The Impact of COVID-19 Vaccination Side-Effects on Work Attendance among Saudi Healthcare Workers.

OBJECTIVE: This cross-sectional-survey-based study aimed to investigate the severity of side-effects from Coronavirus disease (COVID-19) mRNA (Pfizer, Moderna), viral vector DNA (Oxford-AstraZeneca, J&J/Janssen), inactivated virus (Sinopharm, Sinovac), and other vaccines among healthcare workers (HCWs) in Saudi Arabia, focusing on their impact on work attendance. METHODS: A total of 894 HCWs residing in Saudi Arabia participated in this study from March 2023 to May 2023. Participants completed an online questionnaire assessing demographic information, vaccination status, comorbidities, vaccine side-effects, and missed work information after vaccination. Descriptive statistics and chi-square tests were used for data analysis. RESULTS: The majority of participants were female (83.7%) and aged 25-34 years (42.8%). Most participants were predominantly vaccinated with mRNA vaccines. Common side-effects included pain at the injection site, fatigue, fever, and chills. However, no significant association was found between vaccine type, side-effects, and work absenteeism. While demographic factors such as age and healthcare profession did not influence work absenteeism, variations were observed among different racial groups. CONCLUSION: COVID-19 vaccination among HCWs in Saudi Arabia is associated with common side-effects, but their impact on work attendance is not significant. Understanding these implications can inform strategies to support the healthcare workforce and mitigate the impact on patient care and staffing during the ongoing COVID-19 pandemic.

Investigating composite electrode materials of metal oxides for advanced energy storage applications.

Electrochemical energy systems mark a pivotal advancement in the energy sector, delivering substantial improvements over conventional systems. Yet, a major challenge remains the deficiency in storage technology to effectively retain the energy produced. Amongst these are batteries and supercapacitors, renowned for their versatility and efficiency, which depend heavily on the quality of their electrode materials. Metal oxide composites, in particular, have emerged as highly promising due to the synergistic effects that significantly enhance their functionality and efficiency beyond individual components. This review explores the application of metal oxide composites in the electrodes of batteries and SCs, focusing on various material perspectives and synthesis methodologies, including exfoliation and hydrothermal/solvothermal processes. It also examines how these methods influence device performance. Furthermore, the review confronts the challenges and charts future directions for metal oxide composite-based energy storage systems, critically evaluating aspects such as scalability of synthesis, cost-effectiveness, environmental sustainability, and integration with advanced nanomaterials and electrolytes. These factors are crucial for advancing next-generation energy storage technologies, striving to enhance performance while upholding sustainability and economic viability.

hSSB1 (NABP2/OBFC2B) modulates the DNA damage and androgen-induced transcriptional response in prostate cancer.

BACKGROUND: Activation and regulation of androgen receptor (AR) signaling and the DNA damage response impact the prostate cancer (PCa) treatment modalities of androgen deprivation therapy (ADT) and radiotherapy. Here, we have evaluated a role for human single-strand binding protein 1 (hSSB1/NABP2) in modulation of the cellular response to androgens and ionizing radiation (IR). hSSB1 has defined roles in transcription and maintenance of genome stability, yet little is known about this protein in PCa. METHODS: We correlated hSSB1 with measures of genomic instability across available PCa cases from The Cancer Genome Atlas (TCGA). Microarray and subsequent pathway and transcription factor enrichment analysis were performed on LNCaP and DU145 prostate cancer cells. RESULTS: Our data demonstrate that hSSB1 expression in PCa correlates with measures of genomic instability including multigene signatures and genomic scars that are reflective of defects in the repair of DNA double-strand breaks via homologous recombination. In response to IR-induced DNA damage, we demonstrate that hSSB1 regulates cellular pathways that control cell cycle progression and the associated checkpoints. In keeping with a role for hSSB1 in transcription, our analysis revealed that hSSB1 negatively modulates p53 and RNA polymerase II transcription in PCa. Of relevance to PCa pathology, our findings highlight a transcriptional role for hSSB1 in regulating the androgen response. We identified that AR function is predicted to be impacted by hSSB1 depletion, whereby this protein is required to modulate AR gene activity in PCa. CONCLUSIONS: Our findings point to a key role for hSSB1 in mediating the cellular response to androgen and DNA damage via modulation of transcription. Exploiting hSSB1 in PCa might yield benefits as a strategy to ensure a durable response to ADT and/or radiotherapy and improved patient outcomes.

Prevalence and Factors Influencing Smoking Behavior among Female Inmates in Malaysia.

BACKGROUND: Lately, smoking among adolescents is increasing despite various campaigns to address it being carried out. Previously, this habit was common among men, however, nowadays, smoking has become a habit for women as well. The purpose of this study was to determine the prevalence and its associated factors that influence smoking behavior among women inmates in Kelantan. METHODS: A cross-sectional study was carried out among women inmates from Pengkalan Chepa Women's Prison, Kota Bharu, Kelantan. A total of 274 respondents were needed to answer a self-administered questionnaire. The data were analyzed using Multiple Logistic Regression. RESULTS: A total of 183 participants were smokers. Women who were single and divorced had a lower chance of being influenced to smoke compared to married women. Parents with smoking habits were more associated with children who smoked compared to parents who did not smoke. A participant with secondary level education had higher odds of smoking compared to a participant with primary level education. Smoking peers significantly influenced their friends and, therefore, peer practice was a main factor influencing smoking among women inmates. CONCLUSION: The prevalence of smoking among women inmates in Kelantan was found to be quite high. Religion (majority (90.5%) of women in the study were Muslims; it would be inappropriate to draw conclusion that religion is an influencing factor), marital status, parents' practice, peer practice and education significantly influenced women inmates to smoke.

Indications, preferences, global practice patterns and outcomes in retrograde intrarenal surgery (RIRS) for renal stones in adults: results from a multicenter database of 6669 patients of the global FLEXible ureteroscopy Outcomes Registry (FLEXOR).

PURPOSE: To collect a multicentric database on behalf of TOWER research group to assess practice patterns and outcomes of retrograde intrarenal surgery (RIRS) for kidney stones. METHODS: Inclusion criteria: age ≥ 18 years, normal renal/calyceal system anatomy, calculi of any size, number, and position. STUDY PERIOD: January 2018 and August 2021. Stone-free status: absence of fragments > 2 mm, assessed post procedure according to the local protocol (KUB X-Ray and/or ultrasound or non-contrast CT scan). RESULTS: Twenty centers from fifteen countries enrolled 6669 patients. There were 4407 (66.2%) men. Mean age was 49.3 ± 15.59 years. Pain was the most frequent symptom indication for intervention (62.6%). 679 (10.2%) patients underwent RIRS for an incidental finding of stones. 2732 (41.0%) patients had multiple stones. Mean stone size was 10.04 ± 6.84 mm. A reusable flexible ureteroscope was used in 4803 (72.0%) procedures. A sheath-less RIRS was performed in 454 (6.8%) cases. Holmium:YAG laser was used in 4878 (73.1%) cases. A combination of dusting and fragmentation was the most common lithotripsy mode performed (64.3%). Mean operation time was 62.40 ± 17.76 min. 119 (1.8%) patients had an intraoperative injury of the ureter due to UAS insertion. Mean postoperative stay was 3.62 ± 3.47 days. At least one postoperative complication occurred in 535 (8.0%) patients. Sepsis requiring intensive care admission occurred in 84 (1.3%) patients. Residual fragments were detected in 1445 (21.7%) patients. Among the latter, 744 (51.5%) patients required a further intervention. CONCLUSION: Our database contributes real-world data to support to a better understanding of modern RIRS practice and outcomes.

Molecular and hematological studies in a cohort of beta zero South East Asia deletion (ß°-thal SEA) from Malaysian perspective.

Abstract: We report the haematological parameters and molecular characterization of beta zero (ß°) South East Asia (SEA) deletion in the HBB gene cluster with unusually high levels of Hb F compared to a classical heterozygous beta zero (ß°)-thalassaemia. Methods: Retrospective study on 17 cases of (ß°) South East Asia (SEA) deletion from 2016 to 2019 referred to Institute for Medical Research were conducted. The clinical information and haematological profiles were evaluated. The mutation was analyzed, and the results were compared with other ß°-thalassaemia groups. For HBB gene genotyping, all the cases were subjected for multiplex gap-PCR, 5 cases were subjected for HBB gene sequencing for exclusion of compound heterozygous with other beta variants. Co-inheritance of α-thalassaemia were determined using multiplex gap-PCR and multiplex ARMS-PCR. Results: Seventeen cases were positive for ß°-thal SEA deletion. Fifteen cases were heterozygous and two were compound heterozygous for ß°-thal SEA deletion. The results were compared with 182 cases of various heterozygous ß° deletions and mutations. The mean Hb for heterozygous ß°-thal SEA deletion (13.44 ± 1.45 g/dl) was normal and significantly higher than heterozygous IVS 1-1 and Codon 41/42 (post hoc test, p < 0.05). The medians for the MCV and MCH of ß°-thal SEA deletion were significantly higher than for all heterozygote ß°-thalassaemia traits (Mann Whitney test, p < 0.05). Patients with ß°-thal SEA deletion had elevated levels of Hb A2 consistent with ß-thalassaemia traits, with Hb F levels consistent with HPFH or δß-thalassaemia carriers. The median for Hb A2 was 4.00 + 1.00%, similar to that observed in other ß°-thalassaemia groups except for IVS 1-1 mutation (median 5.30 + 0.45%) and ß°-Filipino (∼45 kb deletion) deletion (median 6.00 + 0.58). Interestingly, we found that Hb F levels for ß°-thal SEA deletion were statistically higher than other ß°-thalassaemia mutations (median 19.00 + 5.50%, p < 0.05), except for the ß°-thal 3.5 kb deletion group. Conclusion: We conclude that ß°-thal SEA deletion has a unique haematological parameters of beta zero thalassaemia trait. We affirm to classifying this deletion as SEA-HPFH based on previous studies considering the phenotype features rather than the molecular defect of ß°-thal SEA deletion, as this will make it easier to offer genetic counselling to affected individuals.

A cross sectional study on psychological impact of covid19 on post graduate doctors and Compulsory Rotatory Residential interns in COVID isolation ward of a tertiary care centre, Madurai.

BACKGROUND: COVID-19 pandemic causes major impact on economic, physical, mental well-being of people all over the world. Doctors are working in stressful, unprepared, limited resource setting, and they are under the continuous threat of getting infection. Managing mental health of these warriors is great importance. Hence the present study to estimate the psychological impact of COVID-19* and factors associated with it among doctors in tertiary care hospital, Madurai. METHODS: A Cross-sectional study was conducted during October-November 2020 using a pre-designed semi structured questionnaire and DASS-21 scale which were sent through Google form to doctors who were in their quarantine period after the COVID duty. Totally 292 responses were received. Descriptive statistics done to find frequencies and percentages. Correlation for continuous variables; Univariate and multivariate regression for categorical variables were used to predict the factors influencing the psychological impact. RESULTS: In our study, 42.1% doctors were depressed, 43.8% were stressed and 50.7% had anxiety. Depression*, anxiety*, stress* scores were positively correlated with number of COVID duties(r2 0.163,0.138,0.133), number of elderly persons(r2 0.188,0.169,0.188) in their family and negatively correlated with sleep duration(r 2-0.219,-0.281,-0.239), attitude of study participants(r2-0.319,-0.274,-0.291). Multiple logistic regression showed that disturbed sleep(odd'sratio = 3.931,2.734,3.420) and poor quality of sleep which affect the next day function(odd'sratio = 3.470,2.968,3.122) were significant predictors for all three psychological impacts. CONCLUSION: High prevalence of psychological impact estimated, ensures the requirement of early screening with timely psychological intervention and establishment of guideline policies to support mental health of healthcare workers* for maintaining the functionality of healthcare system.

Turnaround times and modes of reporting critical results in Asian laboratories.

BACKGROUND: Reporting critical results in a timely manner is a crucial role of clinical laboratories. Traditionally, these results were reported using the phone or fax system. However, there are now other modes of communication for this reporting. Quality improvement in any organization is driven by detection of errors and benchmarking against peers. In the case of critical result reporting, there are few current widely used Benchmarking schemes. METHODS: The Roche Clinical Chemistry Benchmarking Survey in 2019 added questions about critical result reporting including the mode of communication and turnaround time key performance index. This survey includes over 1100 laboratories from 20 countries. RESULTS: The survey revealed a range of communication strategies with phone calls still the commonest followed by email. The key performance index for most laboratories was less than 10 min. CONCLUSION: Benchmarking can provide key information for quality improvement activities, particularly pre- and postanalytical.

Limiting Self-Renewal of the Basal Compartment by PKA Activation Induces Differentiation and Alters the Evolution of Mammary Tumors.

Differentiation therapy utilizes our understanding of the hierarchy of cellular systems to pharmacologically induce a shift toward terminal commitment. While this approach has been a paradigm in treating certain hematological malignancies, efforts to translate this success to solid tumors have met with limited success. Mammary-specific activation of PKA in mouse models leads to aberrant differentiation and diminished self-renewing potential of the basal compartment, which harbors mammary repopulating cells. PKA activation results in tumors that are more benign, exhibiting reduced metastatic propensity, loss of tumor-initiating potential, and increased sensitivity to chemotherapy. Analysis of tumor histopathology revealed features of overt differentiation with papillary characteristics. Longitudinal single-cell profiling at the hyperplasia and tumor stages uncovered an altered path of tumor evolution whereby PKA curtails the emergence of aggressive subpopulations. Acting through the repression of SOX4, PKA activation promotes tumor differentiation and represents a possible adjuvant to chemotherapy for certain breast cancers.

Prevalence of 3.7 and 4.2 deletions in Sudanese patients with red cells hypochromia and microcytosis.

OBJECTIVE: Alpha-thalassemia is a genetic disorder characterized by deletions of one or more α globin genes that result in deficient of α globin chains reducing haemoglobin concentration. The study aimed to screen 97 patients with microcytosis and hypochromasia for the 3.7 and 4.2 alpha thalassemia deletion mutations. RESULTS: Out of 97 patients screened, only 7 were carriers for the 3.7 deletion and all patients were negative for the 4.2 deletion. The 3.7 deletion was found in Foor, Hawsa and Rezagat Sudanese tribes. In the carriers of the 3.7 deletion, Red Blood Cells and Haematocrit were significantly increased. The Red Blood Cells were 7.23 ± 0.78 × 1012/L in adult males and 7.21 ± 0.67 × 1012/L in adult females while in children were 5.07 ± 0.87 × 1012/L. The mean cell volume and mean cell haemoglobin were significantly decreased, but the mean cell haemoglobin concentration slightly decreased. Haemoglobin levels didn't revealed statistically significant decrease in adult males (11.7 ± 0.57 g/dL) and adult females (11.25 ± 0.64 g/dL), while in children were (11.6 ± 2.95 g/dL). Haemoglobin electrophoresis revealed two patients of the 3.7 and 4.2 negative were carriers for ß-thalassemia. The study concluded that α3.7 deletion has frequency of 0.07 in Sudanese with hypochromasia and microcytosis.

The BRCA1 and BRCA2 Genes in Early-Onset Breast Cancer Patients.

Approximately 5-10% of breast cancers are attributable to genetic susceptibility. Mutations in the BRCA1 and BRCA2 genes are the best known genetic factors to date. The goal of this study was to determine the structure and distribution of haplotypes of the BRCA1 and BRCA2 genes in early-onset breast cancer patients. We enrolled 70 patients diagnosed with early-onset breast cancer. A total of 21 SNPs (11 on BRCA1 and 10 on BRCA2) and 1 dinucleotide deletion on BRCA1 were genotyped using nested allele-specific PCR methods. Linkage disequilibrium (LD) analysis was conducted, and haplotypes were deduced from the genotype data. Two tightly linked LD blocks were observed on each of the BRCA1 and BRCA2 genes. Variant-free haplotypes (TAT-AG for BRCA1 and ATA-AAT for BRCA2) were observed at a frequency of more than 50% on each gene along with variable frequencies of derived haplotypes. The variant 3'-subhaplotype CGC displayed strong LD with 5'-subhaplotypes GA, AA, and GG on BRCA1 gene. Haplotypes ATA-AGT, ATC-AAT, and ATA-AAC were the variant haplotypes frequent on BRCA2 gene. Although the clinical significance of these derived haplotypes has not yet been established, it is expected that some of these haplotypes, especially the less frequent subhaplotypes, eventually will be shown to be indicative of a predisposition to early-onset breast cancer.

Serum prolactin overestimation and risk of misdiagnosis.

BACKGROUND: Falsely elevated prolactin measurements risk overdiagnosis, and unnecessary imaging and treatment. DESIGN: We conducted a clinical audit of 18 patients who presented with hyperprolactinaemia, followed by a laboratory audit of 40 split samples across a range of serum prolactin (5-5051 mIU/L). In each case (total n = 58), serum prolactin was measured on both Roche and Siemens platforms. RESULTS: Serum prolactin as measured by Roche was higher than the corresponding Siemens value in every case, despite similar reference ranges. The mean discrepancy in serum prolactin by Roche vs. Siemens was +81% in the clinical audit and +50% in the laboratory audit. This led to unnecessary interventions in 7/18 patients (39%) in the clinical audit. CONCLUSIONS: Serum prolactin is overestimated on the Roche relative to the Siemens platform. Laboratories should review Roche reference intervals for serum prolactin, and clinicians should consider repeating serum prolactin on another platform if the serum prolactin is incongruent with the clinical scenario.

Disruption of MAPK1 expression in the ERK signalling pathway and the RUNX1­RUNX1T1 fusion gene attenuate the differentiation and proliferation and induces the growth arrest in t(8;21) leukaemia cells.

The t(8;21) translocation is one of the most frequent chromosome abnormalities associated with acute myeloid leukaemia (AML). This abberation deregulates numerous molecular pathways including the ERK signalling pathway among others. Therefore, the aim of the present study was to investigate the gene expression patterns following siRNA­mediated suppression of RUNX1­RUNX1T1 and MAPK1 in Kasumi­1 and SKNO­1 cells and to determine the differentially expressed genes in enriched biological pathways. BeadChip microarray and gene ontology analysis revealed that RUNX1­RUNX1T1 and MAPK1 suppression reduced the proliferation rate of the t(8;21) cells with deregulated expression of several classical positive regulator genes that are otherwise known to enhance cell proliferation. RUNX1­RUNX1T1 suppression exerted an anti­apoptotic effect through the overexpression of BCL2, BIRC3 and CFLAR genes, while MAPK1 suppression induced apopotosis in t(8;21) cells by the apoptotic mitochondrial changes stimulated by the activity of upregulated TP53 and TNFSF10, and downregulated JUN gene. RUNX1­RUNX1T1 suppression supported myeloid differentiation by the differential expression of CEBPA, CEBPE, ID2, JMJD6, IKZF1, CBFB, KIT and CDK6, while MAPK1 depletion inhibited the differentiation of t(8;21) cells by elevated expression of ADA and downregulation of JUN. RUNX1­RUNX1T1 and MAPK1 depletion induced cell cycle arrest at the G0/G1 phase. Accumulation of cells in the G1 phase was largely the result of downregulated expression of TBRG4, CCNE2, FOXO4, CDK6, ING4, IL8, MAD2L1 and CCNG2 in the case of RUNX1­RUNX1T1 depletion and increased expression of RASSF1, FBXO6, DADD45A and P53 in the case of MAPK1 depletion. Taken together, the current results demonstrate that MAPK1 promotes myeloid cell proliferation and differentiation simultaneously by cell cycle progression while suppresing apoptosis.

Prolactin Biology and Laboratory Measurement: An Update on Physiology and Current Analytical Issues.

Prolactin is a 23 kDa single chain protein of 199 amino acids synthesised and released principally by lactotrophs in the anterior pituitary gland. The secretion is mainly under inhibitory control by hypothalamic dopamine and regulated in a negative feedback manner, with prolactin itself providing the afferent signal: short-loop feedback. The main function of prolactin is during pregnancy and lactation in the development of mammary glands, milk synthesis and maintenance of milk secretion. Serum prolactin levels rise rapidly during pregnancy with increase in the size and number of lactotrophs. During lactation suckling induces rapid secretion of prolactin via a neuroendocrine reflex pathway. In the absence of pregnancy, hyperprolactinaemia may present with symptoms of hypogonadotropic hypogonadism including menstrual disturbance and infertility or visual symptoms from a pituitary mass effect by a prolactinoma, the most common pituitary tumour. Hyperprolactinaemia is diagnosed by laboratory measurement of serum prolactin. There is considerable variability in routinely available prolactin immunoassays as a result of differing reactivity towards monomeric prolactin and macroprolactin and lack of commutability of the WHO 3rd International Standard between routine methods. Macroprolactinaemia is a relatively common cause of interference in the prolactin assay that may lead to incorrect diagnosis and unnecessary investigations. Measurement of prolactin post polyethylene glycol precipitation (PEG) when prolactin levels are above the reference interval is routinely used to identify macroprolactin, however harmonisation of PEG precipitation process and reporting may improve clinical care.

Epimetheus - a multi-profile normalizer for epigenomic sequencing data.

BACKGROUND: Exponentially increasing numbers of NGS-based epigenomic datasets in public repositories like GEO constitute an enormous source of information that is invaluable for integrative and comparative studies of gene regulatory mechanisms. One of today's challenges for such studies is to identify functionally informative local and global patterns of chromatin states in order to describe the regulatory impact of the epigenome in normal cell physiology and in case of pathological aberrations. Critically, the most preferred Chromatin ImmunoPrecipitation-Sequencing (ChIP-Seq) is inherently prone to significant variability between assays, which poses significant challenge on comparative studies. One challenge concerns data normalization to adjust sequencing depth variation. RESULTS: Currently existing tools either apply linear scaling corrections and/or are restricted to specific genomic regions, which can be prone to biases. To overcome these restrictions without any external biases, we developed Epimetheus, a genome-wide quantile-based multi-profile normalization tool for histone modification data and related datasets. CONCLUSIONS: Epimetheus has been successfully used to normalize epigenomics data in previous studies on X inactivation in breast cancer and in integrative studies of neuronal cell fate acquisition and tumorigenic transformation; Epimetheus is freely available to the scientific community.

Do all screening immunoassay positive buprenorphine samples need to be confirmed?

Background Interference from opiates in the Microgenics CEDIA® Buprenorphine assay is known to produce false-positive buprenorphine screening immunoassay results necessitating confirmatory buprenorphine testing by chromatography/mass spectrometry methods. Method We reviewed data on falsely positive buprenorphine immunoassay screen (cut-off ≥ 5 µg/L) but negative for buprenorphine by gas chromatography mass spectrometry (cut-off ≥ 5 µg/L) and had a positive opiate immunoassay result (cut-off ≥ 300 µg/L). The results were collected over three months, and the data were evaluated to determine whether there is an opiate immunoassay screen concentration below which a false-positive buprenorphine result will not occur. Results We found that cross-reactivity in the CEDIA® buprenorphine immunoassay by opiates at concentrations <2000 µg/L will not cause a false-positive buprenorphine result. After changing our practice to not proceed with confirmatory buprenorphine gas chromatography mass spectrometry assay when the opiate screening concentration is below an even more conservative cut-off of <1500 µg/L, we estimate a potential cost-saving of AU$ 17,810 per year without compromising clinical care. Conclusion Samples with CEDIA® opiate immunoassay result <2000 µg/L and a positive CEDIA® buprenorphine immunoassay screen do not require confirmatory testing for buprenorphine.

Reconstructed cell fate-regulatory programs in stem cells reveal hierarchies and key factors of neurogenesis.

Cell lineages, which shape the body architecture and specify cell functions, derive from the integration of a plethora of cell intrinsic and extrinsic signals. These signals trigger a multiplicity of decisions at several levels to modulate the activity of dynamic gene regulatory networks (GRNs), which ensure both general and cell-specific functions within a given lineage, thereby establishing cell fates. Significant knowledge about these events and the involved key drivers comes from homogeneous cell differentiation models. Even a single chemical trigger, such as the morphogen all-trans retinoic acid (RA), can induce the complex network of gene-regulatory decisions that matures a stem/precursor cell to a particular step within a given lineage. Here we have dissected the GRNs involved in the RA-induced neuronal or endodermal cell fate specification by integrating dynamic RXRA binding, chromatin accessibility, epigenetic promoter epigenetic status, and the transcriptional activity inferred from RNA polymerase II mapping and transcription profiling. Our data reveal how RA induces a network of transcription factors (TFs), which direct the temporal organization of cognate GRNs, thereby driving neuronal/endodermal cell fate specification. Modeling signal transduction propagation using the reconstructed GRNs indicated critical TFs for neuronal cell fate specification, which were confirmed by CRISPR/Cas9-mediated genome editing. Overall, this study demonstrates that a systems view of cell fate specification combined with computational signal transduction models provides the necessary insight in cellular plasticity for cell fate engineering. The present integrated approach can be used to monitor the in vitro capacity of (engineered) cells/tissues to establish cell lineages for regenerative medicine.

Reconstruction of gene regulatory networks reveals chromatin remodelers and key transcription factors in tumorigenesis.

BACKGROUND: Alterations in genetic and epigenetic landscapes are known to contribute to the development of different types of cancer. However, the mechanistic links between transcription factors and the epigenome which coordinate the deregulation of gene networks during cell transformation are largely unknown. METHODS: We used an isogenic model of stepwise tumorigenic transformation of human primary cells to monitor the progressive deregulation of gene networks upon immortalization and oncogene-induced transformation. We applied a systems biology approach by combining transcriptome and epigenome data for each step during transformation and integrated transcription factor-target gene associations in order to reconstruct the gene regulatory networks that are at the basis of the transformation process. RESULTS: We identified 142 transcription factors and 24 chromatin remodelers/modifiers (CRMs) which are preferentially associated with specific co-expression pathways that originate from deregulated gene programming during tumorigenesis. These transcription factors are involved in the regulation of divers processes, including cell differentiation, the immune response, and the establishment/modification of the epigenome. Unexpectedly, the analysis of chromatin state dynamics revealed patterns that distinguish groups of genes which are not only co-regulated but also functionally related. Decortication of transcription factor targets enabled us to define potential key regulators of cell transformation which are engaged in RNA metabolism and chromatin remodeling. CONCLUSIONS: We reconstructed gene regulatory networks that reveal the alterations occurring during human cellular tumorigenesis. Using these networks we predicted and validated several transcription factors as key players for the establishment of tumorigenic traits of transformed cells. Our study suggests a direct implication of CRMs in oncogene-induced tumorigenesis and identifies new CRMs involved in this process. This is the first comprehensive view of the gene regulatory network that is altered during the process of stepwise human cellular tumorigenesis in a virtually isogenic system.

NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets.

The combination of massive parallel sequencing with a variety of modern DNA/RNA enrichment technologies provides means for interrogating functional protein-genome interactions (ChIP-seq), genome-wide transcriptional activity (RNA-seq; GRO-seq), chromatin accessibility (DNase-seq, FAIRE-seq, MNase-seq), and more recently the three-dimensional organization of chromatin (Hi-C, ChIA-PET). In systems biology-based approaches several of these readouts are generally cumulated with the aim of describing living systems through a reconstitution of the genome-regulatory functions. However, an issue that is often underestimated is that conclusions drawn from such multidimensional analyses of NGS-derived datasets critically depend on the quality of the compared datasets. To address this problem, we have developed the NGS-QC Generator, a quality control system that infers quality descriptors for any kind of ChIP-sequencing and related datasets. In this chapter we provide a detailed protocol for (1) assessing quality descriptors with the NGS-QC Generator; (2) to interpret the generated reports; and (3) to explore the database of QC indicators (www.ngs-qc.org) for >21,000 publicly available datasets.