Biology subjects

Messing, R. O.

Publications and source records attributed to Messing, R. O..

5 recordsLinked to original sources

bioRxiv2026

The Blood RNA Stability Atlas: defining temporal structure and trait-state programs in the human whole-blood transcriptome

Whole-blood RNA biomarkers are widely used for diagnosis and disease monitoring, but their utility depends not only on abundance but also on temporal stability, a property that is not routinely incorporated into biomarker design. We analyzed 968 longitudinal whole-blood transcriptomes from 165 healthy individuals across eight independent studies spanning diverse platforms, time scales (50 minutes to 16 weeks), and common environmental exposures. Using a cross-study analytical framework integrating variance partitioning, repeatability, and time-associated differential expression, we quantified temporal stability for 6,064 RNAs and classified transcripts into "trait" (stable) and "state" (dynamic) categories representing the extremes of longitudinal changes in transcript abundance. We identified 1,118 trait RNAs exhibiting stable within-individual levels of abundance but substantial inter-individual variability, enriched for whole-blood eGenes (P = 6.0 x 10-{superscript 2}), supporting a genetic basis for stability. In contrast, 1,504 state RNAs showed context-dependent temporal variation and were enriched for translation and RNA-binding pathways. Integration with genetic datasets revealed that 4,395 (72%) blood transcripts were linked to at least one whole-blood eQTL, collectively associated with 18,358 GWAS trait relationships, providing disease-relevant context for transcript stability. We developed the Blood RNA Stability Atlas to integrate these features and demonstrate both top-down (disease-to-gene) and bottom-up (gene-to-context) applications for biomarker prioritization and interpretation. These findings establish temporal stability as a defining property of the blood transcriptome and provide a practical, publicly accessible framework for distinguishing stable baseline abundance levels from context-dependent transcriptional responses, informing biomarker selection, study design, and hypothesis generation.

genomics↗

bioRxiv2026

Alternative polyadenylation in the brain is altered by chronic ethanol exposure in a sex- and cell type-specific manner

Alternative polyadenylation (APA) is a common posttranscriptional mechanism to regulate gene expression. APA generates mRNAs with varying lengths of 3' UTRs or transcripts that encode distinct protein carboxy-terminal ends. APA is especially important in neurons, where different mRNA variants are often asymmetrically localized to dendrites and axons, and can be locally translated into proteins. Local protein synthesis is crucial for axon guidance, synaptic plasticity, and learning and memory, key processes associated with the development of alcohol use disorder (AUD). We investigated the role of APA in AUD using a mouse model of alcohol dependence characterized by increased voluntary drinking after chronic intermittent ethanol (CIE) exposure. We examined APA during protracted withdrawal from alcohol in three brain regions of male and female mice. Our analyses revealed hundreds of genes undergoing APA in males, but substantially fewer in females, suggesting sex-specific effects of CIE on APA. Notably, male and female mice displayed distinct APA signatures. APA genes were different from differentially expressed genes (DEGs), suggesting that these molecular processes are regulated independently. We also determined that the expression of APA genes was associated with neurons, while DEGs were associated with non-neuronal cells. Many of the APA genes were involved in synaptic integrity, neuroplasticity, and neuronal maintenance, which was consistent with their enrichment in neurons. Our study suggests that APA is a crucial sex- and cell type-specific mechanism in AUD with the potential to influence localized neuronal protein expression during protracted withdrawal and to modify alcohol consumption behavior. HIGHLIGHTSO_LIChronic ethanol exposure in mice results in profound changes of APA genes in brain. C_LIO_LICommonly regulated cleavage and polyadenylation sites and genes were identified in male but not in female mice. C_LIO_LIThere was a minimal overlap between APA and differentially expressed genes (DEGs). C_LIO_LIAPA genes were primarily associated with neurons, whereas DEGs were associated with non-neuronal cells. C_LI

neuroscience↗

bioRxiv2025

Alcohol Attenuates CRF-Induced Excitatory Effects from the Extended Amygdala to Dorsostriatal Cholinergic Interneurons

Alcohol relapse is associated with corticotropin-releasing factor (CRF) signaling and altered reward pathway function, though the precise mechanisms remain unclear. Here, we investigated how CRF modulates cholinergic interneurons (CINs) in the dorsal striatum, a region critical in mediating cognitive flexibility and action selection. Using monosynaptic and retrograde circuit tracing, we identified direct inputs from CRF-expressing (CRF) neurons in the central amygdala (CeA) and bed nucleus of the stria terminalis (BNST) to dorsal striatal CINs. We showed that CINs express CRF receptor 1 (CRFR1) and established their functional connectivity with CeA/BNST CRF projections. Functional recordings revealed that CRF enhanced CIN excitability and promoted acetylcholine release in the dorsal striatum. However, acute alcohol exposure and withdrawal attenuated the excitatory effect of CRF on CIN firing, suggesting a mechanism by which alcohol disrupts CRF-dependent neuromodulation. These findings reveal a previously unrecognized CRF-CIN pathway linking the extended amygdala to the dorsal striatum and provide new insight into how CRF and alcohol interact to impair striatal function. This work highlights CRF signaling as a potential target for understanding stress-induced changes to the reward pathway. HighlightsO_LIDorsal striatal CINs receive monosynaptic CRF+ inputs from CeA and BNST neurons. C_LIO_LICRFR1 is expressed in striatal CINs, and CRF+ fibers are present in the dorsal striatum. C_LIO_LICRF enhances dorsal striatal CIN activity via CRFR1 signaling. C_LIO_LIAcute alcohol exposure impairs CRF-induced cholinergic activity. C_LI Significance StatementThe dorsal striatum regulates goal-directed behavior and is implicated in alcohol use disorder (AUD). Within this region, cholinergic interneurons (CINs) support cognitive flexibility and receive input from limbic areas, including the central amygdala (CeA) and bed nucleus of the stria terminalis (BNST). In this study, we identified direct projections from CRF-producing neurons in the CeA and BNST to dorsal striatal CINs, a subset of which express CRF receptor 1 (CRFR1). Electrophysiological recordings confirmed these projections provide functional input that is disrupted by acute alcohol exposure. These findings lay the groundwork for future studies on how CRF and alcohol interact to impair striatal function.

neuroscience↗

bioRxiv2018

Toll-like receptor 3 activation increases voluntary alcohol intake in C57BL/6J male mice

Many genes differentially expressed in brain tissue from human alcoholics and animals that have consumed large amounts of alcohol are components of the innate immune toll-like receptor (TLR) pathway. TLRs initiate inflammatory responses via two branches: (1) MyD88-dependent or (2) TRIF-dependent. All TLRs signal through MyD88 except TLR3. Prior work demonstrated a direct role for MyD88-dependent signaling in regulation of alcohol consumption. However, the role of TLR3 as a potential regulator of excessive alcohol drinking has not previously been investigated. To test the possibility TLR3 activation regulates alcohol consumption, we injected mice with the TLR3 agonist polyinosinic:polycytidylic acid (poly(I:C)) and tested alcohol consumption in an every-other-day two-bottle choice test. Poly(I:C) produced a persistent increase in alcohol intake that developed over several days. Repeated poly(I:C) and ethanol exposure altered innate immune transcript abundance; increased levels of TRIF-dependent pathway components correlated with increased alcohol consumption. Administration of poly(I:C) before exposure to alcohol did not alter alcohol intake, suggesting that poly(I:C) and ethanol must be present together to change drinking behavior. To determine which branch of TLR signaling mediates poly(I:C)-induced changes in drinking behavior, we tested either mice lacking MyD88 or mice administered a TLR3/dsRNA complex inhibitor. MyD88 null mutants showed poly(I:C)-induced increases in alcohol intake. In contrast, mice pretreated with a TLR3/dsRNA complex inhibitor reduced their alcohol intake, suggesting poly(I:C)-induced escalations in alcohol intake function are, at least partially, dependent on TLR3. Together, these results strongly suggest that TLR3-dependent signaling drives excessive alcohol drinking behavior.\n\nHighlightsO_LIActivation of TLR3 via poly(I:C) increased alcohol intake.\nC_LIO_LIPoly(I:C) and ethanol must be present together to change drinking behavior.\nC_LIO_LIIncreased alcohol intake due to poly(I:C) is independent of MYD88.\nC_LIO_LIIncreased alcohol intake due to poly(I:C) is dependent on TLR3.\nC_LI

neuroscience↗

bioRxiv2017

Optogenetic Characterization Of CeA CRF Pathways In Alcohol Dependence

Alcohol withdrawal activates a neuronal ensemble in the central nucleus of the amygdala (CeA) that is responsible for high levels of uncontrolled alcohol drinking. However, the neuronal phenotypes and circuits controlled by these neurons are unknown. We investigated the cellular identity of this CeA neuronal ensemble and found that most neurons expressed corticotropin-releasing factor (CRF). Using Crh-Cre transgenic rats combined with in vivo optogenetics, we tested the role of CeA CRF neurons and their projections in excessive alcohol self-administration during withdrawal. Rats were injected with AAV-DIO-NpHR-eYFP or AAV-DIO-eYFP and implanted with optical fibers over the CeA. Animals were then exposed to chronic intermittent ethanol vapor to induce alcohol dependence. Inactivation of CeA CRF neurons decreased alcohol drinking in dependent rats to non-dependent levels and completely suppressed activation of the CeA neuronal ensemble (Fos+ neurons) during withdrawal. No effects were observed on water or saccharin self-administration. In a second experiment, CeA CRF neurons were infected with AAV-DIO-NpHR-eYFP and optical fibers were implanted into downstream projection regions, including the bed nucleus of the stria terminalis (BNST), lateral hypothalamus (LH), parasubthalamic nucleus (pSTN), substantia innominata (SI), and parabrachial nuclei (PBN). Optogenetic inactivation of CRF terminals in the BNST reduced alcohol drinking and withdrawal signs, whereas inactivation of all other projections had no effect. These results demonstrate that CeA CRF neurons and their projections to the BNST drive excessive alcohol drinking and withdrawal in dependent rats.

neuroscience↗