A-Z of Renal Genetics. Prof Peter Maxwell Nephrology SpR club Belfast 26 February 2011

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1 A-Z of Renal Genetics Prof Peter Maxwell Nephrology SpR club Belfast 26 February 2011

2 A-Z of Renal Genetics Single gene renal disorders Polygenic kidney diseases Gene-environment interactions

3 Glomerular Filtration System. Single-gene kidney disorders Tryggvason K et al. N Engl J Med 2006;354:

4 Single-gene kidney disorders Genotype: mutation Phenotype: the description ( syndrome )

5 Single-gene kidney disorders: Recessive Penetrance full Onset fetus, child Frequency rare Dominant Penetrance sometimes incomplete Onset adult Frequency quite rare

6 Single-gene kidney disorders: potential clinical presentations 1. Proteinuria (fault in glomerular structure) 2. Loss of electrolytes, sugar, amino acids (tubular defects) 3. Blobs on ultrasound (cysts & tumours) 4. Seen on an X-ray (calculi and nephrocalcinosis) 5. Unusual anatomy (congenital CAKUT kids)

7 Single gene glomerular disorders A is for... Alport s syndrome a defect in Type 4 collagen assembly X-linked: COL4A5 Autosomal recessive: COL4A3 or COL4A4 Autosomal dominant: COL4A3 or COL4A4

8 Single gene glomerular disorders Congenital and steroid-resistant nephrotic syndromes Mutations in genes encoding slit diaphragm proteins Nephrin (NPHS1) Podocin (NPHS2) Laminin 2 (LAMB2) actinin (ACTN4) CD-2 associated protein (CD2AP)

9 Single gene kidney disorders: potential clinical presentations 1. Proteinuria (fault in glomerular structure) 2. Loss of electrolytes, sugar, amino acids (tubular defects) 3. Blobs on ultrasound (cysts & tumours) 4. Seen on an X-ray (calculi and nephrocalcinosis) 5. Unusual anatomy (congenital CAKUT kids)

10 Loop diuretic Thiazide

11 Bartter s Gitelman s

12 Na + Na + K + K + Aldosterone sensitive: epithelial sodium channel

13 Na + Na + Na+ Na+ Na + Na + Liddle s syndrome: gain of function mutation in epithelial sodium channel

14 Single gene renal tubular disorders BaGiL syndromes Bartter s (loop of Henle) Gitelman s (distal tubule) Liddle s (collecting duct) Is this stuff on the curriculum? Yes!

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16 Single gene kidney disorders: potential clinical presentations 1. Proteinuria (fault in glomerular structure) 2. Loss of electrolytes, sugar, amino acids (tubular defects) 3. Blobs on ultrasound (cysts & tumours) 4. Seen on an X-ray (calculi and nephrocalcinosis) 5. Unusual anatomy (congenital CAKUT kids)

17 Polycystic kidney disease Prevalence 1/500 1/1000 Most common monogenic cause of ESRD

18 UK Renal Registry data, 2008 New patients starting dialysis Diabetes 24.0% Aetiology uncertain 20.7% Glomerulonephritis (biopsy) 11.8% Pyelonephritis 7.8% Polycystic kidney disease 7.3% Renal vascular disease 6.9% Hypertension 6.0% Other 15.6%

19 PKD: Clinical Implications of Genetics Different prognosis of PKD1 vs. PKD2 gene defect PKD1 (~85% of cases) Earlier onset of ESRD (more severe phenotype) PKD1 females have better renal survival (58 yr vs 54 yr) 1 Higher prevalence of hypertension (compared to PKD2) PKD2 (~15% cases) Later onset ESRD (PKD yr; PKD yr) 2 PKD2 females have better renal survival (76yr vs. 68 yr) 3 1. Reed BY et al. Am J Kid Dis 51: , Hateboer N et al. Lancet 1999; 353: Magistroni R et al. J Am Soc Nephrol 2003; 14:

20 PKD: Practical issues with genetic testing Complex genetics to unravel witin the NHS! PKD1 > 270 mutations reported PKD1 gene is also highly polymorphic PKD2 > 70 mutations reported Majority of mutations are unique to family tested PKD1 gene is adjacent to multiple pseudogene copies on chromosome 16 Some correlations between location of mutation and clinical phenotypes (age of ESRD onset; risk of ICA)

21 Several theories Why are only some tubules affected by cystic change? 1. A two-hit mechanism

22 Individual cyst formation in ADPKD is a two-hit phenomenon ADPKD N PKD PKD At conception (a germline mutation) C PKD PKD After birth (a somatic mutation) PKD = mutant PKD gene

23 Individual cyst formation in ADPKD is a two-hit phenomenon ADPKD N PKD PKD At conception (a germline mutation) C PKD PKD The abnormal cell with two mutant copies of the PKD gene can now multiply rapidly C PKD PKD C PKD PKD C PKD PKD C PKD PKD PKD = mutant PKD gene

24 In this two hit model ADPKD is recessive at the level of an individual cell Somatic mutational events (the second hit ) increase exponentially with age

25 Epithelial cells from individual cysts in ADPKD are monoclonal in origin Single epithelial cell derived from renal tubule Expanded cell mass leads to outpouching from renal tubule Individual cyst eventually forms having severed its connection with the renal tubule

26 Relative contributions of various factors to the resulting phenotypes in autosomal dominant PKD Rossetti, S. et al. J Am Soc Nephrol 2007;18:

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28 Familial renal cancer syndromes

29 Birt-Hogg-Dubé syndrome (BHD) renal cancer, skin lesions and pneumothoraces associated with folliculin gene mutation

30 Single gene kidney disorders: 1. Proteinuria (fault in glomerular structure) 2. Loss of electrolytes, sugar, amino acids (tubular defects) 3. Blobs on ultrasound (cysts & tumours) 4. Seen on an X-ray (calculi and nephrocalcinosis) 5. Unusual anatomy (congenital CAKUT kids)

31 Cystinuria Single gene kidney disorders Stones and abnormal X-rays Nephrocalcinosis Neild GH et al. Nephrol Dial Transplant 2005; 20:2284-5

32 Single gene kidney disorders Dear Dr Smart Renal clinic, Ivory Tower Teaching Hospital Please arrange follow up for this young chap with Dent disease who recently joined our general practice Regards Dr Muggins What s your approach? Google Dent s disease! X-linked recessive Hypercalciuria Nephrolithiasis Nephrocalcinosis Fanconi s syndrome Check out

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35 Single gene kidney disorders: potential clinical presentations 1. Proteinuria (fault in glomerular structure) 2. Loss of electrolytes, sugar, amino acids (tubular defects) 3. Blobs on ultrasound (cysts & tumours) 4. Seen on an X-ray (calculi and nephrocalcinosis) 5. Unusual anatomy

36 Single gene disorders and chromosomal mix-ups Congenital Abnormalities of Kidney and Urinary Tract (CAKUT) vesicoureteral reflux multicystic renal dysplasia

37 Annotated chromosome maps for renal disease. Human Mutation 2009 Mar;30(3): McKnight AJ, O'Donoghue D, Maxwell AP.

38 A-Z of Renal Genetics One gene at a time All genes at once

39 Adjusted incident rates of ESRD due to diabetes, by age & race

40 Adjusted incident rates of ESRD due to diabetes, by age & race Counts & rates of ESRD due to polycystic kidney disease

41 Identifying the genetic contribution to complex polygenic kidney disease

42 Genomewide Association Study (GWAS) Manolio TA. N Engl J Med 2010;363:

43 Meta-Analysis of Genomewide Association Studies Manolio TA. N Engl J Med 2010;363:

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45 Genomewide Association Scans relevant for Renal Disease Hypertension Chronic kidney disease GFR Albuminuria IgA nephropathy Membranous nephropathy Diabetic nephropathy Renal transplant dysfunction

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48 IgA

49 Strong signal of association on chromosome 6p with IgA nephropathy. Feehally J et al. JASN 2010;21: by American Society of Nephrology

50 Multiple SNPs are associated with IgA nephropathy across the MHC region on chromosome 6p. Feehally J et al. JASN 2010;21: by American Society of Nephrology

51 Original Article Risk HLA-DQA1 and PLA 2 R1 Alleles in Idiopathic Membranous Nephropathy Horia C. Stanescu, M.D., Mauricio Arcos-Burgos, M.D., Ph.D., Alan Medlar, M.Sc., Detlef Bockenhauer, M.D., Ph.D., Anna Kottgen, M.D., M.P.H., Liviu Dragomirescu, Ph.D., Catalin Voinescu, B.Sc., Naina Patel, B.Sc., Kerra Pearce, M.Sc., Mike Hubank, Ph.D., Henry A.F. Stephens, Ph.D., Valerie Laundy, F.I.M.L.S., Sandosh Padmanabhan, M.D., Ph.D., Anna Zawadzka, Julia M. Hofstra, M.D., Marieke J.H. Coenen, Ph.D., Martin den Heijer, M.D., Ph.D., Lambertus A.L.M. Kiemeney, Ph.D., Delphine Bacq-Daian, M.Sc., Benedicte Stengel, M.D., Ph.D., Stephen H. Powis, Ph.D., F.R.C.P., Paul Brenchley, Ph.D., John Feehally, D.M., F.R.C.P., Andrew J. Rees, F.R.C.P., F.Med.Sci., Hanna Debiec, Ph.D., Jack F.M. Wetzels, M.D., Ph.D., Pierre Ronco, M.D., Ph.D., Peter W. Mathieson, Ph.D., F.R.C.P., and Robert Kleta, M.D., Ph.D. N Engl J Med Volume 364(7): February 17, 2011

52 Study Overview Independent genomewide association studies were carried out to investigate the genetic basis of idiopathic membranous nephropathy in three groups of white patients. An HLA DQA1 allele on chromosome 6p21 was found to be significantly associated with this disease.

53 Manhattan Plots for Genomewide Association Studies of Idiopathic Membranous Nephropathy (IMN) in Three Groups of Patients and Racially Matched Controls. Stanescu HC et al. N Engl J Med 2011;364:

54 Manhattan Plots for the Joint Genomewide Association Study. Stanescu HC et al. N Engl J Med 2011;364:

55 Odds Ratios for Idiopathic Membranous Nephropathy, According to Single-Nucleotide Polymorphism (SNP) and Genotype Combinations. Stanescu HC et al. N Engl J Med 2011;364:

56 Conclusions An HLA-DQA1 allele on chromosome 6p21 is most closely associated with idiopathic membranous nephropathy in persons of white ancestry. This allele may facilitate an autoimmune response against targets such as variants of PLA2R1. Our findings suggest a basis for understanding this disease and illuminate how adaptive immunity is regulated by HLA.

57 More GWAS data coming!

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59 Renal transplant dysfunction GWAS WTCCC3 study of UK and Ireland patients 2,500 kidney donor-transplant recipient pairs 5000 DNA samples in initial GWAS Exploring the interaction of donor s genome (the graft) with the recipient s genome (host) Replication of top hits in up to 8000 further DNA samples from renal transplant recipients in UK and Ireland

60 Genetic association is NOT causation! SNPs associated with kidney diseases are either directly implicated in pathogenesis or are markers for the genomic regions harbouring gene variants that are important in disease causation Resequencing of the genomic regions required to identify biologic candidate genes (and variants) to test in cell and animal models

61 A-Z of Renal Genetics Single gene renal disorders Polygenic kidney diseases Gene-environment interactions

62 DNA is not static but is constantly being modified in response to environmental stimuli

63 Dutch famine of winter 1944

64 Dutch Hunger Winter: Calories

65 Adverse fetal environment followed by plentiful food in adulthood may be a recipe for adult chronic disease

66 Dutch famine of winter 1944 children of pregnant women exposed to famine were more susceptible to diabetes, obesity, cardiovascular disease, microalbuminuria and other health problems

67 Epigenetic modifications

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72 What might we do with this stuff in 10 years? Genomics Transcriptomics Proteomics Metabolomics It s all just economics Sidney Brenner, Nobel laureate

73 Has fantasy collided with reality?

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76 But...

77 GWAS(s) for egfr & CKD Kottgen et al., New loci associated with kidney function and chronic kidney disease Nature Genetics 42, (2010)

78 For only $985 we scan over one million variants in your genome decodeme

79 Next generation sequencing Complete genome sequence

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81 Genome Sequencing A Reality $68,000 was cost in early

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83 Whole Genome Sequence Costs Sept 2009: $23,000 (~ 14 K) 2010: $10,000 (~ 6 K) Feb 2011: $7,000 (~ 4 K) Dec 2011:???

84 Coming to your clinic within 10 years?

85 Renal genetics: much more to unravel! Epigenetics Pharmacogenetics Whole exome sequencing (rare variants) Whole genome sequencing (rare variants) and personal genome Extreme phenotype studies e.g. rapid progression to ESRD Gene expression profiles e.g. predictive of transplant outcomes

86 A-Z of Renal Genetics Time to go

87 Questions?? A-Z of Renal Genetics Alport s syndrome Birt Hogg Dube syndrome Chromosome Diabetic nephropathy Epigenetics Folliculin gene Genome-wide association scan Hunger IgA nephropathy Junk food Kidney stones Liddle s syndrome Membranous nephropathy Next generation sequencing Orpha.net.org PLA2R1 Q-Q plot Renal transplant GWAS Sodium channel Tests Uromodulin Vorderman WTCCC3 X-linked disease Your future practice? Zebedee