Biology subjects

Ahuja, K.

Publications and source records attributed to Ahuja, K..

10 recordsLinked to original sources

bioRxiv2026

The IFN-γ-inducible GTPase IIGP1 regulates mitochondrial remodeling and immunometabolic reprogramming during inflammatory macrophage polarization

Macrophages are key effector cells of the innate immune system that undergo dynamic polarization into functionally distinct phenotypic states, ranging from classically activated inflammatory (M1) to alternatively activated (M2) macrophages. Inflammatory macrophage polarization requires coordinated integration of cytokine signaling, metabolic reprogramming, and mitochondrial remodeling. However, the molecular effectors that control inflammatory signaling for mitochondrial metabolism and remodeling remain poorly defined. Using quantitative mass spectrometry-based proteomics, we identified Interferon-inducible GTPase 1 (IIGP1) as one of the most robustly induced proteins during inflammatory macrophage polarization. Its expression is governed by the IFN-{gamma}-JAK-STAT1 signaling axis and is crucial for this polarization process. IIGP1-deficient macrophages exhibited significantly impaired iNOS induction, nitric oxide production, pro-inflammatory gene expression, co-stimulatory surface marker expression, and morphological remodeling. Further, IIGP1 associates with mitochondria and its absence impairs key characteristics of inflammatory macrophages, including glycolytic metabolic reprogramming, mitochondrial redox adaptation, membrane potential regulation, and structural remodeling. Consistent with these defects, IIGP1-deficient macrophages displayed impaired intracellular killing of Escherichia coli and Salmonella Typhimurium. Collectively, these results point to IIGP1 as an IFN-{gamma}-inducible effector that facilitates efficient inflammatory macrophage polarization and antibacterial immunity by linking inflammatory signaling to mitochondrial homeostasis and immunometabolic reprogramming.

immunology↗

bioRxiv2026

mito-overview: a mitochondrial report software

Interpreting mitochondrial DNA variation requires relating allele representation and genomic annotation to the sequencing evidence available for each sample. We developed mito-overview to integrate mitochondrial coverage, candidate allele fractions, genomic annotations and long read co-occurrence in mitochondrial genomic reports. Analysis of a subset of public GM12878 long read data from Vandiver and colleagues Cas9 enrichment study of full-length mitochondrial genomes (SRR18110025) identified 16 candidate variants. Among these candidates, co-occurrence analysis showed that m.8860A>G and m.14831G>A occurred together in all 366 jointly callable query names, demonstrating how mito-overview extends individual allele measurements to quantify shared read support between mitochondrial sites. Analysis of public GM11906 short read data (GSE142741), pooled from three single-cell ATAC-seq libraries, recovered the previously characterized disease-associated m.8344A>G variant in MT-TK at an alternate allele fraction of 72.1% (740 of 1,027 callable observations). The recovered variant identity and MT-TK assignment agree with Lareau and colleagues original study, providing a disease-relevant example of mito-overview combined candidate detection and genomic annotation. We also examined ONT data from blood, fibroblast and muscle of one patient using a separate internal workflow. Heteroplasmy was estimated from alternate allele fractions calculated separately for each tissue. The respective analyses yielded 90, 52 and 60 candidates, with 19 candidate identities shared across all three lists. For these shared candidates, the tissue-specific estimates enabled examination of both variant presence and allele representation across the sampled tissues, illustrating the application of mitochondrial genomic reports to heteroplasmy assessment in disease research. By combining candidate identification with allele measurements, genomic annotations and shared read support, mito-overview enables researchers to examine which variants are observed, their representation within a sample and their co-occurrence with other mitochondrial alleles. These complementary measurements support the selection and characterization of candidate variants for further study in mitochondrial disease research.

bioinformatics↗

bioRxiv2026

Progressive neuronal network reorganisation in glioblastoma drives pathological activity in vitro

Glioblastoma (GBM) is the most aggressive primary brain tumour and is frequently accompanied by severe neurological symptoms, including epilepsy and cognitive impairment. Neurological symptoms often persist after surgical resection, indicating that GBM induces durable and self-sustaining changes in the surrounding neuronal networks. However, the mechanisms by which GBM reshapes network structure and function in the tumour periphery remain poorly understood. We present a compartmentalised in vitro platform enabling long-term coculture of iPSC-derived neurons and primary GBM cells to investigate these changes. Placed on high-density microelectrode arrays, the platform permits longitudinal electrophysiological recordings at single-neuron resolution. Using effective network inference, we find that GBM drives a reproducible structural progression: first toward a hyperconnected, hub-dominated architecture, then a collapse of community structure accompanied by a widespread neuron loss. This evolving structure shapes population dynamics, constraining features such as network burst rate and instantaneous synchrony. The reorganisation also carries computational consequences: signal propagation becomes progressively redundant and synergistic rather than unique. As a result, neurons lose the capacity to encode distinct input combinations independently, and the repertoire of accessible network states contracts. Together, these findings reframe GBM as a driver of neuronal network reorganisation rather than uniform hyperexcitability, and establish a compartmentalised, single-neuron-resolution platform for the longitudinal observation, dissection, and ultimately targeting of the network processes that underlie disease progression.

neuroscience↗

bioRxiv2025

MyeliMAP: Studying Oligodendrocyte Function in Brain Networks

Oligodendrocytes are the myelinating glia of the central nervous system (CNS), essential for rapid signal propagation, metabolic support, and neuronal health. While rodent-based cultures and organoid systems have provided insights into oligodendrocyte biology, they fall short of capturing human-specific features of myelination or integrating structural and functional readouts. Here, we present MyeliMAP (Myelination MAPping), a human pluripotent stem cell (hPSC) -derived microphysiological and electrophysiological platform that enables robust modeling of CNS myelination. The system combines inducible hPSC-derived neurons and oligodendrocytes in a custom-engineered microfluidic microstructure designed to mimic the developing brain microenvironment, promoting spatially organized axon-glia interactions and controlled myelin sheath formation. Within six weeks, we demonstrate myelin formation and maturation by immunofluorescence and ultrastructural validation using transmission electron microscopy (TEM), confirming compact multilayered wrapping of human axons. Importantly, the microstructure is directly integrated with a high-density microelectrode array (HD-MEA), enabling real-time, long-term functional assessment of network activity and myelin-dependent changes in signal conduction. This allowed us to demonstrate that oligodendrocyte-based myelinated neurons display enhanced conduction velocity of action potentials compared to neuron monocultures. Moreover, the presence of oligodendrocytes stabilized the temporal neuronal network activity by reducing variability in firing patterns and enhancing synchrony across the culture. This dual structure-function approach surpasses static end-point analyses by coupling morphological validation with dynamic, quantitative measurements of maturing circuit physiology. MyeliMAP provides a reproducible, human-relevant platform to dissect neuron-glia interactions and accelerate discovery of remyelination-promoting strategies for CNS disease.

neuroscience↗

bioRxiv2025

Human Myelin Spheres for In Vitro Oligodendrocyte Maturation, Myelination and Neurological Disease Modeling

Demyelinating diseases, such as multiple sclerosis, damage the protective myelin sheaths of the central nervous system. The development of effective therapies has been hampered by the lack of models that accurately replicate human myelin biology. Here we present a novel method to generate human myelin spheres (MyS) by coculturing of hPSC-derived neuronal and oligodendrocyte precursor cells, to create myelinated neurons. Using multimodal analyses including confocal and (electron)microscopy, single-nuclei transcriptomics, lipidomics, and electrophysiology, we demonstrate myelination in MyS as early as six weeks into coculture. These myelinated structures mature over time into multilamellar and compacted myelin sheaths with lipid compositions and transcriptomic profiles mirror the temporal dynamics of in vivo human oligodendrocyte development and neuronal myelination, resembling those of late fetal/postnatal oligodendrocytes. By employing lysolecithin-induced demyelination and Rabies virus infection experiments, we demonstrate the potential of MyS as an innovative, physiologically relevant platform for studying myelin-related neurodegeneration and neuroinfection.

neuroscience↗

bioRxiv2024

Caveolin-1 regulates context-dependent signaling and survival in Ewing Sarcoma.

Plasticity is a hallmark function of cancer cells, yet the mechanisms that enable dynamic switching between survival states remain incompletely understood. Here, we identify Caveolin-1, a membrane-domain scaffolding protein, as a context-dependent regulator of survival signaling in Ewing sarcoma (EwS). Single-cell analyses reveal a distinct subpopulation of EwS cells marked by high CD99 and elevated Caveolin-1 expression. These CD99High cells exhibit unique morphology, transcriptional programs, and markedly enhanced survival both under chemotherapeutic challenge and in vivo. Importantly, CD99High and CD99Low states are reversible, providing EwS cells with a flexible route to survival-oriented plasticity. Mechanistically, we show that Caveolin-1 in CD99High cells orchestrates PI3K/AKT survival signaling by modulating the spatial organization of PI3K activity on the plasma membrane. We propose that the CD99High state establishes a Caveolin-1-driven signaling architecture that supports survival through mechanisms distinct from those used by CD99Low cells. These findings uncover a dynamic state transition in EwS cells and position Caveolin-1 as a key driver of context-specific survival signaling.

cancer biology↗

bioRxiv2024

A deep phenotyping study in mouse and iPSC models to understand the role of oligodendroglia in optic neuropathy in Wolfram syndrome

Wolfram syndrome (WS) is a rare childhood disease characterized by diabetes mellitus, diabetes insipidus, blindness, deafness, neurodegeneration and eventually early death, due to autosomal recessive mutations in the WFS1 (and WFS2) gene. While it is categorized as a neurodegenerative disease, it is increasingly becoming clear that other cell types besides neurons may be affected and contribute to the pathogenesis. MRI studies in patients and phenotyping studies in WS rodent models indicate white matter/myelin loss, implicating a role for oligodendroglia in WS-associated neurodegeneration. In this study, we sought to determine if oligodendroglia are affected in WS and whether their dysfunction may be the primary cause of the observed optic neuropathy and brain neurodegeneration. We demonstrate that 7.5-month-old Wfs1{Delta}exon8 mice display signs of abnormal myelination and a reduced number of oligodendrocyte precursor cells (OPCs) as well as abnormal axonal conduction in the optic nerve. An MRI study of the brain furthermore revealed grey and white matter loss in the cerebellum, brainstem, and superior colliculus, as is seen in WS patients. To further dissect the role of oligodendroglia in WS, we performed a transcriptomics study of WS patient iPSC-derived OPCs and pre-myelinating oligodendrocytes. Transcriptional changes compared to isogenic control cells were found for genes with a role in ER function. However, a deep phenotyping study of these WS patient iPSC-derived oligodendroglia unveiled normal differentiation, mitochondria-associated endoplasmic reticulum (ER) membrane interactions and mitochondrial function, and no overt signs of ER stress. Overall, the current study indicates that oligodendroglia functions are largely preserved in the WS mouse and patient iPSC-derived models used in this study. These findings do not support a major defect in oligodendroglia function as the primary cause of WS, and warrant further investigation of neurons and neuron-oligodendroglia interactions as a target for future neuroprotective or -restorative treatments for WS.

neuroscience↗

bioRxiv2023

Mitochondrial calcium signaling mediated transcriptional regulation of keratin filaments is a critical determinant of melanogenesis

Mitochondria are versatile organelles that regulate several physiological functions. Many mitochondria-controlled processes are driven by mitochondrial Ca2+ signaling. However, role of mitochondrial Ca2+ signaling in melanosome biology remains unknown. Here, we show that pigmentation requires mitochondrial Ca2+ uptake. In vitro gain and loss of function studies demonstrated that Mitochondrial Ca2+ Uniporter (MCU) is crucial for melanogenesis while the MCU rheostats, MCUb and MICU1 negatively control melanogenesis. Zebrafish and mouse models showed that MCU plays a vital role in pigmentation in vivo. Mechanistically, MCU controls activation of transcription factor NFAT2 to induce expression of three keratins (keratin 5, 7 and 8), which we report as positive regulators of melanogenesis. Interestingly, keratin 5 in turn modulates mitochondrial Ca2+ uptake thereby this signaling module acts as a negative feedback loop that fine-tunes both mitochondrial Ca2+ signaling and melanogenesis. Mitoxantrone, an FDA approved drug that inhibits MCU, decreases physiological melanogenesis. Collectively, our data demonstrates a critical role for mitochondrial Ca2+ signaling in vertebrate pigmentation and reveal the therapeutic potential of targeting MCU for clinical management of pigmentary disorders. Given the centrality of mitochondrial Ca2+ signaling and keratin filaments in cellular physiology, this feedback loop may be functional in a variety of other pathophysiological conditions. HighlightsO_LIMCU complex mediated mitochondrial Ca2+ uptake is a novel regulator of vertebrate pigmentation C_LIO_LIKeratin filaments bridge mitochondrial Ca2+ signaling to melanosome biogenesis and maturation C_LIO_LITranscription factor NFAT2 connects mitochondrial Ca2+ dynamics to keratins expression C_LIO_LIMCU-NFAT2-Keratin 5 signaling module generates a negative feedback loop to maintain mitochondrial Ca2+ homeostasis and to ensure optimal melanogenesis C_LIO_LIInhibiting MCU with mitoxantrone, an FDA approved drug, leads to reduction in physiological pigmentation C_LI

cell biology↗

bioRxiv2023

Methotrimeprazine exerts antiviral and neuroprotective effects in Japanese encephalitis virus infection through activation of adaptive ER stress and autophagy

Japanese encephalitis virus (JEV) is the leading global cause of virus-induced encephalitis. Its pathogenesis is driven by a combination of neuronal cell death and neuroinflammation. We hypothesized that pharmacological upregulation of autophagy could exert a neuroprotective antiviral effect, and tested a panel of forty-two FDA-approved drugs that were shown to induce autophagy. Four drugs were tested in the JE mouse model based on in vitro protective effects on neuronal cell death, inhibition of viral replication, and anti-inflammatory effects in microglial cells. The antipsychotic phenothiazines Methotrimeprazine (MTP) and Trifluoperazine (TFP) showed a significant survival benefit with reduced virus titers in the brain, prevention of blood-brain barrier (BBB) breach, and inhibition of neuroinflammation. Both drugs were potent mTOR-independent autophagy flux inducers. Mechanistically MTP inhibited SERCA channel functioning, thereby resulting in rise in cytosolic calcium levels, and induction of a unique adaptive ER stress response. In virus infected drug treated cells, there was a strong transcriptional downregulation of type I interferon and interferon-stimulated genes and upregulation of cholesterol metabolic pathway genes. The drugs exerted an autophagy-dependent antiviral effect at the level of JEV protein translation/replication complex formation in diverse cell types. Inhibition of inflammatory cytokine/chemokine release from mouse microglial cells was partly autophagy-dependent. Our study suggests that MTP exerts a combined antiviral and anti-inflammatory effect in JEV infection, and has therapeutic potential to be repurposed for JE treatment.

microbiology↗

bioRxiv2022

Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos

The high incidence of aneuploidy in early human development, arising either from errors in meiosis or postzygotic mitosis, is the primary cause of pregnancy loss, miscarriage, and still birth following natural conception as well as in vitro fertilization (IVF). Preimplantation genetic testing for aneuploidy (PGT-A) has confirmed the prevalence of meiotic and mitotic aneuploidies among blastocyst-stage IVF embryos that are candidates for transfer. However, only about half of normally fertilized embryos develop to the blastocyst stage in vitro, while the others arrest at cleavage to late morula or early blastocyst stages. To achieve a more complete view of the impacts of aneuploidy, we applied a validated method of PGT-A to a large series (n = 909) of arrested embryos and trophectoderm biopsies. We then correlated observed aneuploidies with abnormalities of the first two cleavage divisions using time lapse imaging (n = 843). The combined incidence of meiotic and mitotic aneuploidies was strongly associated with blastocyst morphological grading, with the proportion ranging from 20% to 90% for the highest to lowest grades, respectively. In contrast, the incidence of aneuploidy among arrested embryos was exceptionally high (94%), dominated by mitotic aneuploidies affecting multiple chromosomes. In turn, these mitotic aneuploidies were strongly associated with abnormal cleavage divisions, such that 51% of abnormally dividing embryos possessed mitotic aneuploidies compared to only 23% of normally dividing embryos. We conclude that the combination of meiotic and mitotic aneuploidies drives arrest of human embryos in vitro, as development increasingly relies on embryonic gene expression at the blastocyst stage.

genetics↗