Biology subjects

Bresnahan, S. T.

Publications and source records attributed to Bresnahan, S. T..

6 recordsLinked to original sources

bioRxiv2026

Natural variation in transplacental transfer efficiency exposes distinct transcriptional network architectures of PFAS effects on birth weight and gestational age

Per- and polyfluoroalkyl substances (PFAS) are environmental contaminants that produce heterogeneous effects on perinatal outcomes despite chemical similarity. Natural variation in transplacental transfer efficiency (TPTE, the degree to which compounds cross the placental barrier) presents a mechanistic lens for understanding this heterogeneity, but whether TPTE systematically shapes the transcriptional pathways linking exposure to outcomes has not been tested. Using isoform-resolved placental transcriptomics from n = 124 term deliveries with eight PFAS measured in maternal and cord blood, validated against patient-derived placental explants (n = 18) using a tissue-specific long-read transcriptome assembly, we show that PFAS influence perinatal outcomes primarily through co-expression network hubs rather than differentially expressed features, indicating that network position, not fold-change magnitude, determines mediator importance. Leveraging TPTE as a natural experiment, we find that direct fetal exposure recruits increasingly numerous and tightly coordinated transcriptional mediators for both birth weight and gestational age, but the two outcomes diverge in network architecture: network centrality and maternal-fetal compartmentalization scale with TPTE exclusively for birth weight, while gestational age shows no such topological reorganization. These outcome-specific patterns are detectable only at the transcript level, as gene-level aggregation masks systematic TPTE-network relationships. This framework distinguishes which perinatal outcomes are mechanistically vulnerable to fetal exposure dose, with implications for risk assessment and therapeutic target identification for environmental contaminants.

developmental biology↗

bioRxiv2026

Improving isoform-level eQTL and integrative genetic analyses of breast cancer risk with long-read RNA transcript assemblies

Most eQTL and TWAS analyses quantify expression using aggregate, tissue-agnostic transcript annotations and ignore isoform-level regulation, potentially obscuring or misattributing regulatory mechanisms. Here, we developed a framework leveraging publicly available long-read RNA-seq data to perform tissue-informed inference of genetic regulation and prioritize candidate causal isoforms for breast cancer risk. We quantified gene- and isoform-level expression in breast tumor (TCGA), non-cancerous mammary tissue, and cultured fibroblasts (GTEx) using three transcriptome annotations: standard GENCODE, tissue-specific long-read-derived assemblies, and combined annotations incorporating transcript-isoforms from both. While GENCODE cataloged over 250,000 pan-tissue isoforms, the tissue-specific long-read assemblies captured reduced sets of 74,717 isoforms in tumor, 48,057 in fibroblasts, and 22,941 in healthy breast. We performed eQTL mapping and fine-mapping, followed by colocalization with overall and subtype-specific breast cancer GWAS and isoform-level TWAS. While most eGenes were concordant across annotations, approximately 1/3 of lead cis-eQTLs for shared eGenes differed between long-read assemblies and GENCODE. Further, eIsoform discovery was highly annotation-specific. In healthy breast tissue, the gold standard tissue for building gene expression prediction models for TWAS of breast cancer, 46% of eIsoforms identified by the long-read annotation were unique to that annotation even though 93.7% of them are present in GENCODE. Despite combined annotations expanding the GENCODE catalog by only 0.6-7.6% depending on tissue source, 69% of unique significant isoform-trait associations were specific to a single annotation. Long-read-informed annotations uncovered regulatory associations entirely missed by GENCODE, including a candidate regulatory isoform at the MARK1 locus captured only in fibroblasts and a previously unannotated splice variant prioritized as the likely effector transcript at NUP107. These findings demonstrate that transcript annotation is not merely a technical consideration but critically defines the biological hypothesis space for regulatory mechanisms and shapes discovery. Incorporating tissue-resolved isoform annotations from long-read RNA-seq improves the specificity of regulatory inference and enhances identification of candidate causal isoforms at GWAS loci.

genomics↗

bioRxiv2025

Quantification method affects replicability of eQTL analysis, colocalization, and TWAS

eQTL mapping and TWAS are widely used to contextualize GWAS, yet the impact of RNA-seq processing choices remains unexplored. We find that RNA-seq quantification method and transcriptomic reference substantially affect eQTL detection and gene expression prediction with significant downstream impact on colocalization and TWAS results. Our findings demonstrate that seemingly minor methodological decisions substantially affect these common analyses, highlighting the need for standardized practices to ensure reproducible genetic association studies.

genomics↗

bioRxiv2025

Long-read transcriptome assembly reveals vast isoform diversity in the placenta associated with metabolic and endocrine function

The placenta is critical for fetal development and mediates the effects of pregnancy complications on offspring metabolic health, yet it is often poorly characterized in genomic studies. Existing transcriptomic analyses rely on adult tissue-based references, which overlook developmentally important isoform diversity. We used largest-in-class long-read RNA-seq (N=72) to create a comprehensive placental transcriptome reference, identifying 37,661 high-confidence isoforms (14,985 novel) across 12,302 genes (2,759 novel). Contrary to characterizations of the placenta as a "transcriptomic void," we found transcriptional breadth and complexity comparable to adult tissues, with extraordinary splicing diversity in genes controlling obesity, lactogen production and growth, including 108 distinct CSH1 (placental lactogen) isoforms. This improved reference offers two advantages: First, it reduced inferential uncertainty in isoform quantification by 30% and increased the yield of high-confidence transcripts. Applying this reference to short-read RNA-seq datasets (N=344) of gestational diabetes mellitus (GDM), we found that placental transcription mediated 36% of GDM effects on birth weight, with novel CSH1 isoforms identified as key mediators. We further uncovered ancestry-specific effects, with distinct CSH1 isoforms mediating larger effects in European (24.4%) than Asian (13.4%) populations. Our results establish that utilizing long-read-based, tissue-specific transcriptomic annotations is critical, enabling isoform-resolved analyses that provide greater sensitivity than conventional gene-level approaches for understanding placental function and context-specific variation across diverse biobanks.

genomics↗

bioRxiv2024

Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)

Caste determination of honey bees (Apis mellifera) is a prime example of developmental plasticity, where differences in larval diet will result in identical genotypes yielding either long-lived, reproductive queens or short-lived, facultatively sterile workers. Beyond environmental factors, intragenomic conflict between genes inherited from the mother (matrigenes) versus the father (patrigenes) is also hypothesized to generate this plasticity. In honey bees, the Kinship Theory of Intragenomic Conflict predicts selection on patrigenes to enhance traits that result in fitness gained through reproduction, and thus patrigenes should favor the queen caste fate. Here, we conducted allele-specific transcriptome analyses on queen-destined larvae (QL) and worker-destined larvae (WL) at 192 hours post-fertilization (hpf), a critical stage for caste determination. Our findings reveal hundreds of genes with parent-of-origin effects (POEs), with significant patrigene-biased transcription in QL. Genes with POEs in honey bees resemble imprinted genes in other taxa in terms of genomic clustering, recombination rate, intron length and CpG density, and a subset are maintained from 24hpf eggs. Previous studies demonstrated that DNA methylation, the canonical regulatory mechanism underlying transcriptional POEs in placental mammals, angiosperms, and some insects, is not operating in honey bees or other social insects. We use allele-specific ChIP-seq analyses to demonstrate that POEs on caste-specific histone post-translational modification (HPTM) profiles of H3K27me3, H3K4me3 and H3K27ac are associated with POEs on transcription. Together, these findings suggest that parent-of-origin intragenomic conflicts may contribute broadly to phenotypic plasticity and may be associated with HPTMs, suggesting a "non-canonical" genomic imprinting-like system in social insects.

developmental biology↗

bioRxiv2023

Beyond conflict: kinship theory of intragenomic conflict predicts individual variation in altruistic behavior

Studies of the genetic basis of behavioral variation have emphasized gene cooperation within networks, often overlooking gene conflicts. The Kinship Theory of Intragenomic Conflict (KTIC) proposes that conflicts can occur within genes when parent-specific alleles have different strategies for maximizing reproductive fitness. Here, we test a prediction of the KTIC - that selection should favor alleles which promote "altruistic" behaviors that support the reproductive fitness of kin. In honey bee (Apis mellifera) colonies, workers act altruistically when tending to the queen by performing a "retinue" behavior, distributing the queens mandibular pheromone (QMP) throughout the hive. Workers exposed to QMP do not activate their ovaries, ensuring they care for the queens brood instead of competing to lay unfertilized eggs. Thus, the KTIC predicts that response to QMP should be favored by the maternal genome. Using a reciprocal cross design, we tested for parent-of-origin effects on the workers 1) responsiveness to QMP, 2) ovary activation, and 3) brain transcriptome. We hypothesized that QMP-responsive workers have smaller and less active ovaries, influenced by the workers parent-of-origin. With an allele-specific transcriptomic analysis, we tested whether QMP-responsive workers show enriched maternal allele-biased gene expression compared to QMP-unresponsive workers. Finally, we explored how parent-of-origin gene expression patterns are associated with overall gene expression patterns and regulatory networks. We report evidence in support of the KTIC for the retinue behavior and associated conflicts within gene networks. Our study provides new insights into the genetic basis of behavior and the potential for behavioral variation influenced by intragenomic conflict.

animal behavior and cognition↗