Search bioRxiv⌕ Search

Biology subjects

Dubey, P.

Publications and source records attributed to Dubey, P..

At least 19 recordsLinked to original sources
bioRxiv2026

Mapping Light-Induced Conformational Dynamics of Pigeon Cryptochrome 4 by HDX-MS: Structural Transitions from Spin Pair Formation to Activated Conformational States

The navigational prowess of migratory birds is thought to arise from light-dependent radical-pair chemistry in cryptochrome 4 (CRY4), yet the slow structural transitions that couple photochemistry to signaling remain elusive. Here, we combine temperature-controlled steady-state UV-visible spectroscopy and hydrogen-deuterium exchange mass spectrometry (HDX-MS) to elucidate the photochemical and conformational dynamics of pigeon CRY4 (ClCRY4). Steady-state measurements at 5-25 {degrees}C reveal that lower temperatures slow FAD photoreduction and prolong the FAD neutral semiquinone signaling state. This occurs without a solvent kinetic isotope effect, implicating a conformational change rather than proton transfer as the rate determining step in FAD neutral semiquinone formation. Simultaneous HDX-MS under blue-light exposure identifies protection near the FAD-binding site and C-terminal region. To enhance sensitivity, we developed a pump-probe HDX-MS approach at 10 {degrees}C. This reveals eight peptides (within the phosphate-binding loop, protrusion motif, electron-transfer-chain loops and C-terminal tail) that exhibit rapid ([≤]10 s) and sustained light-induced protection, delineating early conformational rearrangements as a prerequisite for FAD neutral semiquinone accumulation. The findings of slower onset HDX protection as well as a bimodal pattern of deuterium uptake in the phosphate-binding loop further identify a local redistribution of conformational substates on the time scale of the accumulation of the signaling species. Site specific mutagenesis within the CTT supports the findings, which lead to a model in which blue light triggers rapid clamping down of protein near the two regions of spin pair separation, followed by a rate limiting closure of a surface loop. The resolution of time-dependent structural transitions that follow photoactivation of CRY4 resolves the interface between quantum radical-pair formation and classical conformational changes, while providing an enhanced structural framework for the molecular events that underlie avian magnetoreception.

biophysics↗
bioRxiv2026

Optimization and Parallelization of Sorting by Interfacial Tension (SIFT) for High-Throughput Metabolic Cell Sorting

A systematic optimization of throughput and operational stability in Sorting by Interfacial Tension (SIFT) is presented. Reducing droplet size and enabling a broader distribution of droplet trajectories increased the number of droplets processed per sorting element, resulting in about a four fold improvement in throughput from 30 to 125 droplets per second. Throughput was further enhanced through device parallelization, with devices incorporating two and four independent sorting regions demonstrated. These configurations distributed droplets evenly across sorting elements that exhibited comparable pH sorting thresholds, indicating similar flow conditions and drag forces within each region. Among the designs evaluated, the two-element configuration provided the optimal balance of throughput, robustness, and simplicity, achieving maximum throughputs of about 250 droplets per second. Throughput and pH sorting thresholds were preserved throughout two hours of continuous sorting. The improved platform was applied to examine the relationship between cellular glycolysis and iron homeostasis at the single-cell level for Jurkat cells, revealing a subpopulation of highly glycolytic cells with significantly elevated iron uptake, consistent with prior reports linking iron regulation and T cell metabolism. Collectively, these advances expand the scale, stability, and biological applicability of SIFT, enabling large-scale functional studies while facilitating the capture of rare and metabolically distinct cell populations.

bioengineering↗
bioRxiv2026

BRD4 represses developmental and neuronal genes through interactions with polycomb complexes

BRD4 is best known as a transcriptional co-activator, yet heterozygous loss-of-function variants cause craniofacial and neurodevelopmental abnormalities through unclear mechanisms. Using human embryonic stem cells and neural organoids as an in vitro model of human embryonic brain development, we show that BRD4 represses polycomb-regulated developmental and neuronal genes. BRD4 co-occupies bivalent promoters with PRC1.6 and directly interacts with PCGF6 and RING1B through its C-terminal domain. H3K23ac contributes to BRD4 recruitment through BD2, linking acetylated chromatin recognition to polycomb-associated repression. Acute BRD4 depletion alters PRC1.6 occupancy, reduces ubiquitination of H2AK119 and rapidly increases developmental gene transcription. In neural organoids, BRD4 BD2 mutations alter neuronal cell composition and increase expression and chromatin accessibility associated with neuronal transcription-factor programmes. These findings establish BRD4 as a context-dependent chromatin regulator that prevents premature activation of developmental genes and provide mechanistic insight into BRD4-associated neurodevelopmental disorders.

molecular biology↗
bioRxiv2025

A yeast model of 5-oxoproline accumulation reveals a general toleration to 5-oxoproline

5-oxoproline (5-OP) or pyroglutamic acid is an intermediate of the degradation arc of the glutathione cycle. It is metabolized into glutamate through the action of the 5-oxoprolinase enzyme, the only enzyme known to act on this metabolite. 5-OP has long been known to be relatively inert with a proposed role as an osomoprotectant. Recent studies on the 5-oxoprolinase enzyme in mammalian cells have, however, shown that knockdown or deletions of the 5-oxoprolinase make mice (and humans) prone to heart failure. This was ascribed to oxidative stress due to a two-fold elevation in 5-OP. To examine the consequences of 5-oxoproline accumulation more rigorously, we have created a yeast model for 5-oxoproline accumulation. We observed retardation of growth only when intracellular levels of 5-OP were increased 12-20 fold over the normal levels. A transcriptomics study was carried out under these conditions. We observed that while a large number of genes were regulated upto 2-fold, there were no single prominent pathways amongst them. Among the key genes upregulated were different efflux pumps. Using knockouts and also overexpression of selected genes, we could observe that many of the upregulated genes were involved in the cellular response to 5-OP accumulation. However, it did not appear that there was any significant oxidative stress response. The study suggests a need to reevaluate previous suppositions of the 5-OP induced oxidative stress response. Instead, we propose an alternative model to explain the possible consequences of 5-oxoprolinase deficiency based on these findings made with the yeast model.

systems biology↗
bioRxiv2025

Caspase-11 Mediated Hyperinflammation Impairs CD8⁺ T Cell Immunity and Viral Clearance in Severe SARS-CoV-2 Infection

Severe SARS-CoV-2 infection is characterized by lung hyperinflammation, impaired interferon responses, and defective T-cell activation, yet the molecular drivers of these immune dysregulations remain incompletely understood. Caspase-11 (CASP11), a key mediator of the non-canonical inflammasome, has been shown to mediate an innate hyperinflammatory response and cytokine release in a non-severe, non-lethal SARS-CoV-2 infection model. However, the role played by CASP11 in severe SARS-CoV-2 disease and how it impacts adaptive immunity is not identified. Here, we newly discover that CASP11 exacerbates severe SARS-CoV-2 pathogenesis by amplifying early innate immune responses while concurrently impairing antiviral CD8 T-cell immunity. Using global knockouts, reciprocal bone marrow chimeras, and phagocyte-monocyte system (PMS) cell-specific CASP11 deletion models, we show that CASP11 deletion in monocyte-derived cells reduces lung inflammation, enhances type I and II interferon signaling, and promotes robust virus-specific effector CD8 T-cell response. This was associated with enhanced viral clearance and improved survival, even under lethal infection conditions. Importantly, CASP11 KO mice also exhibited faster resolution of post-viral inflammation, suggesting a role in long-term immune remodeling. These findings position CASP11 as a promising immunomodulatory target for acute and delayed manifestations of severe SARS-CoV-2.

microbiology↗
bioRxiv2025

Identification of Scaffold Specific Energy Transfer Networks in the Enthalpic Activation of Orotidine 5'-Monophosphate Decarboxylase

AbstractOrotidine 5-monophosphate decarboxylase (OMPDC) is one of the most efficient enzyme systems studied, enhancing the decarboxylation of OMP to uridine 5-monophosphate (UMP) by ca. 17 orders of magnitude, primarily by reducing the enthalpy of activation by ca. 28 kcal/mol. Despite a substantial reduction in activation enthalpy, OMPDC requires 15 kcal/mol of activation energy post- ES complex formation. This study investigates the physical basis of how thermal energy from solvent collisions is directed into the active site of enzyme to enable efficient thermal activation of the reaction. Comparative study of temperature-dependent hydrogen-deuterium exchange mass spectrometry (TDHDX) for WT and mutant forms of enzymes has recently been shown to uncover site specific protein networks for thermal energy transfer from solvent to enzyme active sites. In this study, we interrogate region-specific changes in the enthalpic barrier for local protein flexibility using a native OMPDC from Methanothermobacter thermautotrophicus (Mt-OMPDC) and a single site variant (Leu123Ala) that alters the activation enthalpy for catalytic turnover. The data obtained implicate four spatially resolved, thermally sensitive networks that originate at different protein/solvent interfaces and terminate at sites surrounding the substrate near the substrate phosphate-binding region (R203), the substrate- ribose binding region (K42), and a reaction enhancing loop5 (S127). These are proposed to act synergistically, transiently optimizing the position and electrostatics of the reactive carboxylate of the substrate to facilitate activated complex formation. The uncovered complexity of thermal activation networks in Mt-OMPDC distinguishes this enzyme from other members of the TIM barrel family previously investigated by TDHDX. The new findings extend the essential role of protein scaffold dynamics in orchestrating enzyme activity, with broad implications for the design of highly efficient biocatalysts.

biochemistry↗
bioRxiv2025

Seo1p, a high affinity, plasma membrane transporter of the gamma-Glu-met dipeptide in yeasts and fungi

{gamma}-Glu dipeptides are ubiquitous in nature, and yet their metabolism and transport are poorly understood. Here we investigate this using the dipeptide {gamma}-Glu-met in Saccharomyces cerevisiae. {gamma}-Glu-met was efficiently utilized by S. cerevisiae and its degradation was dependent on both the glutathione degrading cytosolic Dug2p/Dug3p complex, and the vacuolar Ecm38p. Using a transcriptomics approach, followed by a genetic screen, we identified Seo1p, an orphan transporter of yeast, as the transporter of {gamma}-Glu-met. Uptake studies confirmed Seo1p as a high affinity (Km =48uM), highly specific transporter of {gamma}-Glu-met since other analogs like n-Glu-met, {gamma}-Glu-leu, {gamma}-Glu-cys, {gamma}-Glu-met-gly, methionine and methionine sulfoxide were not transported by Seo1p. Candida spp. also encoded a functional Seo1p. A second transporter, Opt2p, identified in the screen, was also investigated. However, Opt2p was not primarily involved in {gamma}-Glu-met uptake. Its deletion affected vacuolar morphology, that interfered with the degradation of the peptide through Ecm38p. These studies demonstrate how organisms have evolved dedicated pathways for the uptake of these unusual peptides.

genetics↗
bioRxiv2024

In vivo changes in zebrafish anesthetic sensitivity in response to the loss of kif5Aa are associated with the alteration of mitochondrial motility

Anesthetic and sedative drugs are small compounds known to bind to hundreds of proteins. One intriguing binding partner of propofol is the kinesin motor domain, kif5A, a neuronal mitochondrial transport protein. Here, we used zebrafish WT and kif5Aa KO larval behavioral assays to assess anesthetic sensitivity and combined that with zebrafish primary neuronal cell culture to probe for alteration in mitochondrial motility. We found that the loss of kif5Aa increases behavioral sensitivity to propofol and etomidate, with etomidate hypersensitivity greater than propofol. In contrast, kif5Aa KO animals were resistant to the behavioral effects of dexmedetomidine. Finally, WT and kif5Aa KO larvae responded similarly to the behavioral effects of ketamine. Propofol inhibited the anterograde motility of mitochondria in WT zebrafish neurons, while etomidate inhibited mitochondrial motility in both anterograde and retrograde directions; neither drug altered mitochondrial motility in the kif5Aa knockout (KO) neurons. In contrast, dexmedetomidine enhanced retrograde mitochondrial motility in both WT and kif5Aa KO animals. Finally, ketamine had little significant effect on mitochondrial motility in either mutant or WT animals. These data demonstrate that each anesthetic/sedative drug affects the motor protein machinery uniquely and is associated with unique changes in behavior. Understanding how different anesthetic compounds alter neuron motor proteins will be important in defining how anesthetics alter neuronal signaling and energetic dynamics.

neuroscience↗
bioRxiv2024

Modelling Amoebic Brain Infection Caused by Balamuthia mandrillaris Using a Human Cerebral Organoid

The lack of disease models adequately resembling human tissue has hindered our understanding of amoebic brain infection. Three-dimensional structured organoids provide a microenvironment similar to human tissue. This study demonstrates the use of cerebral organoids to model a rare brain infection caused by the highly lethal amoeba Balamuthia mandrillaris. Cerebral organoids were generated from human pluripotent stem cells and infected with clinically isolated B. mandrillaris trophozoites. Histological examination showed amoebic invasion and neuron damage following coculture with the trophozoites. The transcript profile suggested an alteration in neuron growth and a proinflammatory response. The release of intracellular proteins specific to neuronal bodies and astrocytes was detected at higher levels postinfection. The amoebicidal effect of the repurposed drug nitroxoline was examined using the human cerebral organoids. Overall, the use of human cerebral organoids helped unravel the host response, identify biomarkers for brain injury, and in the testing of a potential amoebicidal drug in a context similar to the human brain. Author summaryBrain inflammation caused by a free-living amoeba Balamuthia mandrillaris is really rare but life-threatening infectious disease. Given its rarity and difficulty to obtain a clinical isolate for further study, this disease has been neglected despite high mortality rate. Many gaps in our understanding of the disease remain opened. Emergence of the organoid platform allows modelling human diseases in an in vitro setting, leading to identification of potential molecular pathway as drug targets. Thus, this work attempts to deploy a human brain organoid to reveal such pathways, which are altered by the amoeba. A strain of B. mandrillaris was isolated from human biopsied brain. In the co-culture between brain organoid and amoeba, data suggested an alteration in neuron growth and increase of proinflammatory response. Brain organoid release brain trauma biomarkers. Importantly, we show therapeutic effect of the antibiotic nitroxoline using the human cerebral organoids. Thereby, the use of the human cerebral organoids unravels the host response, identify potential biomarkers, and provide an alternative way for testing a potential drug targeting the amoeba. O_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC="FIGDIR/small/588187v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@1ff46eaorg.highwire.dtl.DTLVardef@88ea32org.highwire.dtl.DTLVardef@c78533org.highwire.dtl.DTLVardef@f9fa8c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗
bioRxiv2024

Understanding the effects of oxytocin receptor variants on OXT-OXT receptor binding: A mathematical model

Approximately half of U.S. women giving birth annually receive Pitocin, the synthetic form of oxytocin (OXT), yet its effective dose can vary significantly. This variability presents safety concerns due to unpredictable responses, which may lead to adverse outcomes for both mother and baby. To address the need for improved dosing, we developed a data-driven mathematical model to predict OXT receptor (OXTR) binding. Our study focuses on five prevalent OXTR variants (V45L, P108A, L206V, V281M, and E339K) and their impact on OXT-OXTR binding dynamics in two distinct cell types: human embryonic kidney cells (HEK293T), commonly used in experimental systems, and human myometrial smooth muscle cells, containing endogenous OXTR. We parameterized the model with cell-specific OXTR surface localization measurements. To strengthen the robustness of our study, we conducted a comprehensive meta-analysis of OXT- OXTR binding, enabling parameterization of our model with cell-specific OXT-OXTR binding kinetics (myometrial OXT-OXTR Kd = 1.6 nM, kon = 6.8 x 105 M-1 min-1, and koff = 0.0011 min-1). Our meta-analysis revealed significant homogeneity in OXT-OXTR affinity across experiments and species with a Kd = 0.52 - 9.32 nM and mean Kd = 1.48 {+/-} 0.36 nM. Our model achieves several valuable insights into designing dosage strategies. First, we predicted that the OXTR complex reaches maximum occupancy at 10 nM OXT in myometrial cells and at 1 {micro}M in HEK293T cells. This information is pivotal for guiding experimental design and data interpretation when working with these distinct cell types, emphasizing the need to consider effects for specific cell types when choosing OXTR-transfected cell lines. Second, our model recapitulated the significant effects of genetic variants for both experimental and physiologically relevant systems, with V281M and E339K substantially compromising OXT-OXTR binding capacity. These findings suggest the need for personalized oxytocin dosing based on individual genetic profiles to enhance therapeutic efficacy and reduce risks, especially in the context of labor and delivery. Third, we demonstrated the potential for rescuing the attenuated cell response observed in V281M and E339K variants by increasing the OXT dosage at specific, early time points. Cellular responses to OXT, including Ca2+ release, manifest within minutes. Our model indicates that providing V281M- and E339K-expressing cells with doubled OXT dose during the initial minute of binding can elevate OXT-OXTR complex formation to levels comparable to wild-type OXTR. In summary, our study provides a computational framework for precision oxytocin dosing strategies, paving the way for personalized medicine.

systems biology↗
bioRxiv2024

Opposing effects of acellular and whole cell pertussis vaccines on Bordetella pertussis biofilm formation, Siglec-F+ neutrophil recruitment and bacterial clearance in mouse nasal tissues

Despite global vaccination, pertussis caused by Bordetella pertussis (Bp) is resurging. Pertussis resurgence is correlated with the switch from whole cell vaccines (wPV) that elicit TH1/TH17 polarized immune responses to acellular pertussis vaccines (aPV) that elicit primarily TH2 polarized immune responses. One explanation for the increased incidence in aPV-immunized individuals is the lack of bacterial clearance from the nose. To understand the host and bacterial mechanisms that contribute to Bp persistence, we evaluated bacterial localization and the immune response in the nasal associated tissues (NT) of naive and immunized mice following Bp challenge. Bp resided in the NT of unimmunized and aPV-immunized mice as biofilms. In contrast, Bp biofilms were not observed in wPV-immunized mice. Following infection, Siglec-F+ neutrophils, critical for eliminating Bp from the nose, were recruited to the nose at higher levels in wPV immunized mice compared to aPV immunized mice. Consistent with this observation, the neutrophil chemokine CXCL1 was only detected in the NT of wPV immunized mice. Importantly, the bacteria and immune cells were primarily localized within the NT and were not recovered by nasal lavage (NL). Together, our data suggest that the TH2 polarized immune response generated by aPV vaccination facilitates persistence in the NT by impeding the infiltration of immune effectors and the eradication of biofilms In contrast, the TH1/TH17 immune phenotype generated by wPV, recruits Siglec-F+ neutrophils that rapidly eliminate the bacterial burden and prevent biofilm establishment. Thus, our work shows that aPV and wPV have opposing effects on Bp biofilm formation in the respiratory tract and provides a mechanistic explanation for the inability of aPV vaccination to control bacterial numbers in the nose and prevent transmission. Author SummaryAcellular pertussis vaccine (aPV) immunized individuals maintain a nasal reservoir of Bordetella pertussis (Bp) and thus have the potential to transmit the infection to vulnerable individuals. Here we provide a mechanistic explanation for the inability of aPV to eliminate Bp from the nasal cavity. We show that following bacterial challenge of aPV immunized mice, Siglec-F+ neutrophils and other immune effectors are not recruited to the nose. Consequently, Bp remain in the nose and form biofilms. In contrast, whole cell pertussis (wPV) immunized mice produce immune effectors following bacterial challenge that recruit Siglec-F+ neutrophils to the nose. Bp burden is cleared from the nasal tissues, thereby preventing bacterial persistence and the formation of biofilms.

immunology↗
bioRxiv2022

Prime-pull immunization of mice with a BcfA-adjuvanted vaccine elicits mucosal immunity and prevents SARS CoV-2 infection and pathology

Vaccines against SARS-CoV-2 that induce mucosal immunity capable of preventing infection and disease remain urgently needed. We show that intramuscular priming of mice with an alum and BcfA-adjuvanted Spike subunit vaccine, followed by a BcfA-adjuvanted mucosal booster, generated Th17 polarized tissue resident CD4+ T cells, and mucosal and serum antibodies. The serum antibodies efficiently neutralized SARS-CoV-2 and its Delta variant, suggesting cross-protection against a recent variant of concern (VOC). Immunization with this heterologous vaccine prevented weight loss following challenge with mouse-adapted SARS-CoV-2 and reduced viral replication in the nose and lungs. Histopathology showed a strong leukocyte and polymorphonuclear (PMN) cell infiltrate without epithelial damage in mice immunized with BcfA-containing vaccines. In contrast, viral load was not reduced in the upper respiratory tract of IL-17 knockout mice immunized with the same formulation, suggesting that the Th17 polarized T cell responses are critical for protection. We show that vaccines adjuvanted with alum and BcfA, delivered through a heterologous prime-pull regimen, protect against SARS-CoV-2 infection without causing enhanced respiratory disease. SIGNIFICANCEThere remains a need for SARS CoV-2 booster vaccines that generate mucosal immunity and prevent transmission. We show that systemic priming followed by a mucosal booster with a BcfA-adjuvanted subunit vaccine generates neutralizing antibodies and Th17 polarized systemic and tissue-resident immune responses that provide sterilizing immunity against wildtype SARS CoV-2, and a variant of concern. Importantly, in contrast to alum alone, the addition of BcfA prevents respiratory pathology. These results suggest that a BcfA-adjuvanted mucosal booster may elicit mucosal immunity in individuals previously immunized systemically with approved vaccines. This foundational study in mice sets the stage for testing our vaccine regimen in larger animal models as a booster vaccine.

immunology↗
bioRxiv2022

Bps polysaccharide of Bordetella pertussis resists antimicrobial peptides by functioning as a dual surface shield and decoy and converts Escherichia coli into a respiratory pathogen.

Infections and disease caused by the obligate human pathogen Bordetella pertussis (Bp) are increasing, despite widespread vaccinations. The current acellular pertussis vaccines remain ineffective against nasopharyngeal colonization, carriage, and transmission. In this work, we tested the hypothesis that Bordetella polysaccharide (Bps), a member of the poly-{beta}-1,6-A-acetyl-D-glucosamine (PNAG/PGA) family of polysaccharides promotes respiratory tract colonization of Bp by resisting killing by antimicrobial peptides (AMPs). Genetic deletion of the bpsA-D locus, as well as treatment with the specific glycoside hydrolase Dispersin B, increased susceptibility to AMP-mediated killing. Bps was found to be both cell surface-associated and secreted during laboratory growth and mouse infections. Addition of bacterial supernatants containing Bps and purified Bps increased B. pertussis resistance to AMPs. By utilizing ELISA, immunoblot and flow cytometry assays, we show that Bps functions as a dual surface shield and decoy by inhibiting AMP binding. Co-inoculation of C57BL/6J mice with a Bps-proficient strain enhanced respiratory tract survival of the Bps-deficient strain. In combination, the presented results highlight the critical role of Bps as a central driver of B. pertussis pathogenesis. Heterologous production of Bps in a non-pathogenic E. coli K12 strain increased AMP resistance in vitro, and augmented bacterial survival and pathology in the mouse respiratory tract. Therefore, by conferring virulence traits across bacterial genera, Bps transforms a primarily intestinal and urinary tract bacterium into a respiratory pathogen. These studies can serve as a foundation for other PNAG/PGA polysaccharides and for the development of an effective Bp vaccine that includes Bps. Author summaryPertussis or whooping cough, caused by the obligate human pathogen Bordetella pertussis (Bp), is resurging in many countries. Currently, the mechanism by which B. pertussis subverts and resists host immunity is poorly known. In this manuscript, we examined the role of the B. pertussis polysaccharide Bps in promoting resistance to antimicrobial peptides (AMPs), a critical component of host immune defense. We show that the presence of Bps on the bacterial cell surface enhanced AMP resistance. Bps was secreted both during bacterial growth and during mouse infections. We further found that Bps functioned both as a surface shield and decoy, thereby inhibiting AMP binding. Simultaneous infection of mice with Bps-proficient and Bps- deficient strains resulted in greater survival of the Bps-deficient strain in the mouse respiratory tract. Finally, production of Bps in a non-pathogenic E. coli strain increased AMP resistance in vitro, and increased bacterial survival and heightened pathology in the mouse respiratory tract. Our study provides new insights into how B. pertussis has evolved to survive in the mammalian respiratory tract. Additionally, these studies underscore the potential of a single virulence factor to convert a non-pathogenic bacterium into a respiratory tract pathogen.

microbiology↗
bioRxiv2021

Evaluation of Correlation between CD44, Radiotherapy Response and Survival Rate in Patients with Advanced Stage of Head and Neck Squamous Cell Carcinoma (HNSCC)

PurposeCancer stem cells (CSCs) constitute a distinctive subpopulation of cancer cells that are competent in tumor initiation, invasion, recurrence, and resistance to chemo-radiotherapy. CD44, a hyaluronic acid (HA) receptor has been considered as a potential CSC marker in head and neck cancer. The purpose of this study is to evaluate the correlation between CD44 and clinicopathological parameters, treatment response, survival, and recurrence. MethodsCD44 expression was examined by immunohistochemistry (IHC) in 90 samples of head and neck squamous cell carcinoma (HNSCC) confirmed patients. Expression of CD44 and its association with clinicopathological parameters, treatment response, and survival was determined. ResultsIn all HNSCC patient samples, CD44 was expressed consistently at different intensities. Tumor size (p<0.001), stage (p<0.001) and treatment response (p<0.001) showed statistically significant association with CD44 expression. Alcohol and CD44 were observed as independent predictors of response to radiotherapy by using multivariate ordinal logistic regression analysis. Analysis of 2 years overall survival (OS) showed that CD44 expression (p=0.02), tumor size (p=0.001), lymph node status (p<0.001), stage (p<0.001) and grade (p=0.007) were significantly associated with OS. By using Cox regression analysis, lymph node status (p=0.001), grade (p<0.001), recurrence (p<0.001) and CD44 expression (p=0.003) were found to be potential independent predictors of OS. ConclusionOur findings suggest that CD44 contributes to resistance to radiotherapy and poor OS. The results also suggest that except for CD44 there could be other factors such as lymph node metastasis, grade, and alcohol which should be investigated as potential targets for therapy.

cancer biology↗
bioRxiv2021

The novel leishmanial Copper P-type ATPase plays a vital role in intracellular parasite survival

Copper is essential for all life forms; however in excess it is extremely toxic. Toxic properties of copper are utilized by hosts against various pathogenic invasions. Leishmania, in its both free-living and intracellular forms, was found to exhibit appreciable tolerance towards copper-stress. To determine the mechanism of copper-stress evasion employed by Leishmania we identified and characterized the hitherto unknown Copper-ATPase in Leishmania major and determined its role in parasites survival in host macrophage cells. L. major Cu-ATPase, LmATP7, exhibits high homology with its orthologues at multiple conserved motifs. In promastigotes, LmATP7 localized to the plasma membrane with a fraction in intracellular puncta. Upon copper treatment, LmATP7 expression increases few folds. LmATP7 is capable of complementing copper transport in Cu-ATPase-{Delta} yeast strain. Promastigotes overexpressing LmATP7 exhibits higher survival upon copper stress indicating efficacious copper export compared to wild type and heterozygous LmATP7 knock-out parasites. We explored macrophage-Leishmanial interaction with respect to copper stress subjected by the host upon parasite and the parasites reciprocating response thereon to evade the stress. The Copper-P-type-ATPases ATP7A/7B serve as major copper exporters in mammals that maintain cellular copper levels. We found that Leishmania infection triggers ATP7A upregulation in macrophages. Additionally, as part of host response, ATP7A traffics from trans-Golgi network and transports copper to the endosomal and endolysosomal compartments harbouring the Leishmania amastigotes. Finally, we show LmATP7 overexpression in this parasite increased amastigote survivability within infected macrophages whereas knocking it down reduces that drastically, establishing its role in combating host-induced copper stress.

cell biology↗
bioRxiv2020

Nanoscale indentation of plasma membrane establishes a contractile actomyosin scaffold through selective activation of the Amphiphysin-Rho1-Dia/DAAM and Rok pathway

Nanoscale bending of plasma membrane increases cell adhesion, induces cell-signalling, triggers F-actin assembly and endocytosis in tissue-cultured cells. The underlying mechanisms are not very well understood. Here, we show that stretching the plasma membrane of somatic cyst cell around rigid spermatid heads generates a stable, tubular endomembrane scaffold supported by contractile actomyosin. The structure resembles an actin-basket covering the bundle of spermatid heads. Genetic analysis suggests that the actomyosin organisation is nucleated exclusively by the Formins, Diaphanous and DAAM, downstream of Rho1, recruited by the Bin-Amphiphysin-Rvs (BAR)-domain protein, Amphiphysin, around the spermatid heads. Actomyosin activity at the actin-basket gathers the spermatid heads into a compact bundle and resists the invasion of the somatic cell by the intruding spermatids. These observations revealed a new response mechanism of nanoscale bending of the plasma membrane, which generates a novel cell adhesion strategy through active clamping. HighlightsO_LIStretching the plasma membrane around a spermatid head recruits Amphiphysin and Rho1. C_LIO_LIRho1 activation triggers F-actin assembly in situ through Diaphanous and DAAM. C_LIO_LIRho1-Rok activation assembles actomyosin scaffold around the folded plasma membrane. C_LIO_LIContractile actomyosin enables plasma membrane to clamp onto the spermatid head. C_LI Author summarySperm released from the somatic enclosure is essential for male fertility. During differentiation, the somatic cell membrane, associated with dense F-actin scaffold, tightly hold each spermatid head before release. Kapoor et al., showed that the bending and stretching of the plasma membrane trigger the assembly of an actomyosin scaffold around the bent membrane, which clamps the spermatids together preventing the premature release and somatic cell penetration. This finding provides new insight into the molecular networks activated by mechanical bending of the plasma membrane.

cell biology↗
bioRxiv2020

BAG3-dependent autophagy maintains sarcomere function in cardiomyocytes

The association between reduced myofilament force-generating capacity (Fmax) and heart failure (HF) is clear, however the underlying molecular mechanisms are poorly understood. Here, we show the Fmax decrease arises from impaired BAG3-mediated sarcomere turnover. Myofilament BAG3 decreased in human HF and predicted the extent of Fmax decrease. This relationship was confirmed using BAG3+/- mice, which had reduced Fmax and increased myofilament ubiquitination, suggesting impaired protein turnover. We show cardiac BAG3 operates via the chaperone-assisted selective autophagy complex (CASA), conserved from skeletal muscle, and confirm sarcomeric CASA localization is BAG3/proteotoxic stress-dependent. To determine if increasing BAG3 expression in HF would restore sarcomere proteostasis/Fmax, HF mice were treated with AAV9/BAG3. Gene therapy fully restored Fmax after four weeks and decreased ubiquitination. Using mass spectrometry, we identified several sarcomere proteins with increased ubiquitination in HF and four that decreased with AAV9/BAG3. Our findings indicate BAG3-mediated sarcomere turnover is required for myofilament functional maintenance.

physiology↗