Abstract
Background
Single nucleus RNA sequencing (snRNA‐seq) has the potential to improve our understanding of the cellular‐specific drivers of sporadic Alzheimer’s disease. In this study we ...re‐analyze published snRNA‐seq data from post‐mortem dorsolateral prefrontal cortex tissue from 48 participants in the Religious Order Study and Memory and Aging Project (ROS/MAP) cohorts (Mathys
et al
. 2019) and snRNA‐seq data from prefrontal cortex tissue from 9 participants across the Adult Changes in Thought (ACT), University of Washington Alzheimer’s Disease Research Center (UW‐ADRC), and Seattle Longitudinal Study (SLS) cohorts.
Method
All snRNA‐seq data were normalized using scran, with normalized counts pre‐processed in Monocle 3. Pseudotime lineages were learned separately for male and female patients for each cell subtype with Monocle3. Genes with non‐zero counts in fewer than 10 cells in a subtype were discarded.
Result
We reidentified the ROS/MAP disease‐associated microglia subtype (Mic1) from Mathys
et al
. 2019 in the ACT, UW‐ADRC, and SLS data as determined by Fisher’s exact test overlap of subtype specific gene expression markers (p.adjusted<10
−16
). Furthermore, we identify a trajectory of cellular state (pseudotime) within the Mic1 population that is disease associated (p.adjusted ≤ 3.4 × 10
−11
in females, and p.adjusted ≤ 4.8 × 10
−4
in males) in the Mathys
et al
. data. In female samples in both studies we observed that
APOE
expression has a positive association with Mic1 pseudotime, which we do not see in males. In males we see
MEF2C
expression was negatively associated with Mic1 pseudotime. Lastly, we see both activation of similar Mic1 pseudotime expression patterns in a subpopulation of oligodendroglial cells, as well as a loss of oligodendroglial cells in diseased patients.
Conclusion
We provide increasing evidence implicating a specific microglial subpopulation in the etiology of Alzheimer’s disease. Furthermore, we see that this population has heterogeneity in expression of key Alzheimer’s disease risk genes as a function of sex, and that we can define genes that are specific to this microglial subtype lineage for further functional investigation. Finally, we also see evidence of a similar disease‐associated expression signature in oligodendroglial cells, suggesting potentially an interaction between the disease associated microglia populations and oligodendrocytes in diseased patients that warrants further functional investigation.
Background
Single nucleus RNA sequencing (snRNA‐seq) has the potential to improve our understanding of the cellular‐specific drivers of sporadic Alzheimer’s disease. In this study we re‐analyze ...published snRNA‐seq data from post‐mortem dorsolateral prefrontal cortex tissue from 48 participants in the Religious Order Study and Memory and Aging Project (ROS/MAP) cohorts (Mathys et al. 2019) and snRNA‐seq data from prefrontal cortex tissue from 9 participants across the Adult Changes in Thought (ACT), University of Washington Alzheimer’s Disease Research Center (UW‐ADRC), and Seattle Longitudinal Study (SLS) cohorts.
Method
All snRNA‐seq data were normalized using scran, with normalized counts pre‐processed in Monocle 3. Pseudotime lineages were learned separately for male and female patients for each cell subtype with Monocle3. Genes with non‐zero counts in fewer than 10 cells in a subtype were discarded.
Result
We reidentified the ROS/MAP disease‐associated microglia subtype (Mic1) from Mathys et al. 2019 in the ACT, UW‐ADRC, and SLS data as determined by Fisher’s exact test overlap of subtype specific gene expression markers (p.adjusted<10−16). Furthermore, we identify a trajectory of cellular state (pseudotime) within the Mic1 population that is disease associated (p.adjusted ≤ 3.4 × 10−11 in females, and p.adjusted ≤ 4.8 × 10−4 in males) in the Mathys et al. data. In female samples in both studies we observed that APOE expression has a positive association with Mic1 pseudotime, which we do not see in males. In males we see MEF2C expression was negatively associated with Mic1 pseudotime. Lastly, we see both activation of similar Mic1 pseudotime expression patterns in a subpopulation of oligodendroglial cells, as well as a loss of oligodendroglial cells in diseased patients.
Conclusion
We provide increasing evidence implicating a specific microglial subpopulation in the etiology of Alzheimer’s disease. Furthermore, we see that this population has heterogeneity in expression of key Alzheimer’s disease risk genes as a function of sex, and that we can define genes that are specific to this microglial subtype lineage for further functional investigation. Finally, we also see evidence of a similar disease‐associated expression signature in oligodendroglial cells, suggesting potentially an interaction between the disease associated microglia populations and oligodendrocytes in diseased patients that warrants further functional investigation.
Sub-Saharan Africa bears the highest burden of epilepsy worldwide. A presumed proportion is genetic, but this etiology is buried under the burden of infections and perinatal insults in a setting of ...limited awareness and few options for testing. Children with developmental and epileptic encephalopathies (DEEs) are most severely affected by this diagnostic gap in Africa, because the rate of actionable findings is highest in DEE-associated genes.
We tested 234 genetically naive South African children diagnosed with/possible DEE using gene panels, exome sequencing, and chromosomal microarray. Statistical comparison of electroclinical features in children with and children without candidate variants was performed to identify characteristics most likely predictive of a positive genetic finding.
Of the 41 (of 234) children with likely/pathogenic variants, 26 had variants supporting precision therapy. Multivariate regression modeling highlighted neonatal or infantile-onset seizures and movement abnormalities as predictive of a positive genetic finding. We used this, coupled with an emphasis on precision medicine outcomes, to propose the pragmatic "Think-Genetics" strategy for early recognition of a possible genetic etiology.
Our findings emphasize the importance of an early genetic diagnosis in DEE. We designed the Think-Genetics strategy for early recognition, appropriate interim management, and genetic testing for DEE in resource-constrained settings.
Dubowitz syndrome (DubS) is considered a recognizable syndrome characterized by a distinctive facial appearance and deficits in growth and development. There have been over 200 individuals reported ...with Dubowitz or a “Dubowitz‐like” condition, although no single gene has been implicated as responsible for its cause. We have performed exome (ES) or genome sequencing (GS) for 31 individuals clinically diagnosed with DubS. After genome‐wide sequencing, rare variant filtering and computational and Mendelian genomic analyses, a presumptive molecular diagnosis was made in 13/27 (48%) families. The molecular diagnoses included biallelic variants in SKIV2L, SLC35C1, BRCA1, NSUN2; de novo variants in ARID1B, ARID1A, CREBBP, POGZ, TAF1, HDAC8, and copy‐number variation at1p36.11(ARID1A), 8q22.2(VPS13B), Xp22, and Xq13(HDAC8). Variants of unknown significance in known disease genes, and also in genes of uncertain significance, were observed in 7/27 (26%) additional families. Only one gene, HDAC8, could explain the phenotype in more than one family (N = 2). All but two of the genomic diagnoses were for genes discovered, or for conditions recognized, since the introduction of next‐generation sequencing. Overall, the DubS‐like clinical phenotype is associated with extensive locus heterogeneity and the molecular diagnoses made are for emerging clinical conditions sharing characteristic features that overlap the DubS phenotype.
Sinoatrial node dysfunction and deafness (SANDD) syndrome is rare and characterized by a low heart beat and severe-to-profound deafness. Additional features include fatigue, dizziness, and episodic ...syncope. The sinoatrial node (SAN) drives heart automaticity and continuously regulates heart rate. The CACNA1D gene encoding the Ca
1.3 protein expressed in inner hair cells, atria and SAN, induces loss-of-function in channel activity and underlies SANDD. To date, only one variant c.1208_1209insGGG:p.(G403_V404insG) has been reported for SANDD syndrome. We studied five Pakistani families with SANDD and characterized a new missense variant p.(A376V) in CACNA1D in one family, and further characterized the founder variant p.(G403_V404insG) in four additional pedigrees. We show that affected individuals in the four families which segregate p.(G403_V404insG) share a 1.03 MB haplotype on 3p21.1 suggesting they share a common distant ancestor. In conclusion, we identified new and known variants in CACNA1D in five Pakistani families with SANDD. This study is of clinical importance as the CACNA1D founder variant is only observed in families from the Khyber Pakhtunkhwa (KPK) province, in Pakistan. Therefore, screening patients with congenital deafness for SAN dysfunction in this province could ensure adequate follow-up and prevent cardiac failure associated with SAN.
Abstract
Background
Late‐onset Alzheimer’s disease (AD) is a complex disorder with multiple genetic risk factors. Linkage and association analysis have mapped dozens of loci in pooled analysis of ...many pedigrees or large numbers of unrelated cases and controls. Identification of the underlying DNA risk variants in the regions of interest (ROIs) has been complicated by both the genetic heterogeneity and the cost, until recently, of comprehensive DNA sequencing in ROIs. The known loci also leave much heritability unexplained.
Method
We used the families in the AD Sequencing Project (ADSP) discovery family sample to identify variants of interest from whole genome sequences (WGS), and through the variants, genes implicated in risk. We used SNP‐based multipoint linkage analysis to identify ROIs with rare VOIs, carrying out analysis without trimming pedigrees. We pursued all ROIs with family‐specific lod
max
scores >1.9, reducing the variants of interest by several filters. We carried out pedigree‐based genotype imputation from the available WGS data, followed by family‐based association analysis, filtered for low population minor allele frequency. We prioritized genes with a low false‐discovery rate for association of single‐cell transcription in brain with AD disease state (PMID:31209304), and genes with high expression in bulk brain (PMID: 24309898).
Result
We obtained 46 distinct ROIs representing lod
max
1.9‐3.5 per ROI in each of 26 of the 110 ADSP discovery families analyzed. 29 ROIs further investigated in 16 of the families yielded 59 prioritized genes, with 1‐11 genes/ROI. Only 4 out of 321 variants that passed all filters in these genes were in exons, with minimal overlap with genes identified in AD GWASs. Only one ROI occurred in two families, with evidence for a shared‐haplotype between these families, implicating
FBXO2
and
FBXO44
. Both genes are implicated in ubiquitination, while
FBXO2
interacts with
BACE1
. Multiple pathways, both known and new, are implicated, including the ubiquitin‐proteasome system, neural development and maintenance, and mitochondrial functions.
Conclusion
This analysis underscores the evidence for extensive genetic heterogeneity and rare variants underlying AD risk, along with multiple potential mechanisms. The preponderance of prioritize non‐coding variants suggests alterations in gene regulation and/or expression as an aspect of AD genetic risk.
Background
Late‐onset Alzheimer’s disease (AD) is a complex disorder with multiple genetic risk factors. Linkage and association analysis have mapped dozens of loci in pooled analysis of many ...pedigrees or large numbers of unrelated cases and controls. Identification of the underlying DNA risk variants in the regions of interest (ROIs) has been complicated by both the genetic heterogeneity and the cost, until recently, of comprehensive DNA sequencing in ROIs. The known loci also leave much heritability unexplained.
Method
We used the families in the AD Sequencing Project (ADSP) discovery family sample to identify variants of interest from whole genome sequences (WGS), and through the variants, genes implicated in risk. We used SNP‐based multipoint linkage analysis to identify ROIs with rare VOIs, carrying out analysis without trimming pedigrees. We pursued all ROIs with family‐specific lodmax scores >1.9, reducing the variants of interest by several filters. We carried out pedigree‐based genotype imputation from the available WGS data, followed by family‐based association analysis, filtered for low population minor allele frequency. We prioritized genes with a low false‐discovery rate for association of single‐cell transcription in brain with AD disease state (PMID:31209304), and genes with high expression in bulk brain (PMID: 24309898).
Result
We obtained 46 distinct ROIs representing lodmax1.9‐3.5 per ROI in each of 26 of the 110 ADSP discovery families analyzed. 29 ROIs further investigated in 16 of the families yielded 59 prioritized genes, with 1‐11 genes/ROI. Only 4 out of 321 variants that passed all filters in these genes were in exons, with minimal overlap with genes identified in AD GWASs. Only one ROI occurred in two families, with evidence for a shared‐haplotype between these families, implicating FBXO2 and FBXO44. Both genes are implicated in ubiquitination, while FBXO2 interacts with BACE1. Multiple pathways, both known and new, are implicated, including the ubiquitin‐proteasome system, neural development and maintenance, and mitochondrial functions.
Conclusion
This analysis underscores the evidence for extensive genetic heterogeneity and rare variants underlying AD risk, along with multiple potential mechanisms. The preponderance of prioritize non‐coding variants suggests alterations in gene regulation and/or expression as an aspect of AD genetic risk.
Front Cover, Volume 40, Issue 10 Cox, Timothy C.; Lidral, Andrew C.; McCoy, Jason C. ...
Human Mutation,
October 2019, 2019-10-00, Volume:
40, Issue:
10
Journal Article
Digenic inheritance is the simplest model of oligenic disease. It can be observed when there is a strong epistatic interaction between two loci. For both syndromic and non-syndromic hearing ...impairment, several forms of digenic inheritance have been reported.
We performed exome sequencing in a Pakistani family with profound non-syndromic hereditary hearing impairment to identify the genetic cause of disease.
We found that this family displays digenic inheritance for two trans heterozygous missense mutations, one in PCDH15 p.(Arg1034His) and another in USH1G p.(Asp365Asn). Both of these genes are known to cause autosomal recessive non-syndromic hearing impairment and Usher syndrome. The protein products of PCDH15 and USH1G function together at the stereocilia tips in the hair cells and are necessary for proper mechanotransduction. Epistasis between Pcdh15 and Ush1G has been previously reported in digenic heterozygous mice. The digenic mice displayed a significant decrease in hearing compared to age-matched heterozygous animals. Until now no human examples have been reported.
The discovery of novel digenic inheritance mechanisms in hereditary hearing impairment will aid in understanding the interaction between defective proteins and further define inner ear function and its interactome.
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