CDKN1C Research Articles

The BET protein inhibitor apabetalone (RVX-208) prevents doxorubicin-induced endothelial senescence

Abstract Background Accumulation of senescent endothelial cells (ECs) plays a pivotal role in cardiometabolic disorders and lifespan reduction(1). Yet, only a few senolytics are known to date, partly due to the poor grasp of the molecular mechanisms that control the senescence survival programme. Bromo-and extraterminal domain (BET) proteins, known epigenetic reader proteins, recognize acetylated histone tails and regulate gene transcription. RVX-208, an FDA-approved BET inhibitor, has shown to modulate transcriptional programs involved in inflammation, cancer, and renal disease(2). Yet, its potential role in EC senescence and cardio-oncology remains elusive. Purpose Our study aims to investigate whether pharmacological modulation of BET proteins by RVX-208 can mitigate doxorubicin-induced endothelial senescence. Methods Human aortic endothelial cells (HAECs) were exposed to different concentrations of Doxo (50nM-500nM) for 48 hours. Cell morphology changes, cell cycle arrest, senescence associated secreted phenotype (SASP) release, upregulation of SA-b gal activity, DNA damage response (gH2AX) and expression of p21, p16 and p53 were used as molecular markers of cellular senescence. Conditioned media was collected from Doxo-treated ECs and processed for molecular analyses or used for treatment of healthy, non-senescent ECs. To test whether RVX-208 exerts any senolytic or senomorphic effect, HAECs were treated with Doxo (100 nM) in presence or absence of RVX-208 (5mM-20mM) for 48 hrs. RNA-seq and proteomic profiling were performed in vehicle and Doxo-treated ECs. Results Doxo-treated ECs showed a dose-dependent increase in senescence markers (p16, p21 and p53) and DNA-damage response (gH2AX). FACS analysis revealed an accumulation of cells in G2/M phase in Doxo-treated ECs (100 nM). Of interest, treatment with RVX-208 (15mM) prevented the upregulation of senescent markers (p16, p21 and p53) while rescuing alterations in cell morphology and reducing the number of SA-b gal positive cells. RVX-208 prevented Doxo-induced upregulation of genes involved in inflammation, oxidative stress and mitochondrial dysfunction as shown by RNA-seq and proteomic analysis. Conditioned media from Doxo-treated ECs showed an enrichment of SASP-associated markers (IL6, CCL2, IL8, TIMP2 and PDGF-b) as shown by dot-blot arrays. Exposure of healthy ECs to conditioned media from senescent ECs recapitulated aging features. Notably, RVX-208 blunted the release of SASP markers (IL6, CCL2 and IL8) from Doxo-treated ECs. Mechanistically, we found enhanced BET protein occupancy (BRD4) with concomitant enrichment of activating chromatin marks (H3K27Ac and H3K4me) on the promoter of senescence genes COL1A2, CDKN1C and SESN3. Conclusion Targeting BET proteins with RVX-208 may offer a promising therapeutic strategy to prevent endothelial aging in cancer patients undergoing cardiotoxic therapies.

Isolated Lateralized Overgrowth - Phenotypic Spectrum and Molecular Alterations.

To evaluate the molecular aberrations at 11p15.5 locus in thirty-two patients with isolated lateralized overgrowth (ILO). Among selected 32 cases of ILO, methylation-sensitive multiplex ligation-dependent probe amplification (MS-MLPA) was performed initially followed by short tandem repeats (STR) marker analysis to confirm uniparental disomy (UPD). In those patients with normal MLPA reports, cyclin dependent kinase inhibitor 1C (CDKN1C) gene and whole exome sequencing was performed. Molecular analysis by MS-MLPA showed methylation aberrations in 28% (9/32) of patients. Gain of methylation at IC1 imprinting center (H4, H7) and loss of methylation at IC2 (H6, H9) was observed in 2 patients each. Uniparental disomy was observed in 9% cases. Except one, all patients with methylation aberration had more than one limb hypertrophy. Two patients (H22/H29) also had loss of methylation at IC1. Though this molecular alteration is specifically associated with Silver Russel syndrome (SRS), but the affected children did not completely fulfill the diagnostic criteria for SRS. In a recent study, a discrepancy was reported between the diagnosis of Beckwith-Wiedemann syndrome (BWS)/SRS and the molecular findings in the patients. Many times, it is very difficult to differentiate between hemi hypertrophy/hemi hypotrophy. Patients, in whom no aberrations were detected on MS-MLPA, whole exome sequencing (WES) was performed and no pathogenic variant was identified. Thus, ILO may be considered as a mild presentation on the extreme edge of BWS spectrum with methylation aberration and UPDin one thirdof cases which has implications in follow up.

Identification and characterization of an enhancer element regulating expression of Cdkn1c (p57 gene).

The mammalian p57 protein is a member of the CIP/KIP family of cyclin-dependent kinase inhibitors and plays an essential role in the development of multiple tissues during embryogenesis as well as in the maintenance of tissue stem cells in adults. Although several transcription factors have been implicated in regulating the p57 gene, cis-elements such as enhancers that regulate its expression have remained ill-defined. Here we identify a candidate enhancer for the mouse p57 gene (Cdkn1c) within an intron of the Kcnq1 locus by 4C-seq analysis in mouse embryonic stem cells (mESCs). Deletion of this putative enhancer region with the CRISPR-Cas9 system or its suppression by CRISPR interference resulted in a marked attenuation of Cdkn1c expression in differentiating mESCs. Our results thus suggest that this region may serve as an enhancer for the p57 gene during early mouse embryogenesis.

Clinicopathological and molecular genetic insights into EBV-positive inflammatory follicular dendritic cell sarcoma

Epstein-Barr virus (EBV)-positive inflammatory follicular dendritic cell (FDC) sarcoma (EBV + IFDCS) is a rare entity, and its histopathological characteristics have not been fully described. This study aimed to investigate the clinical characteristics, pathological features, and molecular genetic profiles of EBV + IFDCS to improve our understanding of these lesions. A total of 12 EBV + IFDCS specimens were obtained from patients in our pathology diagnostic center. The clinical data, morphology, immunohistochemistry, in situ hybridization, and high-throughput DNA-targeted sequencing data were collected, and follow-up data were analyzed. These data were compared with those of 6 patients with traditional FDCS. The patients with EBV + IFDCS ranged from 21 to 84 years old, with a mean age of 52.3 years and a male-to-female ratio of 1:5. At the last follow-up, all patients were alive, with 2 experiencing recurrence and metastasis. In these cases, four were classified as the classical subtype, four as the angiomatoid/sclerosing subtype, and four as the lymphoma-like subtype, with two cases also exhibiting epithelioid granulomas. All patients exhibited heterogeneous expression of follicular dendritic cell markers (CD21, CD23, CD35, and CXCL13) alongside the fibroblast marker SMA, with significantly higher expressions of IgG4, EBER, and SMA in EBV + IFDCS patients compared to FDCS patients (P < 0.05). Conversely, SSTR2, EGFR, and STAT3 expression were significantly lower in the EBV + IFDCS group (P < 0.05). The average value of EBER was significantly higher in the classical subtype group (P = 0.022). Among the four cases of EBV + IFDCS analyzed for molecular genetic features, one patient exhibited germline mutations in the CDKN1C, PDGFRA, MSH2, FANCG, MLH1, ALK, and RUNX1 genes; three exhibited simultaneous SNP variations in the MTHFR gene; and two exhibited simultaneous SNP variations in the NQO1 gene. We conducted KEGG pathway analysis on the mutant genes, revealing significant enrichment in the cAMP signaling pathway, which plays a crucial role in tumor development. Survival analysis demonstrated that the median PFS rates were not reached (NR) for EBV + IFDCS patients, compared to 5 months (HR = 7.76) for FDCS patients. The 3-year PFS rates were 66.67% and 16.67%, respectively. Compared with the FDCS group, EBV + IFDCS patients had a significantly longer median PFS time (p < 0.05). In conclusion, EBV + IFDCS represents a group of tumors with unique clinical, morphological, immunological, prognostic, and molecular cytogenetic characteristics.

DCas9-HDAC8-EGFP fusion enables epigenetic editing of breast cancer cells by H3K9 deacetylation

Epigenetic editing is thriving as a robust tool for manipulating transcriptional regulation and cell fate. Despite its regulatory role in gene downregulation, epigenetic editing with histone deacetylation has been sparsely studied, especially in the context of cancer. In this current study, we have reconstructed a dCas9-HDAC8-EGFP fusion to perform histone deacetylation on the promoter of the ESR1, TERT and CDKN1C genes for the first time in breast cancer cell lines MCF-7 and MDA-MB-231 as well as in HEK293T cells. Our results demonstrated that dCas9-HDAC8-EGFP in combination with appropriate gRNAs were able to downregulate the expression of the ESR1, TERT and CDKN1C genes transcriptionally by specifically depleting the H3K9ac level on the recruitment loci. The addition of histone deacetylase inhibitors was found to neutralize the outcomes of dCas9-HDAC8-EGFP-induced epigenetic editing. Furthermore, we observed a significant downregulation of full length ERα expression in epigenetically edited MCF-7 cells with consequential alteration in cellular response toward estradiol and tamoxifen treatment due to dCas9-HDAC8-EGFP mediated epigenetic editing of the ESR1 gene. Overall, dCas9-HDAC8-EGFP is a novel circuit that enabled downregulation of crucial genes with cellular outcome in breast cancer cells by preferentially inducing H3K9 deacetylation of specific promoter regions.

Abstract P454: Screening of risk genes for carotid vulnerable plaque based on transcriptomics and experimental verification

Purpose and background: This study aims to conduct an in-depth analysis of human carotid atherosclerotic plaques using transcriptomic data to elucidate the relationship between hypoxia-related genes and the stability of carotid artery plaques and explore their connection with immune infiltration. Methods: Four GEO datasets (GSE21545, GSE24495, GSE159677, and GSE189300) were used. Initially, gene expression data from carotid artery plaque samples in GSE21545 and GSE24495 were analyzed. Hypoxia-related gene sets were obtained from MSigDB, and the "HALLMARK_HYPOXIA" gene set was explicitly selected. GSEA software was used for ultimately selecting CDKN1C and HAS1 as characteristic genes. Subsequently, sample clustering analysis was conducted to determin the optimal number of clusters. Gene set enrichment and differential analysis were performed. Real-time quantitative polymerase chain reaction (RT-qPCR) and Western blotting experiments were conducted for preliminary validation of CDKN1C and HAS1 expression levels in ApoE knockout mice at 16 and 6 weeks. Subsequently, single-cell data from GSE159677 were processed to determine the differential localization of CDKN1C in carotid atherosclerotic plaques, with functional analysis conducted using GSE189300. Results: CDKN1C and HAS1 genes were found to exhibit differential expression in plaques and were correlated with hypoxia and immune scores. Clustering analysis revealed two main clusters, with patients in cluster A showing a higher risk of adverse events and a stronger association with immunity. Genes with a positive effect on atherosclerosis were highly expressed in poorer prognosis cluster A. Validation dataset GSE24495 also confirmed the grouping ability of CDKN1C and HAS1 genes, showing enrichment in atherosclerosis-related pathways. RT-qPCR and protein immunoblotting experiments demonstrated no significant differences in HAS1 expression levels, while CDKN1C showed lower protein expression in 16-week ApoE knockout mice compared to 6 weeks. Single-cell data from GSE159677 localized differential expression of CDKN1C in plaque cells. Finally, immunofluorescence validation confirmed the coexistence of CDKN1C and vascular smooth muscle cells. Conclusion: This study comprehensively analyzed transcriptomics data from carotid atherosclerotic plaques, revealing the significant roles of CDKN1C and HAS1 genes. Immunofluorescence validation further supported the crucial role of these genes in carotid atherosclerosis.

Transcriptomic analyses of lung tissues reveal key genes associated with progression of systemic sclerosis-interstitial lung disease (SSc-ILD)

Systemic sclerosis-interstitial lung disease (SSc-ILD) is the leading cause of death in SSc, affecting around 50% of the patients. Lung tissue of patients with early-stage SSc-ILD is characterized by a predominant inflammatory response with inconspicuous fibrosis, which may progress to honeycombing fibrosis. Hence, a better understanding of the molecular mechanisms underpinning SSc-ILD pathogenesis is needed to improve treatment options and progression prediction. This transcriptomic study aims to reveal the differential gene expression between control (ctrl) lung tissue and inflammatory, prefibrotic and fibrotic lung tissue to capture progression of early to late phase SSc-ILD. Twelve explanted lungs from patients with SSc-ILD were used to analyze gene expression from formalin-fixed paraffin-embedded lung tissues with varying stages of ILD (n=18) and control lung tissue (n=6). The SSc-ILD tissues were stratified into three ROIs: inflammatory, prefibrotic, and fibrotic using histological assessments to define a longitudinal simulation of early to late phases of SSc-ILD. The nanoString (nS) nCounter Human Fibrosis Panel was used to profile the transcriptome in the regions of interest. Validation of potential targetswas performed with immunohistochemistry in the same tissues that were used for transcriptome analysis. To validate our simulation model, we performed subgroup analysis that showed an incremental increase in pathway scores related to the severity of fibrosis. Ctrl vs SSc-ILD comparison demonstrated 24 differentially expressed genes, two of which had the most pronounced p-values. Cyclin-dependent kinase inhibitor (cdkn2c) was overexpressed (P=0.00052) in SSc-ILD compared to ctrl, while expression of Pellino E3 ubiquitin-protein ligase 1 (peli1) showed lower expression (P=0.0012). Additionally, in all four groups, cdkn2c and peli1 gene expression showed an incremental increase and decrease, respectively. Immunohistochemistry of cdkn2c showed consistent results with the nS analysis. More cdkn2c and less peli1 expression were associated with more advanced stages of SSc-ILD on histologic assessment. We report the potential of the cell cycle inhibitor and senescence marker, cdkn2c (p18) to be associated with fibrosis progression.

Gestational Trophoblastic Disease: Complete versus Partial Hydatidiform Moles.

Hydatidiform moles, including both complete and partial moles, constitute a subset of gestational trophoblastic diseases characterized by abnormal fertilization resulting in villous hydrops and trophoblastic hyperplasia with or without embryonic development. This involves chromosomal abnormalities, where one or two sperms fertilize an empty oocyte (complete hydatidiform mole (CHM); mostly 46,XX) or two sperms fertilize one oocyte (partial hydatidiform mole (PHM); mostly 69,XXY). Notably, recurrent occurrences are associated with abnormal genomic imprinting of maternal effect genes such as NLRP7 (chromosome 19q13.4) and KHDC3L (chromosome 6q1). Ongoing efforts to enhance identification methods have led to the identification of growth-specific markers, including p57 (cyclin-dependent kinase inhibitor 1C; CDKN1C), which shows intact nuclear expression in the villous cytotrophoblast and villous stromal cells in PHMs and loss of expression in CHMs. Treatment of hydatidiform moles includes dilation and curettage for uterine evacuation of the molar pregnancy followed by surveillance of human chorionic gonadotropin (HCG) levels to confirm disease resolution and rule out the development of any gestational trophoblastic neoplasia. In this review, we provide a synopsis of the existing literature on hydatidiform moles, their diagnosis, histopathologic features, and management.

First case report of a successful delivery of a healthy boy by preimplantation genetic testing for Beckwith-Wiedemann syndrome.

To showcase the successful use of ICSI with PGT-M to overcome Beckwith-Wiedemann syndrome (BWS)-related reproductive challenges, resulting in the birth of a healthy baby boy. By targeting the maternally inherited CDKN1C pathogenic gene variant, this report highlights the genetic interventions in BWS reproductive risk management. This case report describes a 41-year-old woman seeking fertility assistance after a previous pregnancy revealed a fetal anomaly related to BWS. Families with BWS recurrence face challenges, as maternally inherited CDKN1C pathogenic variants contribute to approximately 40% of genetic alterations, with a potential recurrence risk as high as 50%. Genetic analysis identified a pathogenic variant in the CDKN1C gene of the fetus that was maternally inherited. The pregnancy was terminated due to the fetal anomalies. The couple underwent intra-cytoplasmic sperm injection (ICSI) combined with preimplantation genetic testing for monogenic diseases (PGT-M) and preimplantation genetic testing for aneuploidy (PGT-A). Two embryos from IVF with low-risk PGT-M and euploid status. One transferred via frozen embryo transfer (FET) in February 2023 resulted in the successful birth of a healthy baby boy. This study reports the first successful delivery of a healthy boy after PGT-M for the CDKN1C gene variant c.79_100delinsGTGACC, contributing to the limited literature on successful outcomes for BWS. Utilizing PGT-M in combination with IVF can lead to favorable outcomes in managing BWS-associated reproductive challenges, offering insights into potential genetic interventions and successful birth.

Cannabinol Regulates the Expression of Cell Cycle-Associated Genes in Motor Neuron-like NSC-34: A Transcriptomic Analysis.

Cannabinoids are reported to have neuroprotective properties and play a role in neurogenesis and neuroplasticity in in vitro and in vivo models. Cannabinol (CBN) is a minor cannabinoid produced by the degradation of Δ9-tetrahydrocannabinol in Cannabis sativa L. and exhibits anti-oxidant, analgesic, anti-bacterial, and anti-inflammatory effects. In this study, we explored the biological effects of 20 µM CBN (6.20 µg/mL) on differentiated NSC-34 cells by MTT assay and next-generation sequencing analysis on the transcriptome. KEGG and Gene Ontology enrichment analyses have been performed to evaluate potential CBN-associated processes. Our results highlighted the absence of any cytotoxic effect of CBN. The comparative transcriptomic analysis pointed out the downregulation of Cdkn2a, Cdkn2c and Cdkn2d genes, which are known to suppress the cell cycle. Ccne2, Cdk2, Cdk7, Anapc11, Anapc10, Cdc23, Cdc16, Anapc4, Cdc27, Stag1, Smc3, Smc1a, Nipbl, Pds5a, Pds5b, and Wapl genes, renowned for their role as cell cycle progression activators, were instead upregulated. Our work suggests that CBN regulates the expression of many genes related to the cell cycle, which are required for axonal maturation, migration, and synaptic plasticity, while not affecting the expression of genes involved in cell death or tumorigenesis.

FOXO3 Inhibits the Cisplatin Resistance and Progression of Melanoma Cells by Promoting CDKN1C Transcription.

Forkhead box O3 (FOXO3) and cyclin dependent kinase inhibitor 1C Gene (CDKN1C) have been shown to be involved in the melanoma process, but their roles in the cisplatin (DDP) resistance of melanoma remain unclear. The mRNA levels of CDKN1C and FOXO3 were measured using quantitative real-time PCR. The protein levels of CDKN1C, FOXO3 and mitochondrial oxidative phosphorylation (mtOXPHOS)-related markers were determinant by western blot analysis. The DDP resistance, proliferation, and apoptosis of melanoma cells were assessed by cell counting kit 8 assay, colony formation assay and flow cytometry. Glucose consumption, lactate production and ATP level were detected to assess glycolysis. The regulation of FOXO3 on CDKN1C was confirmed by ChIP assay and dual-luciferase reporter assay. In vivo experiments were performed to evaluate the effect of FOXO3 on DDP sensitivity in melanoma tumor tissues. CDKN1C and FOXO3 were downregulated in chemoresistant melanoma tissues, and their low expression levels were related to the poor prognosis of melanoma patients. Overexpression of CDKN1C and FOXO3 repressed DDP resistance, proliferation, and glycolysis, while promoted apoptosis and mtOXPHOS in DDP-resistant melanoma cells. Further analysis suggested that FOXO3 could bind to CDKN1C promoter region to enhance its transcription. Besides, CDKN1C knockdown reversed the regulation of FOXO3 on melanoma cell DDP resistance and progression. Moreover, FOXO3 overexpression enhanced the DDP sensitivity of melanoma tumor tissues in vivo. FOXO3 promoted the transcription of CDKN1C, thereby inhibiting the DDP resistance and progression of melanoma cells.

Huge mesenchymal hamartoma in a young adult: a case report

Abstract Mesenchymal hamartoma of the liver (MHL) is rare. Less than 50 adult cases have been described. Due to their potential degeneration or recurrence, a complete surgical resection must be performed. We describe a case of a 26-year-old with a palpable solid lesion, which displaced abdominal organs. Percutaneous needle biopsies suggested the diagnosis of MHL. A right hemi-hepatectomy without segment 1 was performed; the post-operative course was uneventful. The mesenchymal component of the tumour was reactive to desmin and smooth muscle actin. Low proliferation index was confirmed (MIB1). Genetic counselling: the sequencing analysis of DICER1 and CDKN1C gene was negative, DNA methylation analysis on the chromosome 11p15 region was normal. After 42 months, there was no recurrence. In conclusion, clinicians should consider MHL in the differential diagnosis. The dimension and the need of radicality impose major liver resections or liver transplantations, which should be performed in referral centres.

Investigation of Mutations in H19, IGF2, CDKN1C, KCNQ1, and NSD1 Genes in Iranian Children Suspected of Silver-Russell Syndrome (SRS) and Beckwith-Wiedemann Syndrome (BWS) with MS-MLPA

Background: Silver-Russell Syndrome (SRS) and Beckwith-Wiedemann Syndrome (BWS) are two syndromes that are poorly diagnosed in many affected people due to mild and subtle symptoms, genetic complexity, and lack of familiarity with the hallmarks. Objective: The present study was conducted with the aim of determining mutations in H19, IGF2, CDKN1C, KCNQ1, and NSD1 genes in Iranian children suspected of SRS and BWS by the MS-MLPA method. Methods: In this case series study, which was conducted in 2022 in Pars Genome Laboratory, Karaj, Iran, 10 children suspected of SRS or BWS syndrome were included. These 10 Iranian children were referred by pediatric endocrinologists. 5 ml of peripheral blood was taken per patient for DNA extraction. MS-MLPA method was undertaken for possible mutations (methylation and deletion) in H19, IGF2, CDKN1C, KCNQ1, and NSD1 genes. Results: The interpretation of MS-MLPA results showed that out of 10 children (4 boys and 6 girls) suspected of having SRS or BWS syndrome (based on the pediatric endocrinologist’s diagnosis), only 3 children were definitively diagnosed with SRS or BWS syndrome. Based on this, methylation changes in the promoter of ICR1 and ICR2, which are related to the genes H19, IGF2, CDKN1C, KCNQ1, and NSD1, lead to the development of SRS or BWS syndrome. Conclusion: The present findings showed that methylation changes in H19, IGF2, CDKN1C, KCNQ1, and NSD1 genes are associated with the occurrence of SRS or BWS syndrome. In this study, we show that MS-MLPA can serve as a rapid, inexpensive, and reliable method for the molecular diagnosis of these syndromes.

Beckwith-Wiedemann Syndrome: deciphering the genetic and clinical complexity - A case report with literature review

Beckwith-Wiedemann syndrome (BWS) is a rare and heterogeneous genetic condition characterized by overgrowth, organomegaly, and increased vulnerability to embryonal tumors. This review investigates the complex genetic and epigenetic pathways underlying Beckwith-Wiedemann syndrome, focusing on the 11p15.5 region on chromosome 11. Abnormalities in the 11p15.5 area, such as imprinting control region dysregulation and CDKN1C gene mutations, contribute to disrupted growth regulation. This content also provides an overview of the incidence and pathophysiology of this syndrome. Clinical manifestations include macrosomia, macroglossia, and abdominal wall abnormalities. The increased risk of embryonal malignancies, such as Wilms tumor and hepatoblastoma, emphasises the importance of diligent medical observation. Early diagnosis through genetic testing is crucial for tailored management and genetic counseling. This detailed discussion of Beckwith-Wiedemann syndrome sheds light on the molecular complexities of the condition, emphasizing the significance of genetic testing, early detection, and multidisciplinary management for affected infants.

84-OR: Structure–Function Analysis of p57KIP2 in the Human Pancreatic Beta Cell Reveals a Canonical Bipartite Nuclear Localization Sequence (NLS)

p57KIP2 is a canonical cell cycle inhibitor encoded by the CDKN1C gene on chromosome 11. Mutations in CDKN1C underlie multiple pediatric endocrine syndromes including Beckwith-Wiedemann Syndrome (BWS), the Focal Variant of Congenital Hyperinsulinism (FoCHI), Insulinoma, Russel-Silver Syndrome and IMAGe Syndrome. Despite this central role in disease, little is known about the function of p57KIP2 in any cell type, including the human pancreatic beta cell. We hypothesized that p57KIP2 has functions that extend beyond cell cycle control and are unique to the human beta cell. We prepared RIP1 insulin promoter-driven adenoviruses encoding deletions of multiple putatively important and disease-associated but unexplored regions of p57KIP2 (WTp57, p57ΔPAPA, p57ΔCDKI, p57ΔPCNA and p57ΔNLS), and performed the first comprehensive structure-function analysis of CDKN1C/p57KIP2 in the human beta cell. RT-PCR and immunoblot analyses confirmed p57KIP2 overexpression, construct size and beta cell specificity in human islets. By immunocytochemistry, all constructs demonstrated nuclear localization, with the exception of a deletion mutant removing a putative NLS at amino acids 278-281. Unexpectedly, we identified a second NLS at amino acids 312-316. Further analysis showed that each individual NLS is required for nuclear localization of p57KIP2, but neither alone is sufficient to permit nuclear localization of p57KIP2. Finally, constructs containing both the 278-281 and 312-316 sequences were necessary and sufficient to target heterologous proteins to the nucleus of human beta cells. In summary, we discovered that p57KIP2 contains a classic bipartite NLS characterized by two clusters of positively charged amino acids 278KRKRS281 and 312RKRLR316 separated by a proline-rich linker region. Variants in the sequences encoding these two NLS sequences account for functional p57KIP2 loss and beta cell expansion seen in human disease. Disclosure L. Choleva: None. P. Wang: None. H. Liu: None. O. Wood: None. L. Lambertini: None. E. Karakose: None. A.F. Stewart: None.

Promoter methylation and enhanced SKP2 are associated with the downregulation of CDKN1C in cervical squamous cell carcinoma

PurposeCervical Squamous Cell Carcinoma (CSCC) is one of the significant causes of cancer deaths among women. Distinct genetic and epigenetic-altered loci, including chromosomal 11p15.5–15.4, have been identified. CDKN1C (Cyclin-Dependent Kinase Inhibitor 1C, p57KIP2), a member of the CIP/KIP family of cyclin-dependent kinase inhibitors (CDKIs), located at 11p15.4, is a putative tumor suppressor. Apart from transcriptional control, S-Phase Kinase Associated Protein 2 (SKP2), an oncogenic E3 ubiquitin ligase, regulates the protein turnover of CDKN1C. But the molecular status of CDKN1C in CSCC and the underlying mechanistic underpinnings have yet to be explored. MethodsTCGA and other publicly available datasets were analyzed to evaluate the expression of CDKN1C and SKP2. The expression (transcript/protein) was validated in independent CSCC tumors (n = 155). Copy number alteration and promoter methylation were correlated with the expression. Finally, in vitro functional validation was performed. ResultsCDKN1C was down-regulated, and SKP2 was up-regulated at the transcript and protein levels in CSCC tumors and the SiHa cell line. Notably, promoter methylation (50%) was associated with the downregulation of the CDKN1C transcript. However, high expression of SKP2 was found to be associated with the decreased expression of CDKN1C protein. Independent treatments with 5-aza-dC, MG132, and SKP2i (SKPin C1) in SiHa cells led to an enhanced expression of CDKN1C protein, validating the mechanism of down-regulation in CSCC. ConclusionCollectively, CDKN1C was down-regulated due to the synergistic effect of promoter hyper-methylation and SKP2 over-expression in CSCC tumors, paving the way for further studies of its role in the pathogenesis of the disease.

Regulation of Hepatocytes in G0 and G1 Phases by NOTCH3 mRNA, miR-369-3p, and rno-Rmdn2_0006 during the Initial Stage of Rat Liver Regeneration.

The key event of liver regeneration initiation (LRI) is the switch of hepatocytes from the G0 phase to the G1 phase. This study aimed to use the data from large-scale quantitatively detecting and analyzing (LQDA) to reveal the regulation of hepatocytes in the G0 or G1 phase by competing endogenous RNAs (ceRNAs) during LRI. The hepatocytes of the rat liver right lobe were isolated 0, 6, and 24 h after partial hepatectomy. Their ceRNA expression level was measured using LQDA, and the correlation among their expression, interaction, and role was revealed by ceRNA comprehensive analysis. The expression of neurogenic loci notch homologous protein 3 (NOTCH3) mRNA was upregulated in 0 h, but the expression of miR-369-3p and rno-Rmdn2_0006 of hepatocytes did not change significantly. Meanwhile, the expression of the G0 phase-related gene CDKN1c was promoted by NOTCH3 upregulation, and the expression of the G1 phase-related gene PSEN2 was inhibited by NOTCH3 downregulation. On the contrary, the expression of NOTCH3 mRNA and rno-Rmdn2_0006 was upregulated at 6 h, but the expression of miR-136-3p was downregulated. The expression of the G1 phase-related genes CHUK, DDX24, HES1, NET1, and STAT3 was promoted by NOTCH3 upregulation, and the expression of the G0 phase-related gene CDKN1a was inhibited by NOTCH3 downregulation. These results suggested that the ceRNAs and the NOTCH3-regulated G0 phase- and G1 phase-related genes showed a correlation in expression, interaction, and role. They together regulated the hepatocytes in the G0 phase at 0 h and in the G1 phase at 6 h. These findings might help understand the mechanism by which ceRNA together regulated the hepatocytes in the G0 or G1 phase.

The digital expression profile of BMP7, CDKN2C, HIST1H3G, and PKMYT1 genes improves high-grade cervical lesion detection in liquid-based cytology.

Some studies reported that differential gene expression could be used as a biomarker for high-grade cervical lesion identification. The aim was to evaluate the gene expression profile of cervical intraepithelial neoplasia (CIN) to identify a gene expression signature of CIN2+ in liquid-based cytology (LBC) samples. LBC samples (n=85) obtained from women who underwent colposcopy were included with benign (n=13), CIN1 (n=26), CIN2 (n=16), and CIN3 (n=30) diagnoses. After RNA isolation, gene expression profiling was performed using the nCounter PanCancer Pathways, which consists of 730 cancer-related genes. The genes identified were in silico expression evaluated using the UALCAN database. An accurate prediction model to discriminate CIN2+ from <CIN2 lesions was determined. Immunohistochemistry was performed to assess the expression of p16 and Ki67 proteins. This study identified a gene expression profile that significantly differentiates CIN2+ cases from <CIN2. The gene signature comprised 18 genes, two genes downregulated and 16 upregulated. In silico analysis corroborated the differential expression of 11 of those genes. Further observed was that high expression of BMP7 (odds ratio [OR],4.202), CDKN2C (OR,5.326), HIST1H3G (OR,3.522), PKMYT1 (OR,4.247), and menarche age (OR,1.608) were age-adjusted and associated with CIN2+. This model demonstrates a probabilityof43% leading to an area under the curve (of.979; sensitivity of 94.9%, and specificityof91.2% for CIN2+ prediction. It was observed that p16 expression was significantly associated with CDKN2A mRNA overexpression (p=.0015). A gene expression profile that may be helpful in the identification of patients with CIN2+ was identified. This approach could be used together with currently used LBC in a clinical setting, allowing the identification of patients with high risk of CIN2+.

Drug-induced loss of imprinting revealed using bioluminescent reporters of Cdkn1c

Genomic imprinting is an epigenetically mediated mechanism that regulates allelic expression of genes based upon parent-of-origin and provides a paradigm for studying epigenetic silencing and release. Here, bioluminescent reporters for the maternally-expressed imprinted gene Cdkn1c are used to examine the capacity of chromatin-modifying drugs to reverse paternal Cdkn1c silencing. Exposure of reporter mouse embryonic stem cells (mESCs) to 5-Azacytidine, HDAC inhibitors, BET inhibitors or GSK-J4 (KDM6A/B inhibitor) relieved repression of paternal Cdkn1c, either selectively or by inducing biallelic effects. Treatment of reporter fibroblasts with HDAC inhibitors or GSK-J4 resulted in similar paternal Cdkn1c activation, whereas BET inhibitor-induced loss of imprinting was specific to mESCs. Changes in allelic expression were generally not sustained in dividing cultures upon drug removal, indicating that the underlying epigenetic memory of silencing was maintained. In contrast, Cdkn1c de-repression by GSK-J4 was retained in both mESCs and fibroblasts following inhibitor removal, although this impact may be linked to cellular stress and DNA damage. Taken together, these data introduce bioluminescent reporter cells as tools for studying epigenetic silencing and disruption, and demonstrate that Cdkn1c imprinting requires distinct and cell-type specific chromatin features and modifying enzymes to enact and propagate a memory of silencing.

CDKN1C -Related Beckwith-Wiedemann Syndrome: First Patient from India.

Beckwith-Wiedemann syndrome (BWS; MIM# 130650) is a well-characterized pediatric overgrowth disorder. In approximately 5% of the cases, it is caused by pathogenic variants in the CDKN1C (cyclin-dependent kinase inhibitor 1C). CDKN1C gene encodes for a protein p57 (KIP2) that acts as an inhibitor of cyclin-dependent kinases (CDK) that are expressed in the G and S-phase of the cell cycle, thus regulating cellular proliferation. Variants in CDKN1C gene lead to loss of inhibitory function of CDK and thus impair the inhibition of growth, resulting in BWS phenotype. We describe here a 2.5-year-old boy with a maternally inherited variant c.182G > T, p.Trp61Cys in the CDKN1C gene causing BWS. The natural history of the disorder is described along with the gradual change in the facial features. An insight into the genotype-phenotype correlation and disorders to be considered in the differential diagnosis is provided. We describe a common overgrowth syndrome with its rare genetic mechanism and highlight the salient features that help in making a diagnosis and managing patients.