Abstract Background Identifying the genes and biological pathways involved in Alzheimer disease (AD) is critical in the effort to develop effective therapies. Significant work has identified genetic variants conferring risk and protection for AD in individuals of diverse ancestries, but identification of downstream functional effects including modulation of gene regulation is lacking, particularly in individuals of diverse ancestries. Therefore, to explore transcriptional changes between clinically diagnosed AD and cognitively intact age‐matched controls, herein we analyzed RNA sequencing data from peripheral blood collected from individuals of admixed genetic backgrounds. Method Total RNA was extracted from peripheral whole blood stored in PAXGene tubes from 47 Cubans (22 AD and 25 controls), 85 Peruvians (41 AD and 44 controls), and 168 Puerto Ricans (88 AD and 80 controls). PolyA selected mRNA was sequenced to more than 40 million paired end read per sample on the Illumina NovaSeq 6000. The bioinformatic pipeline included mapping to the human reference genome (GRCh38), gene quantifications against the GENCODE v35 annotation set, and differential expression was calculated using DESeq2 with sex, age at blood draw, and count of APOEe4 alleles as covariates. Functional categorization was performed by gene set enrichment of gene ontology and KEGG pathways. Result Across the cohorts, a total of 358 protein‐coding genes (FDR ≤ 0.05, Fold change ≥ 1.25) were differentially expressed with 238 down‐regulated and 120 up‐regulated in AD relative to controls. Despite the few genes overlapping between ethnicities, pathway analysis revealed common pathways including up‐regulation of genes involved in inflammation and RNA processing and down‐regulation of genes involved in cellular detoxification and lipid transport, among others. Interestingly, while few specific genes overlap in differential expression overlap with a published set of genes from non‐Hispanic Europeans and African Americans (Griswold et al, 2018), the pathways identified are similar. Conclusion Our analysis reveals a signature of gene expression that implicates increased inflammation and decreased cellular detoxification based on gene expression analysis in admixed Latinx AD. Convergence of pathways across these and African American and European cohorts supports the idea of distinct genes but similar underlying pathological processes contributing to AD across individuals of diverse ancestries.
Abstract Background Most genome‐wide association studies (GWAS) of Alzheimer’s disease (AD) have been conducted in populations of European ancestry. It is important to determine if known AD‐related variants from these studies are associated with AD biomarkers. Therefore, we investigated the association between known AD risk loci and in vivo brain Aβ deposition in older Korean adults. Method Participants (n = 503) from the Korean Brain Aging Study for the Early Diagnosis and Prediction of Alzheimer’s disease (KBASE) were analyzed. Older adults who were cognitively normal (CN), had mild cognitive impairment (MCI) or AD dementia (264 CN, 148 MCI, 91 AD) underwent comprehensive assessments including 11 C‐PiB‐PET/MRI and blood sampling. Among 76 AD‐related target single nucleotide polymorphisms (SNPs) with genetic evidence compiled by the AD Sequencing Project (ADSP), 38 SNPs with minor allele frequency (MAF)>1% were extracted from TOPMed‐based imputed GWAS genotyping data in KBASE. We employed exploratory univariable logistic regression analysis with Aβ positivity as the dependent variable for each SNP. Then, SNPs with a significance level of p<0.05 were subjected to confirmatory multivariable logistic regression analysis, adjusting for age and sex, with Bonferroni correction. Result In the first step of exploratory analyses, we discovered significant differences in Aβ positivity rates between carriers and noncarriers of minor allele of several loci, including rs16824536 in MME , rs11218343 in SORL1 , rs4985556 in IL34 , rs4277405 in ACE and rs3851179, located in the intergenic region between EED and PICALM . The subsequent confirmatory analysis found an association between these variants and Aβ positivity after adjusting age and sex (Table 1). Notably, the negative association of rs3851179 with Aβ positivity remained significant after correcting for multiple comparisons and after controlling for APOE4 carrier status, age, and sex (OR 0.529, 95% CI 0.345–0.813). Conclusion We identified associations between several known AD risk loci and Aβ positivity on PET. rs3851179, demonstrated a robust association with in vivo brain Aβ positivity that was independent of APOE4 status. Our findings suggest that rs3851179 may be protective for in vivo Aβ accumulation. Additionally, the findings are needed to be replicated in other populations with different ancestries.
Abstract Background The APOE4 gene, the strongest genetic risk factor for late‐onset Alzheimer disease (AD), is highly expressed in astrocytes. The local ancestry (LA) region surrounding APOE4 (Chr19:44‐46Mb) is associated with increased AD risk for European (EU) compared to African (AF) APOE4 carriers. We previously demonstrated that APOE4 expression is higher in astrocytes from EU LA carrier brains using single nuclei RNA (snRNA) sequencing. We investigate whether chromatin accessibility differences could explain the APOE4 expression differences between ancestries. Method We performed snRNA and assays for transposase accessible chromatin sequencing (snATAC) in six EU and six AF APOE4 AD brains. Bioinformatic analysis was performed using Seurat for snRNA and ArchR for snATAC. Result 94,411 and 60,306 nuclei were sequenced by snRNA and snATAC, respectively. Following data integration, we resolved 11 distinct cell type clusters. We confirmed that APOE4 expression in astrocytes was higher in EU (Fold change=1.51; p =1.01x10 ‐113 ) and that chromatin accessibility is indeed higher in EU astrocytes at the APOE4 promoter and surrounding LA. Genome‐wide, astrocytes had the most differentially accessible peaks between ancestries (N=12,518, 95% increased accessibility in EU) representing 2.1% of all peaks. Interestingly, chr19 had the most differentially accessible peaks between ancestries (N=964) with 98% increased accessibility in EU. (EU:245; AF:4) peaks were in the APOE4 LA region with 60% overlapping promoters. Pathway analysis of genes with increased chromatin accessibility in EU LA showed enrichment for lipoprotein assembly, remodeling, and clearance. Conclusion This study represents initial efforts to investigate underlying mechanisms that contribute to the differential expression demonstrated between AF and EU LA brains surrounding APOE4 . Our results suggest that the increased EU APOE4 expression previously observed in EU AD LA APOE4 homozygotes relative to AF LA APOE4 homozygotes in astrocytes is at least partly due to increased EU astrocyte chromatin accessibility in the LA region.
Little is known about the post-transcriptional mechanisms that modulate the genetic effects in the molecular pathways underlying Alzheimer disease (AD), and even less is known about how these changes might differ across diverse populations. RNA editing, the process that alters individual bases of RNA, may contribute to AD pathogenesis due to its roles in neuronal development and immune regulation. Here, we pursued one of the first transcriptome-wide RNA editing studies in AD by examining RNA sequencing data from individuals of both African-American (AA) and non-Hispanic White (NHW) ethnicities. Whole transcriptome RNA sequencing and RNA editing analysis were performed on peripheral blood specimens from 216 AD cases (105 AA, 111 NHW) and 212 gender matched controls (105 AA, 107 NHW). 449 positions in 254 genes and 723 positions in 371 genes were differentially edited in AA and NHW, respectively. While most differentially edited sites localized to different genes in AA and NHW populations, these events converged on the same pathways across both ethnicities, especially endocytic and inflammatory response pathways. Furthermore, these differentially edited sites were preferentially predicted to disrupt miRNA binding and induce nonsynonymous coding changes in genes previously associated with AD in molecular studies, including PAFAH1B2 and HNRNPA1. These findings suggest RNA editing is an important post-transcriptional regulatory program in AD pathogenesis.
Abstract Background Ancestry‐specific Alzheimer Disease (AD) genetic risk is well recognized. Chromatin 3D interaction map in AD‐relevant cells with different ancestries is lacking but needed to understand the genetic/epigenetic basis for AD in diverse populations. We have shown that the local ancestry (LA) block (∼2Mb in size) surrounding APOE confers differential genetic risk for APOE ε4 carriers in Non‐Hispanic Whites (NHW) and African Americans (AA). Recently, we reported that NHW APOE ε4 carriers have a higher APOE ε4 expression and higher number of astrocytes compared to their AA counterparts in the frontal cortex. We therefore sought to characterize chromatin 3D interactions in astrocytes within different APOE LA. Method Induced pluripotent stem cells (iPSCs) with African or European LA block (N=2 individuals for each) were differentiated into astrocytes. Chromatin Hi‐C libraries were constructed with 4‐cutter enzyme and sequenced targeting 500 million pair‐end reads per library. Spatial genome structure was examined at compartment, topological associated domain (TAD), and loop levels. To better define enhancer‐promoter interaction (EPI), high‐resolution contact matrices were built using the HiCorr and DeepLoop algorithms. Result Each library generated over 250 million uniquely mapped, non‐redundant reads for Hi‐C analysis. Compartment and TAD had limited variability among samples (correlation co‐efficiency = 0.62∼0.90 for compartment, 0.84∼0.94 for TAD). Chromatin loop, which usually represents EPI, displays higher variability among samples (correlation co‐efficiency = 0.38∼0.75). In the 5kb‐contact‐matrix analysis, a chromatin interactive event involving APOE was detected, which is supported by Capture‐C data. The higher‐resolution 500bp‐contact‐matrix analysis revealed multiple better‐defined interactions within the event. Of particular interest, an interaction between the 5’end of TOMM40 and CLPTM1 (about 100 kb apart from each other) surrounding APOE is only observed on European but not African LA background. Conclusion Chromatin loop displays more inter‐individual variations compared to other spatial genome structures and therefore is more informative in elucidating the epigenetic basis for inter‐ancestry differences in gene expression regulation. While identifying chromatin loop from Hi‐C data at higher resolution is challenging, it has the potential to delimitate EPI and offers insights on the ancestry‐specific AD genetic risk by providing functional mechanisms underlying AD‐associated genetic variants.
The Infrapatellar Fat Pad (IFP) has until recently been viewed as a densely vascular and innervated intracapsular/extrasynovial tissue with biomechanical roles in the anterior compartment of the knee. Over the last decade, secondary to the proposition that the IFP and synovium function as a single unit, its recognized tight molecular crosstalk with emerging roles in the pathophysiology of joint disease, and the characterization of immune-related resident cells with varying phenotypes (e.g., pro and anti-inflammatory macrophages), this structural complex has gained increasing attention as a potential therapeutic target in patients with various knee pathologies including osteoarthritis (KOA). Furthermore, the description of the presence of mesenchymal stem/stromal cells (MSC) as perivascular cells within the IFP (IFP-MSC), exhibiting immunomodulatory, anti-fibrotic and neutralizing activities over key local mediators, has promoted the IFP as an alternative source of MSC for cell-based therapy protocols. These complementary concepts have supported the growing notion of immune and inflammatory events participating in the pathogenesis of KOA, with the IFP/synovium complex engaging not only in amplifying local pathological responses, but also as a reservoir of potential therapeutic cell-based products. Consequently, the aim of this review is to outline the latest discoveries related with the IFP/synovium complex as both an active participant during KOA initiation and progression thus emerging as a potential target, and a source of therapeutic IFP-MSCs. Finally, we discuss how these notions may help the design of novel treatments for KOA through modulation of local cellular and molecular cascades that ultimately lead to joint destruction.
Abstract Background Prior studies have shown differences in the genetic etiology and clinical presentation of Alzheimer’s Disease across populations. For example, for multiple genetic loci associated with AD, effect sizes can vary drastically between individuals of different ancestral backgrounds. Few investigations into differences in epigenetic features like DNA methylation have been conducted in AD, particularly in diverse individuals. These studies are critical to identify and further characterize mechanisms of disease allowing for development of therapeutic interventions. Method As part of an ongoing study of the genetics and epigenetics of AD in diverse populations, we performed a methylome analysis of 626 individuals. DNA from whole blood was analyzed using the Illumina MethylationEPICv2.0. The cohort consisted of both AD and cognitively unimpaired (CU) individuals of European (68 AD, 67 CU), African (98 AD, 106 CU), or Hispanic (Puerto Rican (85 AD, 76 CU); Peruvian (41 AD, 41 CU); Cuban (22 AD, 22 CU)) backgrounds. We analyzed data using the SeSAMe R package for quality control and statistical analysis. We performed differential methylation analysis between AD and CU in the overall dataset and within each ancestral population using linear models with covariates sex, age of exam, batch effect, global ancestry and estimated immune cell type proportions. Result 878,853 CpG sites were tested for differences between AD status. In a preliminary analysis of these data, we identified 563 CpG sites with nominally significant differences (p‐value ≤ 0.001) between AD and CU. Within each ancestral group, the number of differentially methylated sites differed: European – 442 sites, African – 217 sites, Hispanic – 475. Notably, however, the markers within the ancestral group did not overlap, implying that the AD disease process may be quite different across populations. Conclusion While these results are preliminary, and expansion of the dataset may reveal convergence of methylation patterns across ancestral populations, our analyses suggest the possibility of ancestry specific whole blood DNA methylation patterns as signatures of AD pathogenesis. Ultimately, combining these methylation profiles with existing genomic and transcriptomic data may reveal distinct genes but similar underlying pathological processes contributing to AD across individuals of diverse ancestries.
Summary Kallmann syndrome is a rare genetic condition causing congenital hypogonadotropic hypogonadism. It presents with delayed puberty, anosmia, and infertility. Here, we set out to identify a causative DNA variant for Kallmann syndrome in two affected brothers of Hispanic ancestry. The male siblings presented with a clinical diagnosis of Kallmann syndrome (anosmia, delayed puberty, azoospermia, and undetectable luteinizing hormone and follicle stimulating hormone levels). Genetic variations were investigated by whole exome sequencing. Potentially pathogenic variants were filtered and prioritized followed by validation by Sanger sequencing in the two brothers and their mother. A pathogenic variant was identified in the ANOS1 gene on the X chromosome: c.1267C>T; both brothers were hemizygous, and their mother was heterozygous for the variant. The variant is a single nucleotide change that introduces a stop codon in exon 9 (p.R423*), likely producing a truncated variant of the protein. This variant has only been reported twice in the literature, in the setting of finding genetic causes for other conditions. This result supports the clinical value of whole exome sequencing for identification of genetic pathogenic variants. Genetic diagnosis is the essential first step for genetic counseling, preimplantation diagnosis, and research for a potential treatment.
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