Canonical Factor Research Articles

Body weight variability as a predictor of cardiovascular outcomes in type 1 diabetes: A nationwide cohort study.

Intraindividual body weight variability (BWV), that is, the degree of weight fluctuations over time, is associated with an increased risk of cardiovascular diseases (CVDs) in multiple settings. The impact of BWV on cardiovascular risk in type 1 diabetes (T1D) remains unclear, despite the issues relative to weight management in individuals with this condition. Using data from the Swedish National Diabetes Register, we identified individuals with T1D and without CVD at baseline with at least three measurements of body weight taken over three consecutive years. We estimated BWV as quartiles of the standard deviation of weight measures and explored its longitudinal association with the incidence of CVD during a 12.7 ± 4.6 year follow-up through adjusted Cox regression models. The primary endpoint was the composite of nonfatal myocardial infarction, nonfatal stroke and all-cause mortality. We modelled the function of risk in relation to the magnitude of BWV, testing also whether weight trends, that is, increasing, stable or decreasing, age, sex and glycaemic control modified the association between BWV and the outcome. Among the 36 333 individuals with T1D in the register, we identified 19 373 individuals with at least three measures of body weight and without CVD at baseline. Participants with the highest BWV had a 42% increased risk of reaching the primary endpoint compared to those with the lowest BWV (hazard ratio [HR] = 1.42, 95% confidence interval [CI]: 1.24-1.62). In addition, high BWV was significantly associated with a 51% increased risk of all-cause mortality (HR = 1.51, 95% CI: 1.28-1.78), a 37% increased risk of peripheral artery disease (HR = 1.37, 95% CI: 1.06-1.77) and a 55% increased risk of hospitalization for heart failure (HR = 1.55, 95% CI: 1.20-2.01). BWV showed a quasi-linear association with the primary endpoint. No interaction was observed when comparing subgroups for weight trends, sex or degree of glycaemic control. In the subgroup of elderly individuals, the association of BWV with the primary endpoint was no longer significant. High BWV is associated with an increased risk of CVD and all-cause mortality in individuals with T1D, independently of canonical risk factors. Weight trends, sex and glycaemic control do not modify such association while older age attenuates it.

VHL missense mutation delineate aggressive clear cell renal cell carcinoma subtype with favorable immunotherapeutic response

Backgroundvon Hippel-Lindau (VHL) harbors the highest mutational frequency in clear cell renal cell carcinoma (ccRCC). Although VHL mutational subtypes exert diverse impacts on the functionality of the VHL protein, the...

SHP-1 alleviates acute liver injury caused by Escherichia coli sepsis through negatively regulating the canonical and non-canonical NFκB signaling pathways

SHP-1, as a protein tyrosine phosphatase, plays a key role in inflammation-related diseases. However, its function and regulatory mechanism in the imbalance of inflammatory response and acute liver injury during sepsis are still unknown. Herein, we constructed a murine model of Escherichia coli (E. coli) sepsis and demonstrated the function and novel mechanism of SHP-1 in sepsis. Overexpression of SHP-1 significantly reduced the mortality rate of mice and alleviated the histopathological deterioration of liver. In addition, it inhibited the expression and release of pro-inflammatory mediators in liver tissue and serum, but upregulated the expression of anti-inflammatory molecules. Silencing SHP-1 exhibited the completely opposite effects. Furthermore, the transcriptome data of mice liver showed that SHP-1 suppressed the progression of sepsis by negatively regulating the activation of multiple inflammation-related signaling pathways. More importantly, we fully revealed the regulation mechanism of SHP-1 on both canonical and non-canonical nuclear factor kappa-B (NFκB) signaling pathways during sepsis for the first time. SHP-1 significantly inhibited the phosphorylation and nuclear translocation of p50, while p65 inhibition was mainly achieved by inhibiting its transcription and translation levels. Meanwhile, SHP-1 inhibited the phosphorylation and nuclear translocation of p52, thereby inhibiting the activation of non-canonical NFκB signaling pathways. In summary, SHP-1 negatively regulated canonical and non-canonical NFκB signaling pathways, thereby blocking the occurrence of excessive inflammatory response and acute liver injury caused by E. coli sepsis. Our findings systematically elucidate the role and mechanism of SHP-1 during sepsis, providing new insights into the prevention and treatment of inflammation and immune-related diseases.

Benchmarking multiblock methods with canonical factorization

Data measured on the same observations and organized in blocks of variables — from different measurement sources or deduced from topics specified by the user — are common in practice. Multiblock exploratory methods are useful tools to extract information from data in a reduced and interpretable common space. However, many methods have been proposed independently and the users are often lost in selecting the appropriate one, especially as they do not always lead to the same results or because outputs do not have the same form. For this purpose, the data decomposition by canonical factorization was introduced thus applied to some widely-used methods, CPCA, MCOA, MFA, STATIS and CCSWA. The methods were compared on simulated (resp. real) data whose structure is controlled (resp. known). Theoretical and practical results pinpoint that the block-structure must be carefully explored beforehand. The number of block-variables and the block-variance distribution along dimensions impacts the choice of the block-scaling. The observation-structure within and between blocks impacts the choice of the method. CPCA or MCOA mix common and specific information, STATIS highlights common structure only whereas CCSWA focuses on specific information. To enable these diagnoses, methods and proposed comparison tools are available on R, Matlab or Galaxy.

Pattern recognition-based aptasensor array for discrimination of matrix effect

Nucleic acid aptamers have attracted considerable attention in recent years, particularly in the fields of disease diagnosis and treatment and biosensing. However, complex matrix effects have severely hindered their progress towards practical application. In this study, the novel strategy of a pattern recognition-based aptasensor array was introduced for target recognition based on the predictable selectivity capability of aptamers by circumventing the challenge of the interference of the matrix effect. As one proof of concept, we chose lactoferrin as the target protein, three selected aptamers with differential affinity as its recognition probes, eleven matrix samples of milk powder as the pattern discrimination model, and AuNPs color as the response signals. In the AuNPs colorimetric arrays, the lactoferrin-added milk powder matrix induced different degrees of protection on the surface of AuNPs particles due to different degrees of binding of lactoferrin to the three aptamer sequences and therefore exhibited differentiated red-to-blue color change along with salt-induced aggregation behaviors. The difference in color responses exhibited with and without lactoferrin addition was considered as the fingerprint pattern of the lactoferrin in each milk powder matrix, followed by the supervised machine learning analysis of linear discriminant analysis (LDA) for better orthogonality to complete the identification and prediction of the unknown samples. By this strategy, eleven kinds of milk powder at the added concentration of lactoferrin (50 nmol/L) presented a distinct response pattern and have been identified and classified with accuracies of 100 % via LDA patterns (three aptamers × eleven milk powder matrices × five replicates) with three canonical factors (91.2 %, 8.58 %, and 0.22 %). Furthermore, the accuracy of 22 unknown samples was 100 %, indicating the achievement in differentiating between different milk powder matrices and the identification of each matrix. The proposed aptasensor array complements the traditional “lock-and-key” single aptasensor and opens a new direction for developing sensitive sensing array systems circumventing complex matrix effects.

An effective criterion for a stable factorisation of strictly non-singular 2 × 2 matrix functions: use of the ExactMPF package

In this paper, we propose a method to factorise arbitrary strictly non-singular 2 × 2 matrix functions, allowing for stable factorisation. For this purpose, we use the E x a c t M P F package working within the Maple environment previously developed by the authors and perform an exact factorisation of a non-singular polynomial matrix function. A crucial point in the present analysis is the evaluation of a stability region of the canonical factorisation of the polynomial matrix functions. This, in turn, allows us to propose a sufficient condition for the given matrix function admitting stable factorisation.

A germline PAF1 paralog complex ensures cell type-specific gene expression.

Animal germline development and fertility rely on paralogs of general transcription factors that recruit RNA polymerase II to ensure cell type-specific gene expression. It remains unclear whether gene expression processes downstream from such paralog-based transcription is distinct from that of canonical RNA polymerase II genes. In Drosophila, the testis-specific TBP-associated factors (tTAFs) activate over a thousand spermatocyte-specific gene promoters to enable meiosis and germ cell differentiation. Here, we show that efficient termination of tTAF-activated transcription relies on testis-specific paralogs of canonical polymerase-associated factor 1 complex (PAF1C) proteins, which form a testis-specific PAF1C (tPAF). Consequently, tPAF mutants show aberrant expression of hundreds of downstream genes due to read-in transcription. Furthermore, tPAF facilitates expression of Y-linked male fertility factor genes and thus serves to maintain spermatocyte-specific gene expression. Consistently, tPAF is required for the segregation of meiotic chromosomes and male fertility. Supported by comparative in vivo protein interaction assays, we provide a mechanistic model for the functional divergence of tPAF and the PAF1C and identify transcription termination as a developmentally regulated process required for germline-specific gene expression.

Abstract C016: Pancreatitis-induced resistance to KRAS targeted therapy: The role of cellular plasticity and underlying mechanisms

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease characterized by cell plasticity, particularly the epithelial-to-mesenchymal transition (EMT) phenotype, which significantly contributes to both pancreatic tumorigenesis and therapy resistance. Chronic pancreatitis, a key risk factor for PDAC, induces fibrosis, recruits macrophages, and elevates TGFβ, an EMT master regulator, in the tumor microenvironment (TME). Despite the observed negative correlation between dependence on oncogenic KRAS signaling and the quasi- mesenchymal (QM) subtype, the role of cellular plasticity and the underlying mechanisms of resistance remain unclear. To address this, we employed genetically engineered mouse models that mimic human pancreatitis and PDAC, alongside an in vitro 3-D tumor spheroid culture system. Our study demonstrates that chronic pancreatitis promotes resistance to KRAS- targeted therapy through a canonical TGFβ signaling pathway-dependent mechanism. Nuclear Factor of Activated T Cells 5 (NFAT5) forms a hetero-pentamer with canonical TGFβ factors SMAD3 and SMAD4, inducing EMT and promoting therapy resistance. Analysis of human samples indicates a positive correlation between NFAT5 expression and pancreatic tumorigenesis, with elevated NFAT5 expression correlating with poorer overall survival in the TCGA PDAC dataset. Functional studies reveal that genetic depletion or chemical inhibition of NFAT5 thwarts resistance to KRAS inhibition induced by TGFβ or pancreatitis, impairs the growth of QM-like escaper tumors, and synergizes with KRAS inhibitors to further suppress tumor growth in pre-clinical models. Mechanistically, we identified the chaperone protein and extracellular matrix regulator S100A4 as a key effector transcriptionally activated by the NFAT5- SMAD complex, mediating therapy resistance partially through the activation of key KRAS downstream MAPK and AKT signaling pathways. Furthermore, our investigation reveals that TGFβ stimulates PDAC cells to secrete the chemokine CCL2, which recruits circulating macrophages. In turn, these macrophages support PDAC cells in bypassing KRAS inhibition through paracrine TGFβ and S100A4. Overall, this study establishes a molecular foundation for KRAS-targeted therapy resistance associated with cellular plasticity in PDAC, highlighting pancreatitis as a potential risk factor, and proposes a novel strategy to overcome this resistance through NFAT5 inhibition or S100A4 blockade. Citation Format: Daiyong Deng, Pingping Hou. Pancreatitis-induced resistance to KRAS targeted therapy: The role of cellular plasticity and underlying mechanisms [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C016.

Regulation of outer kinetochore assembly during meiosis I and II by CENP-A and KNL-2/M18BP1 in C. elegans oocytes

During cell division, chromosomes build kinetochores that attach to spindle microtubules. Kinetochores usually form at the centromeres, which contain CENP-A nucleosomes. The outer kinetochore, which is the core attachment site for microtubules, is composed of the KMN network (Knl1c, Mis12c, and Ndc80c complexes) and is recruited downstream of CENP-A and its partner CENP-C. In C.elegans oocytes, kinetochores have been suggested to form independently of CENP-A nucleosomes. Yet kinetochore formation requires CENP-C, which acts in parallel to the nucleoporin MEL-28ELYS. Here, we used a combination of RNAi and Degron-based depletion of CENP-A (or downstream CENP-C) to demonstrate that both proteins are in fact responsible for a portion of outer kinetochore assembly during meiosis I and are essential for accurate chromosome segregation. The remaining part requires the coordinated action of KNL-2 (ortholog of human M18BP1) and of the nucleoporin MEL-28ELYS. Accordingly, co-depletion of CENP-A (or CENP-C) and KNL-2M18BP1 (or MEL-28ELYS) prevented outer kinetochore assembly in oocytes during meiosis I. We further found that KNL-2M18BP1 and MEL-28ELYS are interdependent for kinetochore localization. Using engineered mutants, we demonstrated that KNL-2M18BP1 recruits MEL-28ELYS at meiotic kinetochores through a specific N-terminal domain, independently of its canonical CENP-A loading factor activity. Finally, we found that meiosis II outer kinetochore assembly was solely dependent on the canonical CENP-A/CENP-C pathway. Thus, like in most cells, outer kinetochore assembly in C.elegans oocytes depends on centromeric chromatin. However, during meiosis I, an additional KNL-2M18BP1 and MEL-28ELYS pathway acts in a non-redundant manner and in parallel to canonical centromeric chromatin.

Inhibition of bromodomain and extra-terminal proteins targets constitutively active NFκB and STAT signaling in lymphoma and influences the expression of the antiapoptotic proteins BCL2A1 and c-MYC

The antiapoptotic protein BCL2A1 is highly, but very heterogeneously expressed in Diffuse Large B-cell Lymphoma (DLBCL). Particularly in the context of resistance to current therapies, BCL2A1 appears to play an important role in protecting cancer cells from the induction of cell death. Reducing BCL2A1 levels may have therapeutic potential, however, no specific inhibitor is currently available. In this study, we hypothesized that the signaling network regulated by epigenetic readers may regulate the transcription of BCL2A1 and hence that inhibition of Bromodomain and Extra-Terminal (BET) proteins may reduce BCL2A1 expression thus leading to cell death in DLBCL cell lines. We found that the mechanisms of action of acetyl-lysine competitive BET inhibitors are different from those of proteolysis targeting chimeras (PROTACs) that induce the degradation of BET proteins. Both classes of BETi reduced the expression of BCL2A1 which coincided with a marked downregulation of c-MYC. Mechanistically, BET inhibition attenuated the constitutively active canonical nuclear factor kappa-light-chain-enhancer of activated B-cells (NFκB) signaling pathway and inhibited p65 activation. Furthermore, signal transducer of activated transcription (STAT) signaling was reduced by inhibiting BET proteins, targeting another pathway that is often constitutively active in DLBCL. Both pathways were also inhibited by the IκB kinase inhibitor TPCA-1, resulting in decreased BCL2A1 and c-MYC expression. Taken together, our study highlights a novel complex regulatory network that links BET proteins to both NFκB and STAT survival signaling pathways controlling both BCL2A1 and c-MYC expression in DLBCL.Graphical

Looking back: Selected contributions by C. R. Rao to multivariate analysis

AbstractStatistician C. R. Rao made many contributions to multivariate analysis over the span of his career. Some of his earliest contributions continue to be used and built upon almost 80 years later, while his more recent contributions spur new avenues of research. The present article discusses these contributions, how they helped shape multivariate analysis as we see it today, and what we may learn from reviewing his works. Topics include his extension of linear discriminant analysis, Rao's perimeter test, Rao's U statistic, his asymptotic expansion of Wilks' statistic, canonical factor analysis, functional principal component analysis, redundancy analysis, canonical coordinates, and correspondence analysis. The examination of his works shows that interdisciplinary collaboration and the utilization of real datasets were crucial in almost all of Rao's impactful contributions.

Phosphoproteomic analysis of the response to DNA damage in Trypanosoma brucei

Damage to the genetic material of the cell poses a universal threat to all forms of life. The DNA damage response is a coordinated cellular response to a DNA break, key to which is the phosphorylation signaling cascade. Identifying which proteins are phosphorylated is therefore crucial to understanding the mechanisms that underlie it. We have used stable isotopic labeling of amino acids in cell culture-based quantitative phosphoproteomics to profile changes in phosphorylation site abundance following double stranded DNA breaks, at two distinct loci in the genome of the single cell eukaryote Trypanosoma brucei. Here, we report on the T.brucei phosphoproteome following a single double-strand break at either a chromosome internal or subtelomeric locus, specifically the bloodstream form expression site. We detected >6500 phosphorylation sites, of which 211 form a core set of double-strand break responsive phosphorylation sites. Along with phosphorylation of canonical DNA damage factors, we have identified two novel phosphorylation events on histone H2A and found that in response to a chromosome internal break, proteins are predominantly phosphorylated, while a greater proportion of proteins dephosphorylated following a DNA break at a subtelomeric bloodstream form expression site. Our data represent the first DNA damage phosphoproteome and provides novel insights into repair at distinct chromosomal contexts in T.brucei.

60 Dissecting the Cellular and Epigenetic Landscape of Clear Cell Renal Cell Carcinoma Through Paired snRNA/ATAC-Seq Analysis

Abstract Background Clear cell renal cell carcinoma (ccRCC) stands as one of the most prevalent and aggressive forms of renal malignancies, accounting for a substantial portion of kidney cancer-related mortality worldwide. The heterogeneity within ccRCC poses a significant challenge to understanding its molecular mechanisms and devising effective therapeutic strategies. [1] Previous studies utilizing single nucleus RNA sequencing (snRNA-seq) have revealed transcriptional contributions to cell-type specificity in both mature human and mouse kidneys. Moreover, recent advancements have expanded this approach to single-cell profiling of chromatin accessibility. Single-nuclei assay for transposase-accessible chromatin using sequencing (snATAC-seq) has enabled the measurement of chromatin accessibility in thousands of individual cells, providing insights into the dynamic process that drives nephron development and differentiation. Integration and analysis of multimodal single-cell datasets, such as snRNA-seq and snATAC-seq, allows for the prediction of cell-type-specific cis-regulatory DNA interactions and transcription factor activity, complementing the transcriptional information obtained by snRNA-seq.[2] [3] [1] Yang, Wang, and Yang, “Treatment Strategies for Clear Cell Renal Cell Carcinoma.” [2] Muto et al., “Single Cell Transcriptional and Chromatin Accessibility Profiling Redefine Cellular Heterogeneity in the Adult Human Kidney.” [3] Monteagudo-Sánchez, Noordermeer, and Greenberg, “The Impact of DNA Methylation on CTCF-Mediated 3D Genome Organization.” Methods This study leveraged paired snRNA/ATAC-seq in tumor and normal-adjacent samples from the Renal Tumor Biobank at Dartmouth (n= 63) to explore the ccRCC landscape at single-cell resolution using 10x multiome technology. The snRNA-seq dataset was processed with Seurat v5.0 to remove low-quality nuclei. Doublets were removed with DoubletFinder v2.02, and ambient DNA was removed using decontX from celda. Normalization was conducted via SCTransform, and missing data was imputed with ALRA. Clustering was performed by constructing a KNN graph and running the Louvain algorithm. Cell type assignments were predicted using Azimuth with the human kidney reference dataset. The snATAC-seq data was processed with ArchR v1.0.1, which performed dimensionality reduction and clustering. Cluster identities defined in the Seurat workflow were cross-annotated to the ATAT-seq data, and open peaks were identified within these cell-type clusters using MACS3 v3.0.1. Identification of marker peaks, motif enrichment, and motif enrichment deviations were inferred utilizing ArchR’s getmarkerFeatures, peakAnnoEnrichment, and addMotifAnnotations functions, respectively. Results Motif enrichment analysis revealed canonical cancer-associated transcription factor (TF) dysregulation in tumor cells (nephron loop-like), including enrichment of HNF1B, SMARCC1, FOSL1, and JUND. Interestingly, HNF and SMARCC were also enriched in the lymphoid compartment, indicating possible crosstalk between these two cell types. Previous work has investigated the involvement of the HNF1 in ccRCC and in chromophobe RCC for prognosis,and we plan on investigating the relationship of these enrichments to tumor grade, stage and outcome.[1] Additional TF enrichments included BCL families and ELF within the myeloid compartment, and vascularization related TF families in endothelial cell types including enrichment of various ETS TFs. Investigation of cell-cell interactions between immune and endothelial cell populations as well as between tumor and normal adjacent tissues will be performed to further disentangle the role differentially accessable chromatin plays in ccRCC. [1] Buchner et al., “Downregulation of HNF-1B in Renal Cell Carcinoma Is Associated With Tumor Progression and Poor Prognosis.” Conclusions Our multi-omic approach has several advantages. First, it enables the characterization of cellular heterogeneity within the tumor microenvironment, identifying cell populations and their contributions to disease progression. Secondly, by integrating transcriptomic and epigenomic data, we gain insights into the dynamic interplay between gene expression and chromatin accessibility, uncovering potential therapeutic vulnerabilities and biomarkers for personalized treatment strategies. DOD CDMRP Funding: yes

Exportin-5 binding precedes 5′- and 3′-end processing of tRNA precursors in Drosophila

Exportin5 (Exp5) is the major microRNA (miRNA) nuclear export factor and recognizes structural features of pre-miRNA hairpins, while it also exports other minihelix-containing RNAs. In Drosophila, Exp5 is suggested to play a major role in tRNA export because the gene encoding the canonical tRNA export factor Exportin-t is missing in its genome. To understand molecular functions of fly Exp5, we studied the Exp5/RNA interactome in the cell line S2R+ using the CLIP (crosslinking and immunoprecipitation) technology. The CLIP experiment captured known substrates such as tRNAs and miRNAs, and detected candidates of novel Exp5 substrates including various mRNAs and long non-coding RNAs (lncRNAs). Some mRNAs and lncRNAs enriched PAR-CLIP tags compared to their expression levels, suggesting selective binding of Exp5 to them. Intronless mRNAs tended to enrich PAR-CLIP tags, therefore we proposed that Exp5 might play a role in export of specific classes of mRNAs/lncRNAs. This result suggested that Drosophila Exp5 might have a wider variety of substrates than initially thought. Surprisingly, Exp5 CLIP reads often contained sequences corresponding to the flanking 5’-leaders and 3’-trailers of tRNAs, which were thought to be removed prior to nuclear export. In fact, we found pre-tRNAs before end-processing were present in the cytoplasm, supporting the idea that tRNA end-processing is a cytoplasmic event. In summary, our results provide a genome-wide list of Exp5 substrate candidates, and suggest that flies may lack a mechanism to distinguish pre-tRNAs with or without the flanking sequences.

Unorientable topological gravity and orthogonal random matrix universality

The duality of Jackiw-Teitelboim (JT) gravity and a double scaled matrix integral has led to studies of the canonical spectral form factor (SFF) in the so called τ−scaled limit of large times, t → ∞, and fixed temperature, in order to demonstrate agreement with universal random matrix theory (RMT). Though this has been established for the unitary case, extensions to other symmetry classes requires the inclusion of unorientable manifolds in the sum over geometries, necessary to address time reversal invariance, and regularization of the corresponding prime geometrical objects, the Weil-Petersson (WP) volumes. We report here how universal signatures of quantum chaos, witnessed by the fidelity to the Gaussian orthogonal ensemble, emerge for the low-energy limit of unorientable JT gravity, i.e. the unorientable Airy model/topological gravity. To this end, we implement the loop equations for the corresponding dual (double-scaled) matrix model and find the generic form of the unorientable Airy WP volumes, supported by calculations using unorientable Kontsevich graphs. In an apparent violation of the gravity/chaos duality, the τ−scaled SFF on the gravity side acquires both logarithmic and power law contributions in t, not manifestly present on the RMT side. We show the expressions can be made to agree by means of bootstrapping-like relations hidden in the asymptotic expansions of generalized hypergeometric functions. Thus, we are able to establish strong evidence of the quantum chaotic nature of unorientable topological gravity.

HIF-1 inactivation empowers HIF-2 to drive hypoxia adaptation in aggressive forms of medulloblastoma

Medulloblastoma (MB) is the most prevalent brain cancer in children. Four subgroups of MB have been identified; of these, Group 3 is the most metastatic. Its genetics and biology remain less clear than the other groups, and it has a poor prognosis and few effective treatments available. Tumor hypoxia and the resulting metabolism are known to be important in the growth and survival of tumors but, to date, have been only minimally explored in MB. Here we show that Group 3 MB tumors do not depend on the canonical transcription factor hypoxia-inducible factor-1α (HIF-1α) to mount an adaptive response to hypoxia. We discovered that HIF-1α is rendered inactive either through post-translational methylation, preventing its nuclear localization specifically in Group 3 MB, or by a low expression that prevents modulation of HIF-target genes. Strikingly, we found that HIF-2 takes over the role of HIF-1 in the nucleus and promotes the activation of hypoxia-dependent anabolic pathways. The exclusion of HIF-1 from the nucleus in Group 3 MB cells enhances the reliance on HIF-2’s transcriptional role, making it a viable target for potential anticancer strategies. By combining pharmacological inhibition of HIF-2α with the use of metformin, a mitochondrial complex I inhibitor to block respiration, we effectively induced Group 3 MB cell death, surpassing the effectiveness observed in Non-Group 3 MB cells. Overall, the unique dependence of MB cells, but not normal cells, on HIF-2-mediated anabolic metabolism presents an appealing therapeutic opportunity for treating Group 3 MB patients with minimal toxicity.

A spectrum of clinically-identified cysteine mutations in fibulin-3 (EFEMP1) highlight its disulfide bonding complexity and potential to induce stress response activation.

Fibulin-3 (FBLN3), also known as EFEMP1, is a secreted extracellular matrix (ECM) glycoprotein that contains forty cysteine residues. These cysteines, which are distributed across one atypical and five canonical calcium-binding epidermal growth factor (EGF) domains, are important for regulating FBLN3 structure, secretion, and presumably function. As evidence of this importance, a rare homozygous p.C55R mutation in FBLN3 negates its function, alters disulfide bonding, and causes marfanoid syndrome. Additional studies suggest that heterozygous premature stop codon mutations in FBLN3 may also cause similar, albeit less severe, connective tissue disorders. Interestingly, a series of twenty-four cysteine mutations in FBLN3 have been identified in the human population and published in the Clinical Variation (ClinVar) and gnomAD databases. We tested how seven of these cysteine mutants (five loss-of-cysteine variants: C42Y, C190R, C218R, C252F, and C365S, two gain-of-cysteine variants: R358C, Y369C) and two newly developed mutations (G57C and Y397C) altered FBLN3 secretion, disulfide bonding, MMP2 zymography, and stress response activation Surprisingly, we found a wide variety of biochemical behaviors: i) loss-of-cysteine variants correlated with an increased likelihood of disulfide dimer formation, ii) N-terminal mutations were less likely to disrupt secretion, and were less prone to aggregation, iii) in contrast to wild-type FBLN3, multiple, but not all variants failed to induce MMP2 levels in cell culture, and iv) C-terminal mutations (either loss or gain of cysteines) were more prone to significant secretion defects, intracellular accumulation/misfolding, and stress response activation. These results provide molecular and biochemical insight into FBLN3 folding, secretion, and function for many cysteine mutations found in the human population, some of which may increase the likelihood of subclinical connective tissue or other FBLN3-associated haploinsufficiency diseases.

Short-chain fatty acids abrogate Japanese encephalitis virus-induced inflammation in microglial cells via miR-200a-3p/ZBTB20/IKβα axis.

The gut-brain axis plays a pivotal role in the physiological state of an organism. Gut microbiota-derived metabolites are known to play a role in brain disorders including neuroviral infections. Short-chain fatty acids (SCFAs) appear to quench inflammatory markers in Japanese encephalitis virus-infected microglial cells in vitro. Mechanistically, we demonstrate the interaction between miR-200a-3p and ZBTB20 in regulating the canonical nuclear factor kappa B (NF-κB) signaling pathway via transcriptional regulation of Iκβα. Findings of this study pave the way to a better understanding of SCFA mechanisms that can be used to develop strategies against viral neuroinflammation.

DNA Methylation-derived biological age and long-term mortality risk in subjects with type 2 diabetes

BackgroundIndividuals with type 2 diabetes (T2D) face an increased mortality risk, not fully captured by canonical risk factors. Biological age estimation through DNA methylation (DNAm), i.e. the epigenetic clocks, is emerging as a possible tool to improve risk stratification for multiple outcomes. However, whether these tools predict mortality independently of canonical risk factors in subjects with T2D is unknown.MethodsAmong a cohort of 568 T2D patients followed for 16.8 years, we selected a subgroup of 50 subjects, 27 survived and 23 deceased at present, passing the quality check and balanced for all risk factors after propensity score matching. We analyzed DNAm from peripheral blood leukocytes using the Infinium Human MethylationEPIC BeadChip (Illumina) to evaluate biological aging through previously validated epigenetic clocks and assess the DNAm-estimated levels of selected inflammatory proteins and blood cell counts. We tested the associations of these estimates with mortality using two-stage residual-outcome regression analysis, creating a reference model on data from the group of survived patients. ResultsDeceased subjects had higher median epigenetic age expressed with DNAmPhenoAge algorithm (57.49 [54.72; 60.58] years. vs. 53.40 [49.73; 56.75] years; p = 0.012), and accelerated DunedinPoAm pace of aging (1.05 [1.02; 1.11] vs. 1.02 [0.98; 1.06]; p = 0.012). DNAm PhenoAge (HR 1.16, 95% CI 1.05–1.28; p = 0.004) and DunedinPoAm (HR 3.65, 95% CI 1.43–9.35; p = 0.007) showed an association with mortality independently of canonical risk factors. The epigenetic predictors of 3 chronic inflammation-related proteins, i.e. CXCL10, CXCL11 and enRAGE, C-reactive protein methylation risk score and DNAm-based estimates of exhausted CD8 + T cell counts were higher in deceased subjects when compared to survived.ConclusionsThese findings suggest that biological aging, as estimated through existing epigenetic tools, is associated with mortality risk in individuals with T2D, independently of common risk factors and that increased DNAm-surrogates of inflammatory protein levels characterize deceased T2D patients. Replication in larger cohorts is needed to assess the potential of this approach to refine mortality risk in T2D.

Early Socialization Triggered ROS-Mediated Activation of Canonical NF-κB Pathway Leading to Inflammation of Spleen in Suckling Piglets

Early socialization during lactation is advocated as a feeding strategy to reduce the weaning stress of piglets. However, early socialization has often been accompanied by more frequent aggression between individuals, and its effect on the immune system of piglets has yet to be evaluated. In this study, 89 piglets were raised separately under conventional feeding and early socialization environments. Based on differences in the aggressive behavior of the piglets in different environments during lactation, we further investigated the effects of early socialization on oxidative stress in the spleen of the piglets and the inflammatory responses involved in the canonical nuclear factor kappa-B (NF-κB) signaling pathway. The results revealed that early socialization led to a higher aggression level between individuals (p < 0.01), increased malondialdehyde (MDA) and H2O2 levels and inducible nitric oxide synthase (iNOS) activity, and inhibited glutathione (GSH) levels and the activities of catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GPX) in the piglet spleens (p < 0.05). The mRNA expression levels of the protein kinase A (PKA), inhibitor of kappa B kinase-α (IKK-α), inhibitor of kappa B kinase-β (IKK-β), inhibitor of NF-κB-α (IκB-α), NF-κB(p65), interleukin-1β (IL-1β), interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), cyclooxygenase-2 (COX2), iNOS, and heat shock protein (HSP) genes were significantly up-regulated, as well as the protein levels of P-p65, IKK-β, P-IkB-α, pro-IL-1β, and TNF-α. In summary, early socialization caused oxidative stress and inflammatory responses in the spleen of the piglets by inducing ROS production and the activation of the canonical NF-κB pathway. Our study revealed that early socialization significantly increased the ROS level in the piglet spleens and activated the canonical NF-κB signaling pathway, which induced a high expression of pro-inflammatory cytokines (TNF-α, IL-1β, IL-6, and COX2) and HSP genes regulated by NF-κB signaling, leading to oxidative stress and the inflammatory response.