Biology subjects

Khalil, M. I.

Publications and source records attributed to Khalil, M. I..

13 recordsLinked to original sources

bioRxiv2026

ULK1 drives NDP52-mediated selective autophagic degradation of MHC-I to promote immune evasion in HPV-positive head and neck cancer

Antigen presentation by major histocompatibility complex class I (MHC-I) is critical for tumor cell killing by CD8+ T cells. Accordingly, tumor cells downregulate MHC-I expression through multiple mechanisms, thereby evading the immune response. Importantly, lower levels of MHC-I are associated with poor responses to immune checkpoint inhibitor therapy. Our recent study has shown that the human papillomavirus (HPV) oncoproteins induce MHC-I protein ubiquitination by membrane-associated Ring-CH-type finger 8 (MARCHF8) in HPV-positive head and neck cancer (HPV+ HNC). However, the mechanism by which ubiquitinated MHC-I is degraded remains elusive. By performing genome-wide CRISPR screens, we identified components of the ULK1 and PIK3C3 complexes for autophagy initiation complexes among the top negative regulators of cell-surface MHC-I expression in HPV+ HNC cells. We show that MHC-I is recruited from the ER to autophagosomes by the cargo receptor NDP52, decreasing MHC-I levels. Further, inhibiting the initiation or nucleation steps of autophagy before autophagosome formation is critical for restoring MHC-I levels on the cell surface. Finally, genetic inhibition of autophagy initiation suppresses HPV+ HNC tumor growth in vivo and enhances the CD8+ T cell-mediated antitumor response. Our findings suggest that autophagic degradation of MARCHF8-ubiquitinated MHC-I is a key immune evasion mechanism in HPV+ HNC.

cancer biology↗

bioRxiv2025

Exploration of diuretic potential of different parts (flower, bark, leaf) of Butea Monosperma

Hypertension (HTN) or high blood pressure poses major global health concerns, and the conventional synthetic antihypertensive drugs are effective, though their long-term use is often limited due to adverse effects. Butea monosperma (B. monosperma), commonly known as the Flame of the Forest, the traditional use as medicinal plant for diuresis and other usage in rural areas in South Asia suggests a role for its antihypertensive potential. The study aimed, first to identify the diuretic constituents present from different parts (flower, bark, and leaf) of B. monosperma and to evaluate their diuretic activity through in vivo experimentation. The chemical profiling of the extracts of different parts were performed using Liquid Chromatography Mass Spectrometry (LC-MS/MS), while diuretic efficacy was assessed in Swiss Albino wistar rats. Urinary volume and electrolyte excretion (Na{square}, K{square}, and Cl{square}) were measured to elucidate the possible mechanism of action. Statistical analyses were conducted using one-way ANOVA followed by multiple comparison test, with significance set at p < 0.05. LC MS/MS analysis confirmed the presence of chlorthalidone, a thiazide-like diuretic compound, in all three plant parts under selective ionization mode. In vivo results demonstrated a significant, dose dependent increase in urine output and electrolyte excretion in treated rats compared to controls (p < 0.05). These findings provide both phytochemical and pharmacological evidence that B. monosperma possesses potent diuretic activity, supporting its traditional use and highlighting its potential as a natural source for the development of novel antihypertensive and diuretic therapeutics.

biochemistry↗

bioRxiv2025

Overexpression of GITRL by B cell IgD low (BDL) B cells is a therapeutic strategy to increase endogenous CD4+Foxp3+ T regulatory cells for the treatment of autoimmunity

Autoimmune diseases, such as multiple sclerosis (MS), are often chronic with no cures. An underlying commonality of autoimmune diseases is immune-mediated inflammation. Control of inflammation is achieved by steroids and disease-modifying therapies, which can result in severe side-effects. CD4+Foxp3+ T regulatory cells (Treg), are essential to controlling autoimmune responses and are considered a strong therapeutic target with minimal side effects. To that end, we leveraged our identification of B cell IgD low (BDL) B cells that control Treg homeostatic levels in the mouse spleen in a GITRL-dependent manner to demonstrate that overexpression of GITRL by BDL using a B cell-specific GITRL transgene (tg) was sufficient to increase endogenous Treg numbers and attenuate the disease severity of experimental autoimmune encephalomyelitis (EAE), the mouse model of MS. To determine whether increased GITRL expression by BDL could be a therapeutic strategy, WT mice were transplanted with bone marrow from GITRLtg mice. After reconstitution, GITRL expression was increased on BDL, Treg numbers were significantly elevated, and EAE was dramatically attenuated. These cumulative data further demonstrate that GITRL is a functional receptor on BDL and its overexpression in B cells is a therapeutic strategy to increase endogenous Treg numbers for treating autoimmunity.

immunology↗

bioRxiv2025

3D Tumor-Mimicking Phantom Models for Assessing NIR I/II Nanoparticles in Fluorescence-Guided Surgical Interventions

Fluorescence image-guided surgery (FIGS) offers high spatial resolution and real-time feedback but is limited by shallow tissue penetration and autofluorescence from current clinically approved fluorophores. The near-infrared (NIR) spectrum, specifically the NIR-I (700-900 nm) and NIR-II (950-1700 nm), addresses these limitations with deeper tissue penetration and improved signal-to-noise ratios. However, biological barriers and suboptimal optical performance under surgical conditions have hindered the clinical translation of NIR-I/II nanoprobes. In vivo mouse models have shown promise, but these models do not replicate the complex optical scenarios encountered during real-world surgeries. Existing tissue-mimicking phantoms used to evaluate NIR-I/II imaging systems are useful but fall short when assessing nanoprobes in surgical environments. These phantoms often fail to replicate the tumor microenvironment, limiting their predictive assessment. To overcome these challenges, we propose developing tumor-mimicking phantom models (TMPs) that integrate key tumor features, such as tunable tumor cell densities, in vivo-like nanoparticle concentrations, biologically relevant factors (pH, enzymes), replicate light absorption components (hemoglobin), and light scattering components (intralipid). These TMPs enable more clinically relevant assessments of NIR-I/II nanoprobes, including optical tissue penetration profiling, tumor margin delineation, and ex vivo thoracic surgery on porcine lungs. The components of TMPs can be further modulated to closely match the optical profiles of in vivo and ex vivo tumors. Additionally, 3D bioprinting technology facilitates a high-throughput platform for screening nanoprobes under realistic conditions. This approach will identify high-performing NIR-I/II probes with superior surgical utility, bridging the gap between preclinical findings and clinical applications, and ensuring results extend beyond traditional in vivo mouse studies. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=46 SRC="FIGDIR/small/636085v2_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@12b283aorg.highwire.dtl.DTLVardef@5e2dc7org.highwire.dtl.DTLVardef@10f6c36org.highwire.dtl.DTLVardef@189590d_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

The membrane-associated ubiquitin ligase MARCHF8 promotes cancer immune evasion by degrading MHC class I proteins

The loss of major histocompatibility complex class I (MHC-I) molecules has been proposed as a mechanism by which cancer cells evade tumor-specific T cells in immune checkpoint inhibitor (ICI)-refractory patients. Nevertheless, the mechanism by which cancer cells downregulate MHC-I is poorly understood. We report here that membrane-associated RING-CH-type finger 8 (MARCHF8), upregulated by human papillomavirus (HPV), ubiquitinates and degrades MHC-I proteins in HPV-positive head and neck cancer (HPV+ HNC). MARCHF8 knockdown restores MHC-I levels on HPV+ HNC cells. We further reveal that Marchf8 knockout significantly suppresses tumor growth and increases the infiltration of natural killer (NK) and T cells in the tumor microenvironment (TME). Furthermore, Marchf8 knockout markedly increases crosstalk between the cytotoxic NK cells and CD8+ T cells with macrophages and enhances the tumor cell-killing activity of CD8+ T cells. CD8+ T cell depletion in mice abrogates Marchf8 knockout-driven tumor suppression and T cell infiltration. Interestingly, Marchf8 knockout, in combination with anti-PD-1 treatment, synergistically suppresses tumor growth in mice bearing ICI-refractory tumors. Taken together, our finding suggests that MARCHF8 could be a promising target for novel immunotherapy for HPV+ HNC patients. One Sentence SummaryTargeting MARCHF8 restores MHC-I proteins, induces antitumor CD8+ T cell activity, and suppresses the growth of ICI-refractory tumors.

cancer biology↗

bioRxiv2023

The membrane-associated ubiquitin ligase MARCHF8 stabilizes the human papillomavirus oncoprotein E7 by degrading CUL1 and UBE2L3 in head and neck cancer

The human papillomavirus (HPV) oncoprotein E7 is a relatively short-lived protein required for HPV-driven cancer development and maintenance. E7 is degraded through ubiquitination mediated by cullin 1 (CUL1) and the ubiquitin-conjugating enzyme E2 L3 (UBE2L3). However, E7 proteins are maintained at high levels in most HPV-positive cancer cells. A previous proteomics study has shown that UBE2L3 and CUL1 protein levels are increased by the knockdown of the E3 ubiquitin ligase membrane-associated ring-CH-type finger 8 (MARCHF8). We have recently demonstrated that HPV upregulates MARCHF8 expression in HPV-positive keratinocytes and head and neck cancer (HPV+ HNC) cells. Here, we report that MARCHF8 stabilizes the E7 protein by degrading the components of the SKP1-CUL1-F-box (SCF) ubiquitin ligase complex in HPV+ HNC cells. We found that MARCHF8 knockdown in HPV+ HNC cells drastically decreases the E7 protein level while increasing the CUL1 and UBE2L3 protein levels. We further revealed that the MARCHF8 protein binds to and ubiquitinates CUL1 and UBE2L3 proteins and that MARCHF8 knockdown enhances the ubiquitination of the E7 protein. Conversely, the overexpression of CUL1 and UBE2L3 in HPV+ HNC cells decreases E7 protein levels and suppresses tumor growth in vivo. Our findings suggest that HPV-induced MARCHF8 prevents the degradation of the E7 protein in HPV+ HNC cells by ubiquitinating and degrading CUL1 and UBE2L3 proteins. IMPORTANCESince HPV oncoprotein E7 is essential for virus replication, HPV has to maintain high levels of E7 expression in HPV-infected cells. However, HPV E7 can be efficiently ubiquitinated by a ubiquitin ligase and degraded by proteasomes in the host cell. Mechanistically, the components of the E3 ubiquitin ligase complex CUL1 and UBE2L3 play an essential role in E7 ubiquitination and degradation. Here, we show that the membrane ubiquitin ligase MARCHF8 induced by HPV E6 stabilizes the E7 protein by degrading CUL1 and UBE2L3 and blocking E7 degradation through proteasomes. MARCHF8 knockout restores CUL1 and UBE2L3 expression, decreasing E7 protein levels and inhibiting the proliferation of HPV-positive cancer cells. Additionally, overexpression of CUL1 or UBE2L3 decreases E7 protein levels and suppresses in vivo tumor growth. Our results suggest that HPV maintains high E7 protein levels in the host cell by inducing MARCHF8, which may be critical for cell proliferation and tumorigenesis.

microbiology↗

bioRxiv2022

Asymmetric dimethylation of Ribosomal S6 Kinase 2 regulates its cellular localisation and pro-survival function

Ribosomal S6 Kinases (S6Ks) are critical regulators of cell growth, homeostasis, and survival, with dysregulation of these kinases being associated with various malignancies. While S6K1 has been extensively studied, S6K2 has been neglected despite its reported involvement in cancer progression. Protein arginine methylation is a widespread post-translational modification regulating a plethora of biological responses in mammalian cells. Here we report that p54-S6K2 is asymmetrically dimethylated at Arg-475 and Arg-477, two conserved residues within the AT-hook motif of the S6K2 family and some AT-hook-containing proteins. We demonstrate that PRMT1, PRMT3, and PRMT6 bind to and methylate S6K2 in vitro and in vivo. This methylation localises S6K2 to the nucleus where it rescues cells from starvation-induced cell death. Taken together, our findings highlight a novel mechanism regulating the biological function of p54-S6K2 that may be relevant to cancer where Arg-methylation is often found elevated.

molecular biology↗

bioRxiv2022

The TLK1-MK5 axis regulates motility, invasion, and metastasis of prostate cancer cells

BackgroundMetastatic dissemination of prostate cancer (PCa) accounts for majority of PCa related deaths. However, the exact mechanism of PCa cell spread is still unknown. We uncovered a novel interaction between two unrelated promotility factors, tousled-like kinase 1 (TLK1) and MAPK-activated protein kinase 5 (MK5), which initiates a signaling cascade promoting metastasis. In PCa, TLK1-MK5 signaling might be crucial as androgen deprivation therapy (ADT) leads to increased expression of both TLK1 and MK5 in metastatic patients, but in this work, we directly investigated the motility, invasive, and metastatic capacity of PCa cells following impairment of the TLK1>MK5 axis. ResultsWe conducted scratch wound repair and 3D invasion assays with LNCaP and PC3 cells to determine if TLK1 and MK5 can regulate motility and invasion. Both genetic depletion and pharmacologic inhibition of TLK1 and MK5 resulted in reduced migration and invasion through a Matrigel plug. We further elucidated the potential mechanisms underlying these effects and found that that this is likely due to reorganization of the actin fibers at lamellipodia and the focal adhesions network, in conjunction with increased expression of some MMPs that can affect penetration through the ECM. PC3, a highly metastatic cell line when assayed in xenografts, was further tested in tail-vein injection/lung metastasis model, and we showed that following inoculation, treatment with GLPG (MK5 specific inhibitor) or J54 (TLK1 inhibitor) the resulting lung tumor nodules were greatly diminished in number, and for J54 also in size. ConclusionOur data support that TLK1-MK5 axis is functionally involved in driving PCa cell metastasis and clinical aggressiveness, hence, disruption of this axis may inhibit the metastatic capacity of PCa. SIMPLE SUMMARYRecent work by us and others has illustrated the critical importance of MK5/PRAK in the invasive and motility properties of several cancer cell lines and some mouse models. In our earlier work we also uncovered that TLK1 modulates the activity of MK5 by phosphorylating S354 and two additional sites (S160 and S386).. We have now expanded on the possible mechanisms of the TLK1>MK5 pro-motility and invasive activity, and report that this may be due to reorganization of the actin fibers at lamellipodia and the focal adhesions network, in conjunction with increased expression of some MMPs. Pharmacological or genetic manipulation of prostate cancer (PCa) cell lines, LNCaP and PC3, results in drastic loss of in vitro motility and invasive capacity of these cells concomitant with alterations of their general morphology and reorganization of the focal adhesions distribution. In addition, PC3 used in tail-vein experimental metastases studies show that the use of GLPG (MK5 inhibitor) or J54 (TLK1 inhibitor) results in a drastic reduction of metastatic lung nodules, macroscopically and histologically.

cancer biology↗

bioRxiv2022

SARS-CoV-2 Protein Nsp2 Stimulates Translation Under Normal and Hypoxic Conditions

When viruses like SARS-CoV-2 infect cells, they reprogram the repertoire of cellular and viral transcripts that are being translated to optimize their strategy of replication, often targeting host translation initiation factors, particularly eIF4F complex consisting of eIF4E, eIF4G and eIF4A. A proteomic analysis of SARS-CoV-2/human proteins interaction revealed viral Nsp2 and initiation factor eIF4E2, but a role of Nsp2 in regulating translation is still controversial. HEK293T cells stably expressing Nsp2 were tested for protein synthesis rates of synthetic and endogenous mRNAs known to be translated via cap- or IRES-dependent mechanism under normal and hypoxic conditions. Both cap- and IRES-dependent translation were increased in Nsp2-expressing cells under normal and hypoxic conditions, especially mRNAs that require high levels of eIF4F. This could be exploited by the virus to maintain high translation rates of both viral and cellular proteins, particularly in hypoxic conditions as may arise in SARS-CoV-2 patients with poor lung functioning.

physiology↗

bioRxiv2022

HPV E6 upregulates MARCHF8 ubiquitin ligase and inhibits apoptosis by degrading the death receptors in head and neck cancer

The membrane-associated RING-CH-type finger ubiquitin ligase MARCHF8 is a human homolog of the viral ubiquitin ligases Kaposis sarcoma herpesvirus K3 and K5 that promote host immune evasion. Previous studies have shown that MARCHF8 ubiquitinates several immune receptors, such as the major histocompatibility complex II and CD86. While human papillomavirus (HPV) does not encode any ubiquitin ligase, the viral oncoproteins E6 and E7 are known to regulate host ubiquitin ligases. Here, we report that MARCHF8 expression is upregulated in HPV-positive head and neck cancer patients but not in HPV-negative head and neck cancer patients compared to normal individuals. MARCHF8 expression is highly upregulated by HPV oncoprotein E6-induced MYC/MAX transcriptional activation. The knockdown of MARCHF8 expression in human HPV-positive HNC cells restores cell surface expression of the tumor necrosis factor receptor superfamily (TNFRSF) death receptors, FAS, TRAIL-R1, and TRAIL-R2, and enhances apoptosis. MARCHF8 protein directly interacts with and ubiquitinates the TNFRSF death receptors. Further, MARCHF8 knockout in mouse oral cancer cells expressing HPV16 E6 and E7 augments cancer cell apoptosis and suppresses tumor growth in vivo. Our findings suggest that HPV inhibits host cell apoptosis by upregulating MARCHF8 and degrading TNFRSF death receptors in HPV-positive HNC cells. IMPORTANCESince host cell survival is essential for viruses to replicate persistently, many viruses have evolved to prevent host cell apoptosis. The human papillomavirus (HPV) oncoproteins are known to dysregulate proapoptotic proteins. However, our understanding of detailed mechanisms for HPV to inhibit apoptosis is limited. Here, we report that HPV E6 induces transcription of the membrane-associated ubiquitin ligase MARCHF8, which is upregulated in HPV-positive head and neck cancer. MARCHF8 ubiquitinates the tumor necrosis factor receptor superfamily (TNFRSF) death receptors, FAS, TRAIL-R1, and TRAIL-R2 for degradation. We further revealed that downregulation of the death receptors by MARCHF8 prevents cancer cell apoptosis and that knockout of MARCHF8 expression significantly inhibits in vivo tumor growth and enhances tumor-free survival of mice transplanted with mouse oral cancer cells expressing HPV16 E6 and E7.These results suggest that virus-induced degradation of death receptors leads to cancer cell survival in HPV-positive head and neck cancer.

microbiology↗

bioRxiv2022

Evidence that Nek1 does not phosphorylate Rad54-S572 during recovery from IR

A main focus of the work in our lab is on the activity of Tousled Like Kinase 1 (TLK1) in the area of DNA Damage and Repair. As one of its key interactor, TLK1 phosphorylates NIMA related kinase 1 (Nek1), and Nek1 was reported by Spies et al. to phosphorylate and regulate the activity of the key HRR protein Rad541, which suggested an intriguing signal transduction pathway: TLK1>Nek1>Rad54. In an effort to confirm such relations, we now report that we have not been able to reproduce key findings from that study. Specifically, we found that Nek1 does not phosphorylate RAD54-S572 as was reported. We generated Nek1-KO mouse NT1 cells2 and Nek1-Knock-down in Hek293 (same cells as in Spies et al.), and the pRAD54-S572 signal does not change with our custom Ab, with or w/o IR. When we used an Ab from the Lobrich lab, it detected an immunoreactive band of wrong size for RAD54, which also did not change after IR even in synchronized G2 cells, contrary to their report. We also note that their P-assignment was based on guessing a weak consensus Nek1 sequence, and that site-directed mutagenesis of RAD54-S572 failed to yield biological effects in their in in vitro studies1. To conclusively establish that S572 is not a site of phosphorylation of Nek1, we carried out a IVK with purified Nek1 and RAD54 followed by MS analysis of the phosphatides, which revealed several but not S572. We also could not reproduce their copurification of Nek1-RAD54 by coIP, calling into question this interaction. Neither we could reproduce their results demonstrating the importance of Nek1 for HRR using the same SceI-mediated DR-GFP conversion assays.

molecular biology↗

bioRxiv2021

Rapid and Effective Inactivation of SARS-CoV-2 by a Cationic Conjugated Oligomer with Visible Light: Studies of Antiviral Activity in Solutions and on Supports

This paper presents results of a study of a new cationic oligomer that contains end groups and a chromophore affording inactivation of SARS-Cov-2 by visible light irradiation in solution or as a solid coating on wipes paper and glass fiber filtration substrates. A key finding of this study is that the cationic oligomer with a central thiophene ring and imidazolium charged groups give outstanding performance in both killing of E. coli bacterial cells and inactivation of the virus at very short times. Our introduction of cationic N-Methyl Imidazolium groups enhances the light-activation process for both E. coli and SARS-Cov-2 but dampens the dark killing of the bacteria and eliminates the dark inactivation of the virus. For the studies with this oligomer in solution at concentration of 1 g/mL and E. coli we obtain 3 log killing of the bacteria with 10 min irradiation with LuzChem cool white lights (mimicking indoor illumination). With the oligomer in solution at a concentration of 10 g/mL, we observe 4 logs inactivation (99.99 %) in 5 minutes of irradiation and total inactivation after 10 min. The oligomer is quite active against E. coli on oligomer-coated wipes papers and glass fiber filter supports. The SARS-Cov-2 is also inactivated by the oligomer coated glass fiber filter papers. This study indicates that these oligomer-coated materials may be very useful as wipes and filtration materials.

biochemistry↗

bioRxiv2020

Viral Sequence Identification in Metagenomes using Natural Language Processing Techniques

Viral reads identification is one of the important steps in metagenomic data analysis. It shows up the diversity of the microbial communities and the functional characteristics of microorganisms. There are various tools that can identify viral reads in mixed metagenomic data using similarity and statistical tools. However, the lack of available genome diversity is a serious limitation to the existing techniques. In this work, we applied natural language processing approaches for document classification in analyzing metagenomic sequences. Text featurization is presented by treating DNA similar to natural language. These techniques reveal the importance of using the text feature extraction pipeline in sequence identification by transforming DNA base pairs into a set of characters with a term frequency and inverse document frequency techniques. Various machine learning classification algorithms are applied to viral identification tasks such as logistic regression and multi-layer perceptron. Moreover, we compared classical machine learning algorithms with VirFinder and VirNet, our deep attention model for viral reads identification on generated fragments of viruses and bacteria for benchmarking viral reads identification tools. Then, as a verification of our tool, It was applied to a simulated microbiome and virome data for tool verification and real metagenomic data of Roche 454 and Illumina for a case study.

bioinformatics↗