We are a focused team of researchers with a wide range of skills and experience. We love what we do, and we do it with passion. We look forward to sharing our work with you and are open to future collaborations.
Mutation in CADM3 cause upper limb predominant neuropathy with pyramidal signs
Adriana Rebelo, PhD
The CADM family of proteins consists of four neuronal specific adhesion molecules (CADM1, CADM2, CADM3 and CADM4) that mediate the direct contact and interaction between axons and glia. In the peripheral nerve, axon-Schwann cell interaction is essential for the structural organization of myelinated fibers and it is primarily facilitated via CADM3, expressed in axons, binding to CADM4, expressed by myelinating Schwann cells. We have identified by whole exome sequencing (WES) three families with axonal Charcot-Marie-tooth disease (CMT2) sharing the same private variant in CADM3, Tyr172Cys. This variant is absent in 230,000 alleles in gnomAD and predicted to be pathogenic. Although these CADM3 families have been diagnosed with CMT2, they all share the same peculiar phenotype consisting of axonal motor neuropathy affecting mainly the upper limbs with pyramidal signs. High-resolution mass spectrometry analysis detected a new disulfide bond created in the mutant CADM3 potentially modifying the native protein conformation. This result was supported by significant increased protein retention of the mutant in the endoplasmic reticulum leading to activation of the unfolded protein response (UPR). In addition, Stochastic Optical Reconstruction Microscopy (STORM) imaging revealed decreased co-localization of the mutant CADM3 with CADM4 at the plasma membrane between cell-cell contact sites. Our findings indicate a novel molecular pathway in patients with CMT involving axon-glial interaction abnormalities.
Email me: ARebelo@med.miami.edu
Integrated SNV/structural variation analysis on the genome research platform GENESIS
Matt Danzi, PhD
The diagnostic gap for many rare diseases, especially in the neurodegenerative field, still exceeds 30-50%. These patients do not receive a diagnosis and will not be able to benefit from the upcoming genetic therapy developments. We have created the GEM.app/GENESIS genomic analysis platform to facilitate research diagnosis, gene identification, and data sharing (Gonzalez, 2013, 2015). To date, more than 9,000 exomes, genomes and panels from rare disease patients have been analyzed in GENESIS and are available for gene matching. This has contributed to the identification of 65 Mendelian genes in the past 8 years. Recently, structural variant (SV) analysis of whole genomes has been added for easy querying through a user-friendly web interface. This allows for a fully integrated analysis of SNV, indels, and SV without prior bioinformatics expertise required. SVs have historically been under-studied due to the difficulty of their detection in short-read whole genome sequencing (WGS) data. We are applying the Parliament2 software (Zarate et al., 2018) annotated with population frequency and predicted loss of function data on over 400,000 SVs from gnomAD-SV along with labels of neighboring and overlapping genes and gene regulatory elements as identified by ENCODE. As we reanalyze several hundred WGS samples with this pipeline, we fully expect to diagnose unresolved patients and identify novel genes to be reported in this study in the next 6 months.
Email me: mdanzi@tgp-foundation.org
Mutation burden and oligogenic inheritance in a large inherited axonopathy cohort
Dana Bis-Brewer, PhD
Inherited axonopathies include the clinically distinct phenotypes, Charcot-Marie-Tooth (CMT) and Hereditary Spastic Paraplegia (HSP), which both cause slowly-progressing, length-dependent axonal degeneration. Both phenotypes are genetically and phenotypically diverse with close to 100 Mendelian genes involved for each thus far. Whole-exome sequencing of axonopathy patients may identify more than one rare variant within known disease genes. Occurrence of additional rare variation, also referred to as a ‘mutation burden’, has been reported in two independent CMT cohorts (n £40) supported by functional zebrafish assays. The data indicate that mutation burden may influence clinical heterogeneity and severity of disease. We sought to replicate a mutation burden across inherited axonopathies in a WES cohort 10-fold larger than the original observations (CMT cases = 357, HSP cases = 515, controls = 931). We tested the mutation burden in cases compared to controls for both non-synonymous and loss-of-function variants at ExAC MAF £0.1% and 1%. For each tested variant set, cases harbored a higher average number of qualifying variants (Mann-Whitney, p-value £0.05). The significance of this difference was further evaluated by permutating case/control status over 10,000 iterations (p-value £0.05). Next, we evaluated the possibility of di- and oligogenic inheritance within each cohort. Cases carrying a qualifying variant in ³2 genes were classified as di/oligogenic and in ³3 genes as oligogenic. We observed a difference in the proportion of cases and controls carrying variants for both di/oligogenic and oligogenic inheritance for non-synonymous variation (Chi-squared, p-value £0.05). Neither HSP nor CMT showed evidence of oligogenic inheritance for loss-of-function variation; however, HSP cases were enriched for digenic inheritance (Chi-squared, p-value £0.05). In this study, we provide further evidence of a mutation burden in CMT cases, demonstrate a mutation burden in HSP cases, and explore potential oligogenic inheritance patterns in a large cohort.
Email me: dmb107@miami.edu
Mutational screening of genes associated with hereditary sensory and autonomic neuropathy in a Brazilian population
Vivian Cintra, PhD
Hereditary sensory and autonomic neuropathies (HSAN) are a group of rare genetically and phenotypically heterogeneous disorders characterized by axonal atrophy and degeneration often complicated by ulcers and amputations, with variable motor and autonomic involvement. To date, at least 17 different genes have been associated with HSAN (SPTLC1, SPTLC2, ATL1, DNMT1, ATL3, SCN11A, HSN2/WNK1, FAM134B, KIF1A, SCN9A, IKBKAP, NTRK1, NGF-β, DST, PRDM12, ZFHX2, CLTCL1). The relative frequency of these disorders varies among ethnic and geographical populations probably due to founder effects. However, the epidemiology of HSAN in Brazil is still unknown, since a systematic study has not been conducted yet. In order to evaluate the frequency of mutations in these genes, we performed a systematic mutation screening of their coding sequences in 25 unrelated Brazilian patients diagnosed with HSAN. We identified 10 patients belonging to three unrelated families with mutations in three HSAN disease associated genes: ATL3 (p.Tyr219Cys), SCN9A (p.Trp714Ter; p.Glu982Ter) and SPTLC2 (p.Asn177Asp). The clinical features associated with mutations in ATL3 and SPTLC2 typically consisted of dominant inheritance, frequent traumas in toes with repeated painless infections, including deep foot ulcerations, osteomyelitis, osteonecrosis and acromutilations. We detected a novel mutation in SCN9A (p.Trp714Ter) in compound heterozygous state with the previously described p.Glu982Ter pathogenic variant, leading to an early-onset HSAN phenotype with impairment of pain, temperature and touch sensation, and autonomic involvement, such as urinary incontinence, intestinal constipation and hypohidrosis. We thus identified a pathogenic mutation in 12% of HSAN Brazilian families, which suggests that the vast majority of the cases would be explained by other unknown mutated genes that remain to be discovered. We are currently performing whole genome studies on all remaining cases. Our study characterizes the spectrum of HSAN mutations found in Brazilian patients, and provides additional insights for genotype-phenotype association of the identified mutations.
Email me: vxc371@miami.edu
Mutational screening of genes associated with hereditary sensory and autonomic neuropathy in a Brazilian population
Sarah Fazel, PhD Student
Rare monogenic disorders are largely caused by pathogenic variation in protein coding regions of the genome. Yet, the phenotypes of 30-50% of patients remain unexplained. Thus, we and others have speculated about non-coding sequence contribution to the pathogenic variant spectrum. One such unorthodox mechanism is the expansion of short tandem repeats (STRs) into long repetitive stretches of the wild-type or mutated motif. Only 30 such loci have been linked to diseases thus far. In the past, these repeat expansions have been found primarily through linkage analysis of families. Direct identification from short-read whole genome sequencing data has proven difficult due to the inefficiency of alignment algorithms to correctly match reads to the reference genome. However, with the advance of new tools such as ExpansionHunter, many of these challenges can be overcome. Another challenge has been the lack of an extensive structural variation database focused on repeat sequences in the general population. Here we report a thorough analysis of STR expansions in 1,116 genomes. We find that on average, each genome contains 260 large, repetitive loci; with each new genome containing 3-10 new expansions not seen in our previous analysis. Only 2% of all loci identified are shared amongst all the samples, while more than half are observed only in 1-2 samples. Certain regions in the genome show evidence of expansions in a large number of samples, which could indicate that the reference genome underestimates the number of repeats in these areas. The majority of expansions we identified are intergenic, about 28% are intronic, and less than 1% are exonic. Large expansions were overrepresented near Alu elements, appearing proximal to AluS or AluJ sites over 6 times more often than expected by random chance. We will use this data to identify pathogenic repeat expansions in rare neurological disorders such as axonal neuropathies, motor neuron diseases, and undiagnosed ataxia cases. Because of the considerable diagnostic gap in rare diseases it is likely that repeat expansions as a mutational mechanism play a larger role than currently estimated.
Email me: sxf710@miami.edu
Zuchner Genomics Lab 