Syed Haider
A5052903538- Cancer Genomics and Diagnostics
- Lung Cancer Treatments and Mutations
- Cancer Immunotherapy and Biomarkers
- Advanced Breast Cancer Therapies
- HER2/EGFR in Cancer Research
- RNA modifications and cancer
- Cancer, Hypoxia, and Metabolism
- Radiomics and Machine Learning in Medical Imaging
- Ferroptosis and cancer prognosis
- Cancer Cells and Metastasis
- Radiopharmaceutical Chemistry and Applications
- Cancer-related molecular mechanisms research
- PARP inhibition in cancer therapy
- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- Immune cells in cancer
- DNA Repair Mechanisms
- Cancer, Lipids, and Metabolism
- Lung Cancer Research Studies
- Bioinformatics and Genomic Networks
- Head and Neck Cancer Studies
- BRCA gene mutations in cancer
- Medical Imaging Techniques and Applications
- Cancer Treatment and Pharmacology
- Ubiquitin and proteasome pathways
Breast Cancer Now
2017-2025
Institute of Cancer Research
2015-2025
Australian National University
2025
MRC Weatherall Institute of Molecular Medicine
2013-2024
University of Oxford
2014-2024
SUNY Fredonia
2024
University of Liverpool
2024
Countess of Chester Hospital NHS Foundation Trust
2024
Countess of Chester Hospital
2024
Arkansas Tech University
2024
Abstract Background Biologists need to perform complex queries, often across a variety of databases. Typically, each data resource provides an advanced query interface, which must be learnt by the biologist before they can begin them. Frequently, more than one source is required and for high-throughput analysis, cutting pasting results between websites certainly very time consuming. Therefore, many groups rely on local bioinformatics support process queries accessing resource's programmatic...
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide unified interface biomedical databases that are distributed worldwide. portal provides access numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the independently administered funded their host data federation...
The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created Data Portal. Powered by BioMart software, Portal allows each member institution manage and maintain its own databases locally, while seamlessly presenting all single access point for users. currently contains from 24 projects, including ICGC, Atlas (TCGA), Johns Hopkins University, Tumor Sequencing...
BioMart Central Portal (www.biomart.org) offers a one-stop shop solution to access wide array of biological databases. These include major biomolecular sequence, pathway and annotation databases such as Ensembl, Uniprot, Reactome, HGNC, Wormbase PRIDE; for complete list, visit, http://www.biomart.org/biomart/martview. Moreover, the web server features seamless data federation making cross querying these sources in user friendly unified way. The not only provides through interface (MartView),...
Abstract Activation of cellular transcriptional responses, mediated by hypoxia-inducible factor (HIF), is common in many types cancer, and generally confers a poor prognosis. Known to induce hundreds protein-coding genes, HIF has also recently been shown be key regulator the non-coding response. Here, we show that NEAT1 long RNA (lncRNA) direct target breast cancer cell lines solid tumors. Unlike previously described lncRNAs, regulated principally HIF-2 rather than HIF-1. nuclear lncRNA an...
The epigenome refers to marks on the genome, including DNA methylation and histone modifications, that regulate expression of underlying genes. A consistent profile gene changes in end-stage cardiomyopathy led us hypothesize distinct global patterns may also exist.We constructed genome-wide maps histone-3 lysine-36 trimethylation (H3K36me3) enrichment for cardiomyopathic normal human hearts. More than 506 Mb sequences per library were generated by high-throughput sequencing, allowing assign...
The cyclic GMP-AMP synthase/stimulator of IFN genes (cGAS/STING) pathway detects cytosolic DNA to activate innate immune responses. Poly(ADP-ribose) polymerase inhibitors (PARPi) selectively target cancer cells with repair deficiencies such as those caused by BRCA1 mutations or ERCC1 defects. Using isogenic cell lines and patient-derived samples, we showed that ERCC1-defective non–small lung (NSCLC) exhibit an enhanced type I transcriptomic signature low expression correlates increased...
To identify approaches to target DNA repair vulnerabilities in cancer, we discovered nanomolar potent, selective, low molecular weight (MW), allosteric inhibitors of the polymerase function Polθ, including ART558. ART558 inhibits major Polθ-mediated process, Theta-Mediated End Joining, without targeting Non-Homologous Joining. In addition, elicits damage and synthetic lethality BRCA1- or BRCA2-mutant tumour cells enhances effects a PARP inhibitor. Genetic perturbation screening revealed that...
Radiotherapy and chemotherapy are effective treatment methods for many types of cancer, but resistance is common. Recent findings indicate that antiviral type I interferon (IFN) signaling induced by these treatments. However, the underlying mechanisms still need to be elucidated. Expression a set IFN-stimulated genes comprises an IFN-related DNA damage signature (IRDS), which correlates strongly with radiotherapy across different tumors. Classically, during viral infection, presence foreign...
Abstract Reversion mutations in BRCA1 or BRCA2 are associated with resistance to PARP inhibitors and platinum. To better understand the nature of these mutations, we collated, codified, analyzed more than 300 reversions. This identified reversion “hotspots” “deserts” regions encoding N C terminus, respectively, BRCA2, suggesting that pathogenic may be at higher lower risk reversion. Missense splice-site BRCA1/2 also appeared less likely revert truncating mutations. Most reversions were...
Abstract Immune-checkpoint blockade (ICB) promotes antitumor immune responses and can result in durable patient benefit. However, response rates breast cancer patients remain modest, stimulating efforts to discover novel treatment options. Cancer-associated fibroblasts (CAF) represent a major component of the tumor microenvironment have known immunosuppressive functions addition their well-established roles directly promoting growth metastasis. Here we utilized paired syngeneic mouse mammary...
Abstract Patients with estrogen receptor (ER)-positive breast cancer are at risk of metastatic relapse for decades after primary tumor resection and treatment, a consequence dormant disseminated cells (DTCs) reawakening secondary sites. Here we use syngeneic ER + mouse models in which DTCs display phenotype young mice but accelerated outgrowth an aged or fibrotic microenvironment. In mice, low-level Pdgfc expression by is required their maintenance sites insufficient to support development...
Resistance to therapies that target homologous recombination deficiency (HRD) in breast cancer limits their overall effectiveness. Multiple, preclinically validated, mechanisms of resistance have been proposed, but existence and relative frequency clinical disease are unclear, as is how resistance.
Abstract Cancer differs significantly between men and women; even after adjusting for known epidemiologic risk factors, the sexes differ in incidence, outcome, response to therapy. These differences occur many but not all tumor types, their origins remain largely unknown. Here, we compare somatic mutation profiles tumors arising women. We discovered large density sex biases frequency of specific genes; these may be associated with DNA mismatch repair genes or microsatellite instability....
BackgroundHypoxia is associated with a poor prognosis in prostate cancer. This work aimed to derive and validate hypoxia-related mRNA signature for localized cancer.MethodHypoxia genes were identified vitro via RNA-sequencing combined vivo gene co-expression analysis generate signature. The was independently validated eleven cancer cohorts bladder phase III randomized trial of radiotherapy alone or carbogen nicotinamide (CON).ResultsA 28-gene derived. Patients high scores had poorer...
The availability of bromodomain and extra-terminal inhibitors (BETi) has enabled translational epigenetic studies in cancer. BET proteins regulate transcription by selectively recognizing acetylated lysine residues on chromatin. BETi compete with this process leading to both downregulation upregulation gene expression. Hypoxia enables progression triple negative breast cancer (TNBC), the most aggressive form cancer, partly driving metabolic adaptation, angiogenesis metastasis through...
BackgroundIntegrin αvβ6 promotes migration, invasion, and survival of cancer cells; however, the relevance role has yet to be elucidated in breast cancer.
Restoration of hypoxia-induced apoptosis in tumors harboring p53 mutations has been proposed as a potential therapeutic strategy; however, the transcriptional targets that mediate p53-dependent remain elusive. Here, we demonstrated is reliant on DNA-binding and transactivation domains but not acetylation sites K120 K164, which, contrast, are essential for DNA damage-induced, apoptosis. Evaluation transcripts multiple cell lines identified group genes hypoxia-inducible proapoptotic p53,...
Late-phase clinical trials investigating metformin as a cancer therapy are underway. However, there remains controversy to the mode of action in tumors at doses. We conducted study integrating measurement markers systemic metabolism, dynamic FDG-PET-CT, transcriptomics, and metabolomics paired time points profile bioactivity primary breast cancer. show reduces levels mitochondrial metabolites, activates multiple metabolic pathways, increases 18-FDG flux tumors. Two tumor groups identified...
Tumor heterogeneity is a limiting factor in cancer treatment and the discovery of biomarkers to personalize it. We describe computational purification tool, ISOpure, directly address effects variable normal tissue contamination clinical tumor specimens. ISOpure uses set expression profiles panel healthy generate purified profile for each sample an estimate proportion RNA originating from cancerous cells. Applying before identifying gene signatures leads significant improvements prediction...
Significance The hypoxic microenvironment in solid tumors is known to reduce the efficacy of anticancer treatments many cancer types, including breast cancer. This study shows hypoxia induces an amino acid transporter, SNAT2, which then causes resistance antihormone therapy. We show major interplay between genes induced by estrogen receptor and hypoxia. Hypoxia-inducible factor 1α compensates for loss expression receptor-α (ERα) maintaining SNAT2 under or endocrine therapies. overexpression...