XAB2 functions in mitotic cell cycle progression via transcriptional regulation of CENPE

USP10/XAB2/ANXA2 axis promotes DNA damage repair to enhance chemoresistance to oxaliplatin in colorectal cancer

BACKGROUND

Oxaliplatin-based chemotherapy is the first-line treatment for colorectal cancer (CRC). However, oxaliplatin resistance remains a major challenge contributing to treatment failure and poor prognosis. An increased capacity for DNA damage repair is a key mechanism underlying oxaliplatin resistance. Although XPA binding protein 2 (XAB2) is implicated in various DNA damage repair mechanisms, its specific role in mediating oxaliplatin resistance remains unclear.

METHODS

XAB2 was identified through analysis of public datasets. Western blot analysis and immunohistochemistry were performed to evaluate XAB2 expression, while survival analysis was performed to assess its clinical significance in CRC. Functional experiments were then conducted to assess the impact of XAB2 on proliferation, DNA damage repair, and oxaliplatin resistance in CRC. RNA sequencing (RNA-seq) and Chromatin immunoprecipitation-sequencing (ChIP-seq) were used to identify XAB2 target genes. Co-immunoprecipitation (Co-IP) and mass spectrometry were used to identify the proteins interacting with XAB2. Dual-luciferase reporter assays, ChIP-qPCR, Co-IP, ubiquitination site mass spectrometry, and ubiquitin assays were used to analyse the interactions and potential mechanisms involving XAB2, Annexin A2 (ANXA2), and ubiquitin-specific protease 10 (USP10).

RESULTS

XAB2 was found to be expressed in CRC and was associated with poor prognosis in patients with CRC. XAB2 promoted CRC cell proliferation and enhanced oxaliplatin resistance by promoting DNA damage repair. Mechanistically, CRC cells treated with oxaliplatin exhibited increased USP10 nuclear expression. USP10 bound to XAB2 and deubiquitinated XAB2 K48-linked polyubiquitination at K593, thereby stabilising XAB2 by reducing its degradation via the ubiquitin-proteasome pathway. XAB2 upregulates ANXA2 expression at the transcriptional level by binding to the ANXA2 promoter, thereby promoting DNA damage repair, mitigating oxaliplatin-induced DNA damage, and enhancing oxaliplatin resistance.

CONCLUSIONS

In summary, this study demonstrates that the USP10/XAB2/ANXA2 axis promotes proliferation, DNA damage repair, and oxaliplatin resistance in CRC. These findings uncover a novel mechanism of oxaliplatin resistance in CRC and suggest potential therapeutic targets for improving the efficacy of oxaliplatin in CRC treatment.

Low Temperature Plasma Jet Treatment Promotes Skin Wound Healing by Enhancing Cell Proliferation via the PI3K-AKT and AMPK Pathways

Low temperature plasma jet (LTPJ) treatment can promote skin wound healing, but the underlying molecular mechanisms remain poorly understood. In the present study, we verified the effect of LTPJ in accelerating wound healing and investigated its underlying mechanism. With mouse model, two full-thickness dermal wounds were created in each mouse (n = 8). One wound underwent LTPJ treatment for 10 min, while the other wound without LTPJ treatment served as a control. The percentage of wound closure and collagen content in epidermis increased significantly, which indicated that LTPJ treatment significantly enhanced wound healing through contraction. RNA-seq analysis was conducted to understand the underlying mechanisms. A total of 77 differentially expressed genes (DGEs) were identified. GO and KEGG pathway enrichment analyses revealed that the DGEs were mainly related to the collagen-containing extracellular matrix, cell cycle, PI3K-AKT signalling pathway and AMPK signalling pathway, which are known to be related to wound healing. HaCaT keratinocytes were used to study LTPJ effects on cell proliferation in vitro. In agreement with the in vivo results, the in vitro datas also demonstrated that LTPJ treatment affected the activity of the PI3K-AKT and AMPK pathways. Our findings suggest that LTPJ treatment promotes skin wound healing by inducing genes associated with wound healing, promoting PI3K-AKT signalling, and suppressing the AMPK signalling pathway.

Quantifying Landscape-Flux via Single-Cell Transcriptomics Uncovers the Underlying Mechanism of Cell Cycle

Recent developments in single-cell sequencing technology enable the acquisition of entire transcriptome data. Understanding the underlying mechanism and identifying the driving force of transcriptional regulation governing cell function directly from these data remains challenging. This study reconstructs a continuous vector field of the cell cycle based on discrete single-cell RNA velocity to quantify the single-cell global nonequilibrium dynamic landscape-flux. It reveals that large fluctuations disrupt the global landscape and genetic perturbations alter landscape-flux, thus identifying key genes in maintaining cell cycle dynamics and predicting associated functional effects. Additionally, it quantifies the fundamental energy cost of the cell cycle initiation and unveils that sustaining the cell cycle requires curl flux and dissipation to maintain the oscillatory phase coherence. This study enables the inference of the cell cycle gene regulatory networks directly from the single-cell transcriptomic data, including the feedback mechanisms and interaction intensity. This provides a golden opportunity to experimentally verify the landscape-flux theory and also obtain its associated quantifications. It also offers a unique framework for combining the landscape-flux theory and single-cell high-through sequencing experiments for understanding the underlying mechanisms of the cell cycle and can be extended to other nonequilibrium biological processes, such as differentiation development and disease pathogenesis.

Kinesin-7 CENP-E in tumorigenesis: Chromosome instability, spindle assembly checkpoint, and applications

Kinesin motors are a large family of molecular motors that walk along microtubules to fulfill many roles in intracellular transport, microtubule organization, and chromosome alignment. Kinesin-7 CENP-E (Centromere protein E) is a chromosome scaffold-associated protein that is located in the corona layer of centromeres, which participates in kinetochore-microtubule attachment, chromosome alignment, and spindle assembly checkpoint. Over the past 3 decades, CENP-E has attracted great interest as a promising new mitotic target for cancer therapy and drug development. In this review, we describe expression patterns of CENP-E in multiple tumors and highlight the functions of CENP-E in cancer cell proliferation. We summarize recent advances in structural domains, roles, and functions of CENP-E in cell division. Notably, we describe the dual functions of CENP-E in inhibiting and promoting tumorigenesis. We summarize the mechanisms by which CENP-E affects tumorigenesis through chromosome instability and spindle assembly checkpoints. Finally, we overview and summarize the CENP-E-specific inhibitors, mechanisms of drug resistances and their applications.

Targeting CENP-E augments immunotherapy in non-small cell lung cancer via stabilizing PD-L1

Centromere-associated protein E (CENP-E) plays a critical role in mitosis and chromosome misalignment, which may represent a potential therapeutic target in tumors. CENP-E is frequently overexpressed in lung cancer and act as a driver gene. However, it remains unclear whether CENP-E regulates the immune microenvironment in non-small cell lung cancer (NSCLC). Our study revealed that CENP-E is highly expressed and predicts a worse survival in NSCLC patients; inhibition of CENP-E leads to an upregulation of PD-L1 expression, consequently impacting the immune microenvironment of NSCLC by modulating the balance between CD8+ T cells and regulatory T cells (Tregs). Mechanistically, we demonstrated that downregulation of CENP-E could stabilize PD-L1 mRNA through the targeting of its 3'UTR by TTP. The genetic knockdown or pharmacological inhibition of CENP-E, in combination with PD-L1 antibody, could enhance the antitumor effect in NSCLC. Thus, our findings have revealed a role of CENP-E in immunotherapy and suggest that combination of CENP-E inhibitor with PD-L1 antibody could be an effective treatment option for NSCLC.

scRNA-seq and proteomics reveal the distinction of M2-like macrophages between primary and recurrent malignant glioma and its critical role in the recurrence

AIMS

Tumor-associated macrophages (TAMs) in the immune microenvironment play an important role in the increased drug resistance and recurrence of malignant glioma, but the mechanism remains incompletely inventoried. The focus of this study was to investigate the distinctions of M2-like TAMs in the immune microenvironment between primary and recurrent malignant glioma and its influence in the recurrence.

METHODS

We employed single-cell RNA sequencing to construct a single-cell atlas for a total of 23,010 individual cells from 6 patients with primary or recurrent malignant glioma and identified 5 cell types, including TAMs and malignant cells. Immunohistochemical techniques and proteomics analysis were performed to investigate the role of intercellular interaction between malignant cells and TAMs in the recurrence of malignant glioma.

RESULTS

Six subgroups of TAMs were annotated and M2-like TAMs were found to increase in recurrent malignant glioma significantly. A pseudotime trajectory and a dynamic gene expression profiling during the recurrence of malignant glioma were reconstructed. Up-regulation of several cancer pathways and intercellular interaction-related genes are associated with the recurrence of malignant glioma. Moreover, the M2-like TAMs can activate the PI3K/Akt/HIF-1α/CA9 pathway in the malignant glioma cells via SPP1-CD44-mediated intercellular interaction. Interestingly, high expression of CA9 can trigger the immunosuppressive response in the malignant glioma, thus promoting the degree of malignancy and drug resistance.

CONCLUSION

Our study uncovers the distinction of M2-like TAMs between primary and recurrent glioma, which offers unparalleled insights into the immune microenvironment of primary and recurrent malignant glioma.

Assessing the influence of distinct culture media on human pre-implantation development using single-embryo transcriptomics

The use of assisted reproductive technologies is consistently rising across the world. However, making an informed choice on which embryo culture medium should be preferred to ensure satisfactory pregnancy rates and the health of future children critically lacks scientific background. In particular, embryos within their first days of development are highly sensitive to their micro-environment, and it is unknown how their transcriptome adapts to different embryo culture compositions. Here, we determined the impact of culture media composition on gene expression in human pre-implantation embryos. By employing single-embryo RNA-sequencing after 2 or 5 days of the post-fertilization culture in different commercially available media (Ferticult, Global, and SSM), we revealed medium-specific differences in gene expression changes. Embryos cultured pre-compaction until day 2 in Ferticult or Global media notably displayed 266 differentially expressed genes, which were related to essential developmental pathways. Herein, 19 of them could have a key role in early development, based on their previously described dynamic expression changes across development. When embryos were cultured after day 2 in the same media considered more suitable because of its amino acid enrichment, 18 differentially expressed genes thought to be involved in the transition from early to later embryonic stages were identified. Overall, the differences were reduced at the blastocyst stage, highlighting the ability of embryos conceived in a suboptimal in vitro culture medium to mitigate the transcriptomic profile acquired under different pre-compaction environments.

A pan-cancer landscape of centromere proteins in tumorigenesis and anticancer drug sensitivity

BACKGROUND

During mitosis and meiosis, centromere proteins (CENPs) play a key role in proper chromosome segregation. Abnormal expression of CENPs leads to chromosome instability, which is the main cause of tumorigenesis.

METHODS

To elucidate the functional characteristics of CENPs in pan-cancer, we comprehensively analyzed the expression landscape of CENPs and their relationships with patient survival, genomic alterations, tumor immunity, tumor microenvironment, and anticancer drug sensitivity. The expression patterns and signaling pathways of CENPs were identified through multiple bioinformatics mining and experimental verification. GEPIA2 and PrognoScan were implemented to evaluate the prognostic value of CENPs. The molecular functions of CENPs in pan-cancer were comprehensively assessed using cBioPortal, GSCA, ImmuCellAI, CellMiner, the ROC plotter tool and TIDE.

RESULTS

The results showed that CENPs were upregulated in most tumors compared with normal tissues. We confirmed this conclusion by immunohistochemistry and real-time quantitative PCR. Survival analysis revealed a significant association between high CENP expression and a poor prognosis. CENP expression is related to genome alterations, copy number variation, single nucleotide variation and methylation. Among CENP family genes, CENPF and CENPE are mutated at high frequencies in various tumors, while CENPM and CENPA are less frequently mutated. Furthermore, CENPs regulate the tumor mutational burden, stemness, and microsatellite instability, and are associated with tumor immunity. Most importantly, we revealed that CENP family gene expression was correlated with chemosensitivity and immunotherapy responses.

CONCLUSION

These findings may clarify the role of CENPs in cancer progression and antitumor drug sensitivity and provide evidence for CENPs as a potential target in pan-cancer.

Exploring Potential Biomarkers, Ferroptosis Mechanisms, and Therapeutic Targets Associated with Cutaneous Squamous Cell Carcinoma via Integrated Transcriptomic Analysis

Background

Cutaneous squamous cell carcinoma (cSCC) is the leading cause of death in patients with nonmelanoma skin cancers (NMSC). However, the unclear pathogenesis of cSCC limits the application of molecular targeted therapy.

Methods

Three microarray datasets (GSE2503, GSE45164, and GSE66359) were downloaded from the Gene Expression Omnibus (GEO). After identifying the differentially expressed genes (DEGs) in tumor and nontumor tissues, five kinds of analyses, namely, functional annotation, protein-protein interaction (PPI) network, hub gene selection, TF-miRNA-mRNA regulatory network analysis, and ferroptosis mechanism, were performed.

Results

A total of 146 DEGs were identified with significant differences, including 113 upregulated genes and 33 downregulated genes. The enriched functions and pathways of the DEGs included microtubule-based movement, ATP binding, cell cycle, P53 signaling pathway, oocyte meiosis, and PLK1 signaling events. Nine hub genes were identified (CDK1, AURKA, RRM2, CENPE, CCNB1, KIAA0101, ZWINT, TOP2A, and ASPM). Finally, RRM2, AURKA, and SAT1 were identified as significant ferroptosis-related genes in cSCC. The differential expression of these genes has been verified in two other independent datasets.

Conclusions

By integrated bioinformatic analysis, the hub genes identified in this study elucidated the molecular mechanism of the pathogenesis and progression of cSCC and are expected to become future biomarkers or therapeutic targets.

Genome-wide comparison and in silico analysis of splicing factor SYF2/NTC31/p29 in eukaryotes: Special focus on vertebrates

The gene SYF2—an RNA splicing factor—can interact with Cyclin D-type binding protein 1 (GICP) in many biological processes, including splicing regulation, cell cycle regulation, and DNA damage repair. In our previous study we performed genome-wide identification and functional analysis of SYF2 in plant species. The phylogenetic relationships and expression profiles of SYF2 have not been systematically studied in animals, however. To this end, the gene structure, genes, and protein conserved motifs of 102 SYF2 homologous genes from 91 different animal species were systematically analyzed, along with conserved splicing sites in 45 representative vertebrate species. A differential comparative analysis of expression patterns in humans and mice was made. Molecular bioinformatics analysis of SYF2 showed the gene was conserved and functional in different animal species. In addition, expression pattern analysis found that SYF2 was highly expressed in hematopoietic stem cells, T cells, and lymphoid progenitor cells; in ovary, lung, and spleen; and in other cells and organs. This suggests that changes in SYF2 expression may be associated with disease development in these cells, tissues, or organs. In conclusion, our study analyzes the SYF2 disease resistance genes of different animal species through bioinformatics, reveals the relationship between the SYF2 genotype and the occurrence of certain diseases, and provides a theoretical basis for follow-up study of the relationship between the SYF2 gene and animal diseases.

Upregulated mitosis-associated genes CENPE, CENPF, and DLGAP5 predict poor prognosis and chemotherapy resistance of Acute Myeloid Leukemia

BACKGROUND

Mitosis-associated genes are dysregulated in many types of cancers and play important roles in disease progression and chemotherapy resistance. However, their expression and functions in chemotherapy-resistant Acute Myeloid Leukemia (AML) are still largely undetermined.

OBJECTIVE

This study aims to explore the roles of spindle assembly checkpoint (SAC) genes CENPE, CENPF, and DLGAP5 in chemotherapy-resistant AML.

METHODS

RNA-sequencing (RNA-seq) was performed in patients with chemotherapy-resistant AML and chemotherapy-sensitive AML. AML mRNA data from 151 patients with recurrence were downloaded from TCGA. Integrated analysis of the differentially expressed genes (DEGs), GO and KEGG pathways. CENPE, CENPF, or DLGAP5 knockdown cell lines were used to analyse proliferation, apoptosis and cell cycle alterations.

RESULTS

A total of 87 DEGs (48 upregulated and 39 downregulated) were obtained through gene analysis of R/R-AML and a total of 329 DEGs (202 upregulated and 127 downregulated) were obtained in refractory S-AML. Upregulated DEGs were mainly enriched in cell cycle (GO: 0007049, hsa04110) and mitotic cell cycle (GO: 0000278) processes and pathway. Venn diagram analysis identified the most upregulated DEGs (including CENPE, CENPF, and DLGAP5) in chemoresistant AML. The expression of CENPE, CENPF and DLGAP5 in R-AML (TCGA) was significantly higher than that of primary AML (GEO). The proliferation of K562 cells after CENPE and DLGAP5 knockdown was significantly decreased (P= 0.0001 and P= 0.0006). In THP-1 cells, the CCK-8 values after CENPE, CENPF and DLGAP5 knockdown were significantly decreased (P= 0.01, P= 0.0395 and P= 0.0362). Knockdown of CENPE, CENPF and DLGAP5 significantly increased cell apoptosis by regulating Caspase-9, BAX, TP-53 and bcl-2, and induced cell cycle arrested by regulating CDK1, CDK2, CDKN1A, and CyclinD1.

CONCLUSIONS

In conclusion, the mitotic cell cycle-associated genes CENPE, CENPF, and DLGAP5 were upregulated in chemotherapy-resistant AML patients and might be useful for predicting poor prognosis.

The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing

RNA splicing, transcription and the DNA damage response are intriguingly linked in mammals but the underlying mechanisms remain poorly understood. Using an in vivo biotinylation tagging approach in mice, we show that the splicing factor XAB2 interacts with the core spliceosome and that it binds to spliceosomal U4 and U6 snRNAs and pre-mRNAs in developing livers. XAB2 depletion leads to aberrant intron retention, R-loop formation and DNA damage in cells. Studies in illudin S-treated cells and Csb^m/m developing livers reveal that transcription-blocking DNA lesions trigger the release of XAB2 from all RNA targets tested. Immunoprecipitation studies reveal that XAB2 interacts with ERCC1-XPF and XPG endonucleases outside nucleotide excision repair and that the trimeric protein complex binds RNA:DNA hybrids under conditions that favor the formation of R-loops. Thus, XAB2 functionally links the spliceosomal response to DNA damage with R-loop processing with important ramifications for transcription-coupled DNA repair disorders.

XPA-binding protein (XAB)-2 is the human homologue of the yeast pre-mRNA splicing factor Syf1. Here the authors use an in vivo biotinylation tagging approach to show XAB2’s role in DNA repair, RNA splicing and transcription during mammalian development.

Analyses stratified by maternal age and recombination further characterize genes associated with maternal nondisjunction of chromosome 21

OBJECTIVE

In our previous work, we performed the first genome-wide association study to find genetic risk factors for maternal nondisjunction of chromosome 21. The objective of the current work was to perform stratified analyses of the same dataset to further elucidate potential mechanisms of genetic risk factors.

METHODS

We focused on loci that were statistically significantly associated with maternal nondisjunction based on this same dataset in our previous study and performed stratified association analyses in seven subgroups defined by age and meiotic recombination profile. In each analysis, we contrasted a different subgroup of mothers with the same set of fathers, the mothers serving as cases (phenotype: meiotic nondisjunction of chromosome 21) and the fathers as controls.

RESULTS

Our stratified analyses identified several genes whose patterns of association are consistent with generalized effects across groups, as well as other genes that are consistent with specific effects in certain groups.

CONCLUSIONS

While our results are epidemiological in nature and cannot conclusively prove mechanisms, we identified a number of patterns that are consistent with specific mechanisms. In many cases those mechanisms are strongly supported by available literature on the associated genes.

Dbr1 functions in mRNA processing, intron turnover and human diseases

Pre-mRNA processing and mRNA stability play direct roles in controlling protein abundance in a cell. Before the mRNA can be translated into a protein, the introns in the pre-mRNA transcripts need to be removed by splicing, such that exons can be ligated together and can code for a protein. In this process, the function of the RNA lariat debranching enzyme or Dbr1 provides a rate-limiting step in the intron turnover process and possibly regulating the production of translation competent mRNAs. Surprising new roles of Dbr1 are emerging in cellular metabolism which extends beyond intron turnover processes, ranging from splicing regulation to translational control. In this review, we highlight the importance of the Dbr1 enzyme, its structure and how anomalies in its function could relate to various human diseases.

RHOAming Through the Nucleotide Excision Repair Pathway as a Mechanism of Cellular Response Against the Effects of UV Radiation

Typical Rho GTPases include the enzymes RhoA, Rac1, and Cdc42 that act as molecular switches to regulate essential cellular processes in eukaryotic cells such as actomyosin dynamics, cell cycle, adhesion, death and differentiation. Recently, it has been shown that different conditions modulate the activity of these enzymes, but their functions still need to be better understood. Here we examine the interplay between RhoA and the NER (Nucleotide Excision Repair) pathway in human cells exposed to UVA, UVB or UVC radiation. The results show high levels and accumulation of UV-induced DNA lesions (strand breaks and cyclobutane pyrimidine dimers, CPDs) in different cells with RhoA loss of function (LoF), either by stable overexpression of negative dominant RhoA (RhoA-N19 mutant), by inhibition with C3 toxin or by transient silencing with siRNA. Cells under RhoA LoF showed reduced levels of γH2AX, p-Chk1 (Ser345) and p-p53 (Ser15) that reflected causally in their accumulation in G1/S phases, in low survival rates and in reduced cell proliferation, also in accordance with the energy of applied UV light. Even NER-deficient cells (XPA, XPC) or DNA translesion synthesis (TLS)-deficient cells (XPV) showed substantial hypersensitivity to UV effects when previously submitted to RhoA LoF. In contrast, analyses of apoptosis, necrosis, autophagy and senescence revealed that all cells displaying normal levels of active RhoA (RhoA-GTP) are more resistant to UV-promoted cell death. This work reaffirms the role of RhoA protein signaling in protecting cells from damage caused by UV radiation and demonstrates relevant communicating mechanisms between actin cytoskeleton and genomic stability.

Measuring Cancer Hallmark Mediation of the TET1 Glioma Survival Effect with Linked Neural-Network Based Mediation Experiments

This paper examines the effect of TET1 expression on survival in glioma patients using open-access data from the Genomic Data Commons. A neural network-based survival model was built on expression data from a selection of genes most affected by TET1 knockdown with a median cross-validated survival concordance of 82.5%. A synthetic experiment was then conducted that linked two separately trained neural networks: a multitask model estimating cancer hallmark gene expression from TET1 expression, and a survival neural network. This experiment quantified the mediation of the TET1 survival effect through eight cancer hallmarks: apoptosis, cell cycle, cell death, cell motility, DNA repair, immune response, two phosphorylation pathways, and a randomized gene sets. Immune response, DNA repair, and apoptosis displayed greater mediation than the randomized gene set. Cell motility was inversely associated with only 12.5% mediated concordance. We propose the neural network linkage mediation experiment as an approach to collecting evidence of hazard mediation relationships with prognostic capacity useful for designing interventions.

XAB2 depletion induces intron retention in POLR2A to impair global transcription and promote cellular senescence

XAB2 is a multi-functional protein participating processes including transcription, splicing, DNA repair and mRNA export. Here, we report POLR2A, the largest catalytic subunit of RNA polymerase II, as a major target gene down-regulated after XAB2 depletion. XAB2 depletion led to severe splicing defects of POLR2A with significant intron retention. Such defects resulted in substantial loss of POLR2A at RNA and protein levels, which further impaired global transcription. Treatment of splicing inhibitor madrasin induced similar reduction of POLR2A. Screen using TMT-based quantitative proteomics identified several proteins involved in mRNA surveillance including Dom34 with elevated expression. Inhibition of translation or depletion of Dom34 rescued the expression of POLR2A by stabilizing its mRNA. Immuno-precipitation further confirmed that XAB2 associated with spliceosome components important to POLR2A expression. Domain mapping revealed that TPR motifs 2–4 and 11 of XAB2 were critical for POLR2A expression by interacting with SNW1. Finally, we showed POLR2A mediated cell senescence caused by XAB2 deficiency. Depletion of XAB2 or POLR2A induced cell senescence by up-regulation of p53 and p21, re-expression of POLR2A after XAB2 depletion alleviated cellular senescence. These data together support that XAB2 serves as a guardian of POLR2A expression to ensure global gene expression and antagonize cell senescence.

Single-Cell Transcriptomes Reveal Characteristic Features of Mouse Hepatocytes with Liver Cholestatic Injury

Hepatocytes are the main parenchymal cells of the liver and play important roles in liver homeostasis and disease process. The heterogeneity of normal hepatocytes has been reported, but there is little knowledge about hepatocyte subtype and distinctive functions during liver cholestatic injury. Bile duct ligation (BDL)-induced mouse liver injury model was employed, and single-cell RNA sequencing was performed. Western blot and qPCR were used to study gene expression. Immunofluoresence was employed to detect the expressions of marker genes in hepatocytes. We detected a specific hepatocyte cluster (BDL-6) expressing extracellular matrix genes, indicating these hepatocytes might undergo epithelia-mesenchymal transition. Hepatocytes of BDL-6 also performed tissue repair functions (such as angiogenesis) during cholestatic injury. We also found that four clusters of cholestatic hepatocytes (BDL-2, BDL-3, BDL-4, and BDL-5) were involved in inflammatory process in different ways. To be specific, BDL-2/3/5 were inflammation-regulated hepatocytes, while BDL-4 played a role in cell chemotaxis. Among these four clusters, BDL-5 was special. because the hepatocytes of BDL-5 were proliferating hepatocytes. Our analysis provided more knowledge of hepatocyte distinctive functions in injured liver and gave rise to future treatment aiming at hepatocytes.

Identification and validation of key genes associated with non-small-cell lung cancer

Non-small-cell lung cancer (NSCLC) is one of the main causes of death induced by cancer globally. However, the molecular aberrations in NSCLC patients remain unclearly. In the present study, four messenger RNA microarray datasets (GSE18842, GSE40275, GSE43458, and GSE102287) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between NSCLC tissues and adjacent lung tissues were obtained from GEO2R and the overlapping DEGs were identified. Moreover, functional and pathway enrichment were performed by Funrich, while the protein-protein interaction (PPI) network construction were obtained from STRING and hub genes were visualized and identified by Cytoscape software. Furthermore, validation, overall survival (OS) and tumor staging analysis of selected hub genes were performed by GEPIA. A total of 367 DEGs (95 upregulated and 272 downregulated) were obtained through gene integration analysis. The PPI network consisted of 94 nodes and 1036 edges in the upregulated DEGs and 272 nodes and 464 edges in the downregulated DEGs, respectively. The PPI network identified 46 upregulated and 27 downregulated hub genes among the DEGs, and six (such as CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M) of that have not been identified to be associated with NSCLC so far. Moreover, the expression differences of the mentioned hub genes were consistent with that in lung adenocarcinoma and lung squamous cell carcinoma in the TCGA database. Further analysis showed that all the six hub genes were associated with tumor staging except MYH11, while only the upregulated DEG CENPE was associated with the worse OS of patients with NSCLC. In conclusion, the current study showed that CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M might be the key genes contributed to tumorigenesis or tumor progression in NSCLC, further functional study is needed to explore the involved mechanisms.

Mechanisms of kinesin-7 CENP-E in kinetochore-microtubule capture and chromosome alignment during cell division

Chromosome congression is essential for faithful chromosome segregation and genomic stability in cell division. Centromere-associated protein E (CENP-E), a plus-end-directed kinesin motor, is required for congression of pole-proximal chromosomes in metaphase. CENP-E accumulates at the outer plate of kinetochores and mediates the kinetochore-microtubule capture. CENP-E also transports the chromosomes along spindle microtubules towards the equatorial plate. CENP-E interacts with Bub1-related kinase, Aurora B and core kinetochore components during kinetochore-microtubule attachment. In this review, we introduce the structures and mechanochemistry of kinesin-7 CENP-E. We highlight the complicated interactions between CENP-E and partner proteins during chromosome congression. We summarise the detailed roles and mechanisms of CENP-E in mitosis and meiosis, including the kinetochore-microtubule capture, chromosome congression/alignment in metaphase and the regulation of spindle assembly checkpoint. We also shed a light on the roles of CENP-E in tumourigenesis and CENP-E's specific inhibitors.

CENPE expression is associated with its DNA methylation status in esophageal adenocarcinoma and independently predicts unfavorable overall survival

Centrosome-associated protein E (CENPE) is a plus end-directed kinetochore motor protein, which plays a critical role in mitosis. In this in silico study, using data from the Cancer Genome Atlas-Esophageal Carcinoma (TCGA-ESCA), we analyzed the expression profile of CENPE mRNA in esophageal squamous cell carcinoma (ESCC) and adenocarcinoma (EA), its independent prognostic value and the potential mechanisms of its dysregulation in EA. Results showed that both ESCC and EA tissues had significantly elevated CENPE expression compared with their respective adjacent normal tissues. However, Kaplan-Meier survival curves showed that high CENPE was associated with unfavorable OS in EA. Univariate and multivariate analysis confirmed that CENPE expression was an independent indicator of unfavorable OS in EA patients, as a continuous variable (HR: 1.861, 95%CI: 1.235–2.806, p = 0.003) or as categorical variables (HR: 2.550, 95%CI: 1.294–5.025, p = 0.007). However, CENPE expression had no prognostic value in ESCC. Compared with the methylation status in normal samples, 3 CpG sites were hypomethylated (cg27388036, cg27443373, and cg24651824) in EA, among which two sites (cg27443373 and cg24651824) showed moderately negative correlation with CENPE expression. In addition, we also found that although heterozygous loss (-1) was frequent in EA (50/88, 56.8%), it was not necessarily associated with decreased CENPE expression compared with the copy neutral (0) cases. The methylation of the -1 group was significantly lower than that of the +1/0 group (p = 0.04). Based on these findings, we infer that CENPE upregulation in EA might serve as a valuable indicator of unfavorable OS. The methylation status of cg27443373 and cg24651824 might play a critical role in modulating CENPE expression.

CENP-E as a target for cancer therapy: Where are we now?

In 2015, more than 1.6 million new cancer cases with 589,430 deaths were estimated over worldwide. Cancer is a complex disease with abnormal cell growth control which is hallmarked by chromosome misalignment and consequently genomic instability. Mitosis is a well-known target for chemotherapy as taxol and colchicines inhibit tumor cell division by inhibiting mitotic spindle plasticity. Accumulating evidence has revealed that the Centromere-associated Protein E (CENP-E) is expressed during mitosis and plays critical roles in inaccurate chromosome alignment. Thus, CENP-E might represent a druggable target for several solid tumors which do not have targeted therapy. Moreover, CENP-E appears during the mitotic phase of cell cycle and not implicates in the neuronal function. Hence, we will shed light on CENP-E as an emerging target for chemotherapy in clinical oncology and highlight challenges and excitement down the road.

The Identification of Core Gene Expression Signature in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is one of the most common malignancies, which causes serious financial burden worldwide. This study aims to investigate the potential mechanisms contributing to HCC and identify core biomarkers. The HCC gene expression profile GSE41804 was picked out to analyze the differentially expressed genes (DEGs). Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out using DAVID. We constructed a protein-protein interaction (PPI) network to visualize interactions of the DEGs. The survival analysis of these hub genes was conducted to evaluate their potential effects on HCC. In this analysis, 503 DEGs were captured (360 downregulated genes and 143 upregulated genes). Meanwhile, 15 hub genes were identified. GO analysis showed that the DEGs were mainly enriched in oxidative stress, cell cycle, and extracellular structure. KEGG analysis suggested the DEGs were enriched in the absorption, metabolism, and cell cycle pathway. PPI network disclosed that the top3 modules were mainly enriched in cell cycle, oxidative stress, and liver detoxification. In conclusion, our analysis uncovered that the alterations of oxidative stress and cell cycle are two major signatures of HCC. TOP2A, CCNB1, and KIF4A might promote the development of HCC, especially in proliferation and differentiation, which could be novel biomarkers and targets for diagnosis and treatment of HCC.

Expression signature of ten genes predicts the survival of patients with estrogen receptor positive-breast cancer that were treated with tamoxifen

Although tamoxifen is the most frequently used drug for the treatment of estrogen receptor positive (ER⁺)-breast cancer (BRCA), its efficacy varies between patients. In the present study, Cox multivariate regression of the relative mRNA expression levels in two microarray-based datasets (GSE17005 and GSE26971) was employed to develop a risk score model to evaluate the outcome of patients with BRCA in the GSE17005 dataset. A total of ten genes were used to develop the prediction model for the survival of tamoxifen-treated patients with breast cancer. The survival time of patients in the low risk score group was significantly longer compared with patients in the high risk score group. This observation was validated in three other datasets (GSE26971, GSE22219 and GSE56884). The prognostic effect of the clinicopathological indicators and the risk score were tested with the 5-year event receiving operating characteristic curve, and the risk score had an improved prognostic value in patients with ER⁺-BRCA with an area under the curve value of 0.733 compared with the factors of age, tumor stage, tumor grade, chemotherapy, lymph invasion and tumor size. The risk score was significantly associated with the tumor-node-metastasis stage and grade, but was independent of age, sex, lymph invasion and tumor size. In summary, the risk model for breast cancer using the expression signature of ten genes may be an important indicator for predicting the survival of patients with ER⁺-breast cancer and treated with tamoxifen.

Maintenance of genome stability: the unifying role of interconnections between the DNA damage response and RNA-processing pathways

Endogenous and exogenous factors can severely affect the integrity of genetic information by inducing DNA damage and impairing genome stability. The protection of genome integrity is ensured by the so-called "DNA damage response" (DDR), a set of evolutionary-conserved events that, triggered upon DNA damage detection, arrests the cell cycle, and attempts DNA repair. Here, we review the role of the DDR proteins as post-transcriptional regulators of gene expression, in addition to their roles in DNA damage recognition, signaling, and repair. At the same time, we discuss recent insights into how pre-mRNA splicing factors go beyond their splicing activities and play direct functions in detecting, signaling, and repairing DNA damage. The importance of extensive two-way crosstalk and interaction between the RNA processing and the DDR stems from growing evidence that the defects of their communication lead to genomic instability.

PRPF8 is important for BRCA1-mediated homologous recombination

Disruption of RNA splicing causes genome instability, which could contribute to cancer etiology. Furthermore, RNA splicing is an emerging anti-cancer target. Thus, we have evaluated the influence of the spliceosome factor PRPF8 and the splicing inhibitor Pladienolide B (PlaB) on homologous recombination (HR). We find that PRPF8 depletion and PlaB treatment cause a specific defect in homology-directed repair (HDR), and single strand annealing (SSA), which share end resection as a common intermediate, and BRCA1 as a required factor. Furthermore, PRPF8 depletion and PlaB treatment cause reduced end resection detected as chromatin-bound RPA, BRCA1 foci in response to damage, and histone acetylation marks that are associated with BRCA1-mediated HR. We also identified distinctions between PlaB and PRPF8 depletion, in that PlaB also reduces 53BP1 foci, and BRCA1 expression. Furthermore loss of 53BP1, which rescues SSA in BRCA1 depleted cells, and partially rescues SSA in PRPF8 depleted cells, has no effect on SSA in PlaB treated cells. Finally, while PRPF8 depletion has no obvious effect on the integrity of interchromatin granules, PlaB disrupts these structures. These findings indicate that PRPF8 is important for BRCA1-mediated HR, whereas PlaB also has a more general effect on the DNA damage response and nuclear organization.

Neuroblastoma cells depend on HDAC11 for mitotic cell cycle progression and survival

The number of long-term survivors of high-risk neuroblastoma remains discouraging, with 10-year survival as low as 20%, despite decades of considerable international efforts to improve outcome. Major obstacles remain and include managing resistance to induction therapy, which causes tumor progression and early death in high-risk patients, and managing chemotherapy-resistant relapses, which can occur years after the initial diagnosis. Identifying and validating novel therapeutic targets is essential to improve treatment. Delineating and deciphering specific functions of single histone deacetylases in neuroblastoma may support development of targeted acetylome-modifying therapeutics for patients with molecularly defined high-risk neuroblastoma profiles. We show here that HDAC11 depletion in MYCN-driven neuroblastoma cell lines strongly induces cell death, mostly mediated by apoptotic programs. Genes necessary for mitotic cell cycle progression and cell division were most prominently enriched in at least two of three time points in whole-genome expression data combined from two cell systems, and all nine genes in these functional categories were strongly repressed, including CENPA, KIF14, KIF23 and RACGAP1. Enforced expression of one selected candidate, RACGAP1, partially rescued the induction of apoptosis caused by HDAC11 depletion. High-level expression of all nine genes in primary neuroblastomas significantly correlated with unfavorable overall and event-free survival in patients, suggesting a role in mediating the more aggressive biological and clinical phenotype of these tumors. Our study identified a group of cell cycle-promoting genes regulated by HDAC11, being both predictors of unfavorable patient outcome and essential for tumor cell viability. The data indicate a significant role of HDAC11 for mitotic cell cycle progression and survival of MYCN-amplified neuroblastoma cells, and suggests that HDAC11 could be a valuable drug target.