Biology subjects

O'Farrell, A.

Publications and source records attributed to O'Farrell, A..

10 recordsLinked to original sources

bioRxiv2026

Dorsal and ventral premotor cortices differentially influence contralateral motor cortex excitability

Dorsal (PMd) and ventral (PMv) premotor cortices can modulate contralateral primary motor cortex (M1) excitability, but their distinct interhemispheric influence via transcranial magnetic stimulation (TMS) remains unclear. Single-pulse TMS over PMd, PMv and M1 assessed transcallosal inhibition via the ipsilateral silent period (iSP). Dual-site TMS examined short-(10 ms inter-stimulus interval [ISI]), long-(50 ms ISI) and non-callosal-(0 ms ISI) interhemispheric inhibition (IHI). An iSP was elicited from PMd, PMv, and M1, with distinctly evoked iSP parameters. The iSP magnitude was greatest from M1, followed by PMd and then PMv, while iSP duration was greatest for M1 and showed no differences between PMd and PMv. Dual-site TMS revealed that PMd and M1 inhibited contralateral M1 excitability across all ISIs, while PMv showed inhibition at 0-and 50-ms ISIs. PMd and M1 demonstrated greater short-IHI compared to PMv, all demonstrating similar long-IHI, and PMd demonstrating greater non-callosal-IHI than M1. PMv displayed distinct IHI across ISIs, PMd showed differences across most ISIs and M1 demonstrated the fewest differences across ISIs. Longer iSP duration related to greater long-IHI magnitude elicited from PMd and PMv. Our findings demonstrate differential IHI from PMd and PMv on contralateral M1, which may inform neuromodulation strategies in rehabilitation contexts.

neuroscience↗

bioRxiv2026

Environmental Amino Acid Sensing Regulates the Rate of ASC Translation and NLRP3 Inflammasome Assembly

The NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) inflammasome is a multiprotein signaling complex that triggers pyroptotic cell death and interleukin (IL)-1 family cytokine release during infection and cell injury. Its assembly is driven by the adaptor protein, apoptosis-associated speck-like protein containing a CARD (ASC), whose filamentation forms a supramolecular speck upon NLRP3 activation to amplify inflammasome signaling. While the NLRP3 inflammasome is well appreciated as a sensor of environmental danger and damage, little is known about how homeostatic environmental factors like dietary metabolites regulate its activity. Here, we find that environmental availability of the branched-chain amino acids (BCAAs), leucine, isoleucine, and valine, controls NLRP3 inflammasome assembly. While ASC is typically viewed as a constitutively expressed, unregulated inflammasome component, we find that Toll-like receptor 4 (TLR4) activation triggers localization of ASC mRNA to the perinuclear space. Moreover, our data demonstrate that ASC undergoes TLR4-driven translational bursting from polyribosomes during inflammasome priming. This translational engagement is dependent on BCAA availability and mechanistic target of rapamycin (mTOR) activity, which regulate the kinetics of inflammasome assembly. In contrast, the translation of NLRP3 and caspase-1 is largely insensitive to these inputs. Furthermore, we find that BCAAs regulate NLRP3 inflammasome activation in both mouse and human macrophages, in the context of bacterial infection, and during lipopolysaccharide (LPS)-induced sepsis in vivo. Altogether, this work unveils a novel inflammasome priming event governed by the amino acid environment. These findings further highlight how the activity of proteins maintained in equilibrium like ASC can be dynamically regulated through rapid changes in mRNA translation.

immunology↗

bioRxiv2025

Distinct Motor Cortex Interneuron Plasticity and Its Association with Prefrontal Brain Volume in Parkinson's Disease

Parkinsons disease (PD) is characterized by motor and cognitive deficits, including abnormal primary motor cortex (M1) excitability and diminished sensorimotor neuroplasticity. While paired associative stimulation (PAS) can induce M1 plasticity, people with PD (PwPD) demonstrate variability that cannot be accounted for by disease progression or medication status. Distinct M1 interneuron populations and attention-related brain structures may influence the reduced PAS- induced neuroplasticity. We aimed to characterize M1 interneuron plasticity in PwPD using attention-modulated PAS and identify neurostructural correlates. PwPD underwent MRI, then a PAS protocol with task-relevant attention. Transcranial magnetic stimulation (TMS) assessments of corticospinal excitability using posterior-to-anterior (PA) and anterior-to-posterior (AP) current directions were employed before and three post-PAS time-points. PAS induced distinct time- dependent M1 interneuron excitability changes. PA TMS showed increased corticospinal excitability at all post-PAS time-points; AP TMS increased only at 30 minutes. Rostral middle frontal gyrus volume uniquely explained variance in PA-sensitive M1 interneuron plasticity. In contrast, AP-sensitive plasticity was associated with baseline AP TMS excitability and age. These findings highlight that M1 interneuron circuits show unique neuroplasticity patterns in PwPD and relate to prefrontal brain volume. Our results suggest a complex interplay between motor and cognition-related deficits as interrelated pathophysiological features in PD.

neuroscience↗

bioRxiv2025

Physical exercise and motor learning: A scoping review

Physical exercise can enhance motor learning by inducing neurophysiological changes that facilitate this process. This preregistered scoping review aimed to map current knowledge on the effects of physical exercise on motor learning. Experimental studies and review articles examining any form of physical exercise in healthy or clinical populations were included, with outcomes assessing motor skill acquisition and/or retention. A systematic search across eight databases (e.g., MEDLINE, EMBASE, PsychINFO) identified 66 sources, including 62 experimental studies and 4 reviews. Two researchers independently reviewed articles and extracted data using a pretested data extraction table; disagreements at the study selection or data extraction stages were resolved through discussion with a third researcher. Most studies involved healthy populations (83%), with clinical populations underrepresented (17%). Aerobic exercise was most commonly investigated, particularly lower-limb cycling (73%), while resistance exercise was rarely examined (0.6%). Exercise intensity was predominantly high, although 6% of studies reported intensity not reflecting the prescribed method. Motor learning outcomes varied: 55% assessed both skill acquisition and retention, while 45% relied on retention tests alone at short-term or delayed time points, or both. Infrequent use of long-term retention tests limits understanding of lasting effects. Overall, this review highlights gaps in the literature, including the underrepresentation of clinical populations, inconsistent reporting of exercise intensity, scarce research on resistance exercise, and limited assessment of long-term retention, which may affect interpretation of exercises impact on motor learning. HighlightsO_LIClinical populations were underrepresented in the exercise and motor learning field. C_LIO_LIHigh-intensity lower-limb cycling was the most common exercise studied. C_LIO_LIResistance exercise was underrepresented in the field. C_LIO_LIAccurate prescription of exercise intensity is essential to ensure reliable results. C_LIO_LIFuture research should more frequently use longer-term retention tests. C_LI

neuroscience↗

bioRxiv2025

Eccentric cycling enhances primary motor cortex excitability

Acute aerobic exercise (AAE) can modulate primary motor cortex (M1) excitability. To date, studies evaluating its effects have focused almost exclusively on concentric cycling. Critically, we found that eccentric AAE enhances motor learning more than concentric AAE, possibly explained by enhanced frontal-parietal brain activation during eccentric cycling. Yet, M1 excitability mechanisms underlying this eccentric AAE-enhanced motor learning remain unknown. Thus, this study aimed to evaluate the effect of eccentric cycling AAE on M1 excitability using transcranial magnetic stimulation (TMS). Thirty adults performed three 20 min-conditions: i) eccentric cycling AAE, ii) concentric cycling AAE, and iii) rest. Cycling AAE was carried out at a workload corresponding to 70% of peak heart rate (%HRpeak) measured during concentric incremental cycling exercise. TMS assessments were conducted before (Pre), immediately (Post0) and 20 minutes after (Post20) AAE/rest to evaluate changes in corticospinal excitability (CSE) and short-interval intracortical inhibition (SICI). Overall, we found CSE increased and intracortical inhibition (SICI) was reduced at Post20 to a comparable extent following eccentric and concentric cycling AAE compared to rest. Also, %HRpeak, muscle pain and perceived effort were lower during eccentric cycling AAE compared to concentric cycling AAE. Our results showed that eccentric cycling impacted M1 excitability change to a comparable degree as concentric cycling, while requiring less cardiovascular response, eliciting less muscle pain and lower perceived effort. Taken together, our results suggest that eccentric cycling AAE may be a valuable intervention to modulate M1 excitability for populations with limited cardiovascular capacity and may have potential implications in clinical and sports-related contexts.

neuroscience↗

bioRxiv2025

Lineage memory shapes viral resistance barriers in human skin

Individual cells within a given population exhibit striking variability in viral susceptibility, but it remains unknown whether this heterogeneity reflects memories encoded into the cellular lineage or true probabilistic variability. We used multi-color lineage tracing in a human primary organotypic skin model to reveal that viral resistance is encoded within specific cellular lineages. These lineages create distinct boundaries that block viral spread. Our lineage analyses in vitro confirmed that viral susceptibility exhibits strong heritability across cell generations, with siblings and cousins displaying remarkably similar infection outcomes. ATAC and proteomics profiling of resistant and susceptible clones revealed distinct epigenomic and proteomic states, with the transcription factor AP-1 emerging as a potential central regulator of lineage-encoded viral resistance. Inducing AP-1 activity with PMA rendered cells resistant to viral infection, suggesting a causative role in mediating resistance memory. Our findings demonstrate that antiviral resistance in human skin cells is encoded within cellular lineages and preserved through cell divisions, revealing how cell memory may shape infection dynamics and viral containment in tissues.

bioengineering↗

bioRxiv2025

Innate Immune Memory is Stimulus Specific

Innate immune memory (also termed trained immunity) is defined in part by its ability to cross-protect against heterologous pathogens, and can be generated by many different stimuli, suggesting a "universal" trained state. However, different stimuli could form distinct memories, leading to stimulus-specific trained responses. Here, we use primary human monocyte-derived macrophages to demonstrate phenotypic and epigenetic stimulus specificity of innate immune memory six days after initial exposure. Quantification of cytokine production with single-molecule RNA imaging demonstrates stimulus-specific patterns of response to restimulation at the single cell level. Differential licensing of inflammatory transcription factors is associated with encoding of specificities in chromatin. Trained cells show stronger responses to secondary stimuli that are more similar to the initial stimulus they experienced, suggesting a functional role for these stimulus-specific memories. Rather than activating a universal training state, our findings demonstrate that different stimuli impart specific memories that generate distinct training phenotypes in macrophages.

immunology↗

bioRxiv2024

AP-1 Mediates Cellular Adaptation and Memory Formation During Therapy Resistance

Cellular responses to environmental stimuli are typically thought to be governed by genetically encoded programs. We demonstrate that melanoma cells can form and maintain cellular memories during the acquisition of therapy resistance that exhibit characteristics of cellular learning and are dependent on the transcription factor AP-1. We show that cells exposed to a low dose of therapy adapt to become resistant to a high dose, demonstrating that resistance was not purely selective. The application of therapy itself results in the encoding of transient gene expression into cellular memory and that this encoding occurs for both transiently induced and probabilistically arising expression. Chromatin accessibility showed concomitant persistence. A two-color AP-1 reporter system showed that these memories are encoded in cis, constituting an example of activating cis epigenetics. Our findings establish the formation and maintenance of cellular memories as a critical aspect of gene regulation during the development of therapy resistance.

systems biology↗

bioRxiv2024

Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning

Single-molecule RNA fluorescence in situ hybridization (RNA FISH)-based spatial transcriptomics methods have enabled the accurate quantification of gene expression at single-cell resolution by visualizing transcripts as diffraction-limited spots. While these methods generally scale to large samples, image analysis remains challenging, often requiring manual parameter tuning. We present Piscis, a fully automatic deep learning algorithm for spot detection trained using a novel loss function, the SmoothF1 loss, that approximates the F1 score to directly penalize false positives and false negatives but remains differentiable and hence usable for training by deep learning approaches. Piscis was trained and tested on a diverse dataset composed of 358 manually annotated experimental RNA FISH images representing multiple cell types and 240 additional synthetic images. Piscis outperforms other state-of-the-art spot detection methods, enabling accurate, high-throughput analysis of RNA FISH-derived imaging data without the need for manual parameter tuning.

bioinformatics↗

bioRxiv2022

Lymphatic-Preserving Treatment Sequencing with Immune Checkpoint Inhibition Unleashes cDC1-Dependent Antitumor Immunity in HNSCC

Immune checkpoint inhibition (ICI) with anti-CTLA-4 and anti-PD-1 has revolutionized oncology; however, response rates remain limited in most cancer types, highlighting the need for more effective immune oncology (IO) treatment strategies. Paradoxically, head and neck squamous cell carcinoma (HNSCC), which bears a mutational burden and immune infiltrate commensurate with cancers that respond robustly to ICI, has demonstrated no response to anti- CTLA-4 in any setting or to anti-PD-1 for locally-advanced disease. Scrutiny of the landmark clinical trials defining current IO treatments in HNSCC reveals that recruited patients necessarily received regional ablative therapies per standard of care, prompting us to hypothesize that standard therapies, which by design ablate locoregional lymphatics, may compromise host immunity and the tumor response to ICI. To address this, we employed tobacco-signature HNSCC murine models in which we mapped tumor-draining lymphatics and developed models for regional lymphablation with surgery or radiation. Remarkably, we found that lymphablation eliminates the tumor ICI response, significantly worsening overall survival and repolarizing the tumor- and peripheral-immune compartments. Mechanistically, within tumor-draining lymphatics, we observed an upregulation of cDC1 cells and IFN-I signaling, showed that both are necessary for the ICI response and lost with lymphablation. Ultimately, we defined rational IO sequences that mobilize peripheral immunity, achieve optimal tumor responses, confer durable immunity and control regional lymphatic metastasis. In sum, we provide a mechanistic understanding of how standard regional, lymphablative therapies impact the response to ICI, which affords insights that can be applied to define rational, lymphatic-preserving IO treatment sequences for cancer. One Sentence SummaryDespite the promise of immune checkpoint inhibition, therapeutic responses remain limited, raising the possibility that standard of care treatments delivered in concert may compromise the tumor response; here, we provide a mechanistic understanding of how standard oncologic therapies targeting regional lymphatics impact the tumor response to immune-oncology therapy in order to define rational treatment sequences that mobilize systemic antitumor immunity, achieve optimal tumor responses, confer durable antitumor immunity, and control regional metastatic disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/478744v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@542d71org.highwire.dtl.DTLVardef@737ad0org.highwire.dtl.DTLVardef@183f519org.highwire.dtl.DTLVardef@505ce2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗