Terminal modification, sequence, length, and PIWI-protein identity determine piRNA stability.

In animals, PIWI-interacting RNAs (piRNAs) silence transposons, fight viral infections, and regulate gene expression. piRNA biogenesis concludes with 3' terminal trimming and 2'-O-methylation. Both trimming and methylation influence piRNA stability. Our biochemical data show that multiple mechanisms destabilize unmethylated mouse piRNAs, depending on whether the piRNA 5' or 3' sequence is complementary to a trigger RNA. Unlike target-directed degradation of microRNAs, complementarity-dependent destabilization of piRNAs in mice and flies is blocked by 3' terminal 2'-O-methylation and does not require base pairing to both the piRNA seed and the 3' sequence. In flies, 2'-O-methylation also protects small interfering RNAs (siRNAs) from complementarity-dependent destruction. By contrast, pre-piRNA trimming protects mouse piRNAs from a degradation pathway unaffected by trigger complementarity. In testis lysate and in vivo, internal or 3' terminal uridine- or guanine-rich tracts accelerate pre-piRNA decay. Loss of both trimming and 2'-O-methylation causes the mouse piRNA pathway to collapse, demonstrating that these modifications collaborate to stabilize piRNAs.

GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins.

Argonaute proteins use nucleic acid guides to find and bind specific DNA or RNA target sequences. Argonaute proteins have diverse biological functions and many retain their ancestral endoribonuclease activity, cleaving the phosphodiester bond between target nucleotides t10 and t11. In animals, the PIWI proteins-a specialized class of Argonaute proteins-use 21-35 nucleotide PIWI-interacting RNAs (piRNAs) to direct transposon silencing, protect the germline genome, and regulate gene expression during gametogenesis1. The piRNA pathway is required for fertility in one or both sexes of nearly all animals. Both piRNA production and function require RNA cleavage catalysed by PIWI proteins. Spermatogenesis in mice and other placental mammals requires three distinct, developmentally regulated PIWI proteins: MIWI (PIWIL1), MILI (PIWIL2) and MIWI22-4 (PIWIL4). The piRNA-guided endoribonuclease activities of MIWI and MILI are essential for the production of functional sperm5,6. piRNA-directed silencing in mice and insects also requires GTSF1, a PIWI-associated protein of unknown function7-12. Here we report that GTSF1 potentiates the weak, intrinsic, piRNA-directed RNA cleavage activities of PIWI proteins, transforming them into efficient endoribonucleases. GTSF1 is thus an example of an auxiliary protein that potentiates the catalytic activity of an Argonaute protein.

PIWI-interacting RNAs: small RNAs with big functions.

In animals, PIWI-interacting RNAs (piRNAs) of 21-35 nucleotides in length silence transposable elements, regulate gene expression and fight viral infection. piRNAs guide PIWI proteins to cleave target RNA, promote heterochromatin assembly and methylate DNA. The architecture of the piRNA pathway allows it both to provide adaptive, sequence-based immunity to rapidly evolving viruses and transposons and to regulate conserved host genes. piRNAs silence transposons in the germ line of most animals, whereas somatic piRNA functions have been lost, gained and lost again across evolution. Moreover, most piRNA pathway proteins are deeply conserved, but different animals employ remarkably divergent strategies to produce piRNA precursor transcripts. Here, we discuss how a common piRNA pathway allows animals to recognize diverse targets, ranging from selfish genetic elements to genes essential for gametogenesis.

A-MYB/TCFL5 regulatory architecture ensures the production of pachytene piRNAs in placental mammals.

In male mice, the transcription factor A MYB initiates the transcription of pachytene piRNA genes during meiosis. Here, we report that A MYB activates the transcription factor Tcfl5 produced in pachytene spermatocytes. Subsequently, A MYB and TCFL5 reciprocally reinforce their own transcription to establish a positive feedback circuit that triggers pachytene piRNA production. TCFL5 regulates the expression of genes required for piRNA maturation and promotes transcription of evolutionarily young pachytene piRNA genes, whereas A-MYB activates the transcription of older pachytene piRNA genes. Intriguingly, pachytene piRNAs from TCFL5-dependent young loci initiates the production of piRNAs from A-MYB-dependent older loci ensuring the self-propagation of pachytene piRNAs. A MYB and TCFL5 act via a set of incoherent feedforward loops that drive regulation of gene expression by pachytene piRNAs during spermatogenesis. This regulatory architecture is conserved in rhesus macaque, suggesting that it was present in the last common ancestor of placental mammals.

CRISPR-induced exon skipping of ß-catenin reveals tumorigenic mutants driving distinct subtypes of liver cancer.

CRISPR/Cas9-driven cancer modeling studies are based on the disruption of tumor suppressor genes by small insertions or deletions (indels) that lead to frame-shift mutations. In addition, CRISPR/Cas9 is widely used to define the significance of cancer oncogenes and genetic dependencies in loss-of-function studies. However, how CRISPR/Cas9 influences gain-of-function oncogenic mutations is elusive. Here, we demonstrate that single guide RNA targeting exon 3 of Ctnnb1 (encoding ß-catenin) results in exon skipping and generates gain-of-function isoforms in vivo. CRISPR/Cas9-mediated exon skipping of Ctnnb1 induces liver tumor formation in synergy with YAPS127A in mice. We define two distinct exon skipping-induced tumor subtypes with different histological and transcriptional features. Notably, ectopic expression of two exon-skipped ß-catenin transcript isoforms together with YAPS127A phenocopies the two distinct subtypes of liver cancer. Moreover, we identify similar CTNNB1 exon-skipping events in patients with hepatocellular carcinoma. Collectively, our findings advance our understanding of ß-catenin-related tumorigenesis and reveal that CRISPR/Cas9 can be repurposed, in vivo, to study gain-of-function mutations of oncogenes in cancer. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Rebuilding wellbeing: Understanding the role of self-criticism, anger rumination, and death distress after the February 6, 2023, Türkiye Earthquake.

This study investigated self-criticism, anger rumination, and death distress in wellbeing after one of the most devastating natural disasters of this century. The study included 399 participants from 56 different cities across Türkiye. Participants were from 3 groups: those who themselves or one of their nuclear families are earthquake survivors (group 1), those who had a loved one other than a nuclear family member who was an earthquake survivor (group 2), and those who were deeply affected by the earthquake through media networks (group 3). Results showed that women experienced higher death distress and anger rumination and lower mental wellbeing compared to men post-earthquake. Individuals in group 1 had significantly lower mental wellbeing and higher death distress than groups 2 and 3. However, the effect size of this significant differentiation depending on earthquake experience was small. Moreover, anger rumination and death distress fully mediated the link between self-criticism and mental wellbeing.

Doomscrolling and mental well-being in social media users: A serial mediation through mindfulness and secondary traumatic stress.

Considering that large-scale events such as natural disasters, epidemics, and wars affect people all over the world through online news channels, it is inevitable to investigate the impact of following or avoiding negative news on well-being. This study investigated the effect of doomscrolling on mental well-being and the mediating role of mindfulness and secondary traumatic stress in social media users. A total of 400 Turkish adults completed scales to assess doomscrolling, mental well-being, mindfulness, and secondary traumatic stress. The average age of the participants was 29.42 (SD = 8.38; ranged = 18-65). Structural equation modeling was conducted to examine the mediating roles of mindfulness and secondary traumatic stress in the relationship between doomscrolling and mental well-being. Mindfulness and secondary traumatic stress fully mediated the relationship between doomscrolling and mental well-being. The results are discussed in light of existing knowledge of doomscrolling, mental well-being, mindfulness, and secondary traumatic stress. High levels of doomscrolling, which is related to an individual's mental well-being, can predict the individual's distraction from the here and now and fixation on negative news. This situation, in which mindfulness is low, is related to the individual's indirect traumatization and increased secondary traumatic stress symptoms in the face of the negative news he/she follows.

The MYBL1/TCFL5 transcription network: two collaborative factors with central role in male meiosis.

Male gametogenesis, spermatogenesis, is a stepwise developmental process to generate mature sperm. The most intricate process of spermatogenesis is meiosis during which two successive cell divisions ensue with dramatic cellular and molecular changes to produce haploid cells. After entry into meiosis, several forms of regulatory events control the orderly progression of meiosis and the timely entry into post-meiotic sperm differentiation. Among other mechanisms, changes to gene expression are controlled by key transcription factors. In this review, we will discuss the gene regulatory mechanisms underlying meiotic entry, meiotic progression, and post-meiotic differentiation with a particular emphasis on the MYBL1/TCFL5 regulatory architecture and how this architecture involves in various forms of transcription network motifs to regulate gene expression.

The transcription factor TCFL5 responds to A-MYB to elaborate the male meiotic program in mice.

In brief: The testis-specific transcription factor, TCFL5, expressed in pachytene spermatocytes regulates the meiotic gene expression program in collaboration with the transcription factor A-MYB. Abstract: In male mice, the transcription factors STRA8 and MEISON initiate meiosis I. We report that STRA8/MEISON activates the transcription factors A-MYB and TCFL5, which together reprogram gene expression after spermatogonia enter into meiosis. TCFL5 promotes the transcription of genes required for meiosis, mRNA turnover, miR-34/449 production, meiotic exit, and spermiogenesis. This transcriptional architecture is conserved in rhesus macaque, suggesting TCFL5 plays a central role in meiosis and spermiogenesis in placental mammals. Tcfl5em1/em1 mutants are sterile, and spermatogenesis arrests at the mid- or late-pachytene stage of meiosis. Moreover, Tcfl5+/em1 mutants produce fewer motile sperm.

Relations among self-control, hope, and psychological adjustment: A two-wave longitudinal mediation study.

While the relationships between self-control, hope, and psychological adjustment have been examined in cross-sectional studies, the fact that these variables have not been considered together in any longitudinal research creates a gap in the literature. Therefore, our study aimed to investigate the longitudinal relationships between self-control, hope, and psychological adjustment. Specifically, a cross-lagged panel study in two waves was conducted to examine whether hope mediated the association between self-control and psychological adjustment using a Turkish college sample (N = 349). The results revealed that hope had a significant mediation effect in the longitudinal association between self-control and psychological adjustment. In this direction, self-control indirectly predicts psychological adjustment through hope. This longitudinal study reveals that having self-control may have a positive influence on a person's level of hope and that hope may be a significant predictor of individual psychological adjustment.

Evaluation of the brain cellular damage during liver transplantations.

Background: Neuroinflammation in patients undergoing major surgery can lead to neuronal damage, and neuronal damage can be detected through the measurement of biochemical markers of brain damage. S100 beta (S100 ß), neuron-specific enolase (NSE), and glial fibrillary acidic protein (GFAP) levels are considered good biomarkers to detect brain damage that emerged with neurotoxicity. Aim: To evaluate neuronal damage during liver transplantations. Materials and Methods: After approval of the ethics committee and patient consents, preoperative and postoperative cognitive functions of 33 patients undergoing liver transplantation were measured using the Mini Mental State Examination (MMSE), whereas simultaneous neuronal damage was evaluated through the measurement of S100ß, NSE, and GFAP levels. Results: There was no statistically significant difference between preoperative and postoperative MMSE. There was a statistically significant decrease in postoperative GFAP (P < 0.05) and a statistically significant increase in NSE (P < 0.05) compared to preoperative values. The decrease in S100ß (P > 0.05) level was statistically insignificant. Conclusions: Neuroprotective approaches in anesthesia protocol protect patients from brain damage during liver transplantation and prevent the development of postoperative cognitive dysfunction. Since the significant increase in NSE levels during liver transplantations was deemed to have been associated with causes other than neuronal damage, NSE should not be evaluated as a marker of brain damage in these operations.

YAP1 Withdrawal in Hepatoblastoma Drives Therapeutic Differentiation of Tumor Cells to Functional Hepatocyte-Like Cells.

BACKGROUND AND AIMS: Despite surgical and chemotherapeutic advances, the 5-year survival rate for stage IV hepatoblastoma (HB), the predominant pediatric liver tumor, remains at 27%. Yes-associated protein 1 (YAP1) and ß-catenin co-activation occurs in 80% of children's HB; however, a lack of conditional genetic models precludes tumor maintenance exploration. Thus, the need for a targeted therapy remains unmet. Given the predominance of YAP1 and ß-catenin activation in HB, we sought to evaluate YAP1 as a therapeutic target in HB. APPROACH AND RESULTS: We engineered the conditional HB murine model using hydrodynamic injection to deliver transposon plasmids encoding inducible YAP1S127A , constitutive ß-cateninDelN90 , and a luciferase reporter to murine liver. Tumor regression was evaluated using bioluminescent imaging, tumor landscape characterized using RNA and ATAC sequencing, and DNA footprinting. Here we show that YAP1S127A withdrawal mediates more than 90% tumor regression with survival for 230+ days in mice. YAP1S127A withdrawal promotes apoptosis in a subset of tumor cells, and in remaining cells induces a cell fate switch that drives therapeutic differentiation of HB tumors into Ki-67-negative hepatocyte-like HB cells ("HbHeps") with hepatocyte-like morphology and mature hepatocyte gene expression. YAP1S127A withdrawal drives the formation of hbHeps by modulating liver differentiation transcription factor occupancy. Indeed, tumor-derived hbHeps, consistent with their reprogrammed transcriptional landscape, regain partial hepatocyte function and rescue liver damage in mice. CONCLUSIONS: YAP1S127A withdrawal, without silencing oncogenic ß-catenin, significantly regresses hepatoblastoma, providing in vivo data to support YAP1 as a therapeutic target for HB. YAP1S127A withdrawal alone sufficiently drives long-term regression in HB, as it promotes cell death in a subset of tumor cells and modulates transcription factor occupancy to reverse the fate of residual tumor cells to mimic functional hepatocytes.

Influenza and SARS-CoV-2 Co-infections in California, USA, September 2020-April 2021.

During September 1, 2020-April 30, 2021, the California Department of Public Health, Richmond, California, USA, received 255 positive influenza molecular test results that matched with severe acute respiratory syndrome coronavirus 2 molecular test results; 58 (23%) persons were co-infected. Influenza activity was minimal in California, and co-infections were sporadic.

Depletion of TRRAP Induces p53-Independent Senescence in Liver Cancer by Down-Regulating Mitotic Genes.

Hepatocellular carcinoma (HCC) is an aggressive subtype of liver cancer with few effective treatments, and the underlying mechanisms that drive HCC pathogenesis remain poorly characterized. Identifying genes and pathways essential for HCC cell growth will aid the development of new targeted therapies for HCC. Using a kinome CRISPR screen in three human HCC cell lines, we identified transformation/transcription domain-associated protein (TRRAP) as an essential gene for HCC cell proliferation. TRRAP has been implicated in oncogenic transformation, but how it functions in cancer cell proliferation is not established. Here, we show that depletion of TRRAP or its co-factor, histone acetyltransferase KAT5, inhibits HCC cell growth through induction of p53-independent and p21-independent senescence. Integrated cancer genomics analyses using patient data and RNA sequencing identified mitotic genes as key TRRAP/KAT5 targets in HCC, and subsequent cell cycle analyses revealed that TRRAP-depleted and KAT5-depleted cells are arrested at the G2/M phase. Depletion of topoisomerase II alpha (TOP2A), a mitotic gene and TRRAP/KAT5 target, was sufficient to recapitulate the senescent phenotype of TRRAP/KAT5 knockdown. Conclusion: Our results uncover a role for TRRAP/KAT5 in promoting HCC cell proliferation by activating mitotic genes. Targeting the TRRAP/KAT5 complex is a potential therapeutic strategy for HCC.

Self-compassion, intolerance of uncertainty, fear of COVID-19, and well-being: A serial mediation investigation.

The present study examined the mediating role of intolerance of uncertainty and fear of COVID-19 in the relationship between self-compassion and well-being. The participants were comprised of 667 Turkish individuals (465 females and 202 males; aged between 18 and 73 years) from 75 of 81 cities in Turkey. The model was investigated using bootstrapping. The results showed that self-compassion, intolerance of uncertainty, fear of COVID-19, and well-being are significantly interrelated. Moreover, a serial mediation was found among the variables: individuals with a growth self-compassion to report lower intolerance of uncertainty, which further decreased perceived fear of COVID-19, and subsequently weakened well-being. Results are discussed in the context of COVID-19 and the well-being literature, and theoretical and practical implications were also provided.

Genetic disruption of oncogenic Kras sensitizes lung cancer cells to Fas receptor-mediated apoptosis.

Genetic lesions that activate KRAS account for ∼30% of the 1.6 million annual cases of lung cancer. Despite clinical need, KRAS is still undruggable using traditional small-molecule drugs/inhibitors. When oncogenic Kras is suppressed by RNA interference, tumors initially regress but eventually recur and proliferate despite suppression of Kras Here, we show that tumor cells can survive knockout of oncogenic Kras, indicating the existence of Kras-independent survival pathways. Thus, even if clinical KRAS inhibitors were available, resistance would remain an obstacle to treatment. Kras-independent cancer cells exhibit decreased colony formation in vitro but retain the ability to form tumors in mice. Comparing the transcriptomes of oncogenic Kras cells and Kras knockout cells, we identified 603 genes that were specifically up-regulated in Kras knockout cells, including the Fas gene, which encodes a cell surface death receptor involved in physiological regulation of apoptosis. Antibodies recognizing Fas receptor efficiently induced apoptosis of Kras knockout cells but not oncogenic Kras-expressing cells. Increased Fas expression in Kras knockout cells was attributed to decreased association of repressive epigenetic marks at the Fas promoter. Concordant with this observation, treating oncogenic Kras cells with histone deacetylase inhibitor and Fas-activating antibody efficiently induced apoptosis, thus bypassing the need to inhibit Kras. Our results suggest that activation of Fas could be exploited as an Achilles' heel in tumors initiated by oncogenic Kras.

DEBrowser: interactive differential expression analysis and visualization tool for count data.

BACKGROUND: Sequencing data has become a standard measure of diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by chromatin immunoprecipitation sequencing (ChIP-Seq), protein-RNA interactions by crosslinking immunoprecipitation sequencing (CLIP-Seq) or RNA immunoprecipitation (RIP-Seq) sequencing, DNA accessibility by assay for transposase-accessible chromatin (ATAC-Seq), DNase or MNase sequencing libraries. The processing of these sequencing techniques involves library-specific approaches. However, in all cases, once the sequencing libraries are processed, the result is a count table specifying the estimated number of reads originating from each genomic locus. Differential analysis to determine which loci have different cellular activity under different conditions starts with the count table and iterates through a cycle of data assessment, preparation and analysis. Such complex analysis often relies on multiple programs and is therefore a challenge for those without programming skills. RESULTS: We developed DEBrowser as an R bioconductor project to interactively visualize every step of the differential analysis, without programming. The application provides a rich and interactive web based graphical user interface built on R's shiny infrastructure. DEBrowser allows users to visualize data with various types of graphs that can be explored further by selecting and re-plotting any desired subset of data. Using the visualization approaches provided, users can determine and correct technical variations such as batch effects and sequencing depth that affect differential analysis. We show DEBrowser's ease of use by reproducing the analysis of two previously published data sets. CONCLUSIONS: DEBrowser is a flexible, intuitive, web-based analysis platform that enables an iterative and interactive analysis of count data without any requirement of programming knowledge.

Evaluation of the morphological characteristic and sex differences of sternum by multi-detector computed tomography.

BACKGROUND: Sternum is one of the skeleton parts which have frequently congenital anomalies and variations are commonly used by researchers in determining sex. We evaluated the morphological characteristics and sex-related changes of the sternum in adult individuals using multidetector computed tomography in our study. MATERIALS AND METHODS: Two hundred adults (103 female and 97 male) aged between 18 and 87 years were evaluated. Utilising the morphological characteristics of the sternum based on the multislice images; length, width and the thickness of manubrium, length, width and the thickness of corpus sterni, total length of sternum, sternal angle, sternal index (SI), length of the xiphoid process, the thickness of xiphoid process, the number of indents of xiphoid process were measured and a total of 20 parameters were evaluated by adding age, height and weight to these variables. RESULTS: The mean length of the manubrium, the length of corpus sterni, the length of total sternum, SI, sternal angle were found in females 46.7 ± 5.1, 86.6 ± 9.7, 133.1 ± 1.1, 54.47 ± 10.0 and 163.75 ± 5.79; in males 51.2 ± 6,102.4 ± 13.3, 154.1 ± 13.1, 50.11 ± 10.02 and 162.21 ± 6.17, respectively. We found that Hyrtl's Law and SI did not provide adequate accuracy for sex determination in our patients. It has been detected that the length of the manubrium alone is not helpful for individual samples. Total length of the sternum was found to be more reliable than the length of the manubrium and the length of corpus sterni. We determined sternal cleft and sternal foramen as 0.5% and 3.5%, respectively. CONCLUSIONS: We suggest that the morphometric standards cannot be universally applied and can demonstrate individual differences. The standard rules must be implemented for every population.

Protective effect of glucagon-like peptide-2 in experimental corrosive esophagitis.

Corrosive esophageal injuries are one of the life-threatening morbidities leading to esophageal stricture and perforation affecting all age groups but especially children due to accidental ingestions in this age group. Glucagon-like peptide-2 (GLP-2) is an intestinal polypeptide with potent anti-inflammatory effects. Its effects are studied in various studies but not in corrosive esophagitis. We aimed to investigate whether it has protective effect in experimental corrosive esophagitis, in the absence of existing studies into possible links. Twenty-four Wistar-albino rats, weighing 220-240 g, were randomized into three groups (n = 8 in each). First group is control, second one is sham operated, and the third one is treatment group. Median laparotomy was made in all groups. In sham and treatment groups, esophagus was loosened and suspended from 1 cm proximal to the esophageal junction. The esophagus segment between suspenders was exposed to 0.1 mL 5% NaOH for 10 seconds. In the treatment group, rats were given GLP-2 for 7 days intraperitoneally. After 7 days, all rats were sacrified and esophagi were totally removed. In the histopathologic examination, esophageal tissues were compared in terms of inflammation, muscularis mucosa injury, and collagen deposition of tunica muscularis. Histopathologic changes in the esophageal tissues of groups were compared. Histopathologic injury in the GLP-2 treated group was significantly less than sham group (P < 0.05). There was statistically significant healing in the GLP-2 treatment group. It is concluded that GLP-2 has a preventive effect on inflammation and collagen accumulation in an experimental corrosive esophagitis. In the light of the information that initial lesions in the early phase are predictors of complications, GLP-2 is a promising agent that has an anti-inflammatory effect in caustic injuries.