A-Z of Renal Genetics

Prof Peter Maxwell

Nephrology SpR club

Belfast 26 February 2011

A-Z of Renal Genetics

• Single gene renal disorders

• Polygenic kidney diseases

• Gene-environment interactions

Glomerular Filtration System.

Tryggvason K et al. N Engl J Med 2006;354:1387-1401.

Single-gene kidney disorders

Single-gene kidney disorders

• Genotype: mutation

• Phenotype: the description (“syndrome”)

Single-gene kidney disorders:

• Recessive

• Penetrance – full

• Onset – fetus, child

• Frequency – rare

• Dominant

• Penetrance –sometimes incomplete

• Onset – adult

• Frequency – quite rare

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)

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

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)

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)

Loop diuretic

Thiazide

Bartter’s

Gitelman’s

Na+

Na+

K+

K+

Aldosterone sensitive: epithelial sodium channel

Na+

Na+

Na+

Na+

Na+

Na+

Liddle’s syndrome: gain of function mutation in epithelial sodium channel

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!

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)

Polycystic kidney disease

• Prevalence 1/500 – 1/1000

• Most common monogenic cause of ESRD

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%

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 (PKD1 54.3 yr; PKD2 74.0 yr)2

– PKD2 females have better renal survival (76yr vs. 68 yr)3

1. Reed BY et al. Am J Kid Dis 51: 173-183, 20082. Hateboer N et al. Lancet 1999; 353: 103-1073. Magistroni R et al. J Am Soc Nephrol 2003; 14: 1164-1174

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)

Why are only some tubules affected by cystic change?

• Several theories

1. A “two-hit” mechanism

Individual cyst formation in ADPKD is a “two-hit” phenomenon

PKDPKD

PKDPKD

ADPKD

At conception (a germline mutation)

After birth (a somatic mutation)

N

C

PKD = mutant PKD gene

Individual cyst formation in ADPKD is a “two-hit” phenomenon

PKDPKD

PKDPKD

ADPKD

At conception (a germline mutation)N

C

PKD = mutant PKD gene

PKDPKD

C PKDPKD

C PKDPKD

CPKDPKD

C

The abnormal cell with two mutantcopies of the PKD gene can now multiply rapidly

• 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

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 havingsevered its connection with the renal tubule

Rossetti, S. et al. J Am Soc Nephrol 2007;18:1374-1380

Relative contributions of various factors to the resulting phenotypes in autosomal dominant PKD

Familial renal cancer syndromes

Birt-Hogg-Dubé syndrome (BHD)renal cancer, skin lesions and pneumothoraces

associated with folliculin gene mutation

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)

Single gene kidney disordersStones and abnormal X-rays

• Cystinuria

• Nephrocalcinosis

Neild GH et al. Nephrol Dial Transplant 2005; 20:2284-5

Single gene kidney disorders

• What’s your approach?

• Google Dent’s disease!

• X-linked recessive

• Hypercalciuria

• Nephrolithiasis

• Nephrocalcinosis

• Fanconi’s syndrome

• Check out www.orpha.net.org

• 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

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

Single gene disorders and chromosomal mix-ups

Congenital Abnormalities of Kidney and Urinary Tract (CAKUT)

vesicoureteral reflux

multicystic renal dysplasia

Annotated chromosome maps for renal disease. Human Mutation 2009 Mar;30(3):314-20.

McKnight AJ, O'Donoghue D, Maxwell AP.

A-Z of Renal Genetics

One gene at a time

• All genes at once

Adjusted incident rates of ESRD

due to diabetes, by age & race

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

Counts & rates of ESRD

due to polycystic kidney disease

Identifying the genetic contribution to complex polygenic kidney disease

Genomewide Association Study (GWAS)

Manolio TA. N Engl J Med 2010;363:166-176.

Meta-Analysis of Genomewide Association Studies

Manolio TA. N Engl J Med 2010;363:166-176.

Genomewide Association Scans relevant for Renal Disease

• Hypertension

• Chronic kidney disease

• GFR

• Albuminuria

• IgA nephropathy

• Membranous nephropathy

• Diabetic nephropathy

• Renal transplant dysfunction

2009; 41:712

IgA

Strong signal of association on chromosome 6p

with IgA nephropathy.

Feehally J et al. JASN 2010;21:1791-1797

©2010 by American Society of Nephrology

Multiple SNPs are associated with IgA nephropathy across

the MHC region on chromosome 6p.

Feehally J et al. JASN 2010;21:1791-1797

©2010 by American Society of Nephrology

Original Article

Risk HLA-DQA1 and PLA2R1 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 MedVolume 364(7):616-626

February 17, 2011

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.

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;364:616-626

Manhattan Plots for the Joint Genomewide Association Study.

Stanescu HC et al. N Engl J Med 2011;364:616-626

Odds Ratios for Idiopathic Membranous Nephropathy, According to Single-Nucleotide Polymorphism (SNP) and Genotype Combinations.

Stanescu HC et al. N Engl J Med 2011;364:616-626

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.

More GWAS data coming!

Renal transplant dysfunction GWASWTCCC3 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

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

A-Z of Renal Genetics

Single gene renal disorders

Polygenic kidney diseases

• Gene-environment interactions

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

Dutch famine of winter 1944

Dutch Hunger Winter: Calories

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

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

Epigenetic modifications

What might we do with this stuff in 10 years?

• Genomics

• Transcriptomics

• Proteomics

• Metabolomics

• “It’s all just economics”• Sidney Brenner, Nobel laureate

Has fantasy collided with reality?

http://www.decodeme.com/chronic-kidney-disease

But........

GWAS(s) for eGFR & CKD

Kottgen et al., New loci associated with kidney function and chronic kidney disease Nature Genetics 42, 376 - 384 (2010)

For only

$985 we

scan over

one million

variants in

your

genomedeCODEme

Next generation sequencing

Complete genome sequence

Genome Sequencing A Reality

http://www.scientificamerican.com/blog/60-second-science/post.cfm?id=single-bidder-

pays-68000-to-sequenc-2009-05-06

$68,000 was cost

in early 2009

Whole Genome Sequence Costs

Sept 2009: $23,000 (~ £14 K)

2010: $10,000 (~ £6 K)

Feb 2011: $7,000 (~£4 K)

Dec 2011: ???

Coming to your clinic within 10 years?

• 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

Renal genetics: much more to unravel !

A-Z of Renal Genetics

Time to go

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