46 results on '"Jithesh PV"'
Search Results
2. Identification of a potential DNA methyltransferase (DNMT) inhibitor.
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Jan Z, Ahmed WS, Biswas KH, and Jithesh PV
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- Humans, Protein Binding, DNA Methylation drug effects, Binding Sites, DNA Methyltransferase 3A, Molecular Docking Simulation, Molecular Dynamics Simulation, Enzyme Inhibitors chemistry, Enzyme Inhibitors pharmacology, DNA (Cytosine-5-)-Methyltransferases antagonists & inhibitors, DNA (Cytosine-5-)-Methyltransferases metabolism, DNA (Cytosine-5-)-Methyltransferases chemistry
- Abstract
DNA methyltransferases (DNMTs) play an important role in the epigenetic regulation of gene expression through the methylation of DNA. Since hypermethylation and consequent suppression of tumor suppressor genes are associated with cancer development and progression, DNA hypomethylating agents (HMAs) such as DNMT inhibitors have been proposed for cancer therapy. Two nucleoside analogues approved for the treatment of hematological cancers, decitabine and azacytidine, have poor pharmacokinetic properties, and hence there is a critical need for identifying novel HMAs. Virtual screening of a library of ∼40,000 compounds from the ZINC database, followed by molecular docking of 4,000 compounds having potential druggable properties with DNMT1, DNMT3A and DNMT3B were performed. One unique inhibitor (ZINC167686681) was identified that successfully passed through the Lipinski Rule of 5, geometry constraints as well as ADME/Tox filters and having strong binding energy for DNMTs. Further, molecular dynamics simulations of the docked complexes showed detailed structural features critical for its binding with the DNMTs and the stability of their interaction. Our study identified a compound with potential druggable properties and predicted to bind and inhibit DNMTs. Further investigations involving cellular and animal models of ZINC167686681 will help in potentially taking it into clinical trials for the treatment of cancers.Communicated by Ramaswamy H. Sarma.
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- 2024
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3. Editorial: Precision vaccinology for infectious diseases.
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Rahman M, Adeli M, Schellhorn HE, Jithesh PV, and Levy O
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- Humans, Communicable Diseases immunology, COVID-19 immunology, COVID-19 prevention & control, Precision Medicine methods, Vaccinology methods
- Abstract
Competing Interests: OL is an inventor on patents related to vaccine adjuvants and human in vitro systems that model responses to vaccines and immunomodulatory agents. OL is a co-founder of Ovax Inc and consultant to GlaxoSmithKline GSK and Hillevax. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationship that could be constructed as a potential conflict of interest.
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- 2024
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4. Forging the path to precision medicine in Qatar: a public health perspective on pharmacogenomics initiatives.
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Bastaki K, Velayutham D, Irfan A, Adnan M, Mohammed S, Mbarek H, Qoronfleh MW, and Jithesh PV
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- Humans, Qatar, Public Health, Delivery of Health Care, Precision Medicine, Pharmacogenetics
- Abstract
Pharmacogenomics (PGx) is an important component of precision medicine that promises tailored treatment approaches based on an individual's genetic information. Exploring the initiatives in research that help to integrate PGx test into clinical setting, identifying the potential barriers and challenges as well as planning the future directions, are all important for fruitful PGx implementation in any population. Qatar serves as an exemplar case study for the Middle East, having a small native population compared to a diverse immigrant population, advanced healthcare system, national genome program, and several educational initiatives on PGx and precision medicine. This paper attempts to outline the current state of PGx research and implementation in Qatar within the global context, emphasizing ongoing initiatives and educational efforts. The inclusion of PGx in university curricula and healthcare provider training, alongside precision medicine conferences, showcase Qatar's commitment to advancing this field. However, challenges persist, including the requirement for population specific implementation strategies, complex genetic data interpretation, lack of standardization, and limited awareness. The review suggests policy development for future directions in continued research investment, conducting clinical trials for the feasibility of PGx implementation, ethical considerations, technological advancements, and global collaborations to overcome these barriers., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Bastaki, Velayutham, Irfan, Adnan, Mohammed, Mbarek, Qoronfleh and Jithesh.)
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- 2024
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5. Identification of two novel autism genes, TRPC4 and SCFD2 , in Qatar simplex families through exome sequencing.
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Gupta V, Ben-Mahmoud A, Ku B, Velayutham D, Jan Z, Yousef Aden A, Kubbar A, Alshaban F, Stanton LW, Jithesh PV, Layman LC, and Kim HG
- Abstract
This study investigated the genetic underpinnings of autism spectrum disorder (ASD) in a Middle Eastern cohort in Qatar using exome sequencing. The study identified six candidate autism genes in independent simplex families, including both four known and two novel autosomal dominant and autosomal recessive genes associated with ASD. The variants consisted primarily of de novo and homozygous missense and splice variants. Multiple individuals displayed more than one candidate variant, suggesting the potential involvement of digenic or oligogenic models. These variants were absent in the Genome Aggregation Database (gnomAD) and exhibited extremely low frequencies in the local control population dataset. Two novel autism genes, TRPC4 and SCFD2 , were discovered in two Qatari autism individuals. Furthermore, the D651A substitution in CLCN3 and the splice acceptor variant in DHX30 were identified as likely deleterious mutations. Protein modeling was utilized to evaluate the potential impact of three missense variants in DEAF1 , CLCN3 , and SCFD2 on their respective structures and functions, which strongly supported the pathogenic natures of these variants. The presence of multiple de novo mutations across trios underscored the significant contribution of de novo mutations to the genetic etiology of ASD. Functional assays and further investigations are necessary to confirm the pathogenicity of the identified genes and determine their significance in ASD. Overall, this study sheds light on the genetic factors underlying ASD in Qatar and highlights the importance of considering diverse populations in ASD research., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Gupta, Ben-Mahmoud, Ku, Velayutham, Jan, Yousef Aden, Kubbar, Alshaban, Stanton, Jithesh, Layman and Kim.)
- Published
- 2023
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6. Therapeutic targeting of the TPX2/TTK network in colorectal cancer.
- Author
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Shaath H, Vishnubalaji R, Elango R, Velayutham D, Jithesh PV, and Alajez NM
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- Humans, Molecular Docking Simulation, Cell Proliferation, Gene Expression Regulation, Neoplastic, Microtubule-Associated Proteins genetics, Microtubule-Associated Proteins metabolism, Cell Cycle Proteins genetics, Cell Cycle Proteins metabolism, Protein-Tyrosine Kinases metabolism, Protein Serine-Threonine Kinases metabolism, Colonic Neoplasms genetics, Colorectal Neoplasms drug therapy, Colorectal Neoplasms genetics, Colorectal Neoplasms metabolism, Adenocarcinoma pathology
- Abstract
Background: While the increased screening, changes in lifestyle, and recent advances in treatment regimen have decreased colorectal cancer (CRC) mortality, metastatic disease and recurrence remains a major clinical challenge. In the era of precision medicine, the identification of actionable novel therapeutic targets could ultimately offer an alternative treatment strategy for CRC., Methods: RNA-Seq was conducted using the illumina platform, while bioinformatics analyses were conducted using CLC genomics workbench and iDEP.951. Colony forming unit, flow cytometry, and fluorescent microscopy were used to assess cell proliferation, cell cycle distribution, and cell death, respectively. The growth potential of CRC cells under 3-dimensional (3D) conditions was assessed using Matrigel. STRING database (v11.5) and Ingenuity Pathway Analysis (IPA) tool were used for network and pathway analyses. CRISPR-Cas9 perturbational effects database was used to identify potential therapeutic targets for CRC, through integration with gene-drug interaction database. Structural modeling and molecular docking were used to assess the interaction between candidate drugs and their targets., Results: In the current study, we investigated the therapeutic potential of targeting TPX2, TTK, DDX39A, and LRP8, commonly upregulated genes in CRC identified through differential expression analysis in CRC and adjacent non-cancerous tissue. Targeted depletion of TPX2 and TTK impaired CRC proliferation, cell cycle progression, and organoid formation under 3D culture conditions, while suppression of DDX39A and LRP8 had modest effects on CRC colony formation. Differential expression analysis and bioinformatics on TPX2 and TTK-deficient cells identified cell cycle regulation as the hallmark associated with loss of TPX2 and TTK. Elevated expression of TPX2 and TTK correlated with an oncogenic state in tumor tissue from patients with colon adenocarcinoma, thus corroborating an oncogenic role for the TPX2/TTK network in the pathogenesis of CRC. Gene set enrichment and pathway analysis of TPX2
high /TTKhigh CRC identified numerous additional gene targets as integral components of the TPX2/TTK network. Integration of TPX2/TTK enriched network with CRISPR-Cas9 functional screen data identified numerous novel dependencies for CRC. Additionally, gene-drug interaction analysis identified several druggable gene targets enriched in the TPX2/TTK network, including AURKA, TOP2A, CDK1, BIRC5, and many others., Conclusions: Our data has implicated an essential role for TPX2 and TTK in CRC pathogenesis and identified numerous potential therapeutic targets and their drug interactions, suggesting their potential clinical use as a novel therapeutic strategy for patients with CRC. Video Abstract., (© 2023. The Author(s).)- Published
- 2023
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7. Protegrin-2, a potential inhibitor for targeting SARS-CoV-2 main protease M pro .
- Author
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Jan Z, Geethakumari AM, Biswas KH, and Jithesh PV
- Abstract
Background: SARS-CoV-2 variants continue to spread throughout the world and cause waves of COVID-19 infections. It is important to find effective antiviral drugs to combat SARS-CoV-2 and its variants. The main protease (M
pro ) of SARS-CoV-2 is a promising therapeutic target due to its crucial role in viral replication and its conservation in all the variants. Therefore, the aim of this work was to identify an effective inhibitor of Mpro ., Methods: We studied around 200 antimicrobial peptides using in silico methods including molecular docking and allergenicity and toxicity prediction. One selected antiviral peptide was studied experimentally using a Bioluminescence Resonance Energy Transfer (BRET)-based Mpro biosensor, which reports Mpro activity through a decrease in energy transfer., Results: Molecular docking identified one natural antimicrobial peptide, Protegrin-2, with high binding affinity and stable interactions with Mpro allosteric residues. Furthermore, free energy calculations and molecular dynamics simulation illustrated a high affinity interaction between the two. We also determined the impact of the binding of Protegrin-2 to Mpro using a BRET-based assay, showing that it inhibits the proteolytic cleavage activity of Mpro ., Conclusions: Our in silico and experimental studies identified Protegrin-2 as a potent inhibitor of Mpro that could be pursued further towards drug development against COVID-19 infection., Competing Interests: None to declare., (© 2023 The Authors.)- Published
- 2023
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8. Artificial Intelligence for the Prediction and Early Diagnosis of Pancreatic Cancer: Scoping Review.
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Jan Z, El Assadi F, Abd-Alrazaq A, and Jithesh PV
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- Humans, Early Detection of Cancer, Algorithms, Pancreatic Neoplasms, Artificial Intelligence, Pancreatic Neoplasms diagnosis
- Abstract
Background: Pancreatic cancer is the 12th most common cancer worldwide, with an overall survival rate of 4.9%. Early diagnosis of pancreatic cancer is essential for timely treatment and survival. Artificial intelligence (AI) provides advanced models and algorithms for better diagnosis of pancreatic cancer., Objective: This study aims to explore AI models used for the prediction and early diagnosis of pancreatic cancers as reported in the literature., Methods: A scoping review was conducted and reported in line with the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews) guidelines. PubMed, Google Scholar, Science Direct, BioRXiv, and MedRxiv were explored to identify relevant articles. Study selection and data extraction were independently conducted by 2 reviewers. Data extracted from the included studies were synthesized narratively., Results: Of the 1185 publications, 30 studies were included in the scoping review. The included articles reported the use of AI for 6 different purposes. Of these included articles, AI techniques were mostly used for the diagnosis of pancreatic cancer (14/30, 47%). Radiological images (14/30, 47%) were the most frequently used data in the included articles. Most of the included articles used data sets with a size of <1000 samples (11/30, 37%). Deep learning models were the most prominent branch of AI used for pancreatic cancer diagnosis in the studies, and the convolutional neural network was the most used algorithm (18/30, 60%). Six validation approaches were used in the included studies, of which the most frequently used approaches were k-fold cross-validation (10/30, 33%) and external validation (10/30, 33%). A higher level of accuracy (99%) was found in studies that used support vector machine, decision trees, and k-means clustering algorithms., Conclusions: This review presents an overview of studies based on AI models and algorithms used to predict and diagnose pancreatic cancer patients. AI is expected to play a vital role in advancing pancreatic cancer prediction and diagnosis. Further research is required to provide data that support clinical decisions in health care., (©Zainab Jan, Farah El Assadi, Alaa Abd-alrazaq, Puthen Veettil Jithesh. Originally published in the Journal of Medical Internet Research (https://www.jmir.org), 31.03.2023.)
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- 2023
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9. Human leukocyte antigen class II gene diversity tunes antibody repertoires to common pathogens.
- Author
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Khan T, Rahman M, Ahmed I, Al Ali F, Jithesh PV, and Marr N
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- Adaptive Immunity genetics, Adult, Alleles, Gene Frequency, Haplotypes, Humans, Antibodies genetics, Genes, MHC Class II genetics, HLA Antigens genetics
- Abstract
Allelic diversity of human leukocyte antigen (HLA) class II genes may help maintain humoral immunity against infectious diseases. In this study, we investigated germline genetic variation in classical HLA class II genes and employed a systematic, unbiased approach to explore the relative contribution of this genetic variation in the antibody repertoire to various common pathogens. We leveraged a well-defined cohort of 800 adults representing the general Arab population in which genetic material is shared because of the high frequency of consanguineous unions. By applying a high-throughput method for large-scale antibody profiling to this well-defined cohort, we were able to dissect the overall effect of zygosity for classical HLA class II genes, as well as the effects associated with specific HLA class II alleles, haplotypes and genotypes, on the antimicrobial antibody repertoire breadth and antibody specificity with unprecedented resolution. Our population genetic studies revealed that zygosity of the classical HLA class II genes is a strong predictor of antibody responses to common human pathogens, suggesting that classical HLA class II gene heterozygosity confers a selective advantage. Moreover, we demonstrated that multiple HLA class II alleles can have additive effects on the antibody repertoire to common pathogens. We also identified associations of HLA-DRB1 genotypes with specific antigens. Our findings suggest that HLA class II gene polymorphisms confer specific humoral immunity against common pathogens, which may have contributed to the genetic diversity of HLA class II loci during hominine evolution., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Khan, Rahman, Ahmed, Al Ali, Jithesh and Marr.)
- Published
- 2022
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10. Editorial: Metabolomics in Infectious Diseases.
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Rahman M, Schellhorn H, Jithesh PV, and Rahman MM
- Abstract
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
- Published
- 2022
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11. A population study of clinically actionable genetic variation affecting drug response from the Middle East.
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Jithesh PV, Abuhaliqa M, Syed N, Ahmed I, El Anbari M, Bastaki K, Sherif S, Umlai UK, Jan Z, Gandhi G, Manickam C, Selvaraj S, George C, Bangarusamy D, Abdel-Latif R, Al-Shafai M, Tatari-Calderone Z, Estivill X, and Pirmohamed M
- Abstract
Clinical implementation of pharmacogenomics will help in personalizing drug prescriptions and alleviate the personal and financial burden due to inefficacy and adverse reactions to drugs. However, such implementation is lagging in many parts of the world, including the Middle East, mainly due to the lack of data on the distribution of actionable pharmacogenomic variation in these ethnicities. We analyzed 6,045 whole genomes from the Qatari population for the distribution of allele frequencies of 2,629 variants in 1,026 genes known to affect 559 drugs or classes of drugs. We also performed a focused analysis of genotypes or diplotypes of 15 genes affecting 46 drugs, which have guidelines for clinical implementation and predicted their phenotypic impact. The allele frequencies of 1,320 variants in 703 genes affecting 299 drugs or class of drugs were significantly different between the Qatari population and other world populations. On average, Qataris carry 3.6 actionable genotypes/diplotypes, affecting 13 drugs with guidelines for clinical implementation, and 99.5% of the individuals had at least one clinically actionable genotype/diplotype. Increased risk of simvastatin-induced myopathy could be predicted in ~32% of Qataris from the diplotypes of SLCO1B1, which is higher compared to many other populations, while fewer Qataris may need tacrolimus dosage adjustments for achieving immunosuppression based on the CYP3A5 diplotypes compared to other world populations. Distinct distribution of actionable pharmacogenomic variation was also observed among the Qatari subpopulations. Our comprehensive study of the distribution of actionable genetic variation affecting drugs in a Middle Eastern population has potential implications for preemptive pharmacogenomic implementation in the region and beyond., (© 2022. The Author(s).)
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- 2022
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12. Case Report: Phenotype-Gene Correlation in a Case of Novel Tandem 4q Microduplication With Short Stature, Speech Delay and Microcephaly.
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Umlai UI, Haris B, Hussain K, and Jithesh PV
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- Chromosome Duplication genetics, Humans, Male, Phenotype, Protein Serine-Threonine Kinases, Retrospective Studies, Language Development Disorders genetics, Microcephaly genetics
- Abstract
We describe a sporadic case of a pure, tandem, interstitial chromosome 4q duplication, arr[hg19] 4q28.1q32.3 (127,008,069-165,250,477) x3 in a boy born at 36 weeks of gestation. He presented with microcephaly (head circumference <1
st percentile), short stature (height <2nd percentile) and poor weight gain (weight <3rd percentile). Hypospadias and horseshoe shaped kidneys were also revealed following a urinary tract ultrasound. Biochemical analysis revealed normal growth hormone and thyroid hormone levels. While gross and fine motor skill development was in line with his age, speech delay was observed. This patient adds to a group of more than 30 cases of pure 4q tandem duplication with common and differing phenotypic presentations. Using a retrospective analysis of previous case studies alongside the current case and bioinformatics analysis of the duplicated region, we deduced the most likely dosage sensitive genes for some of the major phenotypes in the patient. The positive predictive value (PPV) was calculated for each gene and phenotype and was derived by comparing the previously reported patients who have gene duplications and an associated phenotype versus those who had the gene duplications but were unaffected. Thus, the growth retardation phenotype may be associated with NAA15 duplication, speech delay with GRIA2 and microcephaly with PLK4 duplication. Functional studies will help in confirming the observations and elucidating the mechanisms. However, our study highlights the importance of analysing case reports with pure duplications in defining phenotype-gene relationships and in improving our knowledge of the function of precise chromosomal regions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Umlai, Haris, Hussain and Jithesh.)- Published
- 2022
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13. Genome sequencing data analysis for rare disease gene discovery.
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Umlai UI, Bangarusamy DK, Estivill X, and Jithesh PV
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- Genetic Association Studies, Genome, High-Throughput Nucleotide Sequencing, Humans, Software, Data Analysis, Rare Diseases diagnosis, Rare Diseases genetics
- Abstract
Rare diseases occur in a smaller proportion of the general population, which is variedly defined as less than 200 000 individuals (US) or in less than 1 in 2000 individuals (Europe). Although rare, they collectively make up to approximately 7000 different disorders, with majority having a genetic origin, and affect roughly 300 million people globally. Most of the patients and their families undergo a long and frustrating diagnostic odyssey. However, advances in the field of genomics have started to facilitate the process of diagnosis, though it is hindered by the difficulty in genome data analysis and interpretation. A major impediment in diagnosis is in the understanding of the diverse approaches, tools and datasets available for variant prioritization, the most important step in the analysis of millions of variants to select a few potential variants. Here we present a review of the latest methodological developments and spectrum of tools available for rare disease genetic variant discovery and recommend appropriate data interpretation methods for variant prioritization. We have categorized the resources based on various steps of the variant interpretation workflow, starting from data processing, variant calling, annotation, filtration and finally prioritization, with a special emphasis on the last two steps. The methods discussed here pertain to elucidating the genetic basis of disease in individual patient cases via trio- or family-based analysis of the genome data. We advocate the use of a combination of tools and datasets and to follow multiple iterative approaches to elucidate the potential causative variant., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)
- Published
- 2022
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14. Prescription Pattern and Off-Label Use of Antipsychotics in a Middle Eastern Population.
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Bastaki K, El Anbari M, Ghuloum S, and Jithesh PV
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Background: Understanding the prescription pattern of medications in a population can help reveal the potential usage scenarios, including off-label prescriptions, and the need for precision medicine implementation. Therefore, the aim of this study was to assess the prescription pattern and off-label use of antipsychotics in the Qatari population. Methods: We performed a cross-sectional study of Qatari patients who received antipsychotic prescriptions from the major healthcare providers in the country during the 2-year period between June 2018 and May 2020. The number of patients, prescriptions dispensed, and clinical indications were collected and statistical analysis using chi-square test was conducted. Results: Among the 9,349 Qatari patients prescribed with antipsychotics during the study period, the majority were female (57%; p < 0.001) and were in the age categories 20-39 and 30-39 years (both 22%; p < 0.001). Among the 35,938 antipsychotic prescriptions dispensed, second-generation antipsychotics were the most highly prescribed (59%), specifically, quetiapine (16%) and olanzapine (12%), but the first-generation antipsychotic prochlorperazine (13%) was also highly prescribed. Most of the indications of antipsychotics (69%) were for off-label use such as for controlling chronic diseases, sleeping disorders, benign paroxysmal positional vertigo and irritable bowel syndrome. Conclusion: Non-mental health and off-label prescriptions of several antipsychotics were observed. Integration of this data with pharmacogenomic and clinical outcome data will help in determining the course of action for implementing personalized and precision medicine in the country and beyond., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Bastaki, El Anbari, Ghuloum and Jithesh.)
- Published
- 2021
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15. Prescription Pattern of Antidepressants and the Potential for Personalized Medicine in the Qatari Population.
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Bastaki K, El Anbari M, Ghuloum S, and Jithesh PV
- Abstract
Studying the prescription pattern of medications will help in understanding potential unnecessary prescriptions, due to the trial-and-error method of prescribing, and the need for personalized medicine in a population. Therefore, in this study, our aim was to explore the prescribing pattern and off-label use of antidepressants in the Qatari population. We conducted a retrospective study of Qatari patients who received prescriptions for antidepressants from the major healthcare providers in Qatar, for a period of 24 months between June 2018 and May 2020. The number of patients, prescriptions, and diagnostic indications were analyzed. The chi-square test was used for identifying statistically significant association of the number of individuals prescribed with age category or gender. Of the 14,601 Qatari patients who were prescribed antidepressants, the majority were female (61%, p < 2.2 × 10
-16 ), and were at or above 60 years of age (27%, p < 2.2 × 10-16 ). More numbers of selective serotonin reuptake inhibitors (SSRIs) (22,085 out of 48,031; 46%), were dispensed than other classes of antidepressants, with escitalopram (26%) at the top of the list. Preponderance of prescription of antidepressants for non-mental health diseases was observed. Population-level prescription trends, as we reported here, when combined with patient genetic variability and outcome data, will have the power to predict the potential for treatment failures and adverse effects of these medications in the population. We also recommend educating non-mental health prescribers about the adherence to evidence and guidelines to ensure patient safety while prescribing antidepressants.- Published
- 2021
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16. First Whole Transcriptome RNAseq on CHD8 Haploinsufficient Patient and Meta-Analyses Across Cellular Models Uncovers Likely Key Pathophysiological Target Genes.
- Author
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Yasin H, Stowe R, Wong CK, Jithesh PV, and Zahir FR
- Abstract
In 2019, we confirmed that the haploinsufficiency of CHD8 does indeed cause the novel syndromic neurodevelopmental disease we first discovered a dozen years before. Here, we report the first whole transcriptome RNAseq gene expression profiling for a patient with this new syndrome, as a preliminary exploration of potential pathophysiological mechanisms. We compared our patient transcriptome profile with that of all publicly available RNAseq datasets from human cellular models including neuronal progenitor cells, neurons and organoids. We compared differential gene expression profiles overall and conducted phenotype-informed data filtration based on the characteristic syndrome presentation. We found that concordance among differential gene expression profiles was poor across all datasets. Nevertheless, remarkably, we show that the patient blood differential gene expression profile most resembled that of the neuronal cell model, a finding that encourages further transcriptome profiling using patient blood samples. In addition, our custom phenotype-informed analyses yielded important, differentially expressed syndrome pathophysiology target genes. Finally, we note that genes dysregulated due to CHD8 heterozygous deletion are linked to known neurological as well as oncological pathways., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2020, Yasin et al.)
- Published
- 2020
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17. Three Copies of Four Interferon Receptor Genes Underlie a Mild Type I Interferonopathy in Down Syndrome.
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Kong XF, Worley L, Rinchai D, Bondet V, Jithesh PV, Goulet M, Nonnotte E, Rebillat AS, Conte M, Mircher C, Gürtler N, Liu L, Migaud M, Elanbari M, Habib T, Ma CS, Bustamante J, Abel L, Ravel A, Lyonnet S, Munnich A, Duffy D, Chaussabel D, Casanova JL, Tangye SG, Boisson-Dupuis S, and Puel A
- Subjects
- Adolescent, Adult, B-Lymphocytes immunology, B-Lymphocytes metabolism, B-Lymphocytes pathology, B-Lymphocytes virology, Child, Child, Preschool, Chromosome Mapping, Cytokines metabolism, Disease Susceptibility, Down Syndrome immunology, Female, Gene Expression Profiling, Genetic Loci, Genetic Predisposition to Disease, Humans, Interferon Type I genetics, Male, Middle Aged, Monocytes immunology, Monocytes metabolism, Receptors, Interferon metabolism, STAT1 Transcription Factor metabolism, T-Lymphocyte Subsets immunology, T-Lymphocyte Subsets metabolism, Transcriptome, Young Adult, Down Syndrome genetics, Down Syndrome metabolism, Gene Dosage, Interferon Type I metabolism, Receptors, Interferon genetics
- Abstract
Down syndrome (DS) is characterized by the occurrence of three copies of human chromosome 21 (HSA21). HSA21 contains a cluster of four interferon receptor (IFN-R) genes: IFNAR1, IFNAR2, IFNGR2, and IL10RB. DS patients often develop mucocutaneous infections and autoimmune diseases, mimicking patients with heterozygous gain-of-function (GOF) STAT1 mutations, which enhance cellular responses to three types of interferon (IFN). A gene dosage effect at these four loci may contribute to the infectious and autoimmune manifestations observed in individuals with DS. We report high levels of IFN-αR1, IFN-αR2, and IFN-γR2 expression on the surface of monocytes and EBV-transformed-B (EBV-B) cells from studying 45 DS patients. Total and phosphorylated STAT1 (STAT1 and pSTAT1) levels were constitutively high in unstimulated and IFN-α- and IFN-γ-stimulated monocytes from DS patients but lower than those in patients with GOF STAT1 mutations. Following stimulation with IFN-α or -γ, but not with IL-6 or IL-21, pSTAT1 and IFN-γ activation factor (GAF) DNA-binding activities were significantly higher in the EBV-B cells of DS patients than in controls. These responses resemble the dysregulated responses observed in patients with STAT1 GOF mutations. Concentrations of plasma type I IFNs were high in 12% of the DS patients tested (1.8% in the healthy controls). Levels of type I IFNs, IFN-Rs, and STAT1 were similar in DS patients with and without recurrent skin infections. We performed a genome-wide transcriptomic analysis based on principal component analysis and interferon modules on circulating monocytes. We found that DS monocytes had levels of both IFN-α- and IFN-γ-inducible ISGs intermediate to those of monocytes from healthy controls and from patients with GOF STAT1 mutations. Unlike patients with GOF STAT1 mutations, patients with DS had normal circulating Th17 counts and a high proportion of terminally differentiated CD8
+ T cells with low levels of STAT1 expression. We conclude a mild interferonopathy in Down syndrome leads to an incomplete penetrance at both cellular and clinical level, which is not correlate with recurrent skin bacterial or fungal infections. The constitutive upregulation of type I and type II IFN-R, at least in monocytes of DS patients, may contribute to the autoimmune diseases observed in these individuals.- Published
- 2020
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18. Integrated omics profiling reveals novel patterns of epigenetic programming in cancer-associated myofibroblasts.
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Najgebauer H, Liloglou T, Jithesh PV, Giger OT, Varro A, and Sanderson CM
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- Cell Movement, Cell Proliferation, DNA Methylation, Epigenomics, Esophageal Neoplasms genetics, Humans, Myofibroblasts metabolism, Stomach Neoplasms genetics, Tumor Cells, Cultured, Tumor Microenvironment, Biomarkers, Tumor genetics, Epigenesis, Genetic, Esophageal Neoplasms pathology, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Myofibroblasts pathology, Stomach Neoplasms pathology
- Abstract
There is increasing evidence that stromal myofibroblasts play a key role in the tumour development however, the mechanisms by which they become reprogrammed to assist in cancer progression remain unclear. As cultured cancer-associated myofibroblasts (CAMs) retain an ability to enhance the proliferation and migration of cancer cells in vitro, it is possible that epigenetic reprogramming of CAMs within the tumour microenvironment may confer long-term pro-tumourigenic changes in gene expression. This study reports the first comparative multi-omics analysis of cancer-related changes in gene expression and DNA methylation in primary myofibroblasts derived from gastric and oesophageal tumours. In addition, we identify novel CAM-specific DNA methylation signatures, which are not observed in patient-matched adjacent tissue-derived myofibroblasts, or corresponding normal tissue-derived myofibroblasts. Analysis of correlated changes in DNA methylation and gene expression shows that different patterns of gene-specific DNA methylation have the potential to confer pro-tumourigenic changes in metabolism, cell signalling and differential responses to hypoxia. These molecular signatures provide new insights into potential mechanisms of stromal reprogramming in gastric and oesophageal cancer, while also providing a new resource to facilitate biomarker identification and future hypothesis-driven studies into mechanisms of stromal reprogramming and tumour progression in solid tumours., (© The Author(s) 2019. Published by Oxford University Press.)
- Published
- 2019
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19. The Unfolded Protein Response: A Novel Therapeutic Target for Poor Prognostic BRAF Mutant Colorectal Cancer.
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Forsythe N, Refaat A, Javadi A, Khawaja H, Weir JA, Emam H, Allen WL, Burkamp F, Popovici V, Jithesh PV, Isella C, Labonte MJ, Mills IG, Johnston PG, and Van Schaeybroeck S
- Subjects
- Antineoplastic Agents pharmacology, Apoptosis drug effects, Apoptosis genetics, Biomarkers, Tumor, Cell Line, Tumor, Cell Survival drug effects, Cell Survival genetics, Colorectal Neoplasms drug therapy, Colorectal Neoplasms mortality, Endoplasmic Reticulum Chaperone BiP, Endoplasmic Reticulum Stress drug effects, Endoplasmic Reticulum Stress genetics, Heat-Shock Proteins genetics, Heat-Shock Proteins metabolism, Humans, Hydroxamic Acids pharmacology, MAP Kinase Signaling System, Models, Biological, Oligopeptides pharmacology, Prognosis, Protein Biosynthesis, Proto-Oncogene Proteins B-raf metabolism, Pyrimidines pharmacology, Signal Transduction drug effects, Transcription Factor CHOP genetics, Transcription Factor CHOP metabolism, Colorectal Neoplasms genetics, Colorectal Neoplasms metabolism, Mutation, Protein Kinase Inhibitors pharmacology, Proto-Oncogene Proteins B-raf antagonists & inhibitors, Proto-Oncogene Proteins B-raf genetics, Unfolded Protein Response drug effects
- Abstract
BRAF
V600E mutations occur in ∼10% of colorectal cancer cases, are associated with poor survival, and have limited responses to BRAF/MEK inhibition with or without EGFR inhibition. There is an unmet need to understand the biology of poor prognostic BRAF MT colorectal cancer. We have used differential gene expression and pathway analyses of untreated stage II and stage III BRAF MT (discovery set: n = 31; validation set: n = 26) colorectal cancer, and an siRNA screen to characterize the biology underpinning the BRAF MT subgroup with poorest outcome. These analyses identified the unfolded protein response (UPR) as a novel and druggable pathway associated with the BRAF MT colorectal cancer subgroup with poorest outcome. We also found that oncogenic BRAF drives endoplasmic reticulum (ER) stress and UPR pathway activation through MEK/ERK. Furthermore, inhibition of GRP78, the master regulator of the UPR, using siRNA or small molecule inhibition, resulted in acute ER stress and apoptosis, in particular in BRAF MT colorectal cancer cells. In addition, dual targeting of protein degradation using combined Carfilzomib (proteasome inhibitor) and ACY-1215 (HDAC6-selective inhibitor) treatment resulted in marked accumulation of protein aggregates, acute ER stress, apoptosis, and therapeutic efficacy in BRAF MT in vitro and xenograft models. Mechanistically, we found that the apoptosis following combined Carfilzomib/ACY-1215 treatment is mediated through increased CHOP expression. Taken together, our findings indicate that oncogenic BRAF induces chronic ER stress and that inducers of acute ER stress could be a novel treatment strategy for poor prognostic BRAF MT colorectal cancer. Mol Cancer Ther; 17(6); 1280-90. ©2018 AACR ., (©2018 American Association for Cancer Research.)- Published
- 2018
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20. Proteomic profiling of rectal cancer reveals acid ceramidase is implicated in radiation response.
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Bowden DL, Sutton PA, Wall MA, Jithesh PV, Jenkins RE, Palmer DH, Goldring CE, Parsons JL, Park BK, Kitteringham NR, and Vimalachandran D
- Subjects
- Aged, Female, Humans, Male, Middle Aged, Acid Ceramidase metabolism, Biomarkers, Tumor metabolism, Chemoradiotherapy, Neoadjuvant Therapy, Neoplasm Proteins metabolism, Proteomics, Rectal Neoplasms metabolism, Rectal Neoplasms pathology, Rectal Neoplasms therapy
- Abstract
Background: Neoadjuvant chemoradiotherapy (CRT) is used in locally advanced rectal cancer when tumours threaten the circumferential resection margin, with varying response to treatment. This experimental study aimed to identify significantly differentially expressed proteins between patients responding and not responding to CRT, and to validate any proteins of interest., Methods: Mass spectrometry (with isobaric tagging for relative quantification) analysis of rectal cancers pre- and post-CRT, and at resection. Validation of proteins of interest was performed by assessing tissue microarray (TMA) immunohistochemistry expression in a further 111 patients with rectal cancer., Results: Proteomic data are available via ProteomeXchange with identifier PXD008436. Reduced abundance of contributing peptide ions for acid ceramidase (AC) (log fold change -1.526, p = 1.17E-02) was observed in CRT responders. Differential expression of AC was confirmed upon analysis of the TMAs. Cancer site expression of AC in stromal cells from post-CRT resection specimens was observed to be relatively low in pathological complete response (p = 0.003), and relatively high with no response to CRT (p = 0.017)., Conclusion: AC may be implicated in the response of rectal cancer to CRT. We propose its further assessment as a novel potential biomarker and therapeutic target., Significance: There is a need for biomarkers to guide the use of chemoradiotherapy in rectal cancer, as none are in routine clinical use. We have determined acid ceramidase may have a role in radiation response, based on novel proteomic profiling and validation in a wider dataset using tissue microarrays. The ability to predict or improve response would positively select those patients who will derive benefit, prevent delays in the local and systemic management of disease in non-responders, and reduce morbidity associated with chemoradiotherapy., (Copyright © 2018 Elsevier B.V. All rights reserved.)
- Published
- 2018
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21. Exome sequencing of synchronously resected primary colorectal tumours and colorectal liver metastases to inform oncosurgical management.
- Author
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Sutton PA, Jithesh PV, Jones RP, Evans JP, Vimalachandran D, Malik HZ, Park BK, Goldring CE, Palmer DH, and Kitteringham NR
- Subjects
- Adenocarcinoma secondary, Adenocarcinoma therapy, Aged, Chemotherapy, Adjuvant, Colorectal Neoplasms pathology, Colorectal Neoplasms therapy, Combined Modality Therapy, Exome, Female, Gene Frequency, Hepatectomy, Humans, Liver Neoplasms secondary, Liver Neoplasms therapy, Male, Middle Aged, Neoplasm Metastasis, Treatment Outcome, Adenocarcinoma genetics, Colectomy methods, Colorectal Neoplasms genetics, DNA, Neoplasm genetics, High-Throughput Nucleotide Sequencing methods, Liver Neoplasms genetics, Mutation
- Abstract
Background: Next generation sequencing technology has facilitated mapping of the colorectal cancer genotype and furthered our understanding of metastogenesis. The aim of this study was to investigate for conserved and different mutations in the exomes of synchronously resected primary colorectal tumour and liver metastases. This information could potentially be utilised to guide the treatment of advanced disease with the help of biological information from the primary tumour., Methods: We performed exome sequencing of synchronously resected primary colorectal cancer and colorectal liver metastases as well as normal colonic mucosa and liver parenchyma, from four patients who had received neo-adjuvant chemotherapy, at a depth of 50X using the Ion Proton platform. Raw data was mapped to the reference genome prior to variant calling, annotation and downstream analysis., Results: Exome sequencing identified 585 non-synonymous missense single nucleotide variants (SNVs), of which 215 (36.8%) were unique to the primary tumour, 226 (38.6%) unique to the metastasis and 81 (13.8%) present in patient matched pairs. SNVs identified in the ErbB pathway appear to be concordant between primary and metastatic tumours., Conclusion: Only 13.8% of the metastatic exome can be predicted by the genotype of the primary tumour. We have demonstrated concordance of a number of SNVs in the ErbB pathway, which may inform selection of therapeutic agents in advanced colorectal cancer., (Copyright © 2017 Elsevier Ltd, BASO ~ The Association for Cancer Surgery, and the European Society of Surgical Oncology. All rights reserved.)
- Published
- 2018
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22. From genomes to genomic medicine: enabling personalized and precision medicine in the Middle East.
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Jithesh PV and Scaria V
- Subjects
- Delivery of Health Care, Genetic Testing, Genomics methods, Humans, Middle East epidemiology, Pharmacogenetics, Genomics trends, Precision Medicine trends
- Published
- 2017
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23. Accelerating next generation sequencing data analysis with system level optimizations.
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Kathiresan N, Temanni R, Almabrazi H, Syed N, Jithesh PV, and Al-Ali R
- Subjects
- Chromosome Mapping, Databases, Genetic, Genomics methods, Genomics standards, Genotyping Techniques, Reproducibility of Results, Software, Workflow, Computational Biology methods, Computational Biology standards, High-Throughput Nucleotide Sequencing standards, Sequence Analysis, DNA standards
- Abstract
Next generation sequencing (NGS) data analysis is highly compute intensive. In-memory computing, vectorization, bulk data transfer, CPU frequency scaling are some of the hardware features in the modern computing architectures. To get the best execution time and utilize these hardware features, it is necessary to tune the system level parameters before running the application. We studied the GATK-HaplotypeCaller which is part of common NGS workflows, that consume more than 43% of the total execution time. Multiple GATK 3.x versions were benchmarked and the execution time of HaplotypeCaller was optimized by various system level parameters which included: (i) tuning the parallel garbage collection and kernel shared memory to simulate in-memory computing, (ii) architecture-specific tuning in the PairHMM library for vectorization, (iii) including Java 1.8 features through GATK source code compilation and building a runtime environment for parallel sorting and bulk data transfer (iv) the default 'on-demand' mode of CPU frequency is over-clocked by using 'performance-mode' to accelerate the Java multi-threads. As a result, the HaplotypeCaller execution time was reduced by 82.66% in GATK 3.3 and 42.61% in GATK 3.7. Overall, the execution time of NGS pipeline was reduced to 70.60% and 34.14% for GATK 3.3 and GATK 3.7 respectively.
- Published
- 2017
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24. Gene expression profiling in bladder cancer identifies potential therapeutic targets.
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Hussain SA, Palmer DH, Syn WK, Sacco JJ, Greensmith RMD, Elmetwali T, Aachi V, Lloyd BH, Jithesh PV, Arrand J, Barton D, Ansari J, Sibson DR, and James ND
- Subjects
- Aged, Aged, 80 and over, Biopsy, Carcinoma drug therapy, Carcinoma metabolism, Carcinoma pathology, Cell Cycle, Cell Proliferation, Cluster Analysis, Complement Pathway, Classical genetics, Cystoscopy, Down-Regulation, Female, Gene Expression Profiling, Humans, Immunohistochemistry, Male, Microarray Analysis, Middle Aged, Neoplasm Grading, Signal Transduction, Transcriptome, Up-Regulation, Urinary Bladder Neoplasms drug therapy, Urinary Bladder Neoplasms metabolism, Urinary Bladder Neoplasms pathology, Urothelium pathology, Carcinoma genetics, Gene Expression Regulation, Neoplastic, Molecular Targeted Therapy, Osteopontin metabolism, Urinary Bladder Neoplasms genetics
- Abstract
Despite advances in management, bladder cancer remains a major cause of cancer related complications. Characterisation of gene expression patterns in bladder cancer allows the identification of pathways involved in its pathogenesis, and may stimulate the development of novel therapies targeting these pathways. Between 2004 and 2005, cystoscopic bladder biopsies were obtained from 19 patients and 11 controls. These were subjected to whole transcript-based microarray analysis. Unsupervised hierarchical clustering was used to identify samples with similar expression profiles. Hypergeometric analysis was used to identify canonical pathways and curated networks having statistically significant enrichment of differentially expressed genes. Osteopontin (OPN) expression was validated by immunohistochemistry. Hierarchical clustering defined signatures, which differentiated between cancer and healthy tissue, muscle-invasive or non-muscle invasive cancer and healthy tissue, grade 1 and grade 3. Pathways associated with cell cycle and proliferation were markedly upregulated in muscle-invasive and grade 3 cancers. Genes associated with the classical complement pathway were downregulated in non-muscle invasive cancer. Osteopontin was markedly overexpressed in invasive cancer compared to healthy tissue. The present study contributes to a growing body of work on gene expression signatures in bladder cancer. The data support an important role for osteopontin in bladder cancer, and identify several pathways worthy of further investigation.
- Published
- 2017
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25. Genome-wide Regulatory Roles of the C2H2-type Zinc Finger Protein ZNF764 on the Glucocorticoid Receptor.
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Fadda A, Syed N, Mackeh R, Papadopoulou A, Suzuki S, Jithesh PV, and Kino T
- Subjects
- Binding Sites, Dexamethasone pharmacology, Glucocorticoids pharmacology, HeLa Cells, Humans, Nucleotide Motifs, Position-Specific Scoring Matrices, Protein Binding, Protein Interaction Domains and Motifs, Regulatory Sequences, Nucleic Acid, Signal Transduction drug effects, Transcription Initiation Site, Transcription, Genetic, Gene Expression Regulation, Genome-Wide Association Study, Receptors, Glucocorticoid metabolism, Zinc Fingers genetics
- Abstract
The C2H2-type zinc finger protein ZNF764 acts as an enhancer for several steroid hormone receptors, and haploinsufficiency of this gene may be responsible for tissue resistance to multiple steroid hormones including glucocorticoids observed in a patient with 16p11.2 microdeletion. We examined genome-wide regulatory actions of ZNF764 on the glucocorticoid receptor (GR) in HeLa cells as a model system. ZNF764- and GR-binding sites demonstrated similar distribution in various genomic features. They positioned predominantly around 50-500 kbs from the transcription start sites of their nearby genes, and were closely localized with each other, overlapping in ~37% of them. ZNF764 demonstrated differential on/off effects on GR-binding and subsequent mRNA expression: some genes were highly dependent on the presence/absence of ZNF764, but others were not. Pathway analysis revealed that these 3 gene groups were involved in distinct cellular activities. ZNF764 physically interacted with GR at ligand-binding domain through its KRAB domain, and both its physical interaction to GR and zinc finger domain appear to be required for ZNF764 to regulate GR transcriptional activity. Thus, ZNF764 is a cofactor directing GR transcriptional activity toward specific biologic pathways by changing GR binding and transcriptional activity on the glucocorticoid-responsive genes., Competing Interests: The authors declare no competing financial interests.
- Published
- 2017
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26. AKT1 has dual actions on the glucocorticoid receptor by cooperating with 14-3-3.
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Habib T, Sadoun A, Nader N, Suzuki S, Liu W, Jithesh PV, and Kino T
- Subjects
- Cell Nucleus metabolism, Chromatin metabolism, E1A-Associated p300 Protein metabolism, Gene Expression Regulation drug effects, Glucocorticoids pharmacology, HCT116 Cells, Histone Code, Humans, Jurkat Cells, Mammary Tumor Virus, Mouse genetics, Mutant Proteins metabolism, Phosphorylation drug effects, Precursor Cell Lymphoblastic Leukemia-Lymphoma genetics, Precursor Cell Lymphoblastic Leukemia-Lymphoma pathology, Promoter Regions, Genetic, Protein Binding drug effects, Protein Domains, Protein Isoforms metabolism, Receptors, Glucocorticoid chemistry, Response Elements genetics, Serine genetics, Transcription, Genetic drug effects, 14-3-3 Proteins metabolism, Biomarkers, Tumor metabolism, Exoribonucleases metabolism, Proto-Oncogene Proteins c-akt metabolism, Receptors, Glucocorticoid metabolism
- Abstract
Glucocorticoids are important therapeutic compounds for acute lymphoblastic leukemia (ALL). AKT1 or the protein kinase B is frequently activated in ALL, and contributes to the development of glucocorticoid resistance. We examined impact of AKT1 on glucocorticoid receptor (GR)-induced transcriptional activity in cooperation with phospho-serine/threonine-binding protein 14-3-3. AKT1 has two distinct actions on GR transcriptional activity, one through segregation of GR in the cytoplasm by phosphorylating GR at Ser-134 and subsequent association of 14-3-3, and the other through direct modulation of GR transcriptional activity in the nucleus. For the latter, AKT1 and 14-3-3 are attracted to DNA-bound GR, accompanied by AKT1-dependent p300 phosphorylation, H3S10 phosphorylation and H3K14 acetylation at the DNA site. These two actions of AKT1 regulate distinct sets of glucocorticoid-responsive genes. Our results suggest that specific inhibition of the AKT1/14-3-3 activity on the cytoplasmic retention of GR may be a promising target for treating glucocorticoid resistance observed in ALL., (Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2017
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27. Ran GTPase promotes cancer progression via Met recepto-rmediated downstream signaling.
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Yuen HF, Chan KK, Platt-Higgins A, Dakir el-H, Matchett KB, Haggag YA, Jithesh PV, Habib T, Faheem A, Dean FA, Morgan R, Rudland PS, and El-Tanani M
- Subjects
- Cell Adhesion drug effects, Cell Adhesion genetics, Cell Line, Tumor, Cell Movement drug effects, Cell Movement genetics, Cell Proliferation, Disease Progression, Drug Resistance, Neoplasm genetics, Gene Expression Regulation, Neoplastic drug effects, Gene Knockdown Techniques, Hepatocyte Growth Factor metabolism, Humans, Neoplasms genetics, Phosphorylation, Protein Kinase Inhibitors pharmacology, Proto-Oncogene Proteins c-akt genetics, Proto-Oncogene Proteins c-akt metabolism, Proto-Oncogene Proteins c-met genetics, ran GTP-Binding Protein genetics, Neoplasms metabolism, Neoplasms pathology, Proto-Oncogene Proteins c-met metabolism, Signal Transduction drug effects, ran GTP-Binding Protein metabolism
- Abstract
It has been shown previously that cancer cells with an activated oncogenic pathway, including Met activation, require Ran for growth and survival.Here, we show that knockdown of Ran leads to a reduction of Met receptor expression in several breast and lung cancer cell lines. This, in turn suppressed HGF expression and the Met-mediated activation of the Akt pathway, as well as cell adhesion, migration, and invasion. In a cell line model where Met amplification has previously been shown to contribute to gefitinib resistance, Ran knockdown sensitized cells to gefitinib-mediated inhibition of Akt and ERK1/2 phosphorylation and consequently reduced cell proliferation. We further demonstrate that Met reduction-mediated by knockdown of Ran, occurs at the post-transcriptional level, probably via a matrix metalloproteinase. Moreover, the level of immunoreactive Ran and Met are positively associated in human breast cancer specimens, suggesting that a high level of Ran may be a pre-requisite for Met overexpression. Interestingly, a high level of immunoreactive Ran dictates the prognostic significance of Met, indicating that the co-overexpression of Met and Ran may be associated with cancer progression and could be used in combination as a prognostic indicator.
- Published
- 2016
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28. KDM6B histone demethylase is an epigenetic regulator of estrogen receptor β expression in human pleural mesothelioma.
- Author
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Manente AG, Pinton G, Zonca S, Tavian D, Habib T, Jithesh PV, Fennell D, Nilsson S, and Moro L
- Subjects
- Basic Helix-Loop-Helix Transcription Factors metabolism, Cell Hypoxia, Cell Line, Tumor, Estrogen Receptor beta metabolism, Histones metabolism, Humans, Jumonji Domain-Containing Histone Demethylases metabolism, Lung Neoplasms metabolism, Mesothelioma metabolism, Mesothelioma, Malignant, Methylation, Protein Processing, Post-Translational, Epigenesis, Genetic, Estrogen Receptor beta genetics, Jumonji Domain-Containing Histone Demethylases genetics, Lung Neoplasms genetics, Mesothelioma genetics
- Abstract
Aim: To assess the correlation between KDM6B and estrogen receptor β (ERβ) expression in malignant pleural mesothelioma (MPM)., Materials & Methods: We evaluated gene expression by in silico analysis of microarray data, real-time PCR and western blot in MPM tumors and cell lines., Results & Conclusion: We report a strong positive correlation between the expression of KDM6B and ERβ in MPM tumors and cell lines. We describe that, in hypoxia, the HIF2α-KDM6B axis induces an epithelioid morphology and ERβ expression in biphasic MPM cells with estrogen receptor-negative phenotype. Reduced histone H3K27 tri-methylation confirms KDM6B activity under hypoxic conditions. Importantly, cells treated during reoxygenation with the selective ERβ agonist, KB9520, maintain ERβ expression and the less aggressive phenotype acquired in hypoxia.
- Published
- 2016
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29. Temple-Baraitser Syndrome and Zimmermann-Laband Syndrome: one clinical entity?
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Mégarbané A, Al-Ali R, Choucair N, Lek M, Wang E, Ladjimi M, Rose CM, Hobeika R, Macary Y, Temanni R, Jithesh PV, Chouchane A, Sastry KS, Thomas R, Tomei S, Liu W, Marincola FM, MacArthur D, and Chouchane L
- Subjects
- Abnormalities, Multiple diagnosis, Craniofacial Abnormalities diagnosis, DNA chemistry, DNA isolation & purification, DNA metabolism, DNA Mutational Analysis, Ether-A-Go-Go Potassium Channels genetics, Fibromatosis, Gingival diagnosis, Hand Deformities, Congenital diagnosis, Humans, Infant, Intellectual Disability diagnosis, Male, Mutation, Missense, Nails, Malformed diagnosis, Protein Serine-Threonine Kinases genetics, Thumb diagnostic imaging, Toes diagnostic imaging, Abnormalities, Multiple genetics, Craniofacial Abnormalities genetics, Fibromatosis, Gingival genetics, Hallux abnormalities, Hand Deformities, Congenital genetics, Intellectual Disability genetics, Nails, Malformed genetics, Thumb abnormalities
- Abstract
Background: KCNH1 encodes a voltage-gated potassium channel that is predominantly expressed in the central nervous system. Mutations in this gene were recently found to be responsible for Temple-Baraitser Syndrome (TMBTS) and Zimmermann-Laband syndrome (ZLS)., Methods: Here, we report a new case of TMBTS diagnosed in a Lebanese child. Whole genome sequencing was carried out on DNA samples of the proband and his parents to identify mutations associated with this disease. Sanger sequencing was performed to confirm the presence of detected variants., Results: Whole genome sequencing revealed three missense mutations in TMBTS patient: c.1042G > A in KCNH1, c.2131 T > C in STK36, and c.726C > A in ZNF517. According to all predictors, mutation in KCNH1 is damaging de novo mutation that results in substitution of Glycine by Arginine, i.e., p.(Gly348Arg). This mutation was already reported in a patient with ZLS that could affect the connecting loop between helices S4-S5 of KCNH1 with a gain of function effect., Conclusions: Our findings demonstrate that KCNH1 mutations cause TMBTS and expand the mutational spectrum of KCNH1 in TMBTS. In addition, all cases of TMBTS were reviewed and compared to ZLS. We suggest that the two syndromes are a continuum and that the variability in the phenotypes is the result of the involvement of genetic modifiers.
- Published
- 2016
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30. Distinct miRNA profiles in normal and gastric cancer myofibroblasts and significance in Wnt signaling.
- Author
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Wang L, Steele I, Kumar JD, Dimaline R, Jithesh PV, Tiszlavicz L, Reisz Z, Dockray GJ, and Varro A
- Subjects
- Cell Proliferation, Cells, Cultured, Chemotaxis, Humans, Myofibroblasts physiology, Stomach Neoplasms genetics, Wnt-5a Protein genetics, Wnt-5a Protein metabolism, MicroRNAs genetics, Myofibroblasts metabolism, Stomach Neoplasms metabolism, Wnt Signaling Pathway
- Abstract
Stromal cells influence epithelial function in both health and disease. Myofibroblasts are abundant stromal cells that influence the cellular microenvironment by release of extracellular matrix (ECM) proteins, growth factors, proteases, cytokines, and chemokines. Cancer-associated myofibroblasts (CAMs) differ from adjacent tissue (ATMs) and normal tissue myofibroblasts (NTMs), but the basis of this is incompletely understood. We report now the differential expression of miRNAs in gastric cancer CAMs. MicroRNA arrays identified differences in the miRNA profile in gastric and esophageal NTMs and in CAMs from stomach compared with NTMs. miR-181d was upregulated in gastric CAMs. Analysis of differentially regulated miRNAs indicated an involvement in Wnt signaling. Examination of a microarray data set then identified Wnt5a as the only consistently upregulated Wnt ligand in gastric CAMs. Wnt5a stimulated miR-181d expression, and knockdown of miR-181d inhibited Wnt5a stimulation of CAM proliferation and migration. Analysis of miR-181d targets suggested a role in chemotaxis. Conditioned medium from CAMs stimulated gastric cancer cell (AGS) migration more than that from ATMs, and miR-181d knockdown reduced the effect of CAM-CM on AGS cell migration but had no effect on AGS cell responses to ATM conditioned media. The data suggest that dysregulation of miRNA expression in gastric CAMs, secondary to Wnt5a signaling, accounts at least in part for the effect of CAMs in promoting cancer cell migration., (Copyright © 2016 the American Physiological Society.)
- Published
- 2016
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31. Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing.
- Author
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Hasan MR, Rawat A, Tang P, Jithesh PV, Thomas E, Tan R, and Tilley P
- Subjects
- Cerebrospinal Fluid microbiology, Cerebrospinal Fluid virology, Humans, Nasopharynx microbiology, Nasopharynx virology, Real-Time Polymerase Chain Reaction, Sensitivity and Specificity, Communicable Diseases diagnosis, High-Throughput Nucleotide Sequencing methods, Molecular Diagnostic Techniques methods, Specimen Handling methods
- Abstract
Next-generation sequencing (NGS) technology has shown promise for the detection of human pathogens from clinical samples. However, one of the major obstacles to the use of NGS in diagnostic microbiology is the low ratio of pathogen DNA to human DNA in most clinical specimens. In this study, we aimed to develop a specimen-processing protocol to remove human DNA and enrich specimens for bacterial and viral DNA for shotgun metagenomic sequencing. Cerebrospinal fluid (CSF) and nasopharyngeal aspirate (NPA) specimens, spiked with control bacterial and viral pathogens, were processed using either a commercially available kit (MolYsis) or various detergents followed by DNase prior to the extraction of DNA. Relative quantities of human DNA and pathogen DNA were determined by real-time PCR. The MolYsis kit did not improve the pathogen-to-human DNA ratio, but significant reductions (>95%;P< 0.001) in human DNA with minimal effect on pathogen DNA were achieved in samples that were treated with 0.025% saponin, a nonionic surfactant. Specimen preprocessing significantly decreased NGS reads mapped to the human genome (P< 0.05) and improved the sensitivity of pathogen detection (P< 0.01), with a 20- to 650-fold increase in the ratio of microbial reads to human reads. Preprocessing also permitted the detection of pathogens that were undetectable in the unprocessed samples. Our results demonstrate a simple method for the reduction of background human DNA for metagenomic detection for a broad range of pathogens in clinical samples., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)
- Published
- 2016
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32. SIRT1 at the crossroads of AKT1 and ERβ in malignant pleural mesothelioma cells.
- Author
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Pinton G, Zonca S, Manente AG, Cavaletto M, Borroni E, Daga A, Jithesh PV, Fennell D, Nilsson S, and Moro L
- Subjects
- Animals, Apoptosis drug effects, Cell Proliferation drug effects, Estrogen Receptor beta agonists, Estrogens pharmacology, Forkhead Box Protein M1 metabolism, Humans, Lung Neoplasms drug therapy, Lung Neoplasms metabolism, Male, Mesothelioma drug therapy, Mesothelioma metabolism, Mesothelioma, Malignant, Mice, Mice, Nude, Pleural Neoplasms drug therapy, Pleural Neoplasms metabolism, Tumor Cells, Cultured, Xenograft Model Antitumor Assays, Biomarkers, Tumor metabolism, Estrogen Receptor beta metabolism, Lung Neoplasms pathology, Mesothelioma pathology, Pleural Neoplasms pathology, Proto-Oncogene Proteins c-akt metabolism, Sirtuin 1 metabolism
- Abstract
In this report, we show that malignant pleural mesothelioma (MPM) patients whose tumors express high levels of AKT1 exhibit a significantly worse prognosis, whereas no significant correlation with AKT3 expression is observed. We provide data that establish a phosphorylation independent role of AKT1 in affecting MPM cell shape and anchorage independent cell growth in vitro and highlight the AKT1 isoform-specific nature of these effects.We describe that AKT1 activity is inhibited by the loss of SIRT1-mediated deacetylation and identify, by mass spectrometry, 11 unique proteins that interact with acetylated AKT1.Our data demonstrate a role of the AKT1/SIRT1/FOXM1 axis in the expression of the tumor suppressor ERβ. We further demonstrate an inhibitory feedback loop by ERβ, activated by the selective agonist KB9520, on this axis both in vitro and in vivo.Our data broaden the current knowledge of ERβ and AKT isoform-specific functions that could be valuable in the design of novel and effective therapeutic strategies for MPM.
- Published
- 2016
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33. Analysis of Gene Expression in 3D Spheroids Highlights a Survival Role for ASS1 in Mesothelioma.
- Author
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Barbone D, Van Dam L, Follo C, Jithesh PV, Zhang SD, Richards WG, Bueno R, Fennell DA, and Broaddus VC
- Subjects
- Annexin A4 metabolism, Cell Line, Tumor, Humans, Mesothelioma pathology, Vault Ribonucleoprotein Particles metabolism, Argininosuccinate Synthase metabolism, Cell Survival, Gene Expression Regulation, Enzymologic, Gene Expression Regulation, Neoplastic, Mesothelioma genetics, Spheroids, Cellular
- Abstract
To investigate the underlying causes of chemoresistance in malignant pleural mesothelioma, we have studied mesothelioma cell lines as 3D spheroids, which acquire increased chemoresistance compared to 2D monolayers. We asked whether the gene expression of 3D spheroids would reveal mechanisms of resistance. To address this, we measured gene expression of three mesothelioma cell lines, M28, REN and VAMT, grown as 2D monolayers and 3D spheroids. A total of 209 genes were differentially expressed in common by the three cell lines in 3D (138 upregulated and 71 downregulated), although a clear resistance pathway was not apparent. We then compared the list of 3D genes with two publicly available datasets of gene expression of 56 pleural mesotheliomas compared to normal tissues. Interestingly, only three genes were increased in both 3D spheroids and human tumors: argininosuccinate synthase 1 (ASS1), annexin A4 (ANXA4) and major vault protein (MVP); of these, ASS1 was the only consistently upregulated of the three genes by qRT-PCR. To measure ASS1 protein expression, we stained 2 sets of tissue microarrays (TMA): one with 88 pleural mesothelioma samples and the other with additional 88 pleural mesotheliomas paired with matched normal tissues. Of the 176 tumors represented on the two TMAs, ASS1 was expressed in 87 (50%; staining greater than 1 up to 3+). For the paired samples, ASS1 expression in mesothelioma was significantly greater than in the normal tissues. Reduction of ASS1 expression by siRNA significantly sensitized mesothelioma spheroids to the pro-apoptotic effects of bortezomib and of cisplatin plus pemetrexed. Although mesothelioma is considered by many to be an ASS1-deficient tumor, our results show that ASS1 is elevated at the mRNA and protein levels in mesothelioma 3D spheroids and in human pleural mesotheliomas. We also have uncovered a survival role for ASS1, which may be amenable to targeting to undermine mesothelioma multicellular resistance.
- Published
- 2016
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34. Total proteome analysis identifies migration defects as a major pathogenetic factor in immunoglobulin heavy chain variable region (IGHV)-unmutated chronic lymphocytic leukemia.
- Author
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Eagle GL, Zhuang J, Jenkins RE, Till KJ, Jithesh PV, Lin K, Johnson GG, Oates M, Park K, Kitteringham NR, and Pettitt AR
- Subjects
- Aged, Blotting, Western, Cell Line, Tumor, Chemokine CCL21 pharmacology, Chemotaxis drug effects, Computational Biology, Female, Humans, Isotope Labeling, Leukemia, Lymphocytic, Chronic, B-Cell pathology, Lymphatic Diseases pathology, Male, Mass Spectrometry, Neoplasm Proteins metabolism, Reproducibility of Results, Cell Movement drug effects, Immunoglobulin Heavy Chains genetics, Immunoglobulin Variable Region genetics, Leukemia, Lymphocytic, Chronic, B-Cell genetics, Mutation genetics, Proteome metabolism, Proteomics methods
- Abstract
The mutational status of the immunoglobulin heavy chain variable region defines two clinically distinct forms of chronic lymphocytic leukemia (CLL) known as mutated (M-CLL) and unmutated (UM-CLL). To elucidate the molecular mechanisms underlying the adverse clinical outcome associated with UM-CLL, total proteomes from nine UM-CLL and nine M-CLL samples were analyzed by isobaric tags for relative and absolute quantification (iTRAQ)-based mass spectrometry. Based on the expression of 3521 identified proteins, principal component analysis separated CLL samples into two groups corresponding to immunoglobulin heavy chain variable region mutational status. Computational analysis showed that 43 cell migration/adhesion pathways were significantly enriched by 39 differentially expressed proteins, 35 of which were expressed at significantly lower levels in UM-CLL samples. Furthermore, UM-CLL cells underexpressed proteins associated with cytoskeletal remodeling and overexpressed proteins associated with transcriptional and translational activity. Taken together, our findings indicate that UM-CLL cells are less migratory and more adhesive than M-CLL cells, resulting in their retention in lymph nodes, where they are exposed to proliferative stimuli. In keeping with this hypothesis, analysis of an extended cohort of 120 CLL patients revealed a strong and specific association between UM-CLL and lymphadenopathy. Our study illustrates the potential of total proteome analysis to elucidate pathogenetic mechanisms in cancer., (© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.)
- Published
- 2015
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35. Identification of RBCK1 as a novel regulator of FKBPL: implications for tumor growth and response to tamoxifen.
- Author
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Donley C, McClelland K, McKeen HD, Nelson L, Yakkundi A, Jithesh PV, Burrows J, McClements L, Valentine A, Prise KM, McCarthy HO, and Robson T
- Subjects
- Animals, Antineoplastic Agents, Hormonal pharmacology, Biomarkers, Tumor genetics, Breast Neoplasms genetics, Breast Neoplasms mortality, COS Cells, Cell Line, Tumor, Cell Proliferation, Chlorocebus aethiops, Estradiol metabolism, Female, Gene Expression Regulation, Neoplastic, HSP90 Heat-Shock Proteins genetics, HSP90 Heat-Shock Proteins metabolism, Humans, Immunophilins biosynthesis, Neovascularization, Pathologic genetics, Promoter Regions, Genetic genetics, RNA Interference, RNA, Small Interfering, Receptors, Estrogen genetics, Signal Transduction genetics, Tacrolimus Binding Proteins, Tamoxifen pharmacology, Transcription Factors biosynthesis, Transcriptional Activation, Treatment Outcome, Trefoil Factor-1, Tumor Suppressor Proteins biosynthesis, Tumor Suppressor Proteins genetics, Ubiquitin-Protein Ligases, Ubiquitination, Antineoplastic Agents, Hormonal therapeutic use, Breast Neoplasms drug therapy, Cyclin-Dependent Kinase Inhibitor p21 biosynthesis, Drug Resistance, Neoplasm genetics, Immunophilins genetics, Tamoxifen therapeutic use, Transcription Factors genetics
- Abstract
FKBPL has been implicated in processes associated with cancer, including regulation of tumor growth and angiogenesis with high levels of FKBPL prognosticating for improved patient survival. Understanding how FKBPL levels are controlled within the cell is therefore critical. We have identified a novel role for RBCK1 as an FKBPL-interacting protein, which regulates FKBPL stability at the post-translational level via ubiquitination. Both RBCK1 and FKBPL are upregulated by 17-β-estradiol and interact within heat shock protein 90 chaperone complexes, together with estrogen receptor-α (ERα). Furthermore, FKBPL and RBCK1 associate with ERα at the promoter of the estrogen responsive gene, pS2, and regulate pS2 levels. MCF-7 clones stably overexpressing RBCK1 were shown to have reduced proliferation and increased levels of FKBPL and p21. Furthermore, these clones were resistant to tamoxifen therapy, suggesting that RBCK1 could be a predictive marker of response to endocrine therapy. RBCK1 knockdown using targeted small interfering RNA resulted in increased proliferation and increased sensitivity to tamoxifen treatment. Moreover, in support of our in vitro data, analysis of mRNA microarray data sets demonstrated that high levels of FKBPL and RBCK1 correlated with increased patient survival, whereas high RBCK1 predicted for a poor response to tamoxifen. Our findings support a role for RBCK1 in the regulation of FKBPL with important implications for estrogen receptor signaling, cell proliferation and response to endocrine therapy.
- Published
- 2014
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36. ADAM17-dependent c-MET-STAT3 signaling mediates resistance to MEK inhibitors in KRAS mutant colorectal cancer.
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Van Schaeybroeck S, Kalimutho M, Dunne PD, Carson R, Allen W, Jithesh PV, Redmond KL, Sasazuki T, Shirasawa S, Blayney J, Michieli P, Fenning C, Lenz HJ, Lawler M, Longley DB, and Johnston PG
- Subjects
- ADAM Proteins genetics, ADAM17 Protein, Animals, Apoptosis drug effects, Cell Proliferation drug effects, Colorectal Neoplasms enzymology, Colorectal Neoplasms genetics, Colorectal Neoplasms metabolism, Drug Resistance, Neoplasm, Female, HCT116 Cells, Humans, MAP Kinase Kinase Kinases metabolism, Male, Mice, Mice, Inbred BALB C, Mice, Nude, Proto-Oncogene Proteins metabolism, Proto-Oncogene Proteins p21(ras), Signal Transduction, Xenograft Model Antitumor Assays, ras Proteins metabolism, ADAM Proteins metabolism, Colorectal Neoplasms drug therapy, MAP Kinase Kinase Kinases antagonists & inhibitors, Protein Kinase Inhibitors pharmacology, Proto-Oncogene Proteins genetics, Proto-Oncogene Proteins c-met metabolism, STAT3 Transcription Factor metabolism, ras Proteins genetics
- Abstract
There are currently no approved targeted therapies for advanced KRAS mutant (KRASMT) colorectal cancer (CRC). Using a unique systems biology approach, we identified JAK1/2-dependent activation of STAT3 as the key mediator of resistance to MEK inhibitors in KRASMT CRC in vitro and in vivo. Further analyses identified acute increases in c-MET activity following treatment with MEK inhibitors in KRASMT CRC models, which was demonstrated to promote JAK1/2-STAT3-mediated resistance. Furthermore, activation of c-MET following MEK inhibition was found to be due to inhibition of the ERK-dependent metalloprotease ADAM17, which normally inhibits c-MET signaling by promoting shedding of its endogenous antagonist, soluble "decoy" MET. Most importantly, pharmacological blockade of this resistance pathway with either c-MET or JAK1/2 inhibitors synergistically increased MEK-inhibitor-induced apoptosis and growth inhibition in vitro and in vivo in KRASMT models, providing clear rationales for the clinical assessment of these combinations in KRASMT CRC patients., (Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2014
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37. Estrogen receptor β activation impairs mitochondrial oxidative metabolism and affects malignant mesothelioma cell growth in vitro and in vivo.
- Author
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Manente AG, Valenti D, Pinton G, Jithesh PV, Daga A, Rossi L, Gray SG, O'Byrne KJ, Fennell DA, Vacca RA, Nilsson S, Mutti L, and Moro L
- Abstract
Estrogen receptor (ER)-β has been shown to possess a tumor suppressive effect, and is a potential target for cancer therapy. Using gene-expression meta-analysis of human malignant pleural mesothelioma, we identified an ESR2 (ERβ coding gene) signature. High ESR2 expression was strongly associated with low succinate dehydrogenase B (SDHB) (which encodes a mitochondrial respiratory chain complex II subunit) expression. We demonstrate that SDHB loss induced ESR2 expression, and that activated ERβ, by over-expression or by selective agonist stimulation, negatively affected oxidative phosphorylation compromising mitochondrial complex II and IV activity. This resulted in reduced mitochondrial ATP production, increased glycolysis dependence and impaired cell proliferation. The observed in vitro effects were phenocopied in vivo using a selective ERβ agonist in a mesothelioma mouse model. On the whole, our data highlight an unforeseen interaction between ERβ-mediated tumor suppression and energy metabolism that may be exploited to improve on the therapy for clinical management of malignant mesothelioma.
- Published
- 2013
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38. Targeting treatment-resistant breast cancer stem cells with FKBPL and its peptide derivative, AD-01, via the CD44 pathway.
- Author
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McClements L, Yakkundi A, Papaspyropoulos A, Harrison H, Ablett MP, Jithesh PV, McKeen HD, Bennett R, Donley C, Kissenpfennig A, McIntosh S, McCarthy HO, O'Neill E, Clarke RB, and Robson T
- Subjects
- Animals, Breast Neoplasms metabolism, Breast Neoplasms mortality, Drug Resistance, Neoplasm, Female, Humans, Immunophilins metabolism, MCF-7 Cells, Mice, Mice, SCID, Radiation Tolerance, Receptors, Notch antagonists & inhibitors, Receptors, Notch metabolism, Signal Transduction, Spheroids, Cellular drug effects, Tacrolimus Binding Proteins, Tumor Burden drug effects, Xenograft Model Antitumor Assays, Antineoplastic Agents pharmacology, Breast Neoplasms drug therapy, Hyaluronan Receptors metabolism, Immunophilins pharmacology, Neoplastic Stem Cells drug effects
- Abstract
Purpose: FK506-binding protein like (FKBPL) and its peptide derivative, AD-01, have already shown tumor growth inhibition and CD44-dependent antiangiogenic activity. Here, we explore the ability of AD-01 to target CD44-positive breast cancer stem cells (BCSC)., Experimental Design: Mammosphere assays and flow cytometry were used to analyze the effect of FKBPL overexpression/knockdown and AD-01 treatment ± other anticancer agents on BCSCs using breast cancer cell lines (MCF-7/MDA-231/ZR-75), primary patient samples, and xenografts. Delays in tumor initiation were evaluated in vivo. The anti-stem cell mechanisms were determined using clonogenic assays, quantitative PCR (qPCR), and immunofluorescence., Results: AD-01 treatment was highly effective at inhibiting the BCSC population by reducing mammosphere-forming efficiency and ESA(+)/CD44(+)/CD24(-) or aldehyde dehydrogenase (ALDH)(+) cell subpopulations in vitro and tumor initiation in vivo. The ability of AD-01 to inhibit the self-renewal capacity of BCSCs was confirmed; mammospheres were completely eradicated by the third generation. The mechanism seems to be due to AD-01-mediated BCSC differentiation shown by a significant decrease in the number of holoclones and an associated increase in meroclones/paraclones; the stem cell markers, Nanog, Oct4, and Sox2, were also significantly reduced. Furthermore, we showed additive inhibitory effects when AD-01 was combined with the Notch inhibitor, DAPT. AD-01 was also able to abrogate a chemo- and radiotherapy-induced enrichment in BCSCs. Finally, FKBPL knockdown led to an increase in Nanog/Oct4/Sox2 and an increase in BCSCs, highlighting a role for endogenous FKBPL in stem cell signaling., Conclusions: AD-01 has dual antiangiogenic and anti-BCSC activity, which will be advantageous as this agent enters clinical trial.
- Published
- 2013
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39. The epigenetic landscape of oral squamous cell carcinoma.
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Jithesh PV, Risk JM, Schache AG, Dhanda J, Lane B, Liloglou T, and Shaw RJ
- Subjects
- Adult, Aged, Aged, 80 and over, Epigenesis, Genetic, Female, Humans, Male, Middle Aged, Neoplasm Recurrence, Local genetics, Papillomavirus Infections, Phenotype, Promoter Regions, Genetic, Proto-Oncogene Proteins genetics, Proto-Oncogene Proteins metabolism, RNA, Messenger genetics, RNA, Messenger metabolism, Receptor, Notch4, Receptors, Notch genetics, Receptors, Notch metabolism, Signal Transduction, Carcinoma, Squamous Cell genetics, CpG Islands genetics, DNA Methylation, Mouth Neoplasms genetics
- Abstract
Background: There is relatively little methylation array data available specifically for oral squamous cell carcinoma (OSCC). This study aims to compare the DNA methylome across a large cohort of tumour/normal pairs., Methods: DNA was extracted from 44 OSCCs and paired normal mucosa. DNA methylation analysis employed the Illumina GoldenGate high-throughput array comprising 1505 CpG loci selected from 807 epigenetically regulated genes. This data was correlated with extracapsular spread (ECS), human papilloma virus (HPV) status, recurrence and 5-year survival., Results: Differential methylation levels of a number of genes distinguished the tumour tissue sample from the matched normal. Putative methylation signatures for ECS and recurrence were identified. The concept of concordant methylation or CpG island methylator phenotype (CIMP) in OSCC is supported by our data, with an association between 'CIMP-high' and worse prognosis. Epigenetic deregulation of NOTCH4 signalling in OSCC was also observed, as part of a possible methylation signature for recurrence, with parallels to recently discovered NOTCH mutations in HNSCC. Differences in methylation in HPV-driven cases were seen, but are less significant than that has been recently proposed in other series., Conclusion: Although OSCC seems as much an 'epigenetic' as a genetic disease, the translational potential of cancer epigenetics has yet to be fully exploited. This data points to the application of epigenetic biomarkers and targets available to further the development of therapy in OSCC.
- Published
- 2013
- Full Text
- View/download PDF
40. Identification of galanin and its receptor GalR1 as novel determinants of resistance to chemotherapy and potential biomarkers in colorectal cancer.
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Stevenson L, Allen WL, Turkington R, Jithesh PV, Proutski I, Stewart G, Lenz HJ, Van Schaeybroeck S, Longley DB, and Johnston PG
- Subjects
- Biomarkers, Pharmacological metabolism, Fluorouracil administration & dosage, Galanin metabolism, Gene Expression Regulation, Neoplastic, HCT116 Cells, HT29 Cells, Humans, Oligonucleotide Array Sequence Analysis, Organoplatinum Compounds administration & dosage, Oxaliplatin, RNA, Small Interfering, Receptor, Galanin, Type 1 metabolism, Signal Transduction, Colorectal Neoplasms drug therapy, Colorectal Neoplasms genetics, Drug Resistance, Neoplasm genetics, Galanin genetics, Receptor, Galanin, Type 1 genetics
- Abstract
Purpose: A major factor limiting the effective clinical management of colorectal cancer (CRC) is resistance to chemotherapy. Therefore, the identification of novel, therapeutically targetable mediators of resistance is vital., Experimental Design: We used a CRC disease-focused microarray platform to transcriptionally profile chemotherapy-responsive and nonresponsive pretreatment metastatic CRC liver biopsies and in vitro samples, both sensitive and resistant to clinically relevant chemotherapeutic drugs (5-FU and oxaliplatin). Pathway and gene set enrichment analyses identified candidate genes within key pathways mediating drug resistance. Functional RNAi screening identified regulators of drug resistance., Results: Mitogen-activated protein kinase signaling, focal adhesion, cell cycle, insulin signaling, and apoptosis were identified as key pathways involved in mediating drug resistance. The G-protein-coupled receptor galanin receptor 1 (GalR1) was identified as a novel regulator of drug resistance. Notably, silencing either GalR1 or its ligand galanin induced apoptosis in drug-sensitive and resistant cell lines and synergistically enhanced the effects of chemotherapy. Mechanistically, GalR1/galanin silencing resulted in downregulation of the endogenous caspase-8 inhibitor FLIP(L), resulting in induction of caspase-8-dependent apoptosis. Galanin mRNA was found to be overexpressed in colorectal tumors, and importantly, high galanin expression correlated with poor disease-free survival of patients with early-stage CRC., Conclusion: This study shows the power of systems biology approaches to identify key pathways and genes that are functionally involved in mediating chemotherapy resistance. Moreover, we have identified a novel role for the GalR1/galanin receptor-ligand axis in chemoresistance, providing evidence to support its further evaluation as a potential therapeutic target and biomarker in CRC.
- Published
- 2012
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41. A systems biology approach identifies SART1 as a novel determinant of both 5-fluorouracil and SN38 drug resistance in colorectal cancer.
- Author
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Allen WL, Stevenson L, Coyle VM, Jithesh PV, Proutski I, Carson G, Gordon MA, Lenz HJ, Van Schaeybroeck S, Longley DB, and Johnston PG
- Subjects
- Antigens, Neoplasm metabolism, Antimetabolites, Antineoplastic pharmacology, Antineoplastic Agents, Phytogenic pharmacology, Apoptosis genetics, CASP8 and FADD-Like Apoptosis Regulating Protein metabolism, Camptothecin pharmacology, Caspase 8 metabolism, Cell Line, Tumor, Colorectal Neoplasms pathology, Humans, Irinotecan, RNA Interference, RNA, Small Interfering, Ribonucleoproteins, Small Nuclear metabolism, Systems Biology, Antigens, Neoplasm genetics, Camptothecin analogs & derivatives, Colorectal Neoplasms metabolism, Drug Resistance, Neoplasm genetics, Fluorouracil pharmacology, Ribonucleoproteins, Small Nuclear genetics
- Abstract
Chemotherapy response rates for advanced colorectal cancer remain disappointingly low, primarily because of drug resistance, so there is an urgent need to improve current treatment strategies. To identify novel determinants of resistance to the clinically relevant drugs 5-fluorouracil (5-FU) and SN38 (the active metabolite of irinotecan), transcriptional profiling experiments were carried out on pretreatment metastatic colorectal cancer biopsies and HCT116 parental and chemotherapy-resistant cell line models using a disease-specific DNA microarray. To enrich for potential chemoresistance-determining genes, an unsupervised bioinformatics approach was used, and 50 genes were selected and then functionally assessed using custom-designed short interfering RNA (siRNA) screens. In the primary siRNA screen, silencing of 21 genes sensitized HCT116 cells to either 5-FU or SN38 treatment. Three genes (RAPGEF2, PTRF, and SART1) were selected for further analysis in a panel of 5 colorectal cancer cell lines. Silencing SART1 sensitized all 5 cell lines to 5-FU treatment and 4/5 cell lines to SN38 treatment. However, silencing of RAPGEF2 or PTRF had no significant effect on 5-FU or SN38 sensitivity in the wider cell line panel. Further functional analysis of SART1 showed that its silencing induced apoptosis that was caspase-8 dependent. Furthermore, silencing of SART1 led to a downregulation of the caspase-8 inhibitor, c-FLIP, which we have previously shown is a key determinant of drug resistance in colorectal cancer. This study shows the power of systems biology approaches for identifying novel genes that regulate drug resistance and identifies SART1 as a previously unidentified regulator of c-FLIP and drug-induced activation of caspase-8., (©2011 AACR.)
- Published
- 2012
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42. Gene expression meta-analysis identifies VDAC1 as a predictor of poor outcome in early stage non-small cell lung cancer.
- Author
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Grills C, Jithesh PV, Blayney J, Zhang SD, and Fennell DA
- Subjects
- Breast Neoplasms genetics, Breast Neoplasms pathology, Carcinoma, Non-Small-Cell Lung genetics, Humans, Lung Neoplasms genetics, Multiple Myeloma genetics, Multiple Myeloma pathology, Prognosis, Carcinoma, Non-Small-Cell Lung pathology, Gene Expression Regulation, Neoplastic, Lung Neoplasms pathology, Predictive Value of Tests, Voltage-Dependent Anion Channel 1 analysis
- Abstract
Background: The bioenergetic status of non-small cell lung cancer correlates with tumour aggressiveness. The voltage dependent anion channel type 1 (VDAC1) is a component of the mitochondrial permeability transition pore, regulates mitochondrial ATP/ADP exchange suggesting that its over-expression could be associated with energy dependent processes including increased proliferation and invasiveness. To test this hypothesis, we conducted an in vivo gene-expression meta-analysis of surgically resected non-small cell lung cancer (NSCLC) using 602 individual expression profiles, to examine the impact of VDAC1 on survival., Methodology/principal Findings: High VDAC1 expression was associated with shorter overall survival with hazard ratio (HR) = 0.6639 (95% confidence interval (CI) 0.4528 to 0.9721), p = 0.035352 corresponding to 52 versus 101 months. VDAC1 predicted shorter time to recurrence and was shown to be an independent prognostic factor compared with histology, gender, age, nodal stage and tumour stage in a Cox multivariate analysis. Supervised analysis of all the datasets identified a 6-gene signature comprising HNRNPC, HSPA4, HSPA9, UBE2D2, CSNK1A1 and G3BP1 with overlapping functions involving regulation of protein turnover, RAS-RAF-MEK pathway and transcription. VDAC1 predicted survival in breast cancer and myeloma and an unsupervised analysis revealed enrichment of the VDAC1 signature in specific subsets., Conclusions: In summary, gene expression analysis identifies VDAC1 gene expression as a predictor of poor outcome in NSCLC and other cancers and is associated with dysregulation of a conserved set of biological pathways, which may be causally associated with aggressive tumour behaviour.
- Published
- 2011
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43. The colorectal cancer disease-specific transcriptome may facilitate the discovery of more biologically and clinically relevant information.
- Author
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Allen WL, Jithesh PV, Oliver GR, Proutski I, Longley DB, Lenz HJ, Proutski V, Harkin P, and Johnston PG
- Subjects
- Antimetabolites, Antineoplastic pharmacology, Antimetabolites, Antineoplastic therapeutic use, Biopsy, Cell Survival drug effects, Colorectal Neoplasms drug therapy, Colorectal Neoplasms pathology, Fluorouracil pharmacology, Genotype, HCT116 Cells, Humans, Insulin-Like Growth Factor Binding Protein 2 genetics, Phenotype, Prognosis, RNA, Antisense metabolism, Reproducibility of Results, Reverse Transcriptase Polymerase Chain Reaction, Colorectal Neoplasms genetics, Drug Resistance, Neoplasm genetics, Gene Expression Profiling methods, Gene Expression Regulation, Neoplastic, Oligonucleotide Array Sequence Analysis
- Abstract
Background: To date, there are no clinically reliable predictive markers of response to the current treatment regimens for advanced colorectal cancer. The aim of the current study was to compare and assess the power of transcriptional profiling using a generic microarray and a disease-specific transcriptome-based microarray. We also examined the biological and clinical relevance of the disease-specific transcriptome., Methods: DNA microarray profiling was carried out on isogenic sensitive and 5-FU-resistant HCT116 colorectal cancer cell lines using the Affymetrix HG-U133 Plus2.0 array and the Almac Diagnostics Colorectal cancer disease specific Research tool. In addition, DNA microarray profiling was also carried out on pre-treatment metastatic colorectal cancer biopsies using the colorectal cancer disease specific Research tool. The two microarray platforms were compared based on detection of probesets and biological information., Results: The results demonstrated that the disease-specific transcriptome-based microarray was able to out-perform the generic genomic-based microarray on a number of levels including detection of transcripts and pathway analysis. In addition, the disease-specific microarray contains a high percentage of antisense transcripts and further analysis demonstrated that a number of these exist in sense:antisense pairs. Comparison between cell line models and metastatic CRC patient biopsies further demonstrated that a number of the identified sense:antisense pairs were also detected in CRC patient biopsies, suggesting potential clinical relevance., Conclusions: Analysis from our in vitro and clinical experiments has demonstrated that many transcripts exist in sense:antisense pairs including IGF2BP2, which may have a direct regulatory function in the context of colorectal cancer. While the functional relevance of the antisense transcripts has been established by many studies, their functional role is currently unclear; however, the numbers that have been detected by the disease-specific microarray would suggest that they may be important regulatory transcripts. This study has demonstrated the power of a disease-specific transcriptome-based approach and highlighted the potential novel biologically and clinically relevant information that is gained when using such a methodology.
- Published
- 2010
- Full Text
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44. FKBPL regulates estrogen receptor signaling and determines response to endocrine therapy.
- Author
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McKeen HD, Byrne C, Jithesh PV, Donley C, Valentine A, Yakkundi A, O'Rourke M, Swanton C, McCarthy HO, Hirst DG, and Robson T
- Subjects
- Antineoplastic Agents, Hormonal pharmacology, Breast Neoplasms genetics, Breast Neoplasms metabolism, Breast Neoplasms pathology, Cathepsin D genetics, Cathepsin D metabolism, Cell Line, Tumor, Cell Proliferation drug effects, Cyclin-Dependent Kinase Inhibitor p21 genetics, Cyclin-Dependent Kinase Inhibitor p21 metabolism, Estradiol analogs & derivatives, Estradiol pharmacology, Estrogens pharmacology, Fulvestrant, Gene Expression Profiling, Gene Expression Regulation, Neoplastic drug effects, HSP90 Heat-Shock Proteins genetics, HSP90 Heat-Shock Proteins metabolism, Humans, Immunophilins genetics, Immunophilins metabolism, Immunoprecipitation, Kaplan-Meier Estimate, Meta-Analysis as Topic, Phosphorylation drug effects, Protein Binding, RNA Interference, Serine metabolism, Signal Transduction genetics, Tacrolimus Binding Proteins, Transfection, Estrogen Receptor alpha metabolism, Immunophilins physiology, Signal Transduction physiology, Tamoxifen pharmacology
- Abstract
The HSP90 chaperone and immunophilin FKBPL is an estrogen-responsive gene that interacts with estogen receptor alpha (ERalpha) and regulates its levels. In this study, we explored the effects of FKBPL on breast cancer proliferation. Breast cancer cells stably overexpressing FKBPL became dependent on estrogen for their growth and were dramatically more sensitive to the antiestrogens tamoxifen and fulvestrant, whereas FKBPL knockdown reverses this phenotype. FKBPL knockdown also decreased the levels of the cell cycle inhibitor p21WAF1 and increased ERalpha phosphorylation on Ser(118) in response to 17beta-estradiol and tamoxifen. In support of the likelihood that these effects explained FKBPL-mediated cell growth inhibition and sensitivity to endocrine therapies, FKBPL expression was correlated with increased overall survival and distant metastasis-free survival in breast cancer patients. Our findings suggest that FKBPL may have prognostic value based on its impact on tumor proliferative capacity and sensitivity to endocrine therapies, which improve outcome.
- Published
- 2010
- Full Text
- View/download PDF
45. Clinical determinants of response to irinotecan-based therapy derived from cell line models.
- Author
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Allen WL, Coyle VM, Jithesh PV, Proutski I, Stevenson L, Fenning C, Longley DB, Wilson RH, Gordon M, Lenz HJ, and Johnston PG
- Subjects
- Biomarkers, Tumor metabolism, Camptothecin therapeutic use, Colorectal Neoplasms metabolism, Gene Expression Profiling, HCT116 Cells drug effects, Humans, Irinotecan, Oligonucleotide Array Sequence Analysis, RNA, Messenger genetics, RNA, Messenger metabolism, RNA, Neoplasm genetics, RNA, Neoplasm metabolism, Retrospective Studies, Reverse Transcriptase Polymerase Chain Reaction, Topoisomerase I Inhibitors, Antineoplastic Agents, Phytogenic therapeutic use, Biomarkers, Tumor genetics, Camptothecin analogs & derivatives, Colorectal Neoplasms drug therapy, Colorectal Neoplasms genetics, Drug Resistance, Neoplasm
- Abstract
Purpose: In an attempt to identify genes that are involved in resistance to SN38, the active metabolite of irinotecan (also known as CPT-11), we carried out DNA microarray profiling of matched HCT116 human colon cancer parental cell lines and SN38-resistant cell lines following treatment with SN38 over time., Experimental Design: Data analysis identified a list of genes that were acutely altered in the parental cells following SN38 treatment as well as constitutively altered in the SN38-resistant cells., Results: Independent validation of 20% of these genes by quantitative reverse transcription-PCR revealed a strong correlation with the microarray results: Pearson's correlation was 0.781 (r(2) = 0.61, P < 0.000001) for those genes that were acutely altered in the parental setting following SN38 treatment and 0.795 (r(2) = 0.63, P < 0.000002) for those genes that were constitutively altered in the SN38-resistant cells. We then assessed the ability of our in vitro-derived gene list to predict clinical response to 5-fluorouracil/irinotecan using pretreatment metastatic biopsies from responding and nonresponding colorectal cancer patients using both unsupervised and supervised approaches. When principal components analysis was used with our in vitro classifier gene list, a good separation between responding and nonresponding patients was obtained, with only one nonresponding and two responding patients separating with the incorrect groups. Supervised class prediction using support vector machines algorithm identified a 16-gene classifier with 75% overall accuracy, 81.8% sensitivity, and 66.6% specificity., Conclusions: These results suggest that in vitro-derived gene lists can be used to predict clinical response to chemotherapy in colorectal cancer.
- Published
- 2008
- Full Text
- View/download PDF
46. Molecular dynamics studies of trinucleotide repeat DNA involved in neurodegenerative disorders.
- Author
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Jithesh PV, Singh P, and Joshi R
- Subjects
- Algorithms, Base Pair Mismatch, Color, Computer Simulation, DNA chemistry, DNA ultrastructure, Humans, Ions chemistry, Models, Molecular, Molecular Sequence Data, Mutation, Nucleic Acid Conformation, Nucleic Acid Heteroduplexes, Thermodynamics, Water chemistry, Neurodegenerative Diseases genetics, Trinucleotide Repeat Expansion genetics
- Abstract
Expansion of trinucleotide repeat DNA of the classes CAG-CTG, CGG-CCG and GAA-TTC are found to be associated with several neurodegenerative disorders. Different mechanisms have been attributed to the expansion of triplets, mainly involving the formation of alternate secondary structures by such repeats. This paper reports the molecular dynamics simulation of triplet repeat DNA sequences to study the basic structural features of DNA that are responsible for the formation of structures such as hairpins and slip-strand DNA leading to expansion. All the triplet repeat sequences studied were found to be more flexible compared to the control sequence unassociated with disease. Moreover, flexibility was found to be in the order CAG-CTG > CGG-CCG approximately GAA-TTC, the highly flexible CAG-CTG repeat being the most common cause of neurodegenerative disorders. In another simulation, a single G-C to T-A mutation at the 9th position of the CAG-CTG repeat exhibited a reduction in bending compared to the pure 15-mer CAG-CTG repeat. EPM1 dodecamer repeat associated with the pathogenesis of progressive myoclonus epilepsy was also simulated and showed flexible nature suggesting a similar expansion mechanism.
- Published
- 2001
- Full Text
- View/download PDF
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