CDK10 in Gastrointestinal Cancers: Dual Roles as a Tumor Suppressor and Oncogene

Biomarker discovery with quantum neural networks: a case-study in CTLA4-activation pathways

BACKGROUND

Biomarker discovery is a challenging task due to the massive search space. Quantum computing and quantum Artificial Intelligence (quantum AI) can be used to address the computational problem of biomarker discovery from genetic data.

METHOD

We propose a Quantum Neural Networks architecture to discover genetic biomarkers for input activation pathways. The Maximum Relevance-Minimum Redundancy criteria score biomarker candidate sets. Our proposed model is economical since the neural solution can be delivered on constrained hardware.

RESULTS

We demonstrate the proof of concept on four activation pathways associated with CTLA4, including (1) CTLA4-activation stand-alone, (2) CTLA4-CD8A-CD8B co-activation, (3) CTLA4-CD2 co-activation, and (4) CTLA4-CD2-CD48-CD53-CD58-CD84 co-activation.

CONCLUSION

The model indicates new genetic biomarkers associated with the mutational activation of CLTA4-associated pathways, including 20 genes: CLIC4, CPE, ETS2, FAM107A, GPR116, HYOU1, LCN2, MACF1, MT1G, NAPA, NDUFS5, PAK1, PFN1, PGAP3, PPM1G, PSMD8, RNF213, SLC25A3, UBA1, and WLS. We open source the implementation at: https://github.com/namnguyen0510/Biomarker-Discovery-with-Quantum-Neural-Networks .

Exercise-Induced miR-210 Promotes Cardiomyocyte Proliferation and Survival and Mediates Exercise-Induced Cardiac Protection against Ischemia/Reperfusion Injury

Exercise can stimulate physiological cardiac growth and provide cardioprotection effect in ischemia/reperfusion (I/R) injury. MiR-210 is regulated in the adaptation process induced by exercise; however, its impact on exercise-induced physiological cardiac growth and its contribution to exercise-driven cardioprotection remain unclear. We investigated the role and mechanism of miR-210 in exercise-induced physiological cardiac growth and explored whether miR-210 contributes to exercise-induced protection in alleviating I/R injury. Here, we first observed that regular swimming exercise can markedly increase miR-210 levels in the heart and blood samples of rats and mice. Circulating miR-210 levels were also elevated after a programmed cardiac rehabilitation in patients that were diagnosed of coronary heart diseases. In 8-week swimming model in wild-type (WT) and miR-210 knockout (KO) rats, we demonstrated that miR-210 was not integral for exercise-induced cardiac hypertrophy but it did influence cardiomyocyte proliferative activity. In neonatal rat cardiomyocytes, miR-210 promoted cell proliferation and suppressed apoptosis while not altering cell size. Additionally, miR-210 promoted cardiomyocyte proliferation and survival in human embryonic stem cell-derived cardiomyocytes (hESC-CMs) and AC16 cell line, indicating its functional roles in human cardiomyocytes. We further identified miR-210 target genes, cyclin-dependent kinase 10 (CDK10) and ephrin-A3 (EFNA3), that regulate cardiomyocyte proliferation and apoptosis. Finally, miR-210 KO and WT rats were subjected to swimming exercise followed by I/R injury. We demonstrated that miR-210 crucially contributed to exercise-driven cardioprotection against I/R injury. In summary, this study elucidates the role of miR-210, an exercise-responsive miRNA, in promoting the proliferative activity of cardiomyocytes during physiological cardiac growth. Furthermore, miR-210 plays an essential role in mediating the protective effects of exercise against cardiac I/R injury. Our findings suggest exercise as a potent nonpharmaceutical intervention for inducing miR-210, which can alleviate I/R injury and promote cardioprotection.

RNF115 aggravates tumor progression through regulation of CDK10 degradation in thyroid carcinoma

BACKGROUND

RING Finger Protein 115 (RNF115), a notable E3 ligase, is known to modulate tumorigenesis and metastasis. In our investigation, we endeavor to unravel the putative function and inherent mechanism through which RNF115 influences the evolution of thyroid carcinoma (THCA).

METHODS

We analyzed RNF115 expression in THCA using the Cancer Genome Atlas (TCGA) database. The influence of RNF115 on the progression of THCA was evaluated using both in vitro and in vivo experimental approaches. The protein regulated by RNF115 was identified through bioinformatics analysis, and its biological significance was further explored.

RESULTS

In both THCA tissues and cells, RNF115 showed elevated expression levels. Enhanced expression of RNF115 fostered cell proliferation, tumor growth, and the exacerbation of epithelial-mesenchymal transition (EMT) in THCA, while also promoting tumor lung metastasis. Bioinformatics analysis identified cyclin-dependent kinase 10 (CDK10) as a downstream target of RNF115, which was found to be ubiquitinated and degraded by RNF115 in THCA cells. Functionally, overexpression of CDK10 was found to counteract the promotion of malignant phenotype in THCA induced by RNF115. From a mechanistic perspective, RNF115 activated the Raf-1 pathway and enhanced cancer cell cycle progression by degrading CDK10 in THCA cells.

CONCLUSION

RNF115 triggers cell proliferation, EMT, and tumor metastasis by ubiquitinating and degrading CDK10. The regulation of the Raf-1 pathway and cell cycle progression in THCA may be profoundly influenced by this process.

CDK10 suppresses metastasis of lung adenocarcinoma through inhibition of the ETS2/c-Raf/p-MEK/p-ERK signaling loop

The repertoire of aberrant signaling underlying the pathogenesis of lung adenocarcinoma remains largely uncharacterized, which precludes an efficient therapy for these patients, especially when distant metastasis occurs. Cyclin-dependent kinase 10 (CDK10) has been reported to modulate the progression of malignant tumors; however, contradictory effects have been found among different types of malignant tumors. In the present study, we found that CDK10 was downregulated in lung adenocarcinoma compared with the paired adjacent normal lung tissue, and lower expression level of CDK10 was associated with more frequent N2 staged lymph node and distant metastasis, higher TNM stage, and shorter overall survival. Further study indicated that CDK10 inhibited the migration and invasion abilities with no impact on the proliferation of lung adenocarcinoma cells. Mechanistically, CDK10 could bind to and promote the degradation of ETS2, a transcription factor for C-RAF and MMP2/9, thereby inactivating the downstream c-Raf/p-MEK/p-ERK pathway that drives epithelial-mesenchymal transition and impairing the expression of matrix metalloproteinases involved in cell invasion. In addition, the p-MEK/p-ERK pathway conducts a positive feedback regulation on the expression of ETS2. Knockdown of CDK10 in human lung adenocarcinoma cells significantly promoted the formation of metastatic foci in lungs in a xenograft mouse model. In conclusion, CDK10 suppresses metastasis of lung adenocarcinoma by disrupting the ETS2/c-Raf/p-MEK/p-ERK/ETS2 signaling and MMP2/9, providing a new therapeutic target for the treatment of lung adenocarcinoma with metastasis.

Copy number variants landscape of multiple cancers and clinical applications based on NGS gene panel

BACKGROUND

The rapid adoption of next-generation sequencing in clinical oncology has enabled detection of molecular biomarkers which are shared between multiple tumour types. Intra-tumour heterogeneity is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the tumour-related copy number variants (CNVs), as key regulators of cancer origination, development, and progression, across various types of cancers are poorly understood.

METHODS

We performed pan-cancer CNV analysis of cancer-related genes in 15 types of cancers including 1438 cancerous patients by next-generation sequencing using a commercially available pan-cancer panel (Onco PanScan™). Downstream bioinformatics analysis was performed in order to detect CNVs, cluster analysis of the found CNVs, and comparison of the frequency of gained CNVs between different types of cancers. LASSO analysis was used for identification of the most important CNVs.

RESULTS

We also identified 523 CNVs among which 16 CNVs were common while 22 CNVs were caner-specific CNVs. Meanwhile, FAM58A was most commonly found in all studied cancers in this study and significant differences were found in FAM58A between female and male patients (p = .001). Common CNVs, such as FOXA1, NFKBIA, HEY1, MECOM, CHD7, AGO2, were mutated in 6.79%, 8.45%, 7.51%, 6.43%, 7.59%, 8.16% of tumours, while most of these mutations have proven roles in positive regulation of transcription from RNA polymerase II promoter. 11 features including sex, DIS3, EPHB1, ERBB2, FLT1, HCK, KEAP1, MYD88, PARP3, TBX3, and TOP2A were found as the key features for classification of cancers using CNVs.

CONCLUSION

The 16 common CNVs between cancers can be used to identify the target of pan-cancer drug design and targeted therapies. Additionally, 22 caner-specific CNVs can be used as unique diagnostic markers for each cancer type.

The roles, molecular interactions, and therapeutic value of CDK16 in human cancers

Cyclin-dependent kinase 16 (CDK16) is an orphan "cyclin-dependent kinase" (CDK) involved in the cell cycle, vesicle trafficking, spindle orientation, skeletal myogenesis, neurite outgrowth, secretory cargo transport, spermatogenesis, glucose transportation, cell apoptosis, cell growth and proliferation, metastasis, and autophagy. Human CDK16 is located on chromosome Xp11.3 and is related to X-linked congenital diseases. CDK16 is commonly expressed in mammalian tissues and may act as an oncoprotein. It is a PCTAIRE kinase in which Cyclin Y or its homologue, Cyclin Y-like 1, regulates activity by binding to the N- and C- terminal regions of CDK16. CDK16 plays a vital role in various cancers, including lung cancer, prostate cancer, breast cancer, malignant melanoma, and hepatocellular carcinoma. CDK16 is a promising biomarker for cancer diagnosis and prognosis. In this review, we summarized and discussed the roles and mechanisms of CDK16 in human cancers.

The Regulation of Cyclins and Cyclin-Dependent Kinases in the Development of Gastric Cancer

Gastric cancer predominantly occurs in adenocarcinoma form and is characterized by uncontrolled growth and metastases of gastric epithelial cells. The growth of gastric cells is regulated by the action of several major cell cycle regulators including Cyclins and Cyclin-dependent kinases (CDKs), which act sequentially to modulate the life cycle of a living cell. It has been reported that inadequate or over-activity of these molecules leads to disturbances in cell cycle dynamics, which consequently results in gastric cancer development. Manny studies have reported the key roles of Cyclins and CDKs in the development and progression of the disease in either in vitro cell culture studies or in vivo models. We aimed to compile the evidence of molecules acting as regulators of both Cyclins and CDKs, i.e., upstream regulators either activating or inhibiting Cyclins and CDKs. The review entails an introduction to gastric cancer, along with an overview of the involvement of cell cycle regulation and focused on the regulation of various Cyclins and CDKs in gastric cancer. It can act as an extensive resource for developing new hypotheses for future studies.

Cyclin-dependent kinases as potential targets for colorectal cancer: past, present and future

Colorectal cancer (CRC) is a common cancer in the world and its prevalence is increasing in developing countries. Deregulated cell cycle traverse is a hallmark of malignant transformation and is often observed in CRC as a result of imprecise activity of cell cycle regulatory components, viz. cyclins and cyclin-dependent kinases (CDKs). Apart from cell cycle regulation, some CDKs also regulate processes such as transcription and have also been shown to be involved in colorectal carcinogenesis. This article aims to review cyclin-dependent kinases as potential targets for CRC. Furthermore, therapeutic candidates to target CDKs are also discussed.

PRES: a webserver for decoding the functional perturbations of RNA editing sites

Rapid progresses in RNA-Seq and computational methods have assisted in quantifying A-to-I RNA editing and altered RNA editing sites have been widely observed in various diseases. Nevertheless, functional characterization of the altered RNA editing sites still remains a challenge. Here, we developed perturbations of RNA editing sites (PRES; http://bio-bigdata.hrbmu.edu.cn/PRES/) as the webserver for decoding functional perturbations of RNA editing sites based on editome profiling. After uploading an editome profile among samples of different groups, PRES will first annotate the editing sites to various genomic elements and detect differential editing sites under the user-selected method and thresholds. Next, the downstream functional perturbations of differential editing sites will be characterized from gain or loss miRNA/RNA binding protein regulation, RNA and protein structure changes, and the perturbed biological pathways. A prioritization module was developed to rank genes based on their functional consequences of RNA editing events. PRES provides user-friendly functionalities, ultra-efficient calculation, intuitive table and figure visualization interface to display the annotated RNA editing events, filtering options and elaborate application notebooks. We anticipate PRES will provide an opportunity for better understanding the regulatory mechanisms of RNA editing in human complex diseases.

Functional characterization of the human Cdk10/Cyclin Q complex

Cyclin-dependent kinases (CDKs) are key players in cell cycle regulation and transcription. The CDK-family member Cdk10 is important for neural development and can act as a tumour suppressor, but the underlying molecular mechanisms are largely unknown. Here, we provide an in-depth analysis of Cdk10 substrate specificity and function. Using recombinant Cdk10/CycQ protein complexes, we characterize RNA pol II CTD, c-MYC and RB1 as in vitro protein substrates. Using an analogue-sensitive mutant kinase, we identify 89 different Cdk10 phosphosites in HEK cells originating from 66 different proteins. Among these, proteins involved in cell cycle, translation, stress response, growth signalling, as well as rRNA, and mRNA transcriptional regulation, are found. Of a set of pan-selective CDK- and Cdk9-specific inhibitors tested, all inhibited Cdk10/CycQ at least five times weaker than their proposed target kinases. We also identify Cdk10 as an in vitro substrate of Cdk1 and Cdk5 at multiple sites, allowing for a potential cross-talk between these CDKs. With this functional characterization, Cdk10 adopts a hybrid position in both cell cycle and transcriptional regulation.