Biology subjects

Hayat, A.

Publications and source records attributed to Hayat, A..

6 recordsLinked to original sources

bioRxiv2024

Integrative proteo-genomic profiling uncovers key biomarkers of lapatinib resistance in HER2-positive breast cancer

Drug resistance is a major obstacle to the long-term effectiveness of cancer therapies. Approximately 70% of breast cancer patients relapse after 5 years of treatment, and the lack of biomarkers associated with drug resistance translates to poor prognosis in clinic. Previous research has utilised omics approaches to uncover biomarkers driving drug resistance, with a strong emphasis on genetic mutations. Here, we identified a nine-marker signature associated with resistance to lapatinib in a HER2-positive breast cancer model using a target discovery approach by employing an integrative multi-omics strategy, combining ATAC-seq, RNA-seq, and proteomics. We found that 7 markers in the drug resistance-signature had not been previously found to be implicated in HER2 positive breast cancer. We counterintuitively found that drug resistant cells have restrictive chromatin accessibility with reduced gene expression associated with limited total proteome changes. However, upon closer look, we identified that the drug resistance-signature had increased chromatin accessibility closer to the transcriptional start sites of those genes and are highly differentially expressed across the three datasets. Our data show that despite the overall transcriptional and proteomic landscape showing limited changes, there are several markers that are highly expressed, which correlate with increased anchorage-independent and invasive phenotype in vitro in lapatinib resistant cells compared to cancer cells. Our results demonstrate that disease aggressiveness can be related to reduced chromatin and gene expression dynamics. We anticipate that the resistant signature identified here using integrative target discovery approach can be applied to complex, representative models and validated before they can be targeted by suitable therapeutic agents.

cancer biology↗

bioRxiv2023

De novo Genome Assembly, Functional Annotation and SSR Mining of Citrus reticulata (Kinnow) from Pakistan

Citrus reticulata (Blanco) fruit is native to South East Asia which owns many of the nutritional, medicinal and economic advantages, locally known as "Kinnow" and one of the priced mandarin varieties (Dancy, Fuetrells Early and Honey) of Citrus genera renowned for its exclusive taste, vitamin richness, thin peel, long shelf-life and seedless characteristics in Pakistan. However, genetic improvement and breeding strategies of this valued variety are lacking due to the in-housed insufficient genomic and technical resources. Therefore, the current research was initiated to provide the base-line de-novo genome assembly of C. reticulata (seedless kinnow) at a depth of 151x with Illumina paired-end short-read sequencing technology using HiSeq 2500. Whole-genome sequencing resulted in 139,436,350 raw reads ([~]20.09 GB) of data, however, after removing the low-quality reads (1.08%), duplicated sequences (10.5%) and Illumina adaptors, 137,901,462 clean reads were obtained with ([~]18.87 GB) of clean data which was further used for downstream variant calling analysis. In total, 348,861 scaffolds were generated with N50 value of 4827 which constitute 263,018,9 contigs ranging from 71-36,213 with total of 179,984,763 nucleotides. The GC content of the final draft assembly at 71-mer was 34.1%. Moreover, annotation was performed with "Hayai-Annotation Plants" tool which marked the whole-genome mapping with three main functional databases of interpro, Pfam and gene ontology. Additionally, in-silico identification of 111,032 Simple Sequence Repeats (SSR) was also accomplished with the help of GMATA tool, which may be used for further screening and genetic improvement of the citrus varieties by means of this current assembly as a resource of local reference genome.

bioinformatics↗

bioRxiv2023

Identification of mammalian transcription factors that bind to inaccessible chromatin

Transcription factors (TFs) are proteins that affect gene expression by binding to regulatory regions of DNA in a sequence specific manner. The binding of TFs to DNA is controlled by many factors, including the DNA sequence, concentration of TF, chromatin accessibility and co-factors. Here, we systematically investigated the binding mechanism of hundreds of TFs by analysing ChIP-seq data with our explainable statistical model, ChIPanalyser. This tool uses as inputs the DNA sequence binding motif; the capacity to distinguish between strong and weak binding sites; the concentration of TF; and chromatin accessibility. We asked whether TFs preferred to bind to DNA in open or dense chromatin conformation and found that approximately one third of TFs are predicted to bind the genome in a DNA accessibility independent fashion. Our model predicted this to be the case when the TF binds to its strongest binding regions in the genome, and only a small number of TFs have the capacity to bind dense chromatin at their weakest binding regions, such as CTCF USF2 and CEBPB. Our study demonstrated that the binding of hundreds of human and mouse TFs is predicted by ChIPanalyser with high accuracy and showed that many TFs can bind dense chromatin.

genomics↗

bioRxiv2022

Whole-Genome Sequencing and Variant Discovery of Citrus reticulata 'Kinnow' from Pakistan

Citrus is a source of many nutritional and medicinal advantages, which is cultivated worldwide with major citrus groups of sweet oranges, mandarins, grapefruits, kumquats, lemons and limes. Pakistan produces all of its major citrus groups with mandarin (Citrus reticulata) being the prominent group that includes local commercial cultivars such as Feutrals Early, Dancy, Honey and Kinnow. The present study was designed to understand the genetic architecture of this unique variety of Citrus reticulata -Kinnow. The whole-genome resequencing and variant calling was performed to map the genomic variability that might be responsible for its particular characteristics like taste, seededness, juice content, thickness of peel and its shelf-life. A total of 139,436,350 raw sequence reads using Illumina platform were generated with 20.9 Gb data in Fastq format having 98% effectiveness and 0.2% base call error rate. Overall, a total of 3,503,033 SNPs, 176,949 MNPs, 323,287 INS and 333,083 DEL were identified using GATK4 variant calling pipeline against Citrus clementina as a reference genome. Further, g:Profiler bioinformatics tool was applied for annotating the newly found variants, harbor genes/transcripts and their involved pathways. A total of 73,864 transcripts harbors 4,336,352 variants, most of the observed variants were predicted in non-coding regions and 1,009 transcripts were found well annotated by different databases. Out of total aforementioned transcripts, 588 involved in biological processes, 234 in molecular functions and 167 transcripts involved in cellular components in Citrus reticulata. In a nutshell, 18,153 high-impact variants and 216 genic-variants found in the current study which may be used for marker assisted breeding programs of Kinnow to identify this particular variety among others and to propagate its valued traits to improve the contemporary citrus varieties as well. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/519411v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1568ae1org.highwire.dtl.DTLVardef@b7d20eorg.highwire.dtl.DTLVardef@3fc3a9org.highwire.dtl.DTLVardef@46ba89_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2022

Low HER2 enables dedifferentiation and transformation of normal breast epithelial cells via chromatin opening

Overexpression of the human epidermal growth factor 2 (HER2) protein in breast cancer patients is a predictor of poor prognosis and resistance to therapies. Despite significant advances in the development of targeted therapies and improvements in the 5-year survival rate of metastatic HER2-positive breast cancer patients, a better understanding of the disease at an early stage is needed to prevent its progression. Here, we used an inducible breast cancer transformation system that allows investigation of early molecular changes at high temporal resolution. HER2 overexpression to similar levels as those observed in a subtype of HER2 positive breast cancer patients induced transformation of MCF10A cells and resulted in gross morphological changes, increased anchorage-independent growth of cells, and altered transcriptional programme of genes associated with oncogenic transformation. Global phosphoproteomic analysis during the first few hours of HER2 induction predominantly detected an increase in protein phosphorylation. Intriguingly, this correlated with a wave of chromatin opening, as measured by ATAC-seq on acini isolated from 3D cell culture. We observed that HER2 overexpression leads to reprogramming of many distal regulatory regions and promotes reprogramming-associated heterogeneity. We found that a subset of cells acquired a dedifferentiated breast stem-like phenotype, making them likely candidates for malignant transformation. Our data show that this population of cells, which counterintuitively enriches for relatively low HER2 protein abundance and increased chromatin accessibility, possesses transformational drive, resulting in increased anchorage-independent growth in vitro compared to cells not displaying a stem-like phenotype. Our data provide a discovery platform for signalling to chromatin pathways in HER2-driven cancers, offering an opportunity for biomarker discovery and identification of novel drug targets.

cancer biology↗

bioRxiv2020

Inhalation: A means to explore and optimize nintedanib's pharmacokinetic/pharmacodynamic relationship

Oral nintedanib is marketed for the treatment of idiopathic pulmonary fibrosis (IPF). While effective slowing fibrosis progression, as an oral medicine nintedanib is limited. To reduce side effects and maximize efficacy, nintedanib was reformulated as a solution for nebulization and inhaled administration. To predict effectiveness treating IPF, the nintedanib pharmacokinetic/pharmacodynamic relationship was dissected. Pharmacokinetic analysis indicated oral-delivered nintedanib plasma exposure and lung tissue partitioning were not dose-proportional and resulting lung levels were substantially higher than blood. Although initial-oral absorbed nintedanib efficiently partitioned into the lung, only a quickly eliminated fraction appeared available to epithelial lining fluid (ELF). Because IPF disease appears to initiate and progress near the epithelial surface, this observation suggests short duration nintedanib exposure (oral portion efficiently partitioned to ELF) is sufficient for IPF efficacy. To test this hypothesis, exposure duration required for nintedanib activity was explored. In vitro, IPF-cellular matrix (IPF-CM) increased primary normal human fibroblast (nHLF) aggregate size and reduced nHLF cell count. IPF-CM also increased nHLF ACTA2 and COL1A expression. Whether short duration (inhalation mimic) or continuous exposure (oral mimic), nintedanib (1-100 nM) reversed these effects. In vivo, intubated silica produced a strong pulmonary fibrotic response. Once-daily (QD) 0.021, 0.21 and 2.1 mg/kg intranasal (IN; short duration inhaled exposure) and twice daily (BID) 30 mg/kg oral (PO; long duration oral exposure) showed that at equivalent-delivered lung concentrations, QD short duration inhaled nintedanib exposure (0.21 mg/kg IN vs. 30 mg/kg PO) exhibited equivalent-to-superior activity as BID oral (reduced silica-induced elastance, alpha-smooth muscle actin, interleukin-1 beta (IL-1{beta}) and soluble collagen, and lung macrophage and neutrophils). An increased lung dose (2.1 mg/kg IN vs. 30 mg/kg PO) exhibited increased effect by further reducing silica-induced elastance, IL-1{beta} and soluble collagen. Neither oral nor inhaled nintedanib reduced silica-induced parenchymal collagen. Both QD inhaled and BID oral nintedanib reduced silica-induced inflammatory index with oral achieving significance. In summary, nintedanib pulmonary anti-fibrotic activity can be achieved using small, infrequent inhaled doses to deliver oral equivalent-to-superior therapeutic effect.

pharmacology and toxicology↗