Genetic Approach to Childhood Interstitial Lung Disease (ChILD)

Transcription

1 Genetic Approach to Childhood Interstitial Lung Disease (ChILD) Lawrence M. Nogee, M.D. Eudowood Neonatal Pulmonary Division Department of Pediatrics Johns Hopkins University School of Medicine Baltimore, MD USA

2 Learning Objectives: Recognize clinical presentations (phenotypes) of children with genetic causes of Childhood Interstitial (Diffuse) Lung Disease. Describe the different kinds of genetic testing currently available. List advantages and disadvantages to genetic testing for childhood DLD.

3 Overview Review data supporting genetic mechanisms are important causes of childhood DLD. Review features of specific disorders. Review approaches to genetic testing and their advantages and disadvantages. Discuss how genetic testing fits into diagnostic approach to childhood DLD.

4 Diffuse Lung Disease in Infancy 11 center, retrospective review of 187 cases < 2 y/o Deutsch, G, Young LR et al., AJRCCM, 2007 Surfactant Dysfunction Not Classifiable Diffuse developmental: Alveolar Cap. Dysplasia Immunocompromised Systemic Disease Associated Growth Abnormalities Chromosomal Congenital Heart Disease BPD Reactive Specific disorders of unknown etiology unique to infancy: NEHI, PIG

5 Results of Genetic Evaluations for Childhood DLD N = 501 NKX2-1 SP-B SP-C Evaluation Incomplete ABCA3 Def ABCA3 likely ABCA3 het No Mutations Identified MARS COPA Other genetic Familial NEHI NEHI Unknown with + Family History ~50% with demonstrated or highly likely genetic mechanism Caveat: Highly selected population

6 Diffuse Developmental Disorders Clinical: Severe neonatal hypoxemic respiratory failure Acinar Dysplasia Arrest of lung development at psuedoglandular to canalicular phase Familial cases reported Genes: FGFR2, TBX4 (complex phenotypes) Congenital Alveolar Dysplasia Arrest of lung development at canalicular to sacular phase Familial cases not recognized (but paucity of reports) Gene:? Alveolar Capillary Dysplasia with Misaligned Pulmonary Veins Pulmonary hypertension in newborn (PPHN); Often severe Other anomalies common (Heart, GI, GU) Gene: Majority FOXF1

7 Alveolar Capillary Dysplasia and FoxF1 Clinical: Severe Neonatal Pulmonary Hypertension 75% + with extra-pulmonary anomalies (Not 100%!) PA PV Majority with with FoxF1 genetic variant DNA sequence variants, genomic/genic deletions, including in 5 UTR, lncrnas. Other genes likely. Majority sporadic: maternal chromosome Familial: imprinted? Sen et al., J Pediatrics 145:646-51, Increasing phenotypic variability: later onset, prolonged survival

8 Surfactant Production and Metabolism C C B B B B B N C ABCA3 NBC NCC AAAA GM-CSF Alveolar Macrophage Type I cell TTF1 Alveolar Type II cell

9 Surfactant Protein B (SP-B) Deficiency Epidemiology: Very rare, < 1 in 1 million live births Clinical: Neonatal RDS Persistent disease 6 hours DOL 2 Genetic: Autosomal Recessive Bi-allelic loss-of-function SFTPB mutations Pathology: Control SP-B Def. Natural history: Usually fatal < 3 months Abnormal lamellar bodies

10 ABCA3 Deficiency Epidemiology: Uncertain, may be as high as ~1 in 4,000 Clinical: Neonatal RDS phenotype, child Genetic: Autosomal Recessive Bi-allelic loss-of-function ABCA3 mutations Pathology: Abnormal lamellar bodies Natural history: Neonatal lethal to prolonged survival

11 Genotype-Phenotype and ABCA3 Deficiency J Wambach, A Casey et al., AJRCCM, % presented after newborn period. Adults with ABCA3 deficiency have been reported. p= Age at Presentation Outcome at age 1 year Children with complete loss-of-function on both alleles (26%): All presented at birth and All died (or were transplanted) by age 1 year.

12 SP-C Dysfunction Epidemiology: Rare, incidence & prevalence unknown Clinical: Neonatal RDS, child, Pulmonary Fibrosis Genetic: Pathology: Natural History: Autosomal Dominant, sporadic Mono-allelic coding SFTPC mutations Common mutation (p.ile73thr) CPI, DIP, NSIP Highly variable, onset neonate to adult Critically ill infants may gradually improve

13 Dominant negative Some mutations SFTPC mutations Disease mechanisms ProSP-C Control SFTPC Δ exon 4 Toxic gain-of-function Abnormal routing to plasma membrane Mature SP-C Abnormal routing and intracellular accumulation WT I73T L188Q Δexon4 Stewart et al., AJRCMB, Misfolded protein, UPR, ER Stress, cell injury/death

14 NKX2.1 (TTF-1, TITF-1, T/EBP) Transcription factor, thyroid, CNS (basal ganglia), Lung Genetic: Sporadic or Autosomal Dominant Deletions or loss-of-function (haploinsufficiency) SP-B BCA3 SP-D Brain Chorea Ataxia Hypotonia Dev Delay nrds Infxn Control P1 P2 21% 22% 1% 4% 41% 6% RDS Infection ILD \ DLD Lung 4% Thyroid Agenesis Hypothyroid Pulmonary phenotype mediated by target gene(s) affected

15 Surfactant Catabolic Disorders GM-CSF Receptor Deficiency Clinical: Gradual onset tachypnea, SOB, cough Onset: Infancy to adult Epidemiology:?, < 20 cases reported α (CSF2RA)* and β c (CSF2RB) # chain Recessive, loss-of-function mutations, deletions Natural history not well definfed; whole lung lavages * Martinez-Moczygemba et al. & Suzuki et al., J Exp Med, 2008, AJRCCM 2010 # Suzuki et al. ERJ, 2011 & Tanaka et al. Hum Mol Genet 2011.

16 Neuroendocrine Cell Hyperplasia of Infancy (NEHI) (Persistent Tachypnea of Infancy) Clinical: Onset Infancy Tachypnea Hypoxemia Failure to thrive No reported mortality Bombesin stain Brody and Crotty, Ped Rad 2006 Popler et al.,ped Pul 2010

17 Familial NEHI and NKX2-1 ILD H&E Bombesin NKX2.1 Homeodomain Sequence p.arg191leu Arg / Leu NKX2-1 sequence normal in other NEHI subjects

18 Other Neonatal ChILD Genes Gene FLNA ITGA3 Protein Function Inheritance Age of onset Pulmonary Phenotype Filamin A Actin Binding Protein X-linked LOF Newborn -> infancy BPD, Growth Disorder Cystic Lung Disease Transmembrane Cytoskeleton -> Extracellular matrix Recessive LOF Newborn -> infancy RDS Growth disorder Other organ Involvement Periventricular heterotopias Skeletal, CVS Skin Renal

19 Newer ChILD Genes Gene MARS COPA TMEM173 Protein Function Methionyl trna Synthetase Transport Golgi > ER STING ER Membrane Signaling Inheritance Age of onset Recessive Dominant Sporadic, Dominant Infancy -> adult Infancy -> adult Infancy Pulmonary Phenotype PAP Hemorrhage ILD ILD Other organ Involvement Liver Dz Anemia Arthritis Immune Dysfunction Autoimmune Vascultis Skin

20 General Approach to child Diagnostic Evaluation Newborn Full-term with RDS, PPHN +/- other anomalies Not clearly infection, MAS Pulmonary Hypoplasia Rapid Deterioration Family history of ChILD disorder or pulmonary fibrosis? Yes Genetic Testing Lung Biopsy (Modeled after Kurland et al., AJRCCM, 2013) Infant ChILD Syndrome Not: Infection, PCD, CF Immunodeficiency Heart Disease No No HRCT Specific Dx (NEHI)

21 Gene Sequencing Standard (Sanger) Targeted region of gene; long reads ( bases) Highly sensitive and accurate (for regions sequenced) May fail to amplify region of interest if primer mismatch CNV not detected Relatively expensive Next Generation methods (multiple platforms) Parallel sequencing multiple DNA fragments Short reads ( bases) and computer alignment Accuracy depends upon depth of coverage CNV detection possible Less expensive (per base) Multiple genes and samples simultaneously Whole exome sequencing (WES) ~1-2% corresponding to protein coding sequence. Different enrichment approaches; coverage not complete. Whole genome sequencing (WGS) All (almost) 3 x 10 9 bases

22 Genetic Approach to child Diagnostic Evaluation Genetic Testing with appropriate NGS Panel Newborn: FOXF1, SFTPB, NKX2-1, ABCA3 Older: ABCA3, SFTPC, NKX2-1, CSF2RA, CSF2RB, SLC7A7, MARS, GATA2 Additional Genes based on other phenotypic features Unrevealing: Consider WES Kurland et al., Am J Respir Crit Care Med 188: , 2013

23 The Problem with Panels 3 m/o with tachypnea, mild retractions PMH: Full-term, uncomplicated perinatal course SpO 2 93% in room air CXR: Increased interstitial markings CT: Ground glass opacities, mainly lower lobes Normal Swallow, IgGs, sweat test Surfactant Genetic studies sent Neonatal Respiratory Distress Panel ordered Results: ABCA3, SFTPB, SFTPC, NKX2-1 all negative FOXF1: c. 52_54insCGG, p.gly17dup More genes means detecting more VUS (increased sensitivity vs. specificity)

24 Genetic Testing: Pros and Cons Advantages: Noninvasive means to establish specific diagnosis. Potentially avoid lung biopsy and associated morbidity. Appropriate counseling re: prognosis, recurrence risk. Information can be helpful to family and providers even if no specific treatment available. Potential Problems: Expensive. Turn-around-times often long. Not 100% sensitive. Interpretation of results not always straight-forward. Variants of Uncertain Significance (VUS)

25 Summary Genetic testing for childhoon DLD is available Multiple labs offering testing. Next Generation panels have supplanted single gene testing and are more cost effective. Knowing (usual) phenotypes still important in determining when to order and which tests. Persistent issues: Turn-around times Costs, reimbursement Sensitivity not 100% CNV better with NGS untranslated regions Interpretation can be problematic Landscape Rapidly changing WES when testing for known disorders negative

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27 OMIM Locus / Protein Genetic Surfactant Dysfunction SMDP1 SMDP3 SMDP2 SFTPB ABCA3 SFTPC B-T-L NKX2-1 2p p13.3 8p23 14q13.3 SP-B ABCA3 SP-C TTF-1 Phenotype RDS RDS > child >> ILD child> ILD >RDS RDS, child Infection CNS (Chorea) Hypothyroid Inheritance Recessive LOF Recessive LOF Dominant/ sporadic Toxic GOF Sporadic/ Dominant LOF Incidence <1 in in 10K-20K?? Outcome Fatal without lung transplant Severe/ variable Variable Variable