LRRK2 Loss-of-Function Variants in Patients with Rare Diseases: No Evidence for a Phenotypic Impact.

Certain missense variants in the LRRK2 gene, which encodes leucine‐rich repeat kinase 2 (LRRK2), are a common cause of Parkinson's disease (PD). As these variants increase the protein's kinase activity, treatment strategies aim at reducing LRRK2 function and/or abundance. Safety concerns for this approach are based on considerable LRRK2 expression in numerous tissues and organs. Indeed, LRRK2 knockout/inhibition in mammalian model organisms has been reported to affect the lungs, the kidneys, and the liver. Findings from two recent studies on LRRK2 loss‐of‐function (LoF) variants in humans have been interpreted as partially alleviating pertinent concerns: Blauwendraat and colleagues showed absence of enrichment of these variants in PD patients, while Whiffin and colleagues revealed that their presence is not associated with reduced life expectancy, abnormal standard laboratory parameters, or common adverse phenotypes in a large cohort of healthy individuals. However, the probably most relevant human subjects, that is, those presenting with (rare) disease phenotypes, have not yet been systematically analyzed. The present study describes the spectrum and frequency of LRRK2 LoF variants in CentoMD®, a data repository for patients with rare disorders, and analyzes the dataset for potential disease associations.

LRRK2 sequencing data from over 70,000 individuals (45,331 patients; 25,043 healthy family members) from diagnostic exome or genome sequencing were interrogated. In 154 cases, good quality LRRK2 LoF variants were present. There were a total of 52 distinct variants (22 nonsense, 20 frameshift, 10 splice‐site) (Fig. S1). The fraction of patients was 0.636 among variant‐positives and 0.644 among variant‐negatives, demonstrating absence of an association of LRRK2 LoF variants with disease. Focusing on only patients, there was no significant difference between variant‐positives and variant‐negatives with respect to age at referral and number of Human Phenotype Ontology (HPO) terms per patient (Fig. 1A,B). Furthermore, none of the HPO terms that were most frequently observed in LRRK2 LoF‐positives was significantly enriched in this cohort (Fig. 1C). Thus, rare disease patients with LRRK2 LoF variants are not affected earlier or more severely than other patients, and do not have specific phenotypes.

FIG. 1

Comparison of LRRK2 LoF‐positive and LRRK2 LoF‐negative patients. (A) Age at referral. (B) Number of Human Phenotype Ontology (HPO) terms per patient. (C) Fractions of patients with HPO terms that are present in at least 10% of LRRK2 LoF‐positive patients. P values are two‐tailed and are not corrected for multiple testing; they are based on Student's t‐test in (A) and (B), and on Fisher's exact test in (C).

Of note, four of the LRKK2 LoF variant‐positives were homozygous (Table S1; Fig. S2), of whom three were patients who did not show any obvious phenotypic overlap. The first patient had received a negative genetic report, while a homozygous variant of uncertain significance was reported in the second and a homozygous pathogenic variant in the third. Importantly, the fourth LRRK2 LoF homozygous individual was a 32‐year‐old healthy father of a patient. Even complete absence of LRRK2 may thus have no overt early phenotypic impact in humans, but further studies are necessary to determine whether the above individuals are indeed “human LRRK2 knockouts.”

Our observations in a large and clinically diverse diagnostic cohort represent conceptually novel support for the safety of currently pursued therapeutic strategies for patients with kinase‐activating LRRK2 mutations. Considering the accumulating evidence for an implication of increased LRRK2 activity also in the pathogenesis of other monogenic and idiopathic forms of PD, our findings are of potentially even broader relevance.

Author Roles

(1) Research Project: A. Conception, B. Organization, C. Execution; (2) Statistical Analysis: A. Design, B. Execution, C. Review and Critique; (3) Manuscript Preparation: A. Writing of the First Draft, B. Review and Critique.

C.B.: 1A, 1B, 1C, 2A, 2B, 3A, 3B

A.W.: 1B, 2C, 3A, 3B

R.A.‐A.: 1B, 1C, 2B, 2C, 3B

N. Ameziane: 1B, 1C, 2B, 2C, 3B

N. Alhashmi: 1B, 1C, 3B

R.‐M.B.: 1B, 1C, 3B

F.A.M.: 1B, 1C, 3B

M.A.: 1B, 1C, 3B

Z.A.‐H.: 1B, 1C, 3B

M.A: 1B, 1C, 3B

K.K.K.: 1B, 1C, 2B, 2C, 3B

O.P.: 1B, 1C, 2C, 3C

V.S.: 1B, 1C, 2C, 3C

A.R.: 1A, 1B, 2A, 2C, 3B

P.B.: 1A, 1B, 2A, 2C, 3A, 3B

Financial Disclosures of All Authors (for the Preceding 12 Months)

Christian Beetz.

Ana Westenberger.

Ruslan Al‐Ali.

Najim Ameziane.

Nadia Al‐Hashmi.

Rose‐Mary Boustany.

Fuad Al‐Mutairi.

Majid Al‐Fadhel.

Zuhair Al‐Hassnan.

Moeenaldin Al‐Sayed.

Krishna K. Kandaswamy.

Omid Paknia.

Volha Skrahina.

Arndt Rolfs.

Peter Bauer.

Figure S1 LRRK2 loss‐of‐function variants (description based on NM_198578.3) as identified in CentoMD®, and number of corresponding variant‐positive individuals

Click here for additional data file.

Figure S2 Confirmation of homozygosity for three LRRK2 loss‐of‐function variants by Sanger sequencing (compare Suppl. Table 1). Affected nucleotides are marked by an arrow

Click here for additional data file.

Table S1 Details for four individuals found to be homozygous for a LRRK2 loss‐of‐function variant

Click here for additional data file.

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Stock Ownership in medically‐related fields
Intellectual Property Rights
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Stock Ownership in medically‐related fields
Intellectual Property Rights
Consultancies
Expert Testimony
Advisory Boards
Employment	CENTOGENE GMBH
Partnerships
Contracts
Honoraria
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Stock Ownership in medically‐related fields
Intellectual Property Rights
Consultancies
Expert Testimony
Advisory Boards
Employment	CENTOGENE GMBH
Partnerships
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Honoraria
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Stock Ownership in medically‐related fields	Yes
Intellectual Property Rights	Yes
Consultancies	CENTOGENE GMBH
Expert Testimony
Advisory Boards
Employment	CENTOGENE GMBH
Partnerships	Yes
Contracts
Honoraria
Royalties
Grants	Yes
Other

Stock Ownership in medically‐related fields	Yes
Intellectual Property Rights	Yes
Consultancies	Yes
Expert Testimony
Advisory Boards
Employment	CENTOGENE GMBH
Partnerships	Yes
Contracts
Honoraria
Royalties
Grants	Yes
Other