Biology subjects

Bettegowda, C.

Publications and source records attributed to Bettegowda, C..

14 recordsLinked to original sources

bioRxiv2026

Toward A Whole-Brain Interface Enabled by High-Resolution Surface Electrophysiology

The goal of building a whole-brain interface - capable of generating a real-time digital representation of the state of the entire central nervous system - has long been framed as a hardware challenge of recording simultaneously from ever-larger numbers of microelectrodes. Advances in high-resolution neural interfaces now enable electrophysiologic interaction with the human nervous system at spatial and temporal resolutions previously unattainable without disrupting tissue architecture or physiology. These capabilities create new opportunities for mechanistic neuroscience, neuroprosthetics, and precision-guided neurosurgery. With the advent of modern microelectrode array technology, however, the whole-brain interface has also become a data challenge. Rather than pursuing large-scale human brain recording purely through a single device placed in a single patient, we demonstrate here that systematic multi-subject aggregation, across brain regions and behavioral paradigms, in a common anatomical framework, can achieve something functionally similar to a whole-brain interface. Here we present an approach to a functional atlas of the human central nervous system derived from high-resolution surface electrophysiology recordings obtained in the first 70 patients implanted with an anatomically conformal, thin-film neural interface positioned in more than 100 locations. The atlas comprises >100,000 electrode deployments and catalogs placement across a broad range of neuroanatomic targets spanning the motor, sensory, language, auditory, and associative domains, as well as brainstem and spinal cord structures that have historically been difficult to access at high electrophysiologic resolution. Across participants, aggregated recordings reveal somatotopic organization, including digit representations that follow a lateral-to-medial ordering consistent with classical homuncular maps, with transitions between adjacent representations occurring over spatial scales of approximately 0.8 - 2.0 mm; canonical frequency-band signatures, such as movement-related beta-band suppression and focal high-gamma (70 - 200 Hz) increases during motor and speech behaviors; and task-modulated population dynamics in both evoked and spontaneous activity across cortical, brainstem, and spinal cord regions. These findings yield insight into patterns of mesoscale electrophysiological dynamics conserved across the entire human central nervous system, suggesting that fine-scale functional organization is preserved across individuals when aligned to common anatomical landmarks. We further demonstrate several applications of these high-resolution recordings, including real-time neural decoding from upper extremity motor cortex to enable real-time neuroprosthetic control, and from ventrolateral cortex to decode cortical correlates of spoken language, facial movements, and complex facial expressions of emotion, supporting initial feasibility of combined verbal and nonverbal communication interfaces. Together, these results establish a paradigm for approaching large-scale interfaces with the human brain, as well as a starting point for a scalable, extensible atlas of human electrophysiologic function designed to accelerate discovery across basic neuroscience, translational research, and clinical neurotechnology.

neuroscience↗

bioRxiv2026

Spatial Regulation of CAR Signaling Enables Logic-Gated Activity

Chimeric antigen receptors (CARs) can induce T cells to kill cancer cells but also to kill normal cells that express the same antigens1. Designing CARs to recognize combinations of antigens, via Boolean logic, can simultaneously expand the scope of targetable antigens and make CAR T cells more specific to cancer2. For example, one antigen may be expressed on cancer cells and normal bone marrow cells, while a second antigen may be present on the same cancer cells but only in normal lungs. If recognition of both antigens is required for T cell activation, only the cancer cells will be killed. Creating such AND-gated CAR T cells has been challenging given the need to engineer non-natural signaling mechanisms that integrate two ligand binding events into a single T cell activation stimulus3-6. Here, we design a fundamentally new AND-gated receptor called Multi-ANtigen Triggered Immune Synapse (MANTIS), which leverages differences in extracellular receptor dimensions to regulate CAR signaling. MANTIS initially prevents CAR activity by steric blocking with a bulky extracellular domain. Upon engagement of the first antigen, MANTIS sheds this blocking domain, releasing a free CAR that can bind a second antigen and activate the T cell in an AND-gated manner. This work demonstrates how differences in extracellular receptor size can be leveraged to spatially regulate intracellular signaling pathways in response to antigen patterns, paving the way for new applications in synthetic biology and cell engineering. One sentence summaryDifferences in extracellular size can be leveraged to regulate CAR T cell activity for precise recognition of antigen patterns.

synthetic biology↗

bioRxiv2025

Engineering immunotoxin-equipped effector cells and evaluation in primary human immune cells

Lethal toxins could become potent therapies against cancer, but their clinical utility is limited by adverse events upon systemic administration. These could be reduced if the toxins were delivered by effector cells that specifically infiltrate cancers, thereby releasing toxins locally into the tumor microenvironment. One of the challenges underlying this strategy is that cells delivering toxins would have to be resistant to them. We address this obstacle by showing that effectors derived from transformed human cell lines genetically engineered for resistance to bacterial adenosine diphosphate ribosylating toxins (ADPRTs), including Pseudomonas aeruginosa exotoxin A (PE), can produce targeted immunotoxins that specifically kill cancer cells expressing cognate tumor-associated antigens. Resistance to immunotoxins was achieved by knockout of genes in the diphthamide biosynthesis pathway (DPH1-4) required for the posttranslational modification of eukaryotic elongation factor 2 (EEF2) that is the target of ADPRTs, or by mutation of EEF2 itself. We show that engineering resistance to ADPRTs, one of the most potent toxins acting on human cells, is essential to achieve robust function of armored effector cell lines. This work establishes a first step on the path to equip effector cells with the ability to deliver powerful toxins to cancer cells and introduces a platform to investigate extension to primary autologous or allogeneic therapeutic cell types.

molecular biology↗

bioRxiv2025

A mouse model of classical trigeminal neuralgia via intradural compression of the trigeminal nerve

IntroductionTrigeminal neuralgia (TN) is a debilitating orofacial pain condition that adversely affects quality of life. Although heterogeneous, the most common form of TN is classical TN, characterized by paroxysmal bouts of pain in response to otherwise innocuous stimuli. It is believed that classical TN results from neurovascular compression of the trigeminal nerve. However, the underlying pathophysiology of TN is not well understood, thus limiting the development of targeted therapies. Current animal models lack translational relevance, particularly in their inability to replicate intradural nerve root compression, a core anatomic component of TN. MethodsWe developed a TN mouse model that achieves intradural nerve root compression via a retro-orbital approach confirmed by anatomic dissection and magnetic resonance imaging. To assess behavioral outcomes, we measured orofacial pain through facial wiping and interaction with a reward stimulus. Pharmacological responsiveness was tested using carbamazepine administration. Mechanistic studies included calcium imaging of trigeminal ganglia (TG), electrophysiologic recordings to measure resting membrane potential and rheobase, and immunohistochemical analysis of the TG. ResultsThe model elicited orofacial neuropathic pain, substantiated by increased facial wiping and reduced interaction with a reward stimulus, behaviors that suggest both spontaneous and evoked pain. Carbamazepine attenuated these behaviors, suggesting pharmacologic relevance to current TN treatment. Calcium imaging showed heightened spontaneous activity in the TG, and electrophysiologic recordings revealed an increased resting membrane potential and a reduced rheobase. Finally, immunohistochemical studies showed infiltration of CD45+ cells, demyelination and an increase in CGRP expression in the TG, supporting the presence of neuroinflammation after nerve root compression. ConclusionThese findings show that our approach replicates the anatomy and clinical presentation of classical TN in humans. This model may represent a new and robust platform for future mechanistic studies of TN and subsequent preclinical evaluation of therapies in mice.

neuroscience↗

bioRxiv2025

Precision targeting of autoreactive B cells in systemic lupus erythematosus using anti-9G4 idiotope synthetic immune receptor T cells

Chimeric antigen receptor (CAR)-T cell therapies can induce drug-free remission in systemic lupus erythematosus (SLE), but indiscriminate B cell targeting causes immunosuppression, unnecessary infections, and cytokine toxicities that preclude widespread use. Here, we overcome this by targeting the 9G4 idiotope, a shared structural feature of pathogenic B cell receptors encoded by the IGHV4-34 gene. We engineered anti-9G4 CAR-T cells and chimeric TCR-T cells to selectively eliminate autoreactive B cells while preserving protective immunity. Both platforms eradicated autoreactive B cells and autoantibodies in vitro and in vivo, spared normal B cells, and markedly reduced cytokine release compared to conventional CAR-T cells. This precision extended to cold agglutinin disease and lymphoma. These findings establish a framework for IGHV idiotope-directed cellular therapies for treating autoimmune and neoplastic diseases while preserving immune competence.

immunology↗

bioRxiv2025

Dual checkpoint blockade of glioblastoma with Anti-PD-1 and Anti-LAG-3 promotes expansion of tumor-reactive T cell clones along a unique pathway of differentiation

IDH-wildtype grade IV glioblastoma is the most aggressive adult primary brain tumor and remains refractory to anti-PD-1 monotherapy despite evidence of limited tumor-specific T cell induction. To determine the impact of immune checkpoint inhibitors (ICIs) on glioblastoma T cell transcriptional landscape and repertoire, we conducted paired single-cell RNA sequencing (scRNA-seq) and T cell receptor sequencing (TCR-seq) of tumor-infiltrating lymphocytes (TILs) from patients with untreated, newly diagnosed glioblastoma and from recurrent glioblastoma treated with dual checkpoint blockade targeting PD-1 and LAG-3. Using a validated transcriptional signature, we found that predicted tumor-reactive T cells (TRC) in untreated glioblastomas reside almost exclusively in a clonally expanded GZMKhi population with developmental plasticity, affording them the potential to differentiate into both tissue-resident and terminal effector T cells. Dual ICI therapy induced substantial clonal remodeling, characterized by the recruitment of new TRC from the periphery into the tumor microenvironment (TME) and differentiation into transitional effectors and ultimately terminal effectors along a gradient characterized by simultaneous acquisition of cytotoxic and exhaustion genes, regulated by specific transcriptional, metabolic, and epigenetic programs. Longitudinal clonal tracking in peripheral blood confirmed that with ICI treatment, most TRC expand transiently in circulation prior to tumor infiltration, with peripherally derived clones becoming the major contributor to the GZMKhi TRC that further expand in the tumor. Our study provides the first comprehensive map of T cell clonal dynamics and differentiation in glioblastoma following dual ICIs and highlights a potential mechanism of immune activation and peripheral recruitment of TRC in glioblastoma not previously described. Our results suggest that therapeutic strategies to sustain these GZMKhi early effector and transitional effector T cells may further enhance ICI therapeutic efficacy in glioblastoma.

immunology↗

bioRxiv2025

Data-driven feedback augments ultrasound nanotheranostics in brain tumors

The blood-brain barrier (BBB) renders the delivery of nanomedicine in the brain ineffective and the detection of circulating disease-related DNA from the brain unreliable. Here, we show that the acoustic emission content of focused ultrasound-controlled microbubble dynamics (MB-FUS) incorporates precursor signals that allow large-data models to predict sonication regimens for safe and effective BBB opening. Crucially, closed-loop MB-FUS controller augmented by machine learning (ML-CL) expands the treatment window (4-fold), as compared to conventional controllers, by persistently and proactively maximizing the BBB permeability while preventing tissue damage. By successfully scaling up from mice to rats and from healthy to diseased brains (glioma), ML-CL rendered the BBB permeable to large nanoparticles and markedly improved the release and detection of tumor DNA in plasma. Together, our findings reveal the potential of data-driven feedback to support the development of next-generation AI-powered ultrasound systems for safe, robust, and efficient nanotheranostic targeting of brain diseases.

bioengineering↗

bioRxiv2023

Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape

Despite exciting developments in cancer immunotherapy, its broad application is limited by the paucity of targetable antigens on the tumor cell surface. As an intrinsic cellular pathway, nonsense-mediated decay (NMD) conceals neoantigens through the destruction of the RNA products from genes harboring truncating mutations. We developed and conducted a high throughput screen, based on the ratiometric analysis of transcripts, to identify critical mediators of NMD. This screen implicated disruption of kinase SMG1s phosphorylation of UPF1 as a potential disruptor of NMD. This led us to design a novel SMG1 inhibitor, KVS0001, that elevates the expression of transcripts and proteins resulting from truncating mutations in vivo and in vitro. Most importantly, KVS0001 concomitantly increased the presentation of immune-targetable HLA class I-associated peptides from NMD-downregulated proteins on the surface of cancer cells. KVS0001 provides new opportunities for studying NMD and the diseases in which NMD plays a role, including cancer and inherited diseases. One Sentence SummaryDisruption of the nonsense-mediated decay pathway with a newly developed SMG1 inhibitor with in-vivo activity increases the expression of T-cell targetable cancer neoantigens resulting from truncating mutations.

cancer biology↗

bioRxiv2023

ME3BP-7 is a targeted cytotoxic agent that rapidly kills pancreatic cancer cells expressing high levels of monocarboxylate transporter MCT1

Nearly 30% of Pancreatic ductal adenocarcinoma (PDAC)s exhibit a marked overexpression of Monocarboxylate Transporter 1 (MCT1) offering a unique opportunity for therapy. However, biochemical inhibitors of MCT1 have proven unsuccessful in clinical trials. In this study we present an alternative approach using 3-Bromopyruvate (3BP) to target MCT1 overexpressing PDACs. 3BP is a cytotoxic agent that is known to be transported into cells via MCT1, but its clinical usefulness has been hampered by difficulties in delivering the drug systemically. We describe here a novel microencapsulated formulation of 3BP (ME3BP-7), that is effective against a variety of PDAC cells in vitro and remains stable in serum. Furthermore, systemically administered ME3BP-7 significantly reduces pancreatic cancer growth and metastatic spread in multiple orthotopic models of pancreatic cancer with manageable toxicity. ME3BP-7 is, therefore, a prototype of a promising new drug, in which the targeting moiety and the cytotoxic moiety are both contained within the same single small molecule. One Sentence SummaryME3BP-7 is a novel formulation of 3BP that resists serum degradation and rapidly kills pancreatic cancer cells expressing high levels of MCT1 with tolerable toxicity in mice.

cancer biology↗

bioRxiv2023

Distinct Myeloid Derived Suppressor Cell Populations Promote Tumor Aggression in Glioblastoma

The diversity of genetic programs and cellular plasticity of glioma-associated myeloid cells, and thus their contribution to tumor growth and immune evasion, is poorly understood. We performed single cell RNA-sequencing of immune and tumor cells from 33 glioma patients of varying tumor grades. We identified two populations characteristic of myeloid derived suppressor cells (MDSC), unique to glioblastoma (GBM) and absent in grades II and III tumors: i) an early progenitor population (E-MDSC) characterized by strong upregulation of multiple catabolic, anabolic, oxidative stress, and hypoxia pathways typically observed within tumor cells themselves, and ii) a monocytic MDSC (M-MDSC) population. The E-MDSCs geographically co-localize with a subset of highly metabolic glioma stem-like tumor cells with a mesenchymal program in the pseudopalisading region, a pathognomonic feature of GBMs associated with poor prognosis. Ligand-receptor interaction analysis revealed symbiotic cross-talk between the stemlike tumor cells and E-MDSCs in GBM, whereby glioma stem cells produce chemokines attracting E-MDSCs, which in turn produce growth and survival factors for the tumor cells. Our large-scale single-cell analysis elucidated unique MDSC populations as key facilitators of GBM progression and mediators of tumor immunosuppression, suggesting that targeting these specific myeloid compartments, including their metabolic programs, may be a promising therapeutic intervention in this deadly cancer. One-Sentence SummaryAggressive glioblastoma harbors two unique myeloid populations capable of promoting stem-like properties of tumor cells and suppressing T cell function in the tumor microenvironment.

immunology↗

bioRxiv2021

An Isogenic Cell Line Panel for Sequence-based Screening of Targeted Anti-cancer Drugs

We describe the creation and characterization of an isogenic cell line panel representing common cancer pathways, with multiple features optimized for high-throughput screening. More than 1,800 cell lines from three normal human cells were generated using CRISPR-technologies. Surprisingly, we discovered most of these lines did not result in complete gene inactivation, despite integration of sgRNA at the desired genomic site. However, a subset of the lines harbored true, biallelic disruptions of the targeted tumor suppressor gene, yielding a final panel of 100 well-characterize lines covering 19 pathways frequently subject to loss of function in cancers. This panel included genetic markers optimized for sequence-based ratiometric assays for drug-based screening assays. To illustrate the potential utility of this panel, we developed a multiplexed high-throughput screen that identified Wee1 inhibitor MK-1775 as a selective growth inhibitor of cells with inactivation of TP53. These cell lines and screening approach should prove useful for researchers studying a variety of cellular and biochemical phenomena.

cancer biology↗

bioRxiv2020

The long non-coding RNA lnc-HLX-2-7 is oncogenic in group 3 medulloblastomas

BackgroundMedulloblastoma (MB) is an aggressive brain tumor that predominantly affects children. Recent high-throughput sequencing studies suggest that the non-coding RNA genome, in particular long non-coding RNAs (lncRNAs), contributes to MB sub-grouping. Here we report the identification of a novel lncRNA, lnc-HLX-2-7, as a potential molecular marker and therapeutic target in group 3 MBs. MethodsPublicly available RNA sequencing (RNA-seq) data from 175 MB patients were interrogated to identify lncRNAs that differentiate between MB subgroups. After characterizing a subset of differentially expressed lncRNAs in vitro and in vivo, the group 3-enriched lncRNA lnc-HLX2-7 was deleted by CRISPR/Cas9 in the MB cell line D425 Med. Intracranially injected tumors were further characterized by bulk and single-cell RNA-sequencing. Resultslnc-HLX-2-7 is highly upregulated in group 3 MB cell lines, patient-derived xenografts, and primary MBs compared to other MB sub-groups as assessed by qRT-PCR, RNA-seq, and RNA fluorescence in situ hybridization (FISH). Depletion of lnc-HLX-2-7 with antisense oligonucleotides or CRISPR/Cas9 significantly reduced cell proliferation and 3D colony formation and induced apoptosis. lnc-HLX-2-7-deleted D425 Med cells injected into mouse cerebella produced smaller tumors than those derived from parental cells. Pathway analysis revealed that lnc-HLX2-7 modulated oxidative phosphorylation, mitochondrial dysfunction, and sirtuin signaling pathways. The MYC oncogene regulated lnc-HLX-2-7, and the small molecule BET-bromodomain (BRD4) inhibitor JQ1 reduced lnc-HLX2-7 expression. Conclusionslnc-HLX-2-7 is oncogenic in MB and represents a promising novel molecular marker and a potential therapeutic target in group 3 MBs in children. Key pointsO_LIlnc-HLX-2-7 is highly upregulated in group 3 medulloblastomas compared to other sub-groups. C_LIO_LIIn vitro and in vivo studies strongly support an oncogenic role for lnc-HLX2-7 in group 3 medulloblastoma. C_LIO_LIlnc-HLX-2-7 may be a novel biomarker and a potential therapeutic target in group 3 medulloblastoma. C_LI Importance of the studyGroup 3 medulloblastomas are associated with poor clinical outcomes, are difficult to subtype clinically, and their biology is poorly understood. In an effort to address these problems, we identified a group 3-specific long non-coding RNA, lnc-HLX-2-7, in an in silico analysis of 175 medulloblastomas and confirmed its expression in group 3 medulloblastoma cell lines, patient-derived xenografts, and FFPE samples. CRISPR/Cas9 deletion and antisense oligonucleotide knockdown of lnc-HLX-2-7 significantly reduced cell growth and 3D colony formation and induced apoptosis. Deletion of lnc-HLX-2-7 in cells injected into mouse cerebellums reduced tumor growth compared to parental cells, and RNA sequencing of these tumors revealed lnc-HLX-2-7-associated modulation of cell viability and cell death signaling pathways. The oncogene MYC regulates lnc-HLX-2-7, and its expression can be controlled by the BET-bromodomain (BRD4) inhibitor JQ1. lnc-HLX-2-7 is a candidate biomarker and a potential therapeutic target in group 3 medulloblastomas in children.

cancer biology↗

bioRxiv2019

Assessing aneuploidy with repetitive element sequencing.

We report a sensitive PCR-based assay that can detect aneuploidy in samples containing as little as 3 picograms of DNA. Using a single primer pair, we amplified [~]750,000 amplicons distributed throughout the genome Aneuploidy was detected in 49% of liquid biopsies from a total of 883 non-metastatic cancers of eight different types. Combining aneuploidy with somatic mutation detection and eight standard protein biomarkers yielded a median sensitivity of 80% at 99% specificity.

cancer biology↗

bioRxiv2018

Integrative analysis of DNA methylation suggests down-regulation of oncogenic pathways and reduced de-novo mutation in survival outliers of glioblastoma

The study of survival outliers of glioblastoma (GBM) can have important implications on gliomagenesis as well as in the identification of ways to alter clinical course on this almost uniformly lethal cancer type. However, current studied epigenetic and genetic signatures of the GBM outliers have failed to identify unifying criteria to characterize this unique group of patients. In this study, we profiled the global DNA methylation pattern of mainly IDH1 wild type survival outliers of glioblastoma and performed comprehensive enrichment analyses with genomic and epigenomic signatures. We found that the genome of long-term survivors in glioblastoma is differentially methylated relative to short-term survivor patients depending on CpG density: hypermethylation near CpG islands (CGIs) and hypomethylation far from CGIs. Interestingly, these two patterns are associated with distinct oncogenic aspects in gliomagenesis. The hypomethylation pattern at the region distant from CGI is associated with lower rates of de novo mutations while the hypermethylation at CGIs correlates with transcriptional downregulation of genes involved in cancer progression pathways. These results extend our understanding of DNA methylation of survival outliers in glioblastoma in a genome-wide level, and provide insight on the potential impact of DNA hypomethylation in cancer genome.

cancer biology↗