Novel genetic mechanisms of congenital Annual US cost is $158 - PowerPoint PPT Presentation

3/8/2019 Congenital diaphragmatic hernia • 1 in 3000 births • 8% of all birth defects Novel genetic mechanisms of congenital • Annual US cost is $158 million diaphragmatic hernia • 20%-40% mortality • 40% -50% Non-isolated Wendy Chung, MD PhD - Up to 25% with CHD Kennedy Family Professor of Pediatrics and Medicine - Developmental delay/ID common Columbia University DHREAMS protocol • Birth cohort L CDH • Neonates affected with diaphragm defects • Samples from affected case and both biological parents (Trio collection) • Developmental assessments at 2 and 5 years • Retrospective cohort • Children and adults with a personal history of a diaphragm defect • Samples from affected case and both biological parents (Trio collection) • Genetic analysis • Natural history studies Chongqing Three Gorges Central Hospital 1

3/8/2019 Study protocol Genetic Evidence for CDH • Eligible subjects • Familial aggregation • Children and fetuses • Protocol • Higher rate of concordance in monozygotic v.s. dizygotic twins • Collection of blood from proband and biological parents • Mouse studies elucidated the role of several genes in • Over 100 data points on prenatal history, NICU stay, surgical report, and family history diaphragm development • Prospective cohort • Coup-TFII, Slit3, Gata4, Fog2, Wt1 • Collection of skin and diaphragm at time of surgery • Chromosome anomalies (10-30%) • Pulmonary Hypertension assessment at 1 and 3 months • 2 year developmental assessment • T21, T18, T13, tetrasomy12p, 15q26, 8p23.1, 1q41-q42 • Vineland Adaptive Behavior Scale II • Single gene disorder (15-??%) • Bayley Scales of Infant Development III • Donnai-Barrow syndrome ( LRP2 2q31), Mathew-Wood syndrome • 5 year developmental assessment ( STRA6 15q24), Denys-Drash ( WT1 , 11q13) • Vineland Adaptive Behavior Scale II • GATA6 , GATA4 , ZFPM2 and others • Child Behavior Check List, Parent and Teacher • Wechsler Preschool and Primary Scale of Intelligence IV Published Current Study Duplication Deletions of 8p23.1 associated with CDH Deletion Translocation/ inversion a p15 8p23.1 8p21.2 4 3 p12=-3.3 9 P22.3 p23.1 p23.1 5 4 3M 9M 12M 15M 18M 21M 6M pter-p22 p21 8,043,620 2 11,883,409 p13 01-0162 15,227,167 192,262 07-0010 7 3 7,256,229 12,077,383 q25-q31.2 q22 4 4 3 3 Wat et al., 2009 [51] q31 q22-q23 6,504,084 12,752,448 4 2 Slavotinek et al., 2005 [53] q41-q42 2 7 4 trisomy q23.3-q25 6,365,021 q37 q35.2 q25.3-qter 12,611,673 Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10 Chr11 q23.3-qter Shimokawa et al., 2005 [16] 17,870,612 Faivre et al., 1998 [54] pks p11-13 ERI1 PRSS55 PINX1 SLC35G5 p13.11-p12.3 CLDN23 TNKS RP1L1 FDFT1 SGK223 MFHAS1 XKR6 BLK DEFB135 C8orf74 p12.3 PPP1R3B MTMR9 q12 GATA4 CTSB MSRA FAM167A DEFB136 q11.1-11.21 NEIL2 pter-q11 SOX7 26 3 q33.3-q34 q26 q32-qter trisomy Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19 Chr20 Chr21 Chr22 trisomy 2

3/8/2019 GATA4 information p.R252W p.R283H p.N248S c.848G>A c.754C>T Whole exome sequencing in familial CDH p.M247T p.Y244S p.N239S p.N285K p.R252P p.A411V p.D425N p.S70T p.P87S p.N239D p.Q316E p.C292R p.S429T p.G69D p.S90R p.G234S p.P407Q c.755G>C p.R320W p.R229S p.A294V p.G64E p.T280M p.G93A p.G296R p.M223T p.K329N p.S52F p.I255T p.H436Y p.D95A p.N273S p.G296S p.H28Y p.G221R p.E359K p.G296C p.S160T p.E216D p.H28D p.L261P p.T277I p.L403M p.A442V p.P163R p.F214S p.C271R p.H302R p.T354A p.G21V p.G16C p.F211L p.V380M p.P163S p.V267M p.F208L p.R260Q p.M310V p.A346V p.A6V p.R266X Exon Exon1 Exon2 Exon3 Exon4 Exon5 Exon6 Exon7 1 1 615 616 783 784 909 910 997 998 1146 1147 1329 c.69_374dupTGCCGC c.677delC c.341_342insA c.1074delC c.1075delG c.366_368dupCGC c.139_141delTCC CZnF NZnF GATA GATA 1 261 265 315 206 211 442 p.R252W p.R283H 240 295 Human A C G L Y H K MN G I N R P L I K P Q R R L S A S R R V G L S C A N C Q T T T T T L WR R N A E G E P V C N A C Chimpanzee A C G L Y H K MN G I N R P L I K P Q R R L S A S R R V G L S C A N C Q T T T T T L WR R N A E G E P V C N A C Rhesus A C G L Y H K MN G I N R P L I K P Q R R L S A S R R V G L S C A N C Q T T T T T L WR R N A E G E P V C N A C Mouse A C G L Y H K MN G I N R P L I K P Q R R L S A S R R V G L S C A N C Q T T T T T L WR R N A E G E P V C N A C Rat A C G L Y H K MN G I N R P L I K P Q R R L S A S R R V G L S C A N C Q T T T T T L WR R N A E G E P V C N A C Rabbit A C G L Y H K MN G I N R P L I K P Q R R L S A S R R V G L S C A N C Q T T T T T L WR R N A E G E P V C N A C Dolphin A C G L Y H K MN G I N R P L I K P Q R R L S A S R R V G L S C A N C Q T T T T T L WR R N A E G E P V C N A C Elephant A C G L Y H K MN G I N R P L I K P Q R R L S A S R R V G L S C A N C Q T T T T T L WR R N A E G E P V C N A C Opossum A C G L Y H K MN G I N R P L I K P Q R R L S A S R R V G L S C A N C Q T T T T T L WR R N A E G E P V C N A C Chicken A C G L Y H K MN G I N R P L F K P Q R R L S A S R R V G L S C A N C H T T T T T L WR R N A E G E P V C N A C X.tropicalis A C G L Y H K MN G I N R P L I K P Q R R L S A S R R V G L S C A N C H T T T T T L WR R N A E G E P V C N A C Zebrafish A C G L Y H K MN G I N R P L V K P Q R R L S A S R R V G L S C T N C Q T T T T T L WR R N A E G E P V C N A C 3

3/8/2019 A GATA4 I 1 2 +/+ • A zinc finger transcription factor that controls gene expression and differentiation in a variety of cell types. • Located at 8p23.1-p22 where there is a recurrent II microdeletion associated with both congenital heart disease 1 +/+ 2 +/+ 3 +/- 4 +/+ and CDH (Wat et al. 2009). • GATA4 is an important component of the retinoic signaling pathway. • ~14% of mice with heterozygous Gata4 +/Δex2 had diaphragm III defects and ~36% had cardiac defect. (Jay et al. 2007). 1 2 +/+ 3 4 +/- 5 +/+ • The N-terminal zinc finger of GATA4 interacts with FOG2 during cardiac morphogenesis (Crispino et al. 2001). FOG2 is an important gene in diaphragm development (Ackerman et al. IV 2005). 1 +/- 2 +/+ GATA4 c.754 C>T p.R252W genotype III.4 Father III.4 Father Not all Genetic Conditions Run in Families A B De novo mutations are common in autism, schizophrenia, intellectual disabilities, seizures, birth defects, syndromes C D II.3 Grandfather II.3 Grandfather 4

3/8/2019 Number Percent Gender Male 212 58.6% Types of Genetic Variants Characteristics Female 150 41.4% CDH classification of CDH Isolated 208 57.5% Complex 149 41.2% Original DNA code patients Unknown 5 1.4% DHREAMS cohort (n=283): Time of recruitment C A G C A G C A G C A G C A G C A G C A G DNA Bases -> (n=362) Neonatal 229 80.9% Fetal 9 3.2% Amino acids -> Gln Gln Gln Gln Gln Gln Gln Child 45 15.9% Discharge vital status (n=283) Survived 241 85.2% Deceased 42 14.8% Likely Gene Disrupting (LGD) Deleterious missense (D-mis) Development assessment ¶ (n=283) At 2 years follow-up 152 53.7% At 5 years follow-up 70 24.7% No assessment at either 2 or 5 years 128 45.2% C A G C A G C G G C A G C A G C A G C A G C A G C A G U A G Additional anomalies in complex cases (n=149) Cardiovascular 66 44.3% Neurodevelopmental § 37 24.8% Gln Gln Arg Gln Gln Gln Gln Gln Gln STOP Skeletal 26 17.4% Genitourinary 14 9.4% Gastrointestinal 13 8.7% Burden of coding LGD and damaging de novo Higher enrichment of damaging variants in complex variants in CDH patients cases and female cases Case group Variant class Number of variants Baseline expectation Fold enrichment P-value Variant class Number of Baseline Fold Gene Sets enrichment P-value Complex Silent 44 44.9 0.98 0.57 variants expectation (n=149) Missense 124 103.1 1.2 0.025 Synonymous 110 109.1 1.01 0.48 D-mis 62 38.5 1.61 3.08E-04 Missense 295 250.6 1.18 3.42E-03 All Genes LGD 23 13.5 1.7 0.012 D-mis 138 93.7 1.47 1.08E-05 Isolated Silent 63 62.7 1.01 0.5 LGD 57 32.9 1.73 8.60E-05 (n=208) Missense 165 144 1.15 0.046 Synonymous 34 38.8 0.88 0.80 D-mis 74 53.8 1.38 5.22E-03 Constrained Missense 112 88.1 1.27 7.91E-03 LGD 31 18.9 1.64 6.52E-03 Genes D-mis 59 38.0 1.55 9.39E-04 Female Silent 44 45.9 0.96 0.63 LGD 30 12.0 2.50 9.05E-06 (n=150) Missense 118 105.6 1.12 0.12 Synonymous 76 70.3 1.08 0.26 D-mis 64 39.3 1.63 1.85E-04 Missense 184 162.6 1.13 0.053 LGD 29 13.9 2.09 2.51E-04 Other Genes D-mis 80 55.7 1.44 1.28E-03 Male Silent 66 63.2 1.04 0.38 LGD 27 20.9 1.29 0.11 (n=212) Missense 177 145.1 1.22 5.63E-03 D-mis 74 54.3 1.36 6.45E-03 LGD 28 19 1.47 0.032 5