Cyclin-dependent kinases

NVP-2, in combination with Orlistat, represents a promising therapeutic strategy for acute myeloid leukemia

Cell cycle dysregulation and the corresponding metabolic reprogramming play significant roles in tumor development and progression. CDK9, a kinase that regulates gene transcription and cell cycle, also induces oncogene transcription and abnormal cell cycle in AML cells. The function of CDK9 for gene regulation in AML cells requires further exploration. In this study, we knocked down the CDK9 to investigate its effects on the growth and survival of AML cells. Through RNA-seq analysis, we identified that in U937 cells CDK9 regulates numerous genes involved in proliferation and apoptosis, including mTOR, SREBF1, and Bcl-2. Furthermore, our results demonstrated that both CDK9 and FASN are crucial for the proliferation and survival of Kasumi-1 and U937 cells. Mechanistically, MCL1, c-Myc, and Akt/mTOR/SREBF1 may be critical factors and pathways in the combined therapy of NVP-2 and Orlistat. In summary, our study revealed that CDK9 and FASN are vital for maintaining AML cell survival and proliferation. Treatment with NVP-2 and Orlistat may be a promising clinical candidate for patients with AML.

Development of 9H-purine scaffold as novel CDK2 inhibitors: Design, synthesis, and biological evaluation

Cyclin-dependent kinase 2 (CDK2), a crucial regulator in multiple oncogenic signaling pathways, has emerged as a promising target for the development of innovative anticancer therapies and overcoming resistance to CDK4/6 inhibitors. In this study, three series of compounds were designed and synthesized, using the CDK2 inhibitor fadraciclib (CYC065) as the lead compound, with 9H-purine as the core structure. The design incorporated reported structure-activity relationship data and utilized computer-aided drug design techniques. Compounds in series 1 explored the binding mode between the ATP ribose binding site in CDK2 and C2 substituents, while compounds in series 2 and 3 validated the feasibility of modifying the specific binding region with different substituents and investigated the effects of filling the CDK2 hydrophobic pocket at the N9 position with alkyl substituents. Three compounds, 1f, 2e, and 3a, demonstrated remarkable activity against CDK2-cyclin E2. Notably, 3a exhibited the most potent effect, with a CDK2-cyclin E2 IC50 value of 6.0 ± 0.1 nM, an MV4-11 IC50 value of 489.2 ± 0.2 nM, and excellent selectivity for CDK2. This study evaluated the impact of substitutions at the 2, 6, and 9 positions of the purine ring on the activity of CDK2 small molecule inhibitors. The findings offer a theoretical foundation for future research, broadening the structural diversity and scope of CDK2 inhibitor studies.

Citrate oscillations during cell cycle are a targetable vulnerability in cancer cells

Cell cycle progression is timely interconnected with oscillations in cellular metabolism. Here, we first describe how these metabolic oscillations allow cycling cells to meet the bioenergetic needs specifically for each phase of the cell cycle. In parallel, we highlight how the cytosolic level of citrate is dynamically regulated during these different phases, being low in G1 phase, increasing in S phase, peaking in G2/M, and decreasing in mitosis. Of note, in cancer cells, a dysregulation of such citrate oscillation can support cell cycle progression by promoting a deregulated Warburg effect (aerobic glycolysis), activating oncogenic signaling pathways (such as PI3K/AKT), and promoting acetyl-CoA production via alternative routes, such as overconsumption of acetate. Then, we review how administration of sodium citrate (at high doses) arrests the cell cycle in G0/G1 or G2/M, inhibits glycolysis and PI3K/AKT, induces apoptosis, and significantly reduces tumor growth in various in vivo models. Last, we reason on the possibility to implement citrate administration to reinforce the effectiveness of cell cycle inhibitors to better cure cancer.

CDK5 targets p21CIP1 to regulate thyroid cancer cell proliferation and malignancy in patients

Cyclin‑dependent kinase 5 (CDK5), known for its role in neuronal function, has emerged as a key player in cancer biology, particularly in thyroid cancer. The present study explored the interaction between CDK5 and the cyclin‑dependent kinase inhibitor p21CIP1 in thyroid cancer (TC). Bioinformatic tools and immunoprecipitation assays were used to confirm that CDK5 targets p21 for ubiquitin‑mediated degradation, reducing its stability and tumor‑suppressive effects. Data from The Cancer Genome Atlas revealed a significant inverse correlation between CDK5 and p21 expression, with higher CDK5 levels linked to increased tumor malignancy and worse survival outcomes; conversely, higher p21 expression was correlated with an improved prognosis. Immunohistochemistry analysis of TC samples further confirmed that increased CDK5 and reduced p21 expression were associated with more advanced tumor stages and aggressive phenotypes. These findings suggested that CDK5‑mediated degradation of p21 contributes to TC progression and malignancy, highlighting the potential of targeting the CDK5‑p21 axis as a therapeutic strategy for management of TC.

Development of Benzothiazole-grafted Pyrazolo[1,5-a]pyrimidines as new CDK2 inhibitors and anti-prostate cancer agents

In the current medical era, CDK2 kinase has emerged as a promising target in the global fight against cancer. Recent research reported the overexpression of CDK2 in prostate cancer cells, which highlighted the potential of CDK2 inhibition as a practical therapeutic approach for this disease that stands out as a challenging global health issue. On account of their interesting biological activities, especially anti-cancer properties, the two privileged scaffolds benzothiazole and pyrazolo[1,5-a]pyrimidine were utilized in this study to develop three series of 16 novel small molecules (8a-k, 12a-c, and 14a-b) as potential anti-prostate cancer agents targeting CDK2. The synthesized derivatives were assessed for cytotoxic effects against two prostate cancer cell lines, DU-145 and PC-3. Compounds 8f, 12c, and 14b exhibited the highest anti-cancer activity. Further investigation showed that these molecules inhibit critical cell cycle regulators by arresting DU-145 cells at the G0/G1 phase. Apoptosis induction was verified using Annexin V-FITC/Propidium iodide (PI) assays, which indicated a noteworthy apoptosis level in DU-145 cells. The compounds were validated as CDK2 inhibitors via in-vitro assays, with 8f demonstrating the highest potency, exceeding that of the reference drug Roscovitine. Molecular docking studies revealed substantial binding affinities of compounds 8f, 12c, and 14b to the ATP-binding site of CDK2, supported by essential hydrogen bonding and hydrophobic interactions. Overall, these study's findings indicate the potential of these benzothiazole-grafted pyrazolo[1,5-a]pyrimidines as effective therapeutic agents for prostate cancer.

Naphthalimide derivative attenuates tumor growth of wild-type p53-expressing U87 glioma cells in vitro and in vivo through a biphasic dose-dependent mechanism: A switch from cell cycle to apoptosis

Glioblastoma multiforme (GBM) is among the most lethal and recurrent malignant solid tumors. Compound 5 is a naphthalimide derivative that has rarely been investigated for glioma treatment. Therefore, we aimed to determine whether compound 5 exhibits anti-glioma activity. The results revealed that compound 5 reduced the cell viability of U87 glioma cells in a concentration-dependent manner. At lower concentrations, compound 5 arrested the G0/G1 phase through p21 upregulation, and at higher concentrations, it arrested the G2/M phase and induced marked apoptosis through p21 downregulation and p53 upregulation and stabilization. Additionally, compound 5 reduced CDK2 expression at lower concentrations but not at higher concentrations, suggesting that CDK2 plays a key role in the entry into the S phase in U87 glioma cells. At higher concentrations, compound 5 also accumulated cyclin B1 and CDK1, which may contribute to mitotic arrest and subsequent apoptosis. Moreover, compound 5 reduced the levels of antiapoptotic Bcl-w and Mcl-1 proteins, as well as those of inhibitors of apoptosis XIAP and survivin, enhancing compound 5-medicated apoptosis. In an in vivo study, compound 5 reduced tumor growth in a mouse xenograft tumor model. This study is the first to demonstrate that compound 5 inhibits the growth of U87 glioma cells in vitro and in vivo through a biphasic dose-dependent switch from cell cycle arrest to apoptosis in a p21 level-dependent manner. These findings suggest that naphthalimide-based compounds can serve as lead compounds for designing new and more potent anti-glioma drugs.

Raddeanin A exerts potent efficacy against non-small cell lung cancer by inhibiting cyclin-dependent kinase 6

PURPOSE

The aim of this study was to investigate the anti-tumor effects and mechanisms of Raddeanin A in NSCLC in vitro and in vivo.

METHODS

The effects of Raddeanin A on cell cycle progression, proliferation, migration and invasion of NSCLC were assessed by flow cytometry and cell biological assays in multiple NSCLC cell lines. To identify possible targets of Raddeanin A in NSCLC, we employed a multifaceted approach incorporating network pharmacology, molecular docking, and molecular dynamics simulation, along with additional techniques such as SPR (Surface Plasmon Resonance), Co-IP (Co-Immunoprecipitation), and immunofluorescence. In vivo effects were investigated using a nude mouse xenograft tumor model.

RESULTS

Raddeanin A inhibits NSCLC cell survival, inhibits invasion and migration and causes cell cycle arrest in G1 phase. Raddeanin A impacts NSCLC cellular activity by inhibiting CDK6, leading to anti-tumor effects. Molecular analysis confirms that the tight binding between Raddeanin A and CDK6, facilitated by specific hydrogen bonds at binding sites including VAL-101, HIS-100, GLN-149, LYS-147, THR-182, VAL-180, and ALA-23, stabilizes within the 40-100 ns interval. In a nude mouse xenograft tumor model, Raddeanin A also demonstrated an inhibitory effect on NSCLC tumor growth.

CONCLUSIONS

Raddeanin A blocks the cell cycle in G1 phase by inhibiting CDK6. Raddeanin A is expected to be a novel antitumor agent against NSCLC.

Natural bioactive gallic acid shows potential anticancer effects by inhibiting the proliferation and invasiveness behavior in human embryonic carcinoma cells

Embryonic cancer stem cells (CSCs), referred to as self‑renewable cells, are commonly found in liquid and solid cancers and can also be attributed to tumor onset, resistance, expansion, recurrence and metastasis following treatment. Cancer therapy targeting CSCs using natural bioactive products is an optimal option for inhibiting cancer recurrence, thereby improving prognosis. Several natural compounds and extracts have been used to identify direct or indirect therapy effects that reduce the pathological activities of CSCs. Natural gallic acid (GA) is noted to have anticancer properties for oncogene expression, cycle arrest, apoptosis, angiogenesis, migration and metastasis in various cancers. The present study demonstrated that GA has various anticancer activities in NTERA‑2 and NCCIT human embryonic carcinoma cells. In two types of embryonic CSCs, GA effectively induced cell death via late apoptosis. Furthermore, GA showed the G0/G1 cell cycle arrest activity in embryonic CSCs by inducing the increase of p21, p27 and p53 expression and the decrease of CDK4, cyclin E and cyclin D1 expression. The present study showed that GA inhibited the expression levels of mRNA and protein for stem cell markers, such as SOX2, NANOG and OCT4, in NTERA‑2 and NCCIT cells. The induction of cellular and mitochondrial reactive oxygen species by GA also activated the cellular DNA damage response pathway by raising the phosphorylated‑BRCA1, ATM, Chk1, Chk2 and histone. Finally, GA inhibited CSCs invasion and migration by inhibiting the expression of matrix metalloproteinase by the downregulation of EGFR/JAK2/STAT5 signaling pathway. Thus, it is hypothesized that GA could be a potential inhibitor of cancer emergence by suppressing CSC properties.

Dynamics insights into CDK4/6-CyclinD1 complex stability modulated by abemaciclib

The CDK4/6-CyclinD1 complex, a fundamental component of the cell cycle regulatory mechanism, is associated with numerous cancers. The synergistic action of P21 and P27 is essential for regulating the G1/S transition in the cell cycle. Current HDX-MS and other experimental studies enhance the understanding of P21 and P27 binding to the CDK4-CyclinD1 complex in response to abemaciclib treatment. However, the existing knowledge of the abemaciclib's effect on the stability of the CDK4/6-CyclinD1-P21/P27 complex is still limited. Here, we utilize molecular dynamics simulations to quantitatively assess specific regions and delineate the roles of individual subsystems or residues through energy decomposition methods. Our results, derived from residue decomposition via molecular dynamics simulations and RIN analysis, reveal that P21 binding to the CDK4 complex involves a broader set of residues and exhibits a higher binding affinity compared to CDK6. Moreover, in the CDK4-CyclinD1-P21 complex, abemaciclib tends to disrupt the C-lobe region of CDK4. To validate this hypothesis, a sequence mutant of the C-terminus of CDK4 was generated, showing that the C-terminus of CDK4 selectively modulates the abemaciclib-mediated decrease in the P21 binding affinity. These findings significantly enhance our understanding of the broader non-catalytic mechanisms underlying second-generation CDK4/6 inhibitors. It is expected that second-generation inhibitors will further destabilize the CDK6-CyclinD1-P21 complex and the P27-containing complex, thereby improving the efficacy of CDK4/6 inhibitors as cancer therapies.

HSC70 Promotes Breast Cancer Progression via PTEN Autophagic Degradation and PI3K/AKT/mTOR Activation

Heat shock cognate protein 70 (HSC70) functions as a molecular chaperone and plays a crucial role in the regulation of intracellular protein modifications that are involved in tumor autophagy. However, its expression and mechanism in breast cancer have not been studied. The expression of HSC70 was verified by TCGA database and breast cancer patient tissue. We established breast cancer cell models and mouse models using knockdown HSC70. The expression and mechanism of HSC70 in breast cancer were investigated by immunocoprecipitation, protein stability, RNA stability, flow cytometry and biogenic analysis. In this study, we found that HSC70 is highly expressed in breast cancer and that high HSC70 expression positive correlated with poor prognosis using TCGA database and patient tissue verification. Subsequent experimental verification demonstrated that HSC70 drives cell cycle progression and promotes proliferation in breast cancer. Further studies revealed that HSC70 significantly promoted the phosphorylation of PI3K, AKT and mTOR but did not affect the total protein levels. Additionally, the AKT agonist SC79 reversed the effects of HSC70 knockdown on proliferation and cell cycle progression of breast cancer cells. Mechanistically, HSC70 reduces the protein stability of PTEN but does not change its mRNA level, suggesting that HSC70 binds to PTEN and promotes its autophagic degradation. More importantly, in vivo experiments demonstrated that HSC70 knockdown results in slower tumor proliferation and growth. In conclusion, HSC70 can bind to PTEN and promote its autophagic degradation, thereby activating the PI3K/AKT/mTOR signaling pathway to promote cell cycle progression and proliferation in breast cancer. These findings suggest that HSC70 may be a feasible target for breast cancer treatment.

Circaea mollis Siebold & Zucc. Induces Apoptosis in Colorectal Cancer Cells by Inhibiting c-Myc Through the Mediation of RPL5

Colorectal cancer remains a significant global health concern. In this study, we investigated the anticancer potential of Circaea mollis Siebold & Zucc. (CS&Z), a traditional medicinal plant known for its anti-inflammatory, anti-arthritic, and antioxidant properties, in the treatment of colorectal cancer. We found that CS&Z induces apoptosis and G1/S phase cell cycle arrest in colorectal cancer cells, primarily through the suppression of the proto-oncogene c-Myc. Specifically, the depletion of RPL5, a ribosomal protein associated with c-Myc regulation, reversed the suppression of c-Myc by CS&Z. Additionally, when co-administered with the standard chemotherapeutic agents doxorubicin and 5-fluorouracil, CS&Z demonstrated synergistic effects, thereby further emphasizing its potential efficacy as a therapeutic option for the treatment of colorectal cancer. Moreover, the constituents of CS&Z, detected through liquid chromatography-mass spectrometry analysis, reportedly exhibit anticancer activities. Taken together, our findings suggest that CS&Z holds promise as a natural product capable of modulating oncogenic signaling in colorectal cancer and may serve as a complementary agent in future therapeutic strategies.

NANS suppresses NF-κB signaling to promote ferroptosis by perturbing iron homeostasis

Metastatic colorectal cancer (CRC) cells endure survival challenges, including treatment-induced ferroptosis. While adaptation to ferroptosis stress facilitates metastasis, reciprocal regulatory mechanisms remain unclear. Here, a CRISPR-Cas9 screen identifies N-acetylneuraminate synthase (NANS) as a ferroptosis promoter in CRC, regardless of its metabolic function. NANS expression is downregulated and correlates with poor prognosis in patients with CRC. Under ferroptotic stress, cyclin-dependent kinase 1 (CDK1) phosphorylates NANS at serine 275 (S275), triggering its dissociation from TAK1. Phosphorylated NANS is ubiquitinated by UBE2N at K246, leading to degradation, which activates TAK1-NF-κB signaling and upregulates the ferroptosis inhibitor FTH1, enabling metastasis via ferroptosis resistance. NANS pS275 levels are associated with tumor aggressiveness and clinical outcomes in patients with CRC. These findings indicate that NANS suppresses CRC metastasis by enhancing ferroptosis susceptibility, while CDK1-mediated phosphorylation at S275 drives adaptive resistance. Targeting this phosphorylation axis may improve ferroptosis-inducing therapies to restrict metastatic progression in CRC.

RNA demethylase ALKBH5 regulates cell cycle progression in DNA damage response

RNA N6-methyladenosine (m6A) modification plays a crucial role in the DNA damage response, while the detailed mechanisms remain to be explored. In this study, we report the involvement of the m6A demethylase ALKBH5 in X-ray-induced DNA damage response. Depletion of ALKBH5 reduces X-ray-induced DNA damage, induces G2/M phase arrest and reduces cell apoptosis. RNA sequencing and m6A sequencing analysis reveal that ALKBH5 removes m6A modifications from its target mRNAs and suppresses their expression. A subset of mRNAs encoding cyclin dependent kinase inhibitors, such as CDKN1A and CDKN2B, show increased stability and expression upon ALKBH5 knockdown. Subsequently, the upregulation of CDKN1A and CDKN2B contributes to G2/M phase arrest to facilitate DNA repair. Our findings unveil the epigenetic regulation of cell cycle checkpoint by ALKBH5 in X-ray-induced DNA damage, offering potential targets for DNA damage-based therapy for cancers.

Protein kinases in neurodegenerative diseases: current understandings and implications for drug discovery

Neurodegenerative diseases (e.g., Alzheimer's, Parkinson's, Huntington's disease, and Amyotrophic Lateral Sclerosis) are major health threats for the aging population and their prevalences continue to rise with the increasing of life expectancy. Although progress has been made, there is still a lack of effective cures to date, and an in-depth understanding of the molecular and cellular mechanisms of these neurodegenerative diseases is imperative for drug development. Protein phosphorylation, regulated by protein kinases and protein phosphatases, participates in most cellular events, whereas aberrant phosphorylation manifests as a main cause of diseases. As evidenced by pharmacological and pathological studies, protein kinases are proven to be promising therapeutic targets for various diseases, such as cancers, central nervous system disorders, and cardiovascular diseases. The mechanisms of protein phosphatases in pathophysiology have been extensively reviewed, but a systematic summary of the role of protein kinases in the nervous system is lacking. Here, we focus on the involvement of protein kinases in neurodegenerative diseases, by summarizing the current knowledge on the major kinases and related regulatory signal transduction pathways implicated in diseases. We further discuss the role and complexity of kinase-kinase networks in the pathogenesis of neurodegenerative diseases, illustrate the advances of clinical applications of protein kinase inhibitors or novel kinase-targeted therapeutic strategies (such as antisense oligonucleotides and gene therapy) for effective prevention and early intervention.

Mechanistic Roles of Transcriptional Cyclin-Dependent Kinases in Oncogenesis: Implications for Cancer Therapy

Cyclin-dependent kinases (CDKs) are pivotal in regulating cell cycle progression and transcription, making them crucial targets in cancer research. The two types of CDKs that regulate different biological activities are transcription-associated CDKs (e.g., CDK7, 8, 9, 12, and 13) and cell cycle-associated CDKs (e.g., CDK1, 2, 4, and 6). One characteristic of cancer is the dysregulation of CDK activity, which results in unchecked cell division and tumor expansion. Targeting transcriptional CDKs, which control RNA polymerase II activity and gene expression essential for cancer cell survival, has shown promise as a therapeutic approach in recent research. While research into selective inhibitors for transcriptional CDKs is ongoing, inhibitors that target CDK4/6, such as palbociclib and ribociclib, have demonstrated encouraging outcomes in treating breast cancer. CDK7, CDK8, and CDK9 are desirable targets for therapy since they have shown oncogenic roles in a variety of cancer types, such as colorectal, ovarian, and breast malignancies. Even with significant advancements, creating selective inhibitors with negligible off-target effects is still difficult. This review highlights the need for more research to optimize therapeutic strategies and improve patient outcomes by giving a thorough overview of the non-transcriptional roles of CDKs in cancer biology, their therapeutic potential, and the difficulties in targeting these kinases for cancer treatment.

Cellular parameters shaping pathways of targeted protein degradation

In recent years the development of proteolysis-targeting chimeras (PROTACs) has enhanced the field of ubiquitin signalling through advancing therapeutic targeted protein degradation (TPD) strategies and generating tools to explore the ubiquitin landscape. However, the interplay between PROTACs and their substrates, and other components of the ubiquitin proteasome system (UPS), raises fundamental questions about cellular parameters that might influence the action of PROTACs and the amenability of a given target to PROTAC-mediated degradation. In this perspective we discuss examples of cellular parameters that have been shown to influence PROTAC sensitivity and consider others likely to be important for PROTAC-mediated target degradation but not yet routinely considered in design of novel TPD strategies: Target localisation and accessibility on the one hand, and expression patterns, localisation and activity of E3 ligases, deubiquitinases (DUBs) and wider ubiquitin machinery on the other, are critical parameters in the exploitation of PROTACs, and establishing a better understanding of these parameters will facilitate the rational design of PROTACs.

Multi-Omics Analysis Reveals Disturbances of Purine Metabolism and Glutamate Metabolism in the Hippocampus of Lipopolysaccharide-Induced Mouse Model of Depression

BACKGROUND

Depression is a global health concern characterized by high incidence, disability, and disease burden. Neuroimmunity, through the secretion of inflammatory mediators and mediation of neuroinflammation, plays a significant role in depression's pathogenesis. However, the underlying molecular mechanisms remain poorly understood.

METHODS

In this pioneering study, we employed a comprehensive multi-omics approach, integrating 2-DE proteomics, liquid chromatography mass spectrometry-based metabolomics, and real-time polymerase chain reaction (PCR) array, to investigate the hippocampal molecular profiles of lipopolysaccharide (LPS)-induced immune inflammation-related depression. This innovative approach aimed to explore the potential pathogenesis of depression by systematically integrating data across multiple molecular layers.

RESULTS

Compared to the control group, we identified 81 differential proteins, 44 differential metabolites, and 4 differential mRNAs in LPS-treated mice. Integrated analysis of these multidimensional data revealed that purine metabolism and glutamate metabolism are the most significantly altered molecular pathways in LPS-induced depression. Additionally, we constructed the corresponding compound-reaction-enzyme-gene regulatory network.

CONCLUSION

This study suggests that purine metabolism and glutamate metabolism may be the underlying mechanisms by which neuroinflammation regulates depression-like behaviors. Our findings confirm the important role of immune inflammation in depression and provide a new clue for the diagnosis and treatment of this disorder. Notably, the multi-omics approach employed in this study represents a pioneering effort in the field, providing unprecedented insights into the molecular mechanisms underlying depression.

Cyclin-dependent kinases as mediators of aberrant transcription in prostate cancer

Transcriptional control of gene expression is fundamental to all cellular processes. Conversely, transcriptional dysregulation is a hallmark of cancer. While this hallmark is a key driver of all malignancy-related process, it also represents a vulnerability that can be exploited therapeutically. Prostate cancer is a prime example of this phenomenon: it is characterised by aberrant transcription and treated with drugs that influence transcriptional pathways. Indeed, the primary oncogenic driver and therapeutic target of prostate cancer, the androgen receptor (AR), is a transcription factor. Moreover, a plethora of other transcriptional regulators, including transcriptional cyclin-dependent kinases (CDK7, CDK8 and CDK9), MYC and Bromodomain-containing protein 4 (BRD4), play prominent roles in disease progression. In this review, we focus on the roles of transcriptional CDKs in prostate cancer growth, metastasis and therapy resistance and discuss their interplay with AR, MYC and BRD4. Additionally, we explore recent advances in the therapeutic targeting of transcriptional CDKs and propose how these strategies could be effectively harnessed for the treatment of prostate cancer.

Discovering potential therapeutic targets in glioblastoma multiforme using a multi-omics approach

BACKGROUND

Glioblastoma multiforme (GBM) is a highly aggressive primary brain tumor associated with high fatality rates, poor prognosis, and limited treatment options. In this study, we utilized RNA-Seq gene count data from GBM patients, sourced from the Gene Expression Omnibus (GEO) database, to conduct an in-depth analysis of gene expression patterns.

METHODS

Our investigation involved stratifying samples into two distinct sets, Group I and Group II, comparing normal, low-grade, and GBM tumor samples, respectively. Subsequently, we performed differential expression analysis and enrichment analysis to uncover significant gene signatures. To elucidate the protein-protein interactions associated with GBM, we used the STRING plugin within Cytoscape for comprehensive network visualization and analysis.

RESULTS

By applying Maximal clique centrality (MCC) scores, we identified a set of 10 hub genes in each group. These hub genes were subjected to survival analysis, highlighting their prognostic relevance. In Group I, comprising BUB1, DLGAP5, BUB1B, CDK1, TOP2A, CDC20, KIF20A, ASPM, BIRC5, and CCNB2, these genes emerged as potential biomarkers associated with the transition to low-grade tumors. In Group II, genes such as LIF, LBP, CSF3, IL6, CCL2, SAA1, CCL20, MMP9, CXCL10, and MMP1 were found to be involved in the transformation to adult glioblastoma. Kaplan-Meier's overall survival analysis of these hub genes revealed that modifications, particularly the upregulation of these candidate genes, were associated with reduced survival in GBM patients.

CONCLUSIONS

The findings established the significance of genomic alterations and differential gene expression in GBM, presenting opportunities for prognostic and targeted therapeutic interventions. This study provides valuable insights into potential avenues for enhancing the clinical management of GBM.

Discovery of 4-(2-(methylamino)thiazol-5-yl)pyrimidin-2-amine derivatives as novel cyclin-dependent kinase 12 (CDK12) inhibitors for the treatment of esophageal squamous cell carcinoma

The transcriptional cyclin-dependent protein kinase 12 (CDK12), a potential target in various cancers, was recently discovered with a dramatic amplification in esophageal cancer (EC). In this study, we conducted an online database analysis that revealed CDK12 to be overexpressed in esophageal squamous cell carcinoma (ESCC) tissue samples from patients. Furthermore, survival analysis indicated that CDK12 can serve as a prognostic indicator for ESCC patients. In addition, CDK12 knockdown had been shown to reduce the proliferation of ESCC cells. The present study also details the design, synthesis, and biological evaluation of new CDK12 inhibitors which bear the scaffold of 4-(2-(methylamino)thiazol-5-yl)pyrimidin-2-amine. Among the synthesized compounds, H63 has been identified as a potent inhibitor of CDK12 with excellent anti-ESCC activity. Mechanistically, H63 blocked transcription elongation, downregulated the G1-phase core genes to induce cell cycle arrest, and altered the CDK12-ATM/ATR-CHEK1/CHEK2 signaling axis to cause DNA damage. In addition, H63 exhibited favorable pharmacokinetic properties, good safety, and prominent anti-ESCC activity in vivo. The present study suggests that CDK12 is a promising target for ESCC treatment, and H63 is a promising candidate for further clinical development as an anti-ESCC drug.

F2-sulfated polysaccharides of Laetiporus sulphureus suppress triple-negative breast cancer cell proliferation and metastasis through the EGFR-mediated signaling pathway

Sulfated polysaccharides (SPS) are a unique secondary metabolite isolated from Laetiporus sulphureus. This study examined the detailed molecular mechanisms of action of F2, a medium molecular weight SPS of L. sulphureus, on breast cancer MDA-MB-231 cell proliferation and metastasis. Results showed that the sulfate and protein content of F2 were 2.1 % and 15.6 %, respectively. F2 had a molecular weight of 23.8 kDa and did not contain a triple helix conformation. The monosaccharide composition of F2 was mannose, galactose, glucose, and fucose. F2 inhibited MDA-MB-231 cell proliferation mainly by blocking the cell cycle at the G0/G1 phase, which was attributed to the down-regulation of CDK4 and cyclin D1 and the up-regulation of p21 protein expression. F2 suppressed epidermal growth factor receptor (EGFR)-mediated intracellular signaling events, such as phosphorylation of ERK1/2, Akt, and GSK-3β and activation of NF-κB and β-catenin, resulting in the cell cycle arrest. Moreover, F2 significantly reduced the EGFR phosphorylation and expression, and the level of mutant p53 protein. F2 also effectively inhibited breast cancer cell migration and invasion through down-regulating MMP-9 and MMP-2 protein expression. In conclusion, this study demonstrated that F2 exhibited anti-proliferative and anti-metastatic activities against MDA-MB-231 cells by inhibiting the activation of EGFR-mediated signaling pathways.

Human ATP-binding proteins: Structural features, functional diversity, and pharmacotherapeutic potential in disease: A review

ATP-binding proteins (ABPs) form diverse and essential protein families across living organisms. Early life forms likely relied on simple chemical reactions for energy, but with the emergence of ABPs and their evolving functions, organisms became capable of more efficient energy storage and utilization, which drove the complexity of metabolic and life processes. By binding and hydrolyzing ATP through conserved structural motifs such as the Walker motifs, ABPs play critical roles in material transport, signal transduction, cellular structure maintenance, motility, and cell cycle regulation. Dysfunctions arising from mutations, deletions, or misregulation of ABPs are linked to a variety of human diseases, including cancer, neurodegenerative disorders, and cardiovascular diseases. The growing recognition of ABPs' significance in disease progression highlights their relevance not only in basic biology but also in clinical applications, particularly as biomarkers and therapeutic targets. This review provides a comprehensive overview of human ABPs, detailing their structural and functional roles, their involvement in disease mechanisms, and the latest advances in understanding their clinical relevance. Additionally, it identifies current research gaps and offers new perspectives for future investigations and therapeutic strategies.

Computational Estimation of Residence Time on Roniciclib and Its Derivatives against CDK2: Extending the Use of Classical and Enhanced Molecular Dynamics Simulations

Residence time is a crucial parameter for assessing the functional efficacy of drugs, quantifying the duration of a drug's binding to its target protein. It is directly related to therapeutic effects and the dosing regimen. Several factors can influence the residence time, including drug-protein binding kinetics and the unbinding pathways. Understanding the efficacy of a drug requires the characterization of both its binding kinetics and unbinding pathways from the drug-protein complex. By employing our previous computational protocol that uses enhanced sampling techniques such as well-tempered metadynamics (WT-MetaD) and classical molecular dynamics (cMD) simulations, it was possible to elucidate the inhibitor unbinding pathways and identify molecular determinants that extend the residence time in a set of cyclin-dependent kinase 2 (CDK2) inhibitors. In this study, using WT-MetaD, the relative residence times of roniciclib and eight derivatives were quantified on the nanosecond timescale. Notably, substituting the R5 position of the aminopyridine core with larger substituents significantly prolonged the computational residence time, which correlated well with experimental data (R 2 = 0.83). Our computational simulations reveal the critical importance of specific amino acids, including Phe80, Lys33, and Asp145, in maintaining the stability of the protein-inhibitor complex. These residues are key in keeping the hydration network around them, affecting the inhibitor binding duration. The hydrogen bond interaction between residue Asp145 and roniciclib and its derivatives is particularly noteworthy, significantly influencing the electrostatic contribution to the binding free energy when the halogen substituent size increases. Furthermore, our analysis of protein flexibility at the C-terminus and N-terminus angles revealed a relationship with the size of the R5 substituent in the bound inhibitor, supported by principal component analysis. Additionally, different unbinding pathways were proposed, where it was found that inhibitors can dissociate from the CDK2 binding site through two principal routes: the α-helix D and β-1 and β-2 segments.

Cell cycle arrest of cardiomyocytes in the context of cardiac regeneration

The limited capacity of adult mammalian cardiomyocytes to undergo cell division and proliferation is one of the key factors contributing to heart failure. In newborn mice, cardiac proliferation occurs during a brief window, but this proliferative capacity diminishes by 7 days after birth. Current studies on cardiac regeneration focused on elucidating changes in regulatory factors within the heart before and after this proliferative window, aiming to determine whether potential association between these factors and cell cycle arrest in cardiomyocytes. Facilitating the re-entry of cardiomyocytes into the cell cycle or reversing their exit from it represents a critical strategy for cardiac regeneration. This paper provides an overview of the role of cell cycle arrest in cardiac regeneration, briefly describes cardiomyocyte proliferation and cardiac regeneration, and systematically summarizes the regulation of the cell cycle arrest in cardiomyocytes, and the potential metabolic mechanisms underlying cardiomyocyte cycle arrest. Additionally, we highlight the development of cardiovascular disease drugs targeting cardiomyocyte cell cycle regulation and their status in clinical treatment. Our goal is to outline strategies for promoting cardiac regeneration and repair following cardiac injury, while also pointing toward future research directions that may offer new technologies and prospects for treating cardiovascular diseases, such as myocardial infarction, arrhythmia and heart failure.

ATG9B-4 accelerates the proliferation and migration of liver cancer cells in an ARNTL-CDK5 pathway-dependent manner: A case-control study

Lnc ATG9B-4 aggravated the progression of liver cancer by up-regulating cyclin-dependent-kinase 5 (CDK5). It could be inferred that ATG9B-4 indirectly regulates the expression of CDK5 via lncRNA-mediated negative regulation of target genes. Therefore, the specific molecular mechanism by which ATG9B-4 regulates the malignant characteristics of liver cancer cells still needs further study. The differentially expressed genes were identified by mRNA sequencing in liver cancer cells transfected with or without ATG9B-4. Liver cancer cells were transfected with ATG9B-4, ARNTL, or si-CDK5. The expression of aryl basic helix-loop-helix ARNT like 1 (BMAL1, also known as ARNTL), CDK5, and ATG9B-4 was analyzed by real-time quantitative PCR and western blotting. The proliferation and invasion of the transfected cells were respectively analyzed by cell counting kit-8 and wound healing assays, respectively. The ARNTL expression was down-regulated in the liver cancer tissues and liver cancer cells transfected with ATG9B-4. Low ARNTL expression indicated poor overall survival in patients with liver cancer. The optical density of cells transfected with ATG9B-4 and ARNTL was significantly lower than that of cells transfected with ATG9B-4. The wound areas of cells transfected with ATG9B-4 and ARNTL were markedly wider than those of cells transfected with ATG9B-4. The expression of CDK5 was down-regulated in cells transfected with ARNTL. CDK5 knockdown partially attenuated the ATG9B-4-induced increase in proliferation and migration in liver cancer cells. ATG9B-4 deteriorated the proliferation and migration of liver cancer cells in an ARNTL-CDK5 pathway-dependent manner.

The involvement of cyclin-dependent kinase 7 (CDK7) and 9 (CDK9) in coordinating transcription and cell cycle checkpoint regulation

Cells regulate the expression of cell cycle-related genes, including cyclins essential for mitosis, through the transcriptional activity of the positive transcription elongation factor b (P-TEFb), a complex comprising CDK9, cyclin T, and transcription factors. P-TEFb cooperates with CDK7 to activate RNA polymerase. In response to DNA stress, the cell cycle shifts from mitosis to repair, triggering cell cycle arrest and the activation of DNA repair genes. This tight coordination between transcription, cell cycle progression, and DNA stress response is crucial for maintaining cellular integrity. Cyclin-dependent kinases CDK7 and CDK9 are central to both transcription and cell cycle regulation. CDK7 functions as the CDK-activating kinase (CAK), essential for activating other CDKs, while CDK9 acts as a critical integrator of signals from both the cell cycle and transcriptional machinery. This review elucidates the mechanisms by which CDK7 and CDK9 regulate the mitotic process and cell cycle checkpoints, emphasizing their roles in balancing cell growth, homeostasis, and DNA repair through transcriptional control.

Decreased Cdk2 Activity Hindered Embryonic Development and Parthenogenesis Induction in Silkworm, Bombyx mori L

Cyclin-dependent protein kinase 2 (Cdk2), an important member of the serine/threonine-specific protein kinase family, plays a critical regulatory role in biological processes. Previous studies have demonstrated that Cdk2 is involved in the arrest and resumption of meiosis in mammalian oocytes. In this study, we explored the function of Cdk2 through parthenogenetic lines (PLs) and corresponding amphigonic lines (ALs) in a model lepidopteran insect silkworm, Bombyx mori L. Our findings revealed a positive correlation between Cdk2 activity and the parthenogenesis induction rate. The pharmacological inhibition of Cdk2 using the specific inhibitor AUZ454 not only significantly reduced the parthenogenesis induction rate but also caused developmental delays in embryos. These results demonstrate that Cdk2 is essential for parthenogenesis success and is a potential target gene for biological reproductive regulation.

Triple-negative breast cancer molecular subtypes and potential detection targets for biological therapy indications

Triple-negative breast cancer (TNBC) is a highly aggressive subtype of breast cancer associated with poor prognosis. While chemotherapy remains the conventional treatment approach, its efficacy is limited and often accompanied by significant toxicity. Advances in precision-targeted therapies have expanded treatment options for TNBC, including immunotherapy, poly (ADP-ribose) polymerase inhibitors, androgen receptor inhibitors, cell cycle-dependent kinase inhibitors, and signaling pathway inhibitors. However, the heterogeneous nature of TNBC contributes to variations in treatment outcomes, underscoring the importance of identifying intrinsic molecular subtypes for personalized therapy. Additionally, due to patient-specific variability, the therapeutic response to targeted treatments is inconsistent. This highlights the need to strategize patients based on potential therapeutic targets for targeted drugs to optimize treatment strategies. This review summarizes the classification strategies and immunohistochemical (IHC) biomarkers for TNBC subtypes, along with potential targets for identifying indications for targeted drug therapy. These insights aim to support the development of personalized treatment approaches for TNBC patients.

c-Jun promotes neuroblastoma cell differentiation by inhibiting APC formation via CDC16 and reduces neuroblastoma malignancy

Neuroblastoma is a pediatric embryonal malignancy characterized by impaired neuronal differentiation. Differentiation status in neuroblastoma strongly affects the clinical outcome, thus, enforcement of differentiation becomes a treatment strategy for this disease. However, the molecular mechanisms that control neuroblastoma differentiation are poorly understood. As an extensively studied protein of the activator protein-1 (AP-1) complex, c-Jun is involved in numerous cell regulations such as proliferation, survival and differentiation. In the current study, we demonstrated that c-Jun expression was upregulated by retinoic acid (RA) and flow cytometry assay indicated c-Jun overexpression arrested cell cycle to G1 phase, which, in turn, promoted the initiation of neuroblastoma cell differentiation. Co-immunoprecipitation (co-IP) assay showed that c-Jun competitively interacted with CDC16, a key subunit in anaphase-promoting complex (APC), resulting in reduced APC formation and inhibition of cell cycle progression. Furthermore, EdU proliferation assay and transwell experiment showed that c-Jun overexpression inhibited neuroblastoma cell proliferation and migration via interacting and sequestering CDC16. These findings identify c-Jun as a key regulator of neuroblastoma cell cycle and differentiation and may represent a promising therapeutic target to induce neuroblastoma differentiation via the interaction between c-Jun and CDC16.

Insights into phosphorylation-induced influences on conformations and inhibitor binding of CDK6 through GaMD trajectory-based deep learning

The phosphorylation of residue T177 produces a significant effect on the conformational dynamics of CDK6. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) are applied to explore the molecular mechanism of the phosphorylation-mediated effect on the conformational dynamics of CDK6 bound by three inhibitors 6ZV, 6ZZ and 0RS, in which 6ZV and 6ZZ have been used to test clinical performance. The DL finds that the β-sheets, αC helix as well as the T-loop are involved in obvious differences of conformation contacts and suggests that the T-loop plays a key role in the function of CDK6. The analyses of free energy landscapes (FELs) reveal that the phosphorylation of T177 leads to alterations of the T-loop conformation and the results from principal component analysis (PCA) indicate that the phosphorylation affects the fluctuation behavior of the β-sheets and the T-loop in CDK6. Interaction networks of inhibitors with CDK6 were analyzed and the information reveals that 6ZV contributes more hydrogen binding interactions (HBIs) and hot interaction spots with CDK6. Our MM-GBSA calculations suggest that the binding ability of 6ZV to CDK6 is stronger than 6ZZ and 0RS. We anticipate that this work could provide useful information for further understanding of CDK6 function and developing new promising inhibitors targeting CDK6.

The Incidence and Clinical Characteristics of Interstitial Lung Disease Associated with CDK4/6 Inhibitors in Breast Cancer Patients: A Retrospective Multicenter Study

Background and Objectives: CDK4/6 inhibitors (CDK4/6i) have revolutionized the treatment of hormone receptor-positive HER2 negative (HR(+)/HER2(-)) breast cancer. Despite their efficacy, interstitial lung disease (ILD) remains a rare but potentially fatal adverse effect. This study aims to evaluate the incidence and clinical characteristics of ILD associated with CDK4/6 inhibitors in breast cancer patients in Turkey. Materials and Methods: A retrospective multicenter analysis included 464 breast cancer patients treated with CDK4/6 inhibitors between January 2017 and April 2024. Patients receiving ribociclib or palbociclib were evaluated for the development of ILD. Radiological assessments were performed to confirm ILD and exclude other conditions. Clinical characteristics, treatment regimens, and outcomes were analyzed. Results: ILD was identified in 10 patients (2.1%). The average age of the affected patients was 62.5 ± 9.85 years. Hypersensitivity pneumonitis and nonspecific interstitial pneumonia (NSIP) were the most common radiological patterns. Palbociclib was implicated in six cases, while ribociclib was associated with four cases. Grade 3 pulmonary toxicity was observed in eight patients, and Grade 4 toxicity in two patients. One patient who was on palbociclib died due to ILD. No significant correlation was found between ILD and age, smoking status, lung metastases, or prior thoracic radiotherapy. Conclusions: The incidence of CDK4/6 inhibitor-associated ILD in Turkish breast cancer patients appears higher than previously reported in clinical trials. More robust, long-term studies are necessary to identify potential risk factors and mitigate ILD-related mortality.

Multi-omics insights into the molecular signature and prognosis of hypopharyngeal squamous cell carcinoma

Approximately two-thirds of hypopharyngeal squamous cell carcinoma (HPSCC) cases are diagnosed at advanced stages, with the worst prognosis among head and neck squamous cell carcinomas (HNSCCs). Identifying biomarkers for high-risk patients requiring aggressive treatment is crucial. We present mutational, transcriptomic, and proteomic studies of 103 Chinese HPSCC patients and observe a higher prevalence and poorer prognosis in males. Estrogen response pathways are up-regulated, and proteins phosphorylated by protein kinase C (PKC) and cyclin-dependent kinases (CDKs) are aberrantly regulated in HPSCC. We identify aberrant copy number regions including SOX2(3q26.33), FGFR(8p11.23), CCND1(11q13.3), CDKN2A/2B(9p21.3), and MYC(8q24.21). Human papillomavirus (HPV) status combined with highly mutated genes, such as SYNE1 in HPV(-) and MUC4 in HPV(+) patients, were assessed as prognosis markers. A predictive model involving clinical factors and expression of six genes was established and cross-site validated. These findings open new opportunities for stratifying high-risk patients and molecular targets for personalized therapeutic strategies.

Recent advances in regulating the cell cycle through inhibiting CDKs for cancer treatment

The inhibition of cyclin-dependent kinases (CDKs) is considered a promising strategy for cancer treatment due to their role in cell cycle regulation. However, CDK inhibitors with no selectivity among CDK families have not been approved. A CDK inhibitor with high selectivity for CDK4/6 exhibited significant treatment effects on breast cancer and has become a heavy bomb on the market. Subsequently, resistance gradually decreased the efficacy of selective CDK4/6 inhibitors in breast cancer treatment. In this review, we first introduce the development of selective CDK4/6 inhibitors and then explain the role of CDK2 activation in inducing resistance to CDK4/6 inhibitors. Moreover, we focused on the development of CDK2/4/6 inhibitors and selective CDK2 inhibitors, which will aid in the discovery of novel CDK inhibitors targeting the cell cycle in the future.

Insights into the selectivity of a brain-penetrant CDK4/6 vs CDK1/2 inhibitor for glioblastoma used in multiple replica molecular dynamics simulations

Cyclin dependent kinases (CDKs) play an important role in cell cycle regulation and their dysfunction is associated with many cancers. That is why CDKs have been attractive targets for the treatment of cancer. Glioblastoma is a cancer caused by the aberrant expression of CDK4/6, so exploring the mechanism of the selection of CDK4/6 toward inhibitors relative to the other family members CDK1/2 is essential. In this work, multiple replica molecular dynamics (MRMD) simulations, principal component analysis (PCA), free energy landscapes (FELs), molecular mechanics Poisson-Boltzmann/Generalized Born surface area (MM-PB/GBSA) and other methods were integrated to decipher the selectively binding mechanism of the inhibitor N1J to CDK4/6 and CDK1/2. Molecular electrostatic potential (MESP) analysis provides an explanation for the N1J selectivity. Residue-based free energy decomposition reveals that most of the hot residues are located at the same location of CDKs proteins, but the different types of residues in different proteins cause changes in binding energy, which is considered as a potential developmental direction to improve the selectivity of inhibitors to CDK4/6. These results provide insights into the source of inhibitor and CDK4/6 selectivity for the future development of more selective inhibitors.

Physiological and pathological roles of the transcriptional kinases CDK12 and CDK13 in the central nervous system

The cyclin-dependent kinases 12 (CDK12) and 13 (CDK13) govern several steps of gene expression, including transcription, RNA processing and translation. The main target of CDK12/13 is the serine 2 residue of the carboxy-terminal domain of RNA polymerase II (RNAPII), thus influencing the directionality, elongation rate and processivity of the enzyme. The CDK12/13-dependent regulation of RNAPII activity influences the expression of selected target genes with important functional roles in the proliferation and viability of all eukaryotic cells. Neuronal cells are particularly affected by the loss of CDK12/13, as result of the high dependency of neuronal genes on RNAPII processivity for their expression. Deregulation of CDK12/13 activity strongly affects brain physiology by influencing the stemness potential and differentiation properties of neuronal precursor cells. Moreover, mounting evidence also suggest the involvement of CDK12/13 in brain tumours. Herein, we discuss the functional role(s) of CDK12 and CDK13 in gene expression regulation and highlight similarities and differences between these highly homologous kinases, with particular attention to their impact on brain physiology and pathology. Lastly, we provide an overview of CDK12/13 inhibitors and of their efficacy in brain tumours and other neoplastic diseases.

Phosphorylated-tau associates with HSV-1 chromatin and correlates with nuclear speckles decondensation in low-density host chromatin regions

Abnormal tau phosphorylation is a key mechanism in neurodegenerative diseases. Evidence implicates infectious agents, such as Herpes Simplex Virus 1 (HSV-1), as co-factors in the onset or the progression of neurodegenerative diseases, including Alzheimer's disease. This has led to divergence in the field regarding the contribution of viruses in the etiology of neurodegenerative diseases. Research indicates that viruses may function as risk factors driving neurodegenerative disease rather than playing a causative role. Investigating HSV-1 in abnormal tau phosphorylation is important for understanding the role of infectious agents in neurodegeneration. We generated cellular models of HSV-1 acute, latent infection, and viral reactivation from latency in cortical brain organoids and investigated the interplay between tau phosphorylation and HSV-1 infection by employing human induced pluripotent stem cell (iPSC)-derived monolayer neuronal cultures and brain organoids. Acute infection with HSV-1 strains 17syn+ and KOS caused nuclear accumulation of phosphorylated tau (p-tau) in neurons and neural precursor cells. Antivirals prevented nuclear accumulation of p-tau. Viral reactivation was accompanied by the nuclear translocation of p-tau. Chromatin immunoprecipitation analysis indicated an interaction of p-tau with the viral chromatin. A reduction in abundance of component of nuclear speckles and their loss of organized morphology in low-denisty host chromatin regions was observed, with strain-specific differences. HSV-1 infection was followed by an increase in the abundance of BRSKs and TAOKs, kinases known to phosphorylate tau. These findings show interaction between p-tau and HSV-1 chromatin and demonstrate the ability of HSV-1 to activate mechanisms that are observed in Alzheimer's disease.

Multimodal mechanisms of human centriole engagement and disengagement

Centrioles are unique cellular structures that replicate to produce identical copies, ensuring accurate chromosome segregation during mitosis. A new centriole, the "daughter", is assembled adjacent to an existing "mother" centriole. Only after the daughter centriole is fully developed as a complete replica, does it disengage and become the core of a new functional centrosome. The mechanisms preventing precocious disengagement of the immature daughter centriole have remained unclear. Here, we identify three key mechanisms maintaining mother-daughter centriole engagement: the cartwheel, the torus, and the pericentriolar material (PCM). Among these, the torus critically establishes the characteristic orthogonal engagement. We also demonstrate that engagement mediated by the cartwheel and torus is progressively released during centriole maturation. This release involves structural changes in the daughter, known as centriole blooming and distancing, respectively. Disrupting these structural transitions blocks subsequent steps, preventing centriole disengagement and centrosome conversion in the G1 phase. This study provides a comprehensive understanding of how the maturing daughter centriole progressively disengages from its mother through multiple steps, ensuring its complete structure and conversion into an independent centrosome.

Targeting cyclin-dependent kinase 2 (CDK2) interactions with cyclins and Speedy 1 (Spy1) for cancer and male contraception

The review discusses progress in discovering cyclin-dependent kinase 2 (CDK2) inhibitors for cancer treatment and their potential for male contraception. It summarizes first-, second-, and third-generation CDK inhibitors and selective CDK2 inhibitors currently in clinical trials for cancer. Novel strategies to discover allosteric inhibitors, covalent inhibitors, and degraders are also discussed.

Cdk6's functions are critically regulated by its unique C-terminus

The vital cell cycle machinery is tightly regulated and alterations of its central signaling hubs are a hallmark of cancer. The activity of CDK6 is controlled by interaction with several partners including cyclins and INK4 proteins, which have been shown to mainly bind to the amino-terminal lobe. We analyzed the impact of CDK6's C-terminus on its functions in a leukemia model, revealing a central role in promoting proliferation. C-terminally truncated Cdk6 (Cdk6 ΔC) shows reduced nuclear translocation and therefore chromatin interaction and fails to enhance proliferation and disease progression. The combination of proteomic analysis and protein modeling highlights that Cdk6's C-terminus is essential for protein flexibility and for its binding potential to cyclin D, p27Kip1 and INK4 proteins but not cyclin B. We demonstrate that the C-terminus is a unique and essential part of the CDK6 protein, regulating interaction partner binding and therefore CDK6's functionality.

CDK13-Related Disorder: Novel Insights From A Series of 27 Cases and Recommendations for Clinical Management

In 2016, Sifrim and colleagues described the first group of patients carrying heterozygous pathogenic variants in CDK13 and sharing major clinical features mainly consisting of congenital heart defects, intellectual disability and peculiar facial features (Congenital Heart Defects, Dysmorphic Facial Features, and Intellectual Developmental Disorder; CHDFIDD, OMIM # 617360). This condition is generally referred to as CDK13-related disorder, and since then other reports have provided further clinical and molecular information. Here we describe a group of 27 previously unreported patients to more accurately profile the clinical spectrum associated with CDK13 variants, disclosing novel associated findings, such as complex craniosynostosis and variable skeletal features (e.g., cranio-cervical anomalies). We also focused on the ocular phenotype that appears to include bilateral congenital glaucoma, posterior embriotoxon, buphthalmos and Duane anomaly. Finally, we observed two cases of mother-to-daughter transmission. Our work clarifies some novel features of CHDFIDD, defines the differential diagnosis of this disorder, and provides recommendations for its clinical management.

Individualized Pooled CRISPR/Cas9 Screenings Identify CDK2 as a Druggable Vulnerability in a Canine Mammary Carcinoma Patient

High-throughput omics approaches have long been used to uncover potential vulnerabilities in human personalized oncology but are often limited by the lack of functional validation. Therefore, we placed our emphasis on functional drug testing using patient-derived organoids (PDOs). However, PDOs generated from tumors mostly lack comparison with matching normal tissue, and the number of testable drugs is limited. Here, we demonstrate how matching the neoplastic and non-neoplastic mammary PDOs derived from the same dog can utilize targeted CRISPR/Cas9 screens to unveil cancer cell specific vulnerabilities. We performed two independent CRISPR/Cas9 dropout screens using sub-libraries targeting the epigenome (n = 1269) or druggable genes (n = 834) in paired PDOs derived from both carcinoma and normal mammary tissues from the same dog. A comparison of essential genes for tumor cells survival identified CDK2 as a functional vulnerability in canine mammary tumors (CMTs) that can be targeted with the PF3600 inhibitor. Additional potential targets were also uncovered, providing insights for personalized cancer treatments in dogs.

Effect of Cdk1 gene disruption on cell cycle progression in newt cells

Cyclin-dependent kinases (CDKs) are key regulators of cell cycle progression, in conjunction with cyclins. The cyclin-CDK system is highly conserved among eukaryotes, and CDK1 is considered essential for progression through the M phase. However, the extent to which cell cycle progression depends on CDK1 varies between cell types. Therefore, a range of cell types must be analyzed to comprehensively elucidate the role of CDK1. Cdk1-knockout mice exhibit lethality at an early developmental stage, specifically before the differentiation of various cell types. The aim of the present study was to characterize the effects of CDK1 deficiency in amphibian newts. Cdk1 was disrupted by injecting fertilized newt eggs with CRISPR/Cas9, and the resulting effects on embryonic development and cell proliferation were then evaluated. In both wild-type and Cdk1-crispant newt embryos, CDK1 protein was either stored in the egg until late embryogenesis or potentially derived from maternal mRNA, which may also be stored during this period. The embryos survived to the hatching stage, during which the cells responsible for forming the basic organs differentiated. To further characterize the long-term effects of Cdk1 knockout, parabiosis experiments were conducted using wild-type embryos and Cdk1 crispants. The results suggested that an endocycle occurred in the crispant larvae, as evidenced by increases in the size of several types of cells. It is anticipated that studies using newts will provide further insights into the role of Cdk1 in regulating the cell cycle.

Emerging roles of cyclin-dependent kinase 7 in health and diseases

Cyclin-dependent kinase 7 (CDK7) regulates cell cycle and transcription, which are central for cancer progression. CDK7 inhibitors exhibit substantial anticancer activities in preclinical studies and are currently being evaluated in clinical trials. CDK7 is widely expressed in the body. However, the impact of CDK7 inhibition on normal tissues has received little attention. Here, we review the biological functions of CDK7, followed by its emerging roles in development, homeostasis and diseases. We discuss the regulatory mechanisms of CDK7 kinase activation and provide an overview of CDK7 substrates identified to date. Moreover, we highlight unanswered questions and propose key areas for future investigation. An advanced understanding of CDK7 will facilitate the pharmaceutical development of CDK7 inhibitors and help minimize undesirable adverse effects.

PI3K/Akt inhibition promotes AR activity and prostate cancer cell proliferation through p35-CDK5 modulation

Aberrant PI3K/Akt activation is linked to prostate cancer (PCa) malignancy, while androgen receptor (AR) is critical in early-stage PCa development. Investigating the interaction between these pathways is crucial for PCa malignancy. Our previous study demonstrated that p35-CDK5 mediates post-translational modifications of AR, STAT3, and p21CIP1, eventually promoting PCa cell growth. This study revealed the role of p35-CDK5 in between PI3K/Akt and AR by utilizing LNCaP and 22Rv1 cells. Through the TCGA database analysis, we observed a positive correlation between PTEN and p35 expression, implying a potential negative correlation between PI3K/Akt activation and p35-CDK5. Inhibiting PI3K/Akt with LY294002, Capivasertib (AZD5363), or using an inactive Akt mutant significantly increased p35 expression and subsequently enhanced AR stability and activation in PCa cells. On the other hand, CDK5-knockdown reversed these effects. The involvement of the β-catenin/Egr1-axis was observed in regulating PI3K/Akt inhibition and p35-CDK5 activation, implying a possible mechanistic connection. Importantly, CDK5 knockdown further reduced PI3K/Akt-inhibition-induced AR and cell viability maintenance, suggesting a compensatory role for CDK5-AR in maintaining cell viability under Akt inhibition. In conclusion, PI3K/Akt inhibition could trigger p35-CDK5-dependent AR activation and cell viability, highlighting p35-CDK5 as a critical link connecting PI3K/Akt inhibition to AR activation and pivotal in PCa cell resistance to PI3K/Akt blockade.

Roles of CDK12 mutations in PCa development and treatment

Prostate cancer (PCa) is one of the most common cancers in men, and cyclin-dependent kinase 12 (CDK12) is emerging as a novel star player in the PCa tumorigenesis and progression to castration-resistant prostate cancer (CRPC). In PCa, CDK12 alterations are mostly loss-of-function mutations featuring intronic polyadenylation (IPA), focal tandem duplications (FTDs), and R-loops formation and transcription-replication conflicts (TRCs). The occurrence of IPA can result in homologous recombination deficiency (HRD) and androgen receptor (AR) variation. FTDs induce neoantigens and increase the expression of the AR, MYC, and other hotspot- associated genes. R-loops lead to TRCs and influence various cellular processes, including gene expression and genome stability. Due to the poor prognosis of CDK12-mutant PCa patients and the mediocre response to classic standard therapies, HRD and increased neoantigen levels have provided clinicians with new insights into alternative systematic treatments for this novel PCa phenotype. In this review, we summarize the roles of CDK12 mutations in PCa and discuss their clinical value, suggesting that CDK12 potentially represents a target for further research and the development of clinical strategies for PCa.

Musculoskeletal adverse events associated with CDK4/6 inhibitors: a real-world study using FDA Adverse Event Reporting System (FAERS) database

OBJECTIVE

Cyclin-dependent kinase (CDK)-4/6 inhibitors have significantly improved outcomes in several cancers but can also induce various organ system toxicities, including musculoskeletal disorders. This study aimed to comprehensively characterize the musculoskeletal adverse events (MSAEs) associated with CDK4/6 inhibitors based on real-world data.

METHODS

Reports of MSAEs linked to CDK4/6 inhibitors from the first quarter (Q1) of 2015 and 2023 Q4 were extracted from the FAERS. Descriptive analyses evaluated report frequencies over time and patient characteristics. Disproportionality analyses using reporting odds ratios (RORs) identified signals for specific musculoskeletal preferred terms (PTs). Time-to-onset analyses examined the temporal patterns of MSAEs.

RESULTS

A total of 10,095 MSAE reports associated with CDK4/6 inhibitors were identified, most involving Palbociclib (n = 7819). The median age of patients was 64 years (IQR: 55-72), predominantly female (97.73%). Most reports were submitted by consumers (47.62%) and the majority of reports were from the United States (71.53%). Disproportionality analyses revealed distinct signals, with Ribociclib showing prominent signals for bone pain and bone lesions, and Abemaciclib for osteonecrosis of the jaw and pathological fractures. Palbociclib demonstrated a consistent but less pronounced signal across musculoskeletal PTs. Time-to-onset analyses demonstrated a significantly longer onset of MSAEs for Palbociclib (median 82 days, IQR[14-311]) compared to Abemaciclib (32.5 days, IQR[12-119]) and Ribociclib (34 days, IQR[8-177]) using the nonparametric Kruskal-Wallis test (P-value = 3.048e-11).

CONCLUSION

Musculoskeletal toxicities is a significant adverse event that affects drug safety. Early identification and proper management of these events are crucial for patients receiving CDK4/6 inhibitors. Further research is warranted to elucidate the underlying mechanisms and improve risk mitigation strategies.

KEAP1-NRF2 Interaction in Cancer: Competitive Interactors and Their Role in Carcinogenesis

An American Cancer Society report estimates the emergence of around 2 million new cancer cases in the US in 2024 [...].

Elucidating Binding Selectivity in Cyclin-Dependent Kinases 4, 6, and 9: Development of Highly Potent and Selective CDK4/9 Inhibitors

CDK4/6 inhibitors are effective in treating HR+/HER2- breast cancer but face limitations due to therapeutic resistance and hematological toxicity, particularly from strong CDK6 inhibition. To address these challenges, designing selective inhibitors targeting specific cyclin-dependent kinases (CDK) members could offer clinical advantages and broaden CDK inhibitor indications. However, the highly conserved binding pockets of CDKs complicate selective targeting. This study leverages in silico modeling and structural analysis of cocrystal data to identify subtle differences in key CDK binding pockets. Notably, a sequence difference in the αD-helix motif between CDK4 and CDK6 provides a targetable "sweet spot" for selectivity. By incorporating a 1,4-trans-cyclohexanediamine side chain, we designed molecules that favor interactions with CDK4 over CDK6 and explored potential dual CDK4/9 inhibition. This approach yielded a lead compound with distinct in vitro selectivity and promising in vivo pharmacokinetics, offering valuable insights for the development of selective next-generation CDK inhibitors.

Targeting cyclin-dependent kinase 11: a computational approach for natural anti-cancer compound discovery

Cancer, a leading global cause of death, presents considerable treatment challenges due to resistance to conventional therapies like chemotherapy and radiotherapy. Cyclin-dependent kinase 11 (CDK11), which plays a pivotal role in cell cycle regulation and transcription, is overexpressed in various cancers and is linked to poor prognosis. This study focused on identifying potential inhibitors of CDK11 using computational drug discovery methods. Techniques such as pharmacophore modeling, virtual screening, molecular docking, ADMET predictions, molecular dynamics simulations, and binding free energy analysis were applied to screen a large natural product database. Three pharmacophore models were validated, leading to the identification of several promising compounds with stronger binding affinities than the reference inhibitor. ADMET profiling indicated favorable drug-like properties, while molecular dynamics simulations confirmed the stability and favorable interactions of top candidates with CDK11. Binding free energy calculations further revealed that UNPD29888 exhibited the strongest binding affinity. In conclusion, the identified compound shows potential as a CDK11 inhibitor based on computational predictions, suggesting their future application in cancer treatment by targeting CDK11. These computational findings encourage further experimental validation as anti-cancer agents.

Role of spindle assembly checkpoint proteins in gametogenesis and embryogenesis

The spindle assembly checkpoint (SAC) is a surveillance mechanism that prevents uneven segregation of sister chromatids between daughter cells during anaphase. This essential regulatory checkpoint prevents aneuploidy which can lead to various congenital defects observed in newborns. Many studies have been carried out to elucidate the role of proteins involved in the SAC as well as the function of the checkpoint during gametogenesis and embryogenesis. In this review, we discuss the role of SAC proteins in regulating both meiotic and mitotic cell division along with several factors that influence the SAC strength in various species. Finally, we outline the role of SAC proteins and the consequences of their absence or insufficiency on proper gametogenesis and embryogenesis in vivo.