Biology subjects

Lim, S.

Publications and source records attributed to Lim, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Genomic Prediction and SNP Importance Analysis for Agronomic Traits in Two Coffea canephora Populations

This study reveals that distinct breeding populations of Coffea canephora can achieve agronomic success through fundamentally different biological strategies. To uncover this, we performed a comparative genomic analysis of two populations ( Premature and Intermediate), integrating single-SNP association, machine learning (Bootstrap Forest), and Gene Ontology (GO) pathway analysis. The genetic architecture of the Premature population was linked to specialized metabolic pathways, including lipid modification and processes within the organelle lumen, a finding supported by the identification of a putative caffeine synthase 3 gene. In contrast, traits in the Intermediate population were governed by variation in core cellular machinery, with significant enrichment for pathways related to actin cytoskeleton regulation and salicylic acid signaling. This discovery provides a new biological context for important candidate genes involved in disease resistance (e.g., RPP13-like, NB-ARC, CERK1). These findings demonstrate that population-specific biological routes underpin agronomic performance, providing a powerful foundation for designing more targeted breeding programs in coffee. We release population-specific, ranked SNP lists and GO gene sets as a reusable resource to enable meta-analyses and benchmarking in coffee and perennial crops.

genetics↗

bioRxiv2025

Circadian phosphotimer generates time cues through PER dimerization-mediated trans-phosphorylation

The circadian clock generates autonomous molecular rhythms that regulate sleep cycles, chronotypes, daily physiology, and expression patterns of almost the entire genome. Temporal phosphorylation of PERIOD (PER) proteins creates a phosphotimer that is critical for clock function. Although previous studies show that PER stably binds the casein kinase CK1, cis-acting phosphorylation of PER by CK1 is not compatible with slow PER phosphorylation extended over 24 hrs. So how can PER phosphorylation be programmed in a slow and controlled manner? Here, we show that the timing cues are encoded by PER-PER dimerization-mediated trans-phosphorylation, which enables the necessary time delay in phosphorylation and slow phosphorylation. When PER dimerization is disrupted, PER phosphorylation and circadian rhythms are severely compromised. In mouse models with point mutations in the PER dimerization domain, circadian period is shortened to [~]20 hrs, and the phase of wake/sleep cycles is dramatically advanced, switching a nocturnal animal to a half diurnal animal.

neuroscience↗

bioRxiv2025

Speaker responses to audience-induced social-evaluative threat: Evidence from scientific presentation tasks in immersive virtual reality

Success in public speaking hinges on engaging an audience - a high-stakes social interaction that remains a significant source of anxiety and stress for many. Using a virtual-reality (VR) paradigm, we tested how speakers delivering scientific talks perceive and respond to supportive vs. unsupportive audiences. We collected behavioral (eye contact, speech rate, motion expressiveness/openness), physiological (heart rate, EEG, breathing rate, pupil dilation), and self-report measures to assess audience effects. The unsupportive audience elicited greater negative affect, arousal, and anxiety, and higher perceived cognitive and social effort. Physiologically and behaviorally, speaking to the unsupportive audience slowed the speaking rate, and acoustic analyses further indicated greater emotional arousal and vocal dominance in the unsupportive condition. Finally, VR exposure reduced speaking anxiety overall. These findings highlight VR combined with physiological measurement as a powerful approach for investigating audience effects and social-communication processes, with clear implications for augmenting social intelligence and communication skills.

scientific communication and education↗

bioRxiv2025

Output-Contingent Working Memory and Decision-Making in Economic Choices

In daily life, economic decisions often unfold sequentially. The brain is thought to compute the subjective value of each option, and comparisons can occur in different reference frames, for example, based on the commodity or presentation order. While primate prefrontal recordings have identified various reference frames for economic choice, it remains unclear how distinct neural mechanisms support them even in similar tasks. To address this, we trained recurrent neural networks (RNNs) on two sequential economic decision-making tasks differing only in output contingencies. Analysis of RNN activity, combined with latent connectivity inference, revealed distinct regimes: commodity-based choices with attractor dynamics and order-based choices with rotational dynamics. Moreover, value and choice representations in the order-based tasks aligned with neural data from a novel experiment where reference frames were not explicitly constrained. Our results suggest that different reference frames emerge depending on task demands and engage distinct working memory and decision-making mechanisms.

neuroscience↗

bioRxiv2025

Angulin-1/LSR inhibition transiently disrupts the blood-tumor barrier to enhance doxil permeability and impair malignant glioma progression

The blood-tumor barrier (BTB) prevents effective central nervous system (CNS) drug delivery, especially in malignant gliomas. Brain endothelium predominates the BTB and connects through bicellular and tricellular tight junctions (TJ). Angulin-1/LSR, is a highly expressed endothelial tricellular TJ. Our studies explore the role of Angubindin-1, an Angulin-1/LSR binder, to disrupt tricellular TJ integrity, increase drug entry and hamper glioma progression. Using rat brain endothelial cells (RBMVEC) we tracked Angulin-1/LSR localization and expression to the membrane; binding tightest to Angubindin-1 2-8 hours post-treatment (p < 0.05). Angubindin-1 dose-dependently reduced bicellular and tricellular TJs 1-4 hours post treatment (p < 0.05), returning to baseline by 24 hours (p < 0.05). In human and rat-derived glioma cells, Angubindin-1 transiently reduced Angulin-1/LSR expression between 2-8 hours (p < 0.05), with return to baseline by 24 hours (p < 0.001). Silenced Angulin-1/LSR expression on endothelium resulted in decreased mRNA levels of bicellular (occludin, claudin-5, ZO-1) and tricellular (tricellulin/MARVELD2, angulin-1/LSR) TJs compared to control (p < 0.01). Angubindin-1 treatment also inhibited efflux transporter P-gp in both RBMVECs and glioma cells with high P-gp expression only. Orthotopic rat glioma models were treated with Doxil (3 mg/kg), Angubindin-1 (10 mg/kg), or combination to evaluate BTB permeability/drug accumulation, and overall survival. Combination therapy enhanced Doxil tumor accumulation by 20% (p < 0.001), reduced tumor volume by day 14 (77.5% vs. 81.6%, p < 0.05), and significantly extended survival compared to Doxil alone (24 days vs. 18 days, p < 0.0001). These findings demonstrate the effects of tricellular tight junction inhibition on disrupting the BTB, enhancing CNS drug delivery, and improving rodent glioma survival. SignificanceThis study demonstrates that Angubindin-1, a targeted modulator of tricellular tight junction protein Angulin-1/LSR, transiently disrupts BTB integrity to enhance chemotherapy delivery and prolong survival in glioma-bearing rats. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/667901v1_ufig1.gif" ALT="Figure 1"> View larger version (76K): org.highwire.dtl.DTLVardef@b1b46corg.highwire.dtl.DTLVardef@bc552dorg.highwire.dtl.DTLVardef@7c1a74org.highwire.dtl.DTLVardef@1ace101_HPS_FORMAT_FIGEXP M_FIG C_FIG Angubindin-1 targets both bicellular tight junctions and the tricellular tight junction protein, Angulin-1/LSR, in brain endothelial and glioma cells leading to transient disruption of the blood-tumor barrier (BTB) and inhibition of P-glycoprotein towards enhanced Doxil penetration and reduced tumor burden.

cell biology↗

bioRxiv2025

PathCLAST: Pathway-Augmented Contrastive Learning with Attention for Spatial Transcriptomics

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSMotivationC_ST_ABSSpatial transcriptomics provides high-resolution insights into tissue architecture and disease progression. While recent computational methods have advanced spatial domain identification, many focus primarily on gene expression alone, which may limit biological interpretability and underexploit complementary data such as histological images and known gene-pathway associations. ResultsWe present PathCLAST (Pathway-Augmented Contrastive Learning with Attention for Spatial Transcriptomics), a novel framework that integrates gene expression, histopathological image features, and curated pathway graphs through a contrastive learning strategy. By embedding gene expression within biologically grounded pathway-level graphs and aligning them with histological features, PathCLAST enhances spatial domain resolution and provides interpretable attention scores over functional pathways. Across three benchmark datasets, PathCLAST consistently outperforms existing methods in clustering accuracy-achieving a 37% improvement over STAGATE on the IDC dataset and uncovers domain-specific signaling programs and spatial heterogeneity. Additional analyses of spatial autocorrelation and inter-domain crosstalk demonstrate its potential to reveal localized biological processes and tumor microenvironmental dynamics. Our code is available at the following link: https://github.com/sslim-aidrug/PathCLAST.

bioinformatics↗

bioRxiv2025

Deep sea anaerobic microbial community couples the degradation of insoluble chitin to extracellular electron transfer

Chitin is a major structural component of arthropod exoskeletons, and an important carbon and nitrogen source in marine environments. In anoxic sediments, its degradation generates chitooligosaccharides and N-acetylglucosamine (GlcNAc), which are fermented into smaller organic molecules and oxidized anaerobically using soluble electron acceptors or insoluble ones such as metal oxides. To date, many aspects of chitin degradation in deep-sea anoxic sediments have been overlooked, including the potential coupling of insoluble chitin degradation to metal oxide reduction, the involvement of extracellular electron transfer (EET), and the spatial organization of the microorganisms involved. Using anoxic deep-sea sediments recovered from a whale fall site, we developed an innovative workflow based on electrochemical reactors, to characterize chitin degradation in these environments. Sediment samples enriched on poorly crystalline iron oxides, and subsequently transferred into an electrochemical reactor poised at +0.22 V vs SHE, showed active anodic current production when supplied with chitin, which increased 2-fold when amended with GlcNAc. Chitin reactors were dominated by Vallitalea (Firmicutes), Spirochaetota, Gammaproteobacteria and Desulfobacterota. Exoenzyme activity assays, metabolite profiling, and continued anodic current production confirmed ongoing chitin degradation linked to EET. We observed metabolic associations between chitin degraders and secondary consumers using in situ imaging (16S rRNA gene FISH coupled with BONCAT and nanoSIMS). These microbial partners, within the electrode-attached community, required close proximity to the poised electrode ([≤] 10 {micro}m) to remain metabolically active. Supporting these observations, cultured isolates of Vallitalea sp. and Trichloromonas sp. recovered from the whale fall site exhibited chitin degradation and electrochemical activity, respectively. When co-cultured in an bioelectrochemical reactor, the acetate produced by Vallitalea sp. during chitin degradation fueled Trichloromonas sp., which facilitated EET, hereby demonstrating that syntrophic interactions are used to couple anoxic chitin degradation to EET in deep-sea sediments. These findings exemplify the interspecies interactions and resource optimization occurring in hard-to-reach and largely unknown deep-sea ecosystems.

microbiology↗

bioRxiv2025

Unveiling differential responses to UVB (305 nm) and UVC (275 nm) in cacao-infecting Colletotrichum gloeosporioides and Pestalotiopsis sp.

Sustainable control of microbial pathogens requires alternatives to chemicals, but physical methods like Ultraviolet-C (UVC) show variable efficacy linked to poorly understood pathogen-specific responses. Here, we investigate differential UVB/UVC responses in plant pathogenic fungi (Colletotrichum gloeosporioides, Pestalotiopsis sp.). Using hyperspectral imaging and machine learning, we dissect the physiological underpinnings of UV sensitivity. UVC proves more potent than UVB, with Pestalotiopsis sp. showing significantly higher resistance than C. gloeosporioides isolates. Crucially, hyperspectral signatures correlated with resistance, revealing UVC-induced photopigment changes, biochemical disruption, and oxidative stress markers in sensitive isolates, contrasting with minimal perturbation in the resistant isolate. Machine learning accurately decoded these complex phenotypes for classification. This understanding enabled enhanced inactivation via optimized pulsed UVC and synergistic sonication. We link distinct physiological states, non-invasively detected via hyperspectral imaging, to fungal UV resistance, demonstrating how integrating advanced phenotyping and machine learning provides a mechanistic basis for optimizing physical pathogen controls.

microbiology↗

bioRxiv2025

Genome-wide association mapping and predictive modeling of wet bean mass in a diverse cacao collection

Improving cacao yield, a key objective in post-domestication crop improvement, remains a primary goal for breeders, but progress is often hindered by the confounding effects of population structure. To overcome this, we analyzed 346 diverse cacao accessions using an ML-based association mapping framework (with and without population structure adjustment) and a phenotype-only ML prediction of yield. By correcting for population structure, our Bootstrap Forest-based GWAS revealed association signals that showed consistent enrichment for ribosome and protein-synthesis functions, and a recurrent subset of SNPs with high importance appeared across multiple yield components, including pod index and seed number. In parallel, a Neural Network model was utilized to identify cotyledon mass and length as the most powerful predictors for total wet bean mass (R{superscript 2} = 0.715 by repeated five-fold cross-validation), suggesting a practical, low-cost screening proxy for breeding). Collectively, this study delivers a robust genetic framework and a novel predictive tool to accelerate the development of high-yielding cacao varieties through the early identification of elite clones.

genomics↗

bioRxiv2025

Loss of tomato geranylgeranyl diphosphate synthase 2 increases monoterpenoid levels and enhances immune responses to bacterial infection

Many plastidial isoprenoids, including diterpenes and photosynthesis-related isoprenoids such as carotenoids and chlorophylls, derive from C20 geranylgeranyl diphosphate (GGPP), produced by GGPP synthase (GGPPS) enzymes. Heterodimers of GGPPS and non-catalytic type I small subunit (SSU-I) proteins produce C10 geranyl diphosphate (GPP), the precursor of monoterpenes. Three plastidial GGPPS isoforms, referred to as SlG1-3, are present in tomato (Solanum lycopersicum). Here we explored their contribution to the production of volatile organic compounds (VOCs) of isoprenoid origin under normal conditions and in response to infection with Pseudomonas syringae pathovar tomato (Pst). Edited lines lacking SlG2 showed a distinctive VOC profile compared to unedited (WT) plants and mutants impaired in SlG1 or SlG3. In particular, only slg2 mutants showed constitutively increased levels of GPP-derived hydroxylated monoterpenes (HMTPs). Upon Pst infection, slg2 plants accumulated higher levels of salicylic acid (SA) and exhibited increase resistance compared to WT controls, resulting in reduced levels of VOCs associated to cell death. Our findings suggest that SlG2 regulates GPP synthesis, potentially by specifically competing with other GGPPS isoforms for heterodimerization with SSU-I. Increased GPP production in slg2 plants could lead to higher HMTPs levels, which may result in elevated SA content, and subsequently enhanced protection against bacterial infection.

plant biology↗

bioRxiv2025

National Scale Genomic Engine for Precision Medicine: Singapore PRECISE-SG100K Experience

The whole-of-nation National Precision Medicine (NPM) programme in Singapore aims to integrate a genomics backbone into standard healthcare. Phase II recently completed the sequencing of 102,202 genomes from the diverse Asian population of Singapore, generating the PRECISE-SG100K dataset. The scaling from the pilot SG10K_Health phase to national production scale demanded a central shift: from earlier generation workflows to an integrated, industrial grade "Genomic Engine". The initiative was co-developed under a public-private partnership model. Our Genomic Engine was designed with an automation-first approach, as a modular platform linking a purpose-built, centralized biospecimen processing and DNA extraction facility (EXTRACT Lab), a high-throughput sequencing operation (Illumina Data Generation Infrastructure, IDGI), with the cloud-native analytics (GRIDS) running on a fully integrated PRECISE Sample Tracking System (STS). Here we describe the key design features of our Genomic Engine. Highlighting the Stress Test phase where the automated DNA extraction yields failed to meet expectations. We share the operational adjustments which were implemented to stabilize production and resulted in a three-fold reduction in sample triage due to improved DNA recovery. Without establishing the operational guardrails during the Stress Test, the Engine would not have reached a steady-state production evidenced by >3,000 genomes per month, median turnaround time 11 days, 99.6% operational success, within in six months. This framework offers a practical blueprint for other population-scale initiatives seeking to bridge the gap between scientific piloting and industrial delivery.

genomics↗

bioRxiv2025

Memory Inception through Gaze-Contingent Message Exposure: Using Virtual Reality to Study Media Influence

The messages we encounter in our environment can shape our knowledge about the world. However, much research on mediadriven influence via messages focuses on population-level effects and aggregate exposure statistics, obscuring how individual and self-determined behaviors affect message intake, processing, and effects. To address this gap, we use virtual reality (VR) to create a controlled messaging environment. Participants navigate a simulated urban street lined with billboard messages while their visual attention is tracked via eye-tracking. We introduce an inception-style manipulation: overlooked billboards are strategically reintroduced, creating additional exposure opportunities. Our results demonstrate that this subtle manipulation - unnoticed by participants - boosts message retention. This study bridges communication theory and psychology, elucidating the blurred line between voluntary and involuntary information intake in the digital age. It also highlights a potential vulnerability in the future metaverse media ecosystem, where undetected information manipulations can influence individual and collective attention and memories.

animal behavior and cognition↗

bioRxiv2025

Characterization of Clinical Fusobacterium nucleatum Isolates from Oral Squamous Cell Carcinoma Patients

Fusobacterium nucleatum (Fn), a Gram-negative anaerobe primarily residing in the oral cavity, has garnered increasing attention for its role in a broad spectrum of human diseases. While typically absent or rarely detected outside the oral cavity in healthy individuals, Fn is frequently found at extra-oral sites under disease conditions and has been implicated in cancer progression and prognosis1. In oral squamous cell carcinoma (OSCC), the abundance of Fn significantly increases as the disease progresses, promoting cell invasion and metastasis. Furthermore, substantial evidence links Fn to accelerated tumor growth and metastatic progression in colorectal cancer (CRC), where its presence is also associated with chemotherapy resistance and poor prognosis. Here, to further elucidate the pathogenic mechanisms of Fn in cancer progression, this study characterized the physiological traits, virulence factor expression, and impacts on cancer cells of 10 Fn strains, including two well-characterized ATCC strains and eight clinical isolates. The clinical isolates consisted of three strains from saliva samples of 117 OSCC patients and five strains from 160 non-cancer individuals. Results indicated that oral isolates, regardless of disease origin, all belong to Fn subspecies polymorphum. The ATCC strains (23726 and 25586) exhibited shorter cell lengths and faster growth rates compared to the clinical isolates. Both ATCC strains formed stable biofilms and expressed key virulence genes, including aim1, fadA, fomA, and radD. All isolates tested showed sensitivity to a panel of eight different antibiotics. Interestingly, only one clinical isolate displayed similar stimulation of CRC cell migration as the two ATCC strains, while the other seven displayed no such ability. Collectively, these findings suggest that the most virulent strains, in terms of biofilm formation and virulence gene expression, are not necessarily the most pathogenic in the context of cancer cell interactions. Future pan-genomic analyses, incorporating whole-genome sequencing of the clinical isolates, will aim to delineate the genetic determinants contributing to the carcinogenic potential of Fn.

microbiology↗

bioRxiv2024

A Co-essentiality Network of Cancer Driver Genes Better Prioritizes Anticancer Drugs

Diverse molecular networks have been extensively studied to discover therapeutic targets and repurpose approved drugs. However, it is necessary to select a suitable network since the performance of network medicine relies heavily on the completeness and characteristics of the selected network. Although a network using gene essentiality from cancer cells could be an effective platform for identifying anticancer targets, efforts to apply these networks in therapeutic applications have been limited. We constructed a phenotype-level network using the co-essentiality relationship between genes in CRISPR screens across 769 cancer cells to discover therapeutic targets for diverse cancer types. Leveraging cancer driver genes and network propagation on the networks, we found that the co-essentiality network better prioritized anticancer targets and biomarkers and predicted more precise drug responses in cancer cells than other molecular networks. The co-essentiality network outperformed conventional molecular networks in drug repurposing, which were validated in silico by clinical trial records. Notably, the co-essentiality network provided 37 repurposed drugs that the other networks have yet to cover, and we showcased three approved drugs repurposed for lung adenocarcinoma (Pioglitazone hydrochloride, Atovaquone, and Eflornithine). Our study provides a novel network for precision oncology to improve the identification of therapeutic targets in specific cancers.

bioinformatics↗

bioRxiv2024

FAK activity exacerbates disturbed flow-mediated atherosclerosis via VEGFR2-Cbl-NF-κB signaling.

Atherosclerosis develops at predictable sites in the vasculature where branch points and curvatures create non-laminar disturbed flow. This disturbed flow causes vascular inflammation by increased endothelial cell (EC) barrier permeability and the expression of inflammatory genes such as vascular cell adhesion molecule-1 (VCAM-1). Vascular endothelial growth factor receptor 2 (VEGFR2) is important for flow-induced EC inflammation; however, there are still some gaps in the signaling pathway. Focal adhesion kinase (FAK) is a protein tyrosine kinase whose expression has been implicated in flow-mediated signaling in ECs. However, the link between FAK and VEGFR2 in flow-mediated inflammation signaling has remained unelucidated. Here we found that priming of VEGFR2 with VEGF was critical for flow-mediated activation of FAK and NF-kB. Mechanistically, FAK activation triggers tyrosine phosphorylation of Casitas B-lineage lymphoma (CBL; an E3 ubiquitin ligase) that interacts with VEGFR2 under flow conditions. Further, Apoe-/- mice fed a western diet (WD) exhibited increased FAK activity within the atheroprone disturbed flow region of the inner aortic arch compared to the outer arch. Disturbed flow-induced FAK activation is associated with elevated VEGFR2 on the surface of ECs of the inner aortic arch, but not in the outer arch. Taken together, these data suggest that suppression of augmented FAK activity under disturbed flow may prove beneficial in reducing pro-inflammatory signaling of the endothelial layer.

cell biology↗

bioRxiv2024

FAK inhibition suppresses breast cancer progression via DNA methylation-mediated DAB2 gene reactivation

Epigenetic silencing of tumor suppressor genes is one of the main drivers of tumor progression. Without these tumor suppressors to reduce proliferation, tumor cells proliferate unchecked. Focal adhesion kinase (FAK) is a tyrosine kinase which is often upregulated in various tumors and promotes cell proliferation and migration. Recent studies have demonstrated that pharmacological or genetic FAK inhibition can reduce suppressive DNA methylation in vascular cells. Mechanistically, this is through nuclear FAK-mediated ubiquitination and proteasomal degradation of DNA methyltransferase 3A (DNMT3A). Treatment of breast cancer cell lines with FAK inhibitor (FAK-I) was able to reduce both FAK activity and DNMT3A protein expression. Further, global DNA methylation was reduced in breast cancer cell lines treated with FAK-I. This decrease in DNA methylation was correlated with decreased cell proliferation. We further showed that FAK-I reduced DNMT3A expression in breast cancer cells and that treatment with the proteasome inhibitor MG132 prevented loss of DNTM3A protein stability. To identify how FAK-I and DNMT3A loss could reduce breast cancer cell growth we compared RNA sequencing data from breast cancer cells treated with or without FAK-I or in shRNA DNMT3A knockdown. We have identified a potential tumor suppressor, DAB2, as being regulated by the nuclear FAK-DNMT3A axis. DAB2 is often downregulated in cancers and has been shown to play a vital role in switching TGF{beta} signaling from proliferative to apoptotic by altering TGF{beta}RI binding partners. Immunoblotting and immunostaining indeed revealed that FAK-I and shDNMT3A could induce DAB2 protein expression. Further, FAK-I treatment showed efficacy in reducing tumor growth in vivo using the murine 4T1 tumor model. Immunostaining of 4T1 tumors showed FAK-I decreased DNMT3A, DNA methylation (5-methylcytosine, 5-mC), and increased DAB2 expression. Taken together, these data suggest that nuclear FAK-mediated regulation of DNMT3A can alter the epigenetic landscape and induce tumor suppressor gene expression.

cancer biology↗

bioRxiv2024

Sensitivity to Vγ9Vδ2TCR T cells is imprinted after single mutations during early oncogenesis

V{gamma}9V{delta}2T cells have the unique ability to recognize a broad range of malignant transformed cells. The tumor targeting event involving BTN2A1 and BTN3A1 dimers on the tumor cell surface is critical, leading to full activation of the TCR. Although the molecular mechanisms governing TCR engagement and T cell activation are well-characterized, the role of V{gamma}9V{delta}2 T cells in cancer immune surveillance remains to be fully elucidated, particularly the mechanisms that enable these cells to discriminate between healthy and malignant cells at an early stage of malignant transformation. We employed two independent, genetically engineered step-wise mutagenesis models of human colorectal and breast cancer that mimic the transformation steps leading to tumor formation. We demonstrate that various single oncogenic mutations introduced into healthy organoids or cells, are sufficient to upregulate surface expressed BTN2A1 and enable V{gamma}9V{delta}2 TCR binding to tumor cells. However, full activation of T cells through a V{gamma}9V{delta}2TCR required additional subsequent phosphorylation of juxtamembrane (JTM) amino acids of BTN3A1, leading to the activating heterodimerization of BTN2A1 and 3A1. Using a protein interactome mapping pipeline, we identified PHLDB2, SYNJ2 and CARMIL1 as key players in controlling these delicate dual surface dynamics of BTN2A1 and 3A1 during early transformation. This mode of action allowed V{gamma}9V{delta}2TCR T cells to control tumors in vitro and in vivo, emphasizing the crucial role of these molecules from early mutagenesis, to advanced cancer stages, and highlighting the therapeutic potential of a V{gamma}9V{delta}2TCR.

cancer biology↗

bioRxiv2024

Prefrontal representations of retrospective spatial working memory in a rodent radial maze task

Working memory is the cognitive capacity for temporarily holding information in mind for processing or use. It has been theorized to depend upon executive and mnemonic subcomponents, although the contextual mapping of these subcomponents is not complete. Perturbations of prefrontal cortex (PFC) delay activity disrupt spatial working memory performance in rodent tasks. However, recordings of unperturbed PFC delay activity do not consistently contain mnemonic representations of spatial information in these tasks, calling into question the role that mnemonic PFC representations play in freely-moving spatial working memory. We hypothesized that increasing task complexity might increase the likelihood of mnemonic PFC representation emergence. We therefore used an automated eight-arm radial maze to implement a novel match-to-sample rodent spatial working memory task with seven options on each trial, and recorded calcium activity in PFC neurons during task performance. We found that the delay-phase activity of PFC neurons indeed contained mnemonic representations of spatial information at the population level. These representations were retrospective rather than prospective, and--surprisingly--were more evident on error trials. Together with previous results, these observations suggest that in freely-moving spatial working memory tasks, PFC mnemonic representations emerge to empower deviation from a routine behavioral strategy. Significance StatementPrefrontal cortex (PFC) activity is necessary for optimal performance of freely-moving spatial working memory tasks in rodents. Despite this, PFC representations of retrospective actions or stimuli--one quintessential working memory hallmark--are only variably observed during task delays, complicating our understanding of the PFCs role in spatial working memory. Here, we examine cellular-resolution PFC activity in a high-optionality match-to-sample radial maze task and find retrospective delay representations. Strikingly, these delay representations are more evident in error trials. This suggests that in the freely-moving context, explicit PFC representations of retrospective information support deviations from an entrained behavioral strategy, rather than equally supporting all spatial working memory-based behavior.

animal behavior and cognition↗