Gene Activation Research Articles

Diversity of endophytic bacteria with antimicrobial potential isolated from marine macroalgae from Yacila and Cangrejos beaches, Piura-Peru.

Endophytic bacteria found in marine macroalgae have been studied for their potential antimicrobial activity, consequently, they could serve as a valuable source of bioactive compounds to control pathogenic bacteria, yeasts, and fungi. Algae endophytic bacteria were isolated from Caulerpa sp., Ulva sp., Ahnfeltiopsis sp., and Chondracantus chamissoi from Yacila and Cangrejo Beaches (Piura, Peru). Antimicrobial assays against pathogenic bacteria were evaluated using cross-culture, over-plate, and volatile organic compound tests. Afterward, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of selected crude extracts were determined, also ITS molecular analysis, antifungal activity, and PCR of iturin, fengycin, and surfactin genes were performed for bacteria strains exhibiting better activity. Forty-six algae endophytic bacteria were isolated from algae. Ten strains inhibited gram-positive pathogenic bacteria (Enterococcus faecalis, Staphylococcus epidermidis, S. aureus, and Listeria monocytogenes), and 12 inhibited gram-negative bacteria (Escherichia coli and Salmonella enteric sv typhimurium). Bacteria with better activity belong to Bacillus sp., Kluyvera ascorbata, Pantoea agglomerans, Leclercia adecarboxylata, and Enterobacter sp., which only four showed antifungal activities against Candida albicans, C. tropicalis, Colletotrichium sp., Fusarium sp., Fusarium oxysporum, and Alternaria sp. Furthermore, K. ascorbata YAFE21 and Bacillus sp. YCFE4 exhibited iturin and fengycin genes. The results indicate that the algae endophytic bacteria found in this study, particularly K. ascorbata YAFE21, Bacillus sp. YCFR6, L. adecarboxylata CUFE2, Bacillus sp. YUFE8, Enterobacter sp. YAFL1, and P. agglomerans YAFL6, could be investigated as potential producers of antimicrobial compounds due to their broad activity against various microorganisms.

Unsupervised clustering of brain tumor leukocytes to reveal atypical lymphoid cell subsets.

25 Background: The brain tumor immune microenvironment (TiME) is characterised by suppression of tumor-infiltrating leukocytes. The lymphocyte niche activity is particularly downregulated within this TiME milieu. Methods: Here, using data-driven approaches in flow cytometry and RNA sequencing analysis, we aimed at dissecting leukocyte cell types infiltrating human brain tumor TiME. Results: Unsupervised clustering provided T lymphocyte subsets including double-negative (CD3+CD4- CD8-) T cells (DNT). Our DNT phenotype was validated with an independent dataset, suggesting DNT to be compatible with γδ T cell phenotype. In our cohort, myeloid immune cell frequencies were associated with malignancy type as previously reported, while a gliosarcoma notably presented unexpectedly high lymphocyte frequencies. Consistently, double-positive (CD4+ CD8+) T cells (DPT) had higher frequency in the gliosarcoma than other tumors. The flow cytometry results were supported by transcriptome patterns and the activity of immune-related genes in these tumors. Conclusions: Our findings feature the benefit of data-driven approaches for brain TiME lymphocyte analysis, and show that primary brain tumors can entail atypical lymphocyte subsets like DNTs and DPT cells. Unbiased lymphocyte characterisation can potentially outline novel targets for immune checkpoint blockade therapy.

Advanced biomimetic design strategies for porous structures promoting bone integration with additive-manufactured Ti6Al4V scaffolds

The natural bone structure exhibits a radial gradient with dense cortical bone externally and porous cancellous bone internally. However, previous studies proposing scaffold designs have predominantly focused on homogeneous porous structures. Moreover, no consensus exists on the optimal structure for gradient porous scaffolds. Our scaffold closely imitated the natural bone structure by incorporating a gradient of pillar diameters. Additionally, we introduced a inverse gradient structure and three uniform diameter pillar structures (400 μm, 600 μm, and 1000 μm) for comparative analysis. Mechanical testing revealed that the compressive strength and elastic modulus of the Ti6Al4V porous scaffolds gradually increased with an increase in pillar diameter. In vitro experiments demonstrated that both the biomimetic gradient and inverse gradient scaffolds promoted osteogenic differentiation, with higher ALP activity (alkaline phosphatase) and osteogenesis-related gene expression compared to the uniform pillar structure scaffolds. The in vivo experiments confirmed these results, highlighting the superior ability of the biomimetic gradient Ti6Al4V porous scaffold to induce new bone formation. Based on our findings, we suggest that the optimal porous structure should have fine-diameter pillars (approximately 400 μm) internally to enhance cell penetration, while coarse-diameter pillars (approximately 800 μm) should be used externally to increase the cell attachment area and enhance mechanical strength. Overall, our study contributes to the field of bone tissue engineering by providing a biomimetic scaffold design that closely imitates the structure of natural bone and promotes osteogenic activity.

From Mild Cases to Critical Cases of COVID-19: The Role of Genes in Inflammasome and Mitochondrial Dynamics

The coronavirus disease 2019 (CVOID-19) has varied clinical manifestations including mild to severe acute respiratory symptoms. Inflammasome complex and mitochondria play an important role in initiating inflammatory responses and could potentially be affected by this infection. To study the inflammasome and mitochondrial fission and fusion gene expression levels in COVID-19 patients, we designed this experiment. The inflammasome and mitochondrial gene expression profiles were determined by real-time polymerase chain reaction in the peripheral blood of 70 hospitalized CVOID-19 patients with mild to moderate symptoms (HOSP) and 30 ICU patients with severe symptoms (ICU) compared to 20 healthy controls (HC). The results indicated that the expression of the dynamin-related protein-1 was extremely suppressed in HOSP while it came back to the normal range in the ICU group. However, the expression of fission 1 protein had a non-significant increase in HOSP and a decrease in the ICU group. The mitofusin-1 and dominant optic atrophy genes showed high expression levels (10-fold) and (70-fold), respectively, in the HOSP group. However, mitofusin-2 significantly decreased in both groups. Although leucine-rich–containing family, pyrin domain–containing-3 (NLRP3) and apoptosis-associated speck-like protein containing a caspase activating and recruitment domain genes dramatically increased in both groups (10 and 4-fold), other inflammasome genes declined in both groups. Finally, Nuclear factor kappa-light-chain-enhancer of activate d B cells (NF-κB) extremely decreased, and Intreleukine-1 showed high expression in ICU patients (3-fold). CVOID-19 infection suppresses the fission genes and elevates the fusion gene expression in mitochondria, and it can cause activation of the inflammasome via the NLRP3 pathway.

The Influence of Chitosan Derivatives in Combination with Bacillus subtilis Bacteria on the Development of Systemic Resistance in Potato Plants with Viral Infection and Drought.

Viral diseases of potatoes are among the main problems causing deterioration in the quality of tubers and loss of yield. The growth and development of potato plants largely depend on soil moisture. Prevention strategies require comprehensive protection against pathogens and abiotic stresses, including modeling the beneficial microbiome of agroecosystems combining microorganisms and immunostimulants. Chitosan and its derivatives have great potential for use in agricultural engineering due to their ability to induce plant immune responses. The effect of chitosan conjugate with caffeic acid (ChCA) in combination with Bacillus subtilis 47 on the transcriptional activity of PR protein genes and changes in the proteome of potato plants during potato virus Y (PVY) infection and drought was studied. The mechanisms of increasing the resistance of potato plants to PVY and lack of moisture are associated with the activation of transcription of genes encoding PR proteins: the main protective protein (PR-1), chitinase (PR-3), thaumatin-like protein (PR-5), protease inhibitor (PR-6), peroxidase (PR-9), and ribonuclease (PR-10), as well as qualitative and quantitative changes in the plant proteome. The revealed activation of the expression of marker genes of systemic acquired resistance and induced systemic resistance under the influence of combined treatment with B. subtilis and chitosan conjugate indicate that, in potato plants, the formation of resistance to viral infection in drought conditions proceeds synergistically. By two-dimensional electrophoresis of S. tuberosum leaf proteins followed by MALDI-TOF analysis, 10 proteins were identified, the content and composition of which differed depending on the experiment variant. In infected plants treated with ChCA, the synthesis of proteinaceous RNase P 1 and oxygen-evolving enhancer protein 2 was enhanced in conditions of normal humidity, and 20 kDa chaperonin and TMV resistance protein N-like was enhanced in conditions of lack of moisture. The virus coat proteins were detected, which intensively accumulated in the leaves of plants infected with potato Y-virus. ChCA treatment reduced the content of these proteins in the leaves, and in plants treated with ChCA in combination with Bacillus subtilis, viral proteins were not detected at all, both in conditions of normal humidity and lack of moisture, which suggests the promising use of chitosan derivatives in combination with B. subtilis bacteria in the regulation of plant resistance.

Systems-Level Modeling for CRISPR-Based Metabolic Engineering.

The CRISPR-Cas system has enabled the development of sophisticated, multigene metabolic engineering programs through the use of guide RNA-directed activation or repression of target genes. To optimize biosynthetic pathways in microbial systems, we need improved models to inform design and implementation of transcriptional programs. Recent progress has resulted in new modeling approaches for identifying gene targets and predicting the efficacy of guide RNA targeting. Genome-scale and flux balance models have successfully been applied to identify targets for improving biosynthetic production yields using combinatorial CRISPR-interference (CRISPRi) programs. The advent of new approaches for tunable and dynamic CRISPR activation (CRISPRa) promises to further advance these engineering capabilities. Once appropriate targets are identified, guide RNA prediction models can lead to increased efficacy in gene targeting. Developing improved models and incorporating approaches from machine learning may be able to overcome current limitations and greatly expand the capabilities of CRISPR-Cas9 tools for metabolic engineering.

SOME SAMPLES OF ASHYG ALESKER'S CREATIVITY, BASED ON LOGIC AND REALITY

İn the article, the material and spiritual existence of the world is divicled into positive and negative poles according to the low of the unity of opposites, and it is shown chat the Turks belong to the positive pole and have active gene carriers. Turks with deep knowledge have had great historical personalities in literature as well as in many areas. One of them is the art of ashıq, which belongs to the spiritual pole and is the food of our soul, and one of those who stand at its peak is Ashıq Alasgar. They did not make a mistake in calling Ashıq Alasgar the real ashiq. By giving logical explanations on selected examples from his work, the authors reveal Ashıq Alasgar knowledge based on sleep logic. This is considered also novelty among the opinions about Ashıq Alasgar based on numerous (any) analyses.

Glutathione S-transferase polymorphisms (GSTM1/GSTT1) outcomes in clinical profile and treatment responsiveness among Tunisian cohort of Parkinson's disease.

Glutathione S-transferases are involved in the oxidative stress which contributes to the pathogenesis of Parkinson's disease (PD). our aim was to investigate the influence of GSTM1 and GSTT1 polymorphisms on the clinical features and treatments outcomes among PD Tunisian patients. We included 300-PD patients followed in neurology department at Razi-University-hospital. GSTM1 and GSTT1 were screened using PCR methods. Correlation between the clinical phenotype and the genotypes was then assessed after adequate parameters adjustment. Individuals carrying inactive GSTT1/GSTM1 were estimated to have 2.5-fold higher risk of developing PD, p = 0.035. The demographic and clinical baseline analysis of GSTM1 polymorphism revealed significant association between the inactive gene and development of tremor as first symptoms (p = 0.046), further, it was correlated to asymmetric start (p = 0.044). The evaluation of the impact of GSTM1/GSTT1 activity among PD at last follow-up revealed the significant variability of motor impairment among cases carrier of the active genes (p = 0.048). As patients with inactive GSTM1/GSTT1 had higher UPDRS-III score. Additionally, higher frequency of cases with good treatment responsiveness was reported among PD with active GSTM1/GSTT1 (p = 0.038).No motor complications were observed among PD by considering the GSTs genotypes (p > 0.05). Finally, we noted significant impairment of memory among cases with inactivate GSTs (p = 0.04), attention deficit (p = 0.013) and impaired judgement (p = 0.0031). This study represents one of the most comprehensive and extensive investigation to date regarding the influence of GSTT1/GSTM1 genotype among PD patients.We speculate that the impact of GSTT1/GSTM1 on PD progression may occur through a cumulative effect, potentially not manifesting during the initial PD stages. Further studies are necessary to validate our conclusions.

The non-canonically organized members of MIR395 gene family in Brassica juncea are associated with developmentally regulated, sulfate-stress responsive bidirectional promoters that exhibit orientation-dependent differential transcriptional activity

Several MICRORNA genes belonging to same family or different families are often found in homologous or non-homologous clusters. Among the various classes, head-to-head arranged genes form one of the largest categories of non-canonically organized genes. Such head-to-head arranged, non-canonically organized genes possibly share cis-regulatory region with the intergenic sequence having the potential to function as bi-directional promoter (BDP). The transcriptional regulation of head-to-head arranged genes, especially with bidirectional promoters, remains an enigma. In the past, bidirectional promoters have been characterized for a small set of protein-coding gene pairs in plants; however, to the best of our knowledge, no such study has been carried so far for MICRORNA genes. The present study thus functionally characterizes bidirectional promoters associated with members of MIR395 family, which is evolutionary conserved and is most frequently occurring cluster across plant kingdom.In Arabidopsis thaliana, the MIR395 gene family contains six members with two head-to-head arranged gene pairs- MIR395A-B and MIR395E-F. This organization was found to be conserved at seven loci for MIR395A-B, and eleven loci for MIR395E-F in five Brassica sps. Sequence analysis of the putative bidirectional promoters revealed variation in length, GC content and distribution of strict TATA-box. Comparatively higher level of conservation at both the ends of the bidirectional promoters, corresponding to ca. 250 bp upstream of 5’end of the respective MIRNA precursor, was observed. These conserved regions harbour several abiotic stress (nutrient, salt, drought) and hormone (ABA, ethylene) responsive cis-motifs. Functional characterization of putative bidirectional promoters associated with MIR395A-B and MIR395E-F from Arabidopsis and their respective orthologs from Brassica juncea (Bj_A08 MIR395A-B, Bj_B03 MIR395A-B, Bj_A07.1 MIR395E-F and Bj_A07.2 MIR395E-F) was carried out using a dual-reporter vector with β-glucuronidase (GUS) and Green Fluorescent Protein (GFP). Analysis of transcriptional regulation of the two reporter genes - GUS and GFP during developmental stages confirmed their bidirectional nature. Orientation-dependent differential reporter activity indicated asymmetric nature of the promoters. Comparison of the reporter activity amongst orthologs, paralogs and homeologs revealed regulatory diversification, an outcome expected in polyploid genomes. Interestingly, reporter gene activities driven by selected bidirectional promoters were also observed in anther and siliques apart vegetative tissues indicating role of miR395 in anther and fruit development. Finally, we evaluated the activity of reporter genes driven under transcriptional regulation of bidirectional promoters under normal and sulfate-deprived conditions which revealed asymmetric inducibility under sulfate-starvation, in agreement with the known role of miR395 in sulfate homeostasis.

Interference of skeleton photoperiod in circadian clock and photosynthetic efficiency of tea plant: in-depth analysis of mathematical model.

The circadian system of plants is a complex physiological mechanism, a biological process in which plants can adjust themselves according to the day and night cycle. To understand the effects of different photoperiods on the biological clock of tea plants, we analyzed the expression levels of core clock genes (CCA1, PRR9, TOC1, ELF4) and photosynthesis-related genes (Lhcb, RbcS, atpA) under normal light (light/dark = 12h/12h, 12L12D) and took the cost function defined by cycle and phase errors as the basic model parameter. In the continuous light environment (24h light, 24L), the peak activity and cycle of key genes that control the biological clock and photosynthesis were delayed by 1-2h. Under a skeleton photoperiod (6L6D, 3L3D), the expression profiles of clock genes and photosynthesis-related genes in tea plants were changed and stomatal opening showed a circadian rhythm. These observations suggest that a skeleton photoperiod may have an effect on the circadian rhythm, photosynthetic efficiency and stomatal regulation of tea plants. Our study and model analyzed the components of circadian rhythms under different photoperiodic pathways, and also revealed the underlying mechanisms of circadian regulation of photosynthesis in tea plants.

Pyrimidine Triones as Potential Activators of p53 Mutants.

p53 is a crucial tumor suppressor in vertebrates that is frequently mutated in human cancers. Most mutations are missense mutations that render p53 inactive in suppressing tumor initiation and progression. Developing small-molecule drugs to convert mutant p53 into an active, wild-type-like conformation is a significant focus for personalized cancer therapy. Prior research indicates that reactivating p53 suppresses cancer cell proliferation and tumor growth in animal models. Early clinical evidence with a compound selectively targeting p53 mutants with substitutions of tyrosine 220 suggests potential therapeutic benefits of reactivating p53 in patients. This study identifies and examines the UCI-1001 compound series as a potential corrector for several p53 mutations. The findings indicate that UCI-1001 treatment in p53 mutant cancer cell lines inhibits growth and reinstates wild-type p53 activities, including DNA binding, target gene activation, and induction of cell death. Cellular thermal shift assays, conformation-specific immunofluorescence staining, and differential scanning fluorometry suggest that UCI-1001 interacts with and alters the conformation of mutant p53 in cancer cells. These initial results identify pyrimidine trione derivatives of the UCI-1001 series as candidates for p53 corrector drug development.

Autophagic genes and antioxidant status during doxorubicin therapy under temperature-stressed conditions in breast cancer cells

ObjectivesAutophagy as a cellular event swings between apoptosis induction and cellular maintenance during chemotherapy. The interplay between autophagy and reactive oxygen species (ROS) remains obscure in cancer progression and treatment. This study aimed to determine the combination effect of chemotherapy and hyperthermia on cancer cell proliferation, autophagy signaling, and oxidative stress status. MethodsTo estimate the autophagic genes' role and antioxidant capacity involvement during chemotherapy, human breast cancer cell lines (MCF7 and CAL51) were exposed to a high temperature at 42 °C and treated with doxorubicin (DOX). The MTT assays were performed to determine the cell survival levels, and the autophagic gene expression levels (ATG5, LC3A, LC3B, and Beclin1) were analyzed. The intracellular TAS (total antioxidant status) and SOD (superoxide dismutase) activities were determined. ResultsThe combined effects of high temperature with chemotherapy significantly reduced cell viability and cell survival compared to cells treated with the chemotherapeutic agent DOX alone. The cell's autophagic gene activities were significantly increased after exposure to 42 °C temperature and DOX-based chemotherapy compared to the cells treated with DOX alone. It was observed that TAS and SOD activities were increased in the cell lines exposed to high temperatures with DOX compared to the cells treated with DOX alone. Increased autophagic gene expression levels and cell death were observed in response to the high temperature and DOX treatment in breast cancer cells. ConclusionThe study may provide a plausible route and treatment plan for the individual adoption of cancer chemotherapy and be developed as part of the personalized medicine protocol.

Comparative Genomics Screens Identify a Novel Small Secretory Peptide, SlSolP12, which Activates Both Local and Systemic Immune Response in Tomatoes and Exhibits Broad-Spectrum Activity.

Small secreted peptides (SSPs) are essential for defense mechanisms in plant-microbe interactions, acting as danger-associated molecular patterns (DAMPs). Despite the first discovery of SSPs over three decades ago, only a limited number of SSP families, particularly within Solanaceae plants, have been identified due to inefficient approaches. This study employed comparative genomics screens with Solanaceae proteomes (tomato, tobacco, and pepper) to discover a novel SSP family, SolP. Bioinformatics analysis suggests that SolP may serve as an endogenous signal initiating the plant PTI response. Interestingly, SolP family members from tomato, tobacco, and pepper share an identical sequence (VTSNALALVNRFAD), named SlSolP12 (also referred to as NtSolP15 or CaSolP1). Biochemical and phenotypic analyses revealed that synthetic SlSolP12 peptide triggers multiple defense responses: ROS burst, MAPK activation, callose deposition, stomatal closure, and expression of immune defense genes. Furthermore, SlSolP12 enhances systemic resistance against Botrytis cinerea infection in tomato plants and interferes with classical peptides, flg22 and Systemin, which modulate the immune response. Remarkably, SolP12 activates ROS in diverse plant species, such as Arabidopsis thaliana, soybean, and rice, showing a broad spectrum of biological activities. This study provides valuable approaches for identifying endogenous SSPs and highlights SlSolP12 as a novel DAMP that could serve as a useful target for crop protection.

Influence of humic acids on growth performance, bravery, stress resistance, antioxidant activity, and immune gene expression in male Siamese fighting fish (Betta splendens)

The current study investigated the effects of a humic acid supplement on the growth performance, antioxidant enzyme activity, immune-related genes, behavior and endocrinology of male Betta splendens fish. Fish species that are naturally exposed to high levels of humic substances in their environment are likely to perform better under captive conditions when given these substances. In this study, fish were fed a diet containing 0, 0.5 %, 1 %, and 1.5 % humic acid for six weeks. The results showed no significant differences in growth and feeding parameters between treatments (p > 0.05). The fish with a diet of 1.5 % humic acid showed more aggressive behavior in the mirror test than the control group (p < 0.05). In contrast, the fish fed a diet containing 1 % and 1.5 % humic acid showed a higher level of activity in the test with new objects than the control group (p < 0.05). The testosterone levels after aggression were significantly higher in the fish fed diets containing 1 % and 1.5 % humic acid than in the control group (p < 0.05). In addition, the humic acid-treated fish showed lower oxidative stress and cortisol production in common aquaculture stressors than the control (p < 0.05). Gene expression analysis showed upregulation of immune-related genes, including β-defensin 1, c-type lysozyme, interleukin-1β, and tumor necrosis factor-α, in response to humic acid supplementation compared to control (p < 0.05). Overall, the results of this study indicate that a diet containing 1 % humic acid has a positive effect on the physiology, immunology, and behavior of male B. splendens.

Transcription factor Ikzf1 associates with Foxp3 to repress gene expression in Treg cells and limit autoimmunity and anti-tumor immunity

The master transcription factor of regulatory T (Treg) cells, forkhead box protein P3 (Foxp3), controls Treg cell function by targeting certain genes for activation or repression, but the specific mechanisms by which it mediates this activation or repression under different conditions remain unclear. We found that Ikzf1 associates with Foxp3 via its exon 5 (IkE5) and that IkE5-deficient Treg cells highly expressed genes that would otherwise be repressed by Foxp3 upon Tcell receptor stimulation, including Ifng. Treg-specific IkE5-deletion caused interferon-γ (IFN-γ) overproduction, which destabilized Foxp3 expression and impaired Treg suppressive function, leading to systemic autoimmune disease and strong anti-tumor immunity. Pomalidomide, which degrades IKZF1 and IKZF3, induced IFN-γ overproduction in human Treg cells. Mechanistically, the Foxp3-Ikzf1-Ikzf3 complex competed with epigenetic co-activators, such as p300, for binding to target gene loci via chromatin remodeling. Therefore, the Ikzf1 association with Foxp3 is essential for the gene-repressive function of Foxp3 and could be exploited to treat autoimmune disease and cancer.

Study of the Effects of Deuterium-Depleted Water on the Expression of GLUT4 and Insulin Resistance in the Muscle Cell Line C2C12.

Deuterium-depleted water (DDW) is used in the treatment of many diseases, including cancer and diabetes. To detect the effect of DDW on gene expression and activation of the insulin-responsive transporter GLUT4 as a mechanism for improving the pathology of diabetes, we investigated the GLUT4 expression and glucose uptake at various concentrations of DDW using the myoblast cell line C2C12 differentiated into myotubes. GLUT4 gene expression significantly increased under deuterium depletion, reaching a maximum value at a deuterium concentration of approximately 50 ppm, which was approximately nine times that of natural water with a deuterium concentration of 150 ppm. GLUT4 protein also showed an increase at similar DDW concentrations. The membrane translocation of GLUT4 by insulin stimulation reached a maximum value at a deuterium concentration of approximately 50-75 ppm, which was approximately 2.2 times that in natural water. Accordingly, glucose uptake also increased by up to 2.2 times at a deuterium concentration of approximately 50 ppm. Drug-induced insulin resistance was attenuated, and the glucose uptake was four times higher in the presence of 10 ng/mL TNF-α and three times higher in the presence of 1 μg/mL resistin at a deuterium concentration of approximately 50 ppm relative to natural water. These results suggest that DDW promotes GLUT4 expression and insulin-stimulated activation in muscle cells and reduces insulin resistance, making it an effective treatment for diabetes.

MicroRNA Analysis of In Vitro Differentiation of Spermatogonial Stem Cells Using a 3D Human Testis Organoid System.

Spermatogenesis produces male gametes from spermatogonial stem cells (SSC), beginning at puberty. Modern-day laboratory techniques allow for the long-term culture of SSC and in vitro spermatogenesis. The specific biochemical processes that occur during spermatogenesis remain poorly understood. One particular element of spermatogenesis that has yet to be characterized is the role of microRNAs (miRNA), short, non-transcribed RNAs that act as post-translational regulators of gene activity. In this study, we seek to describe the presence of miRNA in a two-dimensional (2D) SSC culture and a 3D human testis organoid (HTO) system. Testicular cells were isolated from the frozen tissue of three brain-dead subjects, propagated in cultures for four to five weeks, and used to form 3D HTOs. Following organoid formation, differentiation of testicular cells was induced. RNA was isolated from the whole testis tissue (WT) showing in vivo conditions, HTO Day Zero (2D SSC culture), Day 2 HTOs, and Day 23 differentiated HTOs, then analyzed for changes in miRNA expression using the Nanostring nCounter miRNA panel. One hundred ninety-five miRNAs met the criteria for expression in WT, 186 in 2D culture, 190 in Day 2 HTOs, and 187 in differentiated HTOs. One hundred thirty-three miRNAs were common across all conditions, and 41, 17, 6, and 11 miRNAs were unique for WT, 2D culture, Day 2 HTOs, and differentiated HTOs, respectively. Twenty-two miRNAs were similar between WT and differentiated HTOS. We evaluated the miRNA expression profiles of progressively complex stages of testicular cell culture, culminating in a 3D organoid model capable of meiotic differentiation, and compared these to WT. We identified a great variance between the native tissue and the culture system; however, some miRNAs are preserved. These data may provide avenues for deeper understanding of spermatogenesis and the ability to improve this process in the laboratory. Research on miRNA continues to be an essential avenue for understanding human spermatogenesis.

The role of RNA viruses in human cancers

Many RNA viruses have been reported to be oncogenic (or carcinogenic) in a variety of animal and human cancers. The increase in the incidence and prevalence of cancer-causing viruses in human populations can be known as a key precursor to the development of various cancers. The retrovirus family and Hepatitis C virus (HCV) are also reported to cause cancer. Viral oncoproteins such as Tax of HTLV 1 interacts with cellular ubiquitination complex such as cyclindromatosis tumor suppressor, ubiquitin-specific proteases 7, 11, 15 and 20, A-20 and signal-transducing adaptor molecule binding protein-like-1 in order to improve the cellular signaling pathways. The viral oncoproteins binding to DUB, leading to proliferation of virus-infected cells and cell transformation. Proto-oncogenes (c-onc genes) are the cellular form of v-onc genes. The activation of c-onc genes leads to cell growth. C-onc genes are transformed into an oncogenic form by viral infection. C-onc genes play some roles such as protein kinases, growth factors, growth factor receptors, and DNA binding proteins. The study of transforming retroviruses and their oncogenes and the multiple mechanisms deployed by other RNA viruses to use the growth-suppressive and proapoptotic function of tumor suppressor genes has been added to our current understanding of cancer biology. Oncogenic RNA viruses are important experimental models to study molecular investigation such as cellular networks, including the discovery of oncogenes and tumor suppressors. Understanding of different strategies of RNA viruses as well as the function of their proteins helps to make more extensive plans regarding the adoption of follow-up, prevention and treatment strategies in cancer patients caused by viral origin.

Human induced pluripotent stem cells for live cell cycle monitoring and endogenous gene activation

The fluorescence ubiquitination cell cycle inhibitor (FUCCI) has been introduced to monitor cell cycle activity in living cells, including human induced pluripotent stem cells (hiPSC) and derived cell types. We have recently developed hiPSC with stable expression of dCas9VPR for endogenous gene activation and a Citrine-tagged ACTN2 cell line to monitor sarcomere development and function in muscle cells. Here, we present dual and triple transgenic hiPSC lines developed by genomic integration of FUCCI with and without dCas9VPR into the ROSA26 and AAVS1 loci, respectively, in the previously introduced ACTN2-Citrine line. Functionality of the transgenes was demonstrated in the novel hiPSC line, which we introduce as Myo-CCER and CraCCER.

51 Epigenetic regulation of ribosomal RNA transcription and processing by the tumor suppressor SETD2

Abstract Background The methyltransferase SETD2 was originally identified as a tumor suppressor in clear cell renal cell carcinoma (ccRCC), and ccRCC with SETD2 mutations have increased metastatic potential and poor progression free survival. A known epigenetic regulator, SETD2 interacts with actively transcribing RNA polymerase II (RNAPII) and tri-methylates Histone 3 at Lysine 36 (H3K36me3), a modification that correlates with active gene transcription and is recognized by mRNA methylation and splicing factors. Despite these known roles in mRNA transcription, loss of SETD2 does not alter genic transcription, raising the question of whether or how SETD2 regulates RNA biology. Methods Given that SETD2 influences RNA processing, we sought to identify RNA-protein complexes that are regulated by SETD2. To do this in an unbiased and high-throughput manner, we used orthogonal organic phase separation (OOPS) coupled with mass spectrometry to identify changes in RNA binding proteins and pathways between control and SETD2-knockout cells. Results Corroborating previous findings, we identified that RNA binding proteins governing mRNA splicing and cellular metabolism were dysregulated in SETD2 mutant cells. However, the most robust changes in SETD2 knockout cells occurred in pathways regulated ribosome biogenesis (See Figure, orange highlights), resulting in a significant decrease in binding of ribosomal RNA (rRNA) processing factors to RNA. We confirm these alterations lead to defects in rRNA transcription, processing, and ribosome biogenesis. We identify that loss of SETD2 catalytic activity phenocopies these rRNA processing defects, suggesting H3K36me3 is essential for rRNA processing. Disruptions occur to both the large (60S) and small (40S) ribosome subunits, modifying protein translation. Lastly, we identify synthetic lethality between SETD2 deletion or inhibition and small molecules that interfere with rRNA transcription. Conclusions While the majority of research emphasizes the role SETD2 in the regulation of mRNA, our data identify that SETD2 and its catalytic activity play a critical role in the transcription and processing of rRNA. Importantly, rRNA comprises 80-90% of cellular RNA yet is typically overlooked and understudied. Next-generation RNA sequencing or transcriptional assays investigate mRNA or genic transcription while ignoring rRNA, demonstrating why SETD2-mediated rRNA processing has been unexplored. This may also have important implications for prospective clinical trials that utilized RNA-sequencing to identify optimal therapeutic regimens. Our work also identified that SETD2-mutated cells are more sensitive to compounds that inhibit rRNA transcription, potentially uncovering a new therapeutic vulnerability of ccRCC with mono- and bi-allelic loss of SETD2. Alterations in ribosome biogenesis leads to epithelial-to-mesenchymal transition and metastasis in many tumor types, and our future goal will be to investigate the role of ribosomes and rRNA transcription in transformation and metastasis in ccRCC as well as the molecular mechanisms connecting SETD2 to ribosome fidelity. DOD CDMRP Funding: yes