Serum protein profiles suggest a possible link between qi deficiency constitution and Pi-qi-deficiency syndrome of chronic superficial gastritis

Objective:To identify potential serum protein candidates involved in linking the traditional Chinese medicine(TCM)-defined qi deficiency constitution(QDC)to Pi-qi-deficiency syndrome(PQDS)of chronic superficial gastritis(CSG).Methods:Using participants with the TCM-defined balanced constitution as a control population,labelfree quantitative proteomics was adopted to identify differentially expressed proteins(DEPs)in serum samples from two case populations:case population 1(participants with QDC)and case population 2(patients with PQDS of CSG).The DEPs discovered in both case populations were analyzed to identify common DEPs as potential candidates for proteins involved in the link between QDC and PQDS.Based on Kyoto Encyclopedia of Genes and Genomes pathway(KEGG)and Gene Ontology(GO)enrichment analysis and analysis of proteineprotein interaction networks,we evaluated the possible functions of these potential serum candidates.Results:We discovered 24 and 28 proteins that were differentially expressed in case populations 1 and 2,respectively,compared with the control population.Hierarchical clustering analysis showed that the expression profile of DEPs of individuals from the same population clustered well,while those from different populations were segregated.Furthermore,GO analysis revealed the 10 DEPs that were common to both case populations to be mainly associated with negative regulation of cellular metabolic and immune system processes while KEGG analysis indicated these proteins to be associated with complement and coagulation cascades and peroxisome proliferator-activated receptor signaling.Notably,serum levels of C4b-binding protein beta chain,glycosylphosphatidylinositol-specific phospholipase D1 and MS-F1 light chain variable region proteins were notably higher in the two case populations compared with the control,particularly in the case of CSG with PQDS.Conclusion:The results presented here provide new insights into the molecular mechanisms underlying development of PQDS of CSG from QDC,and suggest candidate serum biomarkers for future application in integrative medicine.

Screening for blood leukocyte microRNA biomarkers responsible for association between qi deficiency constitution and Pi-qi-deficiency syndrome of chronic superficial gastritis

Objective:To screen for blood leukocyte microRNA(miRNA)biomarkers responsible for the association between the traditional Chinese medicine(TCM)qi deficiency constitution(QDC)and the Pi-qi-deficiency syndrome(PQDS)of chronic superficial gastritis(CSG).Methods:Peripheral blood leukocytes were separated from people of two TCM constitutions(balance and qi deficiency)and from CSG patients with PQDS.Total RNA was isolated from the leukocytes and subjected to subsequent high-throughput miRNA sequencing to identify the miRNAs that are specifically and highly expressed in persons of QDC and CSG patients with PQDS.In addition,the target genes of the associated miRNAs were predicted.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway-based enrichment analyses of these target genes were performed to further evaluate the associated miRNA candidates as potential biomarkers responsible for the association between QDC and PQDS of CSG.Results:Compared with the control group with a balance constitution(P<.05,fold change>1.5 or<0.5),31 and 38 differentially expressed miRNAs were found in persons of QDC and CSG patients with PQDS,respectively.In particular,hsa-miR-145-5p and hsa-miR-146a-3p were highly expressed in both the persons of QDC and CSG patients with PQDS.GO analysis of the target genes of the two common miRNAs showed that they were mainly associated with functions related to synthesis and metabolism,such as cellular nitrogen compound metabolic processes,biosynthetic processes,cellular protein modification processes,and cellular component assembly.KEGG analysis identified the common pathways enriched among the target genes,including the Hippo signaling pathway and the transcriptional misregulation pathway.The common target genes of the two miRNAs seemed to be associated with the spliceosome pathway and the RNA degradation pathway.Conclusion:Hsa-miR-145-5p and hsa-miR-146a-3p may serve as candidate biomarkers responsible for the association between QDC and PQDS of CSG.

Disruption of PABPN1 phase separation by SNRPD2 drives colorectal cancer cell proliferation and migration through promoting alternative polyadenylation of CTNNBIP1

Generally shortened 3′UTR due to alternative polyadenylation(APA)is widely observed in cancer,but its regulation mechanisms for cancer are not well characterized.Here,with profiling of APA in colorectal cancer tissues and poly(A)signal editing,we firstly identified that the shortened 3′UTR of CTNNIBP1 in colorectal cancer promotes cell proliferation and migration.We found that liquid-liquid phase separation(LLPS)of PABPN1 is reduced albeit with higher expression in cancer,and the reduction of LLPS leads to the shortened 3′UTR of CTNNBIP1and promotes cell proliferation and migration.Notably,the splicing factor SNRPD2 upregulated in colorectal cancer,can interact with glutamic-proline(EP)domain of PABPN1,and then disrupt LLPS of PABPN1,which attenuates the repression effect of PABPN1 on the proximal poly(A)sites.Our results firstly reveal a new regulation mechanism of APA by disruption of LLPS of PABPN1,suggesting that regulation of APA by interfering LLPS of 3′end processing factor may have the potential as a new way for the treatment of cancer.

Synergistic induction of mitotic pyroptosis and tumor remission by inhibiting proteasome and WEE family kinases

Mitotic catastrophe(MC),which occurs under dysregulated mitosis,represents a fascinating tactic to specifically eradicate tumor cells.Whether pyroptosis can be a death form of MC remains unknown.Proteasome-mediated protein degradation is crucial for M-phase.Bortezomib(BTZ),which inhibits the 20S catalytic particle of proteasome,is approved to treat multiple myeloma and mantle cell lymphoma,but not solid tumors due to primary resistance.To date,whether and how proteasome inhibitor affected the fates of cells in M-phase remains unexplored.Here,we show that BTZ treatment,or silencing of PSMC5,a subunit of 19S regulatory particle of proteasome,causes G2-and M-phase arrest,multi-polar spindle formation,and consequent caspase-3/GSDME-mediated pyroptosis in M-phase(designated as mitotic pyroptosis).Further investigations reveal that inhibitor of WEE1/PKMYT1(PD0166285),but not inhibitor of ATR,CHK1 or CHK2,abrogates the BTZ-induced G2-phase arrest,thus exacerbates the BTZ-induced mitotic arrest and pyroptosis.Combined BTZ and PD0166285 treatment(named BP-Combo)selectively kills various types of solid tumor cells,and significantly lessens the IC50 of both BTZ and PD0166285 compared to BTZ or PD0166285 monotreatment.Studies using various mouse models show that BP-Combo has much stronger inhibition on tumor growth and metastasis than BTZ or PD0166285 monotreatment,and no obvious toxicity is observed in BP-Combo-treated mice.These findings disclose the effect of proteasome inhibitors in inducing pyroptosis in M-phase,characterize pyroptosis as a new death form of mitotic catastrophe,and identify dual inhibition of proteasome and WEE family kinases as a promising anti-cancer strategy to selectively kill solid tumor cells.

Phase-separated nucleocapsid protein of SARS-CoV-2 suppresses cGAS-DNA recognition by disrupting cGAS-G3BP1 complex

Currently,the incidence and fatality rate of SARS-CoV-2 remain continually high worldwide.COVID-19 patients infected with SARS-CoV-2 exhibited decreased type I interferon(IFN-I)signal,along with limited activation of antiviral immune responses as well as enhanced viral infectivity.Dramatic progresses have been made in revealing the multiple strategies employed by SARS-CoV-2 in impairing canonical RNA sensing pathways.However,it remains to be determined about the SARS-CoV-2 antagonism of cGAS-mediated activation of IFN responses during infection.In the current study,we figure out that SARS-CoV-2 infection leads to the accumulation of released mitochondria DNA(mtDNA),which in turn triggers cGAS to activate IFN-I signaling.As countermeasures,SARS-CoV-2 nucleocapsid(N)protein restricts the DNA recognition capacity of cGAS to impair cGAS-induced IFN-I signaling.Mechanically,N protein disrupts the assembly of cGAS with its co-factor G3BP1 by undergoing DNA-induced liquid-liquid phase separation(LLPS),subsequently impairs the double-strand DNA(dsDNA)detection ability of cGAS.Taken together,our findings unravel a novel antagonistic strategy by which SARS-CoV-2 reduces DNA-triggered IFN-I pathway through interfering with cGAS-DNA phase separation.

Systematic identification of CRISPR off-target effects by CROss-seq

DearEditor,The CRISPR-mediated genome editing tools,including nucleases,base editors(ABE/CBE),transposases/recombinases,and prime editor(PE),have been extensively applied in basic and clinical researches,although the off-target effect remains a major concern(Anzalone et al.,2020).Recently,various methods have been developed to assess the specificity and accuracy of different tools(Zhang et al.,2021),yet each method is designed for limited editing systems,and none of them can simultaneously detect off-target sites in vivo and in vitro.A versatile method for profiling genome-wide off-target effects of various tools remains lacking.

c-Myc-driven glycolysis polarizes functional regulatory B cells that trigger pathogenic inflammatory responses

B cells secreting IL-10 functionally are recognized as functional regulatory B(B_(reg))cells;however,direct evidence concerning the phenotype,regulation,and functional and clinical relevance of IL-10-secreting B_(reg)cells in humans is still lacking.Here,we demonstrate that,although IL-10 itself is anti-inflammatory,IL-10+functional B_(reg)cells in patients with systemic lupus erythematosus(SLE)display aggressive inflammatory features;these features shift their functions away from inducing CD8^(+)T cell tolerance and cause them to induce a pathogenic CD4^(+)T cell response.

Establishment of transposase-assisted low-input m^(6)A sequencing technique

RNA modification has been recognized as a pivotal regulator that affects gene expression in a post-transcriptional manner.To date,more than 150 distinct types of RNA modification have been identi-fied,among which N6-methyladenosine(m6 A)is the most abundant and best-characterized internal modification in mRNAs(Boccaletto et al.,2018).Benefit from the fast development of innovative technologies,the prevalence of m6 A has been reported and confirmed repeatedly in diverse organisms.Recent studies reveal that aberrant m6 A modification is associated with various disease progressions such as carcinogenesis and tumorigenesis by disturbing the expression of oncogenes and tumor suppressor genes(Tuncel and Kalkan,2019;Zhao et al.,2020).The m6 A methyltransferase METTL3 is found to be overexpressed in acute myeloid leukemia(AML)(Barbieri et al.,2017;Vu et al.,2017),which consequently elevates the m6 A level of B cell lymphoma 2(BCL2)transcript and promotes the translation effi-ciency。

U1 snRNP proteins promote proximal alternative polyadenylation sites by directly interacting with 3'end processing core factors

In eukaryotic cells,both alternative splicing and alternative polyadenylation(APA)play essential roles in the gene regulation network.U1 small ribonucleoprotein particle(U1 snRNP)is a major component of spliceosome,and U1 snRNP complex can suppress proximal APA sites through crosstalking with 3end processing factors.However,here we show that both knockdown and overexpression of SNRPA,SNRPC,SNRNP70,and SNRPD2,the U1 snRNP proteins,promote the usage of proximal APA sites at the transcriptome level.SNRNP70 can drive the phase transition of PABPN1 from droplet to aggregate,which may reduce the repressive effects of PABPN1 on the proximal APA sites.Additionally,SNRNP70 can also promote the proximal APA sites by recruiting CPSF6,suggesting that the function of CPSF6 on APA is related with other RNA-binding proteins and cell context-dependent.Consequently,these results reveal that,on the contrary to U1 snRNP complex,the free proteins of U1 snRNP complex can promote proximal APA sites through the interaction with 3end processing machinery.