Systematic review and meta-analysis of human transcriptomics reveals neuroinflammation, deficient energy metabolism, and proteostasis failure across neurodegeneration.

Neurodegenerative disorders such as Alzheimer's disease (AD), Lewy body diseases (LBD), and the amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD) spectrum are defined by the accumulation of specific misfolded protein aggregates. However, the mechanisms by which each proteinopathy leads to neurodegeneration remain elusive. We hypothesized that there is a common "pan-neurodegenerative" gene expression signature driving pathophysiology across these clinically and pathologically diverse proteinopathies. To test this hypothesis, we performed a systematic review of human CNS transcriptomics datasets from AD, LBD, and ALS-FTD patients and age-matched controls in the Gene Expression Omnibus (GEO) and ArrayExpress databases, followed by consistent processing of each dataset, meta-analysis, pathway enrichment, and overlap analyses. After applying pre-specified eligibility criteria and stringent data pre-processing, a total of 2600 samples from 26 AD, 21 LBD, and 13 ALS-FTD datasets were included in the meta-analysis. The pan-neurodegenerative gene signature is characterized by an upregulation of innate immunity, cytoskeleton, and transcription and RNA processing genes, and a downregulation of the mitochondrial electron transport chain. Pathway enrichment analyses also revealed the upregulation of neuroinflammation (including Toll-like receptor, TNF, and NFκB signaling) and phagocytosis, and the downregulation of mitochondrial oxidative phosphorylation, lysosomal acidification, and ubiquitin-proteasome pathways. Our findings suggest that neuroinflammation and a failure in both neuronal energy metabolism and protein degradation systems are consistent features underlying neurodegenerative diseases, despite differences in the extent of neuronal loss and brain regions involved.

Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases.

Discovering genetic mechanisms driving complex diseases is a hard problem. Existing methods often lack power to identify the set of responsible genes. Protein-protein interaction networks have been shown to boost power when detecting gene-disease associations. We introduce a Bayesian framework, Conflux, to find disease associated genes from exome sequencing data using networks as a prior. There are two main advantages to using networks within a probabilistic graphical model. First, networks are noisy and incomplete, a substantial impediment to gene discovery. Incorporating networks into the structure of a probabilistic models for gene inference has less impact on the solution than relying on the noisy network structure directly. Second, using a Bayesian framework we can keep track of the uncertainty of each gene being associated with the phenotype rather than returning a fixed list of genes. We first show that using networks clearly improves gene detection compared to individual gene testing. We then show consistently improved performance of Conflux compared to the state-of-the-art diffusion network-based method Hotnet2 and a variety of other network and variant aggregation methods, using randomly generated and literature-reported gene sets. We test Hotnet2 and Conflux on several network configurations to reveal biases and patterns of false positives and false negatives in each case. Our experiments show that our novel Bayesian framework Conflux incorporates many of the advantages of the current state-of-the-art methods, while offering more flexibility and improved power in many gene-disease association scenarios.

Similarity network fusion for aggregating data types on a genomic scale.

Recent technologies have made it cost-effective to collect diverse types of genome-wide data. Computational methods are needed to combine these data to create a comprehensive view of a given disease or a biological process. Similarity network fusion (SNF) solves this problem by constructing networks of samples (e.g., patients) for each available data type and then efficiently fusing these into one network that represents the full spectrum of underlying data. For example, to create a comprehensive view of a disease given a cohort of patients, SNF computes and fuses patient similarity networks obtained from each of their data types separately, taking advantage of the complementarity in the data. We used SNF to combine mRNA expression, DNA methylation and microRNA (miRNA) expression data for five cancer data sets. SNF substantially outperforms single data type analysis and established integrative approaches when identifying cancer subtypes and is effective for predicting survival.

iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data.

High-throughput RNA sequencing (RNA-seq) promises to revolutionize our understanding of genes and their role in human disease by characterizing the RNA content of tissues and cells. The realization of this promise, however, is conditional on the development of effective computational methods for the identification and quantification of transcripts from incomplete and noisy data. In this article, we introduce iReckon, a method for simultaneous determination of the isoforms and estimation of their abundances. Our probabilistic approach incorporates multiple biological and technical phenomena, including novel isoforms, intron retention, unspliced pre-mRNA, PCR amplification biases, and multimapped reads. iReckon utilizes regularized expectation-maximization to accurately estimate the abundances of known and novel isoforms. Our results on simulated and real data demonstrate a superior ability to discover novel isoforms with a significantly reduced number of false-positive predictions, and our abundance accuracy prediction outmatches that of other state-of-the-art tools. Furthermore, we have applied iReckon to two cancer transcriptome data sets, a triple-negative breast cancer patient sample and the MCF7 breast cancer cell line, and show that iReckon is able to reconstruct the complex splicing changes that were not previously identified. QT-PCR validations of the isoforms detected in the MCF7 cell line confirmed all of iReckon's predictions and also showed strong agreement (r(2) = 0.94) with the predicted abundances.

Savant Genome Browser 2: visualization and analysis for population-scale genomics.

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com.

Precision recruitment for high-risk participants in a COVID-19 cohort study.

Background: Studies for developing diagnostics and treatments for infectious diseases usually require observing the onset of infection during the study period. However, when the infection base rate incidence is low, the cohort size required to measure an effect becomes large, and recruitment becomes costly and prolonged. We developed a model for reducing recruiting time and resources in a COVID-19 detection study by targeting recruitment to high-risk individuals. Methods: We conducted an observational longitudinal cohort study at individual sites throughout the U.S., enrolling adults who were members of an online health and research platform. Through direct and longitudinal connection with research participants, we applied machine learning techniques to compute individual risk scores from individually permissioned data about socioeconomic and behavioral data, in combination with predicted local prevalence data. The modeled risk scores were then used to target candidates for enrollment in a hypothetical COVID-19 detection study. The main outcome measure was the incidence rate of COVID-19 according to the risk model compared with incidence rates in actual vaccine trials. Results: When we used risk scores from 66,040 participants to recruit a balanced cohort of participants for a COVID-19 detection study, we obtained a 4- to 7-fold greater COVID-19 infection incidence rate compared with similar real-world study cohorts. Conclusion: This risk model offers the possibility of reducing costs, increasing the power of analyses, and shortening study periods by targeting for recruitment participants at higher risk.

Estimating the Burden of Influenza-like Illness on Daily Activity at the Population Scale Using Commercial Wearable Sensors.

Importance: The severity of viral infections can vary widely, from asymptomatic cases to complications leading to hospitalizations and death. Milder cases, despite being more prevalent, often go undocumented, and their public health burden is not accurately estimated. Objective: To estimate the true burden of influenza-like illness (ILI) in the US population using a surrogate measure of daily steps lost as measured by commercial wearable sensors. Design, Setting, and Participants: This cohort study modeled data from 15 122 US adults who reported ILI symptoms during the 2018-2019 influenza season (before the COVID-19 pandemic) and who had a sufficient density of wearable sensor data at symptom onset. Participants' minute-level step data as measured by commercial wearable sensors were collected from October 1, 2018, through June 30, 2019. Minute-level activity time series were transformed into day-level time series per user, indicating the total number of steps daily. Main Outcomes and Measures: The primary end point was the number of steps lost during the period of 4 days before symptom onset (the latent phase) through 11 days after symptom onset (the symptomatic phase). The association between covariates and steps lost during this interval was also examined. Results: Of the 15 122 participants in this study, 13 108 (86.7%) were women, and the median age was 32 years (IQR, 27-38 years). For their ILI event, 2836 of 15 080 participants (18.8%) sought medical attention, and only 61 (0.4%) were hospitalized. Over the course of an ILI lasting 10 days, the mean cumulative loss was 4437 steps (95% CI, 4143-4731 steps). After weighting, there was an estimated overall nationwide reduction in mobility equivalent to 255.2 billion steps (95% CI, 232.9-277.6 billion steps) lost because of ILI symptoms during the study period. This finding reflects significant changes in routines, mobility, and employment and is equivalent to 15% of the active US population becoming completely immobilized for 1 day. Moreover, 60.6% of this reduction in steps (154.6 billion steps [95% CI, 138.1-171.2 billion steps]) occurred among persons who sought no medical care. Age and educational level were positively associated with steps lost. Conclusions and Relevance: These findings suggest that most of the burden of ILI in this study would have been invisible to health care and public health reporting systems. This approach has applications for public health, health care, and clinical research, from estimating costs of lost productivity at population scale, to measuring effectiveness of anti-ILI treatments, to monitoring recovery after acute viral syndromes such as during long COVID-19.

Finding associations in a heterogeneous setting: statistical test for aberration enrichment.

Most two-group statistical tests find broad patterns such as overall shifts in mean, median, or variance. These tests may not have enough power to detect effects in a small subset of samples, e.g., a drug that works well only on a few patients. We developed a novel statistical test targeting such effects relevant for clinical trials, biomarker discovery, feature selection, etc. We focused on finding meaningful associations in complex genetic diseases in gene expression, miRNA expression, and DNA methylation. Our test outperforms traditional statistical tests in simulated and experimental data and detects potentially disease-relevant genes with heterogeneous effects.

Differential gene expression data from the human central nervous system across Alzheimer's disease, Lewy body diseases, and the amyotrophic lateral sclerosis and frontotemporal dementia spectrum.

In Noori et al. [1], we hypothesized that there is a shared gene expression signature underlying neurodegenerative proteinopathies including Alzheimer's disease (AD), Lewy body diseases (LBD), and the amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD) spectrum. To test this hypothesis, we performed a systematic review and meta-analysis of 60 human central nervous system transcriptomic datasets in the public Gene Expression Omnibus and ArrayExpress repositories, comprising a total of 2,600 AD, LBD, and ALS-FTD patients and age-matched controls which passed our stringent quality control pipeline. Here, we provide the results of differential expression analyses with data quality reports for each of these 60 datasets. This atlas of differential expression across AD, LBD, and ALS-FTD may guide future work to elucidate the pathophysiological drivers of these individual diseases as well as the common substrate of neurodegeneration.

Effect of APOE alleles on the glial transcriptome in normal aging and Alzheimer's disease.

The roles of APOEε4 and APOEε2-the strongest genetic risk and protective factors for Alzheimer's disease-in glial responses remain elusive. We tested the hypothesis that APOE alleles differentially impact glial responses by investigating their effects on the glial transcriptome from elderly control brains with no neuritic amyloid plaques. We identified a cluster of microglial genes that are upregulated in APOEε4 and downregulated in APOEε2 carriers relative to APOEε3 homozygotes. This microglia-APOE cluster is enriched in phagocytosis-including TREM2 and TYROBP-and proinflammatory genes, and is also detectable in brains with frequent neuritic plaques. Next, we tested these findings in APOE knock-in mice exposed to acute (lipopolysaccharide challenge) and chronic (cerebral ß-amyloidosis) insults and found that these mice partially recapitulate human APOE-linked expression patterns. Thus, the APOEε4 allele might prime microglia towards a phagocytic and proinflammatory state through an APOE-TREM2-TYROBP axis in normal aging as well as in Alzheimer's disease.

Characterizing Clinical and Neuropathological Traits of APOE Haplotypes in African Americans and Europeans.

BACKGROUND: The APOEɛ4 allele is the largest genetic risk factor for late-onset Alzheimer's disease (AD). Recent literature suggested that the contribution of APOEɛ4 to AD risk could be population-specific, with ɛ4 conferring a lower risk to Blacks or African Americans. OBJECTIVE: To investigate the effect of APOE haplotypes on AD risk in individuals with European ancestry (EU) and Blacks or African Americans (AA). METHODS: We selected data from 1) the National Alzheimer's Coordinating Center: a total of 3,486 AD cases and 4,511 controls (N = 7,997, 60% female) with genotypes from the Alzheimer's Disease Genetics Consortium (ADGC), and 2) the Rush University Religious Orders Study and Memory and Aging Project (ROSMAP) cohort with 578 AD and 670 controls (N = 1,248, 60% female). Using ɛ3 homozygotes as the reference, we compared the association of various APOE haplotypes with the clinical and neuropathological correlates of dementia in AA and EU. RESULTS: In both cohorts, we find no difference in the odds or age of onset of AD among the ɛ4-linked haplotypes defined by rs769449 within either AA or EU. Additionally, while APOEɛ4 was associated with a faster rate of decline, no differences were found in rate of decline, clinical or neuropathological features among the ɛ4-linked haplotypes. Further analysis with other variants near the APOE locus failed to identify any effect modification. CONCLUSION: Our study finds similar effects of the ɛ4-linked haplotypes defined by rs769449 on AD as compared to ɛ3 in both AA and EU. Future studies are required to understand the heterogeneity of APOE conferred risk of AD among various genotypes and populations.

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Rheumatoid arthritis (RA) affects millions world-wide. While anti-TNF treatment is widely used to reduce disease progression, treatment fails in ∼one-third of patients. No biomarker currently exists that identifies non-responders before treatment. A rigorous community-based assessment of the utility of SNP data for predicting anti-TNF treatment efficacy in RA patients was performed in the context of a DREAM Challenge (http://www.synapse.org/RA_Challenge). An open challenge framework enabled the comparative evaluation of predictions developed by 73 research groups using the most comprehensive available data and covering a wide range of state-of-the-art modelling methodologies. Despite a significant genetic heritability estimate of treatment non-response trait (h(2)=0.18, P value=0.02), no significant genetic contribution to prediction accuracy is observed. Results formally confirm the expectations of the rheumatology community that SNP information does not significantly improve predictive performance relative to standard clinical traits, thereby justifying a refocusing of future efforts on collection of other data.

Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression.

Identifying microRNA signatures for the different types and subtypes of cancer can result in improved detection, characterization and understanding of cancer and move us towards more personalized treatment strategies. However, using microRNA's differential expression (tumour versus normal) to determine these signatures may lead to inaccurate predictions and low interpretability because of the noisy nature of miRNA expression data. We present a method for the selection of biologically active microRNAs using gene expression data and microRNA-to-gene interaction network. Our method is based on a linear regression with an elastic net regularization. Our simulations show that, with our method, the active miRNAs can be detected with high accuracy and our approach is robust to high levels of noise and missing information. Furthermore, our results on real datasets for glioblastoma and prostate cancer are confirmed by microRNA expression measurements. Our method leads to the selection of potentially functionally important microRNAs. The associations of some of our identified miRNAs with cancer mechanisms are already confirmed in other studies (hypoxia related hsa-mir-210 and apoptosis-related hsa-mir-296-5p). We have also identified additional miRNAs that were not previously studied in the context of cancer but are coherently predicted as active by our method and may warrant further investigation. The code is available in Matlab and R and can be downloaded on http://www.cs.toronto.edu/goldenberg/Anna_Goldenberg/Current_Research.html.