Biology subjects

Menon, S.

Publications and source records attributed to Menon, S..

28 records · Page 2Linked to original sources

bioRxiv2023

A host AAA-ATPase exhibits bacteriolytic activity for clearance of microbial infection

An array of host cytosol guarding factors impede bacterial proliferation and preserve cellular sterility. Amongst them, proteasomal degradation of ubiquitinated pathogens has emerged as a critical mechanism for ensuring cytosolic sanctity. We wondered how proteasomes, with their small size and inability to extract membrane-bound proteins, can eradicate pathogens. Here, we unveil a unique strategy, wherein VCP/p97, a host AAA-ATPase, eliminates pathogens by exerting mechanical force that physically unfolds and pulls out ubiquitinated proteins from bacterial membrane. Combining a single-molecule approach along with molecular dynamic simulation and in-vitro reconstitution, we demonstrate that protein extraction by p97 causes extensive membrane lysis and release of cytosolic contents from phylogenetically diverse microbes. Additionally, in an in-vivo mouse sepsis model, this segregase-dependent bactericidal effect of p97 abrogated microbial proliferation in host tissues. Overall, we discovered a distinct innate antimicrobial function of p97, that protects the host against lethal bacterial infections. One Sentence SummaryA host AAA-ATPase exhibits bacteriolytic activity.

microbiology↗

bioRxiv2023

FET fusion oncoproteins disrupt physiologic DNA repair networks and induce ATR synthetic lethality in cancer

In cancers with genetic loss of specific DNA damage response (DDR) genes (i.e., BRCA1/2 tumor suppressor mutations), synthetic lethal targeting of compensatory DDR pathways has translated into clinical benefit for patients. Whether and how growth-promoting oncogenes might also create tumor-specific vulnerabilities within DDR networks is not well understood. Here we focus on Ewing sarcoma, a FET fusion oncoprotein (EWSR1-FLI1) driven pediatric bone tumor, as a model for the class of FET rearranged cancers. Native FET family members are among the earliest factors recruited to DNA double-strand breaks (DSBs), though the function of both native FET proteins and FET fusion oncoproteins in DNA repair remains to be defined. We discover that EWSR1-FLI1 and other FET fusion oncoproteins are recruited to DNA DSBs and impair the activation and downstream signaling of the DNA damage sensor ATM. In multiple FET rearranged cancers, we establish the compensatory ATR signaling axis as a collateral dependency and therapeutic target using patient-derived xenograft models. In summary, we describe how oncogenes can disrupt physiologic DNA repair and provide the preclinical rationale for specifically testing ATR inhibitors in FET rearranged cancers as part of ongoing early phase clinical trials.

cancer biology↗

bioRxiv2022

Small molecule modulates α-Synuclein conformation and its oligomerization via Entropy Expansion

Aberrant misfolding and progressive aggregation of the intrinsically disordered protein (IDP), -synuclein, are associated with the etiology of several neurodegenerative diseases. However, the structurally heterogeneous ensemble of this IDP and lack of a well-defined binding pocket make it difficult to probe the druggability of -synuclein. Here, by building a comprehensive statistical model of the fuzzy ensemble of a millisecond-long atomistic simulation trajectory of monomeric -synuclein interacting with the small-molecule drug fasudil, we identify exhaustive sets of metastable binding-competent states of -synuclein. The model reveals that the interaction with the drug primes this IDP to explore both more compact and more extended conformational sub-ensemble than those in neat water, thereby broadening its structural repertoire in presence of small-molecule via an entropy expansion mechanism. Subsequent simulation of the dimerisation process shows that similar motif of entropic-expansion mechanism helps fasudil to retard the self-aggregation propensity of -synuclein via trapping it into multiple distinct states of diverse compaction featuring aggregation-resistant long-range interactions. Furthermore, small-molecule binding interactions in dimerisation-competent relatively extended states have a screening effect that hinders the formation of stable dimer contacts. Together, the investigation demonstrates the ability of small-molecules to have an ensemble-modulatory effect on IDPs that can be effectively utilised in therapeutic strategies probing aggregation-related diseases.

biophysics↗

bioRxiv2022

Conformational Ensemble of Monomeric α-Synuclein in Aqueous and Crowded Environments as revealed by Markov State Model

140-residue intrinsically disordered protein -synuclein (S) is known to be susceptible to environmental cues/crowders and adopts conformations that are vastly variable in the extent of secondary structure and tertiary interactions. Depending upon the nature of these interactions, some of the conformations may be suitable for its physiological functions while some may be predisposed to aggregate with other partners into higher ordered species or to phase separate. However, the inherently heterogenous and dynamic nature of S has precluded a clear demarcation of its monomeric precursor between aggregation-prone and functionally relevant aggregation-resistant states. Here, we optimally characterise a set of metastable conformations of S by developing a comprehensive Markov state model (MSM) using cumulative 108 {micro}s-long all-atom MD simulation trajectories of monomeric S. Notably, the dimension of the most populated metastable (85%) state (Rg [~] 2.59 ({+/-}0.45) nm) corroborates PRENMR studies of S monomer and undergoes kinetic transition at 0.1-150 {micro}s time-scale with weakly populated (0.06%) random-coil like ensemble (Rg [~] 5.85 ({+/-}0.43) nm) and globular protein-like state (14%) (Rg [~] 1.95 ({+/-}0.08) nm). The inter-residue contact maps identify a set of mutually interconverting aggregation-prone {beta}-sheet networks in the NAC region and aggregation-resistant long-range interactions between N- and C-terminus or helical conformations. The presence of crowding agents compacts the MSM-derived metastable conformations in a non-monotonic fashion and skews the ensemble by either introducing new tertiary contacts or reinforcing the innate contacts to adjust to the excluded-volume effects of such environments. These observations of crucial monomeric states would serve as important steps towards rationalising routes that trigger S-associated pathologies. Significance statement-synuclein, a neuronal protein, is often associated with neurogenerative diseases due to its tendency to self-assemble into higher ordered aggregates. While the monomeric precursor of this protein is intrinsically disordered, it is also known to be susceptible to biological environmental cues and adopts a wide range of conformations that are either primed for aggregation or remain in auto-inhibitory states. However, the inherently heterogenous nature of the monomeric form has prevented a clear dissection of aggregation-prone and functionally relevant aggregation-resistant states. Here, we resolve this via an atomistic characterisation of an optimal set of crucial metastable monomeric conformations via statistical modelling of computer simulated data. The investigation also sheds light on crowding-induced modulation of the ensemble and eventual fibrillation pathways.

biophysics↗

bioRxiv2020

The ubiquitylome of developing cortical neurons

TRIM9 and TRIM67 are neuronally-enriched E3 ubiquitin. Both genes are required for neuronal morphological responses to the axon guidance cue netrin-1. For example, our previously published work demonstrated that the actin polymerase VASP and the netrin receptor DCC exhibit TRIM9 dependent ubiquitylation that is lost upon netrin stimulation. Deletion of either gene in the mouse results in subtle neuroanatomical anomalies yet overt deficits in spatial learning and memory. Despite their role in neuronal form and function, the identity of few TRIM9 or TRIM67 substrates are known. Here we performed ubiquitin remnant profiling approach in cultured wildtype and knockout murine embryonic cortical neurons to identify ubiquitylated peptides and proteins, with the ultimate goal of identifying substrates of TRIM9 and TRIM67 that exhibited reduced ubiquitylation in the absence of the ligase. This work reveals the ubiquitylome of developing cortical neurons.

cell biology↗

bioRxiv2020

TRIM67 Regulates Exocytic Mode and Neuronal Morphogenesis via SNAP47

Neuronal morphogenesis involves dramatic plasma membrane expansion, likely fueled by SNARE-mediated exocytosis. Distinct fusion modes described at neuronal synapses include full-vesicle-fusion (FVF) and kiss-and-run fusion (KNR). During FVF, lumenal cargo is secreted and vesicle membrane incorporates into the plasma membrane. During KNR a transient fusion pore secretes cargo, but closes without membrane addition. In contrast, fusion modes are not described in developing neurons where plasma membrane expansion is significant. Here, we resolve individual exocytic events in developing murine cortical neurons and use new classification tools to identify four distinguishable fusion modes: two FVF-like modes that insert membrane material and two KNR-like modes that do not. Discrete fluorescence profiles suggest distinct behavior of the fusion pore with each mode. Simulations and experiments agree that FVF-like exocytosis provides sufficient membrane material for morphogenesis. We find the E3 ubiquitin ligase TRIM67 promotes FVF-like exocytosis. Our data suggest this is accomplished in part by limiting incorporation of the Qb/Qc SNARE SNAP47 into SNARE complexes and thus, SNAP47 involvement in exocytosis.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cell biology↗

bioRxiv2019

SYCP2 translocation-mediated dysregulation and frameshift variants cause human male infertility

Infertility is one of the most common disorders for men of reproductive age. To identify novel genetic etiologies, we studied a male with severe oligozoospermia and 46, XY,t(20;22)(q13.3;q11.2). We identified exclusive overexpression of SYCP2 from the der(20) allele that is hypothesized to result from enhancer adoption. Modeling the dysregulation in budding yeast resulted in disruption of the synaptonemal complex, a common cause of defective spermatogenesis in mammals. Exome sequencing of infertile males revealed three novel heterozygous SYCP2 frameshift variants in additional subjects with cryptozoospermia and azoospermia. This study provides the first evidence of SYCP2-mediated male infertility in humans.

genetics↗

bioRxiv2019

Onchocerciasis-associated epilepsy in the Democratic Republic of Congo: Clinical description and relationship with microfilarial density

Background: High epilepsy prevalence and incidence were observed in onchocerciasis-endemic villages in the Democratic Republic of Congo (DRC). We sought to investigate the clinical characteristics of onchocerciasis-associated epilepsy (OAE), and the relationship with microfilarial density. Methods: In October 2017, ivermectin-naive persons with epilepsy (PWE) were recruited from onchocerciasis-endemic areas in the Logo health zone in the DRC. Additional PWE were enrolled in the Aketi health zone, where ivermectin had been distributed annually for 14 years. Past medical history, clinical characteristics and skin snips for Onchocerca volvulus detection were obtained from participants. Bivariate and multivariable analyses were used to investigate associations with microfilarial density. Results: Of the 420 PWE in the Logo health zone, 392 were skin snipped (36.5% positive). Generalized motor seizures were most frequent (392 PWE, 93.3%), and nodding seizures were reported in 32 (7.6%) participants. Twelve PWE (3.1%) presented Nakalanga features. More skin snip-positive participants reported a family history of epilepsy (p=0.027). Eighty-one onchocerciasis-infected PWE were recruited in the Aketi health zone. Positive correlations between seizure frequency and microfilarial density were observed in Logo (Spearman-rho=0.181; p=0.0003) and Aketi (Spearman-rho=0.228; p=0.046). In the multivariable analysis which adjusted for age, gender and previous anti-epileptic drug use, factors associated with high seizure frequency included: high microfilarial density (RR=1.004, 95% CI: 1.002-1.007; p<0.001), history of nodding seizures (RR=3.852, 95% CI: 2.926-5.082; p<0.001) and shorter duration of epilepsy (RR=0.948, 95% CI: 0.928-0.968; p<0.001). In Aketi, previous ivermectin use was associated with reduced seizures (RR=0.69, 95% CI: 0.58-0.83; p<0.001). Conclusion: In onchocerciasis-endemic regions in the DRC, a wide spectrum of seizures was observed. Nodding seizures, Nakalanga features, and a positive association between microfilarial density and seizures suggest a high OAE prevalence in the study villages, requiring a double management strategy: treatment with anti-epileptic drugs and stronger onchocerciasis elimination programs.

neuroscience↗

bioRxiv2019

Outcome of radial scar/complex sclerosing lesion associated with epithelial proliferations with atypia diagnosed on breast core biopsy - Results from a multicentric UK based study

AIMS: The clinical significance of radial scar/complex sclerosing lesion (RS/CSL) with high risk lesions (epithelial atypia) diagnosed on needle core biopsy (NCB) is not well defined. We aimed at assessing the upgrade rate to carcinoma in-situ (DCIS) and invasive on the surgical excision specimen in a large cohort of RS/CSL associated with atypia. METHODS: 161 women with NCB diagnosis of a RS/CSL with atypia and follow-up histology were studied. Histological findings including different forms of the atypical lesions and final histological outcome in the excision specimens were retrieved and analysed and the upgrade rate for malignancy and invasive carcinoma calculated. RESULTS: 76% of the cases were associated with an atypical ductal hyperplasia (ADH) whereas lobular neoplasia was seen in 24%. On final histology 38 cases were malignant (overall upgrade rate of 25%); 12 invasive and 27 DCIS. The upgrade differed according to the type of atypia and was highest for ADH (35%). When associated with lobular neoplasia the upgrade rate was 12%. The upgrade rates variability was also considerably lower and showing less variability when considering the upgrade to invasive carcinoma alone. CONCLUSION: The upgrade rate for ADH diagnosed on NCB with RS is similar to that of ADH without RS and therefore should be managed similarly. RS associated with LN is less frequently associated with malignant outcome. Most lesions exhibiting some degree of atypia showed similar upgrade rate to invasive carcinoma. Management of RS should be based on the concurrent atypical lesion.

pathology↗

bioRxiv2017

TRIM9-dependent ubiquitination of DCC constrains kinase signaling, exocytosis, and axon branching

Extracellular netrin-1 and its receptor DCC promote axon branching in developing cortical neurons. Netrin-dependent morphogenesis is preceded by multimerization of DCC, activation of FAK and Src family kinases, and increases in exocytic vesicle fusion, yet how these occurrences are linked is unknown. Here we demonstrate that TRIM9-dependent ubiquitination of DCC blocks the interaction with and phosphorylation of FAK. Upon netrin-1 stimulation TRIM9 promotes DCC multimerization, but TRIM9-dependent ubiquitination of DCC is reduced, which promotes an interaction with FAK and subsequent FAK activation. We found that inhibition of FAK activity blocks elevated frequencies of exocytosis in vitro and elevated axon branching in vitro and in vivo. Although FAK inhibition decreased SNARE-mediated exocytosis, assembled SNARE complexes and vesicles adjacent to the plasma membrane were increased, suggesting a novel role for FAK in the progression from assembled SNARE complexes to vesicle fusion in developing murine neurons.\n\nAbbreviations used in this paper

cell biology↗