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Mekbib KY, Zhao S, Nelson-Williams C, Prendergast A, Zeng X, Rolle M, Shohfi J, Smith H, Ocken J, Moyer Q, Piwowarczyk P, Allington G, Dong W, van der Ent MA, Chen D, Li B, Duran D, Mane SM, Walcott BP, Stapleton CJ, Aagaard-Kienitz B, Rodesch G, Jackson EM, Smith ER, Orbach D, Berenstein A, Bilguvar K, Zhao H, Erson-Omay Z, King PD, Huttner A, Lifton R, Boggon T, Nicoli S, Jin SC, Kahle K. 169 Exome Sequencing Implicates Endothelial Ras Signaling Network in Vein of Galen Aneurysmal Malformation. Neurosurgery 2023. [DOI: 10.1227/neu.0000000000002375_169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
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Wu CHW, Lim TY, Wang C, Seltzsam S, Zheng B, Schierbaum L, Schneider S, Mann N, Connaughton DM, Nakayama M, van der Ven AT, Dai R, Kolvenbach CM, Kause F, Ottlewski I, Stajic N, Soliman NA, Kari JA, El Desoky S, Fathy HM, Milosevic D, Turudic D, Al Saffar M, Awad HS, Eid LA, Ramanathan A, Senguttuvan P, Mane SM, Lee RS, Bauer SB, Lu W, Hilger AC, Tasic V, Shril S, Sanna-Cherchi S, Hildebrandt F. Copy Number Variation Analysis Facilitates Identification of Genetic Causation in Patients with Congenital Anomalies of the Kidney and Urinary Tract. EUR UROL SUPPL 2022; 44:106-112. [PMID: 36185583 PMCID: PMC9520493 DOI: 10.1016/j.euros.2022.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2022] [Indexed: 11/27/2022] Open
Abstract
Background Congenital anomalies of the kidneys and urinary tract (CAKUT) are the most common cause of chronic kidney disease among children and adults younger than 30 yr. In our previous study, whole-exome sequencing (WES) identified a known monogenic cause of isolated or syndromic CAKUT in 13% of families with CAKUT. However, WES has limitations and detection of copy number variations (CNV) is technically challenging, and CNVs causative of CAKUT have previously been detected in up to 16% of cases. Objective To detect CNVs causing CAKUT in this WES cohort and increase the diagnostic yield. Design setting and participants We performed a genome-wide single nucleotide polymorphism (SNP)-based CNV analysis on the same CAKUT cohort for whom WES was previously conducted. Outcome measurements and statistical analysis We evaluated and classified the CNVs using previously published predefined criteria. Results and limitations In a cohort of 170 CAKUT families, we detected a pathogenic CNV known to cause CAKUT in nine families (5.29%, 9/170). There were no competing variants on genome-wide CNV analysis or WES analysis. In addition, we identified novel likely pathogenic CNVs that may cause a CAKUT phenotype in three of the 170 families (1.76%). Conclusions CNV analysis in this cohort of 170 CAKUT families previously examined via WES increased the rate of diagnosis of genetic causes of CAKUT from 13% on WES to 18% on WES + CNV analysis combined. We also identified three candidate loci that may potentially cause CAKUT. Patient summary We conducted a genetics study on families with congenital anomalies of the kidney and urinary tract (CAKUT). We identified gene mutations that can explain CAKUT symptoms in 5.29% of the families, which increased the percentage of genetic causes of CAKUT to 18% from a previous study, so roughly one in five of our patients with CAKUT had a genetic cause. These analyses can help patients with CAKUT and their families in identifying a possible genetic cause.
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Affiliation(s)
- Chen-Han Wilfred Wu
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Urology, Case Western Reserve University and University Hospitals, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University and University Hospitals, Cleveland, OH, USA
| | - Tze Y. Lim
- Division of Nephrology, Columbia University Irving Medical Center, New York, NY, USA
| | - Chunyan Wang
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Steve Seltzsam
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Bixia Zheng
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Luca Schierbaum
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sophia Schneider
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nina Mann
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Dervla M. Connaughton
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Makiko Nakayama
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Amelie T. van der Ven
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Rufeng Dai
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Caroline M. Kolvenbach
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Franziska Kause
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Isabel Ottlewski
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Natasa Stajic
- Department of Pediatric Nephrology, Institute for Mother and Child Health Care, Belgrade, Serbia
| | - Neveen A. Soliman
- Department of Pediatrics, Center of Pediatric Nephrology & Transplantation, Cairo University, Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Jameela A. Kari
- Department of Pediatrics, King AbdulAziz University, Jeddah, Saudi Arabia
| | - Sherif El Desoky
- Department of Pediatrics, King AbdulAziz University, Jeddah, Saudi Arabia
| | - Hanan M. Fathy
- Pediatric Nephrology Unit, University of Alexandria, Alexandria, Egypt
| | - Danko Milosevic
- Department of Pediatric Nephrology, University Hospital Center Zagreb, Zagreb, Croatia
| | - Daniel Turudic
- Department of Pediatric Nephrology, University Hospital Center Zagreb, Zagreb, Croatia
| | - Muna Al Saffar
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Hazem S. Awad
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Loai A. Eid
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
- Department of Pediatrics, Dubai Medical College and Kidney Centre of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, United Arab Emirates
| | - Aravind Ramanathan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Prabha Senguttuvan
- Department of Pediatric Nephrology, Dr. Mehta’s Multi-Specialty Hospital, Chennai, India
| | - Shrikant M. Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Richard S. Lee
- Department of Urology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Stuart B. Bauer
- Department of Urology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Weining Lu
- Renal Section, Department of Medicine, Boston University Medical Center, Boston, MA, USA
| | - Alina C. Hilger
- Department of Pediatric and Adolescent Medicine, Friedrich Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Velibor Tasic
- Medical Faculty Skopje, University Children’s Hospital, Skopje, Macedonia
| | - Shirlee Shril
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Simone Sanna-Cherchi
- Division of Nephrology, Columbia University Irving Medical Center, New York, NY, USA
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Corresponding author. Division of Nephrology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA. Tel. +1 617 3556129; Fax: +1 617 8300365.
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Seltzsam S, Wang C, Zheng B, Mann N, Connaughton DM, Wu CHW, Schneider S, Schierbaum L, Kause F, Kolvenbach CM, Nakayama M, Dai R, Ottlewski I, Schneider R, Deutsch K, Buerger F, Klämbt V, Mao Y, Onuchic-Whitford AC, Nicolas-Frank C, Yousef K, Pantel D, Lai EW, Salmanullah D, Majmundar AJ, Bauer SB, Rodig NM, Somers MJG, Traum AZ, Stein DR, Daga A, Baum MA, Daouk GH, Tasic V, Awad HS, Eid LA, El Desoky S, Shalaby M, Kari JA, Fathy HM, Soliman NA, Mane SM, Shril S, Ferguson MA, Hildebrandt F. Reverse phenotyping facilitates disease allele calling in exome sequencing of patients with CAKUT. Genet Med 2022; 24:307-318. [PMID: 34906515 PMCID: PMC8876311 DOI: 10.1016/j.gim.2021.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/08/2021] [Accepted: 09/14/2021] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Congenital anomalies of the kidneys and urinary tract (CAKUT) constitute the leading cause of chronic kidney disease in children. In total, 174 monogenic causes of isolated or syndromic CAKUT are known. However, syndromic features may be overlooked when the initial clinical diagnosis of CAKUT is made. We hypothesized that the yield of a molecular genetic diagnosis by exome sequencing (ES) can be increased by applying reverse phenotyping, by re-examining the case for signs/symptoms of the suspected clinical syndrome that results from the genetic variant detected by ES. METHODS We conducted ES in an international cohort of 731 unrelated families with CAKUT. We evaluated ES data for variants in 174 genes, in which variants are known to cause isolated or syndromic CAKUT. In cases in which ES suggested a previously unreported syndromic phenotype, we conducted reverse phenotyping. RESULTS In 83 of 731 (11.4%) families, we detected a likely CAKUT-causing genetic variant consistent with an isolated or syndromic CAKUT phenotype. In 19 of these 83 families (22.9%), reverse phenotyping yielded syndromic clinical findings, thereby strengthening the genotype-phenotype correlation. CONCLUSION We conclude that employing reverse phenotyping in the evaluation of syndromic CAKUT genes by ES provides an important tool to facilitate molecular genetic diagnostics in CAKUT.
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Affiliation(s)
- Steve Seltzsam
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Chunyan Wang
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bixia Zheng
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Nina Mann
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Dervla M Connaughton
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Chen-Han Wilfred Wu
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Sophia Schneider
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Luca Schierbaum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Franziska Kause
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Caroline M Kolvenbach
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Makiko Nakayama
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Rufeng Dai
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Isabel Ottlewski
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ronen Schneider
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Konstantin Deutsch
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Florian Buerger
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Verena Klämbt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Youying Mao
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ana C Onuchic-Whitford
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Camille Nicolas-Frank
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Kirollos Yousef
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Dalia Pantel
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Ethan W Lai
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Daanya Salmanullah
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Amar J Majmundar
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Nancy M Rodig
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Michael J G Somers
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Avram Z Traum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Deborah R Stein
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ankana Daga
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Michelle A Baum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ghaleb H Daouk
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, North Macedonia
| | - Hazem S Awad
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Sherif El Desoky
- Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia; Pediatric Nephrology Center of Excellence, Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Mohammed Shalaby
- Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia; Pediatric Nephrology Center of Excellence, Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Jameela A Kari
- Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia; Pediatric Nephrology Center of Excellence, Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Hanan M Fathy
- Pediatric Nephrology Unit, University of Alexandria, Alexandria, Egypt
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Michael A Ferguson
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA.
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4
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Wang C, Seltzsam S, Zheng B, Wu CHW, Nicolas-Frank C, Yousef K, Au KS, Mann N, Pantel D, Schneider S, Schierbaum L, Kitzler TM, Connaughton DM, Mao Y, Dai R, Nakayama M, Kari JA, El Desoky S, Shalaby M, Eid LA, Awad HS, Tasic V, Mane SM, Lifton RP, Baum MA, Shril S, Estrada CR, Hildebrandt F. Whole exome sequencing identifies potential candidate genes for spina bifida derived from mouse models. Am J Med Genet A 2022; 188:1355-1367. [PMID: 35040250 PMCID: PMC8995376 DOI: 10.1002/ajmg.a.62644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 11/11/2022]
Abstract
Spina bifida (SB) is the second most common nonlethal congenital malformation. The existence of monogenic SB mouse models and human monogenic syndromes with SB features indicate that human SB may be caused by monogenic genes. We hypothesized that whole exome sequencing (WES) allows identification of potential candidate genes by (i) generating a list of 136 candidate genes for SB, and (ii) by unbiased exome-wide analysis. We generated a list of 136 potential candidate genes from three categories and evaluated WES data of 50 unrelated SB cases for likely deleterious variants in 136 potential candidate genes, and for potential SB candidate genes exome-wide. We identified 6 likely deleterious variants in 6 of the 136 potential SB candidate genes in 6 of the 50 SB cases, whereof 4 genes were derived from mouse models, 1 gene was derived from human nonsyndromic SB, and 1 gene was derived from candidate genes known to cause human syndromic SB. In addition, by unbiased exome-wide analysis, we identified 12 genes as potential candidates for SB. Identification of these 18 potential candidate genes in larger SB cohorts will help decide which ones can be considered as novel monogenic causes of human SB.
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Affiliation(s)
- Chunyan Wang
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Steve Seltzsam
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bixia Zheng
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chen-Han Wilfred Wu
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Departments of Urology and Genetics, Case Western Reserve University and University Hospitals, Cleveland, Ohio, USA
| | - Camille Nicolas-Frank
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kirollos Yousef
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Nina Mann
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Dalia Pantel
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Sophia Schneider
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Luca Schierbaum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas M Kitzler
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Dervla M Connaughton
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Youying Mao
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rufeng Dai
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Makiko Nakayama
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jameela A Kari
- Department of Pediatrics, King Abdulaziz University, Jeddah, Saudi Arabia.,Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Sherif El Desoky
- Department of Pediatrics, King Abdulaziz University, Jeddah, Saudi Arabia.,Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Mohammed Shalaby
- Department of Pediatrics, King Abdulaziz University, Jeddah, Saudi Arabia.,Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Hazem S Awad
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, North Macedonia
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA
| | - Michelle A Baum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Carlos R Estrada
- Department of Urology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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5
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Richard EM, Bakhtiari S, Marsh APL, Kaiyrzhanov R, Wagner M, Shetty S, Pagnozzi A, Nordlie SM, Guida BS, Cornejo P, Magee H, Liu J, Norton BY, Webster RI, Worgan L, Hakonarson H, Li J, Guo Y, Jain M, Blesson A, Rodan LH, Abbott MA, Comi A, Cohen JS, Alhaddad B, Meitinger T, Lenz D, Ziegler A, Kotzaeridou U, Brunet T, Chassevent A, Smith-Hicks C, Ekstein J, Weiden T, Hahn A, Zharkinbekova N, Turnpenny P, Tucci A, Yelton M, Horvath R, Gungor S, Hiz S, Oktay Y, Lochmuller H, Zollino M, Morleo M, Marangi G, Nigro V, Torella A, Pinelli M, Amenta S, Husain RA, Grossmann B, Rapp M, Steen C, Marquardt I, Grimmel M, Grasshoff U, Korenke GC, Owczarek-Lipska M, Neidhardt J, Radio FC, Mancini C, Claps Sepulveda DJ, McWalter K, Begtrup A, Crunk A, Guillen Sacoto MJ, Person R, Schnur RE, Mancardi MM, Kreuder F, Striano P, Zara F, Chung WK, Marks WA, van Eyk CL, Webber DL, Corbett MA, Harper K, Berry JG, MacLennan AH, Gecz J, Tartaglia M, Salpietro V, Christodoulou J, Kaslin J, Padilla-Lopez S, Bilguvar K, Munchau A, Ahmed ZM, Hufnagel RB, Fahey MC, Maroofian R, Houlden H, Sticht H, Mane SM, Rad A, Vona B, Jin SC, Haack TB, Makowski C, Hirsch Y, Riazuddin S, Kruer MC. Bi-allelic variants in SPATA5L1 lead to intellectual disability, spastic-dystonic cerebral palsy, epilepsy, and hearing loss. Am J Hum Genet 2021; 108:2006-2016. [PMID: 34626583 DOI: 10.1016/j.ajhg.2021.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022] Open
Abstract
Spermatogenesis-associated 5 like 1 (SPATA5L1) represents an orphan gene encoding a protein of unknown function. We report 28 bi-allelic variants in SPATA5L1 associated with sensorineural hearing loss in 47 individuals from 28 (26 unrelated) families. In addition, 25/47 affected individuals (53%) presented with microcephaly, developmental delay/intellectual disability, cerebral palsy, and/or epilepsy. Modeling indicated damaging effect of variants on the protein, largely via destabilizing effects on protein domains. Brain imaging revealed diminished cerebral volume, thin corpus callosum, and periventricular leukomalacia, and quantitative volumetry demonstrated significantly diminished white matter volumes in several individuals. Immunofluorescent imaging in rat hippocampal neurons revealed localization of Spata5l1 in neuronal and glial cell nuclei and more prominent expression in neurons. In the rodent inner ear, Spata5l1 is expressed in the neurosensory hair cells and inner ear supporting cells. Transcriptomic analysis performed with fibroblasts from affected individuals was able to distinguish affected from controls by principal components. Analysis of differentially expressed genes and networks suggested a role for SPATA5L1 in cell surface adhesion receptor function, intracellular focal adhesions, and DNA replication and mitosis. Collectively, our results indicate that bi-allelic SPATA5L1 variants lead to a human disease characterized by sensorineural hearing loss (SNHL) with or without a nonprogressive mixed neurodevelopmental phenotype.
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Affiliation(s)
- Elodie M Richard
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Ashley P L Marsh
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, Queen Square, WC1N 3BG London, UK
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Sheetal Shetty
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Alex Pagnozzi
- CSIRO Health and Biosecurity, The Australian e-Health Research Centre, Brisbane, QLD 4029, Australia
| | - Sandra M Nordlie
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Brandon S Guida
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Patricia Cornejo
- Pediatric Neuroradiology Division, Pediatric Radiology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; University of Arizona College of Medicine, Phoenix, AZ 85004, USA; Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Helen Magee
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - James Liu
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Bethany Y Norton
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Richard I Webster
- Neurology Department, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Lisa Worgan
- Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jiankang Li
- Department of Computer Science, City University of Hong Kong, Kowloon 999077, Hong Kong
| | - Yiran Guo
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Mahim Jain
- Department of Bone and Osteogenesis Imperfecta, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Alyssa Blesson
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, MD 21211, USA
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Mary-Alice Abbott
- University of Massachusetts Medical School - Baystate, Baystate Children's Hospital, Springfield, MA 01107, USA
| | - Anne Comi
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Julie S Cohen
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Bader Alhaddad
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Dominic Lenz
- Centre of Child and Adolescent Medicine, Department of Pediatric Neurology and Metabolic Medicine, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Andreas Ziegler
- Department of Child Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Urania Kotzaeridou
- Department of Child Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Anna Chassevent
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Constance Smith-Hicks
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Joseph Ekstein
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, New York, NY 11211, USA
| | - Tzvi Weiden
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem 9054020, Israel
| | - Andreas Hahn
- Department of Child Neurology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Nazira Zharkinbekova
- Department of Neurology, South Kazakhstan Medical Academy, Shymkent 160001, Kazakhstan
| | - Peter Turnpenny
- Clinical Genetics, Royal Devon & Exeter NHS Foundation Trust, EX1 2ED Exeter, UK
| | - Arianna Tucci
- Clinical Pharmacology, William Harvey Research Institute, Charterhouse Square, School of Medicine and Dentistry Queen Mary University of London, London EC1M 6BQ, UK
| | - Melissa Yelton
- Penn State Health Children's Hospital, Hershey, PA 17033, USA
| | - Rita Horvath
- Department of Clinical Neurosciences, John Van Geest Cambridge Centre for Brain Repair, University of Cambridge School of Clinical Medicine, CB2 0PY Cambridge, UK
| | - Serdal Gungor
- Inonu University, Faculty of Medicine, Turgut Ozal Research Center, Department of Paediatric Neurology, 44280 Malatya, Turkey
| | - Semra Hiz
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, 35340 Izmir, Turkey; Department of Pediatric Neurology, Faculty of Medicine, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Yavuz Oktay
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, 35340 Izmir, Turkey; Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University, 35220 Izmir, Turkey
| | - Hanns Lochmuller
- Children's Hospital of Eastern Ontario Research Institute; Division of Neurology, Department of Medicine, The Ottawa Hospital, and Brain and Mind Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Marcella Zollino
- Università Cattolica Sacro Cuore, Facoltà di Medicina e Chirurgia, Dipartimento Scienze della Vita e Sanità Pubblica, 00168 Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Sezione di Medicina Genomica, 00168 Roma, Italy
| | - Manuela Morleo
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Naples, Italy
| | - Giuseppe Marangi
- Università Cattolica Sacro Cuore, Facoltà di Medicina e Chirurgia, Dipartimento Scienze della Vita e Sanità Pubblica, 00168 Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Sezione di Medicina Genomica, 00168 Roma, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Naples, Italy
| | - Simona Amenta
- Università Cattolica Sacro Cuore, Facoltà di Medicina e Chirurgia, Dipartimento Scienze della Vita e Sanità Pubblica, 00168 Roma, Italy; Fondazione Policlinico A. Gemelli IRCCS, Sezione di Medicina Genomica, 00168 Roma, Italy
| | - Ralf A Husain
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
| | - Benita Grossmann
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tuebingen, Germany
| | - Marion Rapp
- Institute of Systems Motor Science, University of Lübeck, 23538 Lübeck, Germany
| | - Claudia Steen
- Department of Paediatric and Adolescent Medicine, St Joseph Hospital, 12101 Berlin, Germany
| | - Iris Marquardt
- University Children's Hospital Oldenburg, Department of Neuropaediatric and Metabolic Diseases, 26133 Oldenburg, Germany
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tuebingen, Germany
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tuebingen, Germany
| | - G Christoph Korenke
- University Children's Hospital Oldenburg, Department of Neuropaediatric and Metabolic Diseases, 26133 Oldenburg, Germany
| | - Marta Owczarek-Lipska
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, 26129 Oldenburg, Germany; Junior Research Group, Genetics of Childhood Brain Malformations, Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, 26129 Oldenburg, Germany
| | - John Neidhardt
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, 26129 Oldenburg, Germany; Research Center Neurosensory Science, University of Oldenburg, 26129 Oldenburg, Germany
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Cecilia Mancini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | | | - Amber Begtrup
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Amy Crunk
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | | | | | | | - Maria Margherita Mancardi
- Unit of Child Neuropsichiatry, Department of Clinical and Surgical Neurosciences and Rehabilitation, IRCCS Giannina Gaslini, Genoa 16147, Italy
| | - Florian Kreuder
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3168, Australia
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRRCS Istituto Giannina Gaslini, 16148 Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16142 Genoa, Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16142 Genoa, Italy; Unit of Medical Genetics, IRRCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - Warren A Marks
- Department of Neurology, Cook Children's Medical Center, Fort Worth, TX 76104, USA; Department of Pediatrics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Clare L van Eyk
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Dani L Webber
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Mark A Corbett
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Kelly Harper
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Jesia G Berry
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Alastair H MacLennan
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Jozef Gecz
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5006, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia; South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Vincenzo Salpietro
- Pediatric Neurology and Muscular Diseases Unit, IRRCS Istituto Giannina Gaslini, 16148 Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16142 Genoa, Italy
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia; Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Jan Kaslin
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3168, Australia
| | - Sergio Padilla-Lopez
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Alexander Munchau
- Institute of Systems Motor Science, University of Lübeck, 23538 Lübeck, Germany
| | - Zubair M Ahmed
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael C Fahey
- Department of Paediatrics, Monash University, Melbourne, VIC 3168, Australia
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, Queen Square, WC1N 3BG London, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, Queen Square, WC1N 3BG London, UK
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Shrikant M Mane
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Aboulfazl Rad
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Barbara Vona
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tuebingen, Germany; Centre for Rare Diseases, University of Tübingen, 72074 Tuebingen, Germany
| | - Christine Makowski
- Department of Paediatrics, Adolescent Medicine and Neonatology, Munich Clinic, Schwabing Hospital and Technical University of Munich, School of Medicine, 80804 Munich, Germany
| | - Yoel Hirsch
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, New York, NY 11211, USA
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA.
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular, and Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA.
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6
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Mann N, Mzoughi S, Schneider R, Kühl SJ, Schanze D, Klämbt V, Lovric S, Mao Y, Shi S, Tan W, Kühl M, Onuchic-Whitford AC, Treimer E, Kitzler TM, Kause F, Schumann S, Nakayama M, Buerger F, Shril S, van der Ven AT, Majmundar AJ, Holton KM, Kolb A, Braun DA, Rao J, Jobst-Schwan T, Mildenberger E, Lennert T, Kuechler A, Wieczorek D, Gross O, Ermisch-Omran B, Werberger A, Skalej M, Janecke AR, Soliman NA, Mane SM, Lifton RP, Kadlec J, Guccione E, Schmeisser MJ, Zenker M, Hildebrandt F. Mutations in PRDM15 Are a Novel Cause of Galloway-Mowat Syndrome. J Am Soc Nephrol 2021; 32:580-596. [PMID: 33593823 PMCID: PMC7920168 DOI: 10.1681/asn.2020040490] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/18/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Galloway-Mowat syndrome (GAMOS) is characterized by neurodevelopmental defects and a progressive nephropathy, which typically manifests as steroid-resistant nephrotic syndrome. The prognosis of GAMOS is poor, and the majority of children progress to renal failure. The discovery of monogenic causes of GAMOS has uncovered molecular pathways involved in the pathogenesis of disease. METHODS Homozygosity mapping, whole-exome sequencing, and linkage analysis were used to identify mutations in four families with a GAMOS-like phenotype, and high-throughput PCR technology was applied to 91 individuals with GAMOS and 816 individuals with isolated nephrotic syndrome. In vitro and in vivo studies determined the functional significance of the mutations identified. RESULTS Three biallelic variants of the transcriptional regulator PRDM15 were detected in six families with proteinuric kidney disease. Four families with a variant in the protein's zinc-finger (ZNF) domain have additional GAMOS-like features, including brain anomalies, cardiac defects, and skeletal defects. All variants destabilize the PRDM15 protein, and the ZNF variant additionally interferes with transcriptional activation. Morpholino oligonucleotide-mediated knockdown of Prdm15 in Xenopus embryos disrupted pronephric development. Human wild-type PRDM15 RNA rescued the disruption, but the three PRDM15 variants did not. Finally, CRISPR-mediated knockout of PRDM15 in human podocytes led to dysregulation of several renal developmental genes. CONCLUSIONS Variants in PRDM15 can cause either isolated nephrotic syndrome or a GAMOS-type syndrome on an allelic basis. PRDM15 regulates multiple developmental kidney genes, and is likely to play an essential role in renal development in humans.
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Affiliation(s)
- Nina Mann
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Slim Mzoughi
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ronen Schneider
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Susanne J Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Verena Klämbt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Svjetlana Lovric
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Youying Mao
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shasha Shi
- Grenoble Alpes University, National Center for Scientific Research (CNRS), French Alternative Energies and Atomic Energy Commission (CEA), Institute of Structural Biology, Grenoble, France
| | - Weizhen Tan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Ana C Onuchic-Whitford
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ernestine Treimer
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Thomas M Kitzler
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Franziska Kause
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sven Schumann
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Makiko Nakayama
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Florian Buerger
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amelie T van der Ven
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amar J Majmundar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Amy Kolb
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jia Rao
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tilman Jobst-Schwan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eva Mildenberger
- Division of Neonatology, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Thomas Lennert
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Alma Kuechler
- Institute of Human Genetics, University of Duisburg-Essen, Essen, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Faculty of Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Oliver Gross
- Clinic of Nephrology and Rheumatology, University Medical Center Goettingen, University of Goettingen, Goettingen, Germany
| | - Beate Ermisch-Omran
- Department of Pediatric Nephrology, University Children's Hospital, Münster, Germany
| | - Anja Werberger
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Martin Skalej
- Institute of Neuroradiology, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Andreas R Janecke
- Department of Pediatrics I, Medical University of Innsbruck, Innsbruck, Austria
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt
- The Egyption Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
| | - Jan Kadlec
- Grenoble Alpes University, National Center for Scientific Research (CNRS), French Alternative Energies and Atomic Energy Commission (CEA), Institute of Structural Biology, Grenoble, France
| | - Ernesto Guccione
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael J Schmeisser
- Institute for Microscopic Anatomy and Neurobiology, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
- Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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7
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Connaughton DM, Dai R, Owen DJ, Marquez J, Mann N, Graham-Paquin AL, Nakayama M, Coyaud E, Laurent EMN, St-Germain JR, Blok LS, Vino A, Klämbt V, Deutsch K, Wu CHW, Kolvenbach CM, Kause F, Ottlewski I, Schneider R, Kitzler TM, Majmundar AJ, Buerger F, Onuchic-Whitford AC, Youying M, Kolb A, Salmanullah D, Chen E, van der Ven AT, Rao J, Ityel H, Seltzsam S, Rieke JM, Chen J, Vivante A, Hwang DY, Kohl S, Dworschak GC, Hermle T, Alders M, Bartolomaeus T, Bauer SB, Baum MA, Brilstra EH, Challman TD, Zyskind J, Costin CE, Dipple KM, Duijkers FA, Ferguson M, Fitzpatrick DR, Fick R, Glass IA, Hulick PJ, Kline AD, Krey I, Kumar S, Lu W, Marco EJ, Wentzensen IM, Mefford HC, Platzer K, Povolotskaya IS, Savatt JM, Shcherbakova NV, Senguttuvan P, Squire AE, Stein DR, Thiffault I, Voinova VY, Somers MJG, Ferguson MA, Traum AZ, Daouk GH, Daga A, Rodig NM, Terhal PA, van Binsbergen E, Eid LA, Tasic V, Rasouly HM, Lim TY, Ahram DF, Gharavi AG, Reutter HM, Rehm HL, MacArthur DG, Lek M, Laricchia KM, Lifton RP, Xu H, Mane SM, Sanna-Cherchi S, Sharrocks AD, Raught B, Fisher SE, Bouchard M, Khokha MK, Shril S, Hildebrandt F. Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations. Am J Hum Genet 2020; 107:727-742. [PMID: 32891193 PMCID: PMC7536580 DOI: 10.1016/j.ajhg.2020.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/14/2020] [Indexed: 01/10/2023] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) constitute one of the most frequent birth defects and represent the most common cause of chronic kidney disease in the first three decades of life. Despite the discovery of dozens of monogenic causes of CAKUT, most pathogenic pathways remain elusive. We performed whole-exome sequencing (WES) in 551 individuals with CAKUT and identified a heterozygous de novo stop-gain variant in ZMYM2 in two different families with CAKUT. Through collaboration, we identified in total 14 different heterozygous loss-of-function mutations in ZMYM2 in 15 unrelated families. Most mutations occurred de novo, indicating possible interference with reproductive function. Human disease features are replicated in X. tropicalis larvae with morpholino knockdowns, in which expression of truncated ZMYM2 proteins, based on individual mutations, failed to rescue renal and craniofacial defects. Moreover, heterozygous Zmym2-deficient mice recapitulated features of CAKUT with high penetrance. The ZMYM2 protein is a component of a transcriptional corepressor complex recently linked to the silencing of developmentally regulated endogenous retrovirus elements. Using protein-protein interaction assays, we show that ZMYM2 interacts with additional epigenetic silencing complexes, as well as confirming that it binds to FOXP1, a transcription factor that has also been linked to CAKUT. In summary, our findings establish that loss-of-function mutations of ZMYM2, and potentially that of other proteins in its interactome, as causes of human CAKUT, offering new routes for studying the pathogenesis of the disorder.
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Affiliation(s)
- Dervla M Connaughton
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Nephrology, Department of Medicine, University Hospital - London Health Sciences Centre, Schulich School of Medicine & Dentistry, Western University, 339 Windermere Road, London, ON N6A 5A5, Canada
| | - Rufeng Dai
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Nephrology, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Danielle J Owen
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Jonathan Marquez
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nina Mann
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Adda L Graham-Paquin
- Rosalind & Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montréal, QC H3A 1A3, Canada
| | - Makiko Nakayama
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Estelle M N Laurent
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Jonathan R St-Germain
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Lot Snijders Blok
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500HE Nijmegen, the Netherlands; Human Genetics Department, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Arianna Vino
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands
| | - Verena Klämbt
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Konstantin Deutsch
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chen-Han Wilfred Wu
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Caroline M Kolvenbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Franziska Kause
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Isabel Ottlewski
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ronen Schneider
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas M Kitzler
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amar J Majmundar
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Florian Buerger
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ana C Onuchic-Whitford
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mao Youying
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amy Kolb
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daanya Salmanullah
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Evan Chen
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amelie T van der Ven
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jia Rao
- Department of Nephrology, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Hadas Ityel
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Steve Seltzsam
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Johanna M Rieke
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jing Chen
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Asaf Vivante
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Tel Aviv University, Faculty of Medicine, Tel Aviv-Yafo 6997801, Israel
| | - Daw-Yang Hwang
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stefan Kohl
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gabriel C Dworschak
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Tobias Hermle
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mariëlle Alders
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Meibergdreef 9, 1105 Amsterdam, Netherlands
| | - Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal- Straße 55, 04103 Leipzig, Germany
| | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle A Baum
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eva H Brilstra
- Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Thomas D Challman
- Geisinger, Autism & Developmental Medicine Institute, 100 N Academy Avenue, Danville, PA 17822, USA
| | - Jacob Zyskind
- Department of Clinical Genomics, GeneDx, 207 Perry Pkwy, Gaithersburg, MD 20877, USA
| | - Carrie E Costin
- Department of Clinical Genetics, Akron Children's Hospital, One Perkins Square, Akron, OH 44308, USA
| | - Katrina M Dipple
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Floor A Duijkers
- Department of Clinical Genetics, University of Amsterdam, 1012 WX Amsterdam, the Netherlands
| | - Marcia Ferguson
- Department of Clinical Genetics, Harvey Institute for Human Genetics, 6701 Charles St, Towson, MD 21204, USA
| | - David R Fitzpatrick
- MRC Institute of Genetics & Molecular Medicine, Royal Hospital for Sick Children, The University of Edinburgh, 2XU, Crewe Rd S, Edinburgh EH4 2XU, UK
| | - Roger Fick
- Mary Bridge Childrens Hospital, 316 Martin Luther King JR Way, Tacoma, WA 98405, USA
| | - Ian A Glass
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, 1000 Central Street, Suite 610, Evanston, IL 60201, USA
| | - Antonie D Kline
- Department of Clinical Genetics, Harvey Institute for Human Genetics, 6701 Charles St, Towson, MD 21204, USA
| | - Ilona Krey
- Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal- Straße 55, 04103 Leipzig, Germany; Swiss Epilepsy Center, Klinik Lengg, Bleulerstrasse 60, 8000 Zürich, Switzerland
| | - Selvin Kumar
- Department of Pediatric Nephrology, Institute of Child Health and Hospital for Children, Tamil Salai, Egmore, Chennai, Tamil Nadu 600008, India
| | - Weining Lu
- Renal Section, Department of Medicine, Boston University Medical Center, 650 Albany Street, Boston, MA 02118, USA
| | - Elysa J Marco
- Cortica Healthcare, 4000 Civic Center Drive, Ste 100, San Rafael, CA 94939, USA
| | - Ingrid M Wentzensen
- Department of Clinical Genomics, GeneDx, 207 Perry Pkwy, Gaithersburg, MD 20877, USA
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal- Straße 55, 04103 Leipzig, Germany
| | - Inna S Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow 117997, Russia
| | - Juliann M Savatt
- Geisinger, Autism & Developmental Medicine Institute, 100 N Academy Avenue, Danville, PA 17822, USA
| | - Natalia V Shcherbakova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow 117997, Russia
| | - Prabha Senguttuvan
- Department of Pediatric Nephrology, Dr. Mehta's Multi-Specialty Hospital, No.2, Mc Nichols Rd, Chetpet, Chennai, Tamil Nadu 600031, India
| | - Audrey E Squire
- Seattle Children's Hospital, Department of Genetic Medicine, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Deborah R Stein
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, 2401 Gillham Rd, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO 64108, USA; University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, 5000 Holmes St, Kansas City, MO 64110, USA
| | - Victoria Y Voinova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow 117997, Russia
| | - Michael J G Somers
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael A Ferguson
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Avram Z Traum
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ghaleb H Daouk
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ankana Daga
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nancy M Rodig
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Paulien A Terhal
- Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje 1000, North Macedonia
| | - Hila Milo Rasouly
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Tze Y Lim
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Dina F Ahram
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Heiko M Reutter
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany; Section of Neonatology and Pediatric Intensive Care, Clinic for Pediatrics, University Hospital Bonn, Adenauerallee 119, 53313 Bonn, Germany
| | - Heidi L Rehm
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Kristen M Laricchia
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Richard P Lifton
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Hong Xu
- Department of Nephrology, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06510, USA
| | - Simone Sanna-Cherchi
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500HE Nijmegen, the Netherlands
| | - Maxime Bouchard
- Rosalind & Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montréal, QC H3A 1A3, Canada
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shirlee Shril
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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8
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Mann N, Kause F, Henze EK, Gharpure A, Shril S, Connaughton DM, Nakayama M, Klämbt V, Majmundar AJ, Wu CHW, Kolvenbach CM, Dai R, Chen J, van der Ven AT, Ityel H, Tooley MJ, Kari JA, Bownass L, El Desoky S, De Franco E, Shalaby M, Tasic V, Bauer SB, Lee RS, Beckel JM, Yu W, Mane SM, Lifton RP, Reutter H, Ellard S, Hibbs RE, Kawate T, Hildebrandt F. CAKUT and Autonomic Dysfunction Caused by Acetylcholine Receptor Mutations. Am J Hum Genet 2019; 105:1286-1293. [PMID: 31708116 DOI: 10.1016/j.ajhg.2019.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause of chronic kidney disease in the first three decades of life, and in utero obstruction to urine flow is a frequent cause of secondary upper urinary tract malformations. Here, using whole-exome sequencing, we identified three different biallelic mutations in CHRNA3, which encodes the α3 subunit of the nicotinic acetylcholine receptor, in five affected individuals from three unrelated families with functional lower urinary tract obstruction and secondary CAKUT. Four individuals from two families have additional dysautonomic features, including impaired pupillary light reflexes. Functional studies in vitro demonstrated that the mutant nicotinic acetylcholine receptors were unable to generate current following stimulation with acetylcholine. Moreover, the truncating mutations p.Thr337Asnfs∗81 and p.Ser340∗ led to impaired plasma membrane localization of CHRNA3. Although the importance of acetylcholine signaling in normal bladder function has been recognized, we demonstrate for the first time that mutations in CHRNA3 can cause bladder dysfunction, urinary tract malformations, and dysautonomia. These data point to a pathophysiologic sequence by which monogenic mutations in genes that regulate bladder innervation may secondarily cause CAKUT.
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9
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Staretz-Chacham O, Shukrun R, Barel O, Pode-Shakked B, Pleniceanu O, Anikster Y, Shalva N, Ferreira CR, Ben-Haim Kadosh A, Richardson J, Mane SM, Hildebrandt F, Vivante A. Novel homozygous ENPP1 mutation causes generalized arterial calcifications of infancy, thrombocytopenia, and cardiovascular and central nervous system syndrome. Am J Med Genet A 2019; 179:2112-2118. [PMID: 31444901 DOI: 10.1002/ajmg.a.61334] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 07/30/2019] [Accepted: 08/01/2019] [Indexed: 12/19/2022]
Abstract
Generalized arterial calcifications of infancy (GACI) is caused by mutations in ENPP1. Other ENPP1-related phenotypes include pseudoxanthoma elasticum, hypophosphatemic rickets, and Cole disease. We studied four children from two Bedouin consanguineous families who presented with severe clinical phenotype including thrombocytopenia, hypoglycemia, hepatic, and neurologic manifestations. Initial working diagnosis included congenital infection; however, patients remained without a definitive diagnosis despite extensive workup. Consequently, we investigated a potential genetic etiology. Whole exome sequencing (WES) was performed for affected children and their parents. Following the identification of a novel mutation in the ENPP1 gene, we characterized this novel multisystemic presentation and revised relevant imaging studies. Using WES, we identified a novel homozygous mutation (c.556G > C; p.Gly186Arg) in ENPP1 which affects a highly conserved protein domain (somatomedin B2). ENPP1-associated genetic diseases exhibit phenotypic heterogeneity depending on mutation type and location. Follow-up clinical characterization of these families allowed us to revise and detect new features of systemic calcifications, which established the diagnosis of GACI, expanding the phenotypic spectrum associated with ENPP1 mutations. Our findings demonstrate that this novel ENPP1 founder mutation can cause a fatal multisystemic phenotype, mimicking severe congenital infection. This also represents the first reported mutation affecting the SMB2 domain, associated with GACI.
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Affiliation(s)
- Orna Staretz-Chacham
- Metabolic Clinic, Pediatric Division, Soroka Medical Center, Ben-Gurion University, Be'er Sheva, Israel.,Department of Neonatology, Soroka University Medical Center, Faculty of Health Sciences, School of Medicine, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Rachel Shukrun
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat-Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ortal Barel
- The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Ben Pode-Shakked
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat-Gan, Israel.,Talpiot Medical Leadership Program, Department of Pediatrics B and Pediatric Nephrology Unit, Sheba Medical Center, Ramat-Gan, Israel
| | - Oren Pleniceanu
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat-Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yair Anikster
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat-Gan, Israel
| | - Nechama Shalva
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat-Gan, Israel
| | - Carlos R Ferreira
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Admit Ben-Haim Kadosh
- Department of Neonatology, Soroka University Medical Center, Faculty of Health Sciences, School of Medicine, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Justin Richardson
- Department of Neonatology, Soroka University Medical Center, Faculty of Health Sciences, School of Medicine, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Asaf Vivante
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat-Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Talpiot Medical Leadership Program, Department of Pediatrics B and Pediatric Nephrology Unit, Sheba Medical Center, Ramat-Gan, Israel.,Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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10
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Mann N, Braun DA, Amann K, Tan W, Shril S, Connaughton DM, Nakayama M, Schneider R, Kitzler TM, van der Ven AT, Chen J, Ityel H, Vivante A, Majmundar AJ, Daga A, Warejko JK, Lovric S, Ashraf S, Jobst-Schwan T, Widmeier E, Hugo H, Mane SM, Spaneas L, Somers MJG, Ferguson MA, Traum AZ, Stein DR, Baum MA, Daouk GH, Lifton RP, Manzi S, Vakili K, Kim HB, Rodig NM, Hildebrandt F. Whole-Exome Sequencing Enables a Precision Medicine Approach for Kidney Transplant Recipients. J Am Soc Nephrol 2019; 30:201-215. [PMID: 30655312 DOI: 10.1681/asn.2018060575] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/19/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) finds a CKD-related mutation in approximately 20% of patients presenting with CKD before 25 years of age. Although provision of a molecular diagnosis could have important implications for clinical management, evidence is lacking on the diagnostic yield and clinical utility of WES for pediatric renal transplant recipients. METHODS To determine the diagnostic yield of WES in pediatric kidney transplant recipients, we recruited 104 patients who had received a transplant at Boston Children's Hospital from 2007 through 2017, performed WES, and analyzed results for likely deleterious variants in approximately 400 genes known to cause CKD. RESULTS By WES, we identified a genetic cause of CKD in 34 out of 104 (32.7%) transplant recipients. The likelihood of detecting a molecular genetic diagnosis was highest for patients with urinary stone disease (three out of three individuals), followed by renal cystic ciliopathies (seven out of nine individuals), steroid-resistant nephrotic syndrome (nine out of 21 individuals), congenital anomalies of the kidney and urinary tract (ten out of 55 individuals), and chronic glomerulonephritis (one out of seven individuals). WES also yielded a molecular diagnosis for four out of nine individuals with ESRD of unknown etiology. The WES-related molecular genetic diagnosis had implications for clinical care for five patients. CONCLUSIONS Nearly one third of pediatric renal transplant recipients had a genetic cause of their kidney disease identified by WES. Knowledge of this genetic information can help guide management of both transplant patients and potential living related donors.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut; and
| | | | | | | | | | | | | | | | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut; and.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
| | - Shannon Manzi
- Department of Genetics and Genomics, Department of Pharmacy, and
| | - Khashayar Vakili
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Heung Bae Kim
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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11
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Dong W, Nicolson NG, Choi J, Barbieri AL, Kunstman JW, Abou Azar S, Knight J, Bilguvar K, Mane SM, Lifton RP, Korah R, Carling T. Clonal evolution analysis of paired anaplastic and well-differentiated thyroid carcinomas reveals shared common ancestor. Genes Chromosomes Cancer 2018; 57:645-652. [PMID: 30136351 DOI: 10.1002/gcc.22678] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/12/2018] [Accepted: 08/03/2018] [Indexed: 02/04/2023] Open
Abstract
Foci of papillary or follicular thyroid carcinoma are frequently noted in thyroidectomy specimens of anaplastic thyroid carcinoma (ATC). However, whether ATCs evolve from these co-existing well-differentiated thyroid carcinomas (WDTCs) has not been well-understood. To investigate the progression of ATC in patients with co-existing WDTCs, five ATC tumors with co-existing WDTCs and matching normal tissues were whole-exome sequenced. After mapping the somatic alteration landscape, evolutionary lineages were constructed by sub-clone analysis. Though each tumor harbored at least some unique private mutations, all five ATCs demonstrated numerous overlapping mutations with matched WDTCs. Clonal analysis further demonstrated that each ATC/WDTC pair shared a common ancestor, with some pairs diverging early in their evolution and others in which the ATC seems to arise directly from a sub-clone of the WDTC. Though the precise lineal relationship remains ambiguous, based on the genetic relationship, our study clearly suggests a shared origin of ATC and WDTC.
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Affiliation(s)
- Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
| | - Norman G Nicolson
- Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, Connecticut.,Department of Surgery, Yale School of Medicine, New Haven, Connecticut
| | - Jungmin Choi
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
| | - Andrea L Barbieri
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
| | - John W Kunstman
- Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, Connecticut.,Department of Surgery, Yale School of Medicine, New Haven, Connecticut
| | - Sara Abou Azar
- Department of Surgery, Yale School of Medicine, New Haven, Connecticut
| | - James Knight
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut
| | - Kaya Bilguvar
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut.,Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut
| | - Shrikant M Mane
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut.,Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
| | - Reju Korah
- Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, Connecticut.,Department of Surgery, Yale School of Medicine, New Haven, Connecticut
| | - Tobias Carling
- Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, Connecticut.,Department of Surgery, Yale School of Medicine, New Haven, Connecticut
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12
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van der Ven AT, Connaughton DM, Ityel H, Mann N, Nakayama M, Chen J, Vivante A, Hwang DY, Schulz J, Braun DA, Schmidt JM, Schapiro D, Schneider R, Warejko JK, Daga A, Majmundar AJ, Tan W, Jobst-Schwan T, Hermle T, Widmeier E, Ashraf S, Amar A, Hoogstraaten CA, Hugo H, Kitzler TM, Kause F, Kolvenbach CM, Dai R, Spaneas L, Amann K, Stein DR, Baum MA, Somers MJG, Rodig NM, Ferguson MA, Traum AZ, Daouk GH, Bogdanović R, Stajić N, Soliman NA, Kari JA, El Desoky S, Fathy HM, Milosevic D, Al-Saffar M, Awad HS, Eid LA, Selvin A, Senguttuvan P, Sanna-Cherchi S, Rehm HL, MacArthur DG, Lek M, Laricchia KM, Wilson MW, Mane SM, Lifton RP, Lee RS, Bauer SB, Lu W, Reutter HM, Tasic V, Shril S, Hildebrandt F. Whole-Exome Sequencing Identifies Causative Mutations in Families with Congenital Anomalies of the Kidney and Urinary Tract. J Am Soc Nephrol 2018; 29:2348-2361. [PMID: 30143558 PMCID: PMC6115658 DOI: 10.1681/asn.2017121265] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 06/11/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Congenital anomalies of the kidney and urinary tract (CAKUT) are the most prevalent cause of kidney disease in the first three decades of life. Previous gene panel studies showed monogenic causation in up to 12% of patients with CAKUT. METHODS We applied whole-exome sequencing to analyze the genotypes of individuals from 232 families with CAKUT, evaluating for mutations in single genes known to cause human CAKUT and genes known to cause CAKUT in mice. In consanguineous or multiplex families, we additionally performed a search for novel monogenic causes of CAKUT. RESULTS In 29 families (13%), we detected a causative mutation in a known gene for isolated or syndromic CAKUT that sufficiently explained the patient's CAKUT phenotype. In three families (1%), we detected a mutation in a gene reported to cause a phenocopy of CAKUT. In 15 of 155 families with isolated CAKUT, we detected deleterious mutations in syndromic CAKUT genes. Our additional search for novel monogenic causes of CAKUT in consanguineous and multiplex families revealed a potential single, novel monogenic CAKUT gene in 19 of 232 families (8%). CONCLUSIONS We identified monogenic mutations in a known human CAKUT gene or CAKUT phenocopy gene as the cause of disease in 14% of the CAKUT families in this study. Whole-exome sequencing provides an etiologic diagnosis in a high fraction of patients with CAKUT and will provide a new basis for the mechanistic understanding of CAKUT.
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Affiliation(s)
- Amelie T van der Ven
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dervla M Connaughton
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Hadas Ityel
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nina Mann
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Makiko Nakayama
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jing Chen
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daw-Yang Hwang
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Julian Schulz
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - David Schapiro
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ronen Schneider
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jillian K Warejko
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ankana Daga
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amar J Majmundar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Weizhen Tan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tilman Jobst-Schwan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tobias Hermle
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eugen Widmeier
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shazia Ashraf
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ali Amar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Charlotte A Hoogstraaten
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Hannah Hugo
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Thomas M Kitzler
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Franziska Kause
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Caroline M Kolvenbach
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rufeng Dai
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Leslie Spaneas
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kassaundra Amann
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Deborah R Stein
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michelle A Baum
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael J G Somers
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nancy M Rodig
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael A Ferguson
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Avram Z Traum
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ghaleb H Daouk
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Radovan Bogdanović
- Department of Pediatric Nephrology, Institute for Mother and Child Health Care, Belgrade, Serbia
| | - Natasa Stajić
- Department of Pediatric Nephrology, Institute for Mother and Child Health Care, Belgrade, Serbia
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Cairo University, Egypt
- Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Jameela A Kari
- Department of Pediatrics and
- Pediatric Nephrology Center of Excellence, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Sherif El Desoky
- Department of Pediatrics and
- Pediatric Nephrology Center of Excellence, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Hanan M Fathy
- Pediatric Nephrology Unit, University of Alexandria, Alexandria, Egypt
| | - Danko Milosevic
- University of Zagreb School of Medicine, University Hospital Center Zagreb, Zagreb, Croatia
| | - Muna Al-Saffar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Hazem S Awad
- Pediatric Nephrology Department, Dubai Kidney Center Of Excellence, Dubai Hospital, Dubai, United Arab Emirates
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Kidney Center Of Excellence, Dubai Hospital, Dubai, United Arab Emirates
| | - Aravind Selvin
- Department of Pediatric Nephrology, Institute of Child Health and Hospital for Children, The Tamil Nadu Dr. M.G.R. Medical University, Chennai, Tamil Nadu, India
| | - Prabha Senguttuvan
- Department of Pediatric Nephrology, Dr. Mehta's Multi-Specialty Hospital, Chennai, Tamil Nadu, India
| | | | - Heidi L Rehm
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Michael W Wilson
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
- Rockefeller University, New York, New York
| | - Richard S Lee
- Department of Urology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Weining Lu
- Renal Section, Department of Medicine and Pathology, Boston University Medical Center, Boston, Massachusetts
| | - Heiko M Reutter
- Institute of Human Genetics and
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany; and
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, Macedonia
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts;
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13
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Sousa AMM, Zhu Y, Raghanti MA, Kitchen RR, Onorati M, Tebbenkamp ATN, Stutz B, Meyer KA, Li M, Kawasawa YI, Liu F, Perez RG, Mele M, Carvalho T, Skarica M, Gulden FO, Pletikos M, Shibata A, Stephenson AR, Edler MK, Ely JJ, Elsworth JD, Horvath TL, Hof PR, Hyde TM, Kleinman JE, Weinberger DR, Reimers M, Lifton RP, Mane SM, Noonan JP, State MW, Lein ES, Knowles JA, Marques-Bonet T, Sherwood CC, Gerstein MB, Sestan N. Molecular and cellular reorganization of neural circuits in the human lineage. Science 2018; 358:1027-1032. [PMID: 29170230 DOI: 10.1126/science.aan3456] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 10/17/2017] [Indexed: 01/06/2023]
Abstract
To better understand the molecular and cellular differences in brain organization between human and nonhuman primates, we performed transcriptome sequencing of 16 regions of adult human, chimpanzee, and macaque brains. Integration with human single-cell transcriptomic data revealed global, regional, and cell-type-specific species expression differences in genes representing distinct functional categories. We validated and further characterized the human specificity of genes enriched in distinct cell types through histological and functional analyses, including rare subpallial-derived interneurons expressing dopamine biosynthesis genes enriched in the human striatum and absent in the nonhuman African ape neocortex. Our integrated analysis of the generated data revealed diverse molecular and cellular features of the phylogenetic reorganization of the human brain across multiple levels, with relevance for brain function and disease.
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Affiliation(s)
- André M M Sousa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Ying Zhu
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mary Ann Raghanti
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Robert R Kitchen
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA.,Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Marco Onorati
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Department of Biology, Unit of Cell and Developmental Biology, University of Pisa, Pisa, Italy
| | - Andrew T N Tebbenkamp
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Bernardo Stutz
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, New Haven, CT, USA
| | - Kyle A Meyer
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mingfeng Li
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Yuka Imamura Kawasawa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Departments of Pharmacology and Biochemistry and Molecular Biology, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Fuchen Liu
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Raquel Garcia Perez
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | - Marta Mele
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | - Tiago Carvalho
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | - Mario Skarica
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Forrest O Gulden
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mihovil Pletikos
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Akemi Shibata
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Alexa R Stephenson
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Melissa K Edler
- Department of Anthropology and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - John J Ely
- Alamogordo Primate Facility, Holloman Air Force Base, NM, USA
| | - John D Elsworth
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Tamas L Horvath
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, New Haven, CT, USA
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Mark Reimers
- Neuroscience Program, Michigan State University, East Lansing, MI, USA
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Shrikant M Mane
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven, CT, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Matthew W State
- Department of Psychiatry and Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - James A Knowles
- Department of Psychiatry and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain.,Centro Nacional de Analisis Genomico, Barcelona, Catalonia, Spain
| | - Chet C Sherwood
- Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA. .,Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, New Haven, CT, USA.,Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience, Neurodegeneration, and Repair and Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA
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14
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Warejko JK, Schueler M, Vivante A, Tan W, Daga A, Lawson JA, Braun DA, Shril S, Amann K, Somers MJG, Rodig NM, Baum MA, Daouk G, Traum AZ, Kim HB, Vakili K, Porras D, Lock J, Rivkin MJ, Chaudry G, Smoot LB, Singh MN, Smith ER, Mane SM, Lifton RP, Stein DR, Ferguson MA, Hildebrandt F. Whole Exome Sequencing Reveals a Monogenic Cause of Disease in ≈43% of 35 Families With Midaortic Syndrome. Hypertension 2018; 71:691-699. [PMID: 29483232 DOI: 10.1161/hypertensionaha.117.10296] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/06/2017] [Accepted: 01/18/2018] [Indexed: 11/16/2022]
Abstract
Midaortic syndrome (MAS) is a rare cause of severe childhood hypertension characterized by narrowing of the abdominal aorta in children and is associated with extensive vascular disease. It may occur as part of a genetic syndrome, such as neurofibromatosis, or as consequence of a pathological inflammatory disease. However, most cases are considered idiopathic. We hypothesized that in a high percentage of these patients, a monogenic cause of disease may be detected by evaluating whole exome sequencing data for mutations in 1 of 38 candidate genes previously described to cause vasculopathy. We studied a cohort of 36 individuals from 35 different families with MAS by exome sequencing. In 15 of 35 families (42.9%), we detected likely causal dominant mutations. In 15 of 35 (42.9%) families with MAS, whole exome sequencing revealed a mutation in one of the genes previously associated with vascular disease (NF1, JAG1, ELN, GATA6, and RNF213). Ten of the 15 mutations have not previously been reported. This is the first report of ELN, RNF213, or GATA6 mutations in individuals with MAS. Mutations were detected in NF1 (6/15 families), JAG1 (4/15 families), ELN (3/15 families), and one family each for GATA6 and RNF213 Eight individuals had syndromic disease and 7 individuals had isolated MAS. Whole exome sequencing can provide conclusive molecular genetic diagnosis in a high fraction of individuals with syndromic or isolated MAS. Establishing an etiologic diagnosis may reveal genotype/phenotype correlations for MAS in the future and should, therefore, be performed routinely in MAS.
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Affiliation(s)
- Jillian K Warejko
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Markus Schueler
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Asaf Vivante
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Weizhen Tan
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Ankana Daga
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Jennifer A Lawson
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Daniela A Braun
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Shirlee Shril
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Kassaundra Amann
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Michael J G Somers
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Nancy M Rodig
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Michelle A Baum
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Ghaleb Daouk
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Avram Z Traum
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Heung Bae Kim
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Khashayar Vakili
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Diego Porras
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - James Lock
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Michael J Rivkin
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Gulraiz Chaudry
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Leslie B Smoot
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Michael N Singh
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Edward R Smith
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Shrikant M Mane
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Richard P Lifton
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Deborah R Stein
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Michael A Ferguson
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.)
| | - Friedhelm Hildebrandt
- From the Department of Medicine (J.K.W., M.S., A.V., W.T., A.D., J.A.L., D.A.B., S.S., K.A., M.J.G.S., N.M.R., M.A.B., G.D., A.Z.T., D.R.S., M.A.F., F.H.), Department of Surgery (H.B.K., K.V.), Department of Cardiology (D.P., J.L., L.B.S., M.N.S.), Department of Neurology (M.J.R.), Department of Radiology (G.C.), and Department of Neurosurgery (E.R.S.), Boston Children's Hospital, Harvard Medical School, MA; Department of Pediatrics, Yale-New Haven Children's Hospital (J.K.W.) and Department of Genetics (S.M.M., R.P.L.), Yale School of Medicine, CT; Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel (A.V.); and Laboratory of Human Genetics and Genomics, The Rockefeller University, New York (R.P.L.).
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15
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van der Ven AT, Kobbe B, Kohl S, Shril S, Pogoda HM, Imhof T, Ityel H, Vivante A, Chen J, Hwang DY, Connaughton DM, Mann N, Widmeier E, Taglienti M, Schmidt JM, Nakayama M, Senguttuvan P, Kumar S, Tasic V, Kehinde EO, Mane SM, Lifton RP, Soliman N, Lu W, Bauer SB, Hammerschmidt M, Wagener R, Hildebrandt F. A homozygous missense variant in VWA2, encoding an interactor of the Fraser-complex, in a patient with vesicoureteral reflux. PLoS One 2018; 13:e0191224. [PMID: 29351342 PMCID: PMC5774751 DOI: 10.1371/journal.pone.0191224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 06/06/2017] [Accepted: 12/29/2017] [Indexed: 11/18/2022] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause (40-50%) of chronic kidney disease (CKD) in children. About 40 monogenic causes of CAKUT have so far been discovered. To date less than 20% of CAKUT cases can be explained by mutations in these 40 genes. To identify additional monogenic causes of CAKUT, we performed whole exome sequencing (WES) and homozygosity mapping (HM) in a patient with CAKUT from Indian origin and consanguineous descent. We identified a homozygous missense mutation (c.1336C>T, p.Arg446Cys) in the gene Von Willebrand factor A domain containing 2 (VWA2). With immunohistochemistry studies on kidneys of newborn (P1) mice, we show that Vwa2 and Fraser extracellular matrix complex subunit 1 (Fras1) co-localize in the nephrogenic zone of the renal cortex. We identified a pronounced expression of Vwa2 in the basement membrane of the ureteric bud (UB) and derivatives of the metanephric mesenchyme (MM). By applying in vitro assays, we demonstrate that the Arg446Cys mutation decreases translocation of monomeric VWA2 protein and increases translocation of aggregated VWA2 protein into the extracellular space. This is potentially due to the additional, unpaired cysteine residue in the mutated protein that is used for intermolecular disulfide bond formation. VWA2 is a known, direct interactor of FRAS1 of the Fraser-Complex (FC). FC-encoding genes and interacting proteins have previously been implicated in the pathogenesis of syndromic and/or isolated CAKUT phenotypes in humans. VWA2 therefore constitutes a very strong candidate in the search for novel CAKUT-causing genes. Our results from in vitro experiments indicate a dose-dependent neomorphic effect of the Arg446Cys homozygous mutation in VWA2.
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Affiliation(s)
- Amelie T. van der Ven
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Birgit Kobbe
- Center for Biochemistry, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Stefan Kohl
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pediatrics, Cologne Children’s Hospital, Cologne, Germany
| | - Shirlee Shril
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hans-Martin Pogoda
- Institute of Zoology-Developmental Biology, Biocenter Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Thomas Imhof
- Institute for Dental Research and Oral Musculoskeletal Biology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Hadas Ityel
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Asaf Vivante
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel
| | - Jing Chen
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Nephrology, Children’s Hospital of Fudan University, Shanghai, China
| | - Daw-Yang Hwang
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Nephrology, Department of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Dervla M. Connaughton
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nina Mann
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Eugen Widmeier
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mary Taglienti
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Johanna Magdalena Schmidt
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Makiko Nakayama
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Prabha Senguttuvan
- Department of Pediatric Nephrology, Dr. Mehta’s Multispeciality Hospital, Chennai, India
| | - Selvin Kumar
- Department of Pediatric Nephrology, Institute of Child Health and Hospital for Children, the Tamil Nadu Dr. M.G.R. Medical University, Chennai, Tamil Nadu, India
| | - Velibor Tasic
- Medical Faculty Skopje, University Children’s Hospital, Skopje, Macedonia
| | - Elijah O. Kehinde
- Division of Urology, Department of Surgery, Nazarbayev University, Astana, Kazakhstan
| | - Shrikant M. Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Richard P. Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Neveen Soliman
- Department of Pediatrics, Center of Pediatric Nephrology & Transplantation, Cairo University, Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Weining Lu
- Renal Section, Department of Medicine, Boston University Medical Center, Boston, Massachusetts, United States of America
| | - Stuart B. Bauer
- Department of Urology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Matthias Hammerschmidt
- Institute of Zoology-Developmental Biology, Biocenter Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Raimund Wagener
- Center for Biochemistry, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- * E-mail: (RW); (FH)
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (RW); (FH)
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16
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Goldberg SB, Narayan A, Kole AJ, Decker RH, Teysir J, Carriero NJ, Lee A, Nemati R, Nath SK, Mane SM, Deng Y, Sukumar N, Zelterman D, Boffa DJ, Politi K, Gettinger SN, Wilson LD, Herbst RS, Patel AA. Early Assessment of Lung Cancer Immunotherapy Response via Circulating Tumor DNA. Clin Cancer Res 2018; 24:1872-1880. [PMID: 29330207 DOI: 10.1158/1078-0432.ccr-17-1341] [Citation(s) in RCA: 285] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/05/2017] [Accepted: 01/08/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Decisions to continue or suspend therapy with immune checkpoint inhibitors are commonly guided by tumor dynamics seen on serial imaging. However, immunotherapy responses are uniquely challenging to interpret because tumors often shrink slowly or can appear transiently enlarged due to inflammation. We hypothesized that monitoring tumor cell death in real time by quantifying changes in circulating tumor DNA (ctDNA) levels could enable early assessment of immunotherapy efficacy.Experimental Design: We compared longitudinal changes in ctDNA levels with changes in radiographic tumor size and with survival outcomes in 28 patients with metastatic non-small cell lung cancer (NSCLC) receiving immune checkpoint inhibitor therapy. CtDNA was quantified by determining the allele fraction of cancer-associated somatic mutations in plasma using a multigene next-generation sequencing assay. We defined a ctDNA response as a >50% decrease in mutant allele fraction from baseline, with a second confirmatory measurement.Results: Strong agreement was observed between ctDNA response and radiographic response (Cohen's kappa, 0.753). Median time to initial response among patients who achieved responses in both categories was 24.5 days by ctDNA versus 72.5 days by imaging. Time on treatment was significantly longer for ctDNA responders versus nonresponders (median, 205.5 vs. 69 days; P < 0.001). A ctDNA response was associated with superior progression-free survival [hazard ratio (HR), 0.29; 95% CI, 0.09-0.89; P = 0.03], and superior overall survival (HR, 0.17; 95% CI, 0.05-0.62; P = 0.007).Conclusions: A drop in ctDNA level is an early marker of therapeutic efficacy and predicts prolonged survival in patients treated with immune checkpoint inhibitors for NSCLC. Clin Cancer Res; 24(8); 1872-80. ©2018 AACR.
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Affiliation(s)
- Sarah B Goldberg
- Department of Medicine (Medical Oncology), Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Azeet Narayan
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Adam J Kole
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Roy H Decker
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Jimmitti Teysir
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | | | - Angela Lee
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Roxanne Nemati
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Sameer K Nath
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Shrikant M Mane
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Yanhong Deng
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, Connecticut
| | - Nitin Sukumar
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, Connecticut
| | - Daniel Zelterman
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
| | - Daniel J Boffa
- Department of Thoracic Surgery, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Katerina Politi
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Scott N Gettinger
- Department of Medicine (Medical Oncology), Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Lynn D Wilson
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Roy S Herbst
- Department of Medicine (Medical Oncology), Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut.
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17
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Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, Zeng X, Qi H, Chang W, Sierant MC, Hung WC, Haider S, Zhang J, Knight J, Bjornson RD, Castaldi C, Tikhonoa IR, Bilguvar K, Mane SM, Sanders SJ, Mital S, Russell MW, Gaynor JW, Deanfield J, Giardini A, Porter GA, Srivastava D, Lo CW, Shen Y, Watkins WS, Yandell M, Yost HJ, Tristani-Firouzi M, Newburger JW, Roberts AE, Kim R, Zhao H, Kaltman JR, Goldmuntz E, Chung WK, Seidman JG, Gelb BD, Seidman CE, Lifton RP, Brueckner M. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nat Genet 2017; 49:1593-1601. [PMID: 28991257 PMCID: PMC5675000 DOI: 10.1038/ng.3970] [Citation(s) in RCA: 486] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/15/2017] [Indexed: 12/17/2022]
Abstract
Congenital heart disease (CHD) is the leading cause of mortality from birth defects. Exome sequencing of a single cohort of 2,871 CHD probands including 2,645 parent-offspring trios implicated rare inherited mutations in 1.8%, including a recessive founder mutation in GDF1 accounting for ~5% of severe CHD in Ashkenazim, recessive genotypes in MYH6 accounting for ~11% of Shone complex, and dominant FLT4 mutations accounting for 2.3% of Tetralogy of Fallot. De novo mutations (DNMs) accounted for 8% of cases, including ~3% of isolated CHD patients and ~28% with both neurodevelopmental and extra-cardiac congenital anomalies. Seven genes surpassed thresholds for genome-wide significance and 12 genes not previously implicated in CHD had > 70% probability of being disease-related; DNMs in ~440 genes are inferred to contribute to CHD. There was striking overlap between genes with damaging DNMs in probands with CHD and autism.
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Affiliation(s)
- Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jason Homsy
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Samir Zaidi
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Qiongshi Lu
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sarah Morton
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Steven R DePalma
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Xue Zeng
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hongjian Qi
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York, USA
| | - Weni Chang
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Michael C Sierant
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Wei-Chien Hung
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Shozeb Haider
- Department of Computational Chemistry, University College London School of Pharmacy, London, UK
| | - Junhui Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - James Knight
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut, USA
| | - Robert D Bjornson
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut, USA
| | | | - Irina R Tikhonoa
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut, USA
| | - Shrikant M Mane
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut, USA
| | - Stephan J Sanders
- Department of Psychiatry, University of California San Francisco, San Francisco, California, USA
| | - Seema Mital
- Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Mark W Russell
- Division of Pediatric Cardiology, University of Michigan, Ann Arbor, Michigan, USA
| | - J William Gaynor
- Department of Pediatric Cardiac Surgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - John Deanfield
- Department of Cardiology, University College London and Great Ormond Street Hospital, London, UK
| | - Alessandro Giardini
- Department of Cardiology, University College London and Great Ormond Street Hospital, London, UK
| | - George A Porter
- Department of Pediatrics, University of Rochester Medical Center, The School of Medicine and Dentistry, Rochester, New York, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA.,Roddenberry Stem Cell Center at Gladstone, San Francisco, California, USA.,Departments of Pediatrics and Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Cecelia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, New York, USA
| | - W Scott Watkins
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, Utah, USA
| | - Mark Yandell
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, Utah, USA.,USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - H Joseph Yost
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, Utah, USA
| | | | - Jane W Newburger
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Amy E Roberts
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Richard Kim
- Pediatric Cardiac Surgery, Children's Hospital of Los Angeles, Los Angeles, California, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Jonathan R Kaltman
- Heart Development and Structural Diseases Branch, Division of Cardiovascular Sciences, NHLBI/NIH, Bethesda, Maryland, USA
| | - Elizabeth Goldmuntz
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, New York, USA
| | - Jonathan G Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA
| | - Martina Brueckner
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
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18
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Chaste P, Klei L, Sanders SJ, Hus V, Murtha MT, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Mane SM, Martin DM, Morrow EM, Walsh CA, Sutcliffe JS, Martin CL, Beaudet AL, Lord C, State MW, Cook EH, Devlin B. A genome-wide association study of autism using the Simons Simplex Collection: Does reducing phenotypic heterogeneity in autism increase genetic homogeneity? Biol Psychiatry 2015; 77:775-84. [PMID: 25534755 PMCID: PMC4379124 DOI: 10.1016/j.biopsych.2014.09.017] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [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: 05/17/2014] [Revised: 09/02/2014] [Accepted: 09/03/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Phenotypic heterogeneity in autism has long been conjectured to be a major hindrance to the discovery of genetic risk factors, leading to numerous attempts to stratify children based on phenotype to increase power of discovery studies. This approach, however, is based on the hypothesis that phenotypic heterogeneity closely maps to genetic variation, which has not been tested. Our study examines the impact of subphenotyping of a well-characterized autism spectrum disorder (ASD) sample on genetic homogeneity and the ability to discover common genetic variants conferring liability to ASD. METHODS Genome-wide genotypic data of 2576 families from the Simons Simplex Collection were analyzed in the overall sample and phenotypic subgroups defined on the basis of diagnosis, IQ, and symptom profiles. We conducted a family-based association study, as well as estimating heritability and evaluating allele scores for each phenotypic subgroup. RESULTS Association analyses revealed no genome-wide significant association signal. Subphenotyping did not increase power substantially. Moreover, allele scores built from the most associated single nucleotide polymorphisms, based on the odds ratio in the full sample, predicted case status in subsets of the sample equally well and heritability estimates were very similar for all subgroups. CONCLUSIONS In genome-wide association analysis of the Simons Simplex Collection sample, reducing phenotypic heterogeneity had at most a modest impact on genetic homogeneity. Our results are based on a relatively small sample, one with greater homogeneity than the entire population; if they apply more broadly, they imply that analysis of subphenotypes is not a productive path forward for discovering genetic risk variants in ASD.
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Affiliation(s)
- Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; FondaMental Foundation, Créteil; Centre Hospitalier Sainte Anne, Paris, France.
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of
Medicine, Pittsburgh, Pennsylvania, USA
| | - Stephan J. Sanders
- Department of Genetics, Yale University School of Medicine, New
Haven, Connecticut, USA,Department of Psychiatry, University of California at San Francisco,
California, USA
| | - Vanessa Hus
- Department of Psychology, University of Michigan, Ann Arbor, MI,
USA
| | - Michael T. Murtha
- Program on Neurogenetics, Yale University School of Medicine, New
Haven, Connecticut, USA
| | - Jennifer K. Lowe
- Neurogenetics Program, Department of Neurology and Center for Autism
Research and Treatment, Semel Institute, David Geffen School of Medicine, University
of California Los Angeles, Los Angeles, California, USA
| | - A. Jeremy Willsey
- Department of Genetics, Yale University School of Medicine, New
Haven, Connecticut, USA,Department of Psychiatry, University of California at San Francisco,
California, USA
| | - Daniel Moreno-De-Luca
- Program on Neurogenetics, Yale University School of Medicine, New
Haven, Connecticut, USA,Department of Psychiatry, Yale University School of Medicine, New
Haven, Connecticut, USA
| | - Timothy W. Yu
- Division of Genetics, Children's Hospital Boston, Harvard
Medical School, Boston, Massachusetts, USA
| | - Eric Fombonne
- Department of Psychiatry and Institute for Development and
disability, Oregon Health & Science University, Portland, Oregon, USA
| | - Daniel Geschwind
- Neurogenetics Program, Department of Neurology and Center for
Autism Research and Treatment, Semel Institute, David Geffen School of Medicine,
University of California Los Angeles, Los Angeles, California, USA
| | - Dorothy E. Grice
- Department of Psychiatry, Mount Sinai School of Medicine, New York,
New York, USA
| | - David H. Ledbetter
- Autism and Developmental Medicine Institute, Geisinger Health
System, Danville, Pennsylvania, USA
| | | | - Donna M. Martin
- Departments of Pediatrics and Human Genetics, University of
Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Eric M. Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry,
Brown University, Providence, Rhode Island, USA,Department of Psychiatry and Human Behavior, Brown University,
Providence, Rhode Island, USA
| | - Christopher A. Walsh
- Howard Hughes Medical Institute and Division of Genetics,
Children's Hospital Boston, and Neurology and Pediatrics, Harvard Medical
School Center for Life Sciences, Boston, Massachusetts, USA
| | - James S. Sutcliffe
- Departments of Molecular Physiology & Biophysics and
Psychiatry, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN,
USA
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger Health
System, Danville, Pennsylvania, USA
| | - Arthur L. Beaudet
- Department of Human and Molecular Genetics, Baylor College of
Medicine, Houston, Texas, USA
| | - Catherine Lord
- Center for Autism and the Developing Brain, Weill Cornell Medical
College, White Plains, New York, USA
| | - Matthew W. State
- Department of Genetics, Yale University School of Medicine, New
Haven, Connecticut, USA,Department of Psychiatry, University of California at San Francisco,
California, USA
| | - Edwin H. Cook
- Institute for Juvenile Research, Department of Psychiatry,
University of Illinois at Chicago, Chicago, Illinois, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of
Medicine, Pittsburgh, Pennsylvania, USA
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19
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Mishra-Gorur K, Çağlayan AO, Schaffer AE, Chabu C, Henegariu O, Vonhoff F, Akgümüş GT, Nishimura S, Han W, Tu S, Baran B, Gümüş H, Dilber C, Zaki MS, Hossni HAA, Rivière JB, Kayserili H, Spencer EG, Rosti RÖ, Schroth J, Per H, Çağlar C, Çağlar Ç, Dölen D, Baranoski JF, Kumandaş S, Minja FJ, Erson-Omay EZ, Mane SM, Lifton RP, Xu T, Keshishian H, Dobyns WB, Chi NC, Šestan N, Louvi A, Bilgüvar K, Yasuno K, Gleeson JG, Günel M. Mutations in KATNB1 cause complex cerebral malformations by disrupting asymmetrically dividing neural progenitors. Neuron 2015; 84:1226-39. [PMID: 25521378 DOI: 10.1016/j.neuron.2014.12.014] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2014] [Indexed: 01/02/2023]
Abstract
Exome sequencing analysis of over 2,000 children with complex malformations of cortical development identified five independent (four homozygous and one compound heterozygous) deleterious mutations in KATNB1, encoding the regulatory subunit of the microtubule-severing enzyme Katanin. Mitotic spindle formation is defective in patient-derived fibroblasts, a consequence of disrupted interactions of mutant KATNB1 with KATNA1, the catalytic subunit of Katanin, and other microtubule-associated proteins. Loss of KATNB1 orthologs in zebrafish (katnb1) and flies (kat80) results in microcephaly, recapitulating the human phenotype. In the developing Drosophila optic lobe, kat80 loss specifically affects the asymmetrically dividing neuroblasts, which display supernumerary centrosomes and spindle abnormalities during mitosis, leading to cell cycle progression delays and reduced cell numbers. Furthermore, kat80 depletion results in dendritic arborization defects in sensory and motor neurons, affecting neural architecture. Taken together, we provide insight into the mechanisms by which KATNB1 mutations cause human cerebral cortical malformations, demonstrating its fundamental role during brain development.
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Affiliation(s)
- Ketu Mishra-Gorur
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ahmet Okay Çağlayan
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ashleigh E Schaffer
- Neurogenetics Laboratory, Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chiswili Chabu
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT 06510, USA
| | - Octavian Henegariu
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Fernando Vonhoff
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Gözde Tuğce Akgümüş
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sayoko Nishimura
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Wenqi Han
- Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shu Tu
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Burçin Baran
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Hakan Gümüş
- Division of Pediatric Neurology, Department of Pediatrics, Erciyes University Medical Faculty, Kayseri 38039, Turkey
| | - Cengiz Dilber
- Division of Pediatric Neurology, Department of Pediatrics, Sütcü Imam University Medical Faculty, Kahramanmaraş 46100, Turkey
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Center, Cairo 12311, Egypt
| | - Heba A A Hossni
- Department of Neurology, National Institute of Neuromotor System, Cairo 12311, Egypt
| | - Jean-Baptiste Rivière
- Equipe Génétique des Anomalies du Développement, EA 4271, Université de Bourgogne, 21078 Dijon, France
| | - Hülya Kayserili
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul 34093, Turkey
| | - Emily G Spencer
- Neurogenetics Laboratory, Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rasim Ö Rosti
- Neurogenetics Laboratory, Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jana Schroth
- Neurogenetics Laboratory, Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hüseyin Per
- Division of Pediatric Neurology, Department of Pediatrics, Erciyes University Medical Faculty, Kayseri 38039, Turkey
| | - Caner Çağlar
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Çağri Çağlar
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Duygu Dölen
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jacob F Baranoski
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sefer Kumandaş
- Division of Pediatric Neurology, Department of Pediatrics, Erciyes University Medical Faculty, Kayseri 38039, Turkey
| | - Frank J Minja
- Department of Radiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - E Zeynep Erson-Omay
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shrikant M Mane
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT 06510, USA
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT 06510, USA
| | - Tian Xu
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT 06510, USA
| | - Haig Keshishian
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - William B Dobyns
- Departments of Pediatrics and Neurology, University of Washington and Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington 98105, USA
| | - Neil C Chi
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nenad Šestan
- Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Angeliki Louvi
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Kaya Bilgüvar
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT 06510, USA
| | - Katsuhito Yasuno
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Joseph G Gleeson
- Neurogenetics Laboratory, Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA.
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20
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Juhlin CC, Goh G, Healy JM, Fonseca AL, Scholl UI, Stenman A, Kunstman JW, Brown TC, Overton JD, Mane SM, Nelson-Williams C, Bäckdahl M, Suttorp AC, Haase M, Choi M, Schlessinger J, Rimm DL, Höög A, Prasad ML, Korah R, Larsson C, Lifton RP, Carling T. Whole-exome sequencing characterizes the landscape of somatic mutations and copy number alterations in adrenocortical carcinoma. J Clin Endocrinol Metab 2015; 100:E493-502. [PMID: 25490274 PMCID: PMC5393505 DOI: 10.1210/jc.2014-3282] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
CONTEXT Adrenocortical carcinoma (ACC) is a rare and lethal malignancy with a poorly defined etiology, and the molecular genetics of ACC are incompletely understood. OBJECTIVE To utilize whole-exome sequencing for genetic characterization of the underlying somatic mutations and copy number alterations present in ACC. DESIGN Screening for somatic mutation events and copy number alterations (CNAs) was performed by comparative analysis of tumors and matched normal samples from 41 patients with ACC. RESULTS In total, 966 nonsynonymous somatic mutations were detected, including 40 tumors with a mean of 16 mutations per sample and one tumor with 314 mutations. Somatic mutations in ACC-associated genes included TP53 (8/41 tumors, 19.5%) and CTNNB1 (4/41, 9.8%). Genes with potential disease-causing mutations included GNAS, NF2, and RB1, and recurrently mutated genes with unknown roles in tumorigenesis comprised CDC27, SCN7A, and SDK1. Recurrent CNAs included amplification at 5p15.33 including TERT (6/41, 14.6%) and homozygous deletion at 22q12.1 including the Wnt repressors ZNRF3 and KREMEN1 (4/41 9.8% and 3/41, 7.3%, respectively). Somatic mutations in ACC-established genes and recurrent ZNRF3 and TERT loci CNAs were mutually exclusive in the majority of cases. Moreover, gene ontology identified Wnt signaling as the most frequently mutated pathway in ACCs. CONCLUSIONS These findings highlight the importance of Wnt pathway dysregulation in ACC and corroborate the finding of homozygous deletion of Wnt repressors ZNRF3 and KREMEN1. Overall, mutations in either TP53 or CTNNB1 as well as focal CNAs at the ZNRF3 or TERT loci denote mutually exclusive events, suggesting separate mechanisms underlying the development of these tumors.
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Affiliation(s)
- C Christofer Juhlin
- Yale Endocrine Neoplasia Laboratory (C.C.J., J.M.H., A.L.F., J.W.K., T.C.B., R.K., T.C.), Yale School of Medicine, New Haven, Connecticut 06520; Department of Surgery (C.C.J., J.M.H., A.L.F., J.W.K., T.C.B., R.K., T.C.), Yale School of Medicine, New Haven, Connecticut, 06520; Department of Genetics (G.G., C.N.W., M.C., R.P.L.), Yale School of Medicine and Howard Hughes Medical Institute, New Haven, Connecticut, 06520; Department of Oncology-Pathology (C.C.J., A.S., A.H., C.L.), Karolinska Institutet, Karolinska University Hospital, CCK, SE-171 76 Stockholm, Sweden; Yale Center for Genome Analysis (JDO, SMM), Orange, Connecticut, 06477; Department of Pathology (D.L.R., M.L.P.), Yale School of Medicine, New Haven, Connecticut, 06520; Department of Pharmacology (J.S.), Yale School of Medicine, New Haven, Connecticut 06520; Department of Molecular Medicine and Surgery (M.B.), Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden; Division of Nephrology (U.I.S.), University Hospital Düsseldorf, 40225 Düsseldorf, Germany; Department of Pathology (A.C.S.), University Hospital Düsseldorf, 40225 Düsseldorf, Germany; and Division of Endocrinology and Diabetology (M.H.), University Hospital Düsseldorf, 40225 Düsseldorf, Germany
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21
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Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, Gonzalez LE, Mandell JD, Mane SM, Murtha MT, Sullivan CA, Walker MF, Waqar Z, Wei L, Willsey AJ, Yamrom B, Lee YH, Grabowska E, Dalkic E, Wang Z, Marks S, Andrews P, Leotta A, Kendall J, Hakker I, Rosenbaum J, Ma B, Rodgers L, Troge J, Narzisi G, Yoon S, Schatz MC, Ye K, McCombie WR, Shendure J, Eichler EE, State MW, Wigler M. The contribution of de novo coding mutations to autism spectrum disorder. Nature 2014; 515:216-21. [PMID: 25363768 PMCID: PMC4313871 DOI: 10.1038/nature13908] [Citation(s) in RCA: 1663] [Impact Index Per Article: 166.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/03/2014] [Indexed: 12/20/2022]
Abstract
Whole exome sequencing has proven to be a powerful tool for understanding the genetic architecture of human disease. Here we apply it to more than 2,500 simplex families, each having a child with an autistic spectrum disorder. By comparing affected to unaffected siblings, we show that 13% of de novo missense mutations and 43% of de novo likely gene-disrupting (LGD) mutations contribute to 12% and 9% of diagnoses, respectively. Including copy number variants, coding de novo mutations contribute to about 30% of all simplex and 45% of female diagnoses. Almost all LGD mutations occur opposite wild-type alleles. LGD targets in affected females significantly overlap the targets in males of lower intelligence quotient (IQ), but neither overlaps significantly with targets in males of higher IQ. We estimate that LGD mutation in about 400 genes can contribute to the joint class of affected females and males of lower IQ, with an overlapping and similar number of genes vulnerable to contributory missense mutation. LGD targets in the joint class overlap with published targets for intellectual disability and schizophrenia, and are enriched for chromatin modifiers, FMRP-associated genes and embryonically expressed genes. Most of the significance for the latter comes from affected females.
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Affiliation(s)
- Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Brian J O'Roak
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Molecular &Medical Genetics, Oregon Health &Science University, Portland, Oregon 97208, USA
| | - Stephan J Sanders
- 1] Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA [2] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael Ronemus
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Niklas Krumm
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Dan Levy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Holly A Stessman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Kali T Witherspoon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Laura Vives
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Karynne E Patterson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Bryan Paeper
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Jeanselle Dea
- Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Shan Dong
- 1] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA [2] Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Luis E Gonzalez
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Jeffrey D Mandell
- Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Shrikant M Mane
- Yale Center for Genomic Analysis, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael T Murtha
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Catherine A Sullivan
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael F Walker
- Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Zainulabedin Waqar
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Liping Wei
- 1] Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China [2] National Institute of Biological Sciences, Beijing 102206, China
| | - A Jeremy Willsey
- 1] Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA [2] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Boris Yamrom
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Yoon-ha Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ewa Grabowska
- 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] New York Genome Center, New York, New York 10013, USA
| | - Ertugrul Dalkic
- 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] Department of Medical Biology, Bulent Ecevit University School of Medicine, 67600 Zonguldak, Turkey
| | - Zihua Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Steven Marks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Anthony Leotta
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jude Kendall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Inessa Hakker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Julie Rosenbaum
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Beicong Ma
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Linda Rodgers
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jennifer Troge
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Giuseppe Narzisi
- 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] New York Genome Center, New York, New York 10013, USA
| | - Seungtai Yoon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Kenny Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Evan E Eichler
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, Seattle, Washington 98195, USA
| | - Matthew W State
- 1] Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA [2] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA [3] Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA [4] Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael Wigler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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22
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Dong S, Walker MF, Carriero NJ, DiCola M, Willsey AJ, Ye AY, Waqar Z, Gonzalez LE, Overton JD, Frahm S, Keaney JF, Teran NA, Dea J, Mandell JD, Hus Bal V, Sullivan CA, DiLullo NM, Khalil RO, Gockley J, Yuksel Z, Sertel SM, Ercan-Sencicek AG, Gupta AR, Mane SM, Sheldon M, Brooks AI, Roeder K, Devlin B, State MW, Wei L, Sanders SJ. De novo insertions and deletions of predominantly paternal origin are associated with autism spectrum disorder. Cell Rep 2014; 9:16-23. [PMID: 25284784 DOI: 10.1016/j.celrep.2014.08.068] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/04/2014] [Accepted: 08/27/2014] [Indexed: 11/27/2022] Open
Abstract
Whole-exome sequencing (WES) studies have demonstrated the contribution of de novo loss-of-function single-nucleotide variants (SNVs) to autism spectrum disorder (ASD). However, challenges in the reliable detection of de novo insertions and deletions (indels) have limited inclusion of these variants in prior analyses. By applying a robust indel detection method to WES data from 787 ASD families (2,963 individuals), we demonstrate that de novo frameshift indels contribute to ASD risk (OR = 1.6; 95% CI = 1.0-2.7; p = 0.03), are more common in female probands (p = 0.02), are enriched among genes encoding FMRP targets (p = 6 × 10(-9)), and arise predominantly on the paternal chromosome (p < 0.001). On the basis of mutation rates in probands versus unaffected siblings, we conclude that de novo frameshift indels contribute to risk in approximately 3% of individuals with ASD. Finally, by observing clustering of mutations in unrelated probands, we uncover two ASD-associated genes: KMT2E (MLL5), a chromatin regulator, and RIMS1, a regulator of synaptic vesicle release.
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Affiliation(s)
- Shan Dong
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Michael F Walker
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nicholas J Carriero
- Biomedical High Performance Computing Center, W.M. Keck Biotechnology Resource Laboratory, Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Michael DiCola
- Bionomics Research and Technology, Environmental and Occupational Health Sciences Institute, Rutgers University, 170 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - A Jeremy Willsey
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adam Y Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China; National Institute of Biological Sciences, Beijing 102206, People's Republic of China
| | - Zainulabedin Waqar
- Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Luis E Gonzalez
- Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - John D Overton
- Yale Center for Genomic Analysis, Yale University School of Medicine, New Haven, CT 06520, USA; Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Stephanie Frahm
- Bionomics Research and Technology, Environmental and Occupational Health Sciences Institute, Rutgers University, 170 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - John F Keaney
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06520, USA
| | - Nicole A Teran
- Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jeanselle Dea
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jeffrey D Mandell
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Vanessa Hus Bal
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Catherine A Sullivan
- Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nicholas M DiLullo
- Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rehab O Khalil
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Research on Children with Special Needs, National Research Center, Cairo 11787, Egypt
| | - Jake Gockley
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Zafer Yuksel
- Department of Medical Genetics, Gulhane Military Medical Academy, Ankara 06010, Turkey
| | - Sinem M Sertel
- Department of Molecular Biology and Genetics, Bilkent University, Ankara 06800, Turkey
| | - A Gulhan Ercan-Sencicek
- Department of Neurosurgery, Yale Neurogenetics Program, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Abha R Gupta
- Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shrikant M Mane
- Yale Center for Genomic Analysis, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Michael Sheldon
- Department of Genetics and the Human Genetics Institute, Rutgers University, 145 Bevier Road, Room 136, Piscataway, NJ 08854, USA
| | - Andrew I Brooks
- Bionomics Research and Technology, Environmental and Occupational Health Sciences Institute, Rutgers University, 170 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Matthew W State
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA; Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China; National Institute of Biological Sciences, Beijing 102206, People's Republic of China.
| | - Stephan J Sanders
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA.
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23
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Chaste P, Sanders SJ, Mohan KN, Klei L, Song Y, Murtha MT, Hus V, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Lord C, Mane SM, Martin DM, Morrow EM, Walsh CA, Sutcliffe JS, State MW, Martin CL, Devlin B, Beaudet AL, Cook EH, Kim SJ. Modest impact on risk for autism spectrum disorder of rare copy number variants at 15q11.2, specifically breakpoints 1 to 2. Autism Res 2014; 7:355-62. [PMID: 24821083 PMCID: PMC6003409 DOI: 10.1002/aur.1378] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [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: 10/24/2013] [Accepted: 03/19/2014] [Indexed: 01/24/2023]
Abstract
The proximal region of chromosome 15 is one of the genomic hotspots for copy number variants (CNVs). Among the rearrangements observed in this region, CNVs from the interval between the common breakpoints 1 and 2 (BP1 and BP2) have been reported cosegregating with autism spectrum disorder (ASD). Although evidence supporting an association between BP1-BP2 CNVs and autism accumulates, the magnitude of the effect of BP1-BP2 CNVs remains elusive, posing a great challenge to recurrence-risk counseling. To gain further insight into their pathogenicity for ASD, we estimated the penetrance of the BP1-BP2 CNVs for ASD as well as their effects on ASD-related phenotypes in a well-characterized ASD sample (n = 2525 families). Transmission disequilibrium test revealed significant preferential transmission only for the duplicated chromosome in probands (20T:9NT). The penetrance of the BP1-BP2 CNVs for ASD was low, conferring additional risks of 0.3% (deletion) and 0.8% (duplication). Stepwise regression analyses suggest a greater effect of the CNVs on ASD-related phenotype in males and when maternally inherited. Taken together, the results are consistent with BP1-BP2 CNVs as risk factors for autism. However, their effect is modest, more akin to that seen for common variants. To be consistent with the current American College of Medical Genetics guidelines for interpretation of postnatal CNV, the BP1-BP2 deletion and duplication CNVs would probably best be classified as variants of uncertain significance (VOUS): they appear to have an impact on risk, but one so modest that these CNVs do not merit pathogenic status.
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Affiliation(s)
- Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- FondaMental Foundation, Créteil, France
| | - Stephan J. Sanders
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, University of California at San Francisco, California, USA
| | - Kommu N. Mohan
- Department of Biological Sciences, BITS Pilani-Hyderabad Campus, Hyderabad, India
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Youeun Song
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michael T. Murtha
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Vanessa Hus
- Department of Psychology, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer K. Lowe
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - A. Jeremy Willsey
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, University of California at San Francisco, California, USA
| | - Daniel Moreno-De-Luca
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Timothy W. Yu
- Division of Genetics, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric Fombonne
- Department of Psychiatry, Oregon Health & Science University, Portland, Oregon, USA
| | - Daniel Geschwind
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Dorothy E. Grice
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA
| | - David H. Ledbetter
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Catherine Lord
- Center for Autism and the Developing Brain, Weill Cornell Medical College, White Plains, New York, USA
| | | | - Donna M. Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Eric M. Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
- Department of Psychiatry and Human Behavior, Brown University, Providence, Rhode Island, USA
| | - Christopher A. Walsh
- Howard Hughes Medical Institute and Division of Genetics, Children's Hospital Boston, and Neurology and Pediatrics, Harvard Medical School Center for Life Sciences, Boston, Massachusetts, USA
| | - James S. Sutcliffe
- Departments of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Matthew W. State
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, University of California at San Francisco, California, USA
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Arthur L. Beaudet
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Edwin H. Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Soo-Jeong Kim
- Center for Integrative Brain Research, Seattle Children's Research Institute & Department of Psychiatry and Behavioral Science, University of Washington, Seattle, WA, USA
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24
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Willsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, Ercan-Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, Liu W, Liu L, Lu C, Xu X, Zhu Y, Mane SM, Lein ES, Wei L, Noonan JP, Roeder K, Devlin B, Sestan N, State MW. Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell 2014; 155:997-1007. [PMID: 24267886 DOI: 10.1016/j.cell.2013.10.020] [Citation(s) in RCA: 623] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 08/02/2013] [Accepted: 10/07/2013] [Indexed: 01/08/2023]
Abstract
Autism spectrum disorder (ASD) is a complex developmental syndrome of unknown etiology. Recent studies employing exome- and genome-wide sequencing have identified nine high-confidence ASD (hcASD) genes. Working from the hypothesis that ASD-associated mutations in these biologically pleiotropic genes will disrupt intersecting developmental processes to contribute to a common phenotype, we have attempted to identify time periods, brain regions, and cell types in which these genes converge. We have constructed coexpression networks based on the hcASD "seed" genes, leveraging a rich expression data set encompassing multiple human brain regions across human development and into adulthood. By assessing enrichment of an independent set of probable ASD (pASD) genes, derived from the same sequencing studies, we demonstrate a key point of convergence in midfetal layer 5/6 cortical projection neurons. This approach informs when, where, and in what cell types mutations in these specific genes may be productively studied to clarify ASD pathophysiology.
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Affiliation(s)
- A Jeremy Willsey
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
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25
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Chaste P, Klei L, Sanders SJ, Murtha MT, Hus V, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Lord C, Mane SM, Martin CL, Martin DM, Morrow EM, Walsh CA, Sutcliffe JS, State MW, Devlin B, Cook EH, Kim SJ. Adjusting head circumference for covariates in autism: clinical correlates of a highly heritable continuous trait. Biol Psychiatry 2013; 74:576-84. [PMID: 23746936 PMCID: PMC3772969 DOI: 10.1016/j.biopsych.2013.04.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [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: 01/24/2013] [Revised: 03/25/2013] [Accepted: 04/16/2013] [Indexed: 11/29/2022]
Abstract
BACKGROUND Brain development follows a different trajectory in children with autism spectrum disorders (ASD) than in typically developing children. A proxy for neurodevelopment could be head circumference (HC), but studies assessing HC and its clinical correlates in ASD have been inconsistent. This study investigates HC and clinical correlates in the Simons Simplex Collection cohort. METHODS We used a mixed linear model to estimate effects of covariates and the deviation from the expected HC given parental HC (genetic deviation). After excluding individuals with incomplete data, 7225 individuals in 1891 families remained for analysis. We examined the relationship between HC/genetic deviation of HC and clinical parameters. RESULTS Gender, age, height, weight, genetic ancestry, and ASD status were significant predictors of HC (estimate of the ASD effect = .2 cm). HC was approximately normally distributed in probands and unaffected relatives, with only a few outliers. Genetic deviation of HC was also normally distributed, consistent with a random sampling of parental genes. Whereas larger HC than expected was associated with ASD symptom severity and regression, IQ decreased with the absolute value of the genetic deviation of HC. CONCLUSIONS Measured against expected values derived from covariates of ASD subjects, statistical outliers for HC were uncommon. HC is a strongly heritable trait, and population norms for HC would be far more accurate if covariates including genetic ancestry, height, and age were taken into account. The association of diminishing IQ with absolute deviation from predicted HC values suggests HC could reflect subtle underlying brain development and warrants further investigation.
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Affiliation(s)
- Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA, FondaMental Foundation, Créteil, France
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Stephan J. Sanders
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA, Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michael T. Murtha
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Vanessa Hus
- Department of Psychology, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer K. Lowe
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - A. Jeremy Willsey
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Daniel Moreno-De-Luca
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Timothy W. Yu
- Division of Genetics, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric Fombonne
- Department of Psychiatry, Oregon Health & Science University, Portland, Oregon, USA
| | - Daniel Geschwind
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Dorothy E. Grice
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA
| | | | - Catherine Lord
- Center for Autism and the Developing Brain, Weill Cornell Medical College, White Plains, New York, USA
| | | | - Christa Lese Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Donna M. Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Eric M. Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry; and Institute for Brain Science, Brown University, Lab for Molecular Medicine, Providence, Rhode Island, USA, Developmental Disorders Genetics Research Program, Emma Pendleton Bradley Hospital and Department of Psychiatry and Human Behavior, Brown University Medical School, East Providence, Rhode Island, USA
| | - Christopher A. Walsh
- Howard Hughes Medical Institute and Division of Genetics, Children's Hospital Boston, and Neurology and Pediatrics, Harvard Medical School Center for Life Sciences, Boston, Massachusetts, USA
| | - James S. Sutcliffe
- Departments of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Matthew W. State
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA, Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Edwin H. Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Soo-Jeong Kim
- Center for Integrative Brain Research, Seattle Children's Research Institute & Department of Psychiatry and Behavioral Science, University of Washington, Seattle, WA, USA,Corresponding author Soo-Jeong Kim, M.D., Center for Integrative Brain Research, Seattle Children's Research Institute, 1900 9 Ave, Seattle, WA 98101, USA, , Tel: +12068841275, Fax:+12068841210
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Lim YH, Ovejero D, Sugarman JS, Deklotz CMC, Maruri A, Eichenfield LF, Kelley PK, Jüppner H, Gottschalk M, Tifft CJ, Gafni RI, Boyce AM, Cowen EW, Bhattacharyya N, Guthrie LC, Gahl WA, Golas G, Loring EC, Overton JD, Mane SM, Lifton RP, Levy ML, Collins MT, Choate KA. Multilineage somatic activating mutations in HRAS and NRAS cause mosaic cutaneous and skeletal lesions, elevated FGF23 and hypophosphatemia. Hum Mol Genet 2013; 23:397-407. [PMID: 24006476 DOI: 10.1093/hmg/ddt429] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pathologically elevated serum levels of fibroblast growth factor-23 (FGF23), a bone-derived hormone that regulates phosphorus homeostasis, result in renal phosphate wasting and lead to rickets or osteomalacia. Rarely, elevated serum FGF23 levels are found in association with mosaic cutaneous disorders that affect large proportions of the skin and appear in patterns corresponding to the migration of ectodermal progenitors. The cause and source of elevated serum FGF23 is unknown. In those conditions, such as epidermal and large congenital melanocytic nevi, skin lesions are variably associated with other abnormalities in the eye, brain and vasculature. The wide distribution of involved tissues and the appearance of multiple segmental skin and bone lesions suggest that these conditions result from early embryonic somatic mutations. We report five such cases with elevated serum FGF23 and bone lesions, four with large epidermal nevi and one with a giant congenital melanocytic nevus. Exome sequencing of blood and affected skin tissue identified somatic activating mutations of HRAS or NRAS in each case without recurrent secondary mutation, and we further found that the same mutation is present in dysplastic bone. Our finding of somatic activating RAS mutation in bone, the endogenous source of FGF23, provides the first evidence that elevated serum FGF23 levels, hypophosphatemia and osteomalacia are associated with pathologic Ras activation and may provide insight in the heretofore limited understanding of the regulation of FGF23.
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27
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Zaidi S, Choi M, Wakimoto H, Ma L, Jiang J, Overton JD, Romano-Adesman A, Bjornson RD, Breitbart RE, Brown KK, Carriero NJ, Cheung YH, Deanfield J, DePalma S, Fakhro KA, Glessner J, Hakonarson H, Italia MJ, Kaltman JR, Kaski J, Kim R, Kline JK, Lee T, Leipzig J, Lopez A, Mane SM, Mitchell LE, Newburger JW, Parfenov M, Pe'er I, Porter G, Roberts AE, Sachidanandam R, Sanders SJ, Seiden HS, State MW, Subramanian S, Tikhonova IR, Wang W, Warburton D, White PS, Williams IA, Zhao H, Seidman JG, Brueckner M, Chung WK, Gelb BD, Goldmuntz E, Seidman CE, Lifton RP. De novo mutations in histone-modifying genes in congenital heart disease. Nature 2013; 498:220-3. [PMID: 23665959 PMCID: PMC3706629 DOI: 10.1038/nature12141] [Citation(s) in RCA: 636] [Impact Index Per Article: 57.8] [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: 01/16/2013] [Accepted: 04/02/2013] [Indexed: 11/24/2022]
Abstract
Congenital heart disease (CHD) is the most frequent birth defect, affecting 0.8% of live births. Many cases occur sporadically and impair reproductive fitness, suggesting a role for de novo mutations. Here we compare the incidence of de novo mutations in 362 severe CHD cases and 264 controls by analysing exome sequencing of parent-offspring trios. CHD cases show a significant excess of protein-altering de novo mutations in genes expressed in the developing heart, with an odds ratio of 7.5 for damaging (premature termination, frameshift, splice site) mutations. Similar odds ratios are seen across the main classes of severe CHD. We find a marked excess of de novo mutations in genes involved in the production, removal or reading of histone 3 lysine 4 (H3K4) methylation, or ubiquitination of H2BK120, which is required for H3K4 methylation. There are also two de novo mutations in SMAD2, which regulates H3K27 methylation in the embryonic left-right organizer. The combination of both activating (H3K4 methylation) and inactivating (H3K27 methylation) chromatin marks characterizes 'poised' promoters and enhancers, which regulate expression of key developmental genes. These findings implicate de novo point mutations in several hundreds of genes that collectively contribute to approximately 10% of severe CHD.
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Affiliation(s)
- Samir Zaidi
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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Lemaire M, Frémeaux-Bacchi V, Schaefer F, Choi M, Tang WH, Le Quintrec M, Fakhouri F, Taque S, Nobili F, Martinez F, Ji W, Overton JD, Mane SM, Nürnberg G, Altmüller J, Thiele H, Morin D, Deschenes G, Baudouin V, Llanas B, Collard L, Majid MA, Simkova E, Nürnberg P, Rioux-Leclerc N, Moeckel GW, Gubler MC, Hwa J, Loirat C, Lifton RP. Recessive mutations in DGKE cause atypical hemolytic-uremic syndrome. Nat Genet 2013. [PMID: 23542698 DOI: 10.1038/ng.2590)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Pathologic thrombosis is a major cause of mortality. Hemolytic-uremic syndrome (HUS) features episodes of small-vessel thrombosis resulting in microangiopathic hemolytic anemia, thrombocytopenia and renal failure. Atypical HUS (aHUS) can result from genetic or autoimmune factors that lead to pathologic complement cascade activation. Using exome sequencing, we identified recessive mutations in DGKE (encoding diacylglycerol kinase ɛ) that co-segregated with aHUS in nine unrelated kindreds, defining a distinctive Mendelian disease. Affected individuals present with aHUS before age 1 year, have persistent hypertension, hematuria and proteinuria (sometimes in the nephrotic range), and develop chronic kidney disease with age. DGKE is found in endothelium, platelets and podocytes. Arachidonic acid-containing diacylglycerols (DAG) activate protein kinase C (PKC), which promotes thrombosis, and DGKE normally inactivates DAG signaling. We infer that loss of DGKE function results in a prothrombotic state. These findings identify a new mechanism of pathologic thrombosis and kidney failure and have immediate implications for treating individuals with aHUS.
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Affiliation(s)
- Mathieu Lemaire
- Department of Genetics, Yale University School of Medicine, and Howard Hughes Medical Institute, New Haven, Connecticut, USA
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Levinsohn JL, Tian LC, Boyden LM, McNiff JM, Narayan D, Loring ES, Yun D, Sugarman JL, Overton JD, Mane SM, Lifton RP, Paller AS, Wagner AM, Antaya RJ, Choate KA. Whole-exome sequencing reveals somatic mutations in HRAS and KRAS, which cause nevus sebaceus. J Invest Dermatol 2012; 133:827-830. [PMID: 23096712 PMCID: PMC3556376 DOI: 10.1038/jid.2012.379] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Jonathan L Levinsohn
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Li C Tian
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lynn M Boyden
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jennifer M McNiff
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Deepak Narayan
- Department of Surgery, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Erin S Loring
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Duri Yun
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jeffrey L Sugarman
- Departments of Dermatology and Family Medicine, University of California, San Francisco, San Francisco, California, USA
| | - John D Overton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Center for Mendelian Genomics, New Haven, Connecticut, USA
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Center for Mendelian Genomics, New Haven, Connecticut, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Center for Mendelian Genomics, New Haven, Connecticut, USA; Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Amy S Paller
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Annette M Wagner
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Richard J Antaya
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA; Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Keith A Choate
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA.
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Klei L, Sanders SJ, Murtha MT, Hus V, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Lord C, Mane SM, Martin CL, Martin DM, Morrow EM, Walsh CA, Melhem NM, Chaste P, Sutcliffe JS, State MW, Cook EH, Roeder K, Devlin B. Common genetic variants, acting additively, are a major source of risk for autism. Mol Autism 2012; 3:9. [PMID: 23067556 PMCID: PMC3579743 DOI: 10.1186/2040-2392-3-9] [Citation(s) in RCA: 279] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 10/04/2012] [Indexed: 11/10/2022] Open
Abstract
Background Autism spectrum disorders (ASD) are early onset neurodevelopmental syndromes typified by impairments in reciprocal social interaction and communication, accompanied by restricted and repetitive behaviors. While rare and especially de novo genetic variation are known to affect liability, whether common genetic polymorphism plays a substantial role is an open question and the relative contribution of genes and environment is contentious. It is probable that the relative contributions of rare and common variation, as well as environment, differs between ASD families having only a single affected individual (simplex) versus multiplex families who have two or more affected individuals. Methods By using quantitative genetics techniques and the contrast of ASD subjects to controls, we estimate what portion of liability can be explained by additive genetic effects, known as narrow-sense heritability. We evaluate relatives of ASD subjects using the same methods to evaluate the assumptions of the additive model and partition families by simplex/multiplex status to determine how heritability changes with status. Results By analyzing common variation throughout the genome, we show that common genetic polymorphism exerts substantial additive genetic effects on ASD liability and that simplex/multiplex family status has an impact on the identified composition of that risk. As a fraction of the total variation in liability, the estimated narrow-sense heritability exceeds 60% for ASD individuals from multiplex families and is approximately 40% for simplex families. By analyzing parents, unaffected siblings and alleles not transmitted from parents to their affected children, we conclude that the data for simplex ASD families follow the expectation for additive models closely. The data from multiplex families deviate somewhat from an additive model, possibly due to parental assortative mating. Conclusions Our results, when viewed in the context of results from genome-wide association studies, demonstrate that a myriad of common variants of very small effect impacts ASD liability.
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Affiliation(s)
- Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, DiLullo NM, Parikshak NN, Stein JL, Walker MF, Ober GT, Teran NA, Song Y, El-Fishawy P, Murtha RC, Choi M, Overton JD, Bjornson RD, Carriero NJ, Meyer KA, Bilguvar K, Mane SM, Sestan N, Lifton RP, Günel M, Roeder K, Geschwind DH, Devlin B, State MW. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 2012; 485:237-41. [PMID: 22495306 DOI: 10.1038/nature10945] [Citation(s) in RCA: 1434] [Impact Index Per Article: 119.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 02/14/2012] [Indexed: 12/14/2022]
Abstract
Multiple studies have confirmed the contribution of rare de novo copy number variations to the risk for autism spectrum disorders. But whereas de novo single nucleotide variants have been identified in affected individuals, their contribution to risk has yet to be clarified. Specifically, the frequency and distribution of these mutations have not been well characterized in matched unaffected controls, and such data are vital to the interpretation of de novo coding mutations observed in probands. Here we show, using whole-exome sequencing of 928 individuals, including 200 phenotypically discordant sibling pairs, that highly disruptive (nonsense and splice-site) de novo mutations in brain-expressed genes are associated with autism spectrum disorders and carry large effects. On the basis of mutation rates in unaffected individuals, we demonstrate that multiple independent de novo single nucleotide variants in the same gene among unrelated probands reliably identifies risk alleles, providing a clear path forward for gene discovery. Among a total of 279 identified de novo coding mutations, there is a single instance in probands, and none in siblings, in which two independent nonsense variants disrupt the same gene, SCN2A (sodium channel, voltage-gated, type II, α subunit), a result that is highly unlikely by chance.
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Affiliation(s)
- Stephan J Sanders
- Program on Neurogenetics, Child Study Center, Department of Psychiatry, Yale University School of Medicine, 230 South Frontage Road, New Haven, Connecticut 06520, USA
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Fernandez TV, Sanders SJ, Yurkiewicz IR, Ercan-Sencicek AG, Kim YS, Fishman DO, Raubeson MJ, Song Y, Yasuno K, Ho WSC, Bilguvar K, Glessner J, Chu SH, Leckman JF, King RA, Gilbert DL, Heiman GA, Tischfield JA, Hoekstra PJ, Devlin B, Hakonarson H, Mane SM, Günel M, State MW. Rare copy number variants in tourette syndrome disrupt genes in histaminergic pathways and overlap with autism. Biol Psychiatry 2012; 71:392-402. [PMID: 22169095 PMCID: PMC3282144 DOI: 10.1016/j.biopsych.2011.09.034] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 08/26/2011] [Accepted: 09/24/2011] [Indexed: 11/18/2022]
Abstract
BACKGROUND Studies of copy number variation (CNV) have characterized loci and molecular pathways in a range of neuropsychiatric conditions. We analyzed rare CNVs in Tourette syndrome (TS) to identify novel risk regions and relevant pathways, to evaluate burden of structural variation in cases versus controls, and to assess overlap of identified variations with those in other neuropsychiatric syndromes. METHODS We conducted a case-control study of 460 individuals with TS, including 148 parent-child trios and 1131 controls. CNV analysis was undertaken using 370 K to 1 M probe arrays, and genotyping data were used to match cases and controls for ancestry. CNVs present in < 1% of the population were evaluated. RESULTS While there was no significant increase in the number of de novo or transmitted rare CNVs in cases versus controls, pathway analysis using multiple algorithms showed enrichment of genes within histamine receptor (subtypes 1 and 2) signaling pathways (p = 5.8 × 10(-4) - 1.6 × 10(-2)), as well as axon guidance, cell adhesion, nervous system development, and synaptic structure and function processes. Genes mapping within rare CNVs in TS showed significant overlap with those previously identified in autism spectrum disorders but not intellectual disability or schizophrenia. Three large, likely pathogenic, de novo events were identified, including one disrupting multiple gamma-aminobutyric acid receptor genes. CONCLUSIONS We identify further evidence supporting recent findings regarding the involvement of histaminergic and gamma-aminobutyric acidergic mechanisms in the etiology of TS and show an overlap of rare CNVs in TS and autism spectrum disorders.
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Affiliation(s)
- Thomas V Fernandez
- Child Study Center, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA
- Program on Neurogenetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Stephan J Sanders
- Child Study Center, Yale University School of Medicine, New Haven, CT, 06520, USA
- Program on Neurogenetics, Yale University School of Medicine, New Haven, CT, 06520, USA
- Center for Human Genetics and Genomics and Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Ilana R Yurkiewicz
- Child Study Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - A. Gulhan Ercan-Sencicek
- Child Study Center, Yale University School of Medicine, New Haven, CT, 06520, USA
- Program on Neurogenetics, Yale University School of Medicine, New Haven, CT, 06520, USA
- Center for Human Genetics and Genomics and Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Young-Shin Kim
- Child Study Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Daniel O Fishman
- Child Study Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Melanie J Raubeson
- Child Study Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Youeun Song
- Child Study Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Katsuhito Yasuno
- Center for Human Genetics and Genomics and Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Winson SC Ho
- Center for Human Genetics and Genomics and Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Kaya Bilguvar
- Center for Human Genetics and Genomics and Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Joseph Glessner
- The Center for Applied Genomics at The Children’s Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Su Hee Chu
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15232, USA
| | - James F. Leckman
- Child Study Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Robert A King
- Child Study Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Donald L Gilbert
- Division of Neurology, Cincinnati Children’s Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Gary A Heiman
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jay A Tischfield
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Pieter J Hoekstra
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15232, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics at The Children’s Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Shrikant M Mane
- Keck Microarray Center, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Murat Günel
- Program on Neurogenetics, Yale University School of Medicine, New Haven, CT, 06520, USA
- Center for Human Genetics and Genomics and Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Matthew W State
- Child Study Center, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA
- Program on Neurogenetics, Yale University School of Medicine, New Haven, CT, 06520, USA
- Center for Human Genetics and Genomics and Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
- Address correspondence to: Matthew W. State, MD, PhD, 230 S Frontage Road, New Haven, CT 06520, Tel: 203-737-4342, Fax: 203-785-7560,
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Bordner KA, Kitchen RR, Carlyle B, George ED, Mahajan MC, Mane SM, Taylor JR, Simen AA. Parallel declines in cognition, motivation, and locomotion in aging mice: association with immune gene upregulation in the medial prefrontal cortex. Exp Gerontol 2011; 46:643-59. [PMID: 21453768 DOI: 10.1016/j.exger.2011.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 03/15/2011] [Accepted: 03/21/2011] [Indexed: 01/19/2023]
Abstract
Aging in humans is associated with parallel changes in cognition, motivation, and motoric performance. Based on the human aging literature, we hypothesized that this constellation of age-related changes is mediated by the medial prefrontal cortex and that it would be observed in aging mice. Toward this end, we performed detailed assessments of cognition, motivation, and motoric behavior in aging mice. We assessed behavioral and cognitive performance in C57Bl/6 mice aged 6, 18, and 24 months, and followed this with microarray analysis of tissue from the medial prefrontal cortex and analysis of serum cytokine levels. Multivariate modeling of these data suggested that the age-related changes in cognition, motivation, motor performance, and prefrontal immune gene expression were highly correlated. Peripheral cytokine levels were also correlated with these variables, but less strongly than measures of prefrontal immune gene upregulation. To determine whether the observed immune gene expression changes were due to prefrontal microglial cells, we isolated CD11b-positive cells from the prefrontal cortex and subject them to next-generation RNA sequencing. Many of the immune changes present in whole medial prefrontal cortex were enriched in this cell population. These data suggest that, as in humans, cognition, motivation, and motoric performance in the mouse change together with age and are strongly associated with CNS immune gene upregulation.
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Affiliation(s)
- Kelly A Bordner
- Yale University School of Medicine, Department of Psychiatry, New Haven, CT 06511, USA.
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Bordner KA, George ED, Carlyle BC, Duque A, Kitchen RR, Lam TT, Colangelo CM, Stone KL, Abbott TB, Mane SM, Nairn AC, Simen AA. Functional genomic and proteomic analysis reveals disruption of myelin-related genes and translation in a mouse model of early life neglect. Front Psychiatry 2011; 2:18. [PMID: 21629843 PMCID: PMC3098717 DOI: 10.3389/fpsyt.2011.00018] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 04/11/2011] [Indexed: 12/13/2022] Open
Abstract
Early life neglect is an important public health problem which can lead to lasting psychological dysfunction. Good animal models are necessary to understand the mechanisms responsible for the behavioral and anatomical pathology that results. We recently described a novel model of early life neglect, maternal separation with early weaning (MSEW), that produces behavioral changes in the mouse that persist into adulthood. To begin to understand the mechanism by which MSEW leads to these changes we applied cDNA microarray, next-generation RNA-sequencing (RNA-seq), label-free proteomics, multiple reaction monitoring (MRM) proteomics, and methylation analysis to tissue samples obtained from medial prefrontal cortex to determine the molecular changes induced by MSEW that persist into adulthood. The results show that MSEW leads to dysregulation of markers of mature oligodendrocytes and genes involved in protein translation and other categories, an apparent downward biasing of translation, and methylation changes in the promoter regions of selected dysregulated genes. These findings are likely to prove useful in understanding the mechanism by which early life neglect affects brain structure, cognition, and behavior.
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Affiliation(s)
- Kelly A Bordner
- Department of Psychiatry, Yale University School of Medicine New Haven, CT, USA
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Bayrakli F, Bilguvar K, Ceyhan D, Ercan-Sencicek AG, Cankaya T, Bayrakli S, Guney I, Mane SM, State MW, Gunel M. Heterozygous 5p13.3-13.2 deletion in a patient with type I Chiari malformation and bilateral Duane retraction syndrome. Clin Genet 2010; 77:499-502. [PMID: 20447154 DOI: 10.1111/j.1399-0004.2010.01411.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Bayrakli F, Guney I, Bayri Y, Ercan-Sencicek AG, Ceyhan D, Cankaya T, Mason C, Bilguvar K, Bayrakli S, Mane SM, State MW, Gunel M. A novel heterozygous deletion within the 3' region of the PAX6 gene causing isolated aniridia in a large family group. J Clin Neurosci 2009; 16:1610-4. [PMID: 19793656 DOI: 10.1016/j.jocn.2009.03.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 03/10/2009] [Accepted: 03/11/2009] [Indexed: 10/20/2022]
Abstract
Paired box gene 6 (PAX6) is the causative gene of aniridia. It is a dominantly inherited eye abnormality characterized by partial or complete absence of the iris. The PAX6 gene is located on chromosome 11p13 and contains 14 exons. It is expressed mainly in the developing eye and central nervous system. Submicroscopic copy number variations are common in the human genome. Submicroscopic deletions may cause several human diseases, either by disrupting coding sequences or by eliminating regulatory elements essential for expression of the gene in question. Over the past several years, array-based comparative genomic hybridization has become an increasingly useful tool for both identifying normal cytogenetic variations and characterizing chromosomal abnormalities associated with developmental delays and cancer. Our results support the notion that assessing copy number variation of the PAX6 gene itself and also of flanking regions, may contribute to the molecular diagnosis of aniridia.
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Affiliation(s)
- Fatih Bayrakli
- Department of Neurosurgery, Van Military Hospital, Van, Turkey.
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Drozdov I, Kidd M, Nadler B, Camp RL, Mane SM, Hauso O, Gustafsson BI, Modlin IM. Predicting neuroendocrine tumor (carcinoid) neoplasia using gene expression profiling and supervised machine learning. Cancer 2009; 115:1638-50. [PMID: 19197975 DOI: 10.1002/cncr.24180] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND A more accurate taxonomy of small intestinal (SI) neuroendocrine tumors (NETs) is necessary to accurately predict tumor behavior and prognosis and to define therapeutic strategy. In this study, the authors identified a panel of such markers that have been implicated in tumorigenicity, metastasis, and hormone production and hypothesized that transcript levels of the genes melanoma antigen family D2 (MAGE-D2), metastasis-associated 1 (MTA1), nucleosome assembly protein 1-like (NAP1L1), Ki-67 (a marker of proliferation), survivin, frizzled homolog 7 (FZD7), the Kiss1 metastasis suppressor (Kiss1), neuropilin 2 (NRP2), and chromogranin A (CgA) could be used to define primary SI NETs and to predict the development of metastases. METHODS Seventy-three clinically and World Health Organization pathologically classified NET samples (primary tumor, n = 44 samples; liver metastases, n = 29 samples) and 30 normal human enterochromaffin (EC) cell preparations were analyzed using real-time polymerase chain reaction. Transcript levels were normalized to 3 NET housekeeping genes (asparagine-linked glycosylation 9 or ALG9, transcription factor CP2 or TFCP2, and zinc finger protein 410 or ZNF410) using geNorm analysis. A predictive gene-based model was constructed using supervised learning algorithms from the transcript expression levels. RESULTS Primary SI NETs could be differentiated from normal human EC cell preparations with 100% specificity and 92% sensitivity. Well differentiated NETs (WDNETs), well differentiated neuroendocrine carcinomas, and poorly differentiated NETs (PDNETs) were classified with a specificity of 78%, 78%, and 71%, respectively; whereas poorly differentiated neuroendocrine carcinomas were misclassified as either WDNETs or PDNETs. Metastases were predicted in all cases with 100% sensitivity and specificity. CONCLUSIONS The current results indicated that gene expression profiling and supervised machine learning can be used to classify SI NET subtypes and accurately predict metastasis. The authors believe that the application of this technique will facilitate accurate molecular pathologic delineation of NET disease, better define its extent, facilitate the assessment of prognosis, and provide a guide for the identification of appropriate strategies for individualized patient treatment.
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Affiliation(s)
- Ignat Drozdov
- Department of Surgery, Yale University School of Medicine, New Haven, Connecticut 06520-8062, USA
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Yono M, Mane SM, Lin A, Weiss RM, Latifpour J. Differential effects of diabetes induced by streptozotocin and that develops spontaneously on prostate growth in Bio Breeding (BB) rats. Life Sci 2008; 83:192-7. [PMID: 18619471 DOI: 10.1016/j.lfs.2008.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 05/07/2008] [Accepted: 06/05/2008] [Indexed: 11/16/2022]
Abstract
We investigated molecular changes in the response to insulin in prostates of spontaneously developed (Bio Breeding) and streptozotocin (STZ)-induced diabetic rats that received sufficient amounts (euglycemic group), or suboptimal doses (hyperglycemic group) of insulin for 32 weeks, using Affymetrix GeneChip analysis of gene expression. Alterations in gene expression levels identified by microarray analysis, having potential biological relevance to prostate growth, were verified by real-time reverse transcription polymerase chain reaction (RT-PCR). A significant decrease in the weight of ventral prostate was observed in the hyperglycemic STZ-induced but not spontaneously developed diabetic group. Microarray analysis revealed that gene expression profiles were distinctly different in each region of the prostate, and that hyperglycemic diabetes in spontaneously developed and STZ-diabetic rats was associated with differential changes in the prostatic expression levels of 856 genes, of which 35 were related to cell growth, proliferation and death. RT-PCR data verified significant differences in the mRNA expression levels of Igfbp6, Tieg, and Clu between euglycemic and hyperglycemic groups, whereas expression levels of these genes in control and euglycemic diabetic groups were not significantly different. In ventral prostate, the mRNA expression levels of Igfbp6 and Tieg were significantly higher in the hyperglycemic STZ-induced diabetic than in the hyperglycemic spontaneously diabetic BBDP/Wor rats. Our data demonstrate that the diabetes induced by STZ in the BBDR/Wor rats affects prostate growth and the molecular response to insulin differently than that observed in BBDP/Wor rats that develop diabetes spontaneously.
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Affiliation(s)
- Makoto Yono
- Section of Urology, Yale University, New Haven, CT, USA
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Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008; 18:1509-17. [PMID: 18550803 DOI: 10.1101/gr.079558.108] [Citation(s) in RCA: 1947] [Impact Index Per Article: 121.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ultra-high-throughput sequencing is emerging as an attractive alternative to microarrays for genotyping, analysis of methylation patterns, and identification of transcription factor binding sites. Here, we describe an application of the Illumina sequencing (formerly Solexa sequencing) platform to study mRNA expression levels. Our goals were to estimate technical variance associated with Illumina sequencing in this context and to compare its ability to identify differentially expressed genes with existing array technologies. To do so, we estimated gene expression differences between liver and kidney RNA samples using multiple sequencing replicates, and compared the sequencing data to results obtained from Affymetrix arrays using the same RNA samples. We find that the Illumina sequencing data are highly replicable, with relatively little technical variation, and thus, for many purposes, it may suffice to sequence each mRNA sample only once (i.e., using one lane). The information in a single lane of Illumina sequencing data appears comparable to that in a single array in enabling identification of differentially expressed genes, while allowing for additional analyses such as detection of low-expressed genes, alternative splice variants, and novel transcripts. Based on our observations, we propose an empirical protocol and a statistical framework for the analysis of gene expression using ultra-high-throughput sequencing technology.
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Affiliation(s)
- John C Marioni
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
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Bayrakli F, Bilguvar K, Mason CE, DiLuna ML, Bayri Y, Gungor L, Terzi M, Mane SM, Lifton RP, State MW, Gunel M. Rapid identification of disease-causing mutations using copy number analysis within linkage intervals. Hum Mutat 2007; 28:1236-40. [PMID: 17676595 DOI: 10.1002/humu.20592] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
SNP and comparative genome hybridization arrays (aCGH) are powerful techniques for identifying genome rearrangements, deletions, and duplications. We hypothesized that current array-based detection of copy number variation (CNV) could complement parametric linkage analysis and allow the rapid identification of functional mutations in families with inherited disorders. Herein, we demonstrate the utility of this technique by rapidly identifying a disease causing microdeletion within the PARK2 gene in a family with autosomal recessive Parkinsonism.
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Affiliation(s)
- Fatih Bayrakli
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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Stone KL, Bjornson RD, Blasko GG, Bruce C, Cofrancesco R, Carriero NJ, Colangelo CM, Crawford JK, Crawford JM, daSilva NC, Deluca JD, Elliott JI, Elliott MM, Flory PJ, Folta-Stogniew EJ, Gulcicek E, Kong Y, Lam TT, Lee JY, Lin A, LoPresti MB, Mane SM, McMurray WJ, Tikhonova IR, Westman S, Williams NA, Wu TL, Hongyu Z, Williams KR. Keck Foundation Biotechnology Resource Laboratory, Yale University. Yale J Biol Med 2007; 80:195-211. [PMID: 18449392 PMCID: PMC2347368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kathryn L. Stone
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Robert D. Bjornson
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Gregory G. Blasko
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Can Bruce
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Renee Cofrancesco
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Nicholas J. Carriero
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Christopher M. Colangelo
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Janet K. Crawford
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - J. Myron Crawford
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Nancy C. daSilva
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Joseph D. Deluca
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - James I. Elliott
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Margaret M. Elliott
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - P. John Flory
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Ewa J. Folta-Stogniew
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Erol Gulcicek
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Yong Kong
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - TuKiet T. Lam
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Ji Y. Lee
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Aiping Lin
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Mary B. LoPresti
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Shrikant M. Mane
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Walter J. McMurray
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Irina R. Tikhonova
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Sheila Westman
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Nancy A. Williams
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Terence L. Wu
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Zhao Hongyu
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
| | - Kenneth R. Williams
- Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut
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Kidd M, Modlin IM, Pfragner R, Eick GN, Champaneria MC, Chan AK, Camp RL, Mane SM. Small bowel carcinoid (enterochromaffin cell) neoplasia exhibits transforming growth factor-beta1-mediated regulatory abnormalities including up-regulation of C-Myc and MTA1. Cancer 2007; 109:2420-31. [PMID: 17469181 DOI: 10.1002/cncr.22725] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Although it is known that small intestinal carcinoids are derived from enterochromaffin (EC) cells, these cells remain poorly characterized and little is known of the growth regulatory mechanisms of these neuroendocrine cells. Down-regulation or loss of the transforming growth factor-beta1 (TGFbeta1) cytostatic program and activation of TGFbeta-mediated transcriptional networks is associated with uncontrolled growth and metastasis in other neural tumors, glioblastomas. Whether this phenomenon is common to small intestinal carcinoid tumors was investigated. METHODS The effects of TGFbeta1 on cultured normal EC cells (isolated by FACS sorting) and the neoplastic EC cell line, KRJ-I, was assessed using the MTT assay. The TGFbetaRII transcript and protein were identified in tumor cells and the effects of TGFbeta1 on SMAD2 phosphorylation and nuclear translocation quantified. The time-dependent response of SMAD4, SMAD7, c-Myc, and P21(WAF1/CIP1) protein expression and c-Myc and p21(WAF1/CIP1) transcript was measured in response to TGFbeta1 and the transcript expression of candidate downstream targets, MTA1 and E-cadherin, were assessed. RESULTS TGFbeta1 inhibited normal EC cell proliferation (IC(50) = 17 pM) but stimulated neoplastic EC cell proliferation (EC(50) = 22 pM). In tumor cells, significantly decreased transcript (P < .01) of TGFbetaRII was identified, but no receptor mutations were identified and protein expression was evident. TGFbeta1 (1 ng/mL) resulted in SMAD2 phosphorylation and <7% nuclear expression compared with 93% in normal EC cells. In neoplastic cells, TGFbeta1 (1 ng/mL) caused a decrease in SMAD4 (>16%, P < .05), whereas SMAD7 and c-Myc transcript and protein were respectively increased >21% (P < .05) and approximately 40% (P < .002). TGFbeta1 (1 ng/mL) also decreased p21(WAF1/CIP1) transcript by 60% (P < .001) and protein that was undetectable at 24 hours. Expression of the downstream targets of the c-Myc pathway, MTA1, was increased (20%) and E-cadherin decreased (30%). CONCLUSIONS The neoplastic EC cell is characterized by loss of TGFbeta-1-mediated growth inhibition and, similar to glioblastomas, utilizes the TGFbeta system to induce gene responses associated with growth promotion (c-Myc and the ERK pathway), invasion (E-cadherin), and metastasis (MTA1).
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Affiliation(s)
- Mark Kidd
- Department of Surgery, Yale University School of Medicine, New Haven, Connecticut 06520-8062, USA
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Kidd M, Modlin IM, Eick GN, Camp RL, Mane SM. Role of CCN2/CTGF in the proliferation of Mastomys enterochromaffin-like cells and gastric carcinoid development. Am J Physiol Gastrointest Liver Physiol 2007; 292:G191-200. [PMID: 16950763 DOI: 10.1152/ajpgi.00131.2006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Mastomys enterochromaffin-like (ECL) cell proliferation is initially gastrin driven, but once neoplasia develops, cells become gastrin autonomous. We hypothesized that CCN2 (CTGF), a mitogenic growth factor, may regulate ECL cell proliferation. A Mastomys GeneChip database was examined (dCHIP) to identify CCN2 expression levels. CCN2 in normal and tumor ECL cell preparations obtained using FACS (100 nM acridine orange) was examined by real-time PCR. CCN2 protein was identified in mucosal and ECL cell preparations by immunohistochemistry. Short-term cultured cells were stimulated with either CCN2 or CCN2 + EGF, and proliferation was measured (MTT assay). The ERK1/2 inhibitor PD-98059 (0.1-100 microM) was assessed in terms of CCN2 (1 ng/ml)-mediated proliferation and ERK1/2 phosphorylation. CCN2 transcript and protein was then examined in clinical gastric carcinoids. The ccn2 transcript was upregulated in tumor samples compared with the normal mucosa (+2.36-fold, P < 0.01). PCR demonstrated that ccn2 was not expressed in FACS-prepared (>98% pure) normal ECL cells but was elevated in tumor ECL cell fractions (41.3 +/- 10.7-fold). Immunostaining of the Mastomys gastric mucosa and FACS preparations confirmed that CCN2 protein was present in ECL tumors but not in normal ECL cells. Neither CCN2 nor CCN2 + EGF stimulated normal ECL cell proliferation. CCN2 stimulated tumor proliferation (EC50 approximately 0.01 ng/ml); EGF significantly augmented (P < 0.01) CCN2-induced tumor cell proliferation (EC50 = 20 pg/ml). PD-98059 inhibited CCN2-induced proliferation (-12 +/- 3%, P < 0.05) and ERK1/2 phosphorylation (-34 +/- 5%, P < 0.05) in tumor cells. In clinical samples, both CCN2 transcript and protein were elevated in gastrin-autonomous carcinoids (P < 0.02) compared with the normal mucosa. In conclusion, CCN2 may be a proliferative regulator of Mastomys ECL neoplastic proliferation once these cells become autonomous of gastrin regulation. Identification of CCN2 in gastric carcinoid tissue may be useful both as an indicator of ECL cell transformation and may define gastrin autonomy, a criteria of gastric carcinoid malignancy.
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Affiliation(s)
- M Kidd
- Department of Surgery, Yale University School of Medicine, TMP202, 333 Cedar St., New Haven, CT 06520-8062, USA
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Abstract
OBJECTIVE To use differential gene expression of candidate markers to discriminate benign appendiceal carcinoids (APCs) from malignant and mixed cell APCs. SUMMARY BACKGROUND DATA Controversy exists in regard to the appropriate surgical management of APCs since it is sometimes difficult to predict tumor behavior using traditional pathologic criteria. We have identified 5 differentially expressed genes (a mitosis-regulatory gene NAP1L1, an adhesin MAGE-D2, an estrogen-antagonist, the metastasis marker MTA1, the apoptotic marker NALP, and chromogranin A) that define gut neuroendocrine cell behavior. METHODS Total RNA was isolated using TRIzol reagent from 42 appendiceal samples, including appendiceal carcinoids identified at exploration for appendicitis (no evidence of metastasis; n = 16), appendicitis specimens (n = 11), malignant appendiceal tumors (> 1.5 cm, evidence of metastatic invasion; n = 7), and mixed (goblet) cell appendiceal adenocarcinoids (n = 3), normal appendiceal tissue (n = 5), and 5 colorectal cancers. Gene expression (CgA, NAP1L1, MAGE-D2, MTA1, and NALP1) was examined by Q-RT PCR (Applied Biosystems) and quantified against GAPDH. RESULTS CgA message was elevated (> 1000-fold, P < 0.05) in all tumor types. NAP1L1 was elevated (> 10-fold, P < 0.03) in both malignant and goblet cell adenocarcinoids compared with normal and incidental lesions (P < 0.006). MAGE-D2 and MTA1 message were significantly elevated (> 10-fold, P < 0.01) in the malignant and goblet cell adenocarcinoid tumors but not in the appendicitis-associated carcinoids or normal mucosa. The apoptotic marker, NALP1, was overexpressed (> 50-fold, P < 0.05) in the appendicitis-associated and malignant appendiceal carcinoids but was significantly decreased (> 10-fold, P < 0.05) in the goblet cell adenocarcinoids. Elevated CgA transcript and protein levels indicative of a carcinoid tumor were identified in one acute appendicitis sample with no histologic evidence of a tumor. CONCLUSIONS These data demonstrate that malignant APCs and goblet cell adenocarcinoids have elevated expression of NAP1L1, MAGE-D2, and MTA1 compared with appendiceal carcinoids identified at surgery for appendicitis. This and the differences in NALP1 gene expression (decreased in goblet cell adenocarcinoids) provide a series of molecular signatures that differentiate carcinoids of the appendix. CgA identified all appendiceal tumors as well as covert lesions, which may be more prevalent than previously recognized. The molecular delineation of malignant appendiceal tumor potential provides a scientific basis to define the appropriate surgical management as opposed to morphologic assessment alone.
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Affiliation(s)
- Irvin M Modlin
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06520-8062, USA.
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Abstract
BACKGROUND Current techniques to define gastric neoplasia are limited but molecular genetic signatures can categorize tumors and provide biological rationale for predicting clinical behavior. We identified three gene signatures: Chromogranin A (CgA), MAGE-D2 (adhesion), and MTA1 (metastasis) that define gastrointestinal (GI) carcinoids and hypothesize that their expression can delineate gastric neoplasia. This strategy provides a molecular basis to define neuroendocrine gastric carcinoids (GCs), neuronal stromal tumors (GISTs), or epithelial cell (gastric adenocarcinomas [GCAs])-derived tumors. METHODS Total RNA was isolated from 38 GCs: Type I/II (n = 7), Type III/IV (n = 6), GISTs (n = 12), GCAs (n = 13), and normal mucosa (n = 12). Quantitative reverse transcriptase polymerase chain reaction (Q RT-PCR) gene expression was quantified against glyseraldehyde-3-phosphate dehydrogenase (GAPDH) and CgA and MTA1 protein expression levels were analyzed by immunohistochemical analyses of a gastric neoplasia microarray. RESULTS CgA was elevated in Type I/II (10-fold; P < .01) and Type III/IV (100-fold, P < .005), decreased in GISTs (100-fold, P < .03), and unchanged in GCAs. MAGE-D2 was 5-10-fold elevated (P < .05) in Type III/IV, GISTs, and GCAs but not in Type I/II tumors. MTA1 (> 5-fold, P < .01) was elevated in GCs (Type III/IV>I/II, P < .05), in GISTs (> 4-fold, P < .05), and GCAs. CgA protein levels were elevated in GCs (P < .005) but not in GISTs and GCAs. MTA1 levels were elevated in all tumors (P < .02) compared with normal, and especially with tumor invasion (P < .05). CONCLUSION CgA discriminates GCs from other gastric neoplasms; overexpression of MAGE-D2 and MTA1 differentiate Type III/IV from Type I/II GCs. GISTs share similar expression patterns with Type III/IV GCs but have decreased CgA. MTA1 is a marker of tumor invasion.
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Affiliation(s)
- Mark Kidd
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06520, USA
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Kidd M, Modlin IM, Mane SM, Camp RL, Shapiro MD. Q RT-PCR detection of chromogranin A: a new standard in the identification of neuroendocrine tumor disease. Ann Surg 2006; 243:273-80. [PMID: 16432362 PMCID: PMC1448909 DOI: 10.1097/01.sla.0000197734.28551.0f] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Message and protein expression of CgA was examined to evaluate the sensitivity of a PCR-based approach in the detection of covert neuroendocrine (NE) tissue. SUMMARY BACKGROUND DATA Immunohistochemical (IHC) measurement of chromogranin A (CgA) discriminates gastrointestinal (GI) carcinoids from epithelial tumors. IHC is, however, an insensitive technique to identify micrometastases or delineate subpopulations of NE cells. METHODS CgA gene expression was examined by Q-RT PCR in GI carcinoids (small intestinal and metastases, n=17, gastric, n=5), appendiceal tumors (n=10), and adenocarcinomas (gastric, n=5, colorectal, n=6). CgA protein expression levels were quantitatively analyzed following IHC by automated quantitative analysis (AQUA) in 2 tissue microarrays (GI carcinoid and GI adenocarcinoma). RESULTS CgA gene was overexpressed (P<0.001) in GI carcinoids compared with GI adenocarcinomas and normal mucosa. Elevated levels (P<0.00001) were also identified in carcinoid liver and lymph node (LN) metastases. CgA levels were higher (approximately 2-4-fold) in NE appendiceal carcinoids than in adenocarcinoids, but in GI adenocarcinomas were identical to normal mucosa. Histologically normal lymph nodes expressed detectable CgA message in 30% of cases. CgA protein levels were highest in primary GI carcinoids and in liver metastases and significantly elevated (P<0.005) compared with nonmetastatic lesions. Expression in liver and LN metastases was significantly elevated (P<0.000001) compared with normal. Analysis of mRNA by Q-RT PCR was >200-fold more sensitive than by IHC. CONCLUSIONS Overexpression of CgA mRNA and protein in GI carcinoids can identify metastatic cells; thus, PCR for CgA can be used to identify micrometastases not evident by light microscopy or IHC as well as define tumors of ambivalent morphologic phenotype. The use of this sensitive strategy to assess NETs and apparently normal LNs and liver may be of future utility in defining therapeutic strategy.
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Affiliation(s)
- Mark Kidd
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06520-8062, USA
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Kidd M, Modlin IM, Mane SM, Camp RL, Eick G, Latich I. The role of genetic markers--NAP1L1, MAGE-D2, and MTA1--in defining small-intestinal carcinoid neoplasia. Ann Surg Oncol 2006; 13:253-62. [PMID: 16424981 DOI: 10.1245/aso.2006.12.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [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: 12/10/2004] [Accepted: 08/22/2005] [Indexed: 11/18/2022]
Abstract
BACKGROUND Standard clinical and immunohistochemical methods cannot reliably determine whether a small intestinal carcinoid (SIC) is indolent or aggressive. We hypothesized that carcinoid malignancy could be defined by using quantitative reverse transcriptase-polymerase chain reaction (QRT-PCR) and immunohistochemical approaches that evaluate potential marker genes. METHODS Candidate marker gene expression (nucleosome assembly protein 1-like 1 [NAP1L1], melanoma antigen D2 [MAGE-D2], and metastasis-associated protein 1 [MTA1]) identified by Affymetrix transcriptional profiling was examined by QRT-PCR in SIC, liver, and lymph node (LN) metastases, colorectal carcinomas, and healthy tissues. Immunohistochemical expression levels of MTA1 were analyzed quantitatively by a novel automated quantitative analysis in a tissue microarray of 102 gastrointestinal carcinoids and in a breast/prostate carcinoma array. RESULTS Affymetrix transcriptional profiling identified three potentially useful malignancy-marker genes (out of 1709 significantly altered genes). By QRT-PCR, NAP1L1 was significantly (P < .03) overexpressed in SIC compared with colorectal carcinomas and healthy tissue. Increased levels (P < .05) were identified in both liver and LN metastases. Levels in colorectal carcinomas were the same as in healthy mucosa. MAGE-D2 and MTA1 were increased (P < .05) in primary tumors and metastases and overexpressed in carcinomas. Automated quantitative analysis demonstrated the highest levels of MTA1 immunostaining in malignant primary SICs and in metastases to the liver and LN. These were significantly increased (P < .02) compared with nonmetastatic primary tumors. MTA1 was overexpressed in breast and prostate carcinomas (P < .05). CONCLUSIONS SICs overexpress the neoplasia-related genes NAP1L1 (mitotic regulation), MAGE-D2 (adhesion), and MTA1 (estrogen antagonism). The ability to determine the malignant potential of these tumors and their propensity to metastasize provides a biological rationale for the management of carcinoids and may have prognostic utility.
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Affiliation(s)
- Mark Kidd
- Department of Surgery, Yale University School of Medicine, 333 Cedar Street, P.O. Box 208062, New Haven, Connecticut 06520-8062, USA
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Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST, Bracken MB, Ferris FL, Ott J, Barnstable C, Hoh. J. Complement factor H polymorphism in age-related macular degeneration. Science 2005; 308:385-9. [PMID: 15761122 PMCID: PMC1512523 DOI: 10.1126/science.1109557] [Citation(s) in RCA: 2960] [Impact Index Per Article: 155.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Age-related macular degeneration (AMD) is a major cause of blindness in the elderly. We report a genome-wide screen of 96 cases and 50 controls for polymorphisms associated with AMD. Among 116,204 single-nucleotide polymorphisms genotyped, an intronic and common variant in the complement factor H gene (CFH) is strongly associated with AMD (nominal P value <10(-7)). In individuals homozygous for the risk allele, the likelihood of AMD is increased by a factor of 7.4 (95% confidence interval 2.9 to 19). Resequencing revealed a polymorphism in linkage disequilibrium with the risk allele representing a tyrosine-histidine change at amino acid 402. This polymorphism is in a region of CFH that binds heparin and C-reactive protein. The CFH gene is located on chromosome 1 in a region repeatedly linked to AMD in family-based studies.
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Affiliation(s)
- Robert J. Klein
- Laboratory of Statistical Genetics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | - Caroline Zeiss
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, 330 Cedar Street, New Haven, CT 06520, USA
| | - Emily Y. Chew
- National Eye Institute, Building 10, CRC, 10 Center Drive, Bethesda, MD 20892–1204, USA
| | - Jen-Yue Tsai
- Biological Imaging Core, National Eye Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Richard S. Sackler
- Laboratory of Statistical Genetics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | - Chad Haynes
- Laboratory of Statistical Genetics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | - Alice K. Henning
- The EMMES Corporation, 401 North Washington Street, Suite 700, Rockville MD 20850, USA
| | - John Paul SanGiovanni
- National Eye Institute, Building 10, CRC, 10 Center Drive, Bethesda, MD 20892–1204, USA
| | - Shrikant M. Mane
- W. M. Keck Facility, Yale University, 300 George Street, Suite 201, New Haven, CT 06511, USA
| | - Susan T. Mayne
- Department of Epidemiology and Public Health, Yale University School of Medicine, 60 College Street, New Haven, CT 06520, USA
| | - Michael B. Bracken
- Department of Epidemiology and Public Health, Yale University School of Medicine, 60 College Street, New Haven, CT 06520, USA
| | - Frederick L. Ferris
- National Eye Institute, Building 10, CRC, 10 Center Drive, Bethesda, MD 20892–1204, USA
| | - Jurg Ott
- Laboratory of Statistical Genetics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | - Colin Barnstable
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, 330 Cedar Street, New Haven, CT 06520, USA
| | - Josephine Hoh.
- Department of Epidemiology and Public Health, Yale University School of Medicine, 60 College Street, New Haven, CT 06520, USA
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Kidd M, Eick G, Shapiro MD, Camp RL, Mane SM, Modlin IM. Microsatellite instability and gene mutations in transforming growth factor-beta type II receptor are absent in small bowel carcinoid tumors. Cancer 2005; 103:229-36. [PMID: 15599934 DOI: 10.1002/cncr.20750] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Microsatellite instability (MSI) with concomitant mutations in the coding region of transforming growth factor-beta type II receptor (TGFbetaRII) results in an aberrant growth-regulatory phenotype in colorectal carcinomas. The authors postulated that a similar mechanism occurred during the malignant evolution of small bowel carcinoid tumors. METHODS Mutational analysis of two coding regions in the TGFbetaRII gene associated with MSI and BAT-26 within intron 5 of the mismatch repair gene, hMSH2, was undertaken in small bowel carcinoids (n = 14), lymph node metasasis (n = 1) and liver metastases (n = 5). Quantitative PCR analysis [TAQMAN, Applied Biosystems, Foster City, CA] was then undertaken to examine gene alterations in mismatch repair genes (hMLH1 and hMSH2) in small bowel carcinoids (n = 7) and matched normal mucosa (n = 5). Staining was then analyzed using quantitative tissue array profiling (AQUA analysis) in a small bowel EC carcinoid tissue microarray (n = 55 tumors) with immunostaining against TGFbetaRII and MSH2. RESULTS Mutational examination of the TFGbetaRII gene and BAT-26 demonstrated that MSI was not present in any carcinoid material. Q RT-PCR analysis demonstrated statistically significant increased message levels of hMSH2 but not hMLH1 in carcinoid tumors. Quantitative analysis of membrane TGFbetaRII immunostaining using AQUA demonstrated that TGFbetaRII expression was down-regulated (P < 0.0002) in thirty-three primary small bowel carcinoids that exhibited lymph node and liver metastases compared to normal mucosa. AQUA analysis of nuclear MSH2 immunostaining demonstrated no differences for MSH2 between normal tissue and carcinoid tumor metastasis. Small bowel carcinoids characterized by variable expression of TGFbetaRII, did not exhibit MSI and had no differences in MSH2 expression. CONCLUSIONS The molecular events leading to the formation of carcinoid tumors in the small bowel were different from those resulting in epithelial carcinomas. The usually slow-growing and relatively nonaggressive carcinoid tumors had variable expression of TGFbetaRII but were associated with the retention of mismatch repair protein function and a microsatellite-stable phenotype.
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Affiliation(s)
- Mark Kidd
- Department of Surgery, Yale University School of Medicine, New Haven, Connecticut 06520-8062, USA.
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Dorsey JF, Cunnick JM, Mane SM, Wu J. Regulation of the Erk2-Elk1 signaling pathway and megakaryocytic differentiation of Bcr-Abl(+) K562 leukemic cells by Gab2. Blood 2002; 99:1388-97. [PMID: 11830491 DOI: 10.1182/blood.v99.4.1388] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In the blast crisis phase of chronic myelogenous leukemia (CML), Bcr-Abl(+) myeloblasts fail to undergo terminal maturation. The extracellular signal-regulated kinase (Erk) mitogen-activated protein (MAP) kinase has been shown to mediate terminal differentiation of myeloid cells. Interestingly, Bcr-Abl(+) CML cell lines established from blast crisis were found to have low Erk MAP kinase activity. In this study, we analyzed the role of the Gab2 docking protein in regulation of the Erk MAP kinase in Bcr-Abl(+) K562 human CML cells. Overexpression of Gab2 in K562 cells resulted in transcriptional activation of the c-fos serum response element (SRE) promoter, whereas overexpression of SHP2, Grb2, and CrkL had no effect. Activation of the c-fos SRE transcriptional activity by Gab2 required tyrosine 604, which is a SHP2 docking site on Gab2, and the SHP2 tyrosine phosphatase activity. Elk1, c-Jun, and CHOP trans-reporting assays indicated that overexpression of Gab2 selectively activated the Erk2-Elk1 signaling pathway. To determine cellular consequences of elevating the Gab2 level in K562 cells, stable cell lines for doxycycline-inducible expression of the wild-type Gab2 (Gab2WT) and an SHP2-binding defective Gab2 (Gab2Tyr604Phe) were established. Analysis of these cell lines indicated that induction of Gab2WT expression, but not Gab2Tyr604Phe expression, led to Erk activation, growth arrest, cell spreading, and enlargement; expression of megakaryocyte/platelet lineage-specific integrins alphaIIb/beta3 (CD41/CD61); and upregulation of RNA for megakaryocyte/platelet proteins. All of these changes are characteristics of megakaryocytic differentiation. Together, these results reveal Gab2 as a limiting signaling component for Erk MAP kinase activation and terminal differentiation of K562 CML cells.
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Affiliation(s)
- Jay F Dorsey
- Molecular Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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