RETRACTED: This article has been retracted. Please see the Retraction Notice for details. An Expression of Concern was previously published. Previous studies on GTF2E showed that it has association with certain group of diseases such as colon cancer and trichothiodystrophy but what is the global effect of GTF2E on cellular processes is not widely characterized. In this regard, this study aimed to investigate and characterize the affect of GTF2E on transcription level of genes and identify the cellular processes and diseases associated with GTF2E. The HCT116 cell line was used in the study and transfected at 30 nM concentration with siGTF2E1 or non-target negative siRNA. After 72 hours, cells were harvested and prepared for further analysis. Whole transcriptome analysis was performed on the human colorectal carcinoma (HCT116) cell line obtained from siGTF2E1 knockdown HCT116 cells (n=3) and their non-target negative siRNA controls (n=3) using RNA-seq. We tested cell viability using MTS assay. Compared with the control group, 166 genes were identified at the time of GTF2E1 knockdown and expressed differentially in the knockdown group, including 66 up-regulated genes and 100 down-regulated genes. One significantly enriched GO term was identified, involving carbohydrate binding. One oncogene related to B-CLL called BCL11A was identified. Five genes associated with colon carcinoma were determined. Eleven genes involved in the development of atherosclerosis were identified.GTF2E1 knockdown caused a decrease in cell viability. In conclusion, the GTF2E1 knockdown group exhibited an altered expression of multiple genes and some of those genes are related to the development of atherosclerosis, colon carcinoma, and B cell chronic lymphocytic leukemia (B-CLL), which might shed light on the different regulatory affect of GTF2E and its association with certain diseases.

Background and Aim: Systemic sclerosis was found to be associated with an increase in cancer incidence. The target of this study was to investigate the most common malignancies and to identify factors that increase the cancer risk in systemic sclerosis patients. Materials and Methods: In this single-centre retrospective study, we screened 252 patients attending our outpatient clinic between January 2005 and December 2021. Results: A total of 252 systemic sclerosis patients were included in the study. Data for the patients were obtained by evaluating their medical records retrospectively. A total of 252 patients with systemic sclerosis were analysed. Nineteen patients were diagnosed with malignancies. Lung cancer was the most common malignancy among patients. Malignancies were not correlated with sex, follow-up period, type of systemic sclerosis, organ involvement, smoking history, serological tests, comorbidities, dose and duration of disease-modifying antirheumatic drugs (DMARDs), but advanced age at systemic sclerosis diagnosis increased the risk of malignancy (p = 0.017) in systemic sclerosis patients. Conclusion: In the current study, advanced age at systemic sclerosis diagnosis was determined to be an extra risk factor for the initiation of cancer in systemic sclerosis patients. Particularly in this patient group, additional screenings might be helpful for early diagnosis. Treatments such as methotrexate, cyclophosphamide, azathioprine, and mycophenolate mofetil can be used without additional cancer risk.

Purpose: The aim of this study was to determine the association of rheumatoid arthritis–related lung disease (RA-LD) and its subtypes with all-cause mortality. Materials and Methods: For the present analyses, patients with RA who underwent computed tomography of the chest (chest-CT) were evaluated. RA-LD was defined in 4 subtypes as follows: interstitial lung disease (RA-ILD), airway disease (RA-AD), rheumatoid pulmonary nodules (RA-PN), and RA-related pleural disease (RA-PD). The date of RA-LD diagnosis was considered the date of the first chest-CT detecting the pathology. To assess the factors associated with mortality, multivariable logistic regression analyses were performed with variables selected based on their causal associations with the outcome. Results: Of 576 RA patients, 253 (43.9%) had RA-LD (38.7% male; mean age at RA-LD diagnosis, 59.9 ± 9.8 years). The most common subtype was RA-AD, which was detected in 119 (47.0%) patients followed by 107 (42.3%) with RA-ILD, 70 (27.7%) with RA-PN, and 31 (12.3%) with RA-PD. Sixty-one (24.1%) patients had 2+ subtypes. After median follow-up of 10.2 years, 97 (16.8%) died. The existence of at least 1 subtype and 2+ subtypes increased the all-cause mortality, as indicated by odds ratios of 1.60 (95% confidence interval [CI], 1.03–2.48) and 2.39 (95% CI, 1.26–4.54), respectively. Among RA-LD patients, RA-ILD and RA-PD were associated with increased mortality (odds ratios were 2.20 [95% CI, 1.18–4.08] and 1.62 [95% CI, 0.70–3.75], respectively). Conclusions: In this study, RA-AD was the most common subtype, and the presence of RA-LD increased mortality. This effect was particularly pronounced in patients with RA-ILD and RA-PD or those presenting with 2+ subtypes.

Previous studies on transcription factor II E(TFIIE) showed that TFIIE was a general transcription factor and that was involved in the transcription of genes to be transcribed. It is supposed that TFIIE is recruited to promoter sites of genes to be transcribed and plays a role in transcription initiation. The aim of this study was to investigate and identify the disease-specific role of TFIIE rather than its general transcription factor role, and characterize the cellular pathways and genes occupied by TFIIE. In this regards, ChIP-seq analysis was performed. For ChIP-seq data, POLR2A ChIP-seq and eGFP-GTF2E2 ChIP-seq were used on human K562 cell line data obtanined from the ENCODE (Encyclopedia of DNA Elements) Project Consortium database.Six significantly enriched KEGG pathways were identified. These pathways involved splicesomes, alcoholism, ATP-dependent chromatin remodeling, necroptosis, neutrophil extracellular trap formation and systemic lupus erythematosus. Also, sixteen significantly enriched GO terms were identifed, six related to molecular functions, three related to biological processes and seven related to cellular components. The molecular function category contains nucleosomal DNA binding, nucleosome binding, pre-mRNA 5’-splice site binding, pre-mRNA binding, protein heterodimerization activity, and structural constitute of chromatin. The biological process category contains RNA splicing, ribonucleoprotein complex biogenesis, and mRNA 5’-splice site recognition. The cellular component category contains U1-snRNP, nucleosome, spliceosomal snRNP complex, protein-DNA complex, DNA packaging complex, Sm-like protein family complex, and small-nuclear ribonucleoprotein complex. A significant enrichment of 3 motifs was also discovered.The current study revealed TFIIE-associated genes and association of TFIIE with certain groups of cellular pathways.This might shed light on disease specific role of TFIIE and help future studies characterize TFIIE-related human diseases.