The role of PERK in breast cancer tumorigenesis and progression

The major obstacle to effective breast cancer (BC) treatment has been the development of drug resistance, and there is an urgent need to develop treatments able to target resistant cancers. The tumour suppressive transcription factor FOXO3 promotes cell cycle arrest, senescence and cell death, and is often down-regulated as an adaptive response in cancer and particularly in chemotherapeutic drug-resistant cells. My study aimed to examine the role and regulation of ER stress signalling and amino acid metabolism in breast cancer drug resistance. Using a combination of in vitro and in vivo models and techniques, I established the endoplasmic reticulum (ER)-stress defence modulator PERK (eIF2AK3) as a direct downstream transcriptional target of FOXO3. My work therefore reveals a chemotherapeutic drug-resistant cancer cell vulnerability in PERK as it is adaptively downregulated by FOXO3 and suggests PERK as a potential target for cancer therapy, specifically in the context of drug-resistant cancers. Pharmaceutical PERK inhibitors have demonstrated anticancer activities in combination therapies, but their effectiveness as a single agent is limited, suggesting the existence of possible compensatory cellular responses. I found that the eIF2 kinases, PERK and GCN2 (eIF2AK4) function cooperatively to regulate cancer cell clonal renewal as well as cytotoxic drug resistance. Further analysis showed that FOXO3 modulates PERK-GCN2 cross-talk partially via JNK-AKT-FOXO3 axis. I also found GCN2 cooperates with PERK through the JNK-FOXO3 axis in a reciprocal negative feedback loop to mediate cancer chemotherapeutic drug response and clonal survival, advocating the potential of targeting GCN2 as a therapeutic strategy for treating cancer and for overcoming drug resistance. In conclusion, this project unveils a previously unappreciated role of the two eIF2 kinases, PERK and GCN2 in cancer clonal survival and drug resistance. Moreover, my findings can have important implications on developing strategies for targeting cancer and for overcoming cancer drug resistance.Open Acces

Comprehensive Analysis of KCNJ14 Potassium Channel as a Biomarker for Cancer Progression and Development

Cancer is a global epidemic that has affected millions of lives. Discovering novel cancer targets is widely viewed as a key step in developing more effective therapies for cancer and other fatal illnesses. More recently, potassium (K+) channels have been studied as a potential biological target for the creation of cancer treatments. Potassium Inwardly Rectifying Channel Subfamily J Member 14 (KCNJ14) is one of the cancer genome’s least investigated genes. This study conducted a comprehensive examination of the relationships between KCNJ14 gene expression analysis, survival, RNA modification, immunotherapy participation, and cancer stemness using several databases. KCNJ14 was shown to be dysregulated in a variety of cancers, including lung, intestinal, head and neck, oesophageal, and stomach. Additionally, KCNJ14 was shown to be linked to RNA and DNA stemness in 18 and 15 different tumour types, respectively. Moreover, KCNJ14 was discovered to be positively linked with immunological checkpoints and suppressor cells and to have a negative immunophenoscore (IPS). KCNJ14 was linked to tumour mutation burden (TMB), microsatellite instability (MSI), neoantigen (NEO), and programmed death ligand 1 (PD-L1); all four are potential targets for immunotherapies. In addition, a favourable relationship between genomic-instability markers such as heterozygosity (LOH), homologous recombination deficiency (HRD), and mutant-allele tumour heterogeneity (MATH) was demonstrated with KCNJ14. Based on these novel findings, KCNJ14 may be a useful independent prognostic biomarker for a range of cancers

Alternatively Spliced Isoforms of <i>MUC4</i> and <i>ADAM12</i> as Biomarkers for Colorectal Cancer Metastasis

There is a pertinent need to develop prognostic biomarkers for practicing predictive, preventive and personalized medicine (PPPM) in colorectal cancer metastasis. The analysis of isoform expression data governed by alternative splicing provides a high-resolution picture of mRNAs in a defined condition. This information would not be available by studying gene expression changes alone. Hence, we utilized our prior data from an exon microarray and found ADAM12 and MUC4 to be strong biomarker candidates based on their alternative splicing scores and pattern. In this study, we characterized their isoform expression in a cell line model of metastatic colorectal cancer (SW480 & SW620). These two genes were found to be good prognostic indicators in two cohorts from The Cancer Genome Atlas database. We studied their exon structure using sequence information in the NCBI and ENSEMBL genome databases to amplify and validate six isoforms each for the ADAM12 and MUC4 genes. The differential expression of these isoforms was observed between normal, primary and metastatic colorectal cancer cell lines. RNA-Seq analysis further proved the differential expression of the gene isoforms. The isoforms of MUC4 and ADAM12 were found to change expression levels in response to 5-Fluorouracil (5-FU) treatment in a dose-, time- and cell line-dependent manner. Furthermore, we successfully detected the protein isoforms of ADAM12 and MUC4 in cell lysates, reflecting the differential expression at the protein level. The change in the mRNA and protein expression of MUC4 and ADAM12 in primary and metastatic cells and in response to 5-FU qualifies them to be studied as potential biomarkers. This comprehensive study underscores the importance of studying alternatively spliced isoforms and their potential use as prognostic and/or predictive biomarkers in the PPPM approach towards cancer

Risk Factors for Glucose 6-Phosphate Dehydrogenase and COVID-19 Disease—A Retrospective Study at a Major Saudi Tertiary Center

Glucose-6-phosphate dehydrogenase (G6PD) insufficiency is a common enzymatic defect worldwide; it affects over 400 million people and is associated with various disorders. Recent research suggests that G6PD-deficient cells are susceptible to infection by human coronaviruses, as the G6PD enzyme is involved in the metabolism of oxidative stress, which may enhance COVID-19 mortality. This retrospective study aimed to examine the effect of COVID-19 on patients with G6PD deficiency by comparing the laboratory parameters of patients with G6PD enzyme deficiency alone, COVID-19 alone, and those with both COVID-19 and G6PD enzyme deficiency treated at a major Saudi tertiary center. The results indicated significant differences in hematological and biochemical parameters between the three patient groups, indicating that COVID-19 may influence these parameters, and that they could be used to measure the severity of COVID-19 disease. Moreover, this study suggests that patients with G6PD enzyme deficiency may be at higher risk for severe COVID-19 outcomes. Although the study is limited by the lack of a random selection method for group membership, the Kruskal–Wallis H-test was used to statistical assess the data. The study’s findings can enhance the understanding of the relation between COVID-19 infected and G6PD-deficiency patients and inform clinical decision making for an improved patient outcome

Evaluating the Adverse Events Associated with Three Doses of the COVID-19 Vaccination in Adults in the Western Region of Saudi Arabia: A Cross-Sectional Study

The Kingdom of Saudi Arabia was one of the countries earliest affected by the coronavirus 2019 (COVID-19) pandemic and had taken precautions including compulsory COVID-19 vaccination. Both the ChAdOx1 nCoV-19 vaccine (Oxford AstraZeneca) and the BNT162b2 vaccine (Pfizer) were approved by the Saudi Ministry of Health, followed by mRNA-1273 (Moderna), all of which were used for population-wide vaccination. This study aimed to assess the short-term side effects following the COVID-19 vaccinations among participants who had received all three doses in the western region of Saudi Arabia. An online survey was distributed to the participants who received either BNT162b2, ChAdOx1 nCoV-19, or mRNA-1273 vaccines, and the type of side effects and their severity were evaluated. Fatigue and headache, pain at the site of the injection and muscle pain were the most common side effects in all three doses. However, the severity depending on the type of vaccination was significant only for the first and second dose, but not the third dose. In contrast, there was a higher percentage of participants who encountered severe side effects from the third dose compared to the first and second. Nevertheless, the majority of participants described all three doses’ side effects to be moderately severe. A future evaluation could be made to access the individual types of vaccination and compare between the side effects of the BNT162b2, ChAdOx1 nCoV-19, and mRNA-1273 vaccines specifically for the booster dose

Driver Genes from GISTIC analysis showing more than two fold change in expression value as calculated by two different programs – AltAnalyze and Expression Console.

<p>N/A  =  No annotation for these genes were found in the analysis program.</p>a<p>Genes found to be differentially expressed in SAM/LIMMA analyses. CLDN7 and LOX genes were additional driver genes that were differentially expressed.</p>b<p>Genes found to have high splice index values.</p>c<p>Genes found to be eligible as biomarkers for colorectal cancer.</p><p>Driver Genes from GISTIC analysis showing more than two fold change in expression value as calculated by two different programs – AltAnalyze and Expression Console.</p

Gene Regulatory Network Inference diagram for Tumor and Normal Groups.

<p>A hierarchical network topology is used to visualize the degrees of interaction between transcription factor genes and target genes. (a) The inferred network for tumour group showing RUVBL1 as master regulator. (b) The inferred network for normal group showing TSHZ1as master regulator.</p

Differentially regulated genes found to have incoherent expression levels and genomic changes.

<p>AA  =  Fold change value as calculated by AltAnalyze program.</p><p>EC  =  Fold change value as calculated by Expression Console program.</p><p>TF  =  Transcription Factor. Unknown is the TF that is not found in the driver genes.</p><p>Differentially regulated genes found to have incoherent expression levels and genomic changes.</p

Integrated Exon Level Expression Analysis of Driver Genes Explain Their Role in Colorectal Cancer

<div><p>Integrated analysis of genomic and transcriptomic level changes holds promise for a better understanding of colorectal cancer (CRC) biology. There is a pertinent need to explain the functional effect of genome level changes by integrating the information at the transcript level. Using high resolution cytogenetics array, we had earlier identified driver genes by ‘Genomic Identification of Significant Targets In Cancer (GISTIC)’ analysis of paired tumour-normal samples from colorectal cancer patients. In this study, we analyze these driver genes at three levels using exon array data – gene, exon and network. Gene level analysis revealed a small subset to experience differential expression. These results were reinforced by carrying out separate differential expression analyses (SAM and LIMMA). ATP8B1 was found to be the novel gene associated with CRC that shows changes at cytogenetic, gene and exon levels. Splice index of 29 exons corresponding to 13 genes was found to be significantly altered in tumour samples. Driver genes were used to construct regulatory networks for tumour and normal groups. There were rearrangements in transcription factor genes suggesting the presence of regulatory switching. The regulatory pattern of AHR gene was found to have the most significant alteration. Our results integrate data with focus on driver genes resulting in highly enriched novel molecules that need further studies to establish their role in CRC.</p></div