Search

SUMMARYAneuploidy, the presence of chromosome gains or losses, is a hallmark of cancer and congenital syndromes. Here, we describe KaryoCreate (Karyotype CRISPR Engineered Aneuploidy Technology), a system that enables generation of chromosome-specific aneuploidies by co-expression of a sgRNA targeting chromosome-specific CENPA-binding ɑ-satellite repeats together with dCas9 fused to a mutant form of KNL1. We designed unique and highly specific sgRNAs for 19 out of 24 chromosomes. Expression of these sgRNAs with KNL1Mut-dCas9 leads to missegregation and induction of gains or losses of the targeted chromosome in cellular progeny with an average efficiency of 8% and 12% for gains and losses, respectively (up to 20%), tested and validated across 9 chromosomes. Using KaryoCreate in colon epithelial cells, we show that chromosome 18q loss, a frequent occurrence in gastrointestinal cancers, promotes resistance to TGFβ, likely due to synergistic hemizygous deletion of multiple genes. Altogether, we describe a novel technology to create and study chromosome missegregation and aneuploidy in the context of cancer and beyond.HighlightsWe designed sgRNAs targeting chromosome-specific centromeres across 19 human chromosomesKaryoCreate combines chromosome-specific centromeric sgRNAs with dCas9 fused to a mutant form of KNL1.KaryoCreate allows engineering gains and losses of specific human chromosomes.Engineered Chromosome 18q loss promotes tumor-associated phenotypes in colon-derived cells.KaryoCreate is a CRISPR-based technology to foster the study of centromere biology and aneuploidy.

How cells control gene expression is a fundamental question. The relative contribution of protein-level and RNA-level regulation to this process remains unclear. Here, we perform a proteogenomic analysis of tumors and untransformed cells containing somatic copy number alterations (SCNAs). By revealing how cells regulate RNA and protein abundances of genes with SCNAs, we provide insights into the rules of gene regulation. Protein complex genes have a strong protein-level regulation while non-complex genes have a strong RNA-level regulation. Notable exceptions are plasma membrane protein complex genes, which show a weak protein-level regulation and a stronger RNA-level regulation. Strikingly, we find a strong negative association between the degree of RNA-level and protein-level regulation across genes and cellular pathways. Moreover, genes participating in the same pathway show a similar degree of RNA- and protein-level regulation. Pathways including translation, splicing, RNA processing, and mitochondrial function show a stronger protein-level regulation while cell adhesion and migration pathways show a stronger RNA-level regulation. These results suggest that the evolution of gene regulation is shaped by functional constraints and that many cellular pathways tend to evolve one predominant mechanism of gene regulation at the protein level or at the RNA level.

Background Lung cancer is the leading cause of death among cancer patients worldwide. Close to 85% of lung cancer pathology types are non-small cell lung cancer (NSCLC). With advances in medicine, the survival rate of early-stage NSCLC has improved. However, its overall 5-year survival rate and recurrence rate remain high. The search for potential therapeutic targets in the development of NSCLC provides new avenues for clinical treatment. In recent years, related studies have shown that microRNA-486 (miRNA-486) can promote tumor cell proliferation, infiltration, metastasis and drug resistance, and can be used as a new molecular marker for early diagnosis, prognosis and treatment of tumors. However, the expression and prognosis of miRNA-486 in NSCLC are unclear. Therefore, this study further elucidated the relationship between miRNA-486 expression and prognosis in NSCLC through meta-analysis. In addition, the possible molecular mechanism of miRNA-486 was further analyzed by bioinformatics analysis to provide theoretical basis for the diagnosis, treatment and prognosis of NSCLC patients. Methods Wanfang, Chinese Biomedical Literature Database, Chinese National Knowledge Infrastructure, the Chongqing VIP Chinese Science and Technology Periodical Database, PubMed, Embase, and Web of Science databases were searched. The search was scheduled from the establishment of the database to August 2021. Combined hazard ratios (HRs) and 95% confidence intervals (95% CI) were used to evaluate the effect of miRNA-486 on the prognosis of NSCLC. Stata 16.0 software was used for meta-analysis. The expression of miRNA-486 in NSCLC was analyzed using the GEO database and TCGA database. Survival curves of miRNA-486 differential expression were analyzed by OncomiR. Target genes of miRNA-486 were predicted by TargetScan, miRBase, miRTarBase, starBase V2.0 and miRWalk. Target genes were obtained by the intersection of Venn diagrams. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed using the DAVID database. Results The results of this meta-analysis will be submitted to a peer-reviewed journal for publication. Conclusion This study provides high-quality evidence support for the expression of miRNA-486 and the prognosis of NSCLC. Through bioinformatics analysis, we further discussed the mechanism of miRNA-486 in NSCLC and the understanding of related pathways.

Background: The morbidity and mortality of non-small cell lung cancer (NSCLC) are high, platinum-based chemotherapy has reached the efficacy threshold, and its use is limited by drug toxicity, so there is an urgent need to find a new effective and safe treatment. Chemotherapy, antiangiogenic therapy and immunotherapy are the routine methods for the treatment of NSCLC. However, the effect of the combination of the three treatments is currently controversial. Therefore, this study uses meta-analysis to further explore the efficacy and safety of recombinant human endostatin and chemotherapy combined with PD-1 inhibitors in the treatment of NSCLC, so as to provide a reference basis for clinical decision-making. Methods: Relevant publications were searched from the clinical trials. Using computer to retrieve on Cochrane Central Register of Controlled Trials Repositories, PubMed, Embase and Web of Science databases. The retrieval time limit was from the establishment of the database to January 31, 2021. The two researchers independently carried out data extraction and literature quality evaluation on the quality and Meta-analysis of the included literature was carried out using Revman5.3 software. Results: The results of this meta-analysis will be submitted to a peer-reviewed journal for publication. Conclusion: This study will provide reliable evidence-based basis for the clinical application of recombinant human endostatin and chemotherapy combined with PD-1 inhibitors in the treatment of advanced NSCLC.