Short tandem repeat expansions in LRP12 are absent in cohorts of familial and sporadic amyotrophic lateral sclerosis patients of European ancestry

Abstract

In patients of Asian ancestry, a heterozygous CGG repeat expansion of >100 units in LRP12 is the cause of oculopharyngodistal myopathy type 1 (OPDM1). Repeat lengths of between 61 and 100 units have been associated with rare amyotrophic lateral sclerosis (ALS) cases of Asian ancestry, although with unusually long disease duration and without significant upper motor neuron involvement. This study sought to determine whether LRP12 CGG repeat expansions were also present in ALS patients of European ancestry. Whole-genome sequencing data from 608 sporadic ALS patients, 35 familial ALS probands, and 4703 neurologically normal controls were screened for LRP12 CGG expansions using ExpansionHunter v4. All individuals had LRP12 CGG repeat lengths within the normal range of 3–25 units. To date, LRP12 CGG repeat expansions have not been reported in ALS patients of European ancestry and may be limited to rare ALS patients of Asian ancestry and atypical clinical presentations.

Keywords:

• Amyotrophic lateral sclerosis
• short tandem repeat expansions
• LRP12

Introduction

Short tandem repeat (STR) expansions are increasingly being identified in neurodegenerative disorders, in part due to the increasing availability of large whole-genome sequencing datasets and advances in bioinformatic algorithms. A recent publication by Kume et al. (1) implicated LRP12 repeat expansions in amyotrophic lateral sclerosis (ALS). They described LRP12 CGG repeat expansions of 61–100 repeats in ALS patients of Asian ancestry from two ALS families, three progressive muscular atrophy families (PMA, a lower-motor neuron form of ALS) (2) and two sporadic ALS individuals and provided detailed clinical data for 10 patients. LRP12 CGG repeat expansions >100 repeat units had initially been described in patients of Asian ancestry with oculopharyngodistal myopathy type 1 (OPDM1), an autosomal dominant disease characterized by adult-onset ptosis, dysphagia, dysarthria, external ophthalmoplegia, and distal limb muscle weakness and atrophy (3, 4). However, some expansion carriers lacked the distinct oculopharyngeal symptoms and presented as isolated distal myopathies (5).

The genetic landscape of ALS differs in different population groups. In European populations, a pathogenic GGGGCC repeat expansion in C9orf72 is the most common genetic cause of both familial (∼33%) and sporadic ALS (7%) (6), whereas in Asian populations, pathogenic C9orf72 repeat expansions account for only 2.3% of familial ALS and 0.3% of sporadic ALS (7). Considering other major ALS genes, European populations have a higher prevalence of TARDBP mutations as the cause of familial and sporadic ALS compared to Asian populations; conversely, Asian populations have a higher proportion of familial SOD1 and FUS ALS mutations than European populations (7). Therefore, we sought to establish the prevalence of expanded LRP12 CGG repeats in an extensive cohort of ALS patients and controls of European ancestry.

Materials and methods

Our study examined LRP12 CGG repeat expansions in 608 sporadic ALS (sALS) patients, 35 familial ALS (fALS) probands, and 4,703 neurologically normal controls obtained from the NHLBI Trans-Omics for Precision Medicine (TOPMed) studies (dbGaP Study Accessions: phs001368.v3.p2, phs001402.v3.p1, phs001725.v2.p1, phs001024.v5.p1, phs001544.v2.p1 and phs001598.v2.p1). The sporadic ALS and control cohorts were previously described by Henden et al. (8). Samples from all patients and controls in our cohorts underwent short-read whole-genome sequencing and sequence data processing as previously published (8), with LRP12 CGG repeat sizes detected and quantified using ExpansionHunter v4 (9).

Results

We assessed the prevalence of CGG repeat expansions in LRP12 in 608 sALS patients, 35 fALS probands, and 4703 neurologically normal controls. Principal component analysis against the HapMap Phase II and III populations confirmed all ALS patients and controls were of European ancestry. The range of LRP12 CGG repeat allele lengths were between 3 and 25 repeat units across >5000 fALS, sALS, and controls of European ancestry (Table 1), all less than the reported ALS threshold of 61 repeat units by Kume et al. (1).

Table 1. Description of the cohorts assessed and the allele size ranges of the LRP12 CGG repeat.

Cohort of European ancestry	n (% female)	LRP12 CGG repeat allele size range (ExpansionHunter v4)
Sporadic ALS	608 (36.8%)	3–21 repeats
Familial ALS	35 (36.1%)	3–13 repeats
Controls	4703 (50.9%)	3–25 repeats

Discussion

Kume et al. (1) described several Japanese familial and sporadic ALS patients with LRP12 repeat expansions comprising 61–100 repeat units. However, none of the European fALS cases, sALS cases, or controls analyzed here had an allele larger than 25 repeats. The range of LRP12 CGG repeat allele sizes in the European control cohort (3–25 repeats) was concordant with non-Finnish Europeans in gnomAD v3.1.2 (10) (range of 1–29 repeats), as well as two Japanese control cohorts analyzed by Kume et al. (1) (n = 853, range of 5–48 repeats), and Ishiura et al. (3) (n = 998, range of 9–41 repeats). Only one of the 10 patients reported by Kume et al. (1) had typical ALS that progressed to ventilation four years after disease onset. The remaining nine LRP12 expansion patients were still alive between 9 and 31 years after symptom onset, noting that ALS and PMA have similar probabilities of survival after 8 years (2). This differs substantially from our reported sporadic ALS cohort, where only 10% of patients were alive 9 years after disease onset, with <1.5% alive three decades after onset (8). This suggests that LRP12-ALS patients have a very slowly progressive form of ALS. Further supporting atypical disease is that the clinically described LRP12-ALS patients had decreased or normal tendon reflexes, inconsistent with significant upper motor neuron disease.

The absence of LRP12 CGG repeat units larger than 25 repeats in a large ALS and control cohort of European ancestry suggests that ALS-associated CGG expansions in LRP12 may be limited to ALS patients of Asian ancestry and unusually long disease duration, without significant upper motor neuron involvement. Additional genotyping of large and well-phenotyped cohorts, including additional fALS cases of European ancestry, and different population groups, will be required to better understand the genetic contribution and phenotypic variation associated with LRP12 in ALS.

Author contribution

L.H.: Conceptualization, Formal Analysis, Data Curation, Writing – Review & Editing; L.G.F.: Software, Formal Analysis, Data Curation; Writing – Review & Editing; D.S.: Investigation, Writing – Original Draft, Writing – Review & Editing; A.S.: Software, Formal Analysis, Data Curation, Writing – Review & Editing; D.B.R.: Resources, Writing – Review & Editing; M.C.K.: Resources, Investigation, Writing – Review & Editing; R.P.: Resources, Writing – Review & Editing; M.B.: Supervision, Writing – Review & Editing; I.P.B.: Funding acquisition, Resources, Supervision, Writing - Review & Editing; K.L.W.: Conceptualization, Investigation, Data Curation, Funding Acquisition, Resources, Supervision, Writing – Original Draft, Writing – Review & Editing

Acknowledgements

Molecular data for the Trans-Omics in Precision Medicine (TOPMed) program was supported by the National Heart, Lung and Blood Institute (NHLBI). Genome sequencing for “NHLBI TOPMed: Cardiovascular Health Study” (phs001368.v3.p2) was performed at the Baylor College of Medicine Human Genome Sequencing Center (HHSN2682016000331). Funded in part by grants from the National Institutes of Health, National Heart, Lung and Blood Institute (HL66216 and HL83141) and the National Human Genome Research Institute (HG04735). Genome sequencing for “NHLBI TOPMed: Mayo Clinic Venous Thromboembolism Study” (phs001402.v3.p1) was performed at the Baylor College of Medicine Human Genome Sequencing Center (3U54HG003273-12S2, HHSN268201500015C). Genome sequencing for “NHLBI TOPMed: Groningen Genetics of Atrial Fibrillation Study” (phs001725.v2.p1) was performed at the Baylor College of Medicine Human Genome Sequencing Center (3UM1HG008898-01S3). This funding source was an NHLBI supplement to NHGRI’s Centers for Common Disease Genomics (CCDG). Genome sequencing for “NHLBI TOPMed: Partners HealthCare Biobank Study” (phs001024.v5.p1) was performed at the Broad Institute Genomics Platform (3R01HL092577-06S1). Genome sequencing for “NHLBI TOPMed: Malmo Preventive Project” (phs001544.v2.p1) was performed at the Broad Institute Genomics Platform (3UM1HG008895-01S2). This funding source was an NHLBI supplement to NHGRI’s CCDG. Genome sequencing for “NHLBI TOPMed: Johns Hopkins University School of Medicine Atrial Fibrillation Genetics Study” (phs001598.v2.p1) was performed at the Broad Institute Genomics Platform (3UM1HG008895-01S2). This funding source was an NHLBI supplement to NHGRI’s CCDG. Core support including centralized genomic read mapping and genotype calling, along with variant quality metrics and filtering were provided by the TOPMed Informatics Research Center (3R01HL-117626-02S1; contract HHSN268201800002I). Core support including phenotype harmonization, data management, sample-identity QC, and general program, coordination were provided by the TOPMed Administrative Coordinating Center (R01HL-120393; U01HL-120393; contract HHSN268201800001I). We gratefully acknowledge the studies and participants who provided biological samples and data for TOPMed.

Declaration of interests

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article.

Data availability statement

The data and code supporting the findings of this study are available in a Zenodo repository (https://doi.org/10.5281/zenodo.10253473).

Additional information

Funding

This work was supported by National Health and Medical Research Council of Australia grants 1095215 and 1176913 (I.P.B.); National Health and Medical Research Council of Australia grant 1153439 and fellowship 1156093 (M.C.K.); National Health and Medical Research Council of Australia grant 1195236 (M.B.); National Health and Medical Research Council of Australia fellowship 1092023 (K.L.W.); DHB Foundation Centenary Postdoctoral Fellowship (L.G.F.); FightMND, and Motor Neurone Disease Research Australia. This work was undertaken with the assistance of resources and services from the National Computational Infrastructure (NCI), which is supported by the Australian Government. This work was also supported by the Victorian Government’s Operational Infrastructure Support Program and the NHMRC Independent Research Institute Infrastructure Support Scheme (IRIISS).