Biology subjects

Haq, F.

Publications and source records attributed to Haq, F..

4 recordsLinked to original sources

bioRxiv2025

From Metabolism to Malignancy: Profiling Diabetes-Related Genes in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) and diabetes mellitus both affect the liver, a key metabolic organ. This study uses bioinformatics to explore genetic links between Type 1 Diabetes (T1D) and HCC prognosis. Eleven HCC gene expression datasets from GEO and one TCGA-LIHC dataset were analyzed. Gene Set Enrichment Analysis (GSEA) identified up- and downregulated genes after data normalization in R. Four datasets (GSE64041, GSE78737, GSE107170, TCGA) revealed increased expression of T1D-related genes. Ten genes, including HLA-DOB and HLA-DPB1, were consistently upregulated. Statistical analysis (Kruskal-Wallis and Mann-Whitney U tests) showed these two genes were significantly associated with tumor grade and T-stage, with p-values ranging from 0.008 to 0.019. Co-expression analysis with 96 literature-curated T1D genes identified 23 related genes. Survival analysis using Kaplan-Meier curves highlighted five genes (IL7R, CD69, CCR5, RUNX3, PRF1), with CD69 showing strong associations with T-stage and disease-free survival. PRF1, RUNX3, and CCR5 were also linked to survival outcomes. Seven diabetes-related GEO datasets were used for validation. GSEA showed T1D gene enrichment in two datasets (GSE228267, GSE232310), with HLA-DOB significantly expressed in GSE228267 (p = 0.004). These findings suggest that HLA-DOB, HLA-DPB1, and three other T1D-related genes may serve as potential biomarkers for understanding the genetic connection between T1D and HCC. Though computational, this study lays the groundwork for future experimental validation.

bioinformatics↗

bioRxiv2024

Two TAL effectors of Xanthomonas citri pv. malvacearum target GhSWEET15 as the susceptibility genes for bacterial blight of cotton

Bacterial Blight of Cotton (BBC) caused by Xanthomonas citri pv. malvacearum (Xcm) is an important and destructive disease affecting cotton plants. Transcription activator-like effectors (TALEs) released by the pathogen regulate cotton resistance to the susceptibility. In this study, we sequenced the whole genome of Xcm Xss-V2-18 and identified eight tal genes; seven on the plasmids and one on the chromosome. Deletion and complementation experiments of Xss-V2-18 tal genes demonstrated that Tal1b is required for full virulence on cotton. Transcriptome profiling coupled with TALE-binding element prediction revealed that Tal1b targets GhSWEET15A04/D04 and GhSWEET15D02 simultaneously. Expression analysis confirmed the independent inducibility of GhSWEET15A04/D04 and GhSWEET15D02 by Tal1b, whereas GhSWEET15A04/D04 is additionally targeted by Tal1. Moreover, GUS ({beta}-glucuronidase) and Xa10-mediated HR (hypersensitive response) assays indicated that the EBEs are required for the direct and specific activation of the candidate targets by Tal1 and Ta1b. These findings may advance our understanding of the dynamics between TALEs and EBEs, and decipher a simple and effective DNA-binding mechanism that could lead to the development of more efficient methods for gene editing and transgenic research.

pathology↗

bioRxiv2020

Development Optimization and Validation of RT-LAMP based COVID-19 Facility in Pakistan

The pandemic SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) has created a widespread panic across the globe especially in the developing countries like Pakistan. The lack of resources and technical staff are causing havoc challenges in the detection and prevention of this global outbreak. Therefore, a less expensive and massive screening of suspected individuals for COVID-19 is required. In this study, a user-friendly technique of reverse transcription-loop mediated isothermal amplification (RT-LAMP) was designed and validated to suggest a potential RT-qPCR alternate for rapid testing of COVID-19 suspected individuals. A total of 12 COVID-19 negative and 72 COVID-19 suspected individuals were analyzed. Both RT-qPCR and RT-LAMP assays were performed for all the individuals using open reading frame (ORF 1ab), nucleoprotein (N) and Spike (S) genes. All 12 specimens which were negative using RT-qPCR were also found negative using RT-LAMP assay. Overall 62 out of 72 positive samples (detected using RT-qPCR) were found COVID-19 positive using RT-LAMP assay. Interestingly all samples (45) having Ct values less than 30 showed 100% sensitivity. However, samples with weaker Ct values (i.e., => 35) showed 54% concordance, suggesting potential false negatives or false positives in RT-LAMP or RT-qPCR results, respectively. Overall comparative assessment showed that RT-LAMP assay showed strong sensitivity and specificity and can be used as an alternative strategy for rapid COVID-19 testing. Hence, based on fast processing time, minimal risk of specimens transfer and utilizing available resources, LAMP based detection of COVID-19 is strongly advocated especially for developing countries.

molecular biology↗

bioRxiv2018

Bioinformatics Approach to Identify Diseasome and Comorbidities Effect of Mitochondrial Dysfunctions on the Progression of Neurological Disorders

Mitochondrial dysfunction can cause various neurological diseases. We therefore developed a quantitative framework to explore how mitochondrial dysfunction may influence the progression of Alzheimers, Parkinsons, Huntingtons and Lou Gehrigs diseases and cerebral palsy through analysis of genes showing altered expression in these conditions. We sought insights about the gene profiles of mitochondrial and associated neurological diseases by investigating gene-disease networks, KEGG pathways, gene ontologies and protein-protein interaction network. Gene disease networks were constructed to connect shared genes which are commonly found between the neurological diseases and Mitochondrial Dysfunction. We also generated KEGG pathways and gene ontologies to explore functional enrichment among them, and protein-protein interaction networks to identify the shared protein groups of these diseases. Finally, we verified our biomarkers using gold benchmark databases (e.g., OMIM and dbGaP) which identified effective reasons of it. Our network-based methodologies are useful to investigate disease mechanisms, predictions for comorbidities and identified distinct similarities among different neurological disorders for mitochondrial dysfunction.

bioinformatics↗