Citations

ABSTRACTIntroduction/AimsGlucocorticoid (GC)‐related adverse reactions and risks are commonly seen during the treatment of immune‐mediated and inflammatory neuromuscular disorders. There is wide variation in the management of associated complications. The aim of this study is to develop international consensus guidance on the management of GC‐related complications in neuromuscular disorders.MethodsThrough the American Association of Neuromuscular and Electrodiagnostic Medicine (AANEM), an international task force of 15 experts was convened to develop clinical guidance for the management of GC‐related complications in neuromuscular patients. The RAND/UCLA appropriateness method (RAM) was used to develop consensus guidance statements. Initial guidance statements were crafted after a thorough literature review and were modified after anonymous panel input, with up to three rounds of voting via email to achieve consensus.ResultsStatements were developed and achieved consensus for general care, monitoring of patients while on GC, osteoporosis prevention, vaccinations, infection screening, and Pneumocystis jiroveci pneumonia prophylaxis. A multidisciplinary approach to the management of GC‐related complications was emphasized.DiscussionThese formal consensus statements provide guidance to clinicians who use GC in the treatment of neuromuscular diseases regarding prevention and management of the more common associated adverse events and risks that arise with long and short‐term GC use and serve as a springboard for investigation and updates.

Purpose of review Once considered to have only local influences on the gut mucosa, short-chain fatty acids (SCFAs) now appear to have a much wider anti-inflammatory, immune-modulating, systemic effect. This article reviews recent evidence to suggest a much wider clinical application of this valued dietary substrate. Recent findings SCFAs act systemically through stimulation of G protein receptors (GPRs) and inhibition of histone deacetylases (HDACs). SCFAs cause appetite suppression, reduce systemic inflammation, improve insulin sensitivity, increase energy expenditure, promote mitochondrial function, stimulate satiety, reduce blood pressure, and improve cognitive function from various neurologic maladies. Summary Dietary strategies should be implemented to provide this beneficial substrate across a wide spectrum of disease conditions. Use of prebiotic fiber or liquid supplements containing high SCFA-producing organisms should be considered as therapeutic targets for multiple metabolic, immunologic, and neurodegenerative diseases.

Abstract Background Genetic testing has traditionally been divided into molecular genetics and cytogenetics, originally driven by the use of different assays and their associated limitations. Cytogenetic technologies such as karyotyping, fluorescent in situ hybridization or chromosomal microarrays are used to detect large “megabase level” copy number variants and other structural variants such as inversions or translocations. In contrast, molecular methodologies are heavily biased toward subgenic “small variants” such as single nucleotide variants, insertions/deletions, and targeted detection of intragenic, exon level deletions or duplications. The boundaries between these approaches are now increasingly blurred as next-generation sequencing technologies and their use for genome-wide analysis are used by both disciplines, therefore eliminating the historic and somewhat artificial separation driven by variant type. Content This review discusses the history of genomic nomenclature across both fields, summarizes implementation challenges for the clinical genetics community, and identifies key considerations for enabling a seamless connection of the stakeholders that consume variant descriptions. Summary Standardization is naturally a lengthy and complex process that requires consensus building between different stakeholders. Developing a standard that not only fits the multitude of needs across the entities that consume genetic variant information but also works equally well for all genetic variant types is an ambitious goal that calls for revisiting this vision.

Abstract Pharmacogenomics (PGx) is focused on the relationship between an individual's genetic makeup and their response to medications, with the overarching aim of guiding prescribing decisions to improve drug efficacy and reduce adverse events. The PGx and genomic medicine communities have worked independently for over 2 decades, developing separate standards and terminology, making implementation of PGx across all areas of genomic medicine difficult. To address this issue, the Clinical Genome Resource (ClinGen) Pharmacogenomics Working Group (PGxWG) was established by the National Institutes of Health (NIH)-funded ClinGen to initially create frameworks for evaluating gene–drug response clinical validity and actionability aligned with the ClinGen frameworks for evaluating monogenic gene–disease relationships, and a framework for classifying germline PGx variants similar to the American College of Medical Genetics (ACMG) and Association of Molecular Pathology (AMP) system for interpretation of disease-causing variants. These frameworks will leverage decades of work from well-established PGx resources facilitating buy-in among PGx stakeholders. In this report, we describe the background and major activities of the ClinGen PGxWG, and how this initiative will facilitate the critical inclusion of PGx into the larger context of genomic medicine.

Abstract Background Massively parallel sequencing (MPS) of nucleic acids has been a transformative technology for basic and applied genomic science, increasing efficiencies and decreasing costs to enable studies of unprecedented scope and impact. In clinical settings, these technological and scientific advances have led to the development of tests that are increasingly fast, comprehensive, and more frequently employed. Practitioners of genomic medicine have applied these tools across clinical settings, including diagnosis of inherited disorders and cancers and infectious disease detection and surveillance. In recent years, the commercial marketplace for MPS sequencers and reagents has been dominated by a few companies. The growing demand for sequencing has led to the recent emergence of several new sequencing platforms with techniques that may provide alternatives or improvements to existing workflows or allow the adoption of sequencing workflows in new settings. Clinical genomics laboratories will evaluate these platforms from a unique perspective, focusing on how technological advancements can improve patient care. Content This review describes short-read sequencing platforms provided by Illumina, Element Biosciences, MGI, PacBio, Singular Genomics, Thermo Fisher Scientific, and Ultima Genomics. This review discusses their innovative approaches, principles, workflows, and applications. Summary This review aims to inform laboratory geneticists, clinicians, and researchers about emerging short-read technologies and their applications in clinical genomics. By highlighting their principles and potential contributions, we aim to assist laboratories in selecting suitable solutions for their sequencing needs considering key factors such as applications, throughput, and integration with existing laboratory workflows.

AbstractBackgroundAlzheimer’s disease (AD) missing heritability remains extensive despite numerous genetic risk loci identified by genome‐wide association or sequencing studies. This has been attributed, at least partially, to mechanisms not currently investigated by traditional single‐marker/gene approaches. Polygenic Risk Scores (PRS) aggregate sparse genetic information across the genome to identify individual genetic risk profiles for disease prediction and patient risk stratification. Recent advancements have pivoted on innovative approaches utilizing OMICS data to construct such risk scores.MethodWe employed a random forest algorithm to identify a list of gene candidates from bulk RNA sequencing data in prefrontal cortex from 565 AD brain samples (non‐Hispanic Whites, n = 399; Hispanics, n = 113; African American, n = 12) across six U.S. brain banks. Subsequently, we calculated their effect size on Braak staging using regression models to construct a polytranscriptomic risk score (PTRS). We employed two distinct models: “Ethnicity‐Agnostic” Model (randomly assigning samples to training and testing samples) and “Ethnicity‐Aware” Model (assigning NHW samples to training and Hispanics to testing sample). Analysis of variance and the receiver operating characteristics area under the curve (ROC AUC) was used to evaluate PTRS’s classification performances. We validated findings using the Religious Orders Study/Memory and Aging Project study (ROS/MAP, n = 1,095).ResultWe found a significant difference in PTRS between samples with low vs. high Braak stages (≤4 vs. ≥5, p = 1*E‐04; Figure 1 upper panel). AUC was found to be 79‐81%, consistently in both Ethnicity‐Agnostic and Ethnicity‐Aware models (Figure 1 lower panel). Finally, the PTRS in ROS/MAP yielded a similar classification performance (p = 2*E‐04, AUC = 77%).Conclusioncontrary to prior studies, we developed a PTRS with optimal transferability across ethnicities. This underscores the importance of developing novel tools to stratify and harmonize large brain repositories for AD.

AbstractBackgroundDirected by the enzyme pair PINK1 and PRKN, mitophagy is a crucial mitochondrial quality control mechanism that selectively decorates damaged mitochondria with phosphorylated ubiquitin (pS65‐Ub), facilitating their lysosomal degradation. The dynamic pS65‐Ub signal accumulates upon enhanced activation from increased mitochondrial damage or upon reduced autophagic‐lysosomal flux. Previous studies including ours demonstrated altered mitophagy and elevated pS65‐Ub levels in Parkinson’s and Alzheimer’s disease brains that also independently associated with α‐synuclein, tau, or amyloid pathology. However, their combined impact on mitophagy and organelle function remains unclear. Notably these three pathologies often coexist in susceptible brain areas of a neurodegenerative condition named dementia with Lewy bodies (DLB). We herein investigated the interactions of α‐synuclein, tau, and amyloid pathology to uncover their combined effects on mitophagy in a large DLB cohort.MethodThis study included 371 DLB autopsy brains with neurologically normal cases as controls. Immunohistochemistry for the mitophagy marker pS65‐Ub in the hippocampus and amygdala was performed and associations of pS65‐Ub levels with neuropathological measures from the same region were evaluated. Immunofluorescence co‐staining of pS65‐Ub, phospho‐α‐synuclein, and phospho‐tau was conducted to study their interactions at single‐cell level.ResultpS65‐Ub positive cells were significantly more abundant in the hippocampus and amygdala of DLB cases compared to controls. Significant associations were observed between pS65‐Ub levels with age, brain weight, Braak stage, Thal phase as well as counts of Lewy body (LB), neurofibrillary tangle (NFT), and senile plaque (SP) in both regions. Strong synergistic effects of LB and NFT pathologies on pS65‐Ub accumulation were found in the amygdala, while only additive effects of LB and SP pathologies were observed. Single‐cell analysis in the amygdala showed that most affected cells contained either LB or NFT inclusion rather than co‐residing two pathologies within the same cell. Notably, cells harboring LB pathology exhibited mainly smaller, granular pS65‐Ub deposits (type G), possibly associated with increased mitochondrial dysfunction. Conversely, those containing NFT showed larger, vacuolar pS65‐Ub deposits (type V), likely resulting from reduced lysosomal degradation.ConclusionOur study revealed complex interactions of α‐synuclein, tau, and amyloid pathology on mitophagy alteration in DLB brains, highlighting different molecular mechanisms underlying α‐synuclein‐ and tau‐associated mitophagy alterations.

AbstractBackgroundAfrican Americans (AA) and Latin Americans (LA) are at a higher risk of developing AD compared to non‐Hispanic whites (NHW) but are traditionally underrepresented in AD research. The disproportionate risk is likely multifactorial including differences in co‐morbidities and structural and social determinants of health (SSDoH). AD risk is thought to result from multiple genetic and environmental factors, and their interactions (GxE). However, the molecular mechanisms underlying these interactions are largely unknown. The best‐established genetic risk factor for AD is APOE‐ε4, while APOE‐ε2 is protective. Environmental factors, such as living in neighborhoods with greater socioeconomic disadvantage, have been associated with greater AD neuropathology and worse cognitive function. Studying the potential modifying role of neighborhood disadvantage regarding associations of APOE‐ε4 and APOE‐ε2 with AD risk using a socioeconomic metric like the Area Deprivation Index (ADI) in a multiethnic post‐mortem cohort could offer valuable insights for precision medicine.MethodWe analyzed a post‐mortem cohort of 421 multi‐ethnic donors (NHW: N = 234, AD = 70, non‐AD = 164; LA: N = 145, AD = 102, non‐AD = 43; AA: N = 42, AD = 24, non‐AD = 18), from Mayo Clinic Florida, Banner Sun Health Research Institute, and the University of Florida Brain Banks as part of the AMP AD Diversity initiative. This study used the same neuropathological criteria to categorize AD vs. non‐AD as in the MayoRNAseq study (syn5550404). ADI from the Neighborhood Atlas® was obtained from de‐identified addresses. Associations of APOE‐ε4, APOE‐ε2, and ADI with AD risk were examined using logistic regression models adjusted for age‐at‐death, sex, and ethnic group; interactions of APOE genotype with ADI were also assessed.ResultAPOE‐ε4 and APOE‐ε2 showed a significant association with AD diagnosis (APOE‐ε4combined cohort OR = 3.23, P = 3.14E‐08; APOE‐ε2combined cohort OR = 0.30, P = 0.003). However, contrary to prior findings, our study found no association between ADI and AD diagnosis [OR = 1.023 (per each 10 unit increase in ADI), P = 0.629]. No significant interactions of ADI with APOE‐ε4 or APOE‐ε2 regarding association with AD diagnosis were identified (P = 0.083, P = 0.781).ConclusionThis is the first study evaluating the potential interaction of neighborhood disadvantage with APOE on AD risk in a multi‐ethnic autopsy cohort. However, these findings require further investigation in larger, more well‐powered cohorts for validation.

AbstractBackgroundThe aggregation of α‐synuclein protein, encoded by the SNCA gene, forms Lewy bodies (LBs) in neurons and is a key pathological feature of Lewy body dementia (LBD). Interestingly, the apolipoprotein E gene (APOE), primarily expressed in glial cells, is the strongest genetic modifier for LBD. The ε4 allele of this gene (APOE4) notably increases the risk of LBD. However, the specific mechanisms through which APOE‐regulated glial cells affect α‐synuclein aggregation in neurons are not yet fully understood.MethodTo explore this, we conducted spatial transcriptomics using the 10X Genomics Visium CytAssist platform on Formalin‐Fixed Paraffin‐Embedded tissue slides from the temporal cortex of human LBD brains (N = 4 brains in controls and N = 6 brains in LBD group, with an equal ratio of APOE3/3 and APOE3/4 genotypes). We defined the neuronal layers of the gray matter (Layers 1 to 6, L1‐6) and white matter in each brain based on the gene signature of each spot. We also identified LBs from hematoxylin and eosin (H&E) staining on the same slides, and annotated LB‐positive (LB+), LB‐surrounding and LB‐negative (LB‐) spots in each brain using Loupe Browser. We evaluated SNCA and APOE gene expression in each layer and analyzed cell‐cell communication using the CellChat tool across the layers.ResultWe observed that the SNCA gene was highly expressed in L5, which corresponded to the areas where most LBs were found. Notably, within LB+ spots across all layers, both SNCA and APOE gene expression levels were elevated in APOE3/4 cases compared to APOE3/3 cases. Furthermore, we identified cell‐cell communication networks between LB+ and LB‐surrounding spots, particularly in L4 and L5. These networks were enriched by microglia‐related signaling pathways, including APOE signaling, migration inhibitory factor (MIF) signaling, and colony stimulating factor 1 (CSF1) signaling. Interestingly, APOE3/4 brains exhibited significantly reduced interactions and lower interaction strength in these networks compared to APOE3/3 samples.ConclusionOur findings indicate that impaired cell‐cell communication, such as microglia‐mediated immune responses around LB regions, may be associated with the increased risk presented by the APOE4 allele in LBD brains.