ABSTRACT
Objective:To investigate the inhibitory effect and the related mechanism of Yiqi Jianpi Fang on aberrant crypt focus (ACF) in Wister rat colorectal cancer model.Methods:50 Wistar rats were randomly divided into 5 groups:TCM low dose group(TCM solution diluted 3 times,5 mL/kg daily gastric volume),TCM middle dose group (5 mL/kg daily gastric volume),TCM high dose group (15 mL/kg daily gastric volume),model group,normal group.With 10 rats in each group.The colorectal tissues were observed under microscope after methylene blue staining by immunohistochemistry method.Results:Compared with the model group,the number of ACF and large ACF in each TCM group were decreased (P＜0.05),and the number of ACF in the TCM middle dose group reduced most obvious,and the difference was statistically significant (P＜0.05).The proliferation indexs of PCNA in intestinal gland cells 24 h and 48 h after modeling in the TCM groups were higher than those in the model group,and the difference was statistically significant(P＜0.05).The apoptosis index of intestinal gland cells 24 h and 48 h after modeling in the TCM groups were higher than those in the model group,and the difference was statistically significant(P＜0.05).The ectopic expression of β-catenin in TCM groups were lower than that in the model group,and it was highest in the high dose group,than was the low dose group,and the middle group was lowest(P＜0.05).The expression of MMP-7 in TCM groups were lower than that in the model group,and it was highest in the low dose group,than was the high dose group,and the middle dose group was lowest (P＜0.05).Conclusion:Yiqi Jianpi Fang can significantly reduce the number of ACF in Wister rats,inhibit the activation of Wnt signaling in colorectal cancer,reduce the incidence of colorectal cancer,and have a certain preventive effect.
ABSTRACT
While SARS-CoV-2 continues to adapt for human infection and transmission, genetic variation outside of the spike gene remains largely unexplored. This study investigates a highly variable region at residues 203-205 in the SARS-CoV-2 nucleocapsid protein. Recreating a mutation found in the alpha and omicron variants in an early pandemic (WA-1) background, we find that the R203K+G204R mutation is sufficient to enhance replication, fitness, and pathogenesis of SARS-CoV-2. The R203K+G204R mutant corresponds with increased viral RNA and protein both in vitro and in vivo. Importantly, the R203K+G204R mutation increases nucleocapsid phosphorylation and confers resistance to inhibition of the GSK-3 kinase, providing a molecular basis for increased virus replication. Notably, analogous alanine substitutions at positions 203+204 also increase SARS-CoV-2 replication and augment phosphorylation, suggesting that infection is enhanced through ablation of the ancestral RG motif. Overall, these results demonstrate that variant mutations outside spike are key components in SARS-CoV-2s continued adaptation to human infection. Author SummarySince its emergence, SARS-CoV-2 has continued to adapt for human infection resulting in the emergence of variants with unique genetic profiles. Most studies of genetic variation have focused on spike, the target of currently available vaccines, leaving the importance of variation elsewhere understudied. Here, we characterize a highly variable motif at residues 203-205 in nucleocapsid. Recreating the prominent nucleocapsid R203K+G204R mutation in an early pandemic background, we show that this mutation is alone sufficient to enhance SARS-CoV-2 replication and pathogenesis. We also link augmentation of SARS-CoV-2 infection by the R203K+G204R mutation to its modulation of nucleocapsid phosphorylation. Finally, we characterize an analogous alanine double substitution at positions 203-204. This mutant was found to mimic R203K+G204R, suggesting augmentation of infection occurs by disrupting the ancestral sequence. Together, our findings illustrate that mutations outside of spike are key components of SARS-CoV-2s adaptation to human infection.
ABSTRACT
High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for Next-Generation Sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and requires multiple PCR reactions with non-overlapping primer pools. This imparts sensitivity to underlying SNVs and fails to resolve RNA recombination junctions that are not flanked by primer pairs. To address these limitations, we have designed an approach called Tiled-ClickSeq, which uses hundreds of tiled-primers spaced evenly along the virus genome in a single reverse-transcription reaction. The other end of the cDNA amplicon is generated by azido-nucleotides that stochastically terminate cDNA synthesis, removing the need for a paired-primer. A sequencing adaptor containing a Unique Molecular Identifier (UMI) is appended to the cDNA fragment using click-chemistry and a PCR reaction generates a final NGS library. Tiled-ClickSeq provides complete genome coverage, including the 5UTR, at high depth and specificity to the virus on both Illumina and Nanopore NGS platforms. Here, we analyze multiple SARS-CoV-2 isolates and clinical samples to simultaneously characterize minority variants, sub-genomic mRNAs (sgmRNAs), structural variants (SVs) and D-RNAs. Tiled-ClickSeq therefore provides a convenient and robust platform for SARS-CoV-2 genomics that captures the full range of RNA species in a single, simple assay.