Analysis of three genes from the RAS-MAPK signalling pathway that are causative of Noonan/LEOPARD syndromes Sandra Ramos Grade A Project St George’s Hospital, London SW Thames Molecular Genetics Diagnostic Laboratory Aims of the Project • Extend existing Noonan/LEOPARD syndrome screen to include new genes • Test the LightScanner™ (HRM) as a pre-screening tool • Investigate genotype-phenotype correlations • Determine optimal NS/LS future testing strategy SW Thames Molecular Genetics Diagnostic Laboratory Noonan syndrome (NS) • Autosomal dominant • Incidence of 1 in 1000 to 1 in 2500 • Clinically heterogeneous disorder characterized by: - distinct facial features - short stature - congenital heart defects - skeletal abnormalities - bleeding problems Taken from London Medical Database SW Thames Molecular Genetics Diagnostic Laboratory LEOPARD syndrome (LS) • Rare autosomal dominant disease • Characterized by: - Lentigines - ECG conduction abnormalities - Ocular hypertelorism - Pulmonary stenosis - Abnormalities of genitalia - Retardation of growth - Deafness Taken from E. J. of Human Genetics (2004) 12, 1069–1072 SW Thames Molecular Genetics Diagnostic Laboratory Molecular Genetics of NS • Caused by missense gain-of-function mutations in RAS-MAPK pathway • ~ 60% of Noonan syndrome cases are sporadic, presumed to be the result of de novo mutations Molecular Genetics of LS • Caused by loss of function/dominant negative mutations affecting the catalytic activity of PTPN11 SW Thames Molecular Genetics Diagnostic Laboratory RAS-MAPK Signalling Pathway Noonan syndrome RTK SOS1 Shc Grb2 HRAS KRAS Gab2 40 - 50% SHP-2 RAF1 BRAF ~ 90% MEK LEOPARD syndrome ERK Transcription of Target Genes SW Thames Molecular Genetics Diagnostic Laboratory SOS1 gene • SOS1 is located on chromosome 2p22.1 and encodes a major RAS-GEF • Consists of 23 exons of which 9 have reported mutations • Variants disrupt autoinhibition RAS-GEF activity SW Thames Molecular Genetics Diagnostic Laboratory RAS-MAPK Signalling Pathway Noonan syndrome 5 - 10% RTK SOS1 Shc Grb2 HRAS KRAS Gab2 SHP-2 RAF1 BRAF MEK LEOPARD syndrome ERK Transcription of Target Genes SW Thames Molecular Genetics Diagnostic Laboratory KRAS gene • KRAS is located on chromosome 12p12.1 • Encodes a small G protein that is activated by the exchange of bound GDP for GTP • Consists of six exons but RNA splicing reveals two different transcripts – in 98% of transcripts exon 4a is spliced out and exon 4b is translated into protein SW Thames Molecular Genetics Diagnostic Laboratory RAS-MAPK Signalling Pathway Noonan syndrome RTK ~ 1% SOS1 Shc Grb2 HRAS KRAS Gab2 SHP-2 RAF1 BRAF MEK LEOPARD syndrome ERK Transcription of Target Genes SW Thames Molecular Genetics Diagnostic Laboratory RAF1 gene • RAF1 is located on chromosome 3p25 and encodes serine-threonine protein kinase that activates MEK1 and MEK2. • Consists of 17 exons of which 3 have reported mutations • Mutations alter autoinhibition of RAF1 SW Thames Molecular Genetics Diagnostic Laboratory RAS-MAPK Signalling Pathway Noonan syndrome RTK SOS1 Shc Grb2 HRAS KRAS Gab2 3 - 8% SHP-2 RAF1 BRAF MEK LEOPARD syndrome ERK Transcription of Target Genes SW Thames Molecular Genetics Diagnostic Laboratory WAVE v LightScanner™ • Primers designed using LightScanner™ primer design software • CADAMA HotShot mastermix • Idaho Technologies designed Touchdown PCR program • Amplified products were successfully analysed using dHPLC (WAVE) and bidirectional sequencing (ABI3730) SOS1 primers SW Thames Molecular Genetics Diagnostic Laboratory WAVE v LightScanner™ results SOS1 exon 13 LS trace LightScanner™ software missed SOS1 exon 13 variant control (black arrow) SW Thames Molecular Genetics Diagnostic Laboratory SOS1 exon 13 WAVE trace Wave traces for SOS1 exon 13 normal samples and 1 variant control (black arrow) WAVE v LightScanner™ results SOS1 exon 10 LS trace SOS1 exon 10 WAVE trace Visual checks difficult by the lack of uniformity/normalisation in traces SW Thames Molecular Genetics Diagnostic Laboratory WAVE v LightScanner™ results SOS1 exon 16 variant control only detected when sensitivity is increased to 2.40 SW Thames Molecular Genetics Diagnostic Laboratory WAVE v LightScanner™ conclusions LightScanner™ dHPLC WAVE False Variants 10/77 (12.9%) 1/77 (1.2%) Positive Controls detected 5/9 (55%) 9/9 (100%) Fails 1/88 (1.1%) 3/88 (3.4%) SW Thames Molecular Genetics Diagnostic Laboratory Testing • Cohort of 110 patients from SEEGEN region referred for NS/LS testing • All negative for PTPN11 mutations • Screened exons with reported mutations only - SOS1 – 9 Exons (3,6,7,8,10,11,13,14 & 16) - RAF1 – 3 Exons (6,13 & 16) - KRAS – 5 Exons (1,2,3,4a & 4b) Samples pre-screened on the Transgenomic WAVE and variants sequenced using ABI3730 SW Thames Molecular Genetics Diagnostic Laboratory Results 110 patients screened for SOS1, RAF1 and KRAS SOS1 RAF1 7 missense variants identified of which 5 previously reported mutations and 2 novel missense variants 4 missense variants identified of which 3 previously reported mutations and 1 novel missense variant The prevalence of SOS1 mutations found is 6.4% The prevalence of RAF1 mutations found is 3.7% No mutations found in KRAS gene SW Thames Molecular Genetics Diagnostic Laboratory Genotype-Phenotype Clinical features of NS individuals with SOS1 mutations Noonan Syndrome Patient 1 Patient 2 Patient 3 Patient 4 Patient 5 Genotype 1655G>C R552T 1654A>G R552T 1655G>T R552T 1300G>A G434R 305C>G P102R 1867T>A F623I Sex/Age M/2Y M/5Y F/14Y M/2Y F/13Y M/22Y Cardiac Defect - VSD, Mild PVS PVS PVS n.d. ASD HCM Short Stature - + + n.d + + Facial Features + - n.d. + n.d. + Mental Retardation - - n.d. n.d LD - Ptosis, lymphoedema Hydrops, speech delay Others Dev. delay, low factor VIII Patient 6 Pectus excavatum, keratosis VSD/ASD (Ventriculal/Atrial septal defect); PVS (Pulmonary valve stenosis); LD (learning difficulties) SW Thames Molecular Genetics Diagnostic Laboratory Genotype-Phenotype Clinical features of NS/LS individuals with RAF1 mutations Patient 1 LEOPARD Patient 2 Noonan/ LEOPARD Patient 3 Noonan Patient4 Noonan 781C>G P261A 770C>T S257L 770C>T S257L 1835C>G S612C (NV) Sex/Age M/14Y F/ 5months deceased F/17Y M/52Y Cardiac Defect HOCM HOCM, PS HOCM - Short Stature + N/A + + Facial Features + - + + Mental Retardation - N/A LD LD Neck webbing, lentigines, subaortic stenosis Chronic lung disease, failure to thrive Hypertelorism Bilateral ptosis, pectus excavatum, cryptorchidism Genotype Others HOCM (Hypertrophic obstructive cardiomyopathy); PS (Pulmonary stenosis); LD (learning difficulties) SW Thames Molecular Genetics Diagnostic Laboratory Genotype-phenotype SOS1 Mutations RAF1 Mutations Present Study Tartaglia et. al. Present Study Razzaque et. al. Pulmonary Stenosis 2/6 (33%) 10/16 (63%) 1/4 (25%) n.d. HCM/HOCM 1/6 (16%) 2/16 (12.5%) 3/4 (75%) 8/10 (80%) Atrial/ventricular Septal Defect 1/6 (16%) 4/16 (25%) 3/4 (75%) 6/10 (60%) Short Stature 4/6 (66%) 2/15 (13%) 3/4*(75%) 9/10 (90%) Mental retardation 1/6 (16%) 1/16 (6%) 2/4*(50%) 8/10 (80%) (3 LD) Thorax deformity 2/6 (33%) 16/16 (100%) 1/4 (25%) 5/10 (50%) Cryptorchidism 2/4 (50%) n.d. 1/2 (50%) 2/8 (25%) SW Thames Molecular Genetics Diagnostic Laboratory Logging-in / Extraction NS/LS Testing Strategy STAGE 1 dHPLC analysis of exons 2, 3, 4, 7, 8, 12 and 13 of PTPN11 Bidirectional Sequencing of variants (ABI 3730) STAGE 2 dHPLC analysis of exons 3, 6, 10 of SOS1 and 6, 13, 16 of RAF1 Bidirectional Sequencing of variants (ABI 3730) STAGE 3 dHPLC analysis of remaining exons of SOS1 and all exons of KRAS Bidirectional Sequencing of variants (ABI 3730) SW Thames Molecular Genetics Diagnostic Laboratory ~ 40-50% NS cases ~ 90% LS cases ~ 10 % NS cases Exceptional LS cases ~ 1-3 % NS cases Conclusions • Three genes analysed and 9 mutations (plus 3 novel variants) detected in SOS1/RAF1 from 110 samples • Overall pick up rate for our cohort is ~10% • No mutations identified in KRAS • dHPLC WAVE is a more robust pre-screening method compared to LightScanner™ HRM • Complex genotype-phenotype correlation • Three stage screening strategy designed for NS/LS referrals from April 2008 SW Thames Molecular Genetics Diagnostic Laboratory Further Work Taken from EMBO reports 6, 12, 1169–1175 (2005) SW Thames Molecular Genetics Diagnostic Laboratory Acknowledgements Thank you: • John Short • Navaratnam Elanko • Roy Poh • Sally Cottrell • Rohan Taylor • Professor Michael Patton • Kamini Kalidas (Clinical Developmental Sciences, St George’s University of London) • IDEAS Knowledge Park for funding this project and all staff at Molecular Genetics Lab at St George’s SW Thames Molecular Genetics Diagnostic Laboratory