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Yousif, A.

Publications and source records attributed to Yousif, A..

6 recordsLinked to original sources

Vitamin K2 Limits Ferroptosis-Associated Lipid Peroxidation and Attenuates Aortic Valve Stenosis

BackgroundCalcific aortic valve stenosis (AS) is the most common valvular heart disease in the aging population and lacks effective pharmacological therapy. Oxidative stress is a key feature of valvular remodeling, yet the mechanisms linking oxidative injury to calcification remain unclear. Ferroptosis, a lipid peroxidation-driven form of regulated cell death, has emerged as a key mediator of oxidative tissue injury and may contribute to cardiovascular disease. Vitamin K was recently identified as a suppressor of ferroptosis and cardiovascular calcification, but whether ferroptosis links vitamin K status to disease progression in AS remains unknown. Methods and ResultsWe investigated the role of lipid peroxidation and ferroptosis in AS and their modulation by vitamin K2 using a translational approach. In human stenotic aortic valves, lipid peroxidation was markedly increased and localized to calcified regions, consistent with a ferroptosis-associated microenvironment. In primary human valvular interstitial cells (VICs), pro-calcific conditions induced lipid peroxidation and a pro-ferroptotic state. Pharmacological induction of ferroptosis enhanced VIC calcification, whereas its inhibition attenuated mineralization, supporting a causal role in osteogenic remodeling. Impaired vitamin K status was associated with increased valvular lipid peroxidation in AS patients. Conversely, vitamin K2 attenuated lipid peroxidation, preserved cell viability under ferroptotic stress, and partially normalized pro-ferroptotic and inflammatory transcriptional programs in VICs. In a murine model of AS, dietary vitamin K2 supplementation attenuated disease progression, reduced transvalvular gradients, and decreased valvular inflammation and lipid peroxidation-associated pathways. Finally, in a prospective cohort of patients with aortic sclerosis to moderate AS (n = 157), circulating undercarboxylated osteocalcin, a marker of impaired vitamin K status, was independently associated with accelerated disease progression. ConclusionsVitamin K2 counteracts ferroptosis-associated lipid peroxidation in AS and attenuates disease severity in vivo. Impaired vitamin K status is independently associated with accelerated progression in patients. These findings position vitamin K2 as a potential disease-modifying strategy and vitamin K status as a prognostic marker in AS. What Is New?O_LIFerroptotic lipid peroxidation is enriched in calcified regions of human stenotic aortic valves. Pharmacological induction of ferroptosis increases, and its inhibition reduces, calcification of human valvular interstitial cells, indicating a causal contribution to valvular mineralization. C_LIO_LIVitamin K2 suppresses ferroptotic lipid peroxidation, preserves cell viability under ferroptotic stress, and shifts pro-oxidative and pro-inflammatory transcriptional programs in human valvular interstitial cells toward a protective state. C_LIO_LIIn an in vivo model of aortic stenosis, dietary vitamin K2 attenuated hemodynamic progression, with lower peak transvalvular velocity and mean gradient, and reduced valvular inflammation and lipid peroxidation, without affecting coagulation C_LIO_LIIn a prospective cohort of 157 patients with aortic sclerosis to moderate stenosis, impaired vitamin K status, reflected by higher circulating undercarboxylated osteocalcin, was independently associated with accelerated disease progression and with higher rates of mortality. C_LI What Are the Clinical Implications?O_LIAortic stenosis currently has no medical therapy. Vitamin K2, an inexpensive, safe nutrient that does not interfere with anticoagulation, emerges as a candidate disease-modifying strategy that warrants testing in randomized trials. C_LIO_LICirculating undercarboxylated osteocalcin may serve as a biomarker to identify patients at risk of rapid progression and to enrich future vitamin K trials for those most likely to benefit. C_LIO_LITargeting valvular lipid peroxidation, through antioxidant repletion and/or inhibition of lipid-peroxidation enzymes, may be a mechanistically grounded approach to slow calcific aortic valve disease. C_LI

physiology↗

Faithful Modeling of Terminal CD8 T Cell Dysfunction and Epigenetic Stabilization In Vitro

Epigenetic scarring of terminally dysfunctional CD8 T cells hinders long-term protection and response to immune checkpoint blockade during chronic infections and cancer. We developed a faithful in vitro model for CD8 T cell terminal dysfunction as a platform to advance T cell immunotherapy. Using TCR-transgenic CD8 T cells, we found that 1-week peptide stimulation, mimicking conditions in previous models, failed to induce a stable exhaustion program in CD8 T cells. In contrast, prolonged stimulation for 2-3 weeks induced T cell dysfunction but triggered activation-induced cell death, precluding long-term investigation of exhaustion programs. To better mimic in vivo exhaustion, we provided post-effector, chronic TGF{beta}1 signals, enabling survival of chronically stimulated CD8 T cells for over 3 weeks. These conditions induced a stable state of terminal dysfunction (TDysf), marked by a stable loss of effector, cytotoxicity, and memory programs, along with mitochondrial stress and impaired protein translation. Importantly, transcriptomic and epigenetic analyses confirmed the development of terminal exhaustion-specific signatures in TDysf cells. Adoptive transfer of TDysf cells revealed their inability to recall effector functions or proliferate after acute LCMV rechallenge. This novel tractable model system enables investigation of molecular pathways driving T cell terminal dysfunction and discovery of new therapeutic targets for cancer or chronic infections.

immunology↗

CRAM compression: practical across-technologies considerations for large-scale sequencing projects

CRAM is an efficient format to store high-throughput sequencing data and it has been widely adopted. We thus plan to use CRAM for the Emirati Genome Program, which aims to sequence the genomes of ~1 million nationals in the United Arab Emirates using short- and long-read sequencing technologies (Illumina, MGI and Oxford Nanopore Sequencing). We conducted a pilot study on the three technologies before start using CRAM at scale. We found CRAM achieved 40-70% compression depending on the sequencing platform. As expected, CRAM compression was data lossless and did not alter variant calls. In our cloud, we observed compression speeds 0.7-1.4 GB per minute, varying on the sequencing platform too. This translates into ~1-2 hours using a single CPU to compress a ~30X human whole-genome sequencing sample. Despite its wide use, we found little publicly available information about CRAM compression rate, speed, losslessness and parallelization, especially across many sequencing platforms. This work will have direct application for Emirati Genome Program and provide practical considerations for other large-scale sequencing efforts.

bioinformatics↗

The MEK1/2 pathway as a therapeutic target in high-grade serous ovarian carcinoma

RationaleHigh-grade serous ovarian carcinoma (HGSOC) is the deadliest of gynecological cancers due to high rate of recurrence and acquired chemoresistance. Mutation and activation of the RAS/MAPK pathway has been linked to cancer cell proliferation and therapeutic resistance in numerous cancers. While RAS mutations are not commonly observed in HGSOC, less is known about downstream pathway activation. We therefore sought to investigate the role of MEK1/2 signaling in ovarian cancer.\n\nMethodsMEK1/2 pathway activity was evaluated in clinical HGSOC tissue samples and ovarian cancer cell lines by using tissue microarray-based immunohistochemistry, immunoblotting, and RT-qPCR. OVCAR8 and PEO4 HGSOC cell lines were used to assess the effect of MEK1/2 inhibition on cell viability, proliferation rate, and stem-like characteristics. Xenografts were used in mice to investigate the effect of MEK1/2 inhibition on tumor growth in vivo. A drug washout experimental model was used to study the lasting effects of MEK1/2 inhibition therapy.\n\nResultsMEK1/2 signaling is active in a majority of HGSOC tissue samples and cell lines. MEK1/2 is further stimulated by cisplatin treatment, suggesting that MEK1/2 activation may play a role in chemotherapy resistance. The MEK1/2 inhibitor, trametinib, drastically inhibits MEK1/2 downstream signaling activity, causes prominent cell cycle arrest in the G1/0-phase in cell cultures, and reduces the rate of tumor growth in vivo, but does not induce cell death. Cells treated with trametinib display a high CD133+ fraction and increased expression of stemness-associated genes. Transient trametinib treatment causes long-term increases in a high ALDH1 activity subpopulation of cells that possess the capability of surviving and growing in non-adherent conditions.\n\nConclusionsMEK1/2 inhibition in HGSOC cells efficiently inhibits proliferation and tumor growth and therefore may be a promising approach to suppress ovarian cancer cell growth. MEK1/2 inhibition promotes stem-like properties, thus suggesting a possible mechanism of resistance and that a combination with CSC-targeting drugs should be considered.

cancer biology↗

NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization

BackgroundAs high-throughput sequencing applications continue to evolve, the rapid growth in quantity and variety of sequence-based data calls for the development of new software libraries and tools for data analysis and visualization. Often, effective use of these tools requires computational skills beyond those of many researchers. To ease this computational barrier, we have created a dynamic web-based platform, NASQAR (Nucleic Acid SeQuence Analysis Resource). ResultsNASQAR offers a collection of custom and publicly available open-source web applications that make extensive use of a variety of R packages to provide interactive data analysis and visualization. The platform is publicly accessible at http://nasqar.abudhabi.nyu.edu/. Open-source code is on GitHub at https://github.com/nasqar/NASQAR, and the system is also available as a Docker image at https://hub.docker.com/r/aymanm/nasqarall. NASQAR is a collaboration between the core bioinformatics teams of the NYU Abu Dhabi and NYU New York Centers for Genomics and Systems Biology. ConclusionsNASQAR empowers non-programming experts with a versatile and intuitive toolbox to easily and efficiently explore, analyze, and visualize their Transcriptomics data interactively. Popular tools for a variety of applications are currently available, including Transcriptome Data Preprocessing, RNA-seq Analysis (including Single-cell RNA-seq), Metagenomics, and Gene Enrichment.

bioinformatics↗

BioSAILs: versatile workflow management for high-throughput data analysis

MotivationHigh-throughput analysis in the current era of systems biology encompasses a range of analysis workflows for different applications, such as transcriptomics, epigenetics, variant discovery, de novo genome assembly, etc. Many research institutes house a genomics core facility that is responsible for generating high-throughput sequencing data and often includes a core bioinformatics team that carries out data analysis. Core teams must both keep track of data and maintain numerous software packages and databases - which must be scalable according to ever-changing research needs - and they must allocate computational resources to them. Typical data analysis pipelines involve multiple software packages and require the ability to install, execute, and maintain software stacks on a variety of hardware/operating system configurations, including high-performance computing (HPC) facilities, stand-alone servers, and Cloud services. At the same time, individual researchers need to analyze their data and share their analysis steps with collaborators. Having to rely on ad hoc scripts and rigid internally developed pipelines is inefficient, difficult to track and maintain, and ultimately, limits the ability to adapt and evolve as research methods progress.\n\nResultsHere, we present BioSAILs (Bioinformatics Standardized Analysis Information Layers), a scientific workflow management system (WMS) developed by the Core Bioinformatics team at NYU Abu Dhabi. BioSAILs comprises two central components, BioX command and HPCRunner command, supported by BioStacks software stacks. BioX structures executable workflows that may be either run directly on a desktop or lab server, or submitted by HPCRunner to HPC infrastructure or the Cloud. BioSAILs is supported by a range of pre-configured, customizable BioStacks software stacks for various applications (e.g. RNA-seq, de novo genome/transcriptome assembly, variant discovery, etc.) Software stacks are built using Conda and BioConda (6), have been pre-packaged into modules using EasyBuild, and can be deployed with or without BioSAILs. Within the BioSAILs WMS, users can also invoke commands that take advantage of containerized software in Docker (10) and Singularity (8). Finally, the BioSAILs web resource provides documentation, blog posts related to various BioSAILs analysis tasks, forums, knowledge base & FAQs, as well as an interactive web-based workflow editor/creator. BioSAILs is production-level software that has been in use as the main WMS at NYU Abu Dhabi for the past 2 years and is continuously developed and maintained by the core bioinformatics team.\n\nAvailabilityBioSAILs is open source software, available under the GNU license. Online documentation, support and guides can be found at biosails.abudhabi.nyu.edu. The public Github project is available at Github - BioSAILs. HPC-Runner and BioX-Workflow can be installed through Conda using the BioConda channel.

bioinformatics↗