Extracellular RNA in a single droplet of human serum reflects physiologic and disease states.

Extracellular RNAs (exRNAs) are present in human serum. It remains unclear to what extent these circulating exRNAs may reflect human physiologic and disease states. Here, we developed SILVER-seq (Small Input Liquid Volume Extracellular RNA Sequencing) to efficiently sequence both integral and fragmented exRNAs from a small droplet (5 μL to 7 μL) of liquid biopsy. We calibrated SILVER-seq in reference to other RNA sequencing methods based on milliliters of input serum and quantified droplet-to-droplet and donor-to-donor variations. We carried out SILVER-seq on more than 150 serum droplets from male and female donors ranging from 18 y to 48 y of age. SILVER-seq detected exRNAs from more than a quarter of the human genes, including small RNAs and fragments of mRNAs and long noncoding RNAs (lncRNAs). The detected exRNAs included those derived from genes with tissue (e.g., brain)-specific expression. The exRNA expression levels separated the male and female samples and were correlated with chronological age. Noncancer and breast cancer donors exhibited pronounced differences, whereas donors with or without cancer recurrence exhibited moderate differences in exRNA expression patterns. Even without using differentially expressed exRNAs as features, nearly all cancer and noncancer samples and a large portion of the recurrence and nonrecurrence samples could be correctly classified by exRNA expression values. These data suggest the potential of using exRNAs in a single droplet of serum for liquid biopsy-based diagnostics

A novel ZRS variant causes preaxial polydactyly type I by increased sonic hedgehog expression in the developing limb bud.

PurposePreaxial polydactyly (PPD) is a common congenital hand malformation classified into four subtypes (PPD I-IV). Variants in the zone of polarizing activity regulatory sequence (ZRS) within intron 5 of the LMBR1 gene are linked to most PPD types. However, the genes responsible for PPD I and the underlying mechanisms are unknown.MethodsA rare large four-generation family with isolated PPD I was subjected to genome-wide genotyping and sequence analysis. In vitro and in vivo functional studies were performed in Caco-2 cells, 293T cells, and a knockin transgenic mouse model.ResultsA novel g.101779T>A (reference sequence: NG_009240.2; position 446 of the ZRS) variant segregates with all PPD I-affected individuals. The knockin mouse with this ZRS variant exhibited PPD I phenotype accompanying ectopic and excess expression of Shh. We confirmed that HnRNP K can bind the ZRS and SHH promoters. The ZRS mutant enhanced the binding affinity for HnRNP K and upregulated SHH expression.ConclusionOur results identify the first PPD I disease-causing variant. The variant leading to PPD I may be associated with enhancing SHH expression mediated by HnRNP K. This study adds to the ZRS-associated syndromes classification system for PPD and clarifies the underlying molecular mechanisms

NLRP3 Inflammasome Activation-Mediated Pyroptosis Aggravates Myocardial Ischemia/Reperfusion Injury in Diabetic Rats

The reactive oxygen species- (ROS-) induced nod-like receptor protein-3 (NLRP3) inflammasome triggers sterile inflammatory responses and pyroptosis, which is a proinflammatory form of programmed cell death initiated by the activation of inflammatory caspases. NLRP3 inflammasome activation plays an important role in myocardial ischemia/reperfusion (MI/R) injury. Our present study investigated whether diabetes aggravated MI/R injury through NLRP3 inflammasome-mediated pyroptosis. Type 1 diabetic rat model was established by intraperitoneal injection of streptozotocin (60 mg/kg). MI/R was induced by ligating the left anterior descending artery (LAD) for 30 minutes followed by 2 h reperfusion. H9C2 cardiomyocytes were exposed to high glucose (HG, 30 mM) conditions and hypoxia/reoxygenation (H/R) stimulation. The myocardial infarct size, CK-MB, and LDH release in the diabetic rats subjected to MI/R were significantly higher than those in the nondiabetic rats, accompanied with increased NLRP3 inflammasome activation and increased pyroptosis. Inhibition of inflammasome activation with BAY11-7082 significantly decreased the MI/R injury. In vitro studies showed similar effects, as BAY11-7082 or the ROS scavenger N-acetylcysteine, attenuated HG and H/R-induced H9C2 cell injury. In conclusion, hyperglycaemia-induced NLRP3 inflammasome activation may be a ROS-dependent process in pyroptotic cell death, and NLRP3 inflammasome-induced pyroptosis aggravates MI/R injury in diabetic rats

Resilience of infaunal ecosystems during the Early Triassic greenhouse Earth

The Permian-Triassic mass extinction severely depleted biodiversity, primarily observed in the body fossil of well-skeletonized animals. Understanding how whole ecosystems were affected and rebuilt following the crisis requires evidence from both skeletonized and soft-bodied animals; the best comprehensive information on soft-bodied animals comes from ichnofossils. We analyzed abundant trace fossils from 26 sections across the Permian-Triassic boundary in China and report key metrics of ichnodiversity, ichnodisparity, ecospace utilization, and ecosystem engineering. We find that infaunal ecologic structure was well established in the early Smithian. Decoupling of diversity between deposit feeders and suspension feeders in carbonate ramp-platform settings implies that an effect of trophic group amensalism could have delayed the recovery of nonmotile, suspension-feeding epifauna in the Early Triassic. This differential reaction of infaunal ecosystems to variable environmental controls thus played a substantial but heretofore little appreciated evolutionary and ecologic role in the overall recovery in the hot Early Triassic ocean

Comprehensive scientometrics and visualization study profiles lymphoma metabolism and identifies its significant research signatures

BackgroundThere is a wealth of poorly utilized unstructured data on lymphoma metabolism, and scientometrics and visualization study could serve as a robust tool to address this issue. Hence, it was implemented.MethodsAfter strict quality control, numerous data regarding the lymphoma metabolism were mined, quantified, cleaned, fused, and visualized from documents (n = 2925) limited from 2013 to 2022 using R packages, VOSviewer, and GraphPad Prism.ResultsThe linear fitting analysis generated functions predicting the annual publication number (y = 31.685x - 63628, R² = 0.93614, Prediction in 2027: 598) and citation number (y = 1363.7x - 2746019, R² = 0.94956, Prediction in 2027: 18201). In the last decade, the most academically performing author, journal, country, and affiliation were Meignan Michel (n = 35), European Journal of Nuclear Medicine and Molecular Imaging (n = 1653), USA (n = 3114), and University of Pennsylvania (n = 86), respectively. The hierarchical clustering based on unsupervised learning further divided research signatures into five clusters, including the basic study cluster (Cluster 1, Total Link Strength [TLS] = 1670, Total Occurrence [TO] = 832) and clinical study cluster (Cluster 3, TLS = 3496, TO = 1328). The timeline distribution indicated that radiomics and artificial intelligence (Cluster 4, Average Publication Year = 2019.39 ± 0.21) is a relatively new research cluster, and more endeavors deserve. Research signature burst and linear regression analysis further confirmed the findings above and revealed additional important results, such as tumor microenvironment (a = 0.6848, R² = 0.5194, p = 0.019) and immunotherapy (a = 1.036, R² = 0.6687, p = 0.004). More interestingly, by performing a “Walktrap” algorithm, the community map indicated that the “apoptosis, metabolism, chemotherapy” (Centrality = 12, Density = 6), “lymphoma, pet/ct, prognosis” (Centrality = 11, Density = 1), and “genotoxicity, mutagenicity” (Centrality = 9, Density = 4) are crucial but still under-explored, illustrating the potentiality of these research signatures in the field of the lymphoma metabolism.ConclusionThis study comprehensively mines valuable information and offers significant predictions about lymphoma metabolism for its clinical and experimental practice

Black Holes as the source of the dark energy: a stringent test with the high-redshift JWST AGNs

It has been suggested that there is evidence for cosmological coupling of black holes (BHs) with an index of $k\approx 3$ and hence the BHs serve as the astrophysical source of the dark energy. The data sample however is limited for the redshifts $\leq 2.5$. Recently, the James Webb Space Telescope (JWST) has detected more than 180 high-redshift Active Galactic Nuclei (AGNs) and quasars. Among the JWST NIRSpec/NIRCam resolved AGNs, three are identified in early-type host galaxies with a redshift $z\sim 4.5-7$. Their $M_{\star}$ and $M_{\rm BH}$, however, are in tension with the prediction of the cosmological coupling of black holes with $k=3$ at a confidence level of $\sim 3\sigma$, which is not in support of the hypothesis that BHs serve as the origin of dark energy. The future observations of high-redshift AGNs by JWST will further test such a hypothesis by identifying more early-type host galaxies in the higher mass range.Comment: 9 pages, 3 figures, 1 table; Submitted to ApJL. Comments are welcome

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Reproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs). In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values. We recommend the use of FC ranking plus a non-stringent P cutoff as a baseline practice in order to generate more reproducible DEG lists. The FC criterion enhances reproducibility while the P criterion balances sensitivity and specificity