapan
| | - Yoshinao Koike
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical SciencesTokyoJapan
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Elisabet Einarsdottir
- Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of TechnologySolnaSweden
| | - Yanhui Fan
- School of Biomedical Sciences, The University of Hong KongHong Kong SARChina
| | - Lilian Antunes
- Department of Neurology, Washington University in St. LouisSt. LouisUnited States
| | - Yared H Kidane
- Center for Translational Research, Scottish Rite for ChildrenDallasUnited States
| | - Reuel Cornelia
- Center for Translational Research, Scottish Rite for ChildrenDallasUnited States
| | - Rory R Sheng
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Institute for Human Genetics, University of California, San FranciscoSan FranciscoUnited States
| | - Yichi Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Institute for Human Genetics, University of California, San FranciscoSan FranciscoUnited States
- School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
| | - Jimin Pei
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Bret M Evers
- Department of Pathology, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Ophthalmology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Jason Pui Yin Cheung
- Department of Orthopaedics and Traumatology LKS Faculty of Medicine, The University of Hong KongHong Kong SARChina
| | - John A Herring
- Department of Orthopedic Surgery, Scottish Rite for ChildrenDallasUnited States
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical CenterDallasUnited States
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - You-qiang Song
- School of Biomedical Sciences, The University of Hong KongHong Kong SARChina
| | - Christina A Gurnett
- Department of Neurology, Washington University in St. LouisSt. LouisUnited States
| | - Paul Gerdhem
- Department of Surgical Sciences, Uppsala UniversityUppsalaSweden
- Department of Orthopaedics and Hand Surgery, Uppsala University HospitalUppsalaSweden
- Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, Stockholm, Uppsala UniversityUppsalaSweden
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical SciencesTokyoJapan
| | - Jonathan J Rios
- Center for Translational Research, Scottish Rite for ChildrenDallasUnited States
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical CenterDallasUnited States
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Pediatrics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Institute for Human Genetics, University of California, San FranciscoSan FranciscoUnited States
| | - Carol A Wise
- Center for Translational Research, Scottish Rite for ChildrenDallasUnited States
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical CenterDallasUnited States
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Pediatrics, University of Texas Southwestern Medical CenterDallasUnited States
| |
Collapse
|
2
|
Yu H, Khanshour AM, Ushiki A, Otomo N, Koike Y, Einarsdottir E, Fan Y, Antunes L, Kidane YH, Cornelia R, Sheng R, Zhang Y, Pei J, Grishin NV, Evers BM, Cheung JPY, Herring JA, Terao C, Song YQ, Gurnett CA, Gerdhem P, Ikegawa S, Rios JJ, Ahituv N, Wise CA. Association of genetic variation in COL11A1 with adolescent idiopathic scoliosis. bioRxiv 2023:2023.05.26.542293. [PMID: 37292598 PMCID: PMC10245954 DOI: 10.1101/2023.05.26.542293] [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: 06/10/2023]
Abstract
Adolescent idiopathic scoliosis (AIS) is a common and progressive spinal deformity in children that exhibits striking sexual dimorphism, with girls at more than five-fold greater risk of severe disease compared to boys. Despite its medical impact, the molecular mechanisms that drive AIS are largely unknown. We previously defined a female-specific AIS genetic risk locus in an enhancer near the PAX1 gene. Here we sought to define the roles of PAX1 and newly-identified AIS-associated genes in the developmental mechanism of AIS. In a genetic study of 10,519 individuals with AIS and 93,238 unaffected controls, significant association was identified with a variant in COL11A1 encoding collagen (α1) XI (rs3753841; NM_080629.2_c.4004C>T; p.(Pro1335Leu); P=7.07e-11, OR=1.118). Using CRISPR mutagenesis we generated Pax1 knockout mice (Pax1-/-). In postnatal spines we found that PAX1 and collagen (α1) XI protein both localize within the intervertebral disc (IVD)-vertebral junction region encompassing the growth plate, with less collagen (α1) XI detected in Pax1-/- spines compared to wildtype. By genetic targeting we found that wildtype Col11a1 expression in costal chondrocytes suppresses expression of Pax1 and of Mmp3, encoding the matrix metalloproteinase 3 enzyme implicated in matrix remodeling. However, this suppression was abrogated in the presence of the AIS-associated COL11A1P1335L mutant. Further, we found that either knockdown of the estrogen receptor gene Esr2, or tamoxifen treatment, significantly altered Col11a1 and Mmp3 expression in chondrocytes. We propose a new molecular model of AIS pathogenesis wherein genetic variation and estrogen signaling increase disease susceptibility by altering a Pax1-Col11a1-Mmp3 signaling axis in spinal chondrocytes.
Collapse
Affiliation(s)
- Hao Yu
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Anas M Khanshour
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Nao Otomo
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, JP
| | - Yoshinao Koike
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, JP
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, JP
| | - Elisabet Einarsdottir
- Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, Solna, SE
| | - Yanhui Fan
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, CN
| | - Lilian Antunes
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Yared H Kidane
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Reuel Cornelia
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Rory Sheng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yichi Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, CN
| | - Jimin Pei
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bret M Evers
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jason Pui Yin Cheung
- Department of Orthopaedics and Traumatology LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, CN
| | - John A Herring
- Department of Orthopedic Surgery, Scottish Rite for Children, Dallas, TX, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, JP
| | - You-Qiang Song
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, CN
| | - Christina A Gurnett
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Paul Gerdhem
- Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, Stockholm, Uppsala University, Uppsala, SE
- Department of Surgical Sciences, Uppsala University and
- Department of Orthopaedics and Hand Surgery, Uppsala University Hospital, Uppsala, SE
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, JP
| | - Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
3
|
Hachem AA, Filkins LM, Kidane YH, Raj P, Tareen NG, Arana CA, Muthukrishnan G, Copley LA. Staphylococcus aureus isolates from children with clinically differentiated osteomyelitis exhibit distinct transcriptomic signatures. PLoS One 2023; 18:e0288758. [PMID: 37561761 PMCID: PMC10414669 DOI: 10.1371/journal.pone.0288758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/04/2023] [Indexed: 08/12/2023] Open
Abstract
There is substantial genomic heterogeneity among Staphylococcus aureus isolates of children with acute hematogenous osteomyelitis (AHO) but transcriptional behavior of clinically differentiated strains has not been previously described. This study evaluates transcriptional activity of S. aureus isolates of children with AHO that may regulate metabolism, biosynthesis, or virulence during bacterial growth and pathogenesis. In vitro growth kinetics were compared between three S. aureus clinical isolates from children with AHO who had mild, moderate, and severe illness. Total RNA sequencing was performed for each isolate at six separate time points throughout the logarithmic phase of growth. The NASA RNA-Sequencing Consensus Pipeline was used to identify differentially expressed genes allowing for 54 comparisons between the three isolates during growth. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathways were used to evaluate transcriptional variation in metabolism, biosynthesis pathways and virulence potential of the isolates. The S. aureus isolates demonstrated differing growth kinetics under standardized conditions with the mild isolate having higher optical densities with earlier and higher peak rates of growth than that of the other isolates (p<0.001). Enrichment pathway analysis established distinct transcriptional signatures according to both sampling time and clinical severity. Moderate and severe isolates demonstrated pathways of bacterial invasion, S. aureus infection, quorum sensing and two component systems. In comparison, the mild strain favored biosynthesis and metabolism. These findings suggest that transcriptional regulation during the growth of S. aureus may impact the pathogenetic mechanisms involved in the progression of severity of illness in childhood osteomyelitis. The clinical isolates studied demonstrated a tradeoff between growth and virulence. Further investigation is needed to evaluate these transcriptional pathways in an animal model or during active clinical infections of children with AHO.
Collapse
Affiliation(s)
- Ahmad A. Hachem
- Department of Pediatrics, University of Florida College of Medicine –Jacksonville, Jacksonville, FL, United States of America
| | - Laura M. Filkins
- Department of Microbiology, University of Texas Southwestern, Children’s Health System of Texas, Dallas, TX, United States of America
| | - Yared H. Kidane
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, United States of America
| | - Prithvi Raj
- Microbiome Research Laboratory, University of Texas Southwestern, Dallas, TX, United States of America
| | - Naureen G. Tareen
- Department of Pediatric Orthopaedic Surgery, Children’s Health System of Texas, Dallas, TX, United States of America
| | - Carlos A. Arana
- Genomics Core, University of Texas Southwestern, Dallas, TX, United States of America
| | - Gowrishankar Muthukrishnan
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Lawson A. Copley
- Department of Pediatric Orthopaedic Surgery, Children’s Health System of Texas, Dallas, TX, United States of America
- Department of Pediatric Orthopaedic Surgery, University of Texas Southwestern, Dallas, TX, United States of America
| |
Collapse
|
4
|
Paria N, Khalid A, Shen B, Lemoine B, Chan J, Kidane YH, Oxendine I, Cornelia R, Wise CA, Rios JJ. Molecular Dissection of Somatic Skeletal Disease in Neurofibromatosis Type 1. J Bone Miner Res 2023; 38:288-299. [PMID: 36459048 PMCID: PMC9898201 DOI: 10.1002/jbmr.4755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/11/2022] [Accepted: 11/26/2022] [Indexed: 12/04/2022]
Abstract
Neurofibromatosis type 1 (NF1) is a tumor predisposition syndrome caused by heterozygous NF1 gene mutations. Patients with NF1 present with pleiotropic somatic secondary manifestations, including development of bone pseudarthrosis after fracture. Somatic NF1 gene mutations were reproducibly identified in patient-derived pseudarthrosis specimens, suggesting a local mosaic cell population including somatic pathologic cells. The somatic cellular pathogenesis of NF1 pseudarthroses remains unclear, though defects in osteogenesis have been posited. Here, we applied time-series single-cell RNA-sequencing (scRNA-seq) to patient-matched control and pseudarthrosis-derived primary bone stromal cells (BSCs). We show that osteogenic specification to an osteoblast progenitor cell population was evident for control bone-derived cells and haploinsufficient pseudarthrosis-derived cells. Similar results were observed for somatic patient fracture-derived NF1-/- cells; however, expression of genetic pathways associated with skeletal mineralization were significantly reduced in NF1-/- cells compared with fracture-derived NF1+/- cells. In mice, we show that Nf1 expressed in bone marrow osteoprogenitors is required for the maintenance of the adult skeleton. Results from our study implicate impaired Clec11a-Itga11-Wnt signaling in the pathogenesis of NF1-associated skeletal disease. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
Collapse
Affiliation(s)
- Nandina Paria
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Aysha Khalid
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Bo Shen
- Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ben Lemoine
- Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Jinyan Chan
- Baylor Scott & White Research Institute, Dallas, TX, USA.,Institute of Biomedical Studies, Baylor University, Waco, TX, USA
| | - Yared H Kidane
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Ila Oxendine
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Reuel Cornelia
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA.,McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA.,McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
5
|
Guarnieri JW, Dybas JM, Fazelinia H, Kim MS, Frere J, Zhang Y, Albrecht YS, Murdock DG, Angelin A, Singh LN, Weiss SL, Best SM, Lott MT, Cope H, Zaksas V, Saravia-Butler A, Meydan C, Foox J, Mozsary C, Kidane YH, Priebe W, Emmett MR, Meller R, Singh U, Bram Y, tenOever BR, Heise MT, Moorman NJ, Madden EA, Taft-Benz SA, Anderson EJ, Sanders WA, Dickmander RJ, Baxter VK, Baylin SB, Wurtele ES, Moraes-Vieira PM, Taylor D, Mason CE, Schisler JC, Schwartz RE, Beheshti A, Wallace DC. TARGETED DOWN REGULATION OF CORE MITOCHONDRIAL GENES DURING SARS-COV-2 INFECTION. bioRxiv 2022:2022.02.19.481089. [PMID: 35233572 PMCID: PMC8887073 DOI: 10.1101/2022.02.19.481089] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Defects in mitochondrial oxidative phosphorylation (OXPHOS) have been reported in COVID-19 patients, but the timing and organs affected vary among reports. Here, we reveal the dynamics of COVID-19 through transcription profiles in nasopharyngeal and autopsy samples from patients and infected rodent models. While mitochondrial bioenergetics is repressed in the viral nasopharyngeal portal of entry, it is up regulated in autopsy lung tissues from deceased patients. In most disease stages and organs, discrete OXPHOS functions are blocked by the virus, and this is countered by the host broadly up regulating unblocked OXPHOS functions. No such rebound is seen in autopsy heart, results in severe repression of genes across all OXPHOS modules. Hence, targeted enhancement of mitochondrial gene expression may mitigate the pathogenesis of COVID-19.
Collapse
Affiliation(s)
- Joseph W. Guarnieri
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Joseph M. Dybas
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Hossein Fazelinia
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Man S. Kim
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
- Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | | | - Yuanchao Zhang
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Yentli Soto Albrecht
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | | | - Alessia Angelin
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Larry N. Singh
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Scott L. Weiss
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Sonja M. Best
- COVID-19 International Research Team
- Rocky Mountain Laboratories NIAID, Hamilton, MT 59840
| | - Marie T. Lott
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Henry Cope
- University of Nottingham, Nottingham, UK
| | - Viktorija Zaksas
- COVID-19 International Research Team
- University of Chicago, Chicago, IL, 60615, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team
- Logyx, LLC, Mountain View, CA 94043, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Cem Meydan
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
| | | | | | - Yared H. Kidane
- COVID-19 International Research Team
- Scottish Rite for Children, Dallas, TX 75219, USA
| | - Waldemar Priebe
- COVID-19 International Research Team
- University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark R. Emmett
- COVID-19 International Research Team
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert Meller
- COVID-19 International Research Team
- Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Urminder Singh
- COVID-19 International Research Team
- Iowa State University, Ames, IA 50011, USA
| | | | | | - Mark T. Heise
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | - Emily A. Madden
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Wes A. Sanders
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Stephen B. Baylin
- COVID-19 International Research Team
- Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team
- Iowa State University, Ames, IA 50011, USA
| | | | - Deanne Taylor
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Christopher E. Mason
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
- New York Genome Center, NY, USA
| | - Jonathan C. Schisler
- COVID-19 International Research Team
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Robert E. Schwartz
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
| | - Afshin Beheshti
- COVID-19 International Research Team
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- KBR, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Douglas C. Wallace
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
- University of Pennsylvania, Philadelphia, PA 19104 USA
| |
Collapse
|
6
|
Overbey EG, Saravia-Butler AM, Zhang Z, Rathi KS, Fogle H, da Silveira WA, Barker RJ, Bass JJ, Beheshti A, Berrios DC, Blaber EA, Cekanaviciute E, Costa HA, Davin LB, Fisch KM, Gebre SG, Geniza M, Gilbert R, Gilroy S, Hardiman G, Herranz R, Kidane YH, Kruse CPS, Lee MD, Liefeld T, Lewis NG, McDonald JT, Meller R, Mishra T, Perera IY, Ray S, Reinsch SS, Rosenthal SB, Strong M, Szewczyk NJ, Tahimic CGT, Taylor DM, Vandenbrink JP, Villacampa A, Weging S, Wolverton C, Wyatt SE, Zea L, Costes SV, Galazka JM. NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data. iScience 2021; 24:102361. [PMID: 33870146 PMCID: PMC8044432 DOI: 10.1016/j.isci.2021.102361] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/30/2020] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab. Analysis of omics data from different spaceflight studies presents unique challenges A standardized pipeline for RNA-seq analysis eliminates data processing variation The GeneLab RNA-seq pipeline includes QC, trimming, mapping, quantification, and DGE Space-relevant data processed with this pipeline are available at genelab.nasa.gov
Collapse
Affiliation(s)
- Eliah G Overbey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Amanda M Saravia-Butler
- Logyx, LLC, Mountain View, CA 94043, USA.,Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Komal S Rathi
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Homer Fogle
- The Bionetics Corporation, NASA Ames Research Center, Moffett Field, CA 94035, USA.,Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Willian A da Silveira
- Institute for Global Food Security (IGFS) & School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Richard J Barker
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Joseph J Bass
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Royal Derby Hospital, University of Nottingham & National Institute for Health Research Nottingham Biomedical Research Centre, Derby DE22 3DT, UK
| | - Afshin Beheshti
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel C Berrios
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Elizabeth A Blaber
- Center for Biotechnology and Interdisciplinary Studies, Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Helio A Costa
- Departments of Pathology, and of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samrawit G Gebre
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.,KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Rachel Gilbert
- NASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Simon Gilroy
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Gary Hardiman
- Institute for Global Food Security (IGFS) & School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Medical University of South Carolina, Charleston, SC, USA
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Yared H Kidane
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219, USA
| | - Colin P S Kruse
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USA
| | - Michael D Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA 94035, USA.,Blue Marble Space Institute of Science, Seattle, WA 98154, USA
| | - Ted Liefeld
- Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - J Tyson McDonald
- Department of Radiation Medicine, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Robert Meller
- Department of Neurobiology and Pharmacology, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Tejaswini Mishra
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Imara Y Perera
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Shayoni Ray
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
| | - Sigrid S Reinsch
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael Strong
- National Jewish Health, Center for Genes, Environment, and Health, 1400 Jackson Street, Denver, CO 80206, USA
| | - Nathaniel J Szewczyk
- Ohio Musculoskeletal and Neurological Institute and Department of Biomedical Sciences, Ohio University, Athens, OH 43147, USA
| | - Candice G T Tahimic
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Deanne M Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia and the Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Alicia Villacampa
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Silvio Weging
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, Halle 06120, Germany
| | - Chris Wolverton
- Department of Botany and Microbiology, Ohio Wesleyan University, Delaware, OH, USA
| | - Sarah E Wyatt
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA.,Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
| | - Luis Zea
- BioServe Space Technologies, Aerospace Engineering Sciences Department, University of Colorado Boulder, Boulder 80303 USA
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Jonathan M Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| |
Collapse
|
7
|
Khanshour AM, Kidane YH, Kozlitina J, Cornelia R, Rafipay A, De Mello V, Weston M, Paria N, Khalid A, Hecht JT, Dobbs MB, Richards BS, Vargesson N, Hamra FK, Wilson M, Wise C, Gurnett CA, Rios JJ. Genetic association and characterization of FSTL5 in isolated clubfoot. Hum Mol Genet 2020; 29:3717-3728. [PMID: 33105483 DOI: 10.1093/hmg/ddaa236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/28/2020] [Accepted: 10/14/2020] [Indexed: 01/01/2023] Open
Abstract
Talipes equinovarus (clubfoot, TEV) is a congenital rotational foot deformity occurring in 1 per 1000 births with increased prevalence in males compared with females. The genetic etiology of isolated clubfoot (iTEV) remains unclear. Using a genome-wide association study, we identified a locus within FSTL5, encoding follistatin-like 5, significantly associated with iTEV. FSTL5 is an uncharacterized gene whose potential role in embryonic and postnatal development was previously unstudied. Utilizing multiple model systems, we found that Fstl5 was expressed during later stages of embryonic hindlimb development, and, in mice, expression was restricted to the condensing cartilage anlage destined to form the limb skeleton. In the postnatal growth plate, Fstl5 was specifically expressed in prehypertrophic chondrocytes. As Fstl5 knockout rats displayed no gross malformations, we engineered a conditional transgenic mouse line (Fstl5LSL) to overexpress Fstl5 in skeletal osteochondroprogenitors. We observed that hindlimbs were slightly shorter and that bone mineral density was reduced in adult male, but not female, Prrx1-cre;Fstl5LSL mice compared with control. No overt clubfoot-like deformity was observed in Prrx1-cre;Fstl5LSL mice, suggesting FSTL5 may function in other cell types to contribute to iTEV pathogenesis. Interrogating published mouse embryonic single-cell expression data showed that Fstl5 was expressed in cell lineage subclusters whose transcriptomes were associated with neural system development. Moreover, our results suggest that lineage-specific expression of the Fstl genes correlates with their divergent roles as modulators of transforming growth factor beta and bone morphogenetic protein signaling. Results from this study associate FSTL5 with iTEV and suggest a potential sexually dimorphic role for Fstl5 in vivo.
Collapse
Affiliation(s)
- Anas M Khanshour
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Yared H Kidane
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Julia Kozlitina
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Reuel Cornelia
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Alexandra Rafipay
- School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, Scotland, UK
| | - Vanessa De Mello
- School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, Scotland, UK
| | - Mitchell Weston
- Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
| | - Nandina Paria
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Aysha Khalid
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Jacqueline T Hecht
- Department of Pediatrics, McGovern Medical School, University of Texas Health, Houston, TX 77030, USA
| | - Matthew B Dobbs
- Paley Orthopedic and Spine Institute, West Palm Beach, FL 33407, USA
| | - B Stephens Richards
- Department of Orthopaedics, Scottish Rite for Children, Dallas, TX 75219, USA.,Department of Orthopaedic Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Neil Vargesson
- School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, Scotland, UK
| | - F Kent Hamra
- Department of Obstetrics and Gynecology, Cecil H. & Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Megan Wilson
- Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
| | - Carol Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA.,McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Orthopaedic Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christina A Gurnett
- Department of Neurology, School of Medicine, Washington University, St. Louis, MO 63130, USA
| | - Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA.,McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Orthopaedic Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
8
|
Zhao S, Zhang Y, Chen W, Li W, Wang S, Wang L, Zhao Y, Lin M, Ye Y, Lin J, Zheng Y, Liu J, Zhao H, Yan Z, Yang Y, Huang Y, Lin G, Chen Z, Zhang Z, Liu S, Jin L, Wang Z, Chen J, Niu Y, Li X, Wu Y, Wang Y, Du R, Gao N, Zhao H, Yang Y, Liu Y, Tian Y, Li W, Zhao Y, Liu J, Yu B, Zhang N, Yu K, Yang X, Li S, Xu Y, Hu J, Liu Z, Shen J, Zhang S, Su J, Khanshour AM, Kidane YH, Ramo B, Rios JJ, Liu P, Sutton VR, Posey JE, Wu Z, Qiu G, Wise CA, Zhang F, Lupski JR, Zhang J, Wu N. Diagnostic yield and clinical impact of exome sequencing in early-onset scoliosis (EOS). J Med Genet 2020; 58:41-47. [PMID: 32381727 DOI: 10.1136/jmedgenet-2019-106823] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 12/29/2019] [Revised: 02/17/2020] [Accepted: 03/13/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Early-onset scoliosis (EOS), defined by an onset age of scoliosis less than 10 years, conveys significant health risk to affected children. Identification of the molecular aetiology underlying patients with EOS could provide valuable information for both clinical management and prenatal screening. METHODS In this study, we consecutively recruited a cohort of 447 Chinese patients with operative EOS. We performed exome sequencing (ES) screening on these individuals and their available family members (totaling 670 subjects). Another cohort of 13 patients with idiopathic early-onset scoliosis (IEOS) from the USA who underwent ES was also recruited. RESULTS After ES data processing and variant interpretation, we detected molecular diagnostic variants in 92 out of 447 (20.6%) Chinese patients with EOS, including 8 patients with molecular confirmation of their clinical diagnosis and 84 patients with molecular diagnoses of previously unrecognised diseases underlying scoliosis. One out of 13 patients with IEOS from the US cohort was molecularly diagnosed. The age at presentation, the number of organ systems involved and the Cobb angle were the three top features predictive of a molecular diagnosis. CONCLUSION ES enabled the molecular diagnosis/classification of patients with EOS. Specific clinical features/feature pairs are able to indicate the likelihood of gaining a molecular diagnosis through ES.
Collapse
Affiliation(s)
- Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Yuanqiang Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Weiyu Li
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Life Sciences, Shanghai, China
| | - Shengru Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Lianlei Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Yanxue Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Mao Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Yongyu Ye
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Orthopedic Surgery, First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China
| | - Jiachen Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Yu Zheng
- School of Finance, Southwestern University of Finance and Economics, Chengdu, Sichuan, China
| | - Jiaqi Liu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital,Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China.,School of Ophthalmology & Optometry and Eye Hospital, School of BiomedicalEngineering, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zihui Yan
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Graduate School, Peking Union Medical College, Beijing, China
| | - Yongxin Yang
- Machine Intelligence Group, University of Edinburgh, Edinburgh, UK
| | - Yingzhao Huang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Guanfeng Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zefu Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zhen Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Sen Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Lichao Jin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zhaoyang Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Jingdan Chen
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Yipeng Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Na Gao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Hong Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Yang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ye Tian
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Wenli Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jia Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bin Yu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Na Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Keyi Yu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xu Yang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Shugang Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuan Xu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianhua Hu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhe Liu
- Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianxiong Shen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Shuyang Zhang
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Cardiology, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianzhong Su
- School of Ophthalmology & Optometry and Eye Hospital, School of BiomedicalEngineering, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Anas M Khanshour
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, Texas, USA
| | - Yared H Kidane
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, Texas, USA
| | - Brandon Ramo
- Department of Orthopaedic Surgery, Scottish Rite for Children, Dallas, Texas, USA
| | - Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, Texas, USA.,McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing, China
| | | | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, Texas, USA.,McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Life Sciences, Shanghai, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Departments of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | | |
Collapse
|
9
|
Wise CA, Sepich D, Ushiki A, Khanshour AM, Kidane YH, Makki N, Gurnett CA, Gray RS, Rios JJ, Ahituv N, Solnica-Krezel L. The cartilage matrisome in adolescent idiopathic scoliosis. Bone Res 2020; 8:13. [PMID: 32195011 PMCID: PMC7062733 DOI: 10.1038/s41413-020-0089-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/27/2020] [Indexed: 12/13/2022] Open
Abstract
The human spinal column is a dynamic, segmented, bony, and cartilaginous structure that protects the neurologic system and simultaneously provides balance and flexibility. Children with developmental disorders that affect the patterning or shape of the spine can be at risk of neurologic and other physiologic dysfunctions. The most common developmental disorder of the spine is scoliosis, a lateral deformity in the shape of the spinal column. Scoliosis may be part of the clinical spectrum that is observed in many developmental disorders, but typically presents as an isolated symptom in otherwise healthy adolescent children. Adolescent idiopathic scoliosis (AIS) has defied understanding in part due to its genetic complexity. Breakthroughs have come from recent genome-wide association studies (GWAS) and next generation sequencing (NGS) of human AIS cohorts, as well as investigations of animal models. These studies have identified genetic associations with determinants of cartilage biogenesis and development of the intervertebral disc (IVD). Current evidence suggests that a fraction of AIS cases may arise from variation in factors involved in the structural integrity and homeostasis of the cartilaginous extracellular matrix (ECM). Here, we review the development of the spine and spinal cartilages, the composition of the cartilage ECM, the so-called "matrisome" and its functions, and the players involved in the genetic architecture of AIS. We also propose a molecular model by which the cartilage matrisome of the IVD contributes to AIS susceptibility.
Collapse
Affiliation(s)
- Carol A. Wise
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219 USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75235 USA
- Departments of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75235 USA
- Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235 USA
| | - Diane Sepich
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158 USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158 USA
| | - Anas M. Khanshour
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219 USA
| | - Yared H. Kidane
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219 USA
| | - Nadja Makki
- Department of Anatomy and Cell Biology, University of Florida, College of Medicine, Gainesville, FL 32610 USA
| | - Christina A. Gurnett
- Departments of Neurology, Washington University School of Medicine, St Louis, MO 63110 USA
- Pediatrics, Washington University School of Medicine, St Louis, MO 63110 USA
- Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO 63110 USA
| | - Ryan S. Gray
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, TX 78723 USA
| | - Jonathan J. Rios
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219 USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75235 USA
- Departments of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75235 USA
- Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235 USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158 USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158 USA
| | - Lila Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
| |
Collapse
|
10
|
Khanshour AM, Kou I, Fan Y, Einarsdottir E, Makki N, Kidane YH, Kere J, Grauers A, Johnson TA, Paria N, Patel C, Singhania R, Kamiya N, Takeda K, Otomo N, Watanabe K, Luk KDK, Cheung KMC, Herring JA, Rios JJ, Ahituv N, Gerdhem P, Gurnett CA, Song YQ, Ikegawa S, Wise CA. Genome-wide meta-analysis and replication studies in multiple ethnicities identify novel adolescent idiopathic scoliosis susceptibility loci. Hum Mol Genet 2019; 27:3986-3998. [PMID: 30395268 DOI: 10.1093/hmg/ddy306] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is the most common musculoskeletal disorder of childhood development. The genetic architecture of AIS is complex, and the great majority of risk factors are undiscovered. To identify new AIS susceptibility loci, we conducted the first genome-wide meta-analysis of AIS genome-wide association studies, including 7956 cases and 88 459 controls from 3 ancestral groups. Three novel loci that surpassed genome-wide significance were uncovered in intragenic regions of the CDH13 (P-value_rs4513093 = 1.7E-15), ABO (P-value_ rs687621 = 7.3E-10) and SOX6 (P-value_rs1455114 = 2.98E-08) genes. Restricting the analysis to females improved the associations at multiple loci, most notably with variants within CDH13 despite the reduction in sample size. Genome-wide gene-functional enrichment analysis identified significant perturbation of pathways involving cartilage and connective tissue development. Expression of both SOX6 and CDH13 was detected in cartilage chondrocytes and chromatin immunoprecipitation sequencing experiments in that tissue revealed multiple HeK27ac-positive peaks overlapping associated loci. Our results further define the genetic architecture of AIS and highlight the importance of vertebral cartilage development in its pathogenesis.
Collapse
Affiliation(s)
- Anas M Khanshour
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Ikuyo Kou
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Yanhui Fan
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics, University of Helsinki, 00014 University of Helsinki, Finland.,Molecular Neurology Research Program, University of Helsinki, 00014 University of Helsinki, Finland.,Department of Biosciences & Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Nadja Makki
- Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yared H Kidane
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Juha Kere
- Folkhälsan Institute of Genetics, University of Helsinki, 00014 University of Helsinki, Finland.,Molecular Neurology Research Program, University of Helsinki, 00014 University of Helsinki, Finland.,Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK.,Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, K54 Huddinge, Stockholm, Sweden
| | - Anna Grauers
- Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, K54 Huddinge, Stockholm, Sweden.,Department of Orthopedics, Sundsvall and Härnösand County Hospital, Sundsvall, Sweden
| | - Todd A Johnson
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Nandina Paria
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Chandreshkumar Patel
- McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Richa Singhania
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | | | - Kazuki Takeda
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Nao Otomo
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kota Watanabe
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Keith D K Luk
- Department of Orthopaedics & Traumatology, The University of Hong Kong, Hong Kong, China
| | - Kenneth M C Cheung
- Department of Orthopaedics & Traumatology, The University of Hong Kong, Hong Kong, China
| | - John A Herring
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,Department of Orthopaedic Surgery, Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan J Rios
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nadav Ahituv
- Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Paul Gerdhem
- Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, K54 Huddinge, Stockholm, Sweden.,Department of Orthopedics, Karolinska University Hospital, K54 Huddinge, Stockholm, Sweden
| | - Christina A Gurnett
- Department of Neurology, School of Medicine, Washington University, St. Louis, MO, USA
| | - You-Qiang Song
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Shiro Ikegawa
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Carol A Wise
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
11
|
Fenley AT, Anandakrishnan R, Kidane YH, Onufriev AV. Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core. Epigenetics Chromatin 2018; 11:11. [PMID: 29548294 PMCID: PMC5856334 DOI: 10.1186/s13072-018-0181-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [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: 09/28/2017] [Accepted: 03/06/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Controlled modulation of nucleosomal DNA accessibility via post-translational modifications (PTM) is a critical component to many cellular functions. Charge-altering PTMs in the globular histone core-including acetylation, phosphorylation, crotonylation, propionylation, butyrylation, formylation, and citrullination-can alter the strong electrostatic interactions between the oppositely charged nucleosomal DNA and the histone proteins and thus modulate accessibility of the nucleosomal DNA, affecting processes that depend on access to the genetic information, such as transcription. However, direct experimental investigation of the effects of these PTMs is very difficult. Theoretical models can rationalize existing observations, suggest working hypotheses for future experiments, and provide a unifying framework for connecting PTMs with the observed effects. RESULTS A physics-based framework is proposed that predicts the effect of charge-altering PTMs in the histone core, quantitatively for several types of lysine charge-neutralizing PTMs including acetylation, and qualitatively for all phosphorylations, on the nucleosome stability and subsequent changes in DNA accessibility, making a connection to resulting biological phenotypes. The framework takes into account multiple partially assembled states of the nucleosome at the atomic resolution. The framework is validated against experimentally known nucleosome stability changes due to the acetylation of specific lysines, and their effect on transcription. The predicted effect of charge-altering PTMs on DNA accessibility can vary dramatically, from virtually none to a strong, region-dependent increase in accessibility of the nucleosomal DNA; in some cases, e.g., H4K44, H2AK75, and H2BK57, the effect is significantly stronger than that of the extensively studied acetylation sites such H3K56, H3K115 or H3K122. Proximity to the DNA is suggestive of the strength of the PTM effect, but there are many exceptions. For the vast majority of charge-altering PTMs, the predicted increase in the DNA accessibility should be large enough to result in a measurable modulation of transcription. However, a few possible PTMs, such as acetylation of H4K77, counterintuitively decrease the DNA accessibility, suggestive of the repressed chromatin. A structural explanation for the phenomenon is provided. For the majority of charge-altering PTMs, the effect on DNA accessibility is simply additive (noncooperative), but there are exceptions, e.g., simultaneous acetylation of H4K79 and H3K122, where the combined effect is amplified. The amplification is a direct consequence of the nucleosome-DNA complex having more than two structural states. The effect of individual PTMs is classified based on changes in the accessibility of various regions throughout the nucleosomal DNA. The PTM's resulting imprint on the DNA accessibility, "PTMprint," is used to predict effects of many yet unexplored PTMs. For example, acetylation of H4K44 yields a PTMprint similar to the PTMprint of H3K56, and thus acetylation of H4K44 is predicted to lead to a wide range of strong biological effects. CONCLUSION Charge-altering post-translational modifications in the relatively unexplored globular histone core may provide a precision mechanism for controlling accessibility to the nucleosomal DNA.
Collapse
Affiliation(s)
- Andrew T. Fenley
- Department of Physics, Virginia Tech, 2160C Torgersen Hall, Blacksburg, VA 24061 USA
| | | | - Yared H. Kidane
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061 USA
| | - Alexey V. Onufriev
- Department of Physics, Virginia Tech, 2160C Torgersen Hall, Blacksburg, VA 24061 USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061 USA
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061 USA
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061 USA
| |
Collapse
|
12
|
Kidane YH, Lawrence C, Murali TM. Computational approaches for discovery of common immunomodulators in fungal infections: towards broad-spectrum immunotherapeutic interventions. BMC Microbiol 2013; 13:224. [PMID: 24099000 PMCID: PMC3853472 DOI: 10.1186/1471-2180-13-224] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 02/27/2013] [Accepted: 09/17/2013] [Indexed: 01/16/2023] Open
Abstract
Background Fungi are the second most abundant type of human pathogens. Invasive fungal pathogens are leading causes of life-threatening infections in clinical settings. Toxicity to the host and drug-resistance are two major deleterious issues associated with existing antifungal agents. Increasing a host’s tolerance and/or immunity to fungal pathogens has potential to alleviate these problems. A host’s tolerance may be improved by modulating the immune system such that it responds more rapidly and robustly in all facets, ranging from the recognition of pathogens to their clearance from the host. An understanding of biological processes and genes that are perturbed during attempted fungal exposure, colonization, and/or invasion will help guide the identification of endogenous immunomodulators and/or small molecules that activate host-immune responses such as specialized adjuvants. Results In this study, we present computational techniques and approaches using publicly available transcriptional data sets, to predict immunomodulators that may act against multiple fungal pathogens. Our study analyzed data sets derived from host cells exposed to five fungal pathogens, namely, Alternaria alternata, Aspergillus fumigatus, Candida albicans, Pneumocystis jirovecii, and Stachybotrys chartarum. We observed statistically significant associations between host responses to A. fumigatus and C. albicans. Our analysis identified biological processes that were consistently perturbed by these two pathogens. These processes contained both immune response-inducing genes such as MALT1, SERPINE1, ICAM1, and IL8, and immune response-repressing genes such as DUSP8, DUSP6, and SPRED2. We hypothesize that these genes belong to a pool of common immunomodulators that can potentially be activated or suppressed (agonized or antagonized) in order to render the host more tolerant to infections caused by A. fumigatus and C. albicans. Conclusions Our computational approaches and methodologies described here can now be applied to newly generated or expanded data sets for further elucidation of additional drug targets. Moreover, identified immunomodulators may be used to generate experimentally testable hypotheses that could help in the discovery of broad-spectrum immunotherapeutic interventions. All of our results are available at the following supplementary website: http://bioinformatics.cs.vt.edu/~murali/supplements/2013-kidane-bmc
Collapse
Affiliation(s)
- Yared H Kidane
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA.
| | | | | |
Collapse
|
13
|
Kidane YH, Lawrence C, Murali TM. The landscape of host transcriptional response programs commonly perturbed by bacterial pathogens: towards host-oriented broad-spectrum drug targets. PLoS One 2013; 8:e58553. [PMID: 23516507 PMCID: PMC3596304 DOI: 10.1371/journal.pone.0058553] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 02/07/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The emergence of drug-resistant pathogen strains and new infectious agents pose major challenges to public health. A promising approach to combat these problems is to target the host's genes or proteins, especially to discover targets that are effective against multiple pathogens, i.e., host-oriented broad-spectrum (HOBS) drug targets. An important first step in the discovery of such drug targets is the identification of host responses that are commonly perturbed by multiple pathogens. RESULTS In this paper, we present a methodology to identify common host responses elicited by multiple pathogens. First, we identified host responses perturbed by each pathogen using a gene set enrichment analysis of publicly available genome-wide transcriptional datasets. Then, we used biclustering to identify groups of host pathways and biological processes that were perturbed only by a subset of the analyzed pathogens. Finally, we tested the enrichment of each bicluster in human genes that are known drug targets, on the basis of which we elicited putative HOBS targets for specific groups of bacterial pathogens. We identified 84 up-regulated and three down-regulated statistically significant biclusters. Each bicluster contained a group of pathogens that commonly dysregulated a group of biological processes. We validated our approach by checking whether these biclusters correspond to known hallmarks of bacterial infection. Indeed, these biclusters contained biological process such as inflammation, activation of dendritic cells, pro- and anti- apoptotic responses and other innate immune responses. Next, we identified biclusters containing pathogens that infected the same tissue. After a literature-based analysis of the drug targets contained in these biclusters, we suggested new uses of the drugs Anakinra, Etanercept, and Infliximab for gastrointestinal pathogens Yersinia enterocolitica, Helicobacter pylori kx2 strain, and enterohemorrhagic Escherichia coli and the drug Simvastatin for hematopoietic pathogen Ehrlichia chaffeensis. CONCLUSIONS Using a combination of automated analysis of host-response gene expression data and manual study of the literature, we have been able to suggest host-oriented treatments for specific bacterial infections. The analyses and suggestions made in this study may be utilized to generate concrete hypothesis on which gene sets to probe further in the quest for HOBS drug targets for bacterial infections. All our results are available at the following supplementary website: http://bioinformatics.cs.vt.edu/ murali/supplements/2013-kidane-plos-one.
Collapse
Affiliation(s)
- Yared H. Kidane
- Genetics, Bioinformatics, and Computational Biology PhD Program, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Christopher Lawrence
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
- Department of Biology, Virginia Tech, Blacksburg, Virginia, United States of America
| | - T. M. Murali
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
- ICTAS Center for Systems Biology of Engineered Tissues, Virginia Tech, Blacksburg, Virginia, United States of America
| |
Collapse
|