Biology subjects

Doyle, P. H.

Publications and source records attributed to Doyle, P. H..

3 recordsLinked to original sources

bioRxiv2025

Decoding the human PBMC isonome: Isoform-level resolution with single-cell long-read transcriptomics

Long-read single-cell RNA sequencing provides an opportunity to understand human health and disease at a level difficult to resolve with bulk or short-read methods. This approach enables isoform-level investigation of cellular diversity and disease mechanisms and definition of cell-types, rather than using genes alone. Using a modified, microfluidic-free PIPseq workflow and computational pipeline adapted for Oxford Nanopore long-read sequencing, we generated the largest long-read single-cell dataset of human peripheral blood mononuclear cells (PBMCs) to date. This study profiled isoform usage across immune cells, integrating marker expression and isoform discovery. We identified 128 novel isoforms from known and new genes, several with distinct cell-type-specific patterns, and characterized marker gene isoform expression across cell-types. Non-canonical protein-coding variants of GZMB and CD3G were enriched in unexpected cell-types, including megakaryocytes and monocyte-derived populations. We also discovered novel transcripts from CMC1 and LYAR with cell-type-specific signatures that were the predominantly expressed transcript within the gene. This study expands versatility of long-read single-cell studies to not only relay changes in isoform signatures, but to position them within the functional context of the biology they impact. These results demonstrate the power of long-read single-cell sequencing for mapping the isoform landscape--the isonome--across tissues and disease contexts.

genomics↗

bioRxiv2025

A genetically-diverse mouse model reveals a complex gene-environment regulation of cognitive resilience and susceptibility to Alzheimer disease

Alzheimers disease (AD) has a complex etiology arising from largely unknown interactions between genetic and environmental (GxE) factors. Even in populations with causal familial Alzheimers disease mutations, there is variation in disease onset and progression, suggesting that clinical symptoms are modified by genetics and environment. Identification of such modifiers is critical, as mechanisms that promote resilience to high-risk AD mutations, unhealthy diet, or aging represent promising therapeutic targets for AD; global resilience factors that protect against multiple "hits" are among the highest priority for discovery. Both genetic and environmental protective factors in AD have been identified; however, GxE factors are incredibly difficult to study in human populations given complex genomes, poor self-reporting, limited data from underrepresented groups, and incompletely documented exposomes. Here, we (1) validate novel GxE tools using population of mouse strains that model the polygenic nature of human AD, (2) characterize individuals with cognitive resilience to high-risk genetic and dietary perturbations, (3) define and quantitate roles for genetics, sex, age, and diet, and (4) present data for the discovery of complex interactions that are nearly impossible to elucidate from humans or inbred mice. We found that a high-fat high-sugar (HFHS) diet is not universally damaging, as some strains showed an improved AD-related cognitive outcome when fed a HFHS diet, suggesting the need for personalized recommendations for dietary interventions in AD. Cognitive resilience to AD is polygenic; however, we found a locus on Chr 10 that was modestly associated with cognitive resilience to AD in females, and this association was strengthened by HFHS diet, pointing to an unexpected interaction between specific genetic loci and unhealthy diet in AD risk and resilience. This study is the first of its kind to explore characteristics of AD resilience and GxE interactions in a genetically diverse mouse model. We present a subset of strains that exemplify global cognitive resilience to be leveraged for deep mechanistic studies aimed toward development of resilience-based, personalized therapeutic interventions. HighlightsO_LIAD-BXD mouse models and data repository provide unprecedented tools for understanding individual differences arising from Gene x Environment factors in aging and AD. C_LIO_LIEvidence of global cognitive resilience to AD-relevant outcomes that is partially mediated by a resilience to aging and dietary risk factors. C_LIO_LICognitive resilience in AD-BXDs its polygenic nature, with a modest locus on Chr 10 whose association with resilience was amplified by a high-fat/high-sugar diet. C_LIO_LIThe genetic factors mediating resilience to AD in humans also predict cognitive resilience in AD-BXDs, suggesting robust, translatable global resilience factors. C_LI

neuroscience↗

bioRxiv2023

Using deep long-read RNAseq in Alzheimer's disease brain to assess clinical relevance of RNA isoform diversity

Due to alternative splicing, human protein-coding genes average over eight RNA isoforms, resulting in nearly four distinct protein coding sequences per gene. Long-read RNAseq (IsoSeq) enables more accurate quantification of isoforms, shedding light on their specific roles. To assess the medical relevance of measuring RNA isoform expression, we sequenced 12 aged human frontal cortices (6 Alzheimers disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. Our study uncovered 53 new high-confidence RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. Specific examples include WDR4 (61%; microcephaly), MYL3 (44%; hypertrophic cardiomyopathy), and MTHFS (25%; major depression, schizophrenia, bipolar disorder). Other notable genes with new high-confidence isoforms include CPLX2 (10%; schizophrenia, epilepsy) and MAOB (9%; targeted for Parkinsons disease treatment). We identified 1,917 medically relevant genes expressing multiple isoforms in human frontal cortex, where 1,018 had multiple isoforms with different protein coding sequences, demonstrating the need to better understand how individual isoforms from a single gene body are involved in human health and disease, if at all. Exactly 98 of the 1,917 genes are implicated in brain-related diseases, including Alzheimers disease genes such as APP (A{beta} precursor protein; five), MAPT (tau protein; four), and BIN1 (eight). As proof of concept, we also found 99 differentially expressed RNA isoforms between Alzheimers cases and controls, despite the genes themselves not exhibiting differential expression. Our findings highlight the significant knowledge gaps in RNA isoform diversity and their medical relevance. Deep long-read RNA sequencing will be necessary going forward to fully comprehend the medical relevance of individual isoforms for a "single" gene.

genomics↗