Gene Cyclin-dependent Kinase Research Articles

METB-07. FREQUENCY AND OUTCOMES OF CDKN2A/B LOSS IN PEDIATRIC GLIOMA

Abstract BACKGROUND Chromosome 9p21 deletions involving the tumor-suppressor genes cyclin-dependent kinase 2A and 2B (CDKN2A/B) have been identified as a poor prognostic factor in various cancer types, including adult low-grade gliomas. The frequency and influence of CDKN2A/B hemi- and homozygous deletions in pediatric glioma are less well defined. Herein, we report a single-institution evaluation of the frequency and clinical outcomes of CDKN2A/B loss in pediatric gliomas. METHOD We performed a retrospective, IRB-approved single institutional study, utilizing an existing institutional data registry to identify pediatric patients (age < 21) diagnosed with a glioma who had undergone targeted DNA next generation panel sequencing (Oncopanel) between 2013-2023. IDH1/2-mutant gliomas were excluded. Clinical features, treatment details and outcome data were collected and analyzed. RESULTS Oncopanel was performed on 510 pediatric gliomas. Of these, 372 (72.9%) had low-grade and 138 (27%) had high-grade gliomas. Sixty-six (12.9%) gliomas harbored CDKN2A/B hemi-/homozygous loss; this included 26/372 (7%) low-grade and 40/138 (29%) high-grade gliomas. Homozygous loss was seen in 13/372 (3.5%) low-grade and 26/138 (18.8%) high-grade gliomas. The most common co-alteration with CDKN2A/B loss was BRAFV600E (28/66, 42%), followed by TP53 (8/66, 12%). Median follow-up time of the entire cohort was 3.2 years (range:0.1-36). The 10-year overall survival for pLGGs with CDKN2A/B wildtype and CDKN2A/B homozygous deletion were 95% and 85%, respectively (p=0.03). There was no significant difference in survival of pLGGs with CDKN2A/B wildtype and CDKN2A/B hemizygous deletion. For pHGGs, there was no difference in survival outcomes based on CDKN2A/B status. Further univariate and multivariable analyses are underway. Central pathology review and methylation subtyping to confirm rates of malignant transformation are also ongoing. CONCLUSION CDKN2A/B loss is identified in a subset of both pediatric low- and high-grade gliomas. Our data suggest that homozygous CDKN2A/B loss in pLGG is associated with poorer long-term survival.

N6-Methyladenosine modified circ-NAB1 modulates cell cycle and epithelial-mesenchymal transition via CDKN3 in endometrial cancer.

Endometrial cancer (EC) is a common malignant tumor in the female reproductive system. Circular RNAs (circRNAs) and N6-methyladenosine (m6A) modification are widely involved in cancer progression. Nevertheless, the cross-talk between circ-NAB1 and m6A as well as the biological functions of circ-NAB1 in EC remain unclear. Circ-NAB1 was observed to be upregulated in EC tissues and cells by RT-qPCR. MeRIP and RNA pull-down assays were utilized for detecting the m6A modification of circ-NAB1. The interaction between circ-NAB1 and RNAs was also detected. Colony formation, transwell, flow cytometry, and western blot were utilized for measuring EC cell behaviors. Mechanically, we proved the m6A demethylase alkylation repair homolog protein 5 (ALKBH5) can mediate circ-NAB1 expression through an m6A-YTHDF2-dependent manner. Circ-NAB1 overexpression can promote cell proliferation, migration, invasion, epithelial-mesenchymal transition (EMT) process, and cell cycle through functional assays. Circ-NAB1 knockdown exerts the opposite function on EC cells. Furthermore, we proved that circ-NAB1 can sponge miR-876-3p to upregulate the target gene cyclin-dependent kinase inhibitor 3 (CDKN3) in EC cells. CDKN3 overexpression can reverse the impacts of circ-NAB1 depletion on EC cell behaviors. Collectively, we proved that ALKBH5-mediated m6A modification of circ-NAB1 promoted EMT process and cell cycle in EC via targeting the miR-876-3p/CDKN3 axis.

OsMADS6-OsMADS32 and REP1 control palea cellular heterogeneity and morphogenesis in rice

Precise regulation of cell proliferation and differentiation is vital for organ morphology. Rice palea, serving as sepal, comprises two distinct regions: the marginal region (MRP) and body of palea (BOP), housing heterogeneous cell populations, which makes it an ideal system for studying organ morphogenesis. We report that the transcription factor (TF) REP1 promotes epidermal cell proliferation and differentiation inthe BOP,resulting in hard silicified protrusion cells, by regulating the cyclin-dependent kinase gene, OsCDKB1;1. Conversely, TFs OsMADS6 and OsMADS32 are expressed exclusively in the MRP, where they limit celldivision rates by inhibiting OsCDKB2;1 expression and promote endoreduplication, yielding elongatedepidermal cells. Furthermore, reciprocal inhibition between the OsMADS6-OsMADS32 complex andREP1 fine-tunes the balance between cell division and differentiation during palea morphogenesis. Wefurther show the functional conservation of these organ identity genes in heterogeneous cell growthin Arabidopsis, emphasizing a critical framework for controlling cellular heterogeneity in organ morphogenesis.

Genome-Wide Identification, Evolutionary and Expression Analysis of Cyclin-Dependent Kinase Gene Family Members in Moso Bamboo (Phyllostachys edulis)

Genome-Wide Identification, Evolutionary and Expression Analysis of Cyclin-Dependent Kinase Gene Family Members in Moso Bamboo (Phyllostachys edulis)

Hemizygous deletion of cyclin-dependent kinase inhibitor 2A/B with p16 immuno-negative and methylthioadenosine phosphorylase retention predicts poor prognosis in IDH-mutant adult glioma.

Homozygous deletion of the tumor suppression genes cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) is a strong adverse prognostic factor in IDH-mutant gliomas, particularly astrocytoma. However, the impact of hemizygous deletion of CDKN2A/B is unknown. Furthermore, the influence of CDKN2A/B status in IDH-mutant and 1p/19q-codeleted oligodendroglioma remains controversial. We examined the impact of CDKN2A/B status classification, including hemizygous deletions, on the prognosis of IDH-mutant gliomas. We enrolled 101 adults with IDH-mutant glioma between December 2002 and November 2021. CDKN2A/B deletion was evaluated with multiplex ligation-dependent probe amplification (MLPA). Immunohistochemical analysis of p16/MTAP and promoter methylation analysis with methylation-specific MLPA was performed for cases with CDKN2A/B deletion. Kaplan - Meier plots and Cox proportion hazards model analyses were performed to evaluate the impact on overall (OS) and progression-free survival. Of 101 cases, 12 and 4 were classified as hemizygous and homozygous deletion, respectively. Immunohistochemistry revealed p16-negative and MTAP retention in cases with hemizygous deletion, whereas homozygous deletions had p16-negative and MTAP loss. In astrocytoma, OS was shorter in the order of homozygous deletion, hemizygous deletion, and copy-neutral groups (median OS: 38.5, 59.5, and 93.1 months, respectively). Multivariate analysis revealed hazard ratios of 9.30 (P = .0191) and 2.44 (P = .0943) for homozygous and hemizygous deletions, respectively. CDKN2A/B hemizygous deletions exerted a negative impact on OS in astrocytoma. Immunohistochemistry of p16/MTAP can be utilized to validate hemizygous or homozygous deletions in combination with conventional molecular diagnosis.

Sall1 and Sall4 cooperatively interact with Myocd and SRF to promote cardiomyocyte proliferation by regulating CDK and cyclin genes.

Sall1 and Sall4 (Sall1/4), zinc-finger transcription factors, are expressed in the progenitors of the second heart field (SHF) and in cardiomyocytes during the early stages of mouse development. To understand the function of Sall1/4 in heart development, we generated heart-specific Sall1/4 functionally inhibited mice by forced expression of the truncated form of Sall4 (ΔSall4) in the heart. The ΔSall4-overexpression mice exhibited a hypoplastic right ventricle and outflow tract, both of which were derived from the SHF, and a thinner ventricular wall. We found that the numbers of proliferative SHF progenitors and cardiomyocytes were reduced in ΔSall4-overexpression mice. RNA-sequencing data showed that Sall1/4 act upstream of the cyclin-dependent kinase (CDK) and cyclin genes, and of key transcription factor genes for the development of compact cardiomyocytes, including myocardin (Myocd) and serum response factor (Srf). In addition, ChIP-sequencing and co-immunoprecipitation analyses revealed that Sall4 and Myocd form a transcriptional complex with SRF, and directly bind to the upstream regulatory regions of the CDK and cyclin genes (Cdk1 and Ccnb1). These results suggest that Sall1/4 are critical for the proliferation of cardiac cells via regulation of CDK and cyclin genes that interact with Myocd and SRF.

Study on the Interactions of Cyclins with CDKs Involved in Auxin Signal during Leaf Development by WGCNA in Populus alba.

Cell division plays an indispensable role in leaf morphogenesis, which is regulated via the complexes formed by cyclin and cyclin-dependent kinase (CDK). In this study, gene family analysis, exogenous auxin stimulation, RNA-seq and WGCNA analysis were all used to investigate the molecular mechanisms by which cell-cycle-related factors participated in the auxin signaling pathway on leaf morphogenesis. Sixty-three cyclin members and seventeen CDK members in Populus alba were identified and systematically analyzed. During the evolution, WGD was the main reason that resulted in the expansion of cyclin and CDK genes. Firstly, after a short time treating with auxin to matured leaves of seedlings, genes related to cell division including GRF and ARGOS were both upregulated to restart the transition of cells from G1-to-S phase. Secondly, with three days of continuous auxin stimulation to leaves at different developmental stages, leaves area variation, transcriptomes and hormones were analyzed. By PCA, PCoA and WGCNA analyses, the turquoise module was both positively related to leaf development and auxin. Based on the co-expression analysis and Y2H experiment, PoalbCYCD1;4, PoalbCYCD3;3 and PoalbCYCD3;5 were supposed to interact with PoalbCDKA;1, which could be the trigger to promote the G1-to-S phase transition. The ARF transcription factor might play the key role of connecting the auxin signaling pathway and cell division in leaf morphogenesis by affecting CYC-CDK complexes.

Cell cycle-dependent kinase inhibitor GhKRP6, a direct target of GhBES1.4, participates in BR regulation of cell expansion in cotton.

The steroidal hormone brassinosteroid (BR) has been shown to positively regulate cell expansion in plants. However, the specific mechanism by which BR controls this process has not been fully understood. In this study, RNA-seq and DAP-seq analysis of GhBES1.4 (a core transcription factor in BR signaling) were used to identify a cotton cell cycle-dependent kinase inhibitor called GhKRP6. The study found that GhKRP6 was significantly induced by the BR hormone and that GhBES1.4 directly promoted the expression of GhKRP6 by binding to the CACGTG motif in its promoter region. GhKRP6-silenced cotton plants had smaller leaves with more cells and reduced cell size. Furthermore, endoreduplication was inhibited, which affected cell expansion and ultimately decreased fiber length and seed size in GhKRP6-silenced plants compared with the control. The KEGG enrichment results of control and VIGS-GhKRP6 plants revealed differential expression of genes related to cell wall biosynthesis, MAPK, and plant hormone transduction pathways - all of which are related to cell expansion. Additionally, some cyclin-dependent kinase (CDK) genes were upregulated in the plants with silenced GhKRP6. Our study also found that GhKRP6 could interact directly with a cell cycle-dependent kinase called GhCDKG. Taken together, these results suggest that BR signaling influences cell expansion by directly modulating the expression of cell cycle-dependent kinase inhibitor GhKRP6 via GhBES1.4.

Nanohydroxyapatite-Coated Titanium Surface Increases Vascular Endothelial Cells Distinct Signaling Responding to High Glucose Concentration.

The success of dental implants depends on osseointegration can be compromised by well-known related adverse biological processes, such as infection and diabetes. Previously, nanohydroxyapatite-coated titanium surfaces (nHA_DAE) have been shown to contain properties that promote osteogenesis by enhancing osteoblast differentiation. In addition, it was hypothesized to drive angiogenesis in high-glucose microenvironments, mimicking diabetes mellitus (DM). On the other hand, the null hypothesis would be confirmed if no effect was observed in endothelial cells (ECs). Titanium discs presenting the differential surfaces were previously incubated in an FBS-free cell culture medium for up to 24 h, which was, thereafter, supplemented with 30.5 mM of glucose to expose human umbilical vein endothelial cells (HUVECs, ECs) for 72 h. They were then harvested, and the sample was processed to provide molecular activity of specific genes related to EC survival and activity by using qPCR, and the conditioned medium by ECs was used to evaluate the activity of matrix metalloproteinases (MMPs). Our data guaranteed better performance of this nanotechnology-involved titanium surface to this end once the adhesion and survival characteristics were ameliorated by promoting a higher involvement of β1-Integrin (~1.5-fold changes), Focal Adhesion Kinases (FAK; ~1.5-fold changes) and SRC (~2-fold changes) genes. This signaling pathway culminated with the cofilin involvement (~1.5-fold changes), which guaranteed cytoskeleton rearrangement. Furthermore, nHA_DAE triggered signaling that was able to drive the proliferation of endothelial cells once the cyclin-dependent kinase gene was higher in response to it, while the P15 gene was significantly down-regulated with an impact on the statement of angiogenesis. Altogether, our data show that a nanohydroxyapatite-coated titanium surface ameliorates the EC performance in a high-glucose model in vitro, suggesting its potential application in DM patients.

Network Pharmacology and Experimental Validation to Explore the Effect and Mechanism of Kanglaite Injection Against Triple-Negative Breast Cancer.

Kanglaite injection (KLTi), made of Coix seed oil, has been shown to be effective in the treatment of numerous cancers. However, the anticancer mechanism requires further exploration. This study aimed to investigate the underlying anticancer mechanisms of KLTi in triple-negative breast cancer (TNBC) cells. Public databases were searched for active compounds in KLTi, their potential targets and TNBC-related targets. KLTi's core targets and signaling pathways were determined through compound-target network, protein-protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Molecular docking was carried out to predict the binding activity between active ingredients and key targets. In vitro experiments were conducted to further validate the predictions of network pharmacology. Fourteen active components of KLTi were screened from the database. Fifty-three candidate therapeutic targets were selected, and bioinformatics analysis was performed to identify the top two active compounds and three core targets. GO and KEGG enrichment analyses indicated that KLTi exerts therapeutic effects on TNBC through the cell cycle pathway. Molecular docking results showed that the main compounds of KLTi exhibited good binding activity to key target proteins. Results from in vitro experiments showed that KLTi inhibited proliferation and migration of TNBC cell lines 231 and 468, induced apoptosis, blocked cells in the G2/M phase, downregulated the mRNA expression of seven G2/M phase-related genes cyclin-dependent kinase 1 (CDK1), cyclin-dependent kinase 2 (CDK2), and checkpoint kinase 1 (CHEK1), cell division cycle 25A (CDC25A), cell division cycle 25B (CDC25B), maternal embryonic leucine zipper kinase (MELK), and aurora kinase A (AURKA), as well as downregulated CDK1 protein expression and up-regulated protein expression of Phospho-CDK1. By utilizing network pharmacology, molecular docking, and in vitro experiments, KLTi was confirmed to have anti-TNBC effects by arresting cell cycle and inhibiting CDK1 dephosphorylation.

Genome-wide identification, evolutionary and expression analysis of the cyclin-dependent kinase gene family in peanut

BackgroundCyclin-dependent kinases (CDKs) are a predominant group of serine/threonine protein kinases that have multi-faceted functions in eukaryotes. The plant CDK members have well-known roles in cell cycle progression, transcriptional regulation, DNA repair, abiotic stress and defense responses, making them promising targets for developing stress adaptable high-yielding crops. There is relatively sparse information available on the CDK family genes of cultivated oilseed crop peanut and its diploid progenitors.ResultsWe have identified 52 putative cyclin-dependent kinases (CDKs) and CDK-like (CDKLs) genes in Arachis hypogaea (cultivated peanut) and total 26 genes in each diploid parent of cultivated peanut (Arachis duranensis and Arachis ipaensis). Both CDK and CDKL genes were classified into eight groups based on their cyclin binding motifs and their phylogenetic relationship with Arabidopsis counterparts. Genes in the same subgroup displayed similar exon–intron structure and conserved motifs. Further, gene duplication analysis suggested that segmental duplication events played major roles in the expansion and evolution of CDK and CDKL genes in cultivated peanuts. Identification of diverse cis-acting response elements in CDK and CDKL genes promoter indicated their potential fundamental roles in multiple biological processes. Various gene expression patterns of CDKs and CDKLs in different peanut tissues suggested their involvement during growth and development. In addition, qRT-PCR analysis demonstrated that most representing CDK and CDKL gene family members were significantly down-regulated under ABA, PEG and mannitol treatments.ConclusionsGenome-wide analysis offers a comprehensive understanding of the classification, evolution, gene structure, and gene expression profiles of CDK and CDKL genes in cultivated peanut and their diploid progenitors. Additionally, it also provides cell cycle regulatory gene resources for further functional characterization to enhance growth, development and abiotic stress tolerance.

IGF2 interacts with the imprinted gene Cdkn1c to promote terminal differentiation of neural stem cells.

Adult neurogenesis is supported by multipotent neural stem cells (NSCs) with unique properties and growth requirements. Adult NSCs constitute a reversibly quiescent cell population that can be activated by extracellular signals from the microenvironment in which they reside in vivo. Although genomic imprinting plays a role in adult neurogenesis through dose regulation of some relevant signals, the roles of many imprinted genes in the process remain elusive. Insulin-like growth factor 2 (IGF2) is encoded by an imprinted gene that contributes to NSC maintenance in the adult subventricular zone through a biallelic expression in only the vascular compartment. We show here that IGF2 additionally promotes terminal differentiation of NSCs into astrocytes, neurons and oligodendrocytes by inducing the expression of the maternally expressed gene cyclin-dependent kinase inhibitor 1c (Cdkn1c), encoding the cell cycle inhibitor p57. Using intraventricular infusion of recombinant IGF2 in a conditional mutant strain with Cdkn1c-deficient NSCs, we confirm that p57 partially mediates the differentiation effects of IGF2 in NSCs and that this occurs independently of its role in cell-cycle progression, balancing the relationship between astrogliogenesis, neurogenesis and oligodendrogenesis.

Differential expression of cyclins CCNB1 and CCNG1 is involved in the chondrocyte damage of kashin-beck disease.

The purpose of this study was clarify the relationship between the differential expression of cyclins CCNB1 and CCNG1 and chondrocyte damage in Kashin-Beck disease. Systematic review and high-throughput sequencing of chondrocytes derived from Kashin-Beck disease patients were combined to identify the differentially expressed cyclins and cyclin-dependent kinase genes. In parallel, weaned SD rats were treated with low selenium for 4weeks and then T-2 toxin for 4weeks. Knee cartilage was collected to harvest chondrocytes for gene expression profiling. Finally, the protein expression levels of CCNB1 and CCNG1 were verified in knee cartilage tissue of Kashin-Beck disease patients and normal controls by immunohistochemical staining. The systematic review found 52 cartilage disease-related cyclins and cyclin-dependent kinase genes, 23 of which were coexpressed in Kashin-Beck disease, including 15 upregulated and 8 downregulated genes. Under the intervention of a low selenium diet and T-2 toxin exposure, CCNB1 (FC = 0.36) and CCNG1 (FC = 0.73) showed a downward expression trend in rat articular cartilage. Furthermore, compared to normal controls, CCNB1 protein in Kashin-Beck disease articular cartilage was 71.98% and 66.27% downregulated in the superficial and middle zones, respectively, and 12.06% upregulated in the deep zone. CCNG1 protein was 45.66% downregulated in the superficial zone and 12.19% and 9.13% upregulated in the middle and deep zones, respectively. The differential expression of cyclins CCNB1 and CCNG1 may be related to articular cartilage damage in Kashin-Beck disease.

Copy Number Alterations in CDKN2A/2B and MTAP Genes Are Associated With Low MEF2C Expression in T-cell Acute Lymphoblastic Leukemia.

The molecular heterogeneity of T-cell acute lymphoblastic leukemia (T-ALL) makes this disease complex. Early T-cell precursor ALL (ETP-ALL) is a recognized subtype of T-ALL associated with a high probability of induction failure with conventional therapy. Higher expression of myocyte enhancer factor 2C (MEF2C) and the absence of a biallelic deletion (ABD) are the designated markers for the ETP-ALL. Co-deletion of the contiguous genes cyclin-dependent kinase inhibitor 2A/2B (CDKN2A/2B) and the methylthioadenosine phosphorylase (MTAP) cluster, located at 9p21.3, is another common alteration in T-ALL and confers poor response to treatment. We used real-time polymerase chain reaction (PCR) analysis to assess MEF2C mRNA expression and ABD status. Copy number alterations (CNAs) in key genes previously reported to be altered in T-ALL were assessed using multiple ligation probe amplification (MLPA). We observed that CNAs in this co-deletion cluster of CDKN2A/B and MTAP genes exhibited low MEF2C expression while ABD was associated with CNA in the Abelson murine leukemia 1 (ABL1) gene. Assessment of MEF2C expression based on immunophenotype revealed that its association with CDKN2A/2B alteration is present in non-immature immunophenotype. Additionally, ABD was associated with copy number alterations of T-cell acute lymphocytic leukemia protein 1 (TAL1), myeloblastosis (MYB), and LIM domain only 2 (LMO2) genes in immature immunophenotypes. Further, STIL::TAL1fusion was associated with low expression ofMEF2C. These associations may help explain the difficulties in assessing disease heterogeneity and the prognostic importance of 9p21.3 alterations in T-ALL.

Endometrial cancer prognosis prediction using correlation models based on CDK family genes.

Cyclin-dependent kinases (CDKs) play an important role in cell division. Given that abnormal cell proliferation caused by dysregulation of cell division is one of the major causes of endometrial cancer (EC), it is important to elucidate the role of CDK family genes in the diagnosis and prognosis of EC. In this study, The Cancer Genome Atlas (TCGA) database was used to analyze the frequency of copy number variations and somatic mutations in 26 CDK family genes. Subsequently, the expression of these genes in EC was assessed, and their relationship with overall survival (OS) was examined via Kaplan–Meier analysis to assess their prognostic significance. A prognostic model based on seven CDK genes was constructed using Lasso and Cox regression, and the predictive performance of the model was analyzed using Kaplan–Meier analysis and column line plots. The correlation between CDK genes and immune cells was also examined. Patients with EC in the high-risk group had a poorer prognosis. The results of qRT-PCR and immunohistochemical analyses validated that CDK16 is highly expressed in EC tissues. Patients with EC with high CDK16 expression had worse 10-year OS than patients with low CDK16 expression. These findings suggest that the prognostic model constructed based on CDK genes can help to develop individualized and targeted treatment strategies for patients with EC.

Insulin-like growth factor-1 regulates follicle selection of hens by promoting proliferation and inhibiting apoptosis of granulosa cells in prehierarchical follicles in vitro

During the reproduction stage of poultry, a single follicle is selected from a cohort of 6–8 mm small yellow follicles to initiate rapid growth and final ovulation almost daily. In the process, follicle-stimulating hormone (FSH) plays a pivotal role by interacting with intraovarian factors, including insulin-like growth Factor 1 (IGF1). The objective of this study was to analyze whether IGF1 coordinates with FSH to affect the characteristics of granulosa cells from prehierarchical follicles. After treating granulosa cells with 50 ng/mL FSH and 200 ng/mL IGF1, we detected the proliferation and apoptosis of granulosa cells using flow cytometry. The percentage of G1 phase granulosa cells was increased, and the percentage of mitotic cells and apoptotic cells was reduced under IGF1 treatment. The expression levels of the steroidogenic acute regulatory protein gene, cytochrome P450 side-chain cleavage gene and 3β-hydroxysteroid dehydrogenase gene, which are related to steroidogenic synthesis, were reduced by cotreatment with FSH and IGF1. The expression of the cell proliferation- or apoptosis-related genes cyclin dependent kinase 2, cyclin D2, B-cell leukemia/lymphoma 2, and BCL2 like 1 and the ratio of B-cell leukemia/lymphoma 2/BCL2-associated X were increased by treatment with IGF1. There was a decrease in the expression of caspase3 after treatment with FSH and IGF1. All these results showed that IGF1 reduced the expression of genes involved in progesterone synthesis, stimulated proliferation and inhibited apoptosis in granulosa cells. Thus, IGF1 may be one of the factors involved in affecting FSH responsiveness and maintaining the undifferentiated state of prehierarchical follicles before follicle selection.

Study on the interaction preference between CYCD subclass and CDK family members at the poplar genome level

Cyclin-dependent kinases (CDKs) control the progression of the cell cycle. D-type cyclin (CYCD) is generally believed to form a complex with CDK and control the G1/S transition. In plants, CYCD and CDK gene families can be divided into 6 (D1–D7) and 7 (CDKA–CDKG) subclasses, respectively. Different subclasses in the CYCD and CDK families have different numbers, structures and functions. In some heterologous woody plants, the functions of these subclass family members remain unclear. In this study, 43 CYCD and 27 CDK gene family members were identified in the allodiploid Populus tomentosa Carr. Phylogenetic analysis suggested that these CYCDs and CDKs were divided into 6 and 7 subclasses, respectively, which were the same as other species. The analysis of protein properties, gene structure, motifs, domains, cis-acting elements and tissue-specific expression of all members of these CYCDs and CDKs showed that the differences between members of different subclasses varied widely, but members of the same subclass especially in the CDK gene family were very similar. These findings also demonstrated a strong correlation between CYCD and CDK gene family members in response to hormones and specific expression. The collinear analysis of P. tomentosa, Populus trichocarpa and Arabidopsis thaliana showed that the expansion patterns of CYCD and CDK gene families were predominantly whole genome duplications (WGD). The protein interaction prediction results of different subclasses of CYCD and CDKs showed that the interaction between different subclasses of CYCD and CDKs was significantly different. Our previous study found that transgenic PtoCYCD2;1 and PtoCYCD3;3 poplars exhibited opposite phenotypes. Y2H and BIFC results showed that the interaction between PtoCYCD2;1 and PtoCYCD3;3 was significantly different with CDKs. This finding might suggest that the functional differences of different CYCD subclasses in plant growth and development were closely related to the different interactions between CYCD and CDK. Our results provide a good idea and direction for the functional study of CYCD and CDK proteins in woody plants.

Molecular cloning and expression analysis of CDK genes during selective and wild populations of juvenile Meretrix meretrix

The saltwater hard clam Meretrix meretrix is an important commercially bivalve in China. Therefore, identification of key genes involved in growth regulation are the primary prerequisites for further development of phenotype-selective breeding of the clams and understanding molecular mechanisms of growth regulation. In the present study, we cloned the full-length cDNA sequences of the growth-related genes cyclin-dependent kinase 1 and 7 in M. meretrix (MmCDK1 and MmCDK7) and then investigated their gene expression characteristics and associations with growth traits. The full-length cDNA of MmCDK1 was 1623 base pairs (bp), with a 900 bp open reading frame (ORF) encoding 299 amino acids. The full-length MmCDK7 cDNA was 1296 bp, with a 1017 bp ORF encoding 338 amino acids. In adult clams, expression levels of MmCDK1 and MmCDK7 were significantly higher in the gonad than other tissues (p < 0.05). In the eight developmental stages of M. meretrix, MmCDK1 and MmCDK7 had the highest expression levels in the multicellular stage, followed by oosperm, blastula stage and gastrulae stage. The BLAST searches showed that MmCDK1 has high similarity to the cyclin-dependent kinases from Crassostrea gigas (89.26%), and the protein structure of MmCDK7 was similar to the Mizuhopecten yessoensis (75.00%). In addition, the growth trait (shell length) of clams was tested in different cultivation conditions. A 2 × 2 layout was designed including four treatment groups were abbreviated as LHFH (high light and high food), LHFL (high light and low food), LLFH (low light and high food) and LLFL (low light and low food). The shell length of the selective and wild clams in the LHFH group was higher than those in other groups on the 75th day. Moreover, the shell length and MmCDK7 expression levels of the selective clams was higher in the LHFH, LLFH and LHFL groups than the wild clams on the 75th day, significantly (p < 0.05). However, the shell length and relative expression levels of MmCDK7 were no significant differences between the selective clams and the wild clams in the LLFL group (p > 0.05). MmCDK1 expression levels of the selective clams were higher than the wild clams in four treatment groups on the 75th day, significantly (p < 0.05). Further analysis showed that there was a significant linear correlation between shell length and relative expression levels of MmCDKs genes (MmCDK1 and MmCDK7). These results suggest that MmCDK1 and MmCDK7 are key growth-related genes, and they may have potential value in selective breeding to improve growth performance of M. meretrix.

Modulation of atrazine-induced chromosomal aberrations and cyclin-dependent kinases by aqueous extract of Roylea cinerea (D.Don) Baillon leaves in Allium cepa

Roylea cinerea (D.Don) Baillon an indigenous medicinal plant of Lamiaceae family used for the treatment of several diseases. In the present study, its aqueous (leaves) extract was tested for genoprotective action against atrazine-induced chromosomal aberrations in the root tip cells of Allium cepa. Atrazine is a herbicide of triazine class commonly used to inhibit the growth of broad leaf and grassy weeds. In order to find the concentration of atrazine that exhibits maximum toxicity, its different concentrations (1, 5 and 10 µg/mL) were tested. It was observed that 10 µg/mL concentration was more toxic as it reduced the mitotic index and also increased the chromosomal aberrations. Among all the tested concentrations of aqueous (leaves) extracts (0.25. 0.5, 1.0, 1.5 and 3.0 µg/mL), the3.0 µg/mL concentration in both modes of experiments i.e. pre and post showed a significant reduction in chromosomal aberrations induced by atrazine. To understand the mechanism of protection by plant extract on atrazine-induced chromosomal abnormalities the RT-qPCR studies were conducted to observe the expression of marker genes Cyclin-dependent kinases (CDKs) (CDKA:1, CDKB2:1 and CDKD1:1. For this, the RNA was extracted from root tips treated with extract along with atrazine by TRIzol®. It was observed that aqueous extract of Roylea cinerea (D.Don) Baillon leaves upregulated the CDKs gene expression in both the modes i.e. pre and post treatments. A critical analysis of results indicated that aqueous extract ameliorated the chromosomal aberrations caused by atrazine which may be be due to the increased expression level of CDKs genes.

Metformin and Gegen Qinlian Decoction boost islet α-cell proliferation of the STZ induced diabetic rats

BackgroundThe traditional Chinese medicine Gegen Qinlian Decoction (GQD), as well as metformin, had been reported with anti-diabetic effects in clinical practice.ObjectiveTo verify whether these two medicines effectively ameliorate hyperglycemia caused by deficiency of islet β-cell mass which occurs in both type 1 and type 2 diabetes.MethodsSD rats were injected with a single dose of STZ (55 mg/kg) to induce β-cell destruction. The rats were then divided into control, diabetes, GQD and metformin group. GQD and metformin groups were administered with GQD extract or metformin for 6 weeks. The islet α-cell or β-cell mass changes were tested by immunohistochemical and immunofluorescent staining. The potential targets and mechanisms of GQD and metformin on cell proliferation were tested using in silico network pharmacology. Real-time PCR was performed to test the expression of islet cells related genes and targets related genes.ResultsBoth GQD and metformin did not significantly reduce the FBG level caused by β-cell mass reduction, but alleviated liver and pancreas histopathology. Both GQD and metformin did not change the insulin positive cell mass but increased α-cell proliferation of the diabetic rats. Gene expression analysis showed that GQD and metformin significantly increased the targets gene cyclin-dependent kinase 4 (Cdk4) and insulin receptor substrate (Irs1) level.ConclusionThis research indicates that GQD and metformin significantly increased the α-cell proliferation of β-cell deficiency induced diabetic rats by restoring Cdk4 and Irs1 gene expression.