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Background: In medical device validation and verification studies, the area under the receiver operating characteristic curve (AUROC) is often used as a primary endpoint despite multiple reports showing its limitations. Hence, researchers are encouraged to consider alternative metrics as primary endpoints. A new metric called G4 is presented, which is the geometric mean of sensitivity, specificity, the positive predictive value, and the negative predictive value. G4 is part of a balanced metric family which includes the Unified Performance Measure (also known as P4) and the Matthews' Correlation Coefficient (MCC). The purpose of this manuscript is to unveil the benefits of using G4 together with the balanced metric family when analyzing the overall performance of binary classifiers. Results: Simulated datasets encompassing different prevalence rates of the minority class were analyzed under a multi-reader-multi-case study design. In addition, data from an independently published study that tested the performance of a unique ultrasound artificial intelligence algorithm in the context of breast cancer detection was also considered. Within each dataset, AUROC was reported alongside the balanced metric family for comparison. When the dataset prevalence and bias of the minority class approached 50%, all three balanced metrics provided equivalent interpretations of an AI's performance. As the prevalence rate increased / decreased and the data became more imbalanced, AUROC tended to overvalue / undervalue the true classifier performance, while the balanced metric family was resistant to such imbalance. Under certain circumstances where data imbalance was strong (minority-class prevalence < 10%), MCC was preferred for standalone assessments while P4 provided a stronger effect size when evaluating between-groups analyses. G4 acted as a middle ground for maximizing both standalone assessments and between-groups analyses. Conclusions: Use of AUROC as the primary endpoint in binary classification problems provides misleading results as the dataset becomes more imbalanced. This is explicitly noticed when incorporating AUROC in medical device validation and verification studies. G4, P4, and MCC do not share this limitation and paint a more complete picture of a medical device's performance in a clinical setting. Therefore, researchers are encouraged to explore the balanced metric family when evaluating binary classification problems. [ABSTRACT FROM AUTHOR]

Nuclear localization of the metabolic enzyme PKM2 is widely observed in various cancer types. We identify nuclear PKM2 as a non-canonical RNA-binding protein (RBP) that specifically interacts with folded RNA G-quadruplex (rG4) structures in precursor mRNAs (pre-mRNAs). PKM2 occupancy at rG4s prevents the binding of repressive RBPs, such as HNRNPF, and promotes the expression of rG4-containing pre-mRNAs (the "rG4ome"). We observe an upregulation of the rG4ome during epithelial-to-mesenchymal transition and a negative correlation of rG4 abundance with patient survival in different cancer types. By preventing the nuclear accumulation of PKM2, we could repress the rG4ome in triple-negative breast cancer cells and reduce migration and invasion of cancer cells in vitro and in xenograft mouse models. Our data suggest that the balance of folded and unfolded rG4s controlled by RBPs impacts gene expression during tumor progression. [Display omitted] • Nuclear PKM2 binds folded RNA G4s on pre-mRNA • G4 folding during transcription promotes mRNA expression • G4-containing RNAs encode EMT components • Nuclear PKM2 promotes lung metastasis Anastasakis et al. find that PKM2 binds G-quadruplexes (rG4) forming on precursor mRNAs. They show that the balance of folded and unfolded rG4s controls transcriptional output of rG4-containing RNAs (rG4ome). The rG4ome encodes EMT components, and the removal of PKM2 from the nucleus results in reduced tumor growth and metastasis. [ABSTRACT FROM AUTHOR]

We generate new evidence on disagreement among traders in the S&P 500 options market from high-frequency intraday price and volume data. Inference on disagreement is based on a model where investors observe public information but agree to disagree on its interpretation; disagreement among investors is captured by the volume–volatility elasticity. For options, there are two natural variables related to disagreement: moneyness and tenor, which we relate to disagreement about the distribution of the market index at different quantiles and times. The estimated volume–volatility elasticity equals unity for options near the money and close to expiration, which is consistent with the case of no disagreement among investors. In contrast, the elasticity estimates decrease with increases in the absolute value of moneyness, indicating investors have a higher disagreement about rare events. Likewise, the elasticity decreases with increases in tenor, implying higher investors' disagreement about more distant events. [ABSTRACT FROM AUTHOR]

Abstract Background In medical device validation and verification studies, the area under the receiver operating characteristic curve (AUROC) is often used as a primary endpoint despite multiple reports showing its limitations. Hence, researchers are encouraged to consider alternative metrics as primary endpoints. A new metric called G4 is presented, which is the geometric mean of sensitivity, specificity, the positive predictive value, and the negative predictive value. G4 is part of a balanced metric family which includes the Unified Performance Measure (also known as P4) and the Matthews’ Correlation Coefficient (MCC). The purpose of this manuscript is to unveil the benefits of using G4 together with the balanced metric family when analyzing the overall performance of binary classifiers. Results Simulated datasets encompassing different prevalence rates of the minority class were analyzed under a multi-reader-multi-case study design. In addition, data from an independently published study that tested the performance of a unique ultrasound artificial intelligence algorithm in the context of breast cancer detection was also considered. Within each dataset, AUROC was reported alongside the balanced metric family for comparison. When the dataset prevalence and bias of the minority class approached 50%, all three balanced metrics provided equivalent interpretations of an AI’s performance. As the prevalence rate increased / decreased and the data became more imbalanced, AUROC tended to overvalue / undervalue the true classifier performance, while the balanced metric family was resistant to such imbalance. Under certain circumstances where data imbalance was strong (minority-class prevalence

Abstract Background Cis-regulatory elements (CREs) are crucial for regulating gene expression, and G-quadruplexes (G4s), as prototypal non-canonical DNA structures, may play a role in this regulation. However, the relationship between G4s and CREs, especially with non-promoter-like functional elements, requires further systematic investigation. We aimed to investigate the associations between G4s and human cCREs (candidate CREs) inferred from the Encyclopedia of DNA Elements (ENCODE) data. Results We found that G4s are prominently enriched in most types of cCREs, especially those with promoter-like signatures (PLS). The co-occurrence of CTCF signals with H3K4me3 or H3K27ac signals strengthens the association between cCREs and G4s. Genetic variants in G4s, particularly within their G-runs, exhibit higher regulatory potential and deleterious effects compared to cCREs. The G-runs within G4s near transcriptional start sites (TSSs) are more evolutionarily constrained compared to G-runs in cCREs, while those far from the TSS are relatively less conserved. The presence of G4s is often linked to a more favorable local chromatin environment for the activation and execution of regulatory function of cCREs, potentially attributable to the formation of G4 secondary structures. Finally, we discovered that G4-associated cCREs exhibit widespread activation in a variety of cancers. Conclusions Our study suggests that G4s are integral components of human cis-regulatory elements, extending beyond their potential role in promoters. The G4 primary sequences are associated with the localization of CREs, while the G4 structures are linked to the activation of these elements. Therefore, we propose defining G4s as pivotal regulatory elements in the human genome.

Background: Cis-regulatory elements (CREs) are crucial for regulating gene expression, and G-quadruplexes (G4s), as prototypal non-canonical DNA structures, may play a role in this regulation. However, the relationship between G4s and CREs, especially with non-promoter-like functional elements, requires further systematic investigation. We aimed to investigate the associations between G4s and human cCREs (candidate CREs) inferred from the Encyclopedia of DNA Elements (ENCODE) data. Results: We found that G4s are prominently enriched in most types of cCREs, especially those with promoter-like signatures (PLS). The co-occurrence of CTCF signals with H3K4me3 or H3K27ac signals strengthens the association between cCREs and G4s. Genetic variants in G4s, particularly within their G-runs, exhibit higher regulatory potential and deleterious effects compared to cCREs. The G-runs within G4s near transcriptional start sites (TSSs) are more evolutionarily constrained compared to G-runs in cCREs, while those far from the TSS are relatively less conserved. The presence of G4s is often linked to a more favorable local chromatin environment for the activation and execution of regulatory function of cCREs, potentially attributable to the formation of G4 secondary structures. Finally, we discovered that G4-associated cCREs exhibit widespread activation in a variety of cancers. Conclusions: Our study suggests that G4s are integral components of human cis-regulatory elements, extending beyond their potential role in promoters. The G4 primary sequences are associated with the localization of CREs, while the G4 structures are linked to the activation of these elements. Therefore, we propose defining G4s as pivotal regulatory elements in the human genome. [ABSTRACT FROM AUTHOR]

G-quadruplexes (G4) are non-canonical, four-stranded, nucleic acid secondary structures formed in the guanine-rich sequences, where guanine nucleotides associate with each other via Hoogsteen hydrogen bonding. These structures are widely found near the functional regions of the mammalian genome, such as telomeres, oncogenic promoters, and replication origins, and play crucial regulatory roles in replication and transcription. Destabilization of G4 by various carcinogenic agents allows oncogene overexpression and extension of telomeric ends resulting in dysregulation of cellular growth–promoting oncogenesis. Therefore, targeting and stabilizing these G4 structures with potential ligands could aid cancer prevention and therapy. The field of G-quadruplex targeting is relatively nascent, although many articles have demonstrated the effect of G4 stabilization on oncogenic expressions; however, no previous study has provided a comprehensive analysis about the potency of a wide variety of nutraceuticals and some of their derivatives in targeting G4 and the lattice of oncogenic cell signaling cascade affected by them. In this review, we have discussed bioactive G4-stabilizing nutraceuticals, their sources, mode of action, and their influence on cellular signaling, and we believe our insight would bring new light to the current status of the field and motivate researchers to explore this relatively poorly studied arena. Schematic diagram depicting nutraceuticals' role in attenuating cancer progression [ABSTRACT FROM AUTHOR]

The present paper aims to determine what factors affect the success of participatory budgets in Polish cities and what factors affect the size of these budgets. The study covered all 66 cities with powiat rights from 2016 to 2021. A panel data model was used. The first research hypothesis states that the success of participatory budgeting depends on the economic condition of the cities implementing it. The second one states that the success of participatory budgeting depends on the characteristics of the LGUs’ residents. The first hypothesis was confirmed, while the second was partially confirmed. Analyzing four different models with different explanatory variables, it was found that the statistically significant explanatory variables were population, material situation, demographic structure measures, and residents’ economic situation.

Abstract Background G-quadruplex DNA (G4) is a non-canonical structure forming in guanine-rich regions, which play a vital role in cancer biology and are now being acknowledged in both nuclear and mitochondrial (mt) genome. However, the impact of G4-based targeted therapy on both nuclear and mt genome, affecting mt function and its underlying mechanisms remain largely unexplored. Methods The mechanisms of action and therapeutic effects of a G4-binding platinum(II) complex, Pt-ttpy, on mitochondria were conducted through a comprehensive approaches with in vitro and in vivo models, including ICP-MS for platinum measurement, PCR-based genetic analysis, western blotting (WB), confocal microscope for mt morphology study, extracellular flux analyzer, JC1 and Annexin V apoptosis assay, flow cytometry and high content microscope screening with single-cell quantification of both ROS and mt specific ROS, as well as click-chemistry for IF study of mt translation. Decipher Pt-ttpy effects on nuclear-encoded mt related genes expression were undertaken via RNA-seq, Chip-seq and CUT-RUN assays. Results Pt-ttpy, shows a highest accumulation in the mitochondria of A2780 cancer cells as compared with two other platinum(II) complexes with no/weak G4-binding properties, Pt-tpy and cisplatin. Pt-ttpy induces mtDNA deletion, copy reduction and transcription inhibition, hindering mt protein translation. Functional analysis reveals potent mt dysfunction without reactive oxygen species (ROS) induction. Mechanistic study provided first evidence that most of mt ribosome genes are highly enriched in G4 structures in their promoter regions, notably, Pt-ttpy impairs most nuclear-encoded mt ribosome genes’ transcription through dampening the recruiting of transcription initiation and elongation factors of NELFB and TAF1 to their promoter with G4-enriched sequences. In vivo studies show Pt-ttpy’s efficient anti-tumor effects, disrupting mt genome function with fewer side effects than cisplatin. Conclusion This study underscores Pt-ttpy as a G4-binding platinum(II) complex, effectively targeting cancer mitochondria through dual action on mt and nuclear G4-enriched genomes without inducing ROS, offering promise for safer and effective platinum-based G4-targeted cancer therapy. Graphical Abstract

This paper discusses some of the important insights from behavioral finance for international monetary and financial analysis. A broad approach to behavioral finance is advocated which includes analysis of the effects of uncertainty, perverse incentives, and complexity economics as well as the cognitive biases focused on in the initial contributions to behavioral finance. It offers reasons why capital mobility is often not perfect and expectations are sometimes not rational. Correctly interpreted it is not a wholesale attack on efficient market theory but rather argues that markets can behave differently at different times, being efficient sometimes and subject to destabilize or insufficiently stabilizing speculation at others and focuses on the conditions that make different types of behavior more likely. It helps provide insights into issues such as currency crisis, the effects of official intervention in foreign exchange markets, the international monetary trilemma, capital flow surges and reversals, the discipline effects of fixed exchange rates and international financial markets and why uncovered interest rate parity often does not hold.

The study investigates the impact of investor attention on stock trading by modeling the relationship between Google Search intensity and stock return with stocks listed in frontier markets in Vietnam from October 2016 to October 2021. The study has three findings. First, the study confirms the price pressure hypothesis and attention theory that Google Search intensity positively affects stock returns. Second, this study indicates that the impact of Google Search intensity on stock price is short-term. The positive effect is within the week of searching and reverses the following week, although the reverse force is not strong. Third, the relationship is more robust during COVID-19 than in the pre-pandemic period, suggesting that after a shock, more new individual investors enter the market, the impact of GSVI on stock return is more substantial.

The intricate mechanisms underlying transcription‐dependent genome instability involve G‐quadruplexes (G4) and R‐loops. This perspective elucidates the potential link between these structures and genome instability in aging. The co‐occurrence of G4 DNA and RNA–DNA hybrid structures (G‐loop) underscores a complex interplay in genome regulation and instability. Here, we hypothesize that the age‐related decline of sirtuin function leads to an increase in acetylated helicases that bind to G4 DNA and RNA–DNA hybrid structures, but are less efficient in resolving them. We propose that acetylated, less active, helicases induce persistent G‐loop structures, promoting transcription‐dependent genome instability in aging. [ABSTRACT FROM AUTHOR]

Background: G-quadruplex DNA (G4) is a non-canonical structure forming in guanine-rich regions, which play a vital role in cancer biology and are now being acknowledged in both nuclear and mitochondrial (mt) genome. However, the impact of G4-based targeted therapy on both nuclear and mt genome, affecting mt function and its underlying mechanisms remain largely unexplored. Methods: The mechanisms of action and therapeutic effects of a G4-binding platinum(II) complex, Pt-ttpy, on mitochondria were conducted through a comprehensive approaches with in vitro and in vivo models, including ICP-MS for platinum measurement, PCR-based genetic analysis, western blotting (WB), confocal microscope for mt morphology study, extracellular flux analyzer, JC1 and Annexin V apoptosis assay, flow cytometry and high content microscope screening with single-cell quantification of both ROS and mt specific ROS, as well as click-chemistry for IF study of mt translation. Decipher Pt-ttpy effects on nuclear-encoded mt related genes expression were undertaken via RNA-seq, Chip-seq and CUT-RUN assays. Results: Pt-ttpy, shows a highest accumulation in the mitochondria of A2780 cancer cells as compared with two other platinum(II) complexes with no/weak G4-binding properties, Pt-tpy and cisplatin. Pt-ttpy induces mtDNA deletion, copy reduction and transcription inhibition, hindering mt protein translation. Functional analysis reveals potent mt dysfunction without reactive oxygen species (ROS) induction. Mechanistic study provided first evidence that most of mt ribosome genes are highly enriched in G4 structures in their promoter regions, notably, Pt-ttpy impairs most nuclear-encoded mt ribosome genes' transcription through dampening the recruiting of transcription initiation and elongation factors of NELFB and TAF1 to their promoter with G4-enriched sequences. In vivo studies show Pt-ttpy's efficient anti-tumor effects, disrupting mt genome function with fewer side effects than cisplatin. Conclusion: This study underscores Pt-ttpy as a G4-binding platinum(II) complex, effectively targeting cancer mitochondria through dual action on mt and nuclear G4-enriched genomes without inducing ROS, offering promise for safer and effective platinum-based G4-targeted cancer therapy. [ABSTRACT FROM AUTHOR]

Immunoglobulin G4-related disease is an immune-mediated condition comprised of a number of various disorders sharing unique pathologic, serologic, and clinical features. Diagnosis of immunoglobulin G4-related sclerosing mastitis is challenging as the clinical and imaging findings mimic breast malignancies or other types of inflammatory mastitis. Herein, we describe a case of a female patient with a painless palpable mass in her right breast. An excisional core biopsy led to the rare diagnosis of immunoglobulin G4-related sclerosing mastitis, and the patient received steroid treatment for a month. To date, the patient has remained disease-free without any recurrence. As immunoglobulin G4-related sclerosing mastitis is a very rare disease, further studies are needed to reach conclusions about the pathogenesis, diagnosis, and treatment of this entity. [ABSTRACT FROM AUTHOR]

G-quadruplexes or G4s are non-canonical secondary structures of nucleic acids characterized by guanines arranged in stacked tetraplex arrays. Decades of research into these peculiar assemblies of DNA and RNA, fueled by the development and optimization of a vast array of techniques and assays, has resulted in a large amount of information regarding their structure, stability, localization, and biological significance in native systems. A plethora of articles have reported the roles of G-quadruplexes in multiple pathways across several species, ranging from gene expression regulation to RNA biogenesis and trafficking, DNA replication, and genome maintenance. Crucially, a large amount of experimental evidence has highlighted the roles of G-quadruplexes in cancer biology and other pathologies, pointing at these structurally unique guanine assemblies as amenable drug targets. Given the rapid expansion of this field of research, this review aims at summarizing all the relevant aspects of G-quadruplex biology by combining and discussing results from seminal works as well as more recent and cutting-edge experimental evidence. Additionally, the most common methodologies used to study G4s are presented to aid the reader in critically interpreting and integrating experimental data. [ABSTRACT FROM AUTHOR]

G-quadruplexes (G4s) are noncanonical nucleic acid structures that play significant roles in regulating various biological processes, including replication, transcription, translation, and recombination. Recent studies have identified G4s in the genomes of several viruses, such as herpes viruses, hepatitis viruses, and human coronaviruses. These structures are implicated in regulating viral transcription, replication, and virion production, influencing viral infectivity and pathogenesis. G4-stabilizing ligands, like TMPyP4, PhenDC3, and BRACO19, show potential antiviral properties by targeting and stabilizing G4 structures, inhibiting essential viral life-cycle processes. This review delves into the existing literature on G4's involvement in viral regulation, emphasizing specific G4-stabilizing ligands. While progress has been made in understanding how these ligands regulate viruses, further research is needed to elucidate the mechanisms through which G4s impact viral processes. More research is necessary to develop G4-stabilizing ligands as novel antiviral agents. The increasing body of literature underscores the importance of G4s in viral biology and the development of innovative therapeutic strategies against viral infections. Despite some ligands' known regulatory effects on viruses, a deeper comprehension of the multifaceted impact of G4s on viral processes is essential. This review advocates for intensified research to unravel the intricate relationship between G4s and viral processes, paving the way for novel antiviral treatments. [ABSTRACT FROM AUTHOR]

The role of financial experts is to provide their professional judgments with an opinion included in the financial reports after reviewing an entity's financial information, following a specific audit process. We investigate whether confirmation bias (through prior audit opinions) occurs among auditors during the audit process and decision-making, and whether experience mitigates this effect. A total of 175 non-experienced auditors run a 2x4 between-subjects experiment (experiment 1) studying how financial information (IV with two levels: negative and neutral/positive) and previous audit report (IV with four levels: absence, negative, moderately negative, and positive) might influence the issuance of the subsequent decision-making (DV). In addition, a total of 32 junior level 1 auditors (less than one year of experience), 31 junior level 2 auditors (up to 3 years of experience) and 20 senior auditors (more than 3 years of experience) run a 2 × 4 × 3 between-subjects experiment (experiment 2) analyzing if experience (IV with three levels of experience: less than one-year, between one and three years, more than three years) mitigates this effect (experiment 2). Results confirm that the previous-year audit report affect auditors' current assessment, showing that positive and negative prior opinions persuade auditors when suggesting the next one. This finding is relevant as auditors' opinions could be conditioned by prior opinions instead of their own expertise. Our evidence also suggests that professional experience mitigates this influence on auditors' assessments. Consequently, this study has relevant implications for partners, audit professionals and audit firm recruiters. A general implication is that auditor training courses should reinforce the auditor's own expertise and criteria based on the deep analysis of financial and economic data rather than on the work of previous auditors.

We analysed herding behaviour in the recent pandemic and conflict. We employed the cross-sectional dispersion of daily stock returns to estimate herding's intensity in the Saudi stock market. We conducted all analyses for the entire sample and four sub-samples. Additionally, we investigate the existence of the asymmetry in the investors' responses; whether there are differences between up and down markets and between high-volatility and low-volatility days. We found that herding did not occur in the pre-COVID-19, occurred in the during-COVID-19, disappeared in the post-COVID-19 and did not occur during the Russia–Ukraine conflict. Robustness checks confirm our finding that herding manifested in the during-COVID-19 period. Additionally, no difference exists between bearish and bullish or high-and low-volatility days, pushing aside the asymmetry in the investors' responses. This study may raise investors' awareness of their cognitive bias's influence on their decisions, improving market efficiency by increasing the rationality of investors' decisions.

The notable surge in capital flows in recent years has emerged as a key factor shaping the dynamics of international financial markets and influencing economic performance of emerging economies. Even though macroeconomic fundamentals of an economy can explain some of the patterns in international capital flows, behavioral factors also seem to be essential for positioning capital flows across countries. In this study, we aim to examine whether overall economic sentiment towards Turkish economy plays a significant role on net portfolio flows to Türkiye. To this end, we first construct a novel text-based sentiment index called ''Turkish Economic Sentiment Index (TESI)'', to capture the behavioral tendencies of international investors and media towards Türkiye. Our subsequent step integrates TESI into autoregressive distributed lag models (ARDL) alongside major pull-push determinants to assess whether market sentiment holds discernible influence on capital influx into Turkey. The results reveal that the TESI and VIX stand out as pivotal determinants influencing international portfolio flows. The TESI has a positive impact on portfolio flow dynamics, whereas the degree of global risk aversion inversely affects these flows. These findings align with the contention that a favorable sentiment can boost portfolio inflows to emerging markets. Conversely, heightened volatility expectations in global markets can prompt outflows from these economies.

G-quadruplexes or G4s are non-canonical secondary structures of nucleic acids characterized by guanines arranged in stacked tetraplex arrays. Decades of research into these peculiar assemblies of DNA and RNA, fueled by the development and optimization of a vast array of techniques and assays, has resulted in a large amount of information regarding their structure, stability, localization, and biological significance in native systems. A plethora of articles have reported the roles of G-quadruplexes in multiple pathways across several species, ranging from gene expression regulation to RNA biogenesis and trafficking, DNA replication, and genome maintenance. Crucially, a large amount of experimental evidence has highlighted the roles of G-quadruplexes in cancer biology and other pathologies, pointing at these structurally unique guanine assemblies as amenable drug targets. Given the rapid expansion of this field of research, this review aims at summarizing all the relevant aspects of G-quadruplex biology by combining and discussing results from seminal works as well as more recent and cutting-edge experimental evidence. Additionally, the most common methodologies used to study G4s are presented to aid the reader in critically interpreting and integrating experimental data.

G-quadruplexes (G4s) are noncanonical nucleic acid structures that play significant roles in regulating various biological processes, including replication, transcription, translation, and recombination. Recent studies have identified G4s in the genomes of several viruses, such as herpes viruses, hepatitis viruses, and human coronaviruses. These structures are implicated in regulating viral transcription, replication, and virion production, influencing viral infectivity and pathogenesis. G4-stabilizing ligands, like TMPyP4, PhenDC3, and BRACO19, show potential antiviral properties by targeting and stabilizing G4 structures, inhibiting essential viral life-cycle processes. This review delves into the existing literature on G4’s involvement in viral regulation, emphasizing specific G4-stabilizing ligands. While progress has been made in understanding how these ligands regulate viruses, further research is needed to elucidate the mechanisms through which G4s impact viral processes. More research is necessary to develop G4-stabilizing ligands as novel antiviral agents. The increasing body of literature underscores the importance of G4s in viral biology and the development of innovative therapeutic strategies against viral infections. Despite some ligands’ known regulatory effects on viruses, a deeper comprehension of the multifaceted impact of G4s on viral processes is essential. This review advocates for intensified research to unravel the intricate relationship between G4s and viral processes, paving the way for novel antiviral treatments.

Armadillo repeat-containing proteins (ARMCs) are a large family found throughout eukaryotes, which play prominent roles in cell adhesion, signaling and cytoskeletal regulation. The ARMC6 protein is highly conserved in primates, including humans, but to date does not have a clear function beyond initial hints of a link to cancer and telomerase activity. We report here in vitro experiments showing ARMC6 binding to DNA promoter sequences from several cancer-related genes (e.g., EGFR , VEGF and c- MYC) , and also to the telomeric RNA repeat (TERRA). ARMC6 binding activity appears to recognize G-quadruplex motifs, which are being increasingly implicated as structure-based protein binding sites in chromosome maintenance and repair. In vivo investigation of ARMC6 function revealed that when this protein is overexpressed in human cell lines, there is different expression of genes connected with oncogenic pathways and those implicated in downstream non-canonical telomerase pathways (e.g., VEGF , hTERT, c- MYC , ESM1 , MMP3). ARMC6 is already known to interact with human shelterin protein TRF2 and telomerase. The protein binds G-quadruplex structures and does so preferentially to RNA over DNA. As such, this protein may be an example of how a non-canonical nucleic acid structural motif allows mediation between gene regulation and telomeric chromatin rearrangement pathways. [Display omitted] • ARMC6 interacts with telomerase and TRF2 with the potential to regulate gene expression. • ARMC6 binds to specific DNA promoter sequences from cancer related genes in vitro. • ARMC6 recognizes specific structural motifs with preference for G-rich sequences. • ARMC6 binds G4 structures and does so preferentially to RNA over DNA. • ARMC6 overexpression influences VEGF, hTERT, EGFR, c-MYC, ESM1, MMP3 gene expression. [ABSTRACT FROM AUTHOR]

Armadillo repeat-containing proteins (ARMCs) are a large family found throughout eukaryotes, which play prominent roles in cell adhesion, signaling and cytoskeletal regulation. The ARMC6 protein is highly conserved in primates, including humans, but to date does not have a clear function beyond initial hints of a link to cancer and telomerase activity. We report here in vitro experiments showing ARMC6 binding to DNA promoter sequences from several cancer-related genes (e.g., EGFR, VEGF and c-MYC), and also to the telomeric RNA repeat (TERRA). ARMC6 binding activity appears to recognize G-quadruplex motifs, which are being increasingly implicated as structure-based protein binding sites in chromosome maintenance and repair. In vivo investigation of ARMC6 function revealed that when this protein is overexpressed in human cell lines, there is different expression of genes connected with oncogenic pathways and those implicated in downstream non-canonical telomerase pathways (e.g., VEGF, hTERT, c-MYC, ESM1, MMP3). ARMC6 is already known to interact with human shelterin protein TRF2 and telomerase. The protein binds G-quadruplex structures and does so preferentially to RNA over DNA. As such, this protein may be an example of how a non-canonical nucleic acid structural motif allows mediation between gene regulation and telomeric chromatin rearrangement pathways., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

How Polycomb repressive complex 2 (PRC2) is regulated by RNA remains an unsolved problem. Although PRC2 binds G-tracts with the potential to form RNA G-quadruplexes (rG4s), whether rG4s fold extensively in vivo and whether PRC2 binds folded or unfolded rG4 are unknown. Using the X-inactivation model in mouse embryonic stem cells, here we identify multiple folded rG4s in Xist RNA and demonstrate that PRC2 preferentially binds folded rG4s. High-affinity rG4 binding inhibits PRC2's histone methyltransferase activity, and stabilizing rG4 in vivo antagonizes H3 at lysine 27 (H3K27me3) enrichment on the inactive X chromosome. Surprisingly, mutagenizing the rG4 does not affect PRC2 recruitment but promotes its release and catalytic activation on chromatin. H3K27me3 marks are misplaced, however, and gene silencing is compromised. Xist-PRC2 complexes become entrapped in the S1 chromosome compartment, precluding the required translocation into the S2 compartment. Thus, Xist rG4 folding controls PRC2 activity, H3K27me3 enrichment, and the stepwise regulation of chromosome-wide gene silencing. [Display omitted] • RNA G-quadruplex (rG4) folding is tightly regulated and developmentally programmed • Folded rG4s avidly bind PRC2 and inhibit its histone methyltransferase activity • rG4 loss in Xist causes PRC2 hyperactivity on the inactive X chromosome • Xist-PRC2 complexes become spatially entrapped, disrupting X inactivation Lee et al. identify RNA G-quadruplexes (rG4s) in Xist RNA and demonstrate that they are developmentally specific. rG4 folding controls PRC2 activity, H3K27me3 enrichment, and the stepwise regulation of X-linked gene silencing. When the rG4 sequences are mutated in Xist, PRC2 is hyperactivated and becomes spatially entrapped, preventing the progression of X inactivation. [ABSTRACT FROM AUTHOR]

Rationale & Objective: Clinical guidelines define chronic kidney disease (CKD) as abnormalities of kidney structure or function for>3 months. Assessment of the duration criterion may be implemented in different ways, potentially impacting estimates of disease incidence or prevalence in the population, individual diagnosis, and treatment decisions, especially for more severe cases. We investigated differences in incidence and prognosis of CKD stage G4 identified by 1 of 4 algorithms., Study Design: Population-based cohort study in Alberta, Canada., Setting & Participants: Residents>18 years old with incident CKD stage G4 (eGFR 15-29mL/min/1.73m 2 ) diagnosed between April 1, 2015, and March 31, 2018, based on administrative and laboratory data., Exposure: Four outpatient eGFR-based algorithms, increasing in stringency, for defining cohorts with CKD G4 were evaluated: (1) a single test, (2) first eGFR<30mL/min/1.73m 2 and a second eGFR 15-29mL/min/1.73m 2 measured>90 days apart (2 tests), (3) ≥2 eGFR measurements of<30mL/min/1.73m 2 sustained for>90 days (qualifying period) and the last eGFR in the qualifying period of 15-29mL/min/1.73m 2 (relaxed sustained), and (4) ≥2 consecutive measurements of 15-29mL/min/1.73m 2 for>90 days (rigorous sustained)., Outcome: Time to the earliest of death, eGFR improvement (a sustained increase in eGFR to≥30mL/min/1.73m 2 for>90 days and>25% increase from the index eGFR), or kidney failure., Analytical Approach: For each of the 4 cohorts, incidence rates and event-specific cumulative incidence functions at 1 year from cohort entry were estimated., Results: The incidence rates of CKD G4 decreased as algorithms became more stringent, from 190.7 (single test) to 79.9 (rigorous sustained) per 100,000 person-years. The 2 cohorts based on sustained reductions in eGFR were of comparable size and 1-year event-specific probabilities. The 2 cohorts based on a single test and a 2-test sequence were larger and experienced higher probabilities of eGFR improvement., Limitations: A short follow-up period of 1 year and a predominantly White population., Conclusions: The use of more stringent algorithms for defining CKD G4 results in substantially lower estimates of disease incidence, the identification of a group with a lower probability of eGFR improvement, and a higher risk of kidney failure. These findings can inform implementation decisions of disease definitions in clinical reporting systems and research studies., Plain-Language Summary: Although guidelines recommend>3 months to define chronic kidney disease (CKD), the methods for defining specific stages, particularly G4 (eGFR 15-29mL/min/1.73m 2 ) when referral to nephrology services is recommended, have been implemented differently across studies and surveillance programs. We studied differences in incidence and prognosis of CKD G4 cohorts identified by 4 algorithms using administrative and outpatient laboratory databases in Alberta, Canada. We found that, compared with a single-test definition, more stringent definitions resulted in a lower disease incidence and identified a group with worse short-term kidney outcomes. These findings highlight the impact of the choice of algorithm used to define CKD G4 on disease burden estimates at the population level, on individual prognosis, and on treatment/referral decisions., (Copyright © 2023 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.)

G-quadruplex (G4) DNA or RNA poses a unique nucleic acid structure in genomic transactions. Because of the unique topology presented by G4, cells have exquisite mechanisms and pathways to metabolize G4 that arise in guanine-rich regions of the genome such as telomeres, promoter regions, ribosomal DNA, and other chromosomal elements. G4 resolvases are often represented by a class of molecular motors known as helicases that disrupt the Hoogsteen hydrogen bonds in G4 by harnessing the chemical energy of nucleoside triphosphate hydrolysis. Of special interest to researchers in the field, including us, is the human FANCJ DNA helicase that efficiently resolves G4 DNA structures. Notably, FANCJ mutations are linked to Fanconi Anemia and are prominent in breast and ovarian cancer. Since our discovery that FANCJ efficiently resolves G4 DNA structures 15 years ago, we and other labs have characterized mechanistic aspects of FANCJ-catalyzed G4 resolution and its biological importance in genomic integrity and cellular DNA replication. In addition to its G4 resolvase function, FANCJ is also a classic DNA helicase that acts on conventional duplex DNA structures, which are relevant to the enzyme's role in interstrand cross link repair, double-strand break repair via homologous recombination, and response to replication stress. Here, we describe detailed procedures for the purification of recombinant FANCJ protein and characterization of its G4 resolvase and duplex DNA helicase activity., (Copyright © 2024. Published by Elsevier Inc.)

Potential G-quadruplex forming sequences (PQS) are enriched in cancer-related genes and immunoglobulin class-switch recombination. They are prevalent in the 5'UTR of transcriptionally active genes, thereby contributing to the regulation of gene expression. We and others previously demonstrated that the PQS located in the non-template strand leads to an R-loop formation followed by a G-quadruplex (G4) formation during transcription. These structural changes increase mRNA production. Here, we present how single-molecule technique was used to observe cotranscriptional G4 and R-loop formation and to examine the impact on transcription, particularly for the initiation and elongation stages., (Copyright © 2024. Published by Elsevier Inc.)