Cockayne Syndrome Linked to Elevated R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation.

Mutations in the Cockayne Syndrome group B (CSB) gene cause cancer in mice, but premature aging and severe neurodevelopmental defects in humans. CSB, a member of the SWI/SNF family of chromatin remodelers, plays diverse roles in regulating gene expression and transcription-coupled nucleotide excision repair (TC-NER); however, these functions do not explain the distinct phenotypic differences observed between CSB-deficient mice and humans. During investigating Cockayne Syndrome-associated genome instability, we uncover an intrinsic mechanism that involves elongating RNA polymerase II (RNAPII) undergoing transient pauses at internal T-runs where CSB is required to propel RNAPII forward. Consequently, CSB deficiency retards RNAPII elongation in these regions, and when coupled with G-rich sequences upstream, exacerbates genome instability by promoting R-loop formation. These R-loop prone motifs are notably abundant in relatively long genes related to neuronal functions in the human genome, but less prevalent in the mouse genome. These findings provide mechanistic insights into differential impacts of CSB deficiency on mice versus humans and suggest that the manifestation of the Cockayne Syndrome phenotype in humans results from the progressive evolution of mammalian genomes.

KIF2A correlates with lymphovascular invasion and higher tumor stage, and can be used to predict worse prognosis in patients with endometrial carcinoma.

Kinesin family protein 2A (KIF2A) is a microtubule depolymerase that participates in the progression of various cancers; however, its clinical utility in endometrial carcinoma (EC) remains unclear. The aim of the present study was to assess KIF2A expression and its relationship with prognosis in patients with EC. Data from 230 patients with EC who underwent tumor resection were reviewed in the current, retrospective study. KIF2A expression was measured in 230 formalin-fixed paraffin-embedded (FFPE) specimens of tumor tissue and 50 FFPE specimens of non-tumor tissue using immunohistochemistry (IHC). KIF2A expression was elevated in EC tumor tissue vs. non-tumor tissue (P<0.001). Furthermore, tumor KIF2A expression was linked with lymphovascular invasion (P=0.004) and higher International Federation of Gynecology and Obstetrics (FIGO) stage (P=0.001). High tumor KIF2A expression (IHC score>3) was correlated with shorter disease-free survival (DFS; P=0.014) and overall survival (OS; P=0.012). Moreover, the time-dependent receiver operating characteristic curves revealed that tumor KIF2A expression had an acceptable use for estimating the relapse and death risks at each timepoint within 6 years, with each area under the curve remaining stable at ≥0.7. Notably, tumor KIF2A expression (high vs. low) independently forecast shorter DFS (hazard ratio, 2.506; P=0.013), but not OS (P>0.05). Furthermore, information from The Human Protein Atlas database indicated that high tumor KIF2A expression was associated with worse OS in patients with EC (P=0.027). Tumor KIF2A is not only associated with lymphovascular invasion and higher FIGO stage, but also reflects unfavorable survival in patients with EC.

Optimizing calibration of modern skeletal maturity systems.

Purpose: Greulich and Pyle is the most used system to estimate skeletal maturity but has significant drawbacks, prompting the development of newer skeletal maturity systems, such as the modified Fels skeletal maturity systems based on knee radiographs. To create a new skeletal maturity system, an outcome variable, termed a "skeletal maturity standard," must be selected for calibration of the system. Peak height velocity and 90% of final height are both considered reasonable skeletal maturity standards for skeletal maturity system development. We sought to answer two questions: (1) Does a skeletal maturity system developed using 90% of final height estimate skeletal age as well as it would if it was instead developed using peak height velocity? (2) Does a skeletal maturity system developed using 90% of final height perform as well in lower extremity length prediction as it would if it was instead developed using peak height velocity? Methods: The modified Fels knee skeletal maturity system was recalibrated based on 90% of final height and peak height velocity skeletal maturity standards. These models were applied to 133 serially obtained, peripubertal antero-posterior knee radiographs collected from 38 subjects. Each model was used to estimate the skeletal age of each radiograph. Skeletal age estimates were also used to predict each patient's ultimate femoral and tibial length using the White-Menelaus method. Results: The skeletal maturity system calibrated with 90% of final height produced more accurate skeletal age estimates than the same skeletal maturity system calibrated with peak height velocity (p < 0.05). The 90% of final height and peak height velocity models made similar femoral and tibial length predictions (p > 0.05). Conclusion: Using the 90% of final height skeletal maturity standard allows for simpler skeletal maturity system development than peak height velocity with potentially more accuracy.

Probabilistic activity driven model of temporal simplicial networks and its application on higher-order dynamics.

Network modeling characterizes the underlying principles of structural properties and is of vital significance for simulating dynamical processes in real world. However, bridging structure and dynamics is always challenging due to the multiple complexities in real systems. Here, through introducing the individual's activity rate and the possibility of group interaction, we propose a probabilistic activity-driven (PAD) model that could generate temporal higher-order networks with both power-law and high-clustering characteristics, which successfully links the two most critical structural features and a basic dynamical pattern in extensive complex systems. Surprisingly, the power-law exponents and the clustering coefficients of the aggregated PAD network could be tuned in a wide range by altering a set of model parameters. We further provide an approximation algorithm to select the proper parameters that can generate networks with given structural properties, the effectiveness of which is verified by fitting various real-world networks. Finally, we construct the co-evolution framework of the PAD model and higher-order contagion dynamics and derive the critical conditions for phase transition and bistable phenomenon using theoretical and numerical methods. Results show that tendency of participating in higher-order interactions can promote the emergence of bistability but delay the outbreak under heterogeneous activity rates. Our model provides a basic tool to reproduce complex structural properties and to study the widespread higher-order dynamics, which has great potential for applications across fields.

Exploring the Possibility of RNA in Diverse Biological Processes.

The total amount of RNA in a cell is 5 to 10 times greater than that of DNA [...].

NDRG1 facilitates self-renewal of liver cancer stem cells by preventing EpCAM ubiquitination.

BACKGROUND: Portal vein tumour thrombus (PVTT) is the main pathway of HCC intrahepatic metastasis and is responsible for the poor prognosis of patients with HCC. However, the molecular mechanisms underlying PVTT vascular metastases have not been fully elucidated. METHODS: NDRG1 expression was assessed by immunohistochemistry and immunoblotting in clinical specimens obtained from curative surgery. The functional relevance of NDRG1 was evaluated using sphere formation and animal models of tumorigenicity and metastasis. The relationship between NDRG1 and EpCAM was explored using molecular biological techniques. RESULTS: NDRG1 protein was upregulated in HCC samples compared to non-tumorous tissues. Furthermore, NDRG1 expression was enhanced in the PVTT samples. Our functional study showed that NDRG1 was required for the self-renewal of tumour-initiating/cancer stem cells (CSCs). In addition, NDRG1 knockdown inhibited the proliferation and migration of PVTT-1 cells in vitro and in vivo. NDRG1 was found to stabilise the functional tumour-initiating cell marker EpCAM through protein-protein interactions and inhibition of EpCAM ubiquitination. CONCLUSION: Our findings suggest that NDRG1 enhances CSCs expansion, PVTT formation and growth capability through the regulation of EpCAM stability. NDRG1 may be a promising target for the treatment of patients with HCC and PVTT.

Sequential Polyadenylation to Enable Alternative mRNA 3' End Formation.

In eukaryotic cells, a key RNA processing step to generate mature mRNA is the coupled reaction for cleavage and polyadenylation (CPA) at the 3' end of individual transcripts. Many transcripts are alternatively polyadenylated (APA) to produce mRNAs with different 3' ends that may either alter protein coding sequence (CDS-APA) or create different lengths of 3'UTR (tandem-APA). As the CPA reaction is intimately associated with transcriptional termination, it has been widely assumed that APA is regulated cotranscriptionally. Isoforms terminated at different regions may have distinct RNA stability under different conditions, thus altering the ratio of APA isoforms. Such differential impacts on different isoforms have been considered as post-transcriptional APA, but strictly speaking, this can only be considered "apparent" APA, as the choice is not made during the CPA reaction. Interestingly, a recent study reveals sequential APA as a new mechanism for post-transcriptional APA. This minireview will focus on this new mechanism to provide insights into various documented regulatory paradigms.

LncRNA CCTT-mediated RNA-DNA and RNA-protein interactions facilitate the recruitment of CENP-C to centromeric DNA during kinetochore assembly.

Kinetochore assembly on centromeres is central for chromosome segregation, and defects in this process cause mitotic errors and aneuploidy. Besides the well-established protein network, emerging evidence suggests the involvement of regulatory RNA in kinetochore assembly; however, it has remained elusive about the identity of such RNA, let alone its mechanism of action in this critical process. Here, we report CCTT, a previously uncharacterized long non-coding RNA (lncRNA) transcribed from the arm of human chromosome 17, which plays a vital role in kinetochore assembly. We show that CCTT highly localizes to all centromeres via the formation of RNA-DNA triplex and specifically interacts with CENP-C to help engage this blueprint protein in centromeres, and consequently, CCTT loss triggers extensive mitotic errors and aneuploidy. These findings uncover a non-centromere-derived lncRNA that recruits CENP-C to centromeres and shed critical lights on the function of centromeric DNA sequences as anchor points for kinetochore assembly.

RUNX1 deficiency cooperates with SRSF2 mutation to induce multilineage hematopoietic defects characteristic of MDS.

Myelodysplastic syndromes (MDSs) are a heterogeneous group of hematologic malignancies with a propensity to progress to acute myeloid leukemia. Causal mutations in multiple classes of genes have been identified in patients with MDS with some patients harboring more than 1 mutation. Interestingly, double mutations tend to occur in different classes rather than the same class of genes, as exemplified by frequent cooccurring mutations in the transcription factor RUNX1 and the splicing factor SRSF2. This prototypic double mutant provides an opportunity to understand how their divergent functions in transcription and posttranscriptional regulation may be altered to jointly promote MDS. Here, we report a mouse model in which Runx1 knockout was combined with the Srsf2 P95H mutation to cause multilineage hematopoietic defects. Besides their additive and synergistic effects, we also unexpectedly noted a degree of antagonizing activity of single mutations in specific hematopoietic progenitors. To uncover the mechanism, we further developed a cellular model using human K562 cells and performed parallel gene expression and splicing analyses in both human and murine contexts. Strikingly, although RUNX1 deficiency was responsible for altered transcription in both single and double mutants, it also induced dramatic changes in global splicing, as seen with mutant SRSF2, and only their combination induced missplicing of genes selectively enriched in the DNA damage response and cell cycle checkpoint pathways. Collectively, these data reveal the convergent impact of a prototypic MDS-associated double mutant on RNA processing and suggest that aberrant DNA damage repair and cell cycle regulation critically contribute to MDS development.

Inadvertent Transfer of Murine VL30 Retrotransposons to CAR-T Cells.

For more than a decade, genetically engineered autologous T-cells have been successfully employed as immunotherapy drugs for patients with incurable blood cancers. The active components in some of these game-changing medicines are autologous T-cells that express viral vector-delivered chimeric antigen receptors (CARs), which specifically target proteins that are preferentially expressed on cancer cells. Some of these therapeutic CAR expressing T-cells (CAR-Ts) are engineered via transduction with γ-retroviral vectors (γ-RVVs) produced in a stable producer cell line that was derived from murine PG13 packaging cells (ATCC CRL-10686). Earlier studies reported on the copackaging of murine virus-like 30S RNA (VL30) genomes with γ-retroviral vectors generated in murine stable packaging cells. In an earlier study, VL30 mRNA was found to enhance the metastatic potential of human melanoma cells. These findings raise biosafety concerns regarding the possibility that therapeutic CAR-Ts have been inadvertently contaminated with potentially oncogenic VL30 retrotransposons. In this study, we demonstrated the presence of infectious VL30 particles in PG13 cell-conditioned media and observed the ability of these particles to deliver transcriptionally active VL30 genomes to human cells. Notably, VL30 genomes packaged by HIV-1-based vector particles transduced naïve human cells in culture. Furthermore, we detected the transfer and expression of VL30 genomes in clinical-grade CAR-T cells generated by transduction with PG13 cell-derived γ-retroviral vectors. Our findings raise biosafety concerns regarding the use of murine packaging cell lines in ongoing clinical applications.

Local-Forest Method for Superspreaders Identification in Online Social Networks.

Identifying the most influential spreaders in online social networks plays a prominent role in affecting information dissemination and public opinions. Researchers propose many effective identification methods, such as k-shell. However, these methods are usually validated by simulating propagation models, such as epidemic-like models, which rarely consider the Push-Republish mechanism with attenuation characteristic, the unique and widely-existing spreading mechanism in online social media. To address this issue, we first adopt the Push-Republish (PR) model as the underlying spreading process to check the performance of identification methods. Then, we find that the performance of classical identification methods significantly decreases in the PR model compared to epidemic-like models, especially when identifying the top 10% of superspreaders. Furthermore, inspired by the local tree-like structure caused by the PR model, we propose a new identification method, namely the Local-Forest (LF) method, and conduct extensive experiments in four real large networks to evaluate it. Results highlight that the Local-Forest method has the best performance in accurately identifying superspreaders compared with the classical methods.

ZetaSuite: computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics.

Two-dimensional high-throughput data have become increasingly common in functional genomics studies, which raises new challenges in data analysis. Here, we introduce a new statistic called Zeta, initially developed to identify global splicing regulators from a two-dimensional RNAi screen, a high-throughput screen coupled with high-throughput functional readouts, and ZetaSuite, a software package to facilitate general application of the Zeta statistics. We compare our approach with existing methods using multiple benchmarked datasets and then demonstrate the broad utility of ZetaSuite in processing public data from large-scale cancer dependency screens and single-cell transcriptomics studies to elucidate novel biological insights.

Burn Pit Exposure Is Associated With Increased Sinonasal Disease.

OBJECTIVE: The aim of this study was to determine whether self-reported burn pit exposure is associated with increased subjective and objective sinus disease. DESIGN: A cross-sectional study was performed evaluating consecutive adult patients presenting to a US Military rhinology clinic. Demographics, medical histories, sinonasal quality-of-life scores, and nasal endoscopy examinations were obtained. Participants were divided into three cohorts based on self-reported exposure histories and outcomes compared. RESULTS: One hundred eighty-six patients met the inclusion criteria, the majority of whom were male. Patients with burn pit exposure had worse Sinonasal Outcome Test-22 scores (49.9) compared with those deployed without burn pit exposure (31.8) or never deployed (31.5). Endoscopic findings demonstrated worse disease within those exposed (Lund-Kennedy score, 3.3) compared with the other cohorts (1.8 and 1.7, respectively). CONCLUSIONS: These novel findings suggest that deployment-related burn pit exposure is associated with increased subjective and objective sinus disease.

Whole exome sequencing identified a homozygous novel mutation in SUOX gene causes extremely rare autosomal recessive isolated sulfite oxidase deficiency.

BACKGROUND: Isolated sulfite oxidase deficiency (ISOD) is a rare type of life-threatening neurometabolic disorders characterized by neonatal intractable seizures and severe developmental delay with an autosomal recessive mode of inheritance. Germline mutation in SUOX gene causes ISOD. Till date, only 32 mutations of SUOX gene have been identified and reported to be associated with ISOD. METHODS: Here, we investigated a 5-days old Chinese female child, presented with intermittent tremor or seizures of limbs, neonatal encephalopathy, subarachnoid cyst and haemorrhage, dysplasia of corpus callosum, neonatal convulsion, hyperlactatemia, severe metabolic acidosis, hyperglycemia, and hyperkalemia. RESULTS: Whole exome sequencing identified a novel homozygous transition (c.1227G > A) in exon 6 of the SUOX gene in the proband. This novel homozygous variant leads to the formation of a truncated sulfite oxidase (p.Trp409*) of 408 amino acids. This variant causes partial loss of the dimerization domain of sulfite oxidase. Hence, it is a loss-of-function variant. Proband's father and mother is carrying this novel variant in a heterozygous state. This variant was not found in 200 ethnically matched normal healthy control individuals. CONCLUSIONS: Our study not only expanded the mutational spectrum of SUOX gene associated with ISOD, but also strongly suggested the significance of whole exome sequencing for identifying candidate genes and novel disease-causing variants.

Mapping R-Loops Using Catalytically Inactive RNaseH1 (R-ChIP).

R-loops, three-stranded structures containing double-stranded DNA invaded by single-stranded RNA, have been linked to diverse biological processes. They play important roles in regulating gene regulation and DNA repair, contributing to a wide range of diseases. Understanding the formation and dynamic regulation of R-loops is thus a gateway to address many fundamental questions in regulatory biology, which requires the elucidation of the R-loop landscape at the genome scale. To aid in such efforts, this article provides an overview on R-loop mapping strategies along with a detailed protocol based on the use of catalytically inactive RNaseH1, an evolutionarily conserved protein responsible for R-loop recognition and resolution.

The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression.

During an immune response to microbial infection, CD8+ T cells give rise to short-lived effector cells and memory cells that provide sustained protection. Although the transcriptional programs regulating CD8+ T cell differentiation have been extensively characterized, the role of long noncoding RNAs (lncRNAs) in this process remains poorly understood. Using a functional genetic knockdown screen, we identified the lncRNA Malat1 as a regulator of terminal effector cells and the terminal effector memory (t-TEM) circulating memory subset. Evaluation of chromatin-enriched lncRNAs revealed that Malat1 grouped with trans lncRNAs that exhibit increased RNA interactions at gene promoters and gene bodies. Moreover, we observed that Malat1 was associated with increased H3K27me3 deposition at a number of memory cell-associated genes through a direct interaction with Ezh2, thereby promoting terminal effector and t-TEM cell differentiation. Our findings suggest an important functional role of Malat1 in regulating CD8+ T cell differentiation and broaden the knowledge base of lncRNAs in CD8+ T cell biology.

ADAR1-mediated RNA editing links ganglioside catabolism to glioblastoma stem cell maintenance.

Glioblastoma (GBM) is the most common and lethal primary malignant brain tumor, containing GBM stem cells (GSCs) that contribute to therapeutic resistance and relapse. Exposing potential GSC vulnerabilities may provide therapeutic strategies against GBM. Here, we interrogated the role of adenosine-to-inosine (A-to-I) RNA editing mediated by adenosine deaminase acting on RNA 1 (ADAR1) in GSCs and found that both ADAR1 and global RNA editomes were elevated in GSCs compared with normal neural stem cells. ADAR1 inactivation or blocking of the upstream JAK/STAT pathway through TYK2 inhibition impaired GSC self-renewal and stemness. Downstream of ADAR1, RNA editing of the 3'-UTR of GM2A, a key ganglioside catabolism activator, proved to be critical, as interference with ganglioside catabolism and disruption of ADAR1 showed a similar functional impact on GSCs. These findings reveal that RNA editing links ganglioside catabolism to GSC self-renewal and stemness, exposing a potential vulnerability of GBM for therapeutic intervention.

SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling.

Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance of small proteins has been revealed in current years, along with the discovery of their diverse functions. However, systematic annotation of small proteins is still insufficient. SmProt was specially developed to provide valuable information on small proteins for scientific community. Here we present the update of SmProt, which emphasizes reliability of translated sORFs, genetic variants in translated sORFs, disease-specific sORF translation events or sequences, and remarkably increased data volume. More components such as non-ATG translation initiation, function, and new sources are also included. SmProt incorporated 638,958 unique small proteins curated from 3,165,229 primary records, which were computationally predicted from 419 ribosome profiling (Ribo-seq) datasets or collected from literature and other sources from 370 cell lines or tissues in 8 species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio, Saccharomyces cerevisiae, Caenorhabditis elegans, and Escherichia coli). In addition, small protein families identified from human microbiomes were also collected. All datasets in SmProt are free to access, and available for browse, search, and bulk downloads at http://bigdata.ibp.ac.cn/SmProt/.