In the 40years since the discovery of the CENP proteins, many studies have examined the role of these proteins and their interactions with other chromosomal proteins of the centromere and beyond. Together, these studies have yielded vast amounts of sequencing and proteomics data. Typically, each study has focused on a single question and the majority of each dataset remains largely unexplored. Often the interesting details of publicly deposited data are left behind, buried in archives online, while more and more new data are generated. Reanalysing these databases can represent a new paradigm for investigating diverse biological pathways in unprecedented detail. Here, we explore two publicly available pan-cancer proteomic datasets to compare proteins whose abundance correlates with CENP proteins, with a particular focus on CENP-C. Our analysis confirms an expected link between CENP-C and cohesin levels but reveals a surprising and unexpected correlation between CENP-C and proteins of the inner nuclear membrane and the NuMA protein. This guilt-by-association analysis has the potential to identify proteins that act in common pathways but never associate or colocalize and may not even be expressed at the same time in cells. As an example, we show here that it can reveal unexpected links that expand our conception of centromeric chromatin beyond chromosome segregation.

Various long non-coding RNAs (lncRNAs) have indicated their role in different regulatory processes and therapeutics in cervical cancer (CC). This study aims to assess the gene expression and methylation status of LINC00518 & MAFG-AS1 in CC patients. Methylation-specific PCR (MS-PCR) and quantitative real-time PCR (qRT-PCR) were performed on 81 patients. The association of the promoter methylation status of cancer tissues was studied with HPV infection and clinicopathological factors. The Kaplan-Meier curves were used from the GEPIA and TANRIC databases to analyze the overall survival of CC patients. The bioinformatics analysis of relative gene expression was carried out using the GEPIA database. The RNAinter database was also explored to find out the potential interacting partners. This is the first-ever research revealing that hypomethylation of the LINC00518 gene promoter may be relevant to its oncogenic behavior in CC (p < 0.05). However, no significant difference was observed between the MAFG-AS1 methylation status of cancerous and normal tissues. A notable association between the methylation status of LINC00518 promoter and clinicopathological factors, including age (p < 0.001), histological subtypes (p < 0.00001), and differentiation degree (p < 0.00001), has been observed, indicating its possible role in predicting the severity and prognosis of this disease. Overall survival analysis showed a significant value for LINC00518 using GEPIA (p < 0.05). Our findings about the gene expression of LINC00518 and its hypomethylated status in cancerous tissues suggest a potential mechanism that might contribute to its dysregulation in CC and could serve as a potential clinical biomarker.

Esophageal cancer (EC) is still a difficult problem in medicine, depriving many patients of their lives every year. RAD18 and ATM were implicated in cancers including esophageal squamous cell carcinoma (ESCC). However, whether RAD18/ATM axis influences ESCC progression remains unclear. The abundance of genes and proteins was evaluated using RT-qPCR and western blot. Cell proliferation, migration and invasion were examined using clone formation, scratch test and transwell. The level of ATM ubiquitination was verified and experimented using Co-IP. Our findings found that RAD18 expression was enhanced in TCGA database, in ESCC patients and ESCC cells. Similarly, ATM expression was declined in ESCC patients and ESCC cells. RAD18 silencing resulted in suppression of cell proliferation, migration and invasion of ESCC cells, which were abolished by ATM silencing. In addition, ATM silencing promoted malignant behaviors of ESCC cells by activating STAT3/PD-L1 axis, which was reversed by PD-L1 knockdown. Moreover, RAD18 could reduce ATM protein levels. RAD18 mediated ATM ubiquitination to reduce ATM protein level, thereby activating STAT3/PD-L1 axis and strengthening cell proliferation, migration and invasion of ESCC cells.

Overexpression or knockdown of a specific gene is usually helpful in understanding its underlying molecular mechanism. PVT1 gene is regarded as an oncogenic long non-coding RNA (lncRNA) in many cancers, including breast invasive carcinoma (BRCA). We investigated some of the underlying molecular mechanisms of PVT1 in human invasive breast cancer MDA-MB-231 cells. Differentially expressed genes (DEGs) were obtained after PVT1 overexpression and knockdown in MDA-MB-231 cells from the gene expression profiles GSE175736 and GSE97587. RNAInter database was used to predict miRNAs and TFs that have interactions with PVT1. Competing endogenous RNA (ceRNA) and transcription regulatory networks visualized using Cytoscape software. It was found that HLA-G, GBP4, SERPINE1, DHRS2, MT1X, and PRLR were common PVT1 co-upregulated and co-downregulated genes in the two datasets. SERPINE1 was identified as the most positively correlated gene with PVT1 expression in MDA-MB-231 cells. DEGs in overexpressed and silenced PVT1 cells were enriched in the cell adhesion process and JAK-STAT signaling pathway, respectively. In the ceRNA network, PVT1 acts as a competing endogenous RNA for downregulated miR-145-5p, miR-17-5p, and miR-20a-5p. PVT1/miR-145-5p/SERPINE1 was a common axis in ceRNA networks in the two datasets. SERPINIE1 was also a common node between ceRNA and transcription regulatory networks. RT-qPCR validated the anticipated levels of PVT1, miR-145-5p, and SERPINE1 in MDA-MB-231 cancer compared to MCF-10A noncancerous cells. Taken together, the results of this work shed light on the several possible oncogenic mechanisms of PVT1, including its closely related genes and signaling pathways.

Sex chromosomes have independently evolved in various species, displaying unique evolutionary patterns, including differentiation, degeneration, and repetitive DNA accumulation. Pentatomidae hemipterans are characterized by a highly conserved diploid number of 2n = 14 with a XX/XY sex chromosome system, i.e. 2n = 14, 12A + XY. Thus, it represents an interesting group for investigating the reorganization of repeats in conserved karyotypes, i.e. the absence of large chromosomal rearrangements. Using comparative genomic hybridization (CGH) with male and female genomic DNAs (gDNA), this study examined a total of 25 Pentatomidae species to uncover repetitive DNA dynamics and their role in chromosome differentiation, especially sex chromosome differentiation. New karyotype data for nine species reinforces the chromosomal stasis in Pentatomidae for macro-chromosomal structure. However, significant variability in repetitive DNA patterns on autosomes and sex chromosomes has been revealed despite the karyotypic conservation. Autosomal signals varied in intensity and distribution, with some species exhibiting terminal enrichment of repeats, while others displayed dispersed patterns. Sex chromosomes showed distinct hybridization patterns, with the Y chromosome exhibiting more significant variability compared to the X. These findings emphasize the dynamic nature of sex chromosomes and suggest further studies combining genomic sequencing and cytogenetics to uncover sequences and the mechanisms behind their evolution.

Tetraploidisation plays a crucial role in evolution, development, stress adaptation, and disease, but its beneficial or pathological effects in different tissues remain unclear. This study aims to compare physiological and unphysiological tetraploidy in eight steps: 1) mechanisms of diploidy-to-tetraploidy transition, 2) induction and elimination of unphysiological tetraploidy, 3) tetraploid cell characteristics, 4) stress-induced unphysiological tetraploidy, 5) comparison of physiological vs. unphysiological tetraploidy, 6) consequences of unphysiological stress-induced tetraploidy, 7) nutritional or pharmacological prevention strategies of tetraploidisation, and 8) knowledge gaps and future perspectives. Unphysiological tetraploidy is an adaptive stress response at a given threshold, often involving mitotic slippage. If tetraploid cells evade elimination through apoptosis or immune surveillance, they may re-enter the cell cycle, causing genetic instability, micronuclei formation, aneuploidy, modification of the epigenome and the development of diseases. The potential contributions of unphysiological tetraploidy to neurodegenerative, cardiovascular and diabetes related diseases are summarized in schematic figures and contrasted with its role in cancer development. The mechanisms responsible for the transition from physiological to unphysiological tetraploidy and the tolerance to tetraploidisation in unphysiological tetraploidy are not fully understood. Understanding these mechanisms is of critical importance to allow the development of targeted nutritional and pharmacological prevention strategies and therapies.

Some insects have holocentric chromosomes, with multiple kinetochores rather than a single centromere. They also lack the CENP-A and CENP-C proteins, suggesting a kinetochore assembly process different from that of monocentric chromosomes. The homolog of CENP-T was recently shown to bind silent chromatin and to play a key role in kinetochore assembly in Bombyx mori, but its role in other insects with holocentric chromosomes is unknown. We identified kinetochore genes and analyzed their expression in Spodoptera frugiperda. We silenced the kinetochore genes cenp-L, cenp-S, cenp-X and ndc80 and searched for chromosome segregation defects in Sf9 cells. All kinetochore genes except cenp-S were more strongly expressed in gonadal than in somatic tissues. Immunofluorescence microscopy and RT-qPCR demonstrated the effective silencing of the target genes by transfection with dsRNA. In Sf9 cells depleted of CENP-L and NDC80, immunofluorescence microscopy revealed increases in mitotic index and in the proportion of cells with unaligned chromosomes or multipolar spindles. The depletion of CENP-S and CENP-X had no effect on mitotic index and no division defects were observed. This suggests that CENP-L and NDC80 play key roles in chromosome segregation, whereas the functions of CENP-S and CENP-X remain unknown. We have begun to characterize the kinetochore proteins (CENP-L, CENP-S, CENP-X, NDC80), a prerequisite for holocentromere identification in S. frugiperda. This study also provides the first information about the role, in Lepidoptera, of CENP-L, a protein essential to the structure of the constitutive centromere-associated network in species with monocentric chromosomes.