Theme 02 - Genetics and Genomics

Abstract

Background: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder involving upper and lower motor neurons. It is mostly sporadic, tough pathogenic mutations are sometime detectable, mainly in those patients with a positive familiar track record for neurodegenerative disorders. More than 50 genes have been put in relation with ALS so far, among which SOD1, C9Orf72, FUS, ATXN2 and TARDBP are the most frequent. SOD1, encoding for the antioxidant enzyme Cu/ Zn superoxide dismutase and described for the first time in 1993, is the first gene that had been put in rela- tion with ALS. To date, over 180 different SOD1 mutations have been described throughout the five exons of the SOD1 gene. However, the exact pathogenic effect of this gene mutations are still unclear. Recently, a gene therapy targeting SOD1 has been approved for ALS patients carrying any SOD1 mutation. This new therapeutic approach has boosted the number of genetic tests performed, sometimes revealing unexpected positivity and sometimes underlying new genes ’ mutations. Here we describe a case of a woman with a new SOD1 mutation, not described in literature before and con- sidered as pathogenetic in VarSome. Case report: diseases, gait complete neurological dis-closing severe bulbar with anarthria, tongue hyposthenia and oral apraxia. presented mild upper hyposthenia, limbs Hereditary spastic paraplegia (HSP) is a heterogeneous group of genetic neurodegenerative disorders characterized by progressive weakness and spasticity of lower limbs. SPG15 is a rare form of autosomal recessive HSP due to mutations in ZFYVE26 gene, which encodes for spastizin, involved in autophagy and endocytosis (1). Here we describe the case of a 56 years old man who presented to our clinic in November 2020 referring a progressive motor clumsiness of both legs and walking instability during the last five years. No motor impairment at upper limb, no bulbar nor respiratory symptoms. These symptoms had a progressive evolution. In anamnesis only high blood pressure. No familiar history of neurodegenerative diseases. Neurological examination showed a spastic gait, a light hypo-trophy and hyposthenia of the left leg, brisk reflexes at lower limb, no Hoffmann nor Babinski signs, no urinary nor intes- tinal problems. He underwent: blood examination (resulted normal, no HIV, HTLV infections), electroneurography/electro- myography study (signs of chronic neurogenic muscle with apparently sporadic disease have a lower than expected testing yield. Increasing availability of wider genetic panels may confound our results and yield of testing with contemporary approaches may increase. Our data supports testing of individuals with early-onset disease but does not provide strong evidence for testing those without a family history. Interval re-evaluation of this cohort may be of benefit to appreciate the utility of an extended panel (26 genes plus C9orf72 established in 2021). Systematic questioning regarding family history of dementia, other neurological and psychiatric diseases may also help to identify at risk individuals with early-onset disease. Background: Neuronal nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels encoded by different nicotinic cholinergic receptor (CHRN) genes and expressed in both bulbar and spinal motor neurons. They are involved in neuroprotection and in control of the release of many neuro-transmitters, including glutamate. It has been previously postulated that rare variants in the subunits of nAChRs might represent one of several genetic risk factors for Amyotrophic Lateral Sclerosis (ALS) (1). Objective: The aim of this study was to elucidate the contribution of genetic variation of CHRN genes to disease risk in ALS. Methods: We analyzed 935 sporadic ALS patients of Italian origin from the Piemonte and Aosta Register for ALS and 775 ethnically and geographically matched controls. We tested for associations of variants in the CHRN genes cluster using linear regression for common variants and burden analysis for rare (minor allele frequency, MAF, < 1%) variants. Results: No significant association between CHRN genes mutations and ALS was found after appropriate correction for multiple testing. We did not observe a significant excess of rare nonsynonymous variants or an aggregate contribution of rare and common coding variants to the risk for ALS. No effect was detected when applying the combined test at the gene cluster level. Conclusion: Our results indicate that common and rare genetic variations in the CHRN gene cluster do not contribute to ALS pathogenesis. However, further studies are needed to understand the possible effect of genetic variability in nAChRs to motor neuron degeneration. ERLIN1 and UNC13A genes in two different PLS patients. We also investigated the role of pathogenic expansions in PLS. In our PLS cohort no pathogenic expansions were found in the ATXN2 & C9orf72. Finally, we observed that the mean age of onset was 58.4 years and 60.05 years for our PLS and ALS cohort, respectively. This contrasts with the previously reported mean age of onset of 50 years and 60 years between the PLS and ALS patients, respectively. Introduction: Until the emergence of specific drugs for cer- tain genetic pathologies, the request for a genetic study was basically focused on the possibility of being able to carry out adequate genetic counselling. Now that it seems that the antisense oligonucleotide tofersen will soon be available for forms of ALS due to mutations in the copper-zinc superoxide dismutase (SOD1) gene, many scientific societies recommend carrying out a genetic study, at least of this SOD1 gene, in patients with ALS. Materials and methods: We collected transversally the results of the genetic studies carried out on our patients, in June 2022, and compared them with the results in 2019. Results: Of the 36 patients who are being followed up in our ALS unit, only two (5.56%) are positive for some type of genetic mutation (alterations in SOD 1 and in compound het-erozygosity for TANK binding kinase (TBK1) and angiogenin (ANG)), after sequencing in 25 (69.44%) of them, a wide ALS panel, as well as copy number determination for the C9orf72 gene. In absolute values, these are the same patients who had genetic alterations in the past, when compared with the results of 2019. In that moment, only those with a family history underwent a genetic study (in this case, two patients had alterations in C9orf72 and another in SOD1). In addition, patients with genetic alterations in our current cohort also have relevant family history. Conclusions: It seems that despite carrying out more genetic studies, no more patients with ALS due to genetic causes are discovered. However, despite this, it seems reasonable to continue with this behavior, since although the probability is very low (and this must be correctly informed to the patient), the detection of mutations in SOD1, at the present time, can determine a very relevant change in the prognosis of the disease. Background: Amyotrophic lateral sclerosis (ALS) is a rare and fatal neurodegenerative disease. Patients experience progressive motor neuron degeneration, leading to paralysis and death, often from respiratory failure within 3 – 5 years of diagnosis (1). While approximately 10% of ALS cases are familial, the genetic architecture of ALS is still largely unknown, par- ticularly in conjunction with local environmental risk factors that may increase susceptibility to disease. Methods: To address this gap in understanding, we conducted a genome-wide association study to understand the genetic risk factors using a regional cohort of 435 ALS cases and 279 controls primarily based in New England and Ohio. We performed SNP genotyping of 714 subjects using the NeuroChip array, which focuses on curated variants impli- cated in neurological diseases (Illumina Inc.). To minimize the effects of population stratification, we excluded subjects of non-European descent from the analysis. Standard quality control procedures on the genomic data left 242,090 SNPs included in the analysis. We used covariate adjusted logistic regression to screen all the SNPs ’ associations with ALS case-control status. Wald test was used to obtain the p- values followed by Bonferroni correction for multiple comparisons. Covariates included sex, age at symptom onset and the first 10 principal components. The genomic inflation factor was 1.02 after adjusting for covariates. Results: We found a marginally significant (Bonferroni adjusted p -value < 0.1) SNP in the ALS-linked gene, TARDBP : Rs367543041. This SNP was previously reported in association with ALS and was found to share a close affinity with the Sardinian haplotype. Discussion: Our results support future evaluation of genetic risk factors in regional cohorts to better understand potential genetic contributors to ALS risk as well Background: While classic ALS is characterized by varying degrees of upper motor neuron (UMN) and/or lower motor neuron (LMN) dysfunction, primary lateral sclerosis (PLS) and progressive muscular atrophy (PMA) represent extreme phenotypes characterized respectively by pure upper motor neu- ron (UMN) and lower motor neuron (LMN) pathology. Theorizing defects contribute to phenotypic heterogeneity in motor neuron long- read RNA sequencing to accurately capture the full-length transcriptome. Objectives: obtain of versus LMN pathology. Methods: Blood samples from age- and sex-matched individuals with clinical diagnoses of PLS (N (cid:3) 20), classic ALS (N (cid:3) 20) or PMA (N (cid:3) 20) were obtained from the PGB (Phenotype-Genotype-Biomarker, NCT02327845) study of the CReATe (Clinical Research in ALS and Related Disorders for Therapeutic Development) Consortium. RNA was extracted using the PAXgene Blood RNA extraction kit (Qiagen). Only samples with an RNA integrity number (RIN) above 7 were included. Long- read RNA sequencing was