Biology subjects

Roy, I.

Publications and source records attributed to Roy, I..

7 recordsLinked to original sources

bioRxiv2026

(E,E)-bisantrene suppresses MYC expression and displays anti-leukemic activity in acute myeloid leukemia

Background: Acute myeloid leukemia (AML) is genetically diverse with a high unmet clinical need for improved treatment options. Dysregulation of the transcription factor MYC plays a central role in AML progression and therapeutic resistance. (E,E)-bisantrene was recently found to inhibit MYC transcription and downstream activity via G-quadruplex DNA stabilization. This study aimed to evaluate the mechanism of action and preclinical activity of (E,E)-bisantrene in AML. Methods: The in vitro and in vivo activity of (E,E)-bisantrene was determined in a variety of AML models (cell lines, xenograft mouse models, and ex vivo human AML mononuclear cells). Transcriptomic, proteomic and phosphoproteomic analyses were performed after treatment with (E,E)-bisantrene. Analyses of -omics data to identify enriched pathways and upstream regulators were performed. Results: (E,E)-bisantrene demonstrated potent anti-proliferative activity across a panel of AML cell lines, inducing apoptosis and reducing S phase proportions. (E,E)-bisantrene significantly prolonged survival in cell- and patient-derived xenograft models of AML. Mechanistically, RNA-seq and proteomic analysis of MOLM13 and MV4-11 cells treated with (E,E)-bisantrene showed significant reductions in the activity of MYC and E2F, together with the cell cycle regulators CDK1/2/4/5. Transcript and protein levels of MYC were reduced in a dose- and time-dependent manner. TP53 and inflammation-associated transcript signatures were also observed. Conclusion: Anti-proliferative activity of (E,E)-bisantrene in preclinical AML models was associated with a downregulation of MYC, CDK1/2/4/5 and E2F. This study supports the ongoing clinical evaluation of (E,E)-bisantrene in AML where MYC is a clinically relevant driver of disease aggressiveness and therapy resistance.

cancer biology↗

bioRxiv2025

Single nuclear RNA sequencing shows altered microglial and astrocytic functions in post-mortem Parkinson's disease tissue

BackgroundParkinsons disease (PD) is a neurodegenerative disease marked by a progressive loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) and formation of misfolded protein aggregates. A growing body of research has implicated glial cell dysfunction in PD etiology, including the concentration of activated glial cells around protein aggregates in post-mortem tissue. Disruptions in the balance of pro- and anti-inflammatory immune response functions of the microglia and astrocytes is believed to contribute towards neurons being lost as the disease progresses. However, the molecular mechanisms remain unclear. To shed light on the role of inflammation in PD, this study analyses two public single nuclear RNA sequencing datasets of the SNpc from patient and control postmortem brain to identify altered molecular pathways in PD-associated microglia and astrocytes. ResultsThe results show that both cell types have a significant upregulation in heat shock binding and misfolded protein response pathways, likely in response to the accumulation of protein aggregates. Microglia annotated with the MKI67 marker gene show a decreased expression in PD patient derived tissue. Markers associated with activated/reactive states in astrocytes and microglia are upregulated in PD samples. Notably, expression of genes associated with resting state microglia and non-inflammatory reactive state microglia are downregulated in PD microglia, including P2RY12, CSF1R, CSF2RA, CSF3R, and TGFBR1. Concurrently, genes associated with activated microglial states such as HSP90AB1 and GPNMB are upregulated. Among the top downregulated functions, genes associated with ion channel functions are downregulated in both astrocytes and microglia. ConclusionsTaken together, the findings imply that astrocytes and microglia respond to protein misfolding pathology in PD by upregulating chaperone protein folding functions. Additionally, the profile of upregulated genes implies that pathways responding to oxidative stress are also activated. The downregulation of inflammation-associated genes in PD microglia paired with the upregulation of misfolding protein response pathways, suggests a switch from immune receptor functions to protein aggregate clearance by the end of disease stages. Finally, GPNMB emerged as a potential target for therapeutic intervention, as the one primary non-HSP gene that is significantly increased in PD-associated microglia. AbbreviationsParkinsons disease (PD); neurodegenerative diseases (NDD); dopaminergic neurons (DNs); substantia nigra pars compacta (SNpc); microglia (Mg); Lewy body dementia (LBD); single nuclear RNA sequencing (snRNA-seq), single cell RNA sequencing (scRNA-seq); Gene Ontology (GO)

neuroscience↗

bioRxiv2025

TTLL4 glutamyltransferase is a therapeutic target for NPM1-mutated acute myeloid leukemia

NPM1-mutated acute myeloid leukemia (AML) is defined by aberrant cytoplasmic localization of the mutant NPM1c protein, and therapeutic strategies targeting this specific disease remain limited. Here, we identify TTLL4, a mono-glutamate glutamyltransferase, as a selective vulnerability in NPM1c AML. TTLL4 catalyzes post-translational hyper-glutamylation of NPM1c at E126, stabilizes its cytoplasmic localization and promotes a differentiation block in leukemic cells. Multiple genetic TTLL4 inactivation approaches in human NPM1c-mutant cell lines reduce NPM1c glutamylation, trigger myeloid differentiation, and impair proliferation. Transcriptomic analyses show that TTLL4 knockdown pheno-copies NPM1c degradation and aligns with KMT2A and XPO1-targeted gene expression programs. Furthermore, Ttll4 knockout significantly prolonged survival in an NPM1c/NRAS-driven mouse AML model and promoted differentiation. We identify a small molecule, EN7, that selectively inhibits TTLL4 and recapitulates these phenotypes in NPM1c+ cells. These findings identify glutamylation as a new axis of leukemic regulation and highlight TTLL4 as a druggable epigenetic regulator in NPM1c AML.

cancer biology↗

bioRxiv2024

Unambiguous assignment of kinked beta sheets leads to insights into molecular grammar of reversibility in biomolecular condensates

Kinked-{beta} sheets are short peptide motifs that appear as distortions in {beta}-strands and often mediate formation of reversible amyloid fibrils in prion-like proteins. Standard methods for assigning secondary structures cannot distinguish these esoteric motifs. Here, we provide a supervised machine learning based structural quantification map to unambiguously characterize Kinked-{beta} sheets from coordinate data. We find that these motifs, although deviating from standard {beta}-strand region of the Ramachandran plot, scatter around the allowed regions. We also demonstrate the applicability of our technique in wresting out LARKS, which are kinked {beta}-strands with designated sequence. Additionally, from our exhaustive simulation generated conformations, we create a repository of potential kinked peptide-segments that can be used as a screening-library for assigning beta-kinks in unresolved coordinate dataset. Overall, our map for Kinked-{beta} provides a robust framework for detailed structural and kinetics investigation of these important motifs in prion-like proteins that lead to formation of amyloid fibrils.

biophysics↗

bioRxiv2024

Immunomodulatory Role of the Stem Cell Circadian Clock in Muscle Repair

The circadian clock orchestrates vital physiological processes such as metabolism, immune function, and tissue regeneration, aligning them with the optimal time of day. This study identifies an intricate interplay between the circadian clock within muscle stem cells (SCs) and their capacity to modulate the immune microenvironment during muscle regeneration. We uncover that the SC clock provokes time of day-dependent induction of inflammatory response genes following injury, particularly those related to neutrophil activity and chemotaxis. These responses are driven by rhythms of cytosolic regeneration of the signaling metabolite NAD+. We demonstrate that genetically enhancing cytosolic NAD+ regeneration in SCs is sufficient to induce robust inflammatory responses that significantly influence muscle regeneration. Furthermore, using mononuclear single-cell sequencing of the regenerating muscle niche, we uncover a key role for the cytokine CCL2 in mediating SC-neutrophil crosstalk in a time of day-dependent manner. Our findings highlight a crucial intersection between SC metabolic shifts and immune responses within the muscle microenvironment, dictated by the circadian rhythms, and underscore the potential for targeting circadian and metabolic pathways to enhance tissue regeneration.

developmental biology↗

bioRxiv2023

Gait speed is a biomarker of cancer-associated cachexia decline and recovery

BackgroundProgressive functional decline is a key element of cancer-associated cachexia. No therapies have successfully translated to the clinic due to an inability to measure and improve physical function in cachectic patients. Major barriers to translating pre-clinical therapies to the clinic include lack of cancer models that accurately mimic functional decline and use of non-specific outcome measures of function, like grip strength. New approaches are needed to investigate cachexia-related function at both the basic and clinical science levels. MethodsSurvival extension studies were performed by testing multiple cell lines, dilutions, and vehicle-types in orthotopic implantation of K-rasLSL.G12D/+; Trp53R172H/+; Pdx-1-Cre (KPC) derived cells. 128 animals in this new model were then assessed for muscle wasting, inflammation, and functional decline using a battery of biochemical, physiologic, and behavioral techniques. In parallel, we analyzed a 156-subject cohort of cancer patients with a range of cachexia severity, and who required rehabilitation, to determine the relationship between gait speed via six-minute walk test (6MWT), grip strength (hGS), and functional independence measures (FIM). Cachectic patients were identified using the Weight Loss Grading Scale (WLGS), Fearon consensus criteria, and the Prognostic Nutritional Index (PNI). ResultsUsing a 100-cell dose of DT10022 KPC cells, we extended the survival of the KPC orthotopic model to 8-9 weeks post-implantation compared to higher doses used (p<0.001). In this Low-dose Orthotopic (LO) model, both progressive skeletal and cardiac muscle wasting were detected in parallel to systemic inflammation; skeletal muscle atrophy at the fiber level was detected as early as 3 weeks post-implantation compared to controls (p<0.001). Gait speed in LO animals declined as early 2 week post-implantation whereas grip strength change was a late event and related to end of life. Principle component analysis (PCA) revealed distinct cachectic and non-cachectic animal populations, which we leveraged to show that gait speed decline was specific to cachexia (p<0.01) while grip strength decline was not (p=0.19). These data paralleled our observations in cancer patients with cachexia who required rehabilitation. In cachectic patients (identified by WLGS, Fearon criteria, or PNI, change in 6MWT correlated with motor FIM score changes while hGS did not (r2=0.18, p<0.001). This relationship between 6MWT and FIM in cachectic patients was further confirmed through multivariate regression (r2=0.30, p<0.001) controlling for age and cancer burden. ConclusionOutcome measures linked to gait are better associated with cachexia related function and preferred for future pre-clinical and clinical cachexia studies.

cancer biology↗

bioRxiv2023

Atomic-scale structural insights into the functional roles of the full low complexity domain of the hnRNPA1 protein

hnRNPA1, a protein from the heterogeneous-nuclear ribonucleoprotein fam-ily, mediates cellular processes such as RNA metabolism and DNA telomere maintenance. Besides the folded RNA recognition motifs, hnRNPA1 has a [~] 135 amino-acids long low-complexity domain (LCD) consisting of an RGG-rich region and a prion-like domain (PrLD). Biochemical data suggest that RGG-rich region modulates recognition of G-quadruplexes (GQs) in the telomeric repeats. Here, we utilize an in-house developed replica exchange technique (REHT) to generate the heterogeneous conformation ensemble of hnRNPA1-RGG and explore its functional significance in telomere maintenance. Single chain statistics and abundance of structural motifs, as well as consistency with experimentally reported struc-tural data, suggest faithful recapitulation of local interactions. We also introduce a protocol to generate functionally significant IDP-nucleic acid complex structures that corroborate well with the experimental knowledge of their binding. We find that RGG-box preferentially binds to the grooves and loops of GQs providing specificity towards certain GQ structures with its Phe, Tyr, and Asn residues forming essential hydrogen bonds and electrostatic interactions. Several of these residues were also identified as important by the reported HSQC chemical shift data. Our binding and simulations studies also revealed that a minor population of the RGG-box can destabilize telomeric GQs, thereby expediting the unfolding activities of hnRNPA1-UP1 at the telomeric end.

biophysics↗