Biology subjects

Ahuja, A.

Publications and source records attributed to Ahuja, A..

18 recordsLinked to original sources

bioRxiv2026

Linking cross-species hemodynamics with neuronal activity in prefrontal cortex during abstract sequence viewing

The ability to identify and predict abstract sequential patterns enables a wide range of complex cognition and behavior, but the mechanisms mediating it remain poorly understood. Lateral prefrontal cortex (LPFC) has been implicated in abstract sequence tracking in both humans and macaques, but it is unclear whether underlying processes are shared across species. Furthermore, most existing evidence relies on hemodynamic responses, which can have variable relationships with neuronal activity in a region. We leverage a combination of human fMRI, monkey fMRI, and monkey electrophysiology to bridge these gaps. We find that humans and non-human primates show functionally homologous hemodynamic activation in LPFC during abstract sequence viewing, and neuronal responses within fMRI-targeted regions in macaques contain information about sensory and abstract variables in parallel. However, neuronal activity does not directly mirror hemodynamic responses, and abstract sequence responses are found both near and far from fMRI peaks. In contrast, distinct dynamics of spiking activity are selectively present near fMRI peaks, suggesting that temporal coordination across neurons may influence hemodynamic activity in prefrontal cortex. Together, these experiments establish a link between human brain activity, macaque fMRI, and single neuron responses, providing a window into the neural processes that mediate abstract sequence detection.

neuroscience↗

bioRxiv2026

LINE-1 transposable element is expressed in Kaposi's sarcoma and regulates gene expression in KSHV-infected cells

Long interspersed nuclear element-1 (LINE-1/L1) retrotransposons are expressed in various human cancers. Kaposis sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposis Sarcoma (KS) and Primary Effusion Lymphoma (PEL), which are characterized by global transcriptional reprogramming. Previously, we have found upregulation of L1 in PEL. Here, we show that knockdown of L1 in PEL cells significantly impaired their proliferation and induced broad transcriptional changes encompassing DNA replication, mitotic progression, and genome maintenance pathways. Analysis of KSHV-infected mouse and human mesenchymal stem cell models revealed that the KS-mimicking microenvironment robustly upregulates L1 expression, with sustained expression observed in KSHV-induced tumor cells even after the loss of the viral episome. Reanalysis of RNA-seq data from KS patient biopsies further showed elevated L1 expression in both endemic and AIDS-associated epidemic KS, with partial reduction following antiretroviral therapy. L1 ORF1p protein expression was confirmed by immunohistochemistry in KS tissues. Reanalysis of the enzymes that can modulate DNA methylation, a process that regulates L1 expression, revealed upregulation of DNMT3A and TET2 in both mouse KSHV tumor models and human KS. Altogether, our findings establish the L1 activation as a hallmark of KSHV-driven oncogenesis.

microbiology↗

bioRxiv2026

EBV Triggers a Distinct Antiviral Response in HMC3 Cells

Epstein-Barr Virus (EBV) is a gamma herpesvirus found in >90% of the world population that is associated with primary central nervous system (CNS) malignancy development in immunocompromised people. To provide mechanistic links between EBV infection and CNS malignancies, we investigated the capacity for EBV particles to suppress anti-tumor immunity in human microglia through a cell line model. With this approach, we exposed HMC3 cells to EBV-derived glycoprotein 350 (GP350), UV-inactivated EBV (UVi-EBV), and lipoteichoic acid (LTA) for up to 72 hours. Acute impacts of EBV particles and glycoprotein on microglial physiology were characterized at various timepoints in this model through measures of cytokine production, mRNA expression, and endocytosis. We found that UVi-EBV exposure significantly suppressed microglial production of anti-tumor interferons (IFNs) and upregulated microglial expression of the proto-oncogenic immediate early genes FOS and EGR1. Notably, there was no impairment of microglial endocytic functions following UVi-EBV stimulation, suggesting a compartmentalized suppression on IFN signaling. Overall, these findings reveal that the EBV-mediated inhibition of microglial IFN production may contribute to CNS malignancies and emphasize the urgency of innovating therapeutic strategies which target EBV to restore microglial anti-tumoral immunity. ImportanceEvidence linking EBV infection with primary CNS lymphomas and leiomyosarcomas are abundant, yet it is unclear whether EBV infection influences the CNS microenvironment and whether these effects then promote tumorigenesis. This study demonstrates evidence for EBV particle exposure to influence microglial immune phenotypes by suppressing IFN production, providing a putative mechanism for EBV virion expression in the CNS to suppress anti-tumoral immunity against EBV+ cancers. These results are particularly relevant to the etiology of EBV+ primary CNS cancers in immunocompromised people, where microglial play a heightened role in protecting the CNS in the absence of adaptive immunity.

microbiology↗

bioRxiv2026

Archaic translation initiation factor eIF5B supports KSHV late lytic replication and viral oncogenesis by mimicking a hypoxic cellular landscape

Kaposis Sarcoma (KS) Herpesvirus (KSHV) is the etiological agent of KS, an AIDS-defining illness. Recent studies have demonstrated that even during normoxic conditions, KSHV facilitates replication by modulating hypoxia-inducible factors (HIFs), creating a hypoxia-like environment that promotes cellular transformation. KSHV lytic viral genes are favored for protein synthesis during infection by upregulating HIF2 and utilizing the hypoxic eIF4E2 translation initiation complex in oxygen-replete conditions. This translation initiation plasticity (TRIP) links viral replication strategies to angiogenic signaling and oncogenicity. However, the molecular basis of this plasticity remains poorly understood. This study reveals that viral inhibition of eukaryotic initiation factor 2 (eIF2) induces the use of another alternative initiation factor, eIF5B, which canonically mediates delivery of initiator methionine-tRNAiMet during hypoxia. We demonstrate through ribosome density fractionation that eIF2 accumulates in translationally inactive monosome fractions while eIF5B redistributes its translation activity toward polysomes during lytic replication. Progressive dependence on eIF5B during KSHV infection was illustrated by impaired late lytic gene expression, diminished virion production, and altered polysome profiles following eIF5B knockdown. Transcriptomic analyses further reveal that the mRNA landscape in KSHV-infected cells depleted of eIF5B mirrors that of uninfected hypoxic cells. Moreover, silencing of eIF5B in a natural infection model reduces both VEGF secretion and anchorage-independent growth--two hallmarks of KSHV viral oncogenicity. These results demonstrate that eIF5B functions as an essential component of alternative translation initiation machinery activated in response to eIF2 inactivation during KSHV lytic replication, emphasizing its key role in viral pathogenesis and its potential as a novel therapeutic target. IMPORTANCEKaposis Sarcoma Herpesvirus (KSHV) is a human cancer virus that causes severe malignancies in immunocompromised individuals, including the blood vessel cancer Kaposis Sarcoma and a highly aggressive body-cavity lymphoma. Although cells mount a response to infection by shutting down global protein synthesis, how viruses like KSHV continue making viral proteins when this cellular machinery is shutdown remains unclear. This study uncovers that KSHV exploits an ancient cellular factor typically used for protein production under low-oxygen conditions. We identify a previously unrecognized role for the translation factor, eIF5B, in supporting KSHV replication and select production of viral proteins during infection. Our work further demonstrates that KSHVs utilization of eIF5B contributes to a hypoxia-like environment during infection, ultimately contributing to cancer-promoting changes within the cell. These findings highlight a new strategy for tumor-virus reprogramming of host cells, opening an avenue for novel therapeutic targets to eliminate virus-associated cancers.

microbiology↗

bioRxiv2026

Consumption of processed foods impairs memory function through dietary advanced glycation end-products

Consumption of processed foods is associated with dementia, obesity, and other negative health outcomes. Sustained heat treatment, a common food processing approach to enhance flavor, induces the chemical Maillard reaction that promotes the formation of dietary advanced glycation end-products (AGEs). The neurocognitive impacts of consuming dietary AGEs are poorly understood. Here we modeled an AGE-rich diet through heat treatment fed to rats during adolescence, a critical period of neural development, to mechanistically evaluate the long-term impact of early life dietary AGEs on behavioral and neural processes. Consuming the AGE-rich diet impaired hippocampal-dependent memory function and altered the gut microbiome without inducing obesity or nonspecific behavioral deficits. AGE-induced memory deficits were coupled with impaired hippocampal glutamatergic synaptic neurotransmission and altered expression in the synapse-pruning complement system. Hippocampal synaptic deficits likely result from direct AGE-complement interactions, as our extended studies reveal competitive antagonist action of AGEs on complement receptors. Memory impairments were prevented by administration of the AGE-inhibitor, alagebrium, and by supplementation with an AGE-inhibiting bacterial taxon, Lactococcus lactis, which was depleted in the heat-treated diet. These findings reveal a functional connection between early life dietary AGEs, the microbiome, and memory impairments, thus illuminating mechanisms through which food processing negatively impacts neurocognition.

neuroscience↗

bioRxiv2025

NF-kB-Dependent Transcriptional Regulation of Piezo1 Mediates Bacterial Clearance on Stiffened Lung

Respiratory pathogens, such as Pseudomonas aeruginosa damage the alveolar-capillary barrier leading to lung injury and stiffness. Lung stiffness is a key macrophage signal for bacterial clearance, but it remains unknown how stiffness-sensing mechanosensitive ion channels in macrophages are regulated during pneumonia. Macrophage Piezo1 is critical to bacterial clearance in experimental pneumonia in vivo; however, identification of putative matrix-derived signals and the mechanism of their effects remain to be determined. To our knowledge, our work is the first to show that during pneumonia, transcription of the mechanosensitive ion channel Piezo1 is increased in macrophages by the NF-{kappa}B transcription factor, p65, through its signaling adaptor protein, MyD88, leading to increased Piezo1 Ca2+ channel activity. Piezo1 mRNA abundance is increased in association with open chromatin at the Piezo1 promoter in macrophages. The enhanced level of Piezo1 increases the abundance of transcription factor EB (Tfeb) resulting in lysosome biogenesis and stiffness-dependent phagolysosome maturation, a critical step for macrophage bacterial clearance. Our data support the mechanism whereby transcription of macrophage Piezo1 is enhanced by p65 to augment bacterial clearance on an injured, stiffened lung matrix during pneumonia. Therefore, Piezo1 is a future therapeutic target against pneumonia-induced lung injury.

immunology↗

bioRxiv2025

The claudin-like molecule CLC-3 regulates neuromuscular function in Caenorhabditis elegans by modulating cholinergic signalling

Cell adhesion molecules (CAMs play important roles in neurons, contributing to nervous system development, synapse formation, and activity-dependent plasticity. Claudins, the cell-adhesion molecules known for their roles at tight junctions in epithelial and endothelial cells, remain underexplored in neurons, particularly in vertebrates. In contrast, emerging studies in Caenorhabditis elegans have begun to reveal neuronal functions of claudin-like proteins. However, a systematic analysis of their neuronal expression has not been performed. We conducted a transcriptional reporter screen of all claudin-like genes in C. elegans and identified several candidates with previously unreported neuronal expression, highlighting a broader role of this family in the nervous system. One candidate, clc-3, showed robust expression in head, tail, and ventral cord neurons, with no detectable expression in non-neuronal tissues. Functional analyses of clc-3 mutants revealed increased body-bend amplitude and elevated evoked postsynaptic currents at the cholinergic neuromuscular synapses. Imaging and molecular interaction studies demonstrated that CLC-3 localises to the presynaptic membranes in cholinergic neurons, where it interacts with the actin-binding protein NAB-1 and regulates cholinergic signalling. This presynaptic role of CLC-3 likely contributes to the regulation of sinusoidal movement in C. elegans. Our findings identify CLC-3 as a neuronally expressed claudin that regulates motor system output by influencing synaptic vesicle organization and illustrate how changes in synaptic organization are coupled to whole-animal behaviour.

neuroscience↗

bioRxiv2025

HIV Infection and Opioid Treatment Enable the Engraftment of Kaposi Sarcoma-like Tumors into Immunocompetent Mice

The Kaposi Sarcoma herpesvirus (KSHV) causes Kaposi sarcoma (KS), primary effusion lymphoma, a lymphoproliferative disease (KSHV-multicentric Castlemans disease), and a cytokine inflammatory syndrome (KICS). These diseases occur more frequently, though not exclusively, among people living with HIV or other types of immune dysregulation. While limited KS can regress with immune reconstitution, such as through antiretroviral therapy (ART) in people living with HIV, there are currently no curative treatments for advanced KS. Preventive or therapeutic vaccines targeting KSHV could have a significant clinical impact; however, the development and testing of such strategies have been limited by the lack of preclinical models that faithfully recapitulate KS, including the presence of infected spindle cells and a relevant immune microenvironment. HIV/AIDS is an important cofactor for KS, and globally, the majority of individuals with KS are HIV-infected. Current evidence indicates that HIV-1 may enable KS progression through immunosuppression and promote pathogenesis by inducing inflammatory cytokines and producing secreted regulatory proteins like Tat and Nef. The design and testing of new therapeutic approaches based on pathogenesis are hampered by the lack of models that replicate KSHV oncogenesis in the context of HIV/AIDS. In the present study, we demonstrate that KSHV-infected cells can form tumors in an immunocompetent mouse model, but only when these mice are pretreated with EcoHIV and morphine, both of which have immunomodulatory and pro-inflammatory effects. These tumors exhibit gene expression profiles and immune microenvironments that closely resemble those observed in human KS lesions. This novel KSHV tumor model in immunocompetent mice provides a valuable platform to test immunotherapeutic strategies for KS, including immunomodulatory agents, targeted antibody therapies, checkpoint inhibitors, and vaccines. Author SummaryKaposi sarcoma (KS) is a cancer caused by the Kaposis sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus 8 (HHV-8). A vaccine against this virus could prevent or cure this malignancy. However, there are no good animal models with an immune system to test new immunization approaches. The possibility of having KSHV-driven tumors develop in immunocompetent mice due to EcoHIV infection presents a unique opportunity to create an AIDS-KS mouse model suitable for testing immune-based therapies and KSHV vaccines in a scenario that replicates important aspects of AIDS-KS. These first-in-kind murine models incorporating a biologically relevant mouse HIV infection tool make our models unique and original, with the potential to provide novel mechanistic and pathobiological insights.

microbiology↗

bioRxiv2024

Monkey lateral prefrontal cortex subregions differentiate between perceptual exposure to visual stimuli

Each day, humans must parse visual stimuli with varying amounts of perceptual experience, ranging from incredibly familiar to entirely new. Even when choosing a novel to buy at a bookstore, one sees covers they have repeatedly experienced intermixed with recently released titles. Visual exposure to stimuli has distinct neural correlates in the lateral prefrontal cortex (LPFC) of nonhuman primates. However, it is currently unknown if this function may be localized to specific subregions within LPFC. Specifically, we aimed to determine whether the posterior fundus of area 46 (p46f), an area that responds to deviations from learned sequences, also responds to less frequently presented stimuli outside of the sequential context. We compare responses in p46f to the adjacent subregion, posterior ventral area 46 (p46v), which we propose may be more likely to show exposure-dependent responses due to its proximity to novelty responsive regions. To test whether p46f or p46v represent perceptual exposure, we performed awake functional magnetic resonance imaging (fMRI) on three male monkeys as they observed visual stimuli that varied in their number of daily presentations. Here we show that p46v, but not p46f, shows preferential activation to stimuli with low perceptual exposure, further localizing exposure-dependent effects in monkey LPFC. These results align with previous research that has found novelty responses in ventral LPFC and are consistent with the proposal that p46f performs a sequence-specific function. Further, they expand on our knowledge of the specific role of LPFC subregions and localize perceptual exposure processing within this broader brain region.

neuroscience↗

bioRxiv2024

Monkeys engage in visual simulation to solve complex problems

Visual simulation -- i.e., using internal reconstructions of the world to experience potential future versions of events that are not currently happening -- is among the most sophisticated capacities of the human mind. But is this ability in fact uniquely human? To answer this question, we tested monkeys on a series of experiments involving the Planko game, which we have previously used to evoke visual simulation in human participants. We found that monkeys were able to successfully play the game using a simulation strategy, predicting the trajectory of a ball through a field of planks while demonstrating a level of accuracy and behavioral signatures comparable to humans. Computational analyses further revealed that the monkeys strategy while playing Planko aligned with a recurrent neural network (RNN) that approached the task using a spontaneously learned simulation strategy. Finally, we carried out awake functional magnetic resonance imaging while monkeys played Planko. We found activity in motion-sensitive regions of the monkey brain during hypothesized simulation periods, even without any perceived visual motion cues. This neural result closely mirrors previous findings from human research, suggesting a shared mechanism of visual simulation across species. In all, these findings challenge traditional views of animal cognition, proposing that nonhuman primates possess a complex cognitive landscape, capable of invoking imaginative and predictive mental experiences to solve complex everyday problems.

neuroscience↗

bioRxiv2024

Monkey dorsolateral prefrontal cortex shows anatomically and functionally specific responses to sequential but not temporal or image changes

Sequential information permeates daily activities, such as when watching for the correct series of buildings to determine when to get off the bus or train. These sequences include periodicity (the spacing of the buildings), the identity of the stimuli (the kind of house), and higher-order more abstract rules that may not depend on the exact stimulus (e.g. house, house, house, business). Previously, we found that the posterior fundus of area 46 in the monkey lateral prefrontal cortex (LPFC) responds to rule changes in such abstract visual sequences. However, it is unknown if this region responds to other components of the sequence, i.e., image periodicity and identity, in isolation. Further, it is unknown if this region dissociates from other, more ventral LPFC subregions that have been associated with sequences and their components. To address these questions, we used awake functional magnetic resonance imaging in three male macaque monkeys during two no-report visual tasks. One task contained abstract visual sequences, and the other contained no visual sequences but maintained the same image periodicity and identities. We found the fundus of area 46 responded only to abstract sequence rule violations. In contrast, the ventral bank of area 46 responded to changes in image periodicity and identity, but not changes in the abstract sequence. These results suggest a functional specialization within anatomical substructures of LPFC to signal different kinds of stimulus regularities. This specialization may provide key scaffolding to identify abstract patterns and construct complex models of the world for daily living. Significance StatementDaily tasks, such as a bus commute, require tracking or monitoring your place (same, same, same, different building) until your stop. Sequence components such as rule, periodicity (timing), and item identity are involved in this process. While prior work located responses to sequence rule changes to area 46 of monkey lateral prefrontal cortex (LPFC) using awake monkey fMRI, less was known about other components. We found that LPFC subregions differentiated between sequence components. Area 46 posterior fundus responded to abstract visual sequence rule changes, but not to changes in image periodicity or identity. The converse was true for the more ventral, adjacent shoulder region. These results suggest that interactions between adjacent LPFC subregions provide key scaffolding for complex daily behaviors.

neuroscience↗

bioRxiv2023

Early- but not late-adolescent Western diet consumption programs for long-lasting memory impairments in male but not female rats

Early life Western diet (WD) consumption leads to impaired memory function, particularly for processes mediated by the hippocampus. However, the precise critical developmental window(s) during which WD exposure negatively impacts hippocampal function are unknown. Here, we exposed male and female rats to a WD model involving free access to a variety of high-fat and/or high-sugar food and drink items during either the early-adolescent period (postnatal days [PN] 26-41; WD-EA) or late-adolescent period (PN 41-56; WD-LA). Control (CTL) rats were given healthy standard chow throughout both periods. To evaluate long-lasting memory capacity well beyond the early life WD exposure periods, we performed behavioral assessments after both a short (4 weeks for WD-EA, 2 weeks for WD-LA) and long (12 weeks for WD-EA, 10 weeks for WD-LA) period of healthy diet intervention. Results revealed no differences in body weight or body composition between diet groups, regardless of sex. Following the shorter period of healthy diet intervention, both male and female WD-EA and WD-LA rats showed deficits in hippocampal-dependent memory compared to CTL rats. Following the longer healthy diet intervention period, memory impairments persisted in male WD-EA but not WD-LA rats. In contrast, in female rats the longer healthy diet intervention reversed the initial memory impairments in both WD-EA and WD-LA rats. Collectively, these findings reveal that early-adolescence is a critical period of long-lasting hippocampal vulnerability to dietary insults in male but not female rats, thus highlighting developmental- and sex-specific effects mediating the relationship between the early life nutritional environment and long-term cognitive health.

animal behavior and cognition↗

bioRxiv2023

Western diet consumption impairs memory function via dysregulated hippocampus acetylcholine signaling

Western diet (WD) consumption during development yields long-lasting memory impairments, yet the underlying neurobiological mechanisms remain elusive. Here we developed an early life WD rodent model to evaluate whether dysregulated hippocampus (HPC) acetylcholine (ACh) signaling, a pathology associated with memory impairment in human dementia, is causally-related to WD-induced cognitive impairment. Rats received a cafeteria-style WD (access to various high-fat/high-sugar foods; CAF) or healthy chow (CTL) during the juvenile and adolescent periods (postnatal days 26-56). Behavioral, metabolic, and microbiome assessments were performed both before and after a 30-day healthy diet intervention beginning at early adulthood. Results revealed CAF-induced HPC-dependent contextual episodic memory impairments that persisted despite healthy diet intervention, whereas CAF was not associated with long-term changes in body weight, body composition, glucose tolerance, anxiety-like behavior, or gut microbiome. HPC immunoblot analyses after the healthy diet intervention identified reduced levels of vesicular ACh transporter in CAF vs. CTL rats, indicative of chronically reduced HPC ACh tone. To determine whether these changes were functionally related to memory impairments, we evaluated temporal HPC ACh binding via ACh-sensing fluorescent reporter in vivo fiber photometry during memory testing, as well as whether the memory impairments could be rescued pharmacologically. Results revealed dynamic HPC ACh binding during object-contextual novelty recognition was highly predictive of memory performance and was disrupted in CAF vs. CTL rats. Further, HPC alpha-7 nicotinic receptor agonist infusion during consolidation rescued memory deficits in CAF rats. Overall, these findings identify dysregulated HPC ACh signaling as a mechanism underlying early life WD-associated memory impairments.

neuroscience↗

bioRxiv2023

Single-cell RNA sequencing identifies KSHV-infected Mesenchymal stem cell subpopulations precursors of Kaposi's Sarcoma

Kaposis sarcoma (KS) may derive from Kaposis Sarcoma Herpesvirus (KSHV)-infected human Mesenchymal Stem Cells (hMSCs) migrating into an inflammatory and angiogenic site, enhancing KS initiation. KSHV infection of primary hMSCs uncovers specific cell subpopulations, mechanisms, and conditions involved in the first steps of the KSHV-induced transformation and reprogramming process toward KS progenitor cells. The pro-angiogenic environmental conditions allowed KSHV to reprogram hMSCs closer to KS gene expression profiles and points to KSHV infection as an important factor inducing the Mesenchymal-to-Endothelial (MEndT) transition of hMSC. Single-cell RNA-sequencing analysis revealed a subpopulation of infected cells growing in a pro-angiogenic environment with both viral and host oncogenes upregulation. This highlights the importance of this condition in boosting the KSHV-induced transformation and reprogramming of hMSC towards MEndT and closer to KS gene expression profiles, reinforcing the notion of these cell subpopulations as KS precursors.

microbiology↗

bioRxiv2022

Monkey dorsolateral prefrontal cortex represents abstract visual sequences during a no-report task

Monitoring sequential information is an essential component of our daily lives. Many of these sequences are abstract, in that they do not depend on the individual stimuli, but do depend on an ordered set of rules (e.g., chop then stir when cooking). Despite the ubiquity and utility of abstract sequential monitoring, little is known about its neural mechanisms. Human rostrolateral prefrontal cortex (RLPFC) exhibits specific increases in neural activity (i.e., "ramping") during abstract sequences. Monkey dorsolateral prefrontal cortex (DLPFC) has been shown to represent sequential information in motor (not abstract) sequence tasks, and contains a sub-region, area 46, with homologous functional connectivity to human RLPFC. To test the prediction that area 46 may represent abstract sequence information, and do so with parallel dynamics to those found in humans, we conducted functional magnetic resonance imaging (fMRI) in monkeys. When monkeys performed no-report abstract sequence viewing, we found that left and right area 46 responded to abstract sequential changes. Interestingly, responses to rule and number changes overlapped in right area 46 and left area 46 exhibited responses to abstract sequence rules with changes in ramping activation, similar to that observed in humans. Together, these results indicate that monkey DLPFC monitors abstract visual sequential information, potentially with a preference for different dynamics in the two hemispheres. More generally, these results show that abstract sequences are represented in functionally homologous regions across monkeys and humans. Significance StatementDaily, we complete sequences that are "abstract" because they depend on an ordered set of rules (e.g., chop then stir when cooking) rather than the identity of individual items. Little is known about how the brain tracks, or monitors, this abstract sequential information. Based on previous human work showing abstract sequence related dynamics in an analogous area, we tested if monkey dorsolateral prefrontal cortex (DLPFC), specifically area 46, represents abstract sequential information using awake monkey fMRI. We found that area 46 responded to abstract sequence changes, with a preference for more general responses on the right and dynamics similar to humans on the left. These results suggest that abstract sequences are represented in functionally homologous regions across monkeys and humans.

neuroscience↗

bioRxiv2021

A Role for Visual Areas in Physics Simulations

To engage with the world, we must regularly make predictions about the outcomes of physical scenes. How do we make these predictions? Recent evidence points to simulation - the idea that we can introspectively manipulate rich, mental models of the world - as one possible explanation for how such predictions are accomplished. While theories based on simulation are supported by computational models, neuroscientific evidence for simulation is lacking and many important questions remain. For instance, do simulations simply entail a series of abstract computations? Or are they supported by sensory representations of the objects that comprise the scene being simulated? We posit the latter and suggest that the process of simulating a sequence of physical interactions is likely to evoke an imagery-like envisioning of those interactions. Using functional magnetic resonance imaging, we demonstrate that when participants predict how a ball will fall through an obstacle-filled display, motion-sensitive brain regions are activated. We further demonstrate that this activity, which occurs even though no motion is being sensed, resembles activity patterns that arise while participants perceive the balls motion. This finding suggests that the process of simulating the balls movement is accompanied by a sensory representation of this movement. These data thus demonstrate that mental simulations recreate sensory depictions of how a physical scene is likely to unfold.

neuroscience↗

bioRxiv2016

Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade

Immune checkpoint inhibitors are promising treatments for patients with a variety of malignancies. Toward understanding the determinants of response to immune checkpoint inhibitors, it was previously demonstrated that somatic mutation burden is associated with benefit and a hypothesis was posited that neoantigen homology to pathogens may in part explain the link between somatic mutations and response. To further examine this hypothesis, we reanalyzed cancer exome data obtained from a previously published study of 64 melanoma patients treated with CTLA-4 blockade and a new dataset of RNA-Seq data from 24 of those patients. We found that the predictive accuracy does not increase as analysis narrows from somatic mutation burden to predicted MHC Class I neoantigens, expressed neoantigens, or homology to pathogens. Further, the association between somatic mutation burden and response is only found when examining samples obtained prior to treatment. Neoantigen and expressed neoantigen burden are also associated with response, but neither is more predictive than somatic mutation burden. Neither the previously-described tetrapeptide signature nor an updated method to evaluate neoepitope homology to pathogens were more predictive than mutation burden.

cancer biology↗

bioRxiv2016

Multi-omic analysis of urothelial cancer patients treated with PD-L1 blockade demonstrates the contribution of both systemic and somatic factors to the biology of response and resistance

BackgroundInhibition of programmed death-ligand one (PD-L1) with atezolizumab can induce durable clinical benefit (DCB) in patients with metastatic urothelial cancers, including complete remissions in patients with chemotherapy refractory disease. Although mutation load and PD-L1 immune cell (IC) staining have been associated with response, they lack sufficient sensitivity and specificity for clinical use. Thus, there is a need to evaluate the peripheral blood immune environment and to conduct detailed analyses of mutation load, predicted neoantigens and immune cellular infiltration in tumors to enhance our understanding of the biologic underpinnings of response and resistance.\n\nMethods and FindingsThe goals of this study were to (1) evaluate the association of mutation load and predicted neoantigen load with therapeutic benefit, and (2) determine whether intratumoral and peripheral blood T cell receptor (TCR) clonality inform clinical outcomes in urothelial carcinoma treated with atezolizumab. We hypothesized that an elevated mutation load in combination with T cell clonal dominance among intratumoral lymphocytes prior to treatment or among peripheral T cells after treatment would be associated with effective tumor control upon treatment with anti-PD-L1 therapy. We performed whole exome sequencing (WES), RNA sequencing (RNA-seq), and T cell receptor sequencing (TCR-seq) of pre-treatment tumor samples as well as TCR sequencing of matched, serially collected peripheral blood collected before and after treatment with atezolizumab. These parameters were assessed for correlation with DCB (defined as progression free survival (PFS) > 6 months), PFS, and overall survival (OS), both alone and in the context of clinical and intratumoral parameters known to be predictive of survival in this disease state.\n\nPatients with DCB displayed a higher proportion of tumor infiltrating T lymphocytes (TIL) (n=24, Mann-Whitney p=0.047). Pre-treatment peripheral blood TCR clonality below the median was associated with improved PFS (n=29, log-rank p=0.048) and OS (n=29, log-rank p=0.011). Patients with DCB also demonstrated more substantial expansion of tumor-associated TCR clones in the peripheral blood 3 weeks after starting treatment (n=22, Mann-Whitney p=0.022). The combination of high pre-treatment peripheral blood TCR clonality with elevated PD-L1 IC staining in tumor tissue was strongly associated with poor clinical outcomes (n=10, HR (mean)=89.88, HR (median)=23.41, 95% CI (2.43, 506.94), p(HR>1)=0.0014). Marked variations in mutation loads were seen with different somatic variant calling methodologies, which in turn impacted associations with clinical outcomes. Missense mutation load, predicted neoantigen load and expressed neoantigen load did not demonstrate significant association with DCB (n=25, Mann-Whitney p=0.22, n=25, Mann-Whitney p=0.55, and n=25, Mann-Whitney p=0.29 respectively). Instead, we found evidence of time-varying effects of somatic mutation load on progression-free survival in this cohort (n=25, p=0.044). A limitation of our study is its small sample size (n=29), a subset of the patients treated on IMvigor 210 (NCT02108652). Given the number of exploratory analyses performed, we intend for these results to be hypothesis-generating.\n\nConclusionsThese results demonstrate the complex nature of immune response to checkpoint blockade and the compelling need for greater interrogation and data integration of both host and tumor factors. Incorporating these variables in prospective studies will facilitate identification and treatment of resistant patients.

cancer biology↗