Biology subjects

Pal, M.

Publications and source records attributed to Pal, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Regulation of Human Erythroferrone Expression

Erythroferrone (ERFE) is an erythroblast-secreted hormone that suppresses hepatic hepcidin expression to increase iron availability for erythropoiesis, ensuring recovery from anaemia. ERFE excess drives iron overload in disorders of ineffective erythropoiesis. Despite its pivotal role in systemic iron homeostasis and diseases of erythropoiesis, ERFEs molecular regulation has remained undefined. Here, we applied a genomic approach to characterise the molecular mechanisms governing ERFE expression. Using the HUDEP-2 human erythroid progenitor model, integrative ATAC-seq, CUT&RUN and micro capture-C analysis we identified a stage-specific accessible chromatin region within the ERFE 3 UTR that interacts with the promotor. We also identified enhancer-associated chromatin marks including H3K4me1 and H3K27ac in this region, and demonstrate that this cis-regulatory element is bound by key erythroid transcription factors KLF1, GATA1, TAL1 and STAT5. Functional dissection using CRISPR-Cas9-mediated deletion of the central 3 UTR enhancer element led to marked reduction in ERFE mRNA expression, and we show a corresponding reduction in nascent mRNA, confirming a key role for this region in transcriptional regulation. We define the transcriptional regulatory mechanism by which maturing human erythroblasts activate ERFE, the endocrine signal that coordinates erythropoietic demand with systemic iron mobilisation.

molecular biology↗

bioRxiv2025

Epoxyazadiradione ameliorates Parkinson's disease by upregulating heat shock factor 1 and protein degradation pathways in mice.

Parkinsons disease (PD) is a major debilitating health concern for millions of the elderly population all over the world. This progressive neurodegenerative disorder also poses a severe mental and financial burden to caregivers and society. Despite a major thrust on research for therapy development, no significant progress has been made; only temporary management options are currently available. To this end, we have reported azadiradione (AZD), a triterpenoid that we isolated from neem seed extract using a cell-based assay. AZD showed high efficacy in ameliorating protein aggregation-induced pathology and symptoms in fruit flies and mice. Current evidence suggests that AZD functions through activating the transcriptional function of heat shock factor 1 (HSF1), a master regulator of protein quality control pathways, without modulating the cellular redox balance. To better understand the pharmacophore of AZD, a triterpenoid in its observed function, we have analysed various structural derivatives, focusing on their HSF1-activating function in vitro and their efficacies in ameliorating protein aggregation-induced toxicities in cell and mouse models. Our analyses, based on real-time PCR, immunoblots, fluorescent anisotropy, and a mouse model of MPTP-induced PD, highlighted Epoxy-azadiradione (Epoxy) as being as efficient as AZD in in vivo functional tests, albeit activating the promoter binding activity of HSF1 with at least two-fold higher efficacy in vitro. Notably, similar to AZD, Epoxy did not induce cellular redox imbalance. We also incorporated molecular docking analyses involving the published crystal structure of the DNA-binding domain of HSF1 bound to its DNA recognition element to study molecular dynamics-based energy estimation. The analysis revealed a higher energy stability of the epoxy-bound complexes, as indicated by a significant decrease in binding free energy ({Delta}G) estimated from an ensemble of intermediate docked complex structures.

pharmacology and toxicology↗

bioRxiv2025

CCDC103-mediated assembly of the R2C complex links RUVBL1-RUVBL2 to Primary Ciliary Dyskinesia

Primary ciliary dyskinesia (PCD) is a genetic disorder caused by defective cilia motility, powered by axonemal dynein motors. Assembly of these motors is facilitated by the molecular chaperone HSP90, its co-chaperone RUVBL1-RUVBL2 and adaptor proteins such as CCDC103 (aka DNAAF19). Mutations in CCDC103 identified in PCD patients impair dynein assembly, contributing to the disease pathology. Here, we present the cryo-electron microscopy structure of the human RUVBL1-RUVBL2-CCDC103 complex at 3.2[A] resolution, a chaperone assembly we refer to as R2C. It comprises a hetero-hexameric RUVBL1-RUVBL2 ring bound to three CCDC103 molecules via their RUVBL2-binding domains (RBDs), which have additional functions. Unlike RPAP3 of R2TP, a previously defined co-chaperone of HSP90, CCDC103 lacks a PIH1D1-binding motif and TPR domains, but its flexible N-terminal region regulates RUVBL1-RUVBL2 oligomerisation. Our characterisation of the R2C complex presented here enhances understanding of the intricate protein network involved in Hsp90-mediated assembly of dynein motors and how adaptor mutations contribute to PCD.

biochemistry↗

bioRxiv2025

A bipartite, mutation-tolerant NLS regulates interaction of ΔNp63α with importin alpha, nuclear transport and transcriptional activity

{Delta}Np63 is a master regulator of epithelial development, driving the expansion of progenitor cells in stratified epithelia. Mutations in {Delta}Np63 are linked to squamous cell carcinomas (SCCs) and basal cell carcinomas (BCCs), as well as to ectodermal dysplasia syndromes such as ectrodactyly-ectodermal dysplasia-clefting (EEC) and ankyloblepharon-ectodermal dysplasia-clefting (AEC). Although {Delta}Np63 functions as a nuclear transcription factor, the mechanisms underlying its nuclear import remain incompletely understood. By combining imaging, biochemical, structural and functional assays, we have thoroughly characterized {Delta}Np63 nuclear import, as mediated by the importin (IMP) /{beta}1 heterodimer. We also show here that {Delta}Np63 has evolved a peculiar strategy to ensure mutation tolerant nuclear localization, which is essential for DNA binding and transcriptional regulation. Despite a canonical bipartite NLS formed by two stretches of basic amino acids was identified between the DNA binding and oligomerization domains, each of them in sufficient to bind both IMP binding sites upon homodimerization. Therefore, in contrast to most known bipartite NLSs, only simultaneous substitution of both basic stretches of amino acids ablated nuclear localization, interaction with IMP, and decreased transcriptional activity. Since several {Delta}Np63 isoforms which lack the N-terminal basic stretch of amino acids have been described, and a number of mutations in the {Delta}Np63 NLS region have been identified in the Genome Aggregation Database, {Delta}Np63 has specifically evolved to tolerate mutations in its NLS without significantly compromising its ability to localize in the nucleus. GRAPHICAL ABSTRACT

cell biology↗

bioRxiv2025

ALOX12B overexpression in the skin drives inflammasome/Th17 signaling axis to promote inflammation in the mouse model and human patients

Inflammation plays a pivotal role in the etiopathogenesis of chronic inflammatory skin diseases. However, the underlying mechanism remains unclear. Here, we employed Gene expression meta-analysis and clinical validation strategy to dissect the global architecture of immune dysregulation responsible for inflammatory conditions in the skin. Using such approaches, we identified a gene signature comprising of ALOX12B, which is significantly upregulated in psoriatic and atopic dermatitis patient skin samples, and correlates with increased levels of pathological IL-1{beta} and Th17 responses. Surprisingly, ALOX12B is predominantly expressed in the skin. Furthermore, skin-specific overexpression of human ALOX12B in transgenic mice resulted in psoriasis-like inflammatory symptoms, including epidermal hyperplasia, immune cell infiltration, and elevated IL-1{beta}/Th17 responses. ALOX12B is a non-heme iron-containing enzyme that catalyses the production of 12R-HETE from polyunsaturated fatty acids such as arachidonic acid. Mechanistically, we found that ALOX12B/12R-HETE accumulation in the skin acts as an intrinsic danger signal that triggers enhanced IL-1{beta} processing and secretion via ROS generation and NLRP3 inflammasome activation. Increased IL-1{beta} levels in turn drive IL-17 producing T-cell polarization. We further designed a novel first-in-class, potent ALOX12B inhibitor, 6a, which exhibited favorable topical pharmacokinetic and safety profiles. The topical application of 6a reduced inflammation-associated pathologies in Tg-hALOX12B mice by suppressing 12R-HETE-induced IL-1{beta} production and ROS generation. These findings revealed a novel mechanism mediated by ALOX12B/12R-HETE overexpression that controls skin inflammation, thereby providing a promising therapeutic target for treating inflammatory skin diseases. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/658245v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@13cdf3forg.highwire.dtl.DTLVardef@164cac3org.highwire.dtl.DTLVardef@3c0364org.highwire.dtl.DTLVardef@2ca91_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO The proposed mechanism through which ALOX12B modulates the inflammatory pathway in psoriasiform-like inflammatory conditions in the skin. The study provides insight into the role of ALOX12B in skin inflammation. Increased levels of ALOX12B expression in the skin result in 12R-HETE accumulation, which subsequently triggers the IL-1/Th17 inflammatory cascade through ROS generation and inflammasome activation. IL-1 produced by the activated inflammasome leads to the polarization of naive T-cells to activated IL-17 producing CD4+ T-cells, which are involved in the skin-inflammation related pathologies such as keratinocyte proliferation, and cellular infiltration. Hence, we propose ALOX12B as a novel potential therapeutic target for psoriasis-like inflammatory skin disorders. Additionally, we designed a novel first-in-class ALOX12B inhibitor, 6a; which shows a substantial alleviation in ALOX12B enzymatic activity, thereby reducing cellular ROS, which in turn results in reduced levels of IL-1, as a result inhibiting IL-1/Th17 inflammatory pathway and subsequent reduction in pathological inflammatory skin conditions. A portion of the image was created using Biorender.com C_FIG HighlightsO_LIALOX12B is a key gene upregulated in the skin during psoriasis and atopic dermatitis. C_LIO_LITransgenic mice overexpressing ALOX12B in the skin developed Psoriasis-like inflammatory symptoms. C_LIO_LIMechanistically, ALOX12B, through 12R-HETE, enhanced IL-1{beta} production via ROS generation and NLRP3 inflammasome activation. Further elevated IL-1{beta} production promotes Th17 cell polarization. C_LIO_LINovel first-in-class ALOX12B inhibitor alleviates inflammatory symptoms in a transgenic mouse model. C_LIO_LIStudy reveals a crucial ALOX12B/12R-HETE-inflammasome-IL-17 axis involvement in inflammatory skin diseases. C_LI

immunology↗

bioRxiv2025

Azadiradione regulates Heat Shock Factor 1 function by interacting with its DNA-binding domain independent of the oligomerization domain

Heat shock factor 1 (HSF1) masters cellular proteostasis under stress by upregulating the expression of molecular chaperones that help refold or degrade the misfolded proteins. HSF1 activation involves a monomer-to-oligomer transition and binding to its recognition sequence, the heat shock elements (HSEs) on its target gene promoters. HSF1 activity declines with age as well as in neurodegenerative disorders (NDs) such as Parkinsons disease, highlighting the need for strategies to restore its function. Azadiradione (AZD), a limonoid isolated from Azadirachta indica seeds, directly activates HSF1 in cellular and preclinical ND models, unlike other small-molecule activators reported elsewhere. We investigated the molecular basis of AZD-mediated HSF1 activation using purified variants of this protein including those without its oligomerization and transactivation domain. Fluorescence polarization and dynamic light scattering assays revealed that AZD promotes the oligomerization of monomeric HSF1 to enhance its HSE-binding affinity by engaging with its DNA-binding domain (DBD). The oligomerization domain known to be required for stress-induced activation, appears redundant in AZD-mediated activation. Furthermore, evidence suggests AZD-induced conformational alterations in the HSE facilitate its binding to the HSF1 monomer. Notably, AZD reduces the DNA-binding ability of pre-assembled oligomeric HSF1 by triggering its amyloid-like aggregation. This finding also highlighted a potential anticancer effect of AZD, as cancer cells heavily depend on this HSF1 population for rapid proliferation and survival. Overall, these findings offer novel insights into the functional regulation of HSF1 and suggest a framework for developing small-molecule HSF1 activators with therapeutic potential for protein conformation disorders.

biochemistry↗

bioRxiv2025

HSF1 Activator Azadiradione Ameliorates Parkinson Disease and Extends Lifespan in Preclinical Models: Analysis of Underlying Molecular Mechanism

Parkinsons disease (PD) affects millions worldwide, with no efficient therapy currently available. A major cause of the initiation and progression of this degenerative disease is the dysfunctional cellular protein quality control system (PQC), leading to the accumulation of toxic protein aggregates in neurons. We previously reported azadiradione (AZD), a small molecule (MW 451 Da), as a potent inducer of heat shock factor 1 (HSF1) activity, which could alleviate cellular toxicity induced by misfolded proteins by upregulating the levels of inducible molecular chaperones and proteasome activity. Here, we show the multifaceted effect of AZD in enhancing the capacity of PQC machinery in cells, fruit flies, and a PD mouse model. AZD activated HSF1 by promoting its phosphorylation at S326 through MEK. In parallel, AZD boosted protein degradation through increased chymotrypsin-like proteasome activity, upregulation of the ubiquitin ligase CHIP. AZD induced autophagy, marked by elevated levels of Beclin 1, ATG7, and ULK1 phosphorylation at S555, along with mTORC1 inhibition via AMPK activation. Surprisingly, the calorie restriction pathway was also upregulated upon AZD treatment, as demonstrated by the enhanced phosphorylation of FOXO3 and FOXO1, along with increased activity of their target enzymes SOD and catalase. Notably, AKT activity was also suppressed in AZD-treated cells. In vivo, AZD improved motor function, dopaminergic neuron survival, and tyrosine hydroxylase activity in an MPTP-induced mouse model of PD, and extended lifespan in Drosophila without compromising fertility or mobility. These findings highlight AZD as a promising therapeutic candidate for restoring PQC and mitigating PD pathology.

molecular biology↗

bioRxiv2025

Turning blood to brain cells: a plasma mediated reprograming model

The lack of effective stem cell protocols for generating personalized neurovascular niches poses a critical challenge in precision medicine. While iPSC-based methods are explored, their clinical use is hindered by high costs, long timelines, and cancer risks. Recent advancements in plasma-driven differentiation, using circulating monocytes, offer a promising solution as they can be reprogrammed into neuron-like, endothelial-like, and hematopoietic cells without genetic manipulation, by inducing growth factors mediated transdifferentiation. Vasculature is integral to neurodevelopment, with early blood supply transitioning from the perineural to intrinsic vascular plexus, driven by neuro-hematovascular signaling. The choroid plexus selectively transports proteins and growth factors from blood to CSF, supporting neural proliferation and differentiation. Building on these insights, we leveraged the innate reprograming potential of blood-derived cells to generate neuro-hematovascular niches using a novel PITTRep methodology, devoid of transgene and growth factor mediated transdifferentiation opening new avenues for regenerative and investigative neurovascular studies.

cell biology↗

bioRxiv2025

Development of Severity Index for Oral Epithelial Dysplasia Using Fuzzy Group Decision Making Algorithm

BackgroundOral epithelial dysplasia (OED) grading suffers from several levels of uncertainties and imprecision. An index is preferred in this context to improve reliability and reduce subjectivity in diagnostic decision making. In this study, a fuzzy logic-based disease severity index (SI) is formulated considering standard histopathological features used in OED grading. MethodsOral onco-pathologists were asked to independently provide weights of different features, according to their clinical significance in the context of dysplasia. Aggregated weight of each feature was calculated from individual assessment of different onco-pathologists by a fuzzy logic-based group decision making algorithm. Confidence levels of experts were also included to improve robustness of the method. SI was generated by integrating abnormality score of each feature with its weight. Abnormality degree of each feature was expressed in linguistic terms by onco-pathologists which were subsequently represented by a triangular fuzzy number. Fuzzy membership function was used as it can capture the ambiguity of experts opinion regarding abnormality of individual feature. Finally, defuzzification was used to get a crisp index from weighted sum of all features. ResultSI was found to be statistically different (p<0.01) for different grades of dysplasia i.e mild, moderate and severe with added advantage of stratifying each grade in low and high subcategory. ConclusionKey contribution of our work is that we have developed a fuzzy logic-based group consensus process regarding weights of histopathological features for OED grading. Present methodology of developing SI can be applied to other medical decision-making problems as well. HighlightsO_LIA severity index is proposed to improve reproducibility of oral epithelial dysplasia grading. C_LIO_LIClinical significance of each histopathological and cytopathological feature in the context of dysplasia is reflected by its weight. C_LIO_LIA fuzzy logic-based group decision making algorithm is used to reduce subjectivity of features weights. C_LIO_LIConfidence level of oral onco-pathologists are given due importance in derivation of aggregated weight of each feature. C_LIO_LIAbnormality score of each feature is evaluated in fuzzy scale to capture clinicians ambiguity. C_LIO_LIPresent methodology may be useful for developing indices of other diseases. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/633806v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@5a5e28org.highwire.dtl.DTLVardef@dba3a9org.highwire.dtl.DTLVardef@1d5cc7corg.highwire.dtl.DTLVardef@16404b5_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

cancer biology↗

bioRxiv2024

Building neurovascular tissue from autologous blood for modeling brain-activity

There are no faithful individualized stem cell-based bioengineered neuro-vascularized models that can recapitulate the physiological hemodynamic phenomenon of neuro-vascular coupling (NVC)-the principal behind BOLD (blood oxygen level-dependent) signal in functional neuroimaging, thereby dissuading the research in exploring the brain activity-based investigative studies in neurological/neurosensory diseases. This encouraged us to establish a preclinical optoacoustic (Hb/dHb hemoglobin/deoxyhemoglobin) imaging-competent in vitro neuro-vascularized model by employing a novel cellular reprograming PITTRep (Plasma Induced Transcriptomics/ epi-Transcriptomics Reprograming) approach. The current reprograming approach is based on coaxing autologous blood components to ecto-mesodermal lineage intermediates that can subsequently self-pattern into neurovascular tissue by harnessing the hemorheological properties of RBCs. The nature of blood flow is non-Newtonian and is a function of RBC concentration /haematocrit when they flow through the regions of low shear rates as seen in cerebral microcirculation. The current reprograming approach is a modification of our previous cellular reprograming approach that employed a Newtonian plasma fluid. The autologous blood-derived neurovascular tissue is free from exogenous genetic modification, external growth factors, and induced pluripotent stem cell (iPSC) derivation. This model uniquely integrates functional vasculature and neurogenesis. The current reprogramming approach resulted (in part) serendipitously while testing a potential (yet completely unexplored) hypothesis of haemodynamic reprograming by leveraging the fluid mechanic feature of blood erythrocytes as seen in thrombus formation during cerebral ischemic stroke, that is characterized by physiologically intriguing yet clinically meaningful neurological recovery (neuroplasticity) during an early time window. The current study attempted to induce "a post stroke-like model" of adult neurogenesis with functional synaptogenesis by instructing autologous blood components into thrombus formation through incorporation of erythrocytes in varying concentrations. We tried to instruct adult neurogenesis and neuroplasticity (a relatively non-resilient phenomenon under in vitro conditions) by co-induction of a neuro-vascular niche (NVN). These NVNs are marked by dendrites, synapses, astrogliosis, microglia activation, and growth factor signaling, thus phenocopying molecular and cellular aspects of post-stroke recovery window. The induction of neuro-vascularized niches and functional neuro-vascular coupling (NVC) was characterized by confocal microscopy, scanning electron microscopy, proteomic profiling, and Hb/dHb spectra based optoacoustic imaging. The blood thrombus formation was checked by rotational thromboelastometry (ROTEM), and switching of adult-to-embryonic hemoglobin was confirmed by routine hemoglobin typing. We also attempted to establish patient-specific neuro-vascularized niches from autologous blood of sensorineural hearing loss (SNHL) patients. The individualized neovascularised tissues are intended to be employed for investigating deregulated synaptic plasticity/ long term potentiation underlying poor auditory comprehension outcomes in school going kids suffering from SNHL that greatly compromises their academic performance and socio-behavioural-cognitive development. The attendant multiomics of patient-specific NVNs may have potential implications in developing stem-cell based therapies for neurosensory and cerebrovascular diseases.

neuroscience↗

bioRxiv2024

Polyphenol-rich fraction of Bergenia ligulata (Wall.) Engl. sensitizes colon and breast cancer metastasis in vivo: Evidence of cell-type specific mechanism

BackgroundColon and breast cancer are one of the leading causes of mortality worldwide. Limited efficacies of present treatments highlighted an urgent need for improvement. Bergenia ligulata is known for its anticancer properties in Indian traditional and folk medicine though the molecular basis of its effects, particularly its anti-metastatic properties, is not well understood. Anti-prostate cancer activity of a LCMS defined polyphenol-rich fraction from Bergenia ligulata (PFBL) rhizome extract has already been published showing promising results in preclinical models. PurposeThe present study aims to explore anti-cancer activity and anti-metastatic potentials of PFBL against colon and breast cancers in both in vitro and preclinical settings. Study design and methodsPFBL alone or in synergy with standard chemotherapeutic drugs was tasted in CT26 and 4T1 subcutaneous solid tumors in BALB/c mice. The effect of PFBL was analyzed in terms of changes in tumor mass and different molecular marker levels. Anti-metastatic potential of PFBL was evaluated in CT26 and 4T1 lung metastasis model in mice focusing on the number of lung nodules and lung size. ResultsOur results evidenced that PFBL efficiently regressed both CT26 and 4T1-induced solid tumors alone and in combination with 5FU/doxorubicin without affecting the health of normal host. Notably, PFBL suppressed lung metastasis of 4T1 and CT26 cells in mice with great efficacy. Analysis of tumor and cell extracts suggested that colon cancer cells died by autophagy, while breast cancer cells majorly died by caspase-dependent apoptosis. PFBL actions involved AMPK-dependent inhibition of mTORC1 and subsequent increase in LC3II, PARP1, CDK4 and Cyclin D1 levels in both HCT116 and MCF7 cells; an elevation of intracellular ROS level was the major cause of death in both the cancer types. PFBL treatment also reversed the EMT marker expressions in in vivo and in vitro. ConclusionPFBL regressed colon and breast cancer metastasis through distinct mechanisms with little effect on healthy mice. The present study underscored PFBL as a novel anti-tumor and anti-metastasis candidate warranting further testing in clinical settings.

cancer biology↗

bioRxiv2024

Transcriptomic alterations including p53 pathway dysregulation prime DNMT3A mutant cells for transformation

DNMT3A mutations are prevalent in haematologic malignancies. Our mouse model introduced the murine homologue (R878H) of the human hotspot R882H mutation into the mouse Dnmt3a locus, resulting in globally reduced DNA methylation in all tissues. Mice with heterozygous R878H mutations developed {gamma}-radiation induced thymic lymphoma more rapidly than control mice, suggesting a vulnerability to stress stimuli in Dnmt3aR878H/+ cells. In competitive transplantations, Dnmt3aR878H/+ Lin-Sca-1+Kit+ (LSK) cells had a competitive advantage over wt cells, indicating a self-renewal phenotype at the expense of differentiation. RNA-sequencing of Dnmt3aR878H/+ LSKs exposed to low dose {gamma}-radiation showed downregulation of the p53 pathway. Accordingly, reduced PUMA expression was observed by flow cytometry in the bone marrow of {gamma}-irradiated Dnmt3aR878H/+ mice due to altered p53 signalling. These findings provide new insights as to how DNMT3A mutations cause subtle changes in the transcriptome of LSK cells which contribute to their increased self-renewal and propensity for malignant transformation. SIGNIFICANCEHotspot DNMT3A R882H mutations are overrepresented in leukaemia suggesting that they confer a susceptibility to disease if further mutations are acquired. To advance therapies for DNMT3A mutant disease, it is essential to understand the mechanisms by which this mutation primes cells for malignant transformation.

cancer biology↗

bioRxiv2023

Interaction with IP6K1 supports pyrophosphorylation of substrate proteins by the inositol pyrophosphate 5-IP7

Inositol pyrophosphates (PP-IPs) are a sub-family of water soluble inositol phosphates that possess one or more diphosphate groups. PP-IPs can transfer their {beta}-phosphate group to a phosphorylated Ser residue to generate pyrophosphorylated Ser. This unique post-translational modification occurs on Ser residues that lie in acidic stretches within an intrinsically disordered protein sequence. Serine pyrophosphorylation is dependent on the presence of Mg2+ ions, but does not require an enzyme for catalysis. The mechanisms by which cells can regulate this enzyme-independent modification are still unknown. Here, we show that IP6K1, an enzyme responsible for the synthesis of the PP-IP 5-IP7, interacts with several proteins that undergo 5-IP7 mediated pyrophosphorylation, and with CK2, a protein kinase that phosphorylates Ser residues prior to pyrophosphorylation. We characterized the interaction of IP6K1 with AP3B1, the {beta} subunit of the AP3 adaptor protein complex, which is a known pyrophosphorylation substrate. We observe the formation of a protein complex between IP6K1, AP3B1, and the catalytic -subunit of CK2, and show that disrupting IP6K1 binding to AP3B1 lowers its in vivo pyrophosphorylation. We propose that assembly of a substrate-CK2-IP6K complex would allow for coordinated pre-phosphorylation and pyrophosphorylation of the target serine residue, and provide a mechanism to regulate this enzyme-independent modification.

cell biology↗

bioRxiv2023

Analytical Comparability to Evaluate Impact of Manufacturing Changes of ARX788, an Anti-HER2 ADC in Late-Stage Clinical Development

ARX788 is an anti-HER2 antibody drug conjugate (ADC) developed using Ambrx proprietary Engineered Precision Biologics technology. The manufacturing process of ARX788 has been optimized during the course of early to late-phase clinical development. A comprehensive evaluation of side-by-side comparability between pre- and post-change process for ARX788 drug substance and drug product from a quality perspective was conducted based on ICH Q5E guidelines consisting of batch release assays, physicochemical and biophysical characterization, biological characterization, and forced degradation studies. All results have demonstrated a high degree of similarity between the pre- and post-change ARX788 drug substance batches and drug product lots, demonstrating that the process manufacturing changes did not impact product quality.

cancer biology↗

bioRxiv2023

Binding of the TRF2 iDDR motif to RAD50 highlights a convergent evolutionary strategy to inactivate MRN at telomeres

Telomeres protect chromosome ends from unscheduled DNA repair, including from the MRN (MRE11, RAD50, NBS1) complex, which plays a critical role in the processing of double-stranded DNA breaks (DSBs). MRN orchestrates activation of the ATM kinase in the cellular DNA damage response (DDR), promotes DNA end-tethering aiding the nonhomologous end joining (NHEJ) pathway, and initiates DSB resection through the MRE11 nuclease. A previously identified protein motif (MIN, for MRN inhibitor) downregulates MRN activity via binding to RAD50 and has independently arisen at least twice, through convergent evolution of telomeric proteins Rif2 and Taz1, in budding and fission yeast respectively. We now provide a third example of convergent evolution for this binding mechanism for MRN at telomeres, by demonstrating that the iDDR motif of the human shelterin protein TRF2 binds to human RAD50 at the same site engaged by the MIN motif in the yeast proteins, despite lacking sequence homology. Modelling for the human CtIP interaction with RAD50 (necessary for activation of MRE11), and for the budding and fission yeast counterparts Sae2 and Ctp1, indicates that the interaction is mutually exclusive with binding of the iDDR/MIN motifs, pointing to a conserved mechanism for inhibition of MRN nuclease activity at telomeres.

biochemistry↗

bioRxiv2022

Deletion of the transcriptional regulator TFAP4 accelerates c-MYC-driven lymphomagenesis

Many lymphoid malignancies arise from deregulated c-MYC expression in cooperation with additional genetic lesions. While many of these cooperative genetic lesions have been discovered, DNA sequence data suggest that many more do exist. However, their contributions to c-MYC driven lymphomagenesis have not yet been investigated. We identified TFAP4 as a potent suppressor of c-MYC driven lymphoma development in a previous genome-wide CRISPR knockout screen in primary cells in vivo (Mizutani et al, 2022). CRISPR deletion of TFAP4 in E-MYC transgenic hematopoietic stem and progenitor cells (HSPCs) significantly accelerated c-MYC-driven lymphoma development in mice. TFAP4 deficient E-MYC lymphomas all arose at the pre-B cell stage. Characterization of the transcriptional profile of pre-leukemic pre-B cells in E-MYC/Cas9/sgTFAP4 transplanted mice, revealed that TFAP4 deletion reduced expression of several master regulators of B cell differentiation, such as Spi1, SpiB and Pax5, which all have been shown to be bound by TFAP4. We therefore conclude that loss of TFAP4 leads to a block in differentiation during early B cell development, causing accelerated c-MYC-driven lymphoma development.

cancer biology↗

bioRxiv2022

Preclinical efficacy of bacosides-lauric acid nano-herbal formulation incomparison to rivastigmine for treatment of Alzheimer's disease

Despite decades of rigorous scientific endeavors for Alzheimers disease (AD) drug development, massive failures in clinical trials is continuously posing healthcare and societal burden. Currently recommended single targeted drugs including rivastigmine with limited bioavailability can alleviate AD symptoms only for a limited period of time but unable to reverse the disease progression. Recent evidences consider poly-pharmacological and multi-targeted agents aiming at amyloid and tau burden, neuroinflammation, neuroprotection and cognitive enhancement as potential treatment options. In this regard, bioactive herbal compounds with holistic action and minimal adversities have gained prominence, though lacunae in their scientific validation and limited bio-permeability to cross BBB represent major hurdles. Previously, we showed that lactoferrin conjugated PEG-S-S-PLA-PCL-OH efficaciously delivered herbal compounds to brain and such nano-herbal formulation of bacosides-lauric acid (BAN-LAN) attenuated neuronal damages induced by scopolamine in vitro. Here, we tested the preclinical potential of BAN-LAN in reversal of AD pathologies in 5XFAD transgenic mice. Our nano-herbal formulation substantially reduced amyloid burden by clearing A{beta} plaques in the hippocampus of 5XFAD mice and also attenuated a{beta}42 induced alterations in AD associated gene expression in hippocampal neurons in vitro. It showed neuroprotection by rescuing neuronal damage and promoting neurogenesis in the hippocampus of AD transgenic mice. Anti-neuroinflammatory properties were also exhibited by the formulation as evident from inhibition of hippocampal astrocytic and microglial activation in 5XFAD mice. BAN-LAN showed cognitive efficacy by restoring memory impairment in AD transgenic mice and effects were more pronounced than unconjugated natural form and rivastigmine. These findings suggest that BAN-LAN may serve as a promising therapeutic agent for AD with better brain penetration and targeting multiple AD pathways.

pharmacology and toxicology↗

bioRxiv2022

H4K20me1 plays a dual role in transcriptional regulation during regeneration and axispatterning of Hydra

The evolution of the first body axis in the animal kingdom and an extensive ability to regenerate makes Hydra, a Cnidarian, an excellent model system for understanding the underlying epigenetic mechanisms. We identify that SETD8 is critical for regeneration due to its interaction with {beta}-catenin to fine-tune the underlying gene regulatory network. Its target histone mark, H4K20me1, colocalizes with transcriptional activation machinery locally at the {beta}-catenin bound TCF/LEF binding sites on the promoters of head-associated genes, marking an epigenetic activation node. Contrastingly, genome-wide analysis of the H4K20me1 occupancy revealed a negative correlation with transcriptional activation. We propose H4K20me1 as a general repressive histone mark in Cnidaria and describe its dichotomous role in transcriptional regulation in Hydra.

molecular biology↗