Genetics of Nephrolithiasis

Giovanni Gambaro

• Hypercalciuria in 40-75% (?)

• Hyperoxaluria in ~5% (?)

• Hyperuricosuria in ~10% (URAT1)

• Hypocitraturia in ~20% (Na-DC1)

Stone risk

- FAMILIAL -

In up to 50% of SF

Heritability of renal stones (Iceland)

(Edvardsson et al, Scand J Urol Nephrol, 2009)

Risk Ratio - 5954 all SF

Risk Ratio - 2959 Ca SF

Goldfarb et al. A twin study of genetic and dietary influenceson nephrolithiasis: a report from the Vietnam Era Twin (VET) Registry. Kidney Int 67: 1053-61, 2005

Total

number of

pairs

Pairs

concordant

for stones

Pairs

discordant

for stones

Proband

concordance

Monozygotic 1928 39 163 32.4

Dizygotic 1463 17 162 17.3

Idiopthic calcium nephrolithiasis

Heritability 56%

Environmental effects 44%

Idiopathic hypercalciuria & calcium stonedisease

• Monogenic forms of renal stone disease (calcium

and non-calcium stones) were previously thought to

account for just 2% of all renal stones

• PolygenicOne or few genes playing a major role

Additional genes contributing to the disease risk

Complex (multifactorial and polygenic) conditionIt is the consequence of dietary-environmental factors

in a genetically predisposed subject

Genes previously associated with calcium

nephrolithiasis identified by genome-wide

association studies (GWAS)

CLDN14, Iceland-The Netherlands

AQP1, Japan

DGKH, Japan

Uromodulin, Iceland

ALPL (alkaline phosphatase isoenzyme), Iceland, China

CASR (possible association), Iceland

SLC34A1 (sodium-dependent phosphate cotransporter type

2), Iceland, Japan

TRPV5 (transient receptor potential cation channel V5, i.e.

epithelial calcium channel 1), Iceland

Taguchi K et al. Genetic Risk Factors for Idiopathic

Urolithiasis: A Systematic Review of the Literature and

Causal Network Analysis. Eur Urol Focus 3(2017) 72-81

GWAS studies in renal stone

disease: the Icelandic study

Oddsson et al Nat Comms 2015

GWAS using data from whole-genome sequencing of

Icelander

sample size of 5419 patients

identification of an intronic sequence variant (rs1256328) in

ALPL (encoding an alkaline phosphatase isoenzyme)

Common allele

Rare allele

ALPL (alias TNAP tissue non-

specific Alk phosphatase)

Hydrolyses pyrophosphate to free

phosphate

Rare loss of function mutations in

patients with hypophosphatasia

(syndrome with decreased ALP and

elevated urine pyrophosphate, early

loss of teeth, chondrocalcinosis, poor

bone mineralisation)

ALPL expressed in proximal tubule

Mutations in ABCC6 lead to pseudoksanthoma elasticum,

low pyrophosphate levels and soft tissue calcification

Affect skin, retina and arteries but many pts get renal stones

Humans and KO mice had papillary calcifications (Randall’s

plaques)

exon sequencing in gene panels

30 genes were investigated (candidate genes)

whole exome sequencing

WES evaluates all 20,000 human genes

How to discover the monogenic

forms of nephrolithiasis?

Recent genetic studies by the same consortium

show that the likelyhood to identify monogenic

forms of renal stone disease depend on patient

selection

Halbritter J et al. Fourteen monogenic genesaccount for 15% of nephrolithiasis/nephrocalcinosis. J Am SocNephrol. 26:543-551, 2015

Braun et al. Monogenetic Genes in Early-Onset Urinary Stone Disease. Clin J Am Soc Nephrol 11: 664–672, 2016

Daga et al. Whole exome sequencing frequently detects a monogenic cause in early onset nephrolithiasis and nephrocalcinosis. Kidney Int 2017 35%

Fourteen monogenic genes cause ~15% of stones

256 consecutive recurrent SF;

16 nephrocalcinosis;

166 adults

106 children

30 genesGLUT9 NHERF1 NaPi2c Adenylate cyclase 10

Paediatric

Adult

(Halbritter et al, JASN, 2015)

40 cases of inherited

disorders

14 different disorders

(22 cystinuria)

Cys tp B 19 cases Cys tp A 3 cases

Lieske et al. Stone composition as a function of

age and sex. Clin J Am Soc Nephrol. 2014 Dec

5;9(12):2141-6.

No. of stone

analyzed

% cystine

stones

Spivacow

SR

Argentina, 2016 715 0.6

Rellum

DM

The Netherlands

2014

71 children 10

Sun X China 2011 189 children 9

Zafar MN Pakistan 2017 976 children 1.2

Genetic disorders1. dRTA with deafness

2. Hypophosphatemic nephrolithiasis/osteoporosis-1, NPHLOP1 / Fanconi

renotubular syndrome 2

3. Renal hypouricemia, RHUC2

4. Dent disease, tp 1

5. Familial hypomagnesemia with hypercalciuria & nephrocalcinosis

6. Hypophosphatemic nephrolithiasis/osteoporosis-2, NPHLOP2

7. Primary hyperoxaluria, type 1

8. 1,25-(OH) D-24 hydroxylase deficiency , infantile Hypercalcemia

9. Hypophosphatemic rickets with hypercalciuria

10. Renal hypouricemia, RHUC1

11. Cystinuria, type B

12. Primary dRTA, dominant / recessive

13. Cystinuria, type A

14. Idiopathic (absorptive) hypercalciuria, susceptibility

65 individuals from 51 families (some with consanguinity)

with NL or a finding of NC (27 cases) on renal ultrasound or

both, who manifested before the age of 25 years.

1. Families with pts with recurrent

NL

2. Families with NC

3. Consanguinity

4. NL/NC manifested before the

age of 25 years

Daga et al. Whole exome sequencing frequently

detects a monogenic cause in early onset

nephrolithiasis and nephrocalcinosis Kidney Int 2017

Daga et al. Whole exome sequencing frequently

detects a monogenic cause in early onset

nephrolithiasis and nephrocalcinosis Kidney Int 2017

10 genes

were mutated Total cases solved 34%

Finding in a Pakistani

cohort

7%

2/3 of cases: Idiopathic infantile

hypercalcemia (with hypercalciuria)

(NaP 2a carrier; SLC34A1)

1 cystinuria

The ability to identify causative

mutations by genetic tests

depends on the selection criteria

of the studied population.

HIGHER DETECTION RATES IN:

• YOUNGER AGE OF ONSET OF NL/NC (<3 YRS: 58%)

• PRESENCE OF MULTIPLE MEMBERS AFFECTED IN A

FAMILY (41%)

• PRESENCE OF CONSANGUINITY (75%)

• TERTIARY REFERRAL CENTER

Toka HR, Genovese G, Mount DB, Pollak MR, Curhan GC.

Frequency of rare allelic variation in candidate genes among

individuals with low and high urinary calcium excretion.

PLoS One. 2013

association of rare allelic variants with extremes of 24-hour urinary calcium excretion …. 40 candidate genes potentially related to urinary calcium excretion …….480 hypercalciuric stone formers from the Nurses’ Health Studies I & II and the Health Professionals Follow-up Study…..primers were designed to target all 497 exons of the 40 candidate genes, including, 50 bp of intronic sequence flanking each exon.

Our study does not support the hypothesis that rare, presumably functional allelic variants in the

tested genes influence urinary Ca2+

excretion.

In stone formers diagnosing a monogenic disease allows to

provide a specific etiologic diagnosis in NL/NC

delay progression to CKD/ESRD

enable personalization of the treatment plan

A detailed clinical and biochemical phenotyping of renal stone formers and the familial pattern of inheritance are still very important since they can point toward an underlying molecular genetic diagnosis.

Send all stones for analysis

Measure Calcium, PTH

Spot urine for cystine is useful in all

Beware ESKD with a history of

stones/nephrocalcinosis/crystal deposition on renal

biopsy

Clues of inherited renal stones

Early onset

Family cases

Consanguinity of parents

Highly active stone disease (bilateral, multiple stones, very recurrent)

Associated nephrocalcinosis

Renal hyperechogenicity

Tubular dysfunction and related manifestations (statural growth deficit, poliuria)

Renal failure

Extrarenal manifestations (Sensorineural hearing disorders, ocular abnormalities, neurological disorders)

Stone composition

Crystalluria

Monohydrate CaOx (whewellite)

Cystine

Dihydroxyadenine

Xanthine

Which approach to genetics in

diagnosing nephrolithiasis?

Rapidly evolving

Targeted panel/Candidate gene approach will solve 10-20%

GWAS Individualised genetic risk profile

(SNP/WES/WGS) will give “predictive” info on

remaining

Which approach to genetics in

diagnosing nephrolithiasis?

Rapidly evolving

Targeted panel/Candidate gene approach will solve 10-20% in selected cases

GWAS Individualised genetic risk profile

(SNP/WES/WGS) will give “predictive” info on

remaining