TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs.

Eukaryotic genomes contain several types of recurrent sequence motifs, e.g. transcription factor motifs, miRNA binding sites, repetitive elements. CRISPR/Cas9 can facilitate identification and study of crucial motifs. We present transCRISPR, the first online tool dedicated to search for sequence motifs in the user-provided genomic regions and design optimal sgRNAs targeting them. Users can obtain sgRNAs for chosen motifs, for up to tens of thousands of target regions in 30 genomes, either for the Cas9 or dCas9 system. TransCRISPR provides user-friendly tables and visualizations, summarizing features of identified motifs and designed sgRNAs such as genomic localization, quality scores, closest transcription start sites and others. Experimental validation of sgRNAs for MYC binding sites designed with transCRISPR confirmed efficient disruption of the targeted motifs and effect on expression of MYC-regulated genes. TransCRISPR is available from https://transcrispr.igcz.poznan.pl/transcrispr/.

Core regions in immunoglobulin heavy chain enhancers essential for survival of non-Hodgkin lymphoma cells are identified by a CRISPR interference screen.

Chromosomal translocations in non-Hodgkin lymphoma (NHL) result in activation of oncogenes by placing them under the regulation of immunoglobulin heavy chain (IGH) super-enhancers. Aberrant expression of translocated oncogenes induced by enhancer activity can contribute to lymphomagenesis. The role of the IGH enhancers in normal B-cell development is well established, but knowledge regarding the precise mechanisms of their involvement in control of the translocated oncogenes is limited. The goal of this project was to define the critical regions in the IGH regulatory elements and identify enhancer RNAs (eRNA). We designed a sgRNA library densely covering the IGH enhancers and performed tiling CRISPR interference screens in three NHL cell lines. This revealed three regions crucial for NHL cell growth. With chromatin-enriched RNA-Seq we showed transcription from the core enhancer regions and subsequently validated expression of the eRNAs in a panel of NHL cell lines and tissue samples. Inhibition of the essential IGH enhancer regions decreased expression of eRNAs and translocated oncogenes in several NHL cell lines. The observed expression and growth patterns were consistent with the breakpoints in the IGH locus. Moreover, targeting the Eµ enhancer resulted in loss of B-cell receptor expression. In a Burkitt lymphoma cell line, MYC overexpression partially rescued the phenotype induced by IGH enhancer inhibition. Our results indicated the most critical regions in the IGH enhancers and provided new insights into the current understanding of the role of IGH enhancers in B-cell NHL. As such, this study forms a basis for development of potential therapeutic approaches.

Human Long Noncoding RNA Interactome: Detection, Characterization and Function.

The application of a new generation of sequencing techniques has revealed that most of the genome has already been transcribed. However, only a small part of the genome codes proteins. The rest of the genome "dark matter" belongs to divergent groups of non-coding RNA (ncRNA), that is not translated into proteins. There are two groups of ncRNAs, which include small and long non-coding RNAs (sncRNA and lncRNA respectively). Over the last decade, there has been an increased interest in lncRNAs and their interaction with cellular components. In this review, we presented the newest information about the human lncRNA interactome. The term lncRNA interactome refers to cellular biomolecules, such as nucleic acids, proteins, and peptides that interact with lncRNA. The lncRNA interactome was characterized in the last decade, however, understanding what role the biomolecules associated with lncRNA play and the nature of these interactions will allow us to better understand lncRNA's biological functions in the cell. We also describe a set of methods currently used for the detection of lncRNA interactome components and the analysis of their interactions. We think that such a holistic and integrated analysis of the lncRNA interactome will help to better understand its potential role in the development of organisms and cancers.

tRNA-derived short RNAs bind to Saccharomyces cerevisiae ribosomes in a stress-dependent manner and inhibit protein synthesis in vitro.

Recently, a number of ribosome-associated non-coding RNAs (rancRNAs) have been discovered in all three domains of life. In our previous studies, we have described several types of rancRNAs in Saccharomyces cerevisiae, derived from many cellular RNAs, including mRNAs, rRNAs, tRNAs and snoRNAs. Here, we present the evidence that the tRNA fragments from simple eukaryotic organism S. cerevisiae directly bind to the ribosomes. Interestingly, rancRNA-tRFs in yeast are derived from both, 5'- and 3'-part of the tRNAs and both types of tRFs associate with the ribosomes in vitro The location of tRFs within the ribosomes is distinct from classical A- and P-tRNA binding sites. Moreover, 3'-tRFs bind to the distinct site than 5'-tRFs. These interactions are stress dependent and as a consequence, provoke regulation of protein biosynthesis. We observe strong correlation between tRF binding to the ribosomes and inhibition of protein biosynthesis in particular environmental conditions. These results implicate the existence of an ancient and conserved mechanism of translation regulation with the involvement of ribosome-associating tRNA-derived fragments.

Metabolic Syndrome in Polish Ischemic Stroke Patients.

BACKGROUND: Metabolic syndrome (MetS) predisposes individuals to cardiovascular disease or stroke development. We aimed at evaluating the prevalence of MetS in a population of acute ischemic stroke (IS) patients from central Poland and at estimating the relationship between MetS and stroke risk. METHODS: We analyzed 672 IS patients who were consecutively admitted to stroke units. The control group was composed of 612 patients with other neurologic disorders. MetS was diagnosed if 3 of 5 factors were present (obesity, increased blood pressure, increased triglycerides, low high-density lipoprotein [HDL] cholesterol, and fasting hyperglycemia) according to the Unified Criteria for Clinical Diagnosis of the Metabolic Syndrome (2009). RESULTS: MetS was diagnosed in 61.2% of stroke patients versus 18.1% of the control group (P < .001). Multiple logistic regression showed that MetS was 1.8 times more common in women than in men (odds ratio [OR], 1.8; 95% confidence interval [CI], 1.4-2.5). The adjusted OR (95% CI) associated with MetS was 2.44 (1.48-3.64; P < .001) for IS. Hypertension and hypertriglyceridemia were the most frequent disturbances of IS patients (87.2% and 68.2%, respectively). The analysis of the interaction between MetS and its components showed significant associations with hypertension (OR, 2.15; 95% CI, .98-4.24; P < .01), high triglyceride levels (OR, 4.35; 95% CI, 2.87-9.43; P < .0001), and low HDL cholesterol levels (OR, 5.12; 95% CI, 3.15-8.20; P < .001). CONCLUSIONS: Over 60% of Polish IS patients have MetS. The prevalence of MetS was significantly higher in women than in men. Thus, MetS may be a risk factor for IS.

[The role of vitamin D in the pathogenesis and course of multiple sclerosis]. / Wplyw witaminy D na patogeneze i przebieg stwardnienia rozsianego.

Multiple sclerosis (MS) is a progressive, inflammatory demyelinating disease of the central nervous system, with an unknown aetiology. The pathogenesis of MS is mainly related with the autoimmune process, environmental factors and genetic predispositions. In recentyears, hypovitaminosis D has been considered as an independent factor increasing the risk of multiple sclerosis. Hypovitaminosis D is defined as a condition in which the concentration of 25(OH)D in serum is lower than 75 nmol/l (30 ng/ml). Numerous studies have documented the relation between the occurrence of MS, its course and activity, and vitamin D concentration dependent on sunlight and dietary intake. Conclusions from research on the effectiveness of supplementation have also been presented. They indicate the necessity of using higher doses of calcitriol. Most authors consider a preventive dose of 4000 IU daily as safe and well-tolerated by people living in low-insolation latitudes. It has been pointed out that vitamin D supplementation is indicated and effective only in cases of actual deficiency. The low risk and low cost of vitamin D supplementation, as well as patients' positive attitude towards it, makes it a promising strategy for decreasing the incidence and alleviating the signs and symptoms of multiple sclerosis.

Lithium cation conducting TDI anion-based ionic liquids.

In this paper we present the synthesis route and electrochemical properties of new class of ionic liquids (ILs) obtained from lithium derivate TDI (4,5-dicyano-2-(trifluoromethyl)imidazolium) anion. ILs synthesized by us were EMImTDI, PMImTDI and BMImTDI, i.e. TDI anion with 1-alkyl-3-methylimidazolium cations, where alkyl meant ethyl, propyl and butyl groups. TDI anion contains fewer fluorine atoms than LiPF6 and thanks to C-F instead of P-F bond, they are less prone to emit fluorine or hydrogen fluoride due to the rise in temperature. Use of IL results in non-flammability, which is making such electrolyte even safer for both application and environment. The thermal stability of synthesized compounds was tested by DSC and TGA and no signal of decomposition was observed up to 250 °C. The LiTDI salt was added to ILs to form complete electrolytes. The structures of tailored ILs with lithium salt were confirmed by X-ray diffraction patterns. The electrolytes showed excellent properties regarding their ionic conductivity (over 3 mS cm(-1) at room temperature after lithium salt addition), lithium cation transference number (over 0.1), low viscosity and broad electrochemical stability window. The ionic conductivity and viscosity measurements of pure ILs are reported for reference.

[RNA processing - unusual mechanism of generation of novel classes of noncoding RNAs from functional RNAs]. / Przetwarzanie RNA - niezwykly mechanizm powstawania nowych klas niekodujacych RNA z funkejonalnych RNA.

Non-coding RNAs (ncRNAs) play regulatory roles at all stages of the genetic information transmission from DNA to proteins. The ncRNA-mediated mechanisms leading to specific expression or silencing of particular genes seem to be of special importance. In addition to well-known and well-understood functions of RNAs, we recently discover new and nonobvious aspects and possibilities of regulating cellular processes. One example is the processing of various RNAs, the mechanism of formation of short non-coding RNAs from existing functional RNAs. Both: the sources of these short RNAs and the functions performed by them are diverse. Their presence greatly enriches the possibilities of gene expression regulation, as it turns out, at all stages.

Inhibition of the glutamate-cysteine ligase catalytic subunit with buthionine sulfoximine enhances the cytotoxic effect of doxorubicin and cyclophosphamide in Burkitt lymphoma cells.

Burkitt lymphoma (BL) is a highly aggressive lymphoma that mainly affects children and young adults. Chemotherapy is effective in young BL patients but the outcome in adults is less satisfactory. Therefore, there is a need to enhance the cytotoxic effect of drugs used in BL treatment. Glutathione (GSH) is an important antioxidant involved in processes such as regulation of oxidative stress and drug detoxification. Elevated GSH levels have been observed in many cancers and were associated with chemoresistance. We previously identified GCLC, encoding an enzyme involved in GSH biosynthesis, as an essential gene in BL. We now confirm that knockout of GCLC decreases viability of BL cells and that the GCLC protein is overexpressed in BL tissues. Moreover, we demonstrate that buthionine sulfoximine (BSO), a known inhibitor of GCLC, decreases growth of BL cells but does not affect control B cells. Furthermore, we show for the first time that BSO enhances the cytotoxicity of compounds commonly used in BL treatment, doxorubicin, and cyclophosphamide. Given the fact that BSO itself was not toxic to control cells and well-tolerated in clinical trials, combination of chemotherapy with BSO may allow reduction of the doses of cytotoxic drugs required to obtain effective responses in BL patients.

Identification of ATM-dependent long non-coding RNAs induced in response to DNA damage.

DNA damage response (DDR) is a complex process, essential for cell survival. Especially deleterious type of DNA damage are DNA double-strand breaks (DSB), which can lead to genomic instability and malignant transformation if not repaired correctly. The central player in DSB detection and repair is the ATM kinase which orchestrates the action of several downstream factors. Recent studies have suggested that long non-coding RNAs (lncRNAs) are involved in DDR. Here, we aimed to identify lncRNAs induced upon DNA damage in an ATM-dependent manner. DNA damage was induced by ionizing radiation (IR) in immortalized lymphoblastoid cell lines derived from 4 patients with ataxia-telangiectasia (AT) and 4 healthy donors. RNA-seq revealed 10 lncRNAs significantly induced 1 h after IR in healthy donors, whereas none in AT patients. 149 lncRNAs were induced 8 h after IR in the control group, while only three in AT patients. Among IR-induced mRNAs, we found several genes with well-known functions in DDR. Gene Set Enrichment Analysis and Gene Ontology revealed delayed induction of key DDR pathways in AT patients compared to controls. The induction and dynamics of selected 9 lncRNAs were confirmed by RT-qPCR. Moreover, using a specific ATM inhibitor we proved that the induction of those lncRNAs is dependent on ATM. Some of the detected lncRNA genes are localized next to protein-coding genes involved in DDR. We observed that induction of lncRNAs after IR preceded changes in expression of adjacent genes. This indicates that IR-induced lncRNAs may regulate the transcription of nearby genes. Subcellular fractionation into chromatin, nuclear, and cytoplasmic fractions revealed that the majority of studied lncRNAs are localized in chromatin. In summary, our study revealed several lncRNAs induced by IR in an ATM-dependent manner. Their genomic co-localization and co-expression with genes involved in DDR suggest that those lncRNAs may be important players in cellular response to DNA damage.

[Differential diagnosis of multiple sclerosis and autoimmune rheumatic diseases]. / Diagnostyka róznicowa stwardnienia rozsianego i chorób reumatycznych o podlozu autoimmunologicznym.

Multiple sclerosis (MS) is a progressive demyelinating-inflammatory disease of the central nervous system, probably of autoimmune etiology. Characteristic qualities include multifocal demyelination, which result in varied clinical pictures of the disease. MS must be differentiated from chronic or recurring diseases, as well as from those with multifocal neurological manifestations and multifocal lesions revealed in a MR scan. Particular signs may precede the development of the full-blown MS, but they may be initial manifestations of autoimmune disease such as systemic lupus, antiphospholipid syndrome, Behçet's disease or Sjögren's syndrome as well. Diagnosis is easier in the later stages due to appearance of characteristic manifestations, absent in the course of MS. Nevertheless, the mildly symptomatic nature of those diseases may lead to misdiagnosis, putting the patient at risk of an expensive and inefficient treatment, which may only exacerbate the symptoms. In many cases a long-term follow-up is necessary to confirm the diagnosis.

CRISPR/Cas9 screen for genome-wide interrogation of essential MYC-bound E-boxes in cancer cells.

The transcription factor MYC is a proto-oncogene with a well-documented essential role in the pathogenesis and maintenance of several types of cancer. MYC binds to specific E-box sequences in the genome to regulate gene expression in a cell-type- and developmental-stage-specific manner. To date, a combined analysis of essential MYC-bound E-boxes and their downstream target genes important for growth of different types of cancer is missing. In this study, we designed a CRISPR/Cas9 library to destroy E-box sequences in a genome-wide fashion. In parallel, we used the Brunello library to knock out protein-coding genes. We performed high-throughput screens with these libraries in four MYC-dependent cancer cell lines-K562, ST486, HepG2, and MCF7-which revealed several essential E-boxes and genes. Among them, we pinpointed crucial common and cell-type-specific MYC-regulated genes involved in pathways associated with cancer development. Extensive validation of our approach confirmed that E-box disruption affects MYC binding, target-gene expression, and cell proliferation in vitro as well as tumor growth in vivo. Our unique, well-validated tool opens new possibilities to gain novel insights into MYC-dependent vulnerabilities in cancer cells.

Adar-mediated A-to-I editing is required for embryonic patterning and innate immune response regulation in zebrafish.

Adenosine deaminases (ADARs) catalyze the deamination of adenosine to inosine, also known as A-to-I editing, in RNA. Although A-to-I editing occurs widely across animals and is well studied, new biological roles are still being discovered. Here, we study the role of A-to-I editing in early zebrafish development. We demonstrate that Adar, the zebrafish orthologue of mammalian ADAR1, is essential for establishing the antero-posterior and dorso-ventral axes and patterning. Genome-wide editing discovery reveals pervasive editing in maternal and the earliest zygotic transcripts, the majority of which occurred in the 3'-UTR. Interestingly, transcripts implicated in gastrulation as well as dorso-ventral and antero-posterior patterning are found to contain multiple editing sites. Adar knockdown or overexpression affect gene expression by 12 hpf. Analysis of adar-/- zygotic mutants further reveals that the previously described role of Adar in mammals in regulating the innate immune response is conserved in zebrafish. Our study therefore establishes distinct maternal and zygotic functions of RNA editing by Adar in embryonic patterning along the zebrafish antero-posterior and dorso-ventral axes, and in the regulation of the innate immune response, respectively.

Enhancing B-Cell Malignancies-On Repurposing Enhancer Activity towards Cancer.

B-cell lymphomas and leukemias derive from B cells at various stages of maturation and are the 6th most common cancer-related cause of death. While the role of several oncogenes and tumor suppressors in the pathogenesis of B-cell neoplasms was established, recent research indicated the involvement of non-coding, regulatory sequences. Enhancers are DNA elements controlling gene expression in a cell type- and developmental stage-specific manner. They ensure proper differentiation and maturation of B cells, resulting in production of high affinity antibodies. However, the activity of enhancers can be redirected, setting B cells on the path towards cancer. In this review we discuss different mechanisms through which enhancers are exploited in malignant B cells, from the well-studied translocations juxtaposing oncogenes to immunoglobulin loci, through enhancer dysregulation by sequence variants and mutations, to enhancer hijacking by viruses. We also highlight the potential of therapeutic targeting of enhancers as a direction for future investigation.

7-[[(4-methyl-2-pyridinyl)amino](2-pyridinyl)methyl]-8-quinolinol (compound 30666) inhibits enhancer activity and reduces B-cell lymphoma growth - A question of specificity.

B-cell non-Hodgkin lymphoma (NHL) is among the ten most common malignancies. Survival rates range from very poor to over 90% and highly depend on the stage and subtype. Characteristic features of NHL are recurrent translocations juxtaposing an oncogene (e.g. MYC, BCL2) to the enhancers in the immunoglobulin heavy chain (IGH) locus. Survival and proliferation of many B-cell lymphomas depend on the expression of the translocated oncogene. Thus, targeting IGH enhancers as an anti-lymphoma treatment seems a promising strategy. Recently, a small molecule - 7-[[(4-methyl-2-pyridinyl)amino](2-pyridinyl)methyl]-8-quinolinol (compound 30666) was identified to decrease activity of the Eµ enhancer and reduce the expression of translocated oncogenes in multiple myeloma and some NHL cell lines (Dolloff, 2019). Here, we aimed to test the effect of compound 30666 in Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL) and shed light on its mechanism of action. We report that both IGH-translocation positive NHL cells as well as IGH-translocation negative B cells and non-B cell controls treated with compound 30666 exhibited consistent growth inhibition. A statistically significant increase in cell percentage in sub-G1 phase of cell cycle was observed, suggesting induction of apoptosis. Compound 30666 downregulated MYC levels in BL cell lines and altered IGH enhancer RNA expression. Moreover, a global decrease of H3K27ac and an increase of H3K4me1 was observed upon 30666 treatment, which suggests switching enhancers to a poised or primed state. Altogether, our findings indicate that 30666 inhibitor affects enhancer activity but might not be as specific for IGH enhancers as previously reported.

[Cachexia in chronic cardiac disease. Ancient syndrome new idea?]. / Kacheksja w przewleklej niewydolnosci serca. Stary zespól, nowe spojrzenie?

Cachexia has long been recognized as serious complication of chronic illness. Cardiac cachexia is a syndrome of generalised wasting which carries a poor prognosis of the chronic heart disease. Characteristic features of cachexia include the activation of the immune system associated with raised plasma concentriations of tumor necrosis factor alpha (TNF(alpha) and other plasma cytokines. Another crucial issue is muscle wasting through the ubiquitin proteasome pathway. The prevention or attenuation of disease related skeletal muscle degeneration has been a common goal in the treatment of cardiac cachexia.

The widespread occurrence of tRNA-derived fragments in Saccharomyces cerevisiae.

Short RNAs derived from the cleavage of tRNA molecules are observed in most organisms. Their occurrence seems to be induced by stress conditions, but still little is known about their biogenesis and functions. We find that the recovery of tRNA fragments depends on the RNA isolation method. Using an optimized RNA extraction protocol and northern blot hybridization technique, we show that the tRNA-derived fragments in yeast are widespread in 12 different growth conditions. We did not observe significant stress-dependent changes in the amounts of tRNA fragments pool. Instead, we show the differential processing of almost all individual tRNAs. We also provide evidence that 3'-part-derived tRNA fragments are as abundant as the 5'- one in Saccharomyces cerevisiae. The resulting set of S. cerevisiae tRNA fragments provides a robust basis for further experimental studies on biological functions of tRFs.