Increased ZNF84 expression in cervical cancer

Massive Loss of Transcription Factors Promotes the Initial Diversification of Placental Mammals

As one of the most successful group of organisms, mammals occupy a variety of niches on Earth as a result of macroevolution. Transcription factors (TFs), the fundamental regulators of gene expression, may also have evolved. To examine the relationship between TFs and mammalian macroevolution, we analyzed 140,821 de novo-identified TFs and their birth and death histories from 96 mammalian species. Gene tree vs. species tree reconciliation revealed that placental mammals experienced an upsurge in TF losses around 100 million years ago (Mya) and also near the Cretaceous–Paleogene boundary (K–Pg boundary, 66 Mya). Early Euarchontoglires, Laurasiatheria and marsupials appeared between 100 and 95 Mya and underwent initial diversification. The K-Pg boundary was associated with the massive extinction of dinosaurs, which lead to adaptive radiation of mammals. Surprisingly, TF loss decelerated, rather than accelerated, molecular evolutionary rates of their target genes. As the rate of molecular evolution is affected by the mutation rate, the proportion of neutral mutations and the population size, the decrease in molecular evolution may reflect increased functional constraints to survive target genes.

KRAB-ZFPs and cancer stem cells identity

Studies on carcinogenesis continue to provide new information about different disease-related processes. Among others, much research has focused on the involvement of cancer stem cells (CSCs) in tumor initiation and progression. Studying the similarities and differences between CSCs and physiological stem cells (SCs) allows for a better understanding of cancer biology. Recently, it was shown that stem cell identity is partially governed by the Krϋppel-associated box domain zinc finger proteins (KRAB-ZFPs), the biggest family of transcription regulators. Several KRAB-ZFP factors exert a known effect in tumor cells, acting as tumor suppressor genes (TSGs) or oncogenes, yet their role in CSCs is still poorly characterized. Here, we review recent studies regarding the influence of KRAB-ZFPs and their cofactor protein TRIM28 on CSCs phenotype, stemness features, migration and invasion potential, metastasis, and expression of parental markers.

Leveraging Methylation Alterations to Discover Potential Causal Genes Associated With the Survival Risk of Cervical Cancer in TCGA Through a Two-Stage Inference Approach

BACKGROUND

Multiple genes were previously identified to be associated with cervical cancer; however, the genetic architecture of cervical cancer remains unknown and many potential causal genes are yet to be discovered.

METHODS

To explore potential causal genes related to cervical cancer, a two-stage causal inference approach was proposed within the framework of Mendelian randomization, where the gene expression was treated as exposure, with methylations located within the promoter regions of genes serving as instrumental variables. Five prediction models were first utilized to characterize the relationship between the expression and methylations for each gene; then, the methylation-regulated gene expression (MReX) was obtained and the association was evaluated via Cox mixed-effect model based on MReX. We further implemented the aggregated Cauchy association test (ACAT) combination to take advantage of respective strengths of these prediction models while accounting for dependency among the p-values.

RESULTS

A total of 14 potential causal genes were discovered to be associated with the survival risk of cervical cancer in TCGA when the five prediction models were separately employed. The total number of potential causal genes was brought to 23 when conducting ACAT. Some of the newly discovered genes may be novel (e.g., YJEFN3, SPATA5L1, IMMP1L, C5orf55, PPIP5K2, ZNF330, CRYZL1, PPM1A, ESCO2, ZNF605, ZNF225, ZNF266, FICD, and OSTC). Functional analyses showed that these genes were enriched in tumor-associated pathways. Additionally, four genes (i.e., COL6A1, SYDE1, ESCO2, and GIPC1) were differentially expressed between tumor and normal tissues.

CONCLUSION

Our study discovered promising candidate genes that were causally associated with the survival risk of cervical cancer and thus provided new insights into the genetic etiology of cervical cancer.

Chromatin-Directed Proteomics Identifies ZNF84 as a p53-Independent Regulator of p21 in Genotoxic Stress Response

Simple Summary

Chemotherapy is a commonly applied anticancer treatment, however therapy-induced senescent growth arrest has been associated with aggressive disease recurrence. The p21 protein, encoded by CDKN1A, plays a vital role in the induction of senescence. Its transcriptional control by p53 is well-established. However, in many cancers where TP53 is mutated, p21 expression must be triggered by p53-independent mechanisms. We here used a chromatin-directed proteomic approach and identified ZNF84 as a regulator of CDKN1A gene expression in various p53-deficient cell lines. Knock-down of ZNF84, an as-yet un-characterized protein, inhibited p21 gene and protein expression in response to doxorubicin and facilitated senescence bypass. Intriguingly, ZNF84 depletion diminished genotoxic burden evoked by doxorubicin. Clinical data association studies indicated the relevance of ZNF84 expression for patient survival. Collectively, we identified ZNF84 as a critical regulator of senescence-proliferation outcome of chemotherapy, opening possibilities for its targeting in novel anti-cancer therapies of p53-mutated tumours.

Abstract

The p21^WAF1/Cip1 protein, encoded by CDKN1A, plays a vital role in senescence, and its transcriptional control by the tumour suppressor p53 is well-established. However, p21 can also be regulated in a p53-independent manner, by mechanisms that still remain less understood. We aimed to expand the knowledge about p53-independent senescence by looking for novel players involved in CDKN1A regulation. We used a chromatin-directed proteomic approach and identified ZNF84 as a novel regulator of p21 in various p53-deficient cell lines treated with cytostatic dose of doxorubicin. Knock-down of ZNF84, an as-yet un-characterized protein, inhibited p21 gene and protein expression in response to doxorubicin, it attenuated senescence and was associated with enhanced proliferation, indicating that ZNF84-deficiency can favor senescence bypass. ZNF84 deficiency was also associated with transcriptomic changes in genes governing various cancer-relevant processes e.g., mitosis. In cells with ZNF84 knock-down we discovered significantly lower level of H2AX Ser139 phosphorylation (γH2AX), which is triggered by DNA double strand breaks. Intriguingly, we observed a reverse correlation between the level of ZNF84 expression and survival rate of colon cancer patients. In conclusion, ZNF84, whose function was previously not recognized, was identified here as a critical p53-independent regulator of senescence, opening possibilities for its targeting in novel therapies of p53-null cancers.

Decreased IL-37 expression in hepatocellular carcinoma tissues and liver cancer cell lines

The role of IL-37 in cancer is currently largely unknown. The present study aimed to investigate IL-37 expression in hepatocellular carcinoma (HCC), paracancerous tissues (PT) and liver cancer cell lines, and their associations between IL-37 and NF-κB. A total of 65 HCC and 65 PT tissues were collected. The expression of IL-37 and NF-κB in tissues was detected by immunohistochemistry (IHC) and the data was analyzed using SPSS software. In the in vitro studies, IL-37 gene was transfected into HepG2 and MHCC97H cell lines with Lipofectamine 3000, and the protein regulation of NF-κB by IL-37 was verified by immunofluorescence (IF) and western blotting. In HCC, the positive expression rates of IL-37 and NF-kB were 21.5 and 95.4%, respectively. In PT, strong positive staining of IL-37and weak positive staining of NF-κB were observed. The normal expression levels of IL-37 and NF-κB, the increased IL-37 and decreased NF-κB induced by IL-37 gene transfection were observed through IF in cell lines. In terms of clinical significance, the difference in IL-37 expression between HCC and PT was statistically significant (χ²=55.05; P<0.001). IL-37 expression in HCC but not PT was negatively associated with serum AFP (χ²=6.522; P=0.039). IL-37 expression in PT was associated with sex (χ²=13.12; P=0.003) and tumor size (χ²=7.996; P=0.045). NF-κB expression in PT was associated with age, sex and BCLC stage. Notably, there was a negative correlation between IL-37 and NF-κB in HCC (r=-0.277; P=0.029) but not in PT (P>0.05). IL-37 overexpression downregulated the NF-κB protein by 56.50% in HepG2 cells (P<0.05) and 30.52% in MHCC97H cells (P<0.05). In conclusion, the expression of IL-37 in HCC and PT was specifically associated with serum AFP and tumor size, respectively. IL-37 expression was negatively correlated with NF-κB protein expression in HCC tissues and liver cancer cell lines.

Uncovering missed indels by leveraging unmapped reads

In current practice, Next Generation Sequencing (NGS) applications start with mapping/aligning short reads to the reference genome, with the aim of identifying genetic variants. Although existing alignment tools have shown great accuracy in mapping short reads to the reference genome, a significant number of short reads still remain unmapped and are often excluded from downstream analyses thereby causing nonnegligible information loss in the subsequent variant calling procedure. This paper describes Genesis-indel, a computational pipeline that explores the unmapped reads to identify novel indels that are initially missed in the original procedure. Genesis-indel is applied to the unmapped reads of 30 breast cancer patients from TCGA. Results show that the unmapped reads are conserved between the two subtypes of breast cancer investigated in this study and might contribute to the divergence between the subtypes. Genesis-indel identifies 72,997 novel high-quality indels previously not found, among which 16,141 have not been annotated in the widely used mutation database. Statistical analysis of these indels shows significant enrichment of indels residing in oncogenes and tumour suppressor genes. Functional annotation further reveals that these indels are strongly correlated with pathways of cancer and can have high to moderate impact on protein functions. Additionally, some of the indels overlap with the genes that do not have any indel mutations called from the originally mapped reads but have been shown to contribute to the tumorigenesis in multiple carcinomas, further emphasizing the importance of rescuing indels hidden in the unmapped reads in cancer and disease studies.