Homozygous RFC1 AAGGG Repeat Expansions Are Common in Idiopathic Peripheral Neuropathy.

Biallelic intronic AAGGG repeat expansions in RFC1 cause Cerebellar Ataxia with Neuropathy and Vestibular Areflexia Syndrome and may also contribute to isolated sensory neuropathy. The clinical significance of both heterozygous and biallelic RFC1 expansions in more diverse patient populations remains unclear-partly due to the absence of accurate, user-friendly computational tools specifically tailored for tandem repeat analysis. To discern the relationship between RFC1 expansions and idiopathic peripheral neuropathy (iPN), we performed whole-genome sequencing (WGS) followed by PCR-based confirmation in a large, well-characterized U.S. cohort consisting of 788 iPN patients (369 pure small fiber neuropathy (SFN), 266 sensorimotor, 144 pure sensory, and 9 pure motor). We developed an integrative pipeline combining ExpansionHunter Denovo and Expansion Hunter coupled with unsupervised clustering to reliably detect and genotype RFC1 expansions from short-read WGS data, achieving 98.2% concordance with repeat-primed PCR based validation. Biallelic RFC1 expansions were absent in 879 controls but present in 2.8% of iPN patients (Fisher's exact p = 5.9×10 -8 ), including 6.2% of pure sensory, 2.2% of SFN, and 1.5% of sensorimotor neuropathy, indicating that motor nerve involvement should not exclude patients from RFC1 repeat screening. We also observed a markedly increased frequency of monoallelic expansions in iPN compared to controls (13.2% versus 2.5%; Fisher's exact p = 3.4×10 -17 ), without evidence of secondary mutations or expansions on the other allele. Our approach provides a robust, cost-effective method for detecting RFC1 expansions from WGS data. Our findings indicate that both heterozygous and homozygous AAGGG repeat expansions in RFC1 can contribute to development of iPN.

Detection of trait-associated structural variations using short-read sequencing

The foot and ankle surgeon can see peripheral neuropathy in the treatment of foot and ankle conditions. The purpose of this study was (1) to evaluate the demographics and presenting complaints of patients diagnosed with idiopathic peripheral neuropathy during an examination by a foot and ankle surgeon and (2) to identify the type and frequency of subsequent diagnosis of medical causes of neuropathy. This was a retrospective study of patients diagnosed with idiopathic peripheral neuropathy in our practice between January 1997 and December 2008. Ninety-five patients were identified, and demographic data, presenting complaints, and medical comorbidities were extracted from the medical record. Examination findings of decreased sensation to Semmes Weinstein 5.07 monofilament testing were documented, and electromyogram and nerve conduction study results were reviewed when available. Laboratory values were noted, as were neurologic evaluations performed to diagnose medical conditions associated with peripheral neuropathy. The most common presentation was foot pain, in 36 patients (38%). Ninety-one patients had Semmes Weinstein 5.07 monofilament testing, with loss of protective sensation reported in 75 of the 91 tested (82%). Only 30 of the 95 patients had electromyogram and nerve conduction study results available, with a test positive for peripheral neuropathy in 20 of the 30 tested. Thirty-two patients were evaluated by a neurologist. A specific cause was identified in 12 of the 32 seen by a neurologist. Of the total group of 95 patients, 31 patients (33%) were diagnosed with a condition that may be associated with peripheral neuropathy. Thirty-three percent of the patients presenting to our clinic and given a diagnosis of idiopathic peripheral neuropathy were ultimately diagnosed with a medical cause of neuropathy-most commonly, diabetes. For those patients with idiopathic neuropathy, a spectrum of disease was encountered, including pain, ulcer, infection, and Charcot neuroarthropathy. Level IV, retrospective case series.

Immune reactivity to gluten in the development of peripheral neuropathies and cerebellar ataxia has been suggested for decades, but evidence is scarce. The aim of the current study was to test the prevalence of tissue transglutaminase 2 (anti-TG2), tissue transglutaminase 6 (anti-TG6), and gliadin antibodies (anti-gliadin) in a large cross-sectional study. The sera of patients with idiopathic cerebellar ataxia, idiopathic small fibre neuropathy (SFN) and chronic idiopathic axonal polyneuropathy (CIAP), and controls with a comparable age distribution and men/women ratio were collected. The sera were analysed for anti-gliadin IgA/IgG (manufacturer’s and lower cut-off), anti-TG2 IgA and anti-TG6 IgA/IgG. In total, 683 samples were analysed: 476 patients (249 SFN, 161 CIAP and 66 idiopathic cerebellar ataxia) and 195 controls. There were no differences between disease and control group in the prevalence of elevated anti-TG6, anti-TG2 and anti-gliadin using the manufacturer’s cut-off. Using a lower cut-off of 3 U/mL, previously used by others for gluten-related neurological disorders, anti-gliadin IgA was positive in 20.8% patients vs 12.8% controls (p = 0.017) and anti-gliadin IgG in 7.6% vs 2.6% (p = 0.013), respectively. In subgroup analyses, significant differences were only observed in SFN for anti-gliadin IgA and in idiopathic cerebellar ataxia for anti-gliadin IgG using this lower cut-off after adjusting for sex and age. In conclusion, no difference in anti-TG2, anti-TG6 and anti-gliadin levels were observed between patients and controls. Only when using the lower cut-off (3 U/mL), the patients with SFN and idiopathic cerebellar ataxia were more often positive for anti-gliadin than controls. Whether these low-titre antibodies are gluten related, have any pathophysiological relevance, or reflect an epiphenomenon of neurodegeneration or gut inflammation is unknown.

biallelic mutation/expansion of the gene RFC1 has been described in association with a spectrum of manifestation ranging from isolate sensory neuro(no)pathy to a complex presentation as Cerebellar Ataxia with Neuropathy and Vestibular Areflexia Syndrome (CANVAS). Our aim was to define the frequency and characteristics of small fiber neuropathy (SFN) in RFC1-disease at different stages. RFC1-cases were screened for SFN using the Neuropathic Pain Symptom Inventory (NPSI) and Composite Autonomic Symptom Score-31 (COMPASS-31) questionnaires. Clinical data were retrospectively collected. If available, lower limb skin biopsy samples were evaluated for somatic epidermal and autonomic subepidermal structures innervation and compared to healthy controls (HC). we enrolled 40 patients, median age at onset 54 years (IQR 49-61) and disease duration 10 years (IQR 6-16). Mild-to-moderate positive symptoms (median NPSI score 12.1/50, IQR 5.5-22.3) and relevant autonomic disturbances (median COMPASS-31 score 37.0/100, IQR 17.7-44.3) were frequently reported and showed scarce correlation with disease duration. A non-length-dependent impairment in nociception was evident on both clinical and paraclinical investigations. An extreme somatic denervation was observed in all patients at both proximal (fibers/mm RFC1-cases 0.0 vs HC 20.5, p < .0001) and distal sites (fibers/mm RFC1-cases 0.0 vs HC 13.1, p < .0001), instead only a slight decrease was observed in cholinergic and adrenergic innervation of autonomic structures. RFC1-disease is characterized by a severe and widespread somatic SFN. Skin denervation may potentially represent the earliest feature and drive towards the suspicion of this disorder.

Understanding the individual- and population-level polymorphisms of major histocompatibility complex (MHC) genes is crucial for identifying associations between MHC variations and immune phenotypes. To support this, we developed NGSMHC, a streamlined bioinformatics tool for efficient and accurate MHC genotyping using nextgeneration sequencing (NGS) data in non-human species. NGSMHC constructs phased haplotype contigs of selected MHC genes from BAM-format mapping data and determines the best matching MHC alleles and genotypes via nucleotide BLAST analysis against a user-provided reference set of MHC alleles. We evaluated NGSMHC using short-read whole-genome sequencing (WGS) data from 12 pigs, focusing on swine leukocyte antigen (SLA) genes. The typing results from NGSMHC were compared to those obtained using polymerase chain reaction sequence-based typing (PCR-SBT). In addition, we tested NGSMHC on a publicly available long-read WGS dataset with known SLA genotypes. The short-read WGS data showed an average read depth of 20.9× across the SLA region, enabling typing of SLA-2, SLA-3, SLA-DRB1, and SLA-DQB1 using NGSMHC. The concordance rates between NGSMHC and PCR-SBT were 88% for SLA-3, 92% for SLA-DRB1, and 100% for SLA-DQB1. However, SLA-2 typing showed lower concordance (58%), likely due to its high sequence similarity with other SLA class I genes and complex intra-locus polymorphisms. In contrast, NGSMHC accurately identified all tested SLA genotypes-including SLA-1, SLA-2, SLA-3, SLA-DRA, SLA-DRB1, SLA-DQA, and SLADQB1-when applied to the long-read WGS data. NGSMHC is a simple and effective tool for MHC genotyping using NGS data, particularly for non-human species. Its accuracy is significantly improved by longread sequencing, underscoring the importance of read length in precise MHC allele determination.

Background:In small fiber neuropathy (SFN), thinly myelinated Aδ and unmyelinated C fibers are primarily affected, resulting in sensory and/or autonomic symptoms. Various etiologies have been shown to be associated with SFN. This study was aimed to analyze a variety of features in peripheral neuropathy (PN) with small fiber involvement, and to compare disease severity among patients with idiopathic PN, PN associated with impaired glucose tolerance (IGT), and metabolic syndrome (MS) PN.Methods:Thirty-eight PN patients with small fiber involvement were enrolled from December 20, 2013 to May 31, 2016. Patients were divided into idiopathic PN, IGT-related PN, and MS-related PN groups. Detailed medical history and small fiber neuropathy were investigated, and symptom inventory questionnaire was conducted, as well as the visual analog scale. Nerve conduction studies and skin biopsies were also performed. The differences among the groups were analyzed using analysis of variance and Kruskal-Wallis test.Results:Eight patients were diagnosed with pure SFN. Intraepidermal nerve fiber density (IENFD) weakly correlated with motor conduction velocity (MCV) (r = 0.372, P = 0.025), and proximal (r = 0.383, P = 0.021) and distal (r = 0.358, P = 0.032) compound muscle action potential (CMAP) of the tibial nerve. IENFD also weakly correlated with MCV of the peroneal nerve (r = 0.399, P = 0.016). IENFD was shown to be significantly different among all groups (χ2 = 9.901, P = 0.007). IENFD was significantly decreased (χ2 = 23.000, P = 0.003) in the MS-related PN group compared to the idiopathic PN group. The MCV of the tibial nerve was significantly different among all groups (χ2 = 8.172, P < 0.017). The proximal (F = 4.336, P = 0.021) and distal (F = 3.262, P = 0.049) CMAP of the tibial nerve was also significantly different among all groups.Conclusions:IENFD of patients included in the present study weakly correlated with various electrophysiological parameters. Small and large fibers are more involved in patients with MS-related PN than in patients with idiopathic PN.

Can Whole Genome and Whole Transcriptome Sequencing Replace Standard Procedures in CLL Diagnostics?

The RFC1 spectrum has become considerably expanded as multisystemic features beyond the triad of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) have started to be unveiled, although many still require clinical replication. Here, we aimed to clinically characterize a cohort of RFC1-positive patients by addressing both classic and multisystemic features. In a second part of this study, we prospectively assessed small nerve fibers (SNF) and autonomic function in a subset of these RFC1-related patients. We retrospectively enrolled 67 RFC1-positive patients from multiple neurologic centers in Portugal. All patients underwent full neurologic and vestibular evaluation, as well as neuroimaging and neurophysiologic studies. For SNF and autonomic testing (n = 15), we performed skin biopsies, quantitative sensory testing, sudoscan, sympathetic skin response, heart rate deep breathing, and tilt test. Multisystemic features beyond CANVAS were present in 82% of the patients, mainly chronic cough (66%) and dysautonomia (43%). Other features included motor neuron (MN) affection and motor neuropathy (18%), hyperkinetic movement disorders (16%), sleep apnea (6%), REM and non-REM sleep disorders (5%), and cranial neuropathy (5%). Ten patients reported an inverse association between cough and ataxia severity. A very severe epidermal denervation was found in skin biopsies of all patients. Autonomic dysfunction comprised cardiovascular (67%), cardiovagal (54%), and/or sudomotor (50%) systems. The presence of MN involvement, motor neuropathy, small fiber neuropathy, or extrapyramidal signs should not preclude RFC1 testing in cases of sensory neuronopathy. Indeed, the RFC1 spectrum can overlap not only with multiple system atrophy but also with hereditary motor and sensory neuropathy, hereditary sensory and autonomic neuropathy, and feeding dystonia phenotypes. Some clinical-paraclinical dissociations can pose diagnostic challenges, namely large and small fiber neuropathy and sudomotor dysfunction which are usually subclinical.

CefiderocolFinder: a tool for detecting genetic adaptations implicated in cefiderocol resistance.

<strong>BACKGROUND: </strong>Small-fiber neuropathies (SFNs), affecting thinly myelinated Ad fibers and unmyelinated C fibers, often manifest with sensory or autonomic symptoms in varied patterns. Diagnostic tools comprise skin biopsy, quantitative sensory, autonomic testing, and biochemical markers. Spinal cord stimulation (SCS), particularly high-frequency SCS, has emerged as a pivotal therapeutic intervention. <strong>CASE REPORT: </strong>This study delves into a 49-year-old woman diagnosed with idiopathic asymmetrical SF peripheral neuropathy, examining her 12-month postoperative trajectory after SCS implantation. Postsurgical assessment revealed substantial improvements: baseline pain (Numeric Rating Scale 7) decreased to 4 at 3 months, indicating reduced intensity; Oswestry Disability Index improved from 38% to 4%, highlighting enhanced functionality; Patient-Specific Questionnaire 3 average score dropped from 35 to 2, indicating improved outcomes in specific pain-related concerns. <strong>CONCLUSIONS:</strong> This case report underscores the efficacy of SCS in managing idiopathic asymmetrical SFN, demonstrating significant symptomatic relief over a 12-month postoperative period. <strong>KEY WORDS: </strong>Small-fiber neuropathy, spinal cord stimulation, HF10 SCS, idiopathic asymmetrical small-fiber neuropathy, pain management.

Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) refers to a sporadic or autosomal recessive disorder characterized by the involvement of multiple systems including the cerebellum, somatosensory nerves, and vestibular system. 1 Affected patients mostly report severe imbalance due to combined cerebellar and sensory ataxia. 1 Chronic cough is another characteristic finding, which can appear years before the neurological manifestation. 2 CANVAS was clinically characterized in 2011, 1 but the underlying biallelic pentanucleotide (AAGGG) expansion in intron 2 of the replication factor C subunit 1 (RFC1) gene was not identified until 2019. 3We report the first genetically confirmed case of CANVAS in South Korea, and discuss the clinical and laboratory findings.A 64-year-old female presented with worsening unsteadiness and occasional falls with a 9-year history.She reported experiencing a chronic nonproductive cough since her thirties, but no significant medical or neurological histories in her immediate family members.A physical examination showed mild dysarthria, gaze-evoked and rebound nystagmus, and downbeat nystagmus during lateral gaze (Supplementary Video 1 in the online-only Data Supplement).Smooth pursuit was impaired in both the horizontal and vertical directions (Supplementary Video 2 in the online-only Data Supplement).Horizontal and vertical saccades were hypometric, and the velocities of vertical saccades were slightly decreased.Clinical head impulse tests (HITs) were positive bilaterally.The visually enhanced vestibulo-ocular reflex was impaired bilaterally (Fig. 1A and Supplementary Video 3 in the online-only Data Supplement).Horizontal head oscillation at about 1 Hz decreased the visual acuity from 20/20 to 2/20.All extremities had normal power, tone, sensation, and deep tendon reflexes.Mild dysmetria was noted in the upper extremities.Her gait was ataxic and a tandem gait was impossible.The Romberg test was positive.Video HITs revealed decreased gains and overt corrective saccades for all six semicircular canals (Fig. 1B).Bithermal caloric tests indicated complete canal paralysis bilaterally (Fig. 1C).Rotatory chair tests showed reduced gains of the horizontal vestibulo-ocular reflex.Nerve conduction studies revealed that sensory action potentials were either absent or decreased in all extremities.Magnetic resonance imaging showed mild atrophy of the anterior and dorsal cerebellar vermis and spinal cord (Fig. 1D).Whole-genome sequencing (WGS) confirmed biallelic intronic AAGGG expansions in RFC1 (Fig. 1E).Short-tandem-repeat analysis using Expansion Hunter revealed that the expansion size was around 20 or more in smaller alleles.Our patient showed the typical characteristics of CANVAS that included cerebellar ataxia, sensory neuropathy, bilateral vestibulopathy, and chronic cough.Even though we could not determine the expansion size due to WGS limitations, our patient had at least 20 biallelic AAGGG expansions in intron 2 of RFC1; determination of the exact expansion size

Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers

PurposeBiallelic repeat expansions in the Replication Factor C Subunit 1 (RFC1) gene are associated with cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS). Recent studies have shown that chronic cough often precedes neurological symptoms in CANVAS by 10–20 years, suggesting a potential link between RFC1 repeat expansion and chronic cough. However, the prevalence and clinical relevance of RFC1 expansions in chronic cough, particularly in non-Caucasian populations, remain unknown.MethodsWe analyzed 128 consecutive patients with chronic cough who were enrolled in the Korean Chronic Cough Registry at 2 tertiary clinics. All patients underwent a comprehensive clinical evaluation and were followed up for at least 6 months to assess treatment response and to identify the diagnosis of refractory chronic cough (RCC). RFC1 repeat expansions, including both biallelic and monoallelic variants, were assessed using flanking and repeat-primed polymerase chain reactions. Whole genome sequencing (WGS) was performed in selected cases to explore additional genetic variants.ResultsRFC1 repeat expansions were identified in 12 patients with chronic cough, comprising 3 biallelic (2.3%), and 9 monoallelic (7.0%) carriers. RCC was diagnosed in 55 of the 109 subjects who completed follow-up. The percentage of RFC1 expansions was significantly higher in RCC than in non-RCC (18.2% vs. 1.9%, P = 0.005), comprising 5.5% biallelic and 12.7% monoallelic expansions in the RCC group. Carriers had longer cough duration (11.0 vs. 4.0 years, P = 0.048) and poorer cough-specific quality of life (Leicester Cough Questionnaire score: 8.5 ± 2.2 vs. 10.5 ± 3.4; P = 0.027). All of the biallelic carriers were diagnosed with RCC and showed poor response to antitussive therapies. WGS identified no additional pathogenic variants in most cases.ConclusionsThis is the first study to evaluate RFC1 repeat expansions in non-Caucasian patients with chronic cough. The findings suggest that RFC1 expansions may define a distinct, treatment-refractory phenotype of chronic cough.

“Intravenous Immunoglobulin Therapy in Patients With Painful Idiopathic Small Fiber Neuropathy” by Geerts et al. compared the administration of IVIG with placebo for patients with idiopathic small fiber neuropathy (SFN) and found no significant difference in the Pain Intensity Numerical Rating Scale score. We summarized (1) an exchange about these findings between Wilder-Smith and Spoendlin and Faber (a coauthor on the article) in the October 19, 2021, Editors' Note and (2) an exchange between Wilder-Smith et al. and Faber et al. in the January 18, 2022, Editors' Note.[1][1],[2][2] Oaklander et al. now comment that while the trial used a subjective outcome (pain intensity), an objective assessment (such as autonomic function test scores) could have enhanced the methodology. They also advocate against the extrapolation of these results to all patients with SFN, noting that patients with autoimmune disorders who may benefit from IVIG may not be readily apparent, so it is beneficial to create guidelines triaging patients with SFN who may benefit from a time-limited trial of IVIG. Finally, they express concern that payors may deny treatment to some patients who could benefit, particularly those who are immune-mediated. Faber et al. respond that changes in the Pain Intensity Numerical Rating Scale score are clinically relevant and the sensitivity of autonomic function testing results in isolation to detect autonomic dysfunction in SFN is low in clinical practice. They agree that patients with immune-mediated SFN may benefit from IVIG and emphasize that their study was not intended to focus on that patient population. However, they suggest that randomized studies with valid and reliable outcome measures are needed to evaluate the role of IVIG in patients with SFN that could potentially be immune-mediated. “Intravenous Immunoglobulin Therapy in Patients With Painful Idiopathic Small Fiber Neuropathy” by Geerts et al. compared the administration of IVIG with placebo for patients with idiopathic small fiber neuropathy (SFN) and found no significant difference in the Pain Intensity Numerical Rating Scale score. We summarized (1) an exchange about these findings between Wilder-Smith and Spoendlin and Faber (a coauthor on the article) in the October 19, 2021, Editors' Note and (2) an exchange between Wilder-Smith et al. and Faber et al. in the January 18, 2022, Editors' Note.1,2 Oaklander et al. now comment that while the trial used a subjective outcome (pain intensity), an objective assessment (such as autonomic function test scores) could have enhanced the methodology. They also advocate against the extrapolation of these results to all patients with SFN, noting that patients with autoimmune disorders who may benefit from IVIG may not be readily apparent, so it is beneficial to create guidelines triaging patients with SFN who may benefit from a time-limited trial of IVIG. Finally, they express concern that payors may deny treatment to some patients who could benefit, particularly those who are immune-mediated. Faber et al. respond that changes in the Pain Intensity Numerical Rating Scale score are clinically relevant and the sensitivity of autonomic function testing results in isolation to detect autonomic dysfunction in SFN is low in clinical practice. They agree that patients with immune-mediated SFN may benefit from IVIG and emphasize that their study was not intended to focus on that patient population. However, they suggest that randomized studies with valid and reliable outcome measures are needed to evaluate the role of IVIG in patients with SFN that could potentially be immune-mediated. [1]: #ref-1 [2]: #ref-2