Biology subjects

Haldar, K.

Publications and source records attributed to Haldar, K..

13 recordsLinked to original sources

bioRxiv2025

A Plasmodium falciparum molecular mechanism of heme binding and sensitivity to artemisinins

Mutations in Plasmodium falciparum Kelch13 (K13) confer artemisinin resistance (ART-R) which threatens global malaria control, but known K13 functions fail to explain clinical ART-R. We reported that K13 binds the oxidant heme in vitro, however, its functions in redox-stress, cell survival and death remained unknown. Since taut control of free heme is not feasible in infected erythrocytes, we utilized a non-erythroid cell model to show that K13 directly binds and is stabilized by nanomolar heme levels. K13 also binds and regulates a major redox transcription factor, which is displaced by heme into the nucleus, to raise redox-stress responses that become suppressed during artemisinin-induced death (ART-death). K13s evolutionarily conserved kelch domain confers heme-binding and ART-death characteristics to its mammalian orthologue KEAP1. Chemical or genetic elevation of K13, fuels ART-death proportionate to K13 levels even in vast excess of heme, suggesting a novel plasmodial redox-survival mechanism licenses ART-death in clinical ART-R.

cell biology↗

bioRxiv2025

Multi-team conflict resolution is ineffective for stable decision making

Competition between distinct groups is fundamental to complex systems, from political coalitions and economic markets to gene regulatory networks (GRNs) controlling cell fate. Strikingly, cell-fate decision systems predominantly employ binary competition between two mutually inhibitory teams of genes, despite multi-team competition being common in social and ecological contexts. This raises a fundamental question: does binary decision-making offer functional advantages over multi-team systems? We systematically analyzed multi-team competitive networks using Boolean dynamics on signed directed graphs, extending well-characterized two-team GRN architectures to systems with three or more mutually inhibitory teams. Three-team networks produced significantly less stable outcomes than two-team systems, with steady states showing higher structural frustration and increased sensitivity to perturbations. Multi-team systems exhibited unpredictable transitions even under controlled perturbations, especially at lower densities typical of real networks. Networks with four or more teams failed to maintain distinct stable states entirely. Using spectral analysis, we show that team structure can be predicted from network eigenproperties, extending structural balance theory to directed signed networks. Our findings explain why binary decisions dominate biology and provide insights into coalition instability in social systems, market dynamics, and organizational structures. This work establishes fundamental stability principles for competitive networks across disciplines.

systems biology↗

bioRxiv2025

Variants in glycine decarboxylase activate mechanisms of mitochondrial energy metabolism in the brain.

Brain energy metabolism is produced from glucose by mitochondrial oxidative phosphorylation. Variants in the mitochondrial enzyme glycine decarboxylase (GLDC) cause a rare neurological disease, non-ketotic hyperglycinemia (NKH), with expected hallmarks of brain glycine elevation and responsiveness to folate deficiency that are equivalent to the severity of Gldc mutations. We remarkably find that brains of young- attenuated mutant mice with a 1.5-fold increase in glycine are reduced > 5-fold in GLDC, show a decline in both the mitochondrial lipoyl-transfer protein GCSH and lipoylation of the pyruvate dehydrogenase (PDH) complex, as well as concomitant rise in signatures of astrocyte mitochondrial {beta}-oxidation of fatty acids and activation of neuronal PDH. Our findings suggest a novel GLDC mechanism of remodeling mitochondrial energy systems throughout the brain, established early in and sustained throughout post-natal NKH disease.

neuroscience↗

bioRxiv2025

Chronic HDACi emends microglial differentiation and neurological disease in a mouse model of intellectual disability

Defect in lysine-specific methyltransferase 2D (KMT2D) underlies a rare intellectual disability disorder, Kabuki Syndrome (KS). We show that in addition to reduction in post-natal neurogenesis, KS mice present small, arrested hippocampal microglia which single cell RNA sequence analyses revealed as globally downregulated, occupying neither activated nor surveillance states. Weekly administration of a triple combination formulation (TCF) containing the FDA-approved HDAC inhibitor Vorinostat, HPBCD and PEG-400 for three months, boosted microglia. Transcriptomic, pseudotime cell trajectory analyses, imaging and behavioral data suggest that TCF differentiated KS microglia from arrested to non-diseased and non-activated surveillance forms by selective acetylation of histone H3, that restored the open chromatin mark H3K4me3 independent of Kmt2D, to improve cognitive and nociceptive responses. Wild-type microglia showed no substantial transcriptional or histone changes, intimating normal heterochromatin resisted TCF. These findings reveal a novel chromatin-mediated mechanism of microglial differentiation uncoupled from activation, with therapeutic potential for KS and related disorders.

neuroscience↗

bioRxiv2025

Astrocyte and neurogenic mechanisms of protective gene therapy prevent brain disease and death due to non-ketotic hyperglycinemia

Genetic defects in glycine decarboxylase (GLDC) cause non-ketotic hyperglycinemia (NKH), a rare and frequently fatal neurometabolic disease, which lacks FDA-approved therapies. We characterized CRISPR Cas9-edited humanized mice expressing a prevalent clinical mutation after administration with a single intraperitoneal dose of a novel recombinant of adeno-associated viral vector 9 expressing GLDC (rAAV9-GLDC). Long term biological activity of rAAV9-GLDC was first validated by assessment of its systemic efficacy over five and ten months in mice. Access of rAAV9 to the brain was confirmed by tracking green fluorescent protein (GFP) after a single intraperitoneal dose of rAAV9-GFP. Over five months, control mock treated GFP-mice showed reduction in astrocytes but not microglia, oligodendrocytes or neurons in the brain. 37% of these animals suffered long term neurological disease and/or death. rAAV9-GLDC boosts astrogenesis without triggering an inflammatory response and confers 100% protection against disease progression and fatality due to NKH.

neuroscience↗

bioRxiv2023

Long-range action of an HDAC inhibitor treats chronic pain in a spared nerve injury rat model

Histone deacetylase inhibitors (HDACi) that modulate epigenetic regulation and are approved for treating rare cancers have, in disease models, also been shown to mitigate neurological conditions, including chronic pain. They are of interest as non-opioid treatments, but achieving long-term efficacy with limited dosing has remained elusive. Here we utilize a triple combination formulation (TCF) comprised of a pan-HDACi vorinostat (Vo at its FDA-approved daily dose of 50mg/Kg), the caging agent 2-hydroxypropyl-{beta}-cyclodextrin (HPBCD) and polyethylene glycol (PEG) known to boost plasma and brain exposure and efficacy of Vo in mice and rats, of various ages, spared nerve injury (SNI) model of chronic neuropathic pain. Administration of the TCF (but not HPBCD and PEG) decreased mechanical allodynia for 4 weeks without antagonizing weight, anxiety, or mobility. This was achieved at less than 1% of the total dose of Vo approved for 4 weeks of tumor treatment and associated with decreased levels of major inflammatory markers and microglia in ipsilateral (but not contralateral) spinal cord regions. A single TCF injection was sufficient for 3-4 weeks of efficacy: this was mirrored in repeat injections, specific for the injured paw and not seen on sham treatment. Pharmacodynamics in an SNI mouse model suggested pain relief was sustained for days to weeks after Vo elimination. Doubling Vo in a single TCF injection proved effectiveness was limited to male rats, where the response amplitude tripled and remained effective for > 2 months, an efficacy that outperforms all currently available chronic pain pharmacotherapies. Together, these data suggest that through pharmacological modulation of Vo, the TCF enables single-dose effectiveness with extended action, reduces long-term HDACi dosage, and presents excellent potential to develop as a non-opioid treatment option for chronic pain.

neuroscience↗

bioRxiv2022

Simultaneous adjunctive treatment of malaria and its co-evolved genetic disorder sickle cell anaemia

Effective treatments for genetic disorders that co-evolved with pathogens require simultaneous betterment of both conditions. Hydroxyurea (HU) offers safe and efficacious treatment for sickle cell anemia (SCA) by reducing clinical complications, transfusions, and death. Despite concerns that HU-treatment for SCA would increase infection risk by the human malaria Plasmodium falciparum, (the genetic driver of the sickle mutation), HU instead reduced clinical malaria. We show that at physiologically relevant exposures, HU (and other ribonucleotide reductase inhibitors) have significant, intrinsic killing activity in vitro against blood stages of P. falciparum, with low risk of eliciting stably resistant parasites or compromising potency of current antimalarial drugs. Additive activity devoid of antagonism by HU was observed with a wide spectrum of commonly used antimalarial treatments. These data endorse broad, safe, long-term use of HU for SCA in malaria endemic countries and provide a novel biological model for simultaneous, adjunct therapy of a life-threatening infection and concomitant management of a co-evolved genetic disorder. SignificanceGenetic disorders are increasingly being treated in global health settings. Hydroxyurea (HU; a ribonucleotide reductase inhibitor) is safe and efficacious for treating sickle cell anemia (SCA). Since the sickle mutation co-evolved with the human malaria parasite Plasmodium falciparum, HU-treatment may potentially have increased malarial infection in SCA patients. However, HU reduced clinical malaria, but why this occurred was not understood. We discovered that in doses used in patients, HU kills P. falciparum and shows strong potential for safe, adjunctive use with current antimalarial drugs. Our findings endorse, long-term use of HU for SCA in malaria-endemic countries and a novel model for simultaneous, adjunct treatment of a life-threatening infection like malaria with concomitant management of multiple genetic hematological disorders of global proportions.

microbiology↗

bioRxiv2020

Somatic chromosomal number alterations affecting driver genes inform in-vitro and clinical drug response in high-grade serous ovarian cancer

The genomic complexity and heterogeneity of high-grade serous ovarian cancer (HGSOC) has hampered the realisation of successful therapies and effective personalised treatment is an unmet clinical need. Here we show that primary HGSOC spheroid models can be used to predict drug response and use them to demonstrate that somatic copy number alterations (SCNAs) in frequently amplified HGSOC cancer genes significantly correlate with gene expression and drug response. These genes are often located in areas of the genome with frequent clonal SCNAs. MYC chromosomal copy number is associated with ex-vivo and clinical response to paclitaxel and ex-vivo response to mTORC1/2 inhibition. Activation of the mTOR survival pathway in the context to MYC-amplified HGSOC is mostly due to increased prevalence of SCNAs in genes from the PI3K pathway. These results suggest that SCNAs encompassing driver genes could be used to inform therapeutic response in the context of clinical trials testing personalised medicines.

cancer biology↗

bioRxiv2020

Genomic analyses of glycine decarboxylase neurogenic mutations yield a large scale prediction model for prenatal disease.

Glycine decarboxylase (GLDC) is a mitochondrial protein, hundreds of mutations in which cause a neurometabolic disorder Non-ketotic Hyperglycinemia (NKH), associated with elevation of plasma glycine. But why a mutation induces severe or attenuated neurological disease is poorly understood. We combined a human multiparametric mutation scale that separates severe from attenuated clinical, neurological disease, with new in silico tools to assess 238 of 255 NKH mutations in murine GLDC. We unified novel murine and human genome level-analyses across a linear scale of neurological severity, with in vivo evidence from mice engineered with a top-ranking attenuated mutation and another mutation >10 times more pathogenic and integrated the data in a model of pre- and post-natal disease outcomes, relevant for over a hundred major and minor neurogenic mutations. Our findings suggest that highly severe neurogenic mutations predict fatal, prenatal disease that can be remedied by metabolic supplementation of dams, in absence of amelioration of persistent and age-dependent elevation of plasma glycine.

bioinformatics↗

bioRxiv2020

Algorithmic Assessment of Missense Mutation Severity in the Von-Hippel Lindau Protein

Von Hippel-Lindau disease (VHL) is an autosomal dominant rare disease that causes the formation of angiogenic tumors. When functional, pVHL acts as an E3 ubiquitin ligase that negatively regulates hypoxia inducible factor (HIF). Genetic mutations that perturb the structure of pVHL result in dysregulation of HIF, causing a wide array of tumor pathologies including retinal angioma, pheochromocytoma, central nervous system hemangioblastoma, and clear cell renal carcinoma. These VHL-related cancers occur throughout the lifetime of the patient, requiring frequent intervention procedures, such as surgery, to remove the tumors. Although VHL is classified as a rare disease (1 in 39,000 to 1 in 91,000 affected) there is a large heterogeneity in genetic mutations listed for observed pathologies. Understanding how these specific mutations correlate with the myriad of observed pathologies for VHL could provide clinicians insight into the potential severity and onset of disease. Using a set of 285 ClinVar mutations in VHL, we developed a multiparametric scoring algorithm to evaluate the overall clinical severity of missense mutations in pVHL. The mutations were assessed according to eight weighted parameters as a comprehensive evaluation of protein misfolding and malfunction. Higher mutation scores were strongly associated with pathogenicity. Our approach establishes a novel in silico method by which VHL-specific mutations can be assessed for their severity and effect on the biophysical functions of the VHL protein.View Full Text

pathology↗

bioRxiv2019

Large scale analyses of genotype-phenotype relationships of glycine decarboxylase mutations and neurological disease severity.

Monogenetic diseases provide unique opportunity for studying complex, clinical states that underlie neurological severity. Loss of glycine decarboxylase (GLDC) can severely impact neurological development as seen in non-ketotic hyperglycinemia (NKH). NKH is a neuro-metabolic disorder lacking quantitative predictors of disease states. It is characterized by elevation of glycine, seizures and failure to thrive, but glycine reduction often fails to confer neurological benefit, suggesting need for alternate tools to distinguish severe from attenuated disease. A major challenge has been that there are 255 unique disease-causing missense mutations in GLDC, of which 206 remain entirely uncharacterized. Here we report a Multiparametric Mutation Score (MMS) developed by combining in silico predictions of stability, evolutionary conservation and protein interaction models and suitable to assess 251 of 255 mutations. In addition, we created a quantitative scale of clinical disease severity comprising of four major disease domains (seizure, cognitive failure, muscular and motor control and brain-malformation) to comprehensively score patient symptoms identified in 131 clinical reports published over the last 15 years. The resulting patient Clinical Outcomes Scores (COS) were used to optimize the MMS for biological and clinical relevance and yield a patient Weighted Multiparametric Mutation Score (WMMS) that separates severe from attenuated neurological disease (p < 3.5e-5). Our study provides understanding for developing quantitative tools to predict clinical severity of neurological disease and a clinical scale that advances monitoring disease progression needed to evaluate new treatments for NKH.

bioinformatics↗

bioRxiv2017

Tolerance of chronic HDACi-administration used for treatment of neurological and visceral disease including lung pathogenesis.

Histone deacetylase (HDAC) inhibitors are of significant interest as drugs. However, their use in neurological disorders has raised concern because HDACs are required for brain function. We have previously shown that a triple combination formulation (TCF) of the pan HDACi vorinostat (Vo) improves pharmacokinetic exposure and entry of Vo into the brain. TCF treatment significantly delayed both neurodegeneration and death in the Npc1nmf164 murine model of Niemann Pick Type C (NPC) disease. The TCF induces no metabolic toxicity, but its risk to normal brain functions and potential utility in treating lung disease, a major NPC clinical complication, remain unknown. Here we report that TCF administered for 8-10 months was not detrimental to brain or neuromuscular functions of healthy mice, based on quantitative analyses of major Purkinje neurons in the cerebellum, inflammation in the hippocampus and symptoms of progressive neurocognitive/muscular disease. The TCF was also not injurious to lung tissue but rather improved delivery of Vo to lungs and reduced accumulation of foamy macrophages in Npc1nmf164 mice. Together these data support feasibility of tolerable, chronic administration of an HDACi formulation to treat brain and systemic disease including lung pathology, a frequent cause of death in NPC and possibly other neurological diseases.

neuroscience↗

bioRxiv2017

Characterization of polymorphisms in Plasmodium falciparum artemisinin resistance marker kelch13 in asymptomatic infections in a rural area of Cameroon

BackgroundThe genetic variability of the artemisinin resistance (AR) molecular marker kelch13 has been extensively investigated in Plasmodium falciparum malaria parasites from symptomatic infections in South East (SE) Asia where AR is highly prevalent, as well as in Africa where evidence of AR has emerged only recently. However, molecular surveillance and risk of transmission of AR also require monitoring asymptomatic infection. Here, molecular analyses were used to investigate polymorphisms in kelch13 and their potential for transmission in asymptomatic adults in Bolifamba, Cameroon in Central Africa.\n\nMethodsUsing polymerase chain reaction (PCR), we amplified and sequenced the full length of kelch13 from P. falciparum infections detected in the blood of 33 asymptomatic adults (age: 18-55 years-old) collected in a cross-sectional study from July 2008 to October 2009. Risk of increased transmission was assessed by quantifying gametocytes by qPCR. Quantitative ELISA was used to detect plasma levels of PfHRP2 to establish total parasite burdens associated with asymptomatic infection.\n\nResultsOut of 33 isolates tested, 14 (42.4%) presented at least a single nucleotide polymorphism (SNP) in kelch13. Five non-synonymous SNPs were detected (K189T/N, N217H, R393K and E433K). None were located in the beta-propeller domain, where AR mutations have been detected in both SE Asian and, more recently, African parasites. K189T/N and N217H have been previously reported in African strains, but R393K and E433K are new polymorphisms. Gametocytes were detected in 24.2% of infections, without a significant association with detected Kelch13 polymorphisms. Notably, polymorphisms detected in kelch13 were associated with a significant increase of PfHRP2 plasma levels.\n\nConclusionsThis study provides the baseline prevalence of kelch13 polymorphisms in asymptomatic infection for molecular surveillance in tracking AR, and suggests the need for additional studies to explore the association of kelch13 polymorphisms with P. falciparum burden independent of AR, in this region of Cameroon.

microbiology↗