Biology subjects

Vo, K.

Publications and source records attributed to Vo, K..

7 recordsLinked to original sources

bioRxiv2025

Aging alters mRNA processing in the mouse ovary

Aging in females predominantly impacts the ovaries before any other organ systems. This has profound implications for womens reproductive health. This phenomenon is closely linked to a gradual depletion of the ovarian follicle reserve and a notable diminishment of oocyte quality. Studies have shown that cellular changes within ovaries can manifest even before the observable depletion of ovarian follicles. To understand the molecular mechanisms underlying these changes, we have conducted a comprehensive analysis of the changes in gene expression in aging mouse ovaries. Using efficient genomics software such as CLC Genomic Workbench, we could detect not only the differentially expressed genes but also delineate the various transcript variants present in the transcriptome of aging ovaries. We verified the results by comparing coding sequences of selected transcripts with the coding sequences of their canonical counterparts from young and aged mice. In general, the analysis methods yielded similar observations. Our findings revealed that traditional gene expression analyses often overlook the differential expression of numerous transcript variants. We identified significant alterations in the expression patterns of alternative transcripts in aging ovaries and found coding sequences that lead to profound functional outcomes. Notably, most of these differentially expressed transcript variants were affected upstream epigenetically and transcriptionally, then generated through alternative splicing events. This suggests that aging may lead to alterations in RNA-binding proteins and spliceosome components, which play a crucial role in mRNA processing within the mouse ovary. Our observations highlight the necessity of focusing on transcript variants and their functions in aging research, as they provide a more nuanced understanding of the biological processes at play.

molecular biology↗

bioRxiv2025

Functional synaptic connectivity of engrafted spinal cord neurons with locomotor circuitry in the injured spinal cord

Spinal cord injury (SCI) results in significant neurological deficits, with no currently available curative therapies. Neural progenitor cell (NPC) transplantation has emerged as a promising approach for neural repair, as graft-derived neurons (GDNs) can integrate into the host spinal cord and support axon regeneration. However, the mechanisms underlying functional recovery remain poorly understood. In this study, we investigate the synaptic integration of NPC-derived neurons into locomotor circuits, the projection patterns of distinct neuronal subtypes, and their potential to modulate motor circuit activity. Using transsynaptic tracing in a mouse thoracic contusion SCI model, we found that NPC-derived neurons form synaptic connections with host locomotor circuits, albeit at low frequencies. Furthermore, we mapped the axon projections of V0C and V2a interneurons, revealing distinct termination patterns within host spinal cord laminae. To assess functional integration, we employed chemogenetic activation of GDNs, which induced muscle activity in a subset of transplanted animals. However, NPC transplantation alone did not significantly improve locomotor recovery, highlighting a key challenge in the field. Our findings suggest that while GDNs can integrate into host circuits and modulate motor activity, synaptic connectivity remains a limiting factor in functional recovery. Future studies should focus on enhancing graft-host connectivity and optimizing transplantation strategies to maximize therapeutic benefits for SCI.

neuroscience↗

bioRxiv2024

Ethanol drinking sex-dependently alters cortical IL-1β synaptic signaling and cognitive behavior in mice

Individuals with alcohol use disorder (AUD) struggle with inhibitory control, decision making, and emotional processing. These cognitive symptoms reduce treatment adherence, worsen clinical outcomes, and promote relapse. Neuroimmune activation is a key factor in the pathophysiology of AUD, and targeting this modulatory system is less likely to produce unwanted side effects compared to directly targeting neurotransmitter dysfunction. Notably, the cytokine interleukin-1{beta} (IL-1{beta}) has been broadly associated with the cognitive symptoms of AUD, though the underlying mechanisms are not well understood. Here we investigated how chronic intermittent 24-hour access two bottle choice ethanol drinking affects medial prefrontal cortex (mPFC)-related cognitive function and IL-1 synaptic signaling in male and female C57BL/6J mice. In both sexes, ethanol drinking decreased reference memory and increased mPFC IL-1 receptor 1 (IL-1R1) mRNA levels. In neurons, IL-1{beta} can activate either pro-inflammatory or neuroprotective intracellular pathways depending on the isoform of the accessory protein (IL-1RAcP) recruited to the IL-1R1 complex. Moreover, ethanol drinking sex-dependently shifted mPFC IL-1RAcP isoform gene expression and IL-1{beta} regulation of mPFC GABA synapses, both of which may contribute to female mPFC resiliency and male mPFC susceptibility. This type of signaling bias has become a recent focus of rational drug development. Therefore, in addition to increasing our understanding of how IL-1{beta} sex-dependently contributes to mPFC dysfunction in AUD, our current findings also support the development of a new class of pharmacotherapeutics based on biased IL-1 signaling. Highlights- Female mice consumed more ethanol, but were less cognitively impaired than males - Ethanol altered IL-1{beta} effects at mPFC GABA synapses, with females less sensitive than males - Ethanol altered mPFC Il1rap mRNA to promote female neuroprotection and male neuroinflammation

neuroscience↗

bioRxiv2024

Epigenetic and transcriptional regulation of ovarian development altered in ErβKO ovaries

We analyzed the transcriptome of wildtype and estrogen receptor {beta} knockout (Er{beta}KO) rat ovaries during the early postnatal period and detected remarkable changes in epigenetic regulators and transcription factors. Compared to postnatal day (PD) 4.5 wildtype ovaries, 17 differentially expressed epigenetic regulators (DEERs), and 23 differentially expressed transcription factors (DETFs) were detected in PD6.5 wildtype ovaries. Subsequently, compared to PD 6.5 wildtype ovaries, 24 DEERs and 68 DETFs were detected in PD8.5 ovaries. Changes in DEERs and DEFTs resulted in 581 differentially expressed downstream genes (DEDGs) in PD6.5 and 920 DEDGs in wildtype PD8.5 ovaries. The DEERs, DETFs, and DEDGs in wildtype ovaries represented primordial follicle activation (PFA) and development of the first-wave follicles because the second-wave follicles remain dormant during this period. However, the changes in DEERs, DETFs, and DEDGs during this postnatal period were markedly different in Er{beta}KO rat ovaries, which suffered from increased PFA in both waves. Compared to 17 DEERs and 23 DETFs in wildtype, 46 DEERs and 55 DETFs were identified in PD 6.5 Er{beta}KO ovaries. The differences were more remarkable in PD 8.5 Er{beta}KO ovaries; compared to 24 DEERS and 68 DETFs in wildtype, only 8 DEERs and 10 DETFs were detected in Er{beta}KO ovaries. Such dysregulation resulted in altered DEDGs in PD 6.5 (581 vs. 744) and in PD8.5 (920 vs. 191) Er{beta}KO ovaries. These findings also suggest that the number of DEDGs depends directly on the numbers of DEERS and DETFs. In addition to the quantitative differences in DEERs and DETFs between the wildtype and Er{beta}KO ovaries, we detected distinct differences in the identities of the regulators. Our observations indicate that loss of ER{beta} dysregulates the epigenetic regulators and transcription factors in Er{beta}KO ovaries, which disrupts the downstream genes in ovarian follicles and increases follicle activation.

developmental biology↗

bioRxiv2024

Importance of transcript variants in transcriptome analyses

RNA sequencing (RNA-Seq) has become a widely adopted genome-wide technique for investigating gene expression patterns. However, conventional RNA-Seq analyses typically rely on gene expression (GE) values that aggregate all the transcripts produced by a gene under a single identifier, overlooking the complexity of transcript variants arising from different transcription start sites and alternative splicing events. In this study, we explored the implications of neglecting transcript variants in RNA-Seq analyses. Among the 1334 transcription factor (TF) genes expressed in mouse embryonic stem (ES) or trophoblast stem (TS) cells, 652 were reported to be differentially expressed in TS cells based on GE values (365 upregulated and 287 downregulated, [≥]2-fold, FDR p-value [≤]0.05). Intriguingly, differential gene expression analysis revealed that of the 365 upregulated genes, 883 transcript variants were expressed, with only 174 (<20%) variants exhibiting upregulation based on transcript expression (TE) values. The remaining 709 (>80%) variants were either down-regulated or showed no significant change in expression analysis. Similarly, the 287 genes reported to be downregulated expressed 856 transcript variants, with only 153 (<20%) downregulated variants and 703 (>82%) variants that were upregulated or showed no significant changes. Additionally, the 682 TF genes that did not show significant changes between ES and TS cells (GE values < 2-fold changes and/or FDR p-values >0.05) expressed 2215 transcript variants, which included 477 (>21%) that were differentially expressed (276 upregulated and 201 downregulated, [≥]2-fold, FDR p-value [≤]0.05). Notably, a particular gene does not express just one protein; rather its transcript variants encode multiple proteins with distinct functional domains, including non-coding regulatory RNAs. Our findings underscore the critical necessity of considering transcript variants in RNA-Seq analyses. Doing so may enable a more precise understanding of the intricate functional and regulatory landscape of genes; ignoring the variants may result in an erroneous interpretation. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/603122v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1371b9corg.highwire.dtl.DTLVardef@f5c037org.highwire.dtl.DTLVardef@1e5f79org.highwire.dtl.DTLVardef@e20cb_HPS_FORMAT_FIGEXP M_FIG C_FIG Differential expression of transcription factors (TFs) between mouse embryonic stem (ES) cells and trophoblast stem (TS) cells. This graphic presentation clearly demonstrates the importance of including transcript variants during RNA sequencing (RNA-Seq) analyses. Panel A represents the conventional differential gene expression analysis approach after RNA-Seq, where all transcript reads are taken under a single gene name. Panel B takes differential gene expression analysis one step further by examining all the transcript variants that were previously hidden under the main gene name. Our results indicate that exclusive gene expression (GE) analysis inaccurately defines over 80% of the transcript expression (TE). Without analyses of all the transcript variants reads, we fail to uncover the functional importance of the variants and the regulation of their expression. Both GE and TE values are expressed as transcript per million (TPM). Data analyses were performed by using CLC Genomics Workbench.

bioinformatics↗

bioRxiv2021

Leukocyte proliferation mediates disease pathogenesis in the Ndufs4(KO) mouse model of Leigh syndrome

Symmetric, progressive, necrotizing lesions in the brainstem are a defining feature of Leigh syndrome (LS). A mechanistic understanding of the pathogenesis of these lesions has been elusive. Here, we report that leukocyte proliferation is causally involved in the pathogenesis of Leigh syndrome. Directly depleting leukocytes with a colony-stimulating factor 1 receptor (CSF1R) inhibitor dramatically attenuates disease, including complete prevention of CNS lesion formation and substantial extension of survival. Leukocyte depletion rescues a range of symptoms including hyperlactemia, seizures, respiratory function, and neurologic symptoms. These data provide a mechanistic explanation for the beneficial effects of mTOR inhibition. More importantly, these findings dramatically alter our understanding of the pathogenesis of LS, demonstrating that immune involvement directly drives disease. These findings have significant implication for the mechanisms of disease resulting from mitochondrial dysfunction, and may lead to novel therapeutic strategies. One-Sentence SummaryPharmacologic targeting of leukocytes prevents CNS lesions, neurological disease, and metabolic dysfunction in the Ndufs4(KO) mouse model of Leigh syndrome.

pathology↗

bioRxiv2021

A Novel Art of Electrocardiogram Assessment in Zebrafish for Cardiovascular Disease Studies and Drug Screening

The zebrafish (Dario rerio) has proven to be an excellent animal model for biological research owing to its small size, low cost for maintenance, short generation time, amenable genetics, and optical transparency. Zebrafish have been extensively used in cardiovascular studies in which mutant lines with cardiovascular defects were introduced and analyzed. Despite the small size, technological advances have paved the way to effectively assess cardiac functions of zebrafish. Here, we present a novel art for long-term simultaneous monitoring and analysis of electrocardiogram (ECG) in multiple zebrafish with controlled environment. The system helps minimize the effect of anesthetic drug and temperature to cardiac rhythm side effects as well as save time and efforts by 40-50 fold compared with the conventional approach. We further employed the system to study the Na+ sensitivity in the development of sinus arrest in Tg(SCN5A-D1275N) fish, a study model of the sick sinus syndrome, as well as the relationship between this variant and drug administration. The novel ECG system developed in this study holds promise to greatly accelerate other cardiovascular studies and drug screening using zebrafish.

bioengineering↗