CpG Site-Specific Methylation-Modulated Divergent Expression of PRSS3 Transcript Variants Facilitates Nongenetic Intratumor Heterogeneity in Human Hepatocellular Carcinoma.

Background: Hepatocellular carcinoma (HCC) is one of the most lethal human tumors with extensive intratumor heterogeneity (ITH). Serine protease 3 (PRSS3) is an indispensable member of the trypsin family and has been implicated in the pathogenesis of several malignancies, including HCC. However, the paradoxical effects of PRSS3 on carcinogenesis due to an unclear molecular basis impede the utilization of its biomarker potential. We hereby explored the contribution of PRSS3 transcripts to tumor functional heterogeneity by systematically dissecting the expression of four known splice variants of PRSS3 (PRSS3-SVs, V1~V4) and their functional relevance to HCC. Methods: The expression and DNA methylation of PRSS3 transcripts and their associated clinical relevance in HCC were analyzed using several publicly available datasets and validated using qPCR-based assays. Functional experiments were performed in gain- and loss-of-function cell models, in which PRSS3 transcript constructs were separately transfected after deleting PRSS3 expression by CRISPR/Cas9 editing. Results: PRSS3 was aberrantly differentially expressed toward bipolarity from very low (PRSS3Low ) to very high (PRSS3High ) expression across HCC cell lines and tissues. This was attributable to the disruption of PRSS3-SVs, in which PRSS3-V2 and/or PRSS3-V1 were dominant transcripts leading to PRSS3 expression, whereas PRSS3-V3 and -V4 were rarely or minimally expressed. The expression of PRSS3-V2 or -V1 was inversely associated with site-specific CpG methylation at the PRSS3 promoter region that distinguished HCC cells and tissues phenotypically between hypermethylated low-expression (mPRSS3-SVLow ) and hypomethylated high-expression (umPRSS3-SVHigh ) groups. PRSS3-SVs displayed distinct functions from oncogenic PRSS3-V2 to tumor-suppressive PRSS3-V1, -V3 or PRSS3-V4 in HCC cells. Clinically, aberrant expression of PRSS3-SVs was translated into divergent relevance in patients with HCC, in which significant epigenetic downregulation of PRSS3-V2 was seen in early HCC and was associated with favorable patient outcome. Conclusions: These results provide the first evidence for the transcriptional and functional characterization of PRSS3 transcripts in HCC. Aberrant expression of divergent PRSS3-SVs disrupted by site-specific CpG methylation may integrate the effects of oncogenic PRSS3-V2 and tumor-suppressive PRSS3-V1, resulting in the molecular diversity and functional plasticity of PRSS3 in HCC. Dysregulated expression of PRSS3-V2 by site-specific CpG methylation may have potential diagnostic value for patients with early HCC.

Analysis of Continuous Mutation and Evolution on Circulating SARS-CoV-2.

Monitoring the mutation and evolution of the virus is important for tracing its ongoing transmission and facilitating effective vaccine development. A total of 342 complete genomic sequences of SARS-CoV-2 were analyzed in this study. Compared to the reference genome reported in December 2019, 465 mutations were found, among which, 347 occurred in only 1 sequence, while 26 occurred in more than 5 sequences. For these 26 further identified as SNPs, 14 were closely linked and were grouped into 5 profiles. Phylogenetic analysis revealed the sequences formed 2 major groups. Most of the sequences in late period (March and April) constituted the Cluster II, while the sequences before March in this study and the reported S/L and A/B/C types in previous studies were all in Cluster I. The distributions of some mutations were specific geographically or temporally, the potential effect of which on the transmission and pathogenicity of SARS-CoV-2 deserves further evaluation and monitoring. Two mutations were found in the receptor-binding domain (RBD) but outside the receptor-binding motif (RBM), indicating that mutations may only have marginal biological effects but merit further attention. The observed novel sequence divergence is of great significance to the study of the transmission, pathogenicity, and development of an effective vaccine for SARS-CoV-2.

Electrochemical method for the quantitative determination of Escherichia coli based on gold functionalized FTO substrate.

This work presents a novel rapid and sensitive label-free electrochemical method for the detection of bacteria on surface nanostructures. A simple electrochemical deposition and calcination method is employed to prepare different gold nanostructures on FTO substrate. The sensor based on nanostructure gold exhibits excellent linear relation between E. coli DH5α bacteria and the changes of ΔRct, especially FTO-GEDC-D30, with a correction coefficient R2 = 0.998. Both the spectrophotometric (OD600 methods) and fluorescence-staining methods also verified the reliability of electrochemical impedance spectroscopy (EIS) methods for evaluating the antibacterial activity of the gold nanostructure.

Analyzing the role of soil and rice cadmium pollution on human renal dysfunction by correlation and path analysis.

The aim of this study was to investigate the role of soil and rice pollution on human renal dysfunction. The participants were 97 inhabitants (46 men and 51 women) who are aged 50 to 60 years old and have been living in Xiaogan (Hubei, China) from birth. We collected samples of soil, rice, and urinary correspondingly. Urinary N-acetyl-ß-D-glucosaminidase (NAG) and ß-2-microglobulin (ß2MG) were used as indicators of renal dysfunction, and urinary cadmium (U-Cd) was used as indicator of total internal cadmium exposure. We made a hypothesis that soil cadmium concentration (S-Cd) and rice cadmium concentration (R-Cd) could be used as indicators of environmental cadmium exposure. Correlation and path analysis were used to estimate the relationships among the levels of rice cadmium (R-Cd), soil cadmium (S-Cd), urinary cadmium (U-Cd), and renal damage indicators (NAG and ß2MG). Our results showed that there was positive significant relationship between S-Cd (R-Cd, U-Cd), and U-NAG (U-ß2MG). The standard multiple regression describing the relationship between S-Cd (R-Cd, U-Cd) and U-NAG was Y1 = 1.26X1-6.53X2 + 9.32, where Y is U-NAG, X1 is U-Cd, X2 is S-Cd. The equation of U-ß2MG was Y = 49.32X1 + 3085.99X2 + 143.42, where Y is U-ß2MG, X1 is U-Cd, X2 is R-Cd. It is obvious that the effect of S-Cd and R-Cd on NAG or U-ß2MG cannot be ignored. Through our study, we can find that the effects of S-Cd on renal health even as significant as R-Cd. To protect people from the damage of cadmium pollution, it is vital to monitor the situation of soil and rice cadmium pollution.

Non-Catalytic RISCs and Kinetics Determine Mammalian siRNA Sub-Cellular Localization.

Small interfering RNAs (siRNAs) are fundamental to the regulation of cell function. Much is known about its gene interfering mechanism, but a kinetic description of it is still lacking. Here, we derived a set of reaction-diffusion equations for multiple RNA-induced silencing complex (RISC) pathways that give quantitative temporal and spatial descriptions of the siRNA process in mammalian cell, and are able to correctly describe all salient experimentally observed patterns of sub-cellular siRNA localization, including those that, at first glance, appear irreconcilable. These results suggest siRNA sub-cellular localization mainly concerns the non-catalytic RISC-target complex, and is caused by the selectiveness of RISC-target interaction and the permeability of the nuclear membrane to siRNA strands but not to RISC-target complexes. Our method is expected to be useful in devising RNAi based cell regulation strategies.

Web resources for stem cell research.

In this short review, we have presented a brief overview on major web resources relevant to stem cell research. To facilitate more efficient use of these resources, we have provided a preliminary rating based on our own user experience of the overall quality for each resource. We plan to update the information on an annual basis.

The generation of continuous-variable entanglement frequency comb.

Continuous-variable (CV) entanglement frequency comb can be produced by enhanced Raman scattering in an above-threshold optical oscillator cavity in which a hexagonally-poled LiTaO3 crystal resides as a Raman gain medium. The Stokes and anti-Stokes Raman signals are enhanced by a coupled quasi-phase-matching optical parametric process and the entanglement natures among these Raman signals and pump are demonstrated by applying a sufficient inseparability criterion for CV entanglement. Such entanglement frequency comb source with different frequencies and continuously tunable frequency interval may be very significant for the applications in quantum communication and networks.

Minimal model for genome evolution and growth.

Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random mutation but primarily grows by random segmental duplication. That genomes grew mostly by duplication is consistent with the observation that repeat sequences in all genomes are widespread and intragenomic and intergenomic homologous genes are preponderant across all life forms.