PCTAIRE1-knockdown sensitizes cancer cells to TNF family cytokines

Insights into the structural and functional activities of forgotten Kinases: PCTAIREs CDKs

In cells, signal transduction heavily relies on the intricate regulation of protein kinases, which provide the fundamental framework for modulating most signaling pathways. Dysregulation of kinase activity has been implicated in numerous pathological conditions, particularly in cancer. The druggable nature of most kinases positions them into a focal point during the process of drug development. However, a significant challenge persists, as the role and biological function of nearly one third of human kinases remains largely unknown.Within this diverse landscape, cyclin-dependent kinases (CDKs) emerge as an intriguing molecular subgroup. In human, this kinase family encompasses 21 members, involved in several key biological processes. Remarkably, 13 of these CDKs belong to the category of understudied kinases, and only 5 having undergone broad investigation to date. This knowledge gap underscores the pressing need to delve into the study of these kinases, starting with a comprehensive review of the less-explored ones.Here, we will focus on the PCTAIRE subfamily of CDKs, which includes CDK16, CDK17, and CDK18, arguably among the most understudied CDKs members. To contextualize PCTAIREs within the spectrum of human pathophysiology, we conducted an exhaustive review of the existing literature and examined available databases. This approach resulted in an articulate depiction of these PCTAIREs, encompassing their expression patterns, 3D configurations, mechanisms of activation, and potential functions in normal tissues and in cancer.We propose that this effort offers the possibility of identifying promising areas of future research that extend from basic research to potential clinical and therapeutic applications.

PCTAIRE Protein Kinase 1 (PCTK1) Suppresses Proliferation, Stemness, and Chemoresistance in Colorectal Cancer through the BMPR1B-Smad1/5/8 Signaling Pathway

Colorectal cancer (CRC) is the third most common cancer and a leading cause of cancer-related mortality worldwide. Even with advances in therapy, CRC mortality remains high. Therefore, there is an urgent need to develop effective therapeutics for CRC. PCTAIRE protein kinase 1 (PCTK1) is an atypical member of the cyclin-dependent kinase (CDK) family, and the function of PCTK1 in CRC is poorly understood. In this study, we found that patients with elevated PCTK1 levels had a better overall survival rate in CRC based on the TCGA dataset. Functional analysis also showed that PCTK1 suppressed cancer stemness and cell proliferation by using PCTK1 knockdown (PCTK1-KD) or knockout (PCTK1-KO) and PCTK1 overexpression (PCTK1-over) CRC cell lines. Furthermore, overexpression of PCTK1 decreased xenograft tumor growth and knockout of PCTK1 significantly increased in vivo tumor growth. Moreover, knockout of PCTK1 was observed to increase the resistance of CRC cells to both irinotecan (CPT-11) alone and in combination with 5-fluorouracil (5-FU). Additionally, the fold change of the anti-apoptotic molecules (Bcl-2 and Bcl-xL) and the proapoptotic molecules (Bax, c-PARP, p53, and c-caspase3) was reflected in the chemoresistance of PCTK1-KO CRC cells. PCTK1 signaling in the regulation of cancer progression and chemoresponse was analyzed using RNA sequencing and gene set enrichment analysis (GSEA). Furthermore, PCTK1 and Bone Morphogenetic Protein Receptor Type 1B (BMPR1B) in CRC tumors were negatively correlated in CRC patients from the Timer2.0 and cBioPortal database. We also found that BMPR1B was negatively correlated with PCTK1 in CRC cells, and BMPR1B expression was upregulated in PCTK1-KO cells and xenograft tumor tissues. Finally, BMPR1B-KD partially reversed cell proliferation, cancer stemness, and chemoresistance in PCTK1-KO cells. Moreover, the nuclear translocation of Smad1/5/8, a downstream molecule of BMPR1B, was increased in PCTK1-KO cells. Pharmacological inhibition of Smad1/5/8 also suppressed the malignant progression of CRC. Taken together, our results indicated that PCTK1 suppresses proliferation and cancer stemness and increases the chemoresponse of CRC through the BMPR1B-Smad1/5/8 signaling pathway.

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.

PCTAIRE1 promotes mitotic progression and resistance against antimitotic and apoptotic signals

PCTAIRE1 (also known as CDK16) is a serine-threonine kinase implicated in physiological processes like neuronal development, vesicle trafficking, spermatogenesis and cell proliferation. However, its exact role in cell division remains unclear. In this study, using a library screening approach, we identified PCTAIRE1 among several candidates that resisted mitotic arrest and mitotic cell death induced by polyomavirus small T (PolST) expression in mammalian cells. Our study showed that PCTAIRE1 is a mitotic kinase that localizes at centrosomes during G2 and at spindle poles as the cells enter mitosis, and then at the midbody during cytokinesis. We also report that PCTAIRE1 protein levels fluctuate through the cell cycle and reach their peak at mitosis, during which there is an increase in PCTAIRE1 phosphorylation as well. Interestingly, knockdown of PCTAIRE1 resulted in aberrant mitosis by interfering with spindle assembly and chromosome segregation. Further, we found that PCTAIRE1 promotes resistance of cancer cells to antimitotic drugs, and this underscores the significance of PCTAIRE1 as a potential drug target for overcoming chemotherapeutic resistance. Taken together, these studies establish PCTAIRE1 as a critical mediator of mitotic progression and highlight its role in chemotherapeutic resistance. This article has an associated First Person interview with the first author of the paper.

Cetuximab-siRNA Conjugate Linked Through Cationized Gelatin Knocks Down KRAS G12C Mutation in NSCLC Sensitizing the Cells Toward Gefitinib

Delivery of small-interfering RNA (siRNA) has been of great interest in the past decade for effective gene silencing. To overcome synthetic and regulatory challenges posed by nanoparticle-mediated siRNA delivery, antibody–siRNA conjugate (ARC) platform is emerging as a potential siRNA delivery system suitable for clinical translation. Herein, we have developed a delivery technology based on the ARC platform for stable delivery of siRNA called as Gelatin-Antibody Delivery System (GADS). In GADS, positively charged gelatin acts as a linker between antibody–siRNA and enables the endosomal escape of siRNA for gene silencing postcellular internalization. For proof of concept, we synthesized a scalable GADS conjugate comprising of Cetuximab (CTB), cationized gelatin (cGel) and NSCLC KRAS_G12C-specific siRNA. CTB was chemically conjugated to cGel through an amide link to form the CTB–cGel complex. Thereafter, siRNA was chemically conjugated to the cGel moiety of the complex through the thioether link to form CTB–cGel–siRNA conjugate. RP-HPLC analysis was used to monitor the reaction while gel retardation assay was used to determine siRNA loading capacity. SPR analysis showed the preservation of ligand binding affinity of antibody conjugates with K_D of ∼0.3 nM. Furthermore, cellular internalization study using florescent microscopy revealed receptor-mediated endocytosis. The conjugate targeted EGFR receptor of KRAS mutant NSCLC to specifically knockdown G12C mutation. The oncogene knockdown sensitized the cells toward small molecule inhibitor—Gefitinib causing ∼70% loss in cell viability. Western blot analysis revealed significant downregulation for various RAS downstream proteins postoncogene knockdown. Comparison of the efficiency of GADS vis-à-vis positive siRNA control and CRISPR–Cas9-based knockout of KRAS Exon 2 in the NCI-H23 NSCLC cell line suggests GADS as a potential technology for clinical translation of gene therapy.

Transcriptomic Analysis in Liquid Biopsy Identifies Circulating PCTAIRE-1 mRNA as a Biomarker in NSCLC

BACKGROUND/AIM

Circulating mRNA can be a useful source of cancer biomarkers. We took advantage of direct transcriptomic analysis in plasma RNA to identify novel mRNA markers for non-small cell lung cancer (NSCLC).

PATIENTS AND METHODS

Plasma RNA from NSCLC patients and healthy individuals was profiled with cDNA-mediated annealing, selection, extension and ligation (DASL) microarrays. The microarray results were further validated in plasma RNA.

RESULTS

Through RNA profiling and online database mining, four gene transcripts were filtered as candidate markers of NSCLC. After validation, the PCTAIRE-1 transcript was identified as a circulating mRNA marker. The diagnostic potential of PCTAIRE-1 was evaluated by receiver operating characteristic curve analysis, which gave a sensitivity and specificity of 60% and 85%, respectively. In addition, high plasma PCTK1 levels were also correlated with poor progression-free survival (p=0.008).

CONCLUSION

Circulating mRNA can be profiled with the DASL assay. From the profile, PCTAIRE-1 RNA in the plasma we discovered as a novel diagnostic/prognostic biomarker and an indicator of poor survival in NSCLC patients.

The Roles of Cyclin-Dependent Kinases in Cell-Cycle Progression and Therapeutic Strategies in Human Breast Cancer

Cyclin-dependent kinases (CDKs) are serine/threonine kinases whose catalytic activities are regulated by interactions with cyclins and CDK inhibitors (CKIs). CDKs are key regulatory enzymes involved in cell proliferation through regulating cell-cycle checkpoints and transcriptional events in response to extracellular and intracellular signals. Not surprisingly, the dysregulation of CDKs is a hallmark of cancers, and inhibition of specific members is considered an attractive target in cancer therapy. In breast cancer (BC), dual CDK4/6 inhibitors, palbociclib, ribociclib, and abemaciclib, combined with other agents, were approved by the Food and Drug Administration (FDA) recently for the treatment of hormone receptor positive (HR+) advanced or metastatic breast cancer (A/MBC), as well as other sub-types of breast cancer. Furthermore, ongoing studies identified more selective CDK inhibitors as promising clinical targets. In this review, we focus on the roles of CDKs in driving cell-cycle progression, cell-cycle checkpoints, and transcriptional regulation, a highlight of dysregulated CDK activation in BC. We also discuss the most relevant CDK inhibitors currently in clinical BC trials, with special emphasis on CDK4/6 inhibitors used for the treatment of estrogen receptor-positive (ER+)/human epidermal growth factor 2-negative (HER2−) M/ABC patients, as well as more emerging precise therapeutic strategies, such as combination therapies and microRNA (miRNA) therapy.

The role of phospholipase Cβ on the plasma membrane and in the cytosol: How modular domains enable novel functions

Phospholipase Cβ (PLCβ) is a signaling enzyme activated by G proteins to generate calcium signals. The catalytic core of PLCβ is surrounded by modular domains that mediate the interaction of the enzyme with known protein partners on the plasma membrane. The C-terminal region PLCβ contains a novel coiled-coil domain that is required for Gαq binding and activation. Recent work has shown that this domain also binds a number of cytosolic proteins that regulate protein translation, and that these proteins compete with Gαq for PLCβ binding. The ability of PLCβ to shuttle between the cytosol to impact protein translation and the plasma membrane to mediate calcium signals puts PLCβ in a central role in cell function.

Novel Therapeutic Targets in Cutaneous Squamous Cell Carcinoma

Cutaneous squamous cell carcinoma (SCC) is one of the common cancers in Caucasians, accounting for 20–30% of cutaneous malignancies. The risk of metastasis is low in most patients; however, aggressive SCC is associated with very high mortality and morbidity. Although cutaneous SCC can be treated with surgical removal, radiation and chemotherapy singly or in combination, the prognosis of patients with metastatic SCC is poor. Recently, the usage of immune checkpoint blockades has come under consideration. To develop effective therapies that are less toxic than existing ones, it is crucial to achieve a detailed characterization of the molecular mechanisms that are involved in cutaneous SCC pathogenesis and to identify new drug targets. Recent studies have identified novel molecules that are associated with SCC carcinogenesis and progression. This review focuses on recent advances in molecular studies involving SCC tumor development, as well as in new therapeutics that have become available to clinicians.

Long non-coding RNA KCNQ1OT1 mediates the growth of hepatocellular carcinoma by functioning as a competing endogenous RNA of miR-504

Accumulating evidence highlights the fact that long non‑coding RNAs (lncRNAs) serve as critical factors in the growth of hepatocellular carcinoma (HCC). The dysregulation of lncRNA KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1) has been reported in numerous human benign diseases. However, the role of KCNQ1OT1 in human HCC remains poorly understood. In this study, we demonstrated that the expression of KCNQ1OT1 was abnormally increased in HCC tissues. The ectopic high expression of KCNQ1OT1 was associated with liver cirrhosis, a larger tumor size, an advanced TNM stage, and a worse overall survival and tumor‑free survival. For the first time, to the best of our knowledge, we report that KCNQ1OT1 knockdown results in a decreased cell viability and colony formation ability, and an increased rate of apoptosis in vitro. The results from our in vivo results demonstrated that KCNQ1OT1 silencing attenuated tumor growth by impairing cell proliferation. Additionally, we found that KCNQ1OT1 exerted its effects partly by relying on the microRNA‑504 (miR‑504)‑mediated regulation of cyclin‑dependent kinase 16 (CDK16), in addition to the regulation of the glycogen synthase kinase 3β (GSK3β)/β‑catenin/Bcl‑2 signaling pathway. The present study revealed the functions and mechanisms of action of lncRNA KCNQ1OT1 regarding its role in promoting the growth of HCC. Thus, lncRNA KCNQ1OT1 may prove to be a potential therapeutic target for human HCC.

Phospholipase Cβ1 regulates proliferation of neuronal cells

Cells have developed lineage-specific mechanisms to control proliferation and drive morphologic changes upon differentiation. A hallmark of differentiation is the assembly of signaling molecules that transduce extracellular signals, such as the production of the G protein-regulated enzyme phospholipase Cβ (PLCβ), which generates calcium signals from sensory stimuli. We found that in most cancerous cell lines there is positive correlation between PLCβ1 levels and cell proliferation. In cells of neuronal lineage, however, reducing PLCβ1 levels increases the rate of proliferation. Using a combination of biochemical and biophysical methods, we find that, in the G₁ phase, a cytosolic population of PLCβ1 associates with cyclin-dependent kinase 16 (CDK16), a neuron-specific enzyme that is activated by cyclin Y to inactivate the antioncogenic protein p27^Kip1. Binding of PLCβ1 directly inhibits CDK16 activity and in turn reduces the ability of cells to enter the S phase. Activation of Gα_q by carbachol causes movement of PLCβ from the cytosol to the plasma membrane, reducing its association with CDK16. Similarly, the overexpression of activated Gα_q moves PLCβ1 to the membrane, reverses G₁ arrest, and promotes proliferation, thereby connecting external stimuli with cell proliferation. Our results present a model in which the transient high expression of PLCβ1 that occurs at the onset of differentiation arrests cells in the G₁ phase through its association with CDK16 and allows CDK16 to transition to its postmitotic function of neurite outgrowth and trafficking of synaptic vesicles. The novel role of PLCβ1 in neuronal cell proliferation offers a unique interaction that can be manipulated to guide cells into a neuronal phenotype or to develop therapies for neuroblastomas.-Garwain, O., Valla, K., Scarlata, S. Phospholipase Cβ1 regulates proliferation of neuronal cells.

Up-regulation of CDK16 by multiple mechanisms in hepatocellular carcinoma promotes tumor progression

Background

Hepatocellular carcinoma (HCC) remains difficult to cure due to lack of effective treatment and the molecular mechanisms are complex and not completely understood. In this study, We investigated the role of CDK16 in tumor progression of HCC.

Methods

We interrogated the expression level of CDK16 by polymerase chain reaction and immunohistochemistry(IHC) and studied its clinical significance. The functional role of CDK16 on HCC was studied via gain and loss of function in vitro and in vivo. Luciferase reporter assay and Chromatin immunoprecipitation(ChIP) assay were performed to investigate the transcriptional and post-transcriptional mechanisms involved in the regulation of CDK16.

Results

CDK16 expression was significantly up-regulated in HCC and higher expression of CDK16 was positively correlated with aggressive clinicopathological phenotype and poorer survival rates. Functionally, knockdown of CDK16 suppressed proliferation in vitro and in vivo. Inactivation of CDK16 also induced apoptosis and cell cycle arrest. Most importantly, CDK16 promoted epithelial mesenchymal transition and tumor invasion by activating β-catenin signaling. In addition, We identified E2F1 as a positive transcriptional regulator of CDK16. Moreover, down regulation of miR-125b-5p enhanced CDK16 expression at post-transcriptional level.

Conclusion

We provided the first evidence that CDK16 is an bona fide oncogene in HCC, and multiple activating mechanisms at transcriptional and posttranscriptional levels together contributes to CDK16 up-regulation in HCC.

Electronic supplementary material

The online version of this article (doi:10.1186/s13046-017-0569-2) contains supplementary material, which is available to authorized users.

Poly-dimensional network comparative analysis reveals the pure pharmacological mechanism of baicalin in the targeted network of mouse cerebral ischemia

AIM

This study aimed to investigate the pure pharmacological mechanisms of baicalin/baicalein (BA) in the targeted network of mouse cerebral ischemia using a poly-dimensional network comparative analysis.

METHODS

Eighty mice with induced focal cerebral ischemia were randomly divided into four groups: BA, Concha Margaritifera (CM), vehicle and sham group. A poly-dimensional comparative analysis of the expression levels of 374 stroke-related genes in each of the four groups was performed using MetaCore.

RESULTS

BA significantly reduced the ischemic infarct volume (P<0.05), whereas CM was ineffective. Two processes and 10 network nodes were shared between "BA vs CM" and vehicle, but there were no overlapping pathways. Two pathways, three processes and 12 network nodes overlapped in "BA vs CM" and BA. The pure pharmacological mechanism of BA resulted in targeting of pathways related to development, G-protein signaling, apoptosis, signal transduction and immunity. The biological processes affected by BA were primarily found to correlate with apoptotic, anti-apoptotic and neurophysiological processes. Three network nodes changed from up-regulation to down-regulation, while mitogen-activated protein kinase kinase 6 (MAP2K6, also known as MEK6) changed from down-regulation to up-regulation in "BA vs CM" and vehicle. The changed nodes were all related to cell death and development.

CONCLUSION

The pure pharmacological mechanism of BA is related to immunity, apoptosis, development, cytoskeletal remodeling, transduction and neurophysiology, as ascertained using a poly-dimensional network comparative analysis.

Targeting Cyclin-Dependent Kinases in Ovarian Cancer

Ovarian cancer is the most common gynecological malignancy in the United States, and prognosis is generally poor because the disease is often diagnosed at an advanced stage. Cyclin-dependent kinases (CDKs) are a family of serine/threonine kinases whose activity is regulated by CDK inhibitors (CKIs) and cyclins. Generally, cyclins and CKIs promote and inhibit CDK activation, respectively. Since cancer commonly involves dysregulation of cell cycle, cyclins and CDKs have been targeted in a variety of tumors using small molecules, peptides, immunotherapy, and CKIs. In this review we discuss the significance of cell cycle dysregulation in ovarian cancer as well as recent advances targeting CDKs in ovarian cancer and potential future directions. Although many of the studies assessing CDK-targeting therapies in ovarian cancer are at an early preclinical stage, there is significant evidence that targeting CDKs, particularly in combination with traditional platinum-based drugs, could have significant efficacy in ovarian cancer. Nevertheless, before these agents can be investigated in humans, additional preclinical development is needed, including using in vivo tumor models and additional studies into their mechanism of action.

Differential Impacts of Alternative Splicing Networks on Apoptosis

Apoptosis functions as a common mechanism to eliminate unnecessary or damaged cells during cell renewal and tissue development in multicellular organisms. More than 200 proteins constitute complex networks involved in apoptotic regulation. Imbalanced expressions of apoptosis-related factors frequently lead to malignant diseases. The biological functions of several apoptotic factors are manipulated through alternative splicing mechanisms which expand gene diversity by generating discrete variants from one messenger RNA precursor. It is widely observed that alternatively-spliced variants encoded from apoptosis-related genes exhibit differential effects on apoptotic regulation. Alternative splicing events are meticulously regulated by the interplay between trans-splicing factors and cis-responsive elements surrounding the regulated exons. The major focus of this review is to highlight recent studies that illustrate the influences of alternative splicing networks on apoptotic regulation which participates in diverse cellular processes and diseases.

New Frontiers in Promoting TRAIL-Mediated Cell Death: Focus on Natural Sensitizers, miRNAs, and Nanotechnological Advancements

Cancer is a multifaceted and genomically complex disease, and rapidly emerging scientific evidence is emphasizing on intra-tumor heterogeneity within subpopulations of tumor cells and rapidly developing resistance against different molecular therapeutics. There is an overwhelmingly increasing list of agents currently being tested for efficacy against cancer. In accordance with the concept that therapeutic agents must have fewer off target effects and considerable efficacy, TRAIL has emerged as one among the most deeply investigated proteins reportedly involved in differential killing of tumor cells. Considerable killing activity of TRAIL against different cancers advocated its entry into clinical trials. However, data obtained through preclinical and cell culture studies are deepening our understanding of wide-ranging mechanisms which induce resistance against TRAIL-based therapeutics. These include downregulation of death receptors, overexpression of oncogenes, inactivation of tumor suppressor genes, imbalance of pro- and anti-apoptotic proteins, and inactivation of intrinsic and extrinsic pathways. Substantial fraction of information has been added into existing pool of knowledge related to TRAIL biology and recently accumulating evidence is adding new layers to regulation of TRAIL-induced apoptosis. Certain hints have emerged underscoring miR135a-3p- and miR-143-mediated regulation of TRAIL-induced apoptosis, and natural agents have shown remarkable efficacy in improving TRAIL-based therapeutics by increasing expression of tumor suppressor miRNAs. In this review, we summarize most recent breakthroughs related to naturopathy and strategies to nanotechnologically deliver TRAIL to the target site in xenografted mice. We also set spotlight on positive and negative regulators of TRAIL-mediated signaling. Comprehensive knowledge of genetics and proteomics of TRAIL-based signaling network obtained from cancer patients of different populations will be helpful in getting a step closer to personalized medicine.

Lipid Nanoparticle-mediated siRNA Transfer Against PCTAIRE1/PCTK1/Cdk16 Inhibits In Vivo Cancer Growth

PCTAIRE1/CDK16/PCTK1 plays critical roles in cancer cell proliferation and antiapoptosis. To advance our previously published in vitro results with PCTAIRE1 silencing, we examined the in vivo therapeutic potential of this approach by using small interfering RNA (siRNA) encapsulated by lipid nanoparticles. Therapy experiments of PCTAIRE1 siRNA were performed using human HCT116 colorectal cancer cells and human A2058 melanoma cells. A single dose of PCTAIRE1 siRNA-lipid nanoparticles was found to be highly effective in reducing in vivo PCTAIRE1 expression for up to 4 days as assayed by immunoblotting. Therapy experiments were started 4 days after subcutaneous injection of cancer cells. Treatment with PCTAIRE1 siRNA-lipid nanoparticles (0.5 mg/kg RNA, twice a week) reduced tumor volume and weight significantly compared with the scramble-control group. Histopathological analysis (terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling) showed increased apoptosis of tumor cells treated with PCTAIRE1-siRNA. Overall, our results demonstrate that siRNA treatment targeting PCTAIRE1 is effective in vivo, suggesting that PCTAIRE1 siRNA-lipid nanoparticles might be a novel therapeutic approach against cancer cells.