Razan Sheta - Academia.edu (original) (raw)

Papers by Razan Sheta

Additional file 8. Comparative canonical pathway analysis for a dataset of differentially express... more Additional file 8. Comparative canonical pathway analysis for a dataset of differentially expressed genes (≥ 1.5-fold; p

Additional file 2. Primers used for qPCR. All primers used for qPCR experiments performed in the ... more Additional file 2. Primers used for qPCR. All primers used for qPCR experiments performed in the study. The table includes a list of the genes primers were designed for, the perimers primer melting temperature (Tm), and the design of the forward and reverse primers.

Additional file 6. Genes, differentially expressed between Sensitive (S) and resistant (R) AsPCs ... more Additional file 6. Genes, differentially expressed between Sensitive (S) and resistant (R) AsPCs (≥ 1.5 fold, p ≤ 0.05). Table presenting the subset of differentially expressed genes that were selected by initial filtering on confidence at p-value ≤ 0.05, followed by filtering of expression level (≥ 1.5 fold). Using these selection criteria, the table lists 240 upregulated genes and 583 downregulated genes in the PARPis-sensitive AsPCs, as compared to the PARPis-resistant AsPCs.

Additional file 4. PARPis sensitive and resistant AsPCs present with different EMT features. (A) ... more Additional file 4. PARPis sensitive and resistant AsPCs present with different EMT features. (A) Western blot protein expression analysis of the two EMT markers, N-cadherin and E-cadherin in resistant (R) and sensitive (S) PARPis AsPCs. Actin was used as the loading control (n = 3). Histograms represent 6 resistant (R) and 6 sensitive (S) AsPCs, and the protein expression levels were normalized to actin. The two-tailed unpaired t-test was used for statistical analysis. All values were expressed as the means ± S.D. *p

Additional file 3. Comparative analysis of PARPis-sensitive and resistant AsPCs, as examined in m... more Additional file 3. Comparative analysis of PARPis-sensitive and resistant AsPCs, as examined in monolayer vs. 3D culture. (A) Total number of AsPCs determined as resistant or sensitive to treatment with the two PARPis olaparib and niraparib when grown in monolayer. Olaparib resistant AsPCs showed to be 36% higher in total number to niraparib resistant AsPCs, likewise niraparib sensitive AsPCs showed to be 36% higher in total number to olaparib sensitive AsPCs. (B) Total number of AsPCs determined as resistant or sensitive to treatment with the two PARPis olaparib and niraparib when treated in 3D. Olaparib resistant AsPCs showed to be 28% higher in total number to niraparib resistant AsPCs, likewise niraparib sensitive AsPCs showed to be 28% higher in total number to olaparib sensitive AsPCs.

Additional file 5. The effect of olaparib and niraparib on EMT in PARPis-resistant AsPCs. AsPCs w... more Additional file 5. The effect of olaparib and niraparib on EMT in PARPis-resistant AsPCs. AsPCs were grown in monolayers for 48 h and then treated with either olaparib at a concentration of 50 μM for a period of 24 h, or niraparib at a concentration of 25 μM for a period of 24 h, as non-treated AsPCs were used as controls. Western blot protein expression analysis of the two EMT markers, (A) olaparib resistant and (B) niraparib resistant AsPCs. Actin was used as the loading control.

Additional file 1. Antibodies used for Western Blots, immunohistochemistry and immunofluorescence... more Additional file 1. Antibodies used for Western Blots, immunohistochemistry and immunofluorescence. The Table includes list and detailed description of the antibodies used in the study, including their dilutions and incubation periods applied, for WB, IHC and IF.

Additional file 10. Original blots from Fig. 4, Additional file 4 and Additional file 5.

Journal of Molecular and Cellular Cardiology, 2014

The key information processing units within gene regulatory networks are enhancers. Enhancer acti... more The key information processing units within gene regulatory networks are enhancers. Enhancer activity is associated with the production of tissue-specific noncoding RNAs, yet the existence of such transcripts during cardiac development has not been established. Using an integrated genomic approach, we demonstrate that fetal cardiac enhancers generate long noncoding RNAs (IncRNAs) during cardiac differentiation and morphogenesis. Enhancer expression correlates with the emergence of active enhancer chromatin states, the initiation of RNA polymerase II at enhancer loci and expression of target genes. Orthologous human sequences are also transcribed in fetal human hearts and cardiac progenitor cells. Through a systematic bioinformatic analysis, we identified and characterized, for the first time, a catalog of IncRNAs that are expressed during embryonic stem cell differentiation into cardiomyocytes and associated with active cardiac enhancer sequences. RNA-sequencing demonstrates that many of these transcripts are polyadenylated, multi-exonic long noncoding RNAs. Moreover, knockdown of two enhancerassociated IncRNAs resulted in the specific downregulation of their predicted target genes. Interestingly, the reactivation of the fetal gene program, a hallmark of the stress response in the adult heart, is accompanied by increased expression of fetal cardiac enhancer transcripts. Altogether, these findings demonstrate that the activity of cardiac enhancers and expression of their target genes are associated with the production of enhancer-derived IncRNAs.

PLOS Biology, 2022

Neurodegenerative disorders refer to a group of diseases commonly associated with abnormal protei... more Neurodegenerative disorders refer to a group of diseases commonly associated with abnormal protein accumulation and aggregation in the central nervous system. However, the exact role of protein aggregation in the pathophysiology of these disorders remains unclear. This gap in knowledge is due to the lack of experimental models that allow for the spatiotemporal control of protein aggregation, and the investigation of early dynamic events associated with inclusion formation. Here, we report on the development of a light-inducible protein aggregation (LIPA) system that enables spatiotemporal control of α-synuclein (α-syn) aggregation into insoluble deposits called Lewy bodies (LBs), the pathological hallmark of Parkinson disease (PD) and other proteinopathies. We demonstrate that LIPA-α-syn inclusions mimic key biochemical, biophysical, and ultrastructural features of authentic LBs observed in PD-diseased brains. In vivo, LIPA-α-syn aggregates compromise nigrostriatal transmission, ind...

Background Poly(ADP-ribose) polymerase inhibitors (PARPis) specifically target homologous recombi... more Background Poly(ADP-ribose) polymerase inhibitors (PARPis) specifically target homologous recombination deficiency (HRD) cells and display good therapeutic effect in women with advanced-stage BRCA1/2-mutated breast and epithelial ovarian cancer (EOC). However, about 50% of high grade serous ovarian cancers (HGSOC) present with HRD due to epigenetic BRCA1 inactivation, as well as genetic/epigenetic inactivation(s) of other HR genes, a feature known as “BRCAness”. Therefore, there is a potential for extending the use of PARPis to these patients if HR status can be identified. Methods We have developed a 3D (spheroid) functional assay to assess the sensitivity of two PARPis (niraparib and olaparib) in ascites-derived primary cell cultures (AsPCs) from HGSOC patients. A method for AsPCs preparation was established based on a matrix (agarose), allowing for easy isolation and successive propagation of monolayer and 3D AsPCs. Based on this method, we performed cytotoxicity assays on 42 AsP...

Biomolecules

Abnormal accumulation of the protein α- synuclein (α-syn) into proteinaceous inclusions called Le... more Abnormal accumulation of the protein α- synuclein (α-syn) into proteinaceous inclusions called Lewy bodies (LB) is the neuropathological hallmark of Parkinson’s disease (PD) and related disorders. Interestingly, a growing body of evidence suggests that LB are also composed of other cellular components such as cellular membrane fragments and vesicular structures, suggesting that dysfunction of the endolysosomal system might also play a role in LB formation and neuronal degeneration. Yet the link between α-syn aggregation and the endolysosomal system disruption is not fully elucidated. In this review, we discuss the potential interaction between α-syn and the endolysosomal system and its impact on PD pathogenesis. We propose that the accumulation of monomeric and aggregated α-syn disrupt vesicles trafficking, docking, and recycling, leading to the impairment of the endolysosomal system, notably the autophagy-lysosomal degradation pathway. Reciprocally, PD-linked mutations in key endos...

Oncotarget

The molecular basis of epithelial ovarian cancer (EOC) dissemination is still poorly understood. ... more The molecular basis of epithelial ovarian cancer (EOC) dissemination is still poorly understood. We have previously identified the hydrogen peroxide-inducible clone-5 (Hic-5) gene as hypomethylated in high-grade (HG) serous EOC tumors, compared to normal ovarian tissues. Hic-5 is a focal adhesion scaffold protein and has been primarily studied for its role as a key mediator of TGF-β-induced epithelialto-mesenchymal transition (EMT) in epithelial cells of both normal and malignant origin; however, its role in EOC has been never investigated. Here we demonstrate that Hic-5 is overexpressed in advanced EOC, and that Hic-5 is upregulated upon TGFβ1 treatment in the EOC cell line with epithelial morphology (A2780s), associated with EMT induction. However, ectopic expression of Hic-5 in A2780s cells induces EMT independently of TGFβ1, accompanied with enhancement of cellular proliferation rate and migratory/invasive capacity and increased resistance to chemotherapeutic drugs. Moreover, Hic-5 knockdown in the EOC cells with mesenchymal morphology (SKOV3) was accompanied by induction of mesenchymalto-epithelial transition (MET), followed by a reduction of their proliferative, migratory/ invasive capacity, and increased drugs sensitivity in vitro, as well as enhanced tumor cell colonization and metastatic growth in vivo. The modulation of Hic-5 expression in EOC cells resulted in altered regulation of numerous EMT-related canonical pathways and was indicative for a possible role of Hic-5 in controlling EMT through a RhoA/ ROCK mediated mechanism. To our knowledge, this is the first report examining the role of Hic-5 in EOC, and its role in maintaining the mesenchymal phenotype of EOC cells independently of exogenous TGFβ1 treatment.

Data in Brief, 2016

This article contains raw and processed data related to research published in "Role of the polype... more This article contains raw and processed data related to research published in "Role of the polypeptide N-acetylgalactosaminyltransferase 3 in ovarian cancer progression: possible implications in abnormal mucin Oglycosylation" [1]. The data presented here was obtained with the application of a bioorthogonal chemical reporter strategy analyzing differential glycoprotein expression following the knock-down (KD) of the GALNT3 gene in the epithelial ovarian cancer (EOC) cell line A2780s. LC-MS/MS mass spectrometry analysis was then performed and the processed data related to the identified glycoproteins show that several hundred proteins are differentially expressed between control and GALNT3 KD A2780s cells. The obtained data also uncover numerous novel glycoproteins; some of which could represent new potential EOC biomarkers and/or therapeutic targets.

Journal of Proteomics, 2016

Epithelial ovarian cancer (EOC) is a disease responsible for more deaths among women in the Weste... more Epithelial ovarian cancer (EOC) is a disease responsible for more deaths among women in the Western world than all other gynecologic malignancies. There is urgent need for new therapeutic targets and a better understanding of EOC initiation and progression. We have previously identified the polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3) gene, a member of the GalNAc-transferases (GalNAc-Ts) gene family, as hypomethylated and overexpressed in high-grade serous EOC tumors, compared to low malignant potential EOC tumors and normal ovarian tissues. This data also suggested for a role of GALNT3 in aberrant EOC glycosylation, possibly implicated in disease progression. To evaluate differential glycosylation in EOC caused by modulations in GALNT3 expression, we used a metabolic labeling strategy for enrichment and mass spectrometry-based characterization of glycoproteins following GALNT3 gene knockdown (KD) in A2780s EOC cells. A total of 589 differentially expressed glycoproteins were identified upon GALNT3 KD. Most identified proteins were involved in mechanisms of cellular metabolic functions, post-translational modifications, and some have been reported to be implicated in EOC etiology. The GALNT3-dependent glycoproteins identified by this metabolic labeling approach support the oncogenic role of GALNT3 in EOC dissemination and may be pursued as novel EOC biomarkers and/or therapeutic targets. Knowledge of the O-glycoproteome has been relatively elusive, and the functions of the individual polypeptide GalNAc-Ts have been poorly characterized. Alterations in GalNAc-Ts expression were shown to provide huge variability in the O-glycoproteome in various pathologies, including cancer. The application of a chemical biology approach for the metabolic labeling and subsequent characterization of O-glycoproteins in EOC using the Ac4GalNAz metabolite has provided a strategy allowing for proteomic discovery of GalNAc-Ts specific functions. Our study supports an essential role of one of the GalNAc-Ts - GALNT3, in EOC dissemination, including its implication in modulating PTMs and EOC metabolism. Our approach validates the use of the applied metabolic strategy to identify important functions of GalNAc-Ts in normal and pathological conditions.

International journal of oncology, Jan 9, 2017

Protein glycosylation perturbations are implicated in a variety of diseases, including cancer. Ab... more Protein glycosylation perturbations are implicated in a variety of diseases, including cancer. Aberrant glycosylation in cancer is frequently attributed to altered expression of polypeptide GalNAc transferases (GalNAc‑Ts) - enzymes initiating mucin-type O-glycosylation. A previous study from our group demonstrated that one member of this family (GALNT3) is overexpressed in epithelial ovarian cancer (EOC), and GALNT3 expression correlated with shorter progression-free survival (PFS) in EOC patients with advanced disease. As considerable degree of redundancy between members of the GalNAc‑Ts gene family has been frequently observed, we decided to investigate whether other members of this family are essential in EOC progression. In silico analysis based on publically available data was indicative for altered expression of five GalNAc‑Ts (GALNT2, T4, T6, T9 and T14) in ovarian high-grade serous carcinoma (HGSC) samples compared to non-tumoral (control) ovarian tissue. We analyzed protein...