Actin and myosin in transcription and chromatin regulation

In mammalian cells, actin and myosin have emerged as regulators of nuclear structure and function, involved in chromatin remodeling and histone modifications, and in different phases of gene transcription. Actin and myosin have also been shown to be incorporated into nascent ribonucleoprotein complexes. In the cell nucleus, actin undergoes regulated polymerization and this may be linked to yet unknown mechanisms of nuclear reprogramming. The aims of this thesis were to gain further insights into the functions of actin and myosin in transcription by RNA polymerase I and II (RNAP) and how these mechanisms are regulated. We investigated, in particular, the interplay between actin and a form of myosin 1c, termed nuclear myosin 1 (NM1), which localizes to the cell nucleus. We found that NM1 interacts with the chromatin and with actin to facilitate association of the RNAP with the gene promoter and the transcription start site. At this specific location, NM1 also promotes a chromatin state compatible with transcription activation. NM1 accomplishes this by facilitating chromatin remodeling by the WICH complex, with the subunits WSTF and SNF2h, and by promoting epigenetic reprogramming. In paper I and in paper IV, we show that these mechanisms apply to both RNAP I and RNAP II transcription activation. In paper II, we show that NM1 is regulated by GSK3β through a specific phosphorylation in the NM1 C-terminus that stabilizes the interaction of NM1 with rDNA chromatin. Finally, we show in paper III that knocking down the β-actin gene has a negative effect on transcription by RNAP I, which leads to a delay in cell cycle progression and defects in cell growth and proliferation

Biallelic variants in four genes underlying recessive osteogenesis imperfecta

Peer reviewe

Mini percutaneous nephrolithotripsy as treatment modality for kidney stones

Cilj: Prikazati naše rezultate u liječenju pacijenata s bubrežnim kamencima metodom miniperkutane nefrolitotripsije (miniPCNL). Pacijenti i metode: Retrospektivnim istraživanjem obuhvatili smo pacijente Klinike za urologiju, Kliničkog bolničkog centra u Rijeci koji su između 1. kolovoza 2015. i 31. prosinca 2016. godine zbog bubrežnih kamenaca liječeni metodom miniPCNL-a. Rezultati: U promatranom razdoblju u našem centru operirano je 6 pacijenata ovom metodom, od kojih je jedan bio s transplantiranim bubregom. U svih pacijenata uspješno je učinjena litotripsija s holmium-laserom. Na kontrolnom RTG-u nije bilo ostatnih fragmenata. U četvoro pacijenata poslijeoperativno je došlo do razvoja febriliteta koji je uspješno liječen antibiotskom terapijom. Niti u jednog pacijenta nije bila potrebna reoperacija, dodatne procedure niti potreba za davanjem krvi. Zaključak: Miniperkutana nefrolitotripsija je minimalno invazivna metoda koja se pokazala uspješnom i sigurnom u liječenju nefrolitijaze.Aim: To present our results in the treatment of nephrolithiasis using mini percutaneous nephrolithotripsy (miniPCNL). Patients and methods: We retrospectively analyzed all patients with nephrolithiasis treated with miniPCNL in Department of Urology, University Hospital Rijeka from August 1st 2015 to December 31st 2016. Results: In observed period 6 patients were operated with this novel method and one has transplanted kidney. In allpatients lithotripsy was successfully performed with holmium laser. On the control x-ray the residual fragments were not found in any patients. Postoperatively, in four patients febrility was noticed and successfully treated with antibiotics. Neither the one patient need reoperation, auxiliary procedures or blood transfusion. Conclusion: Mini percutaneous nephrolithotripsy is a minimally-invasive method which is successfull and safe method in the treatment of kidney stones

Nuclear Wiskott–Aldrich syndrome protein co-regulates T cell factor 1-mediated transcription in T cells

Background: The Wiskott–Aldrich syndrome protein (WASp) family of actin-nucleating factors are present in the cytoplasm and in the nucleus. The role of nuclear WASp for T cell development remains incompletely defined. Methods: We performed WASp chromatin immunoprecipitation and deep sequencing (ChIP-seq) in thymocytes and spleen CD4+ T cells. Results: WASp was enriched at genic and intergenic regions and associated with the transcription start sites of protein-coding genes. Thymocytes and spleen CD4+ T cells showed 15 common WASp-interacting genes, including the gene encoding T cell factor (TCF)12. WASp KO thymocytes had reduced nuclear TCF12 whereas thymocytes expressing constitutively active WASpL272P and WASpI296T had increased nuclear TCF12, suggesting that regulated WASp activity controlled nuclear TCF12. We identify a putative DNA element enriched in WASp ChIP-seq samples identical to a TCF1-binding site and we show that WASp directly interacted with TCF1 in the nucleus. Conclusions: These data place nuclear WASp in proximity with TCF1 and TCF12, essential factors for T cell development. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0481-6) contains supplementary material, which is available to authorized users

A novel interstitial deletion of chromosome 2q21.1‐q23.3: Case report and literature review

Abstract Background Interstitial deletions of 2q are rare. Those that have been reported show varying clinical manifestations according to the size of the deletion and the genomic region involved. Method and Results We describe a preterm male harboring a novel interstitial deletion encompassing the 2q21.2‐q23.3 region of 2q, a deletion that has not been described previously. The patient had multiple congenital anomalies including agenesis of the corpus callosum, congenital cardiac defects, bilateral hydronephrosis, spontaneous intestinal perforation, hypospadias and cryptorchidism, sacral dimple and rocker‐bottom feet. Array comparative genomic hybridization (aCGH) analysis revealed a de novo >18 Mb deletion at 2q21.1–q23.3, a region that included (605802, 611472 and 604593) OMIM genes. Conclusion To the best of our knowledge this is the first report of a de novo interstitial deletion at 2q21.1–q23.3 in which haploinsufficiency of dose‐sensitive genes is shown to contribute to the patient's phenotype

Identification of CSF3R Mutations in B-Lineage Acute Lymphoblastic Leukemia Using Comprehensive Cancer Panel and Next-Generation Sequencing

B-lineage acute lymphocytic leukemia (B-ALL) is characterized by different genetic aberrations at a chromosomal and gene level which are very crucial for diagnosis, prognosis and risk assessment of the disease. However, there is still controversial arguments in regard to disease outcomes in specific genetic abnormalities, e.g., 9p-deletion. Moreover, in absence of cytogenetic abnormalities it is difficult to predict B-ALL progression. Here, we use the advantage of Next-generation sequencing (NGS) technology to study the mutation landscape of 12 patients with B-ALL using Comprehensive Cancer Panel (CCP) which covers the most common mutated cancer genes. Our results describe new mutations in CSF3R gene including S661N, S557G, and Q170X which might be associated with disease progression

Additional file 1: of Nuclear Wiskott–Aldrich syndrome protein co-regulates T cell factor 1-mediated transcription in T cells

Supplementary Figures S1–S7. (PDF 1766 kb

Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel

Biomarker discovery would be an important tool in advancing and utilizing the concept of precision and personalized medicine in the clinic. Discovery of novel variants in local population provides confident targets for developing biomarkers for personalized medicine. We identified the need to generate high-quality sequencing data from local colorectal cancer patients and understand the pattern of occurrence of variants. In this report, we used archived samples from Saudi Arabia and used the AmpliSeq comprehensive cancer panel to identify novel somatic variants. We report a comprehensive analysis of next-generation sequencing results with a coverage of >300X. We identified 466 novel variants which were previously unreported in COSMIC and ICGC databases. We analyzed the genes associated with these variants in terms of their frequency of occurrence, probable pathogenicity, and clinicopathological features. Among pathogenic somatic variants, 174 were identified for the first time in the large intestine. APC, RET, and EGFR genes were most frequently mutated. A higher number of variants were identified in the left colon. Occurrence of variants in ERBB2 was significantly correlated with those of EGFR and ATR genes. Network analyses of the identified genes provide functional perspective of the identified genes and suggest affected pathways and probable biomarker candidates. This report lays the ground work for biomarker discovery and identification of driver gene mutations in local population

Pancytopenia, Recurrent Infection, Poor Wound Healing, Heterotopia of the Brain Probably Associated with A Candidate Novel de Novo CDC42 Gene Defect: Expanding the Molecular and Phenotypic Spectrum

CDC42 (cell division cycle protein 42) belongs to the Rho GTPase family that is known to control the signaling axis that regulates several cellular functions, including cell cycle progression, migration, and proliferation. However, the functional characterization of the CDC42 gene in mammalian physiology remains largely unclear. Here, we report the genetic and functional characterization of a non-consanguineous Saudi family with a single affected individual. Clinical examinations revealed poor wound healing, heterotopia of the brain, pancytopenia, and recurrent infections. Whole exome sequencing revealed a de novo missense variant (c.101C > A, p.Pro34Gln) in the CDC42 gene. The functional assays revealed a substantial reduction in the growth and motility of the patient cells as compared to the normal cells control. Homology three-dimensional (3-D) modeling of CDC42 revealed that the Pro34 is important for the proper protein secondary structure. In conclusion, we report a candidate disease-causing variant, which requires further confirmation for the etiology of CDC42 pathogenesis. This represents the first case from the Saudi population. The current study adds to the spectrum of mutations in the CDC42 gene that might help in genetic counseling and contributes to the CDC42-related genetic and functional characterization. However, further studies into the molecular mechanisms that are involved are needed in order to determine the role of the CDC42 gene associated with aberrant cell migration and immune response