Cell Cycle-associated Genes Research Articles

Abstract PD2-06: Efficacy of abemaciclib based on genomic alterations detected in baseline circulating tumor DNA from the MONARCH 3 study of abemaciclib plus nonsteroidal aromatase inhibitor

Abstract Background: Combination treatments of CDK4 & 6 inhibitors (CDK4 & 6i) with endocrine therapy (ET) have improved outcomes in patients with HR-positive (HR+), HER2-negative (HER2-) advanced breast cancer (ABC). Aside from estrogen receptor positivity (ER+), predictive biomarkers of clinical benefit from CDK4 & 6i in combination with ET remain elusive. We assessed clinical outcomes by genomic alterations detected in baseline circulating tumor DNA (ctDNA) from patients treated with abemaciclib plus a nonsteroidal aromatase inhibitor (NSAI) versus placebo plus NSAI in the Phase 3 study MONARCH 3 (NCT02246621). Methods: MONARCH 3 randomized 493 postmenopausal women with HR+, HER2- ABC who had no prior systemic therapy in the advanced setting to treatment with abemaciclib plus NSAI or placebo plus NSAI. Biomarker analysis of baseline ctDNA was an exploratory objective; plasma was analyzed by the Guardant360 next-generation sequencing (NGS)-based assay to identify potential tumor-related (i.e., somatic) genomic alterations including point mutations (SNV), indels, amplifications, and fusions in over 70 cancer-related genes. Genomic alterations detected in baseline ctDNA were associated with clinical outcomes including progression-free survival (PFS) and objective response rate (ORR). Results: Baseline ctDNA results were available for 295 patients (201 abemaciclib; 94 placebo) with 83% of patients harboring one or more detectable genomic alterations. Commonly altered genes of interest (% frequency) detected in baseline ctDNA included: PIK3CA (38%); TP53 (26%); EGFR (15%); FGFR1 (12%); NF1 (12%); MYC (9%); CCND1 (9%); ESR1 (5%).Overall, patients treated with placebo plus NSAI who harbored detectable ctDNA genomic alterations had shorter median PFS compared to patients without detectable genomic alterations, as shown in the Table (14.9 months [95% CI: 11.0-23.1] vs 19.2 months [95% CI 9.4-NR]). Moreover, genomic alterations in EGFR, FGFR1, MYC, and CCND1 were associated with median PFS <12 months with placebo plus NSAI. However, consistent with the intent-to-treat population, the addition of abemaciclib to NSAI benefitted these genomic subgroups, regardless of ctDNA gene alterations. Additional genomic results, including alterations in cell cycle-associated genes, will be presented. Conclusions: In this exploratory subgroup analysis, the presence of detectable ctDNA genomic alterations was associated with shorter PFS with placebo plus NSAI. Consistently, abemaciclib added to NSAI improved outcomes for genomically identified subgroups. In contrast to prior studies, there was no subgroup (e.g., patients harboring FGFR1 alterations) that did not derive benefit from abemaciclib, supporting the efficacy of abemaciclib, including in difficult to treat tumors. These findings are hypothesis-generating and warrant further investigations in clinical studies of CDK4 & 6i in combination with ET. TableAbemaciclib + NSAIPlacebo + NSAIEvents, n/NMedian PFS (95% CI)Events, n/NMedian PFS (95% CI)Hazard Ratio (95% CI)OVERALLITT population170 / 32828.2 (23.7 - 33.9)123 / 16514.8 (11.2 - 19.2)0.52 (0.42 - 0.66)TR population93 / 20138.7 (31.1 - NR)71 / 9416.5 (11.7 - 23.1)0.45 (0.33 - 0.61)Any Gene AlterationDetected83 / 16634.1 (27.2 - 40.0)62 / 7914.9 (11.0 - 23.1)0.47 (0.34 - 0.66)Not detected10 / 35NR (36.4 - NR)9 / 1519.2 (9.40 - NR)0.31 (0.13 - 0.78)TP53Detected29 / 5327.0 (14.1 - NR)19 / 2315.4 (5.7 - 30.4)0.53 (0.30 - 0.95)Not detected64 / 14839.9 (34.1 - NR)52 / 7117.5 (11.7 - 24.2)0.42 (0.29 - 0.60)EGFRDetected10 / 26NR (32.4 - NR)16 / 1710.9 (2.1 - 24.7)0.20 (0.09 - 0.47)Not detected83 / 17536.4 (27.7 - NR)55 / 7717.6 (14.6 - 25.5)0.52 (0.37 - 0.73)FGFR1Detected15 / 2532.8 (10.1 - NR)10 / 117.6 (1.9 - 15.4)0.37 (0.16 - 0.85)Not detected78 / 17639.9 (31.1 - NR)61 / 8319.2 (14.6 - 26.5)0.45 (0.32 - 0.63)NF1Detected10 / 2435.9 (27 - NR)8 / 1014.6 (1.6 - 33.4)0.33 (0.13 - 0.84)Not detected83 / 17738.7 (30.8 - NR)63 / 8417.5 (11.7 - 24.2)0.47 (0.33 - 0.65)MYCDetected11 / 1720.1 (5.5 - NR)9 / 106.5 (1.2 - 15.7)0.33 (0.13 - 0.86)Not detected82 / 18438.9 (32.9 - NR)62 / 8419.2 (14.6 - 26.5)0.45 (0.32 - 0.63)CCND1Detected8 / 1632.8 (5.5 - NR)10 / 107.2 (3.6 - 9.0)0.28 (0.10 - 0.77)Not detected85 / 18538.7 (31.1 - NR)61 / 8417.6 (14.6 - 25.5)0.48 (0.34 - 0.67)n = number of patients with events; N = total number of patients in the corresponding population and treatment arm; NR = not reached. TR population consists of patients in the ITT population from whom a valid baseline ctDNA result has been obtained. Citation Format: Matthew P Goetz, J. Thaddeus Beck, Mario Campone, Sara Hurvitz, Seock-Ah Im, Stephen Johnston, Antonio Llombart-Cussac, Miguel Martin, Joohyuk Sohn, Masakazu Toi, Lacey M Litchfield, Hillary T Graham, Hong Wang, Sameera R Wijayawardana, Valerie M Jansen, Angelo Di Leo. Efficacy of abemaciclib based on genomic alterations detected in baseline circulating tumor DNA from the MONARCH 3 study of abemaciclib plus nonsteroidal aromatase inhibitor [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr PD2-06.

Gestation and lactation exposure to nicotine induces transient postnatal changes in lung alveolar development.

Harmful consequences of cigarette smoke (CS) exposure during lung development can already manifest in infancy. In particular, early life exposure to nicotine, the main component of CS, was shown to affect lung development in animal models. We aimed to characterize the effect of nicotine on alveoli formation. We analyzed the kinetics of normal alveolar development during the alveolarization phase and then looked at the effect of nicotine in a mouse model of gestational and early life exposure. Immunohistochemical staining revealed that the wave of cell proliferation [i.e., vascular endothelial cells, alveolar epithelial cells (AEC) type II and mesenchymal cell] occurs at postnatal day (pnd) 8 in control and nicotine-exposed lungs. However, FACS analysis of individual epithelial alveolar cells revealed nicotine-induced transient increase of AEC type I proliferation and decrease of vascular endothelial cell proliferation at pnd8. Furthermore, nicotine increased the percentage of endothelial cells at pnd2. Transcriptomic data also showed significant changes in nicotine samples compared with the controls on cell cycle-associated genes at pnd2 but not anymore at pnd16. Accordingly, the expression of survivin, involved in cell cycle regulation, also follows a different kinetics in nicotine lung extracts. These changes resulted in an increased lung size detected by stereology at pnd16 but no longer in adult age, suggesting that nicotine can act on the pace of lung maturation. Taken together, our results indicate that early life nicotine exposure could be harmful to alveolar development independently from other toxicants contained in CS.

SCARA5 is a Novel Biomarker in Colorectal Cancer by Comprehensive Analysis.

SCARA5 has been demonstrated to be a tumor suppressor gene, with its expression downregulated in many cancer types. However, only few studies have investigated its role in colorectal cancer (CRC). The current study evaluated SCARA5 expression levels in CRC and its potential value as a diagnostic biomarker for CRC. Data were downloaded from the TCGA, GEO, and Oncomine databases to evaluate SCARA5 mRNA expression levels in CRC. The prognosis value of SCARA5 was assessed using the online tool Cutoff Finder via the Kaplan-Meier plotter (n = 484). Immunohistochemistry was performed to analyze and compare the SCARA5 protein expression levels in CRC and normal tissues from 67 CRC clinical specimens. Relevant CRC CNV data were downloaded from TCGA and cBioPortal for Cancer Genomics databases to assess the associated genetic alterations. GSEA was used to explore the underlying molecular mechanisms of SCARA5. The correlation between SCARA5 mRNA levels and cell cycle-associated genes was explored using GEPIA database. SCARA5 mRNA levels were found to be downregulated in CRC tissues compared with normal tissues. Survival analysis showed that low SCARA5 expression was associated with poor prognosis. These results were validated in clinical specimens, wherein the SCARA5 protein levels were significantly downregulated in CRC tissues compared with paracarcinoma tissues. Deep deletion was the most common genetic alteration and was consistent with the downregulated SCARA5 expression in CRC tissues. GSEA indicated that the gene sets of CELL CYCLE, G2M CHECKPOINT, and E2F TARGETS were negatively related to SCARA5 mRNA expression. GEPIA indicated that the mRNA expression of some cell cycle-associated genes was negatively correlated with that of SCARA5 in CRC. Thus, SCARA5 may act as a human cancer suppressor gene in CRC, and its expression level may be a reliable adjuvant parameter to diagnose CRC and predict tumor metastasis and prognosis.

Zinc finger protein RP-8, the Bombyx mori ortholog of programmed cell death 2, regulates cell proliferation

Programmed cell death 2 (PDCD2) is a highly conserved eukaryotic protein indispensable for various physiological processes such as cell proliferation, development, and apoptosis. In the present study, we identified a Zinc finger protein RP-8 from the silkworm, Bombyx mori (BmZfrp8), the ortholog of PDCD2 protein. The quantitative real-time PCR analysis revealed the ubiquitous distribution of BmZfrp8 in the different tissues; however, the gene's transcription level was highest in those of the silk gland, testis, and ovary. Additionally, the expression levels of BmZfrp8 were unequal on different days of embryonic development, and it reached the highest level on the 5th day of early development. The challenge with pathogens influenced the expression level of BmZfrp8 in both hemocyte and fat body when compared with the control. Administration of 20-hydroxyecdysone significantly enhanced the BmZfrp8 expression in hemocyte. The knock-down of BmZfrp8 by double-stranded RNA suppressed the expression of developmental pathway associated genes as well as cell cycle-associated genes. Furthermore, the RNAi treated cells also showed cell cycle arrest compared to the control group. Taken together, BmZfrp8 may have a critical biological role in of B. mori, since it regulates the expression of the developmental pathway and cell cycle-associated genes.

LukS-PV induces cell cycle arrest and apoptosis through p38/ERK MAPK signaling pathway in NSCLC cells

Non-small-cell lung cancer (NSCLC) accounts for nearly 85% of lung cancer cases. LukS-PV, one of the two components of Panton-Valentine leucocidin (PVL), is produced by Staphylococcus aureus. The present study showed that LukS-PV can induce apoptosis in human acute myeloid leukemia (AML) lines (THP-1 and HL-60). However, the role of LukS-PV in NSCLC is unclear. In this study, we treated NSCLC cell lines A549 and H460 and a normal lung cell line, 16HBE, with LukS-PV and investigated the biological roles of LukS-PV in NSCLC. Cells were treated with varying concentrations of LukS-PV and cell viability was evaluated by CCK8 and EdU assay. Flow cytometry was used to detect cell apoptosis and analyze the cell cycle, and the expression of apoptosis and cell cycle-associated proteins and genes were identified by western blotting analysis and qRT-polymerase chain reaction, respectively. We found that LukS-PV inhibited the proliferation of NSCLC cells but had little cytotoxicity in normal lung cells. LukS-PV induced NSCLC cell apoptosis and increased the BAX/BCL-2 ratio, triggering S-phase arrest in A549 and H460 cells while increasing P21 expression and decreasing CDK2, cyclin D1, and cyclin A2 expression. We also observed increased P-p38 and P-ERK in NSCLC cells treated with LukS-PV. Treatment of NSCLC with LukS-PV combined with p38 and ERK inhibitors reversed the pro-apoptotic and pro-cell cycle arrest effects of LukS-PV. Overall, these findings indicate that LukS-PV has anti-tumor effects in NSCLC and may contribute to the development of anti-cancer agents.

TNF-α Differentially Regulates Cell Cycle Genes in Promyelocytic and Granulocytic HL-60/S4 Cells.

Tumor necrosis factor alpha (TNF-α) is a potent cytokine involved in systemic inflammation and immune modulation. Signaling responses that involve TNF-α are context dependent and capable of stimulating pathways promoting both cell death and survival. TNF-α treatment has been investigated as part of a combined therapy for acute myeloid leukemia due to its modifying effects on all-trans retinoic acid (ATRA) mediated differentiation into granulocytes. To investigate the interaction between cellular differentiation and TNF-α, we performed RNA-sequencing on two forms of the human HL-60/S4 promyelocytic leukemia cell line treated with TNF-α. The ATRA-differentiated granulocytic form of HL-60/S4 cells had an enhanced transcriptional response to TNF-α treatment compared to the undifferentiated promyelocytes. The observed TNF-α responses included differential expression of cell cycle gene sets, which were generally upregulated in TNF-α treated promyelocytes, and downregulated in TNF-α treated granulocytes. This is consistent with TNF-α induced cell cycle repression in granulocytes and cell cycle progression in promyelocytes. Moreover, we found evidence that TNF-α treatment of granulocytes shifts the transcriptome toward that of a macrophage. We conclude that TNF-α treatment promotes a divergent transcriptional program in promyelocytes and granulocytes. TNF-α promotes cell cycle associated gene expression in promyelocytes. In contrast, TNF-α stimulated granulocytes have reduced cell cycle gene expression, and a macrophage-like transcriptional program.

Ivermectin induces apoptosis of porcine trophectoderm and uterine luminal epithelial cells through loss of mitochondrial membrane potential, mitochondrial calcium ion overload, and reactive oxygen species generation

Ivermectin is a pesticide that has been used for over 30 years in livestock. Although there are a number of studies on the therapeutic potential of ivermectin, little is known about the effects of the drug during the early stage of pregnancy. In this study, we investigated the detrimental effects of ivermectin on porcine trophectoderm (pTr) and uterine luminal epithelial (pLE) cells. Ivermectin not only inhibited the proliferation of both cells via the regulation of cell cycle-associated genes, but also induced apoptosis in pTr and pLE cells. We also verified its effect on mitochondrial dysfunction as shown by loss of mitochondrial membrane potential, mitochondrial Ca2+ overload, and reactive oxygen species (ROS) generation in pTr and pLE cells. As a mechanistic approach, we evaluated ivermectin-mediated cell signaling interactions including PI3K, AKT and MAPK pathways. Overall, our results suggest that constant exposure to and accumulation of ivermectin may cause abnormal fetal morphogenesis and placentation during the early stages of pregnancy. Our results may further provide a comprehensive understanding of the detrimental effects of ivermectin during pregnancy and will contribute to the establishment of a complete safety profile for ivermectin and its association with environmental pollution and public health in humans and livestock.

Knockdown of long non-coding RNA PVT1 inhibits the proliferation of Raji cells through cell cycle regulation.

Long non-coding RNA plasmacytoma variant translocation 1 (PVT1) has been reported to be associated with oncogenesis. However, the functional role of PVT1 in Burkitt lymphoma has not yet been addressed. The purpose of the present study was to investigate the effect of PVT1 knockdown by small interfering RNA (siRNA) on the proliferation of Burkitt lymphoma Raji cells and to explore its possible mechanism of action. An effective siRNA targeting PVT1 was screened and the corresponding short hairpin RNA (shRNA) was reconstructed into a lentiviral vector. Cell proliferation and cell cycle distribution were assessed by Cell Counting kit-8 assay and flow cytometry, respectively. Protein expression levels of c-Myc, cyclin-dependent kinase inhibitor1A (CDKN1A, P21) and cyclin E1 (CCNE1) were detected by western blotting. A polymerase chain reaction (PCR) array was used to analyse the expression of genes associated with the cell cycle. PVT1 knockdown markedly suppressed proliferation, and induced cell cycle arrest at the G0/G1 phase in Raji cells. Protein expression levels of c-Myc and CCNE1 were reduced, whereas P21 protein expression was markedly increased following downregulation of PVT1 in Raji cells. The cell cycle PCR array revealed that 54 genes were upregulated and 26 genes were downregulated in Raji cells following PVT1 knockdown. Reverse transcription-quantitative PCR demonstrated that cyclin G2 (CCNG2), CDKN1A, Retinoblastoma-like 2 (RBL2, p130), HUS1 checkpoint homolog, cyclin dependent kinase inhibitor 3 (CDKN3) and cyclin dependent kinase inhibitor 1B (CDKN1B) expression were upregulated, whereas the expression levels of CCNE1, cyclin D1 (CCND1) and cell division cycle 20 (CDC20) were downregulated in Raji cells with PVT1 knockdown. In conclusion, PVT1 knockdown may inhibit the proliferation of Raji cells by arresting cells in G0/G1 phase. Furthermore, inhibition of cell proliferation may be associated with a reduction inc-Myc expression and alterations in the expression levels of cell cycle-associated genes.

PCGF6 regulates stem cell pluripotency as a transcription activator via super-enhancer dependent chromatin interactions

ABSTRACTPolycomb group (PcG) ring finger protein 6 (PCGF6), though known as a member of the transcription-repressing complexes, PcG, also has activation function in regulating pluripotency gene expression. However, the mechanism underlying the activation function of PCGF6 is poorly understood. Here, we found that PCGF6 co-localizes to gene activation regions along with pluripotency factors such as OCT4. In addition, PCGF6 was recruited to a subset of the super-enhancer (SE) regions upstream of cell cycle-associated genes by OCT4, and increased their expression. By combining with promoter capture Hi-C data, we found that PCGF6 activates cell cycle genes by regulating SE-promoter interactions via 3D chromatin. Our findings highlight a novel mechanism of PcG protein in regulating pluripotency, and provide a research basis for the therapeutic application of pluripotent stem cells.

PHD finger protein 5A promoted lung adenocarcinoma progression via alternative splicing.

Alternative splicing (AS) and the regulation of AS by splicing factors play critical roles in cancer. Plant homeodomain (PHD)–finger domain protein PHF5A, a critical splicing factor involved in AS, has been demonstrated to play an oncogenic role in glioblastoma multiforme and breast cancer, but its biological function in lung cancer remains unclear. In the present study, we systematically analyzed the biological function and clinical relevance of PHF5A in non–small cell lung cancer (NSCLC). We found that PHF5A was significantly upregulated in NSCLC tumors compared with normal tissues in both TCGA data set and tissue microarrays. Upregulation of PHF5A was negatively correlated to the overall survival (OS) of lung adenocarcinoma (LUAD) patients. Loss‐of‐function and gain‐of‐function experiments confirmed that PHF5A functioned as an oncoprotein by promoting LUAD cell proliferation, migration and invasion, inducing G0/G1 cell cycle progression and inhibiting cisplatin–induced apoptosis. RNA–seq analysis identified many essential genes whose AS was dysregulated by PHF5A, including cell cycle–associated genes such as SKP2, CHEK2, ATR and apoptosis–associated genes such as API5 and BCL2L13. Additionally, pladienolide, a small molecular inhibitor of PHF5A, inhibited LUAD cell proliferation in a dose–dependent manner and induced AS changes similar to PHF5A knockdown. In conclusion, we validated that PHF5A played an oncogenic role via AS in LUAD and suggested that PHF5A might serve as a potential drug target with a promising anticancer therapeutic effect.

Genomic aberrations in cell cycle genes predict progression of KIT-mutant gastrointestinal stromal tumors (GISTs)

BackgroundActivating mutations of the receptor tyrosine kinase KIT are early events in the development of most gastrointestinal stromal tumors (GISTs). Although GISTs generally remain dependent on oncogenic KIT during tumor progression, KIT mutations alone are insufficient to induce malignant behavior. This is evidenced by KIT-mutant micro-GISTs, which are present in up to one-third of normal individuals, but virtually never progress to malignancy.MethodsWe performed whole exome sequencing on 29 tumors obtained from 21 patients with high grade or metastatic KIT-mutant GIST (discovery set). We further validated the frequency and potential prognostic significance of aberrations in CDKN2A/B, RB1, and TP53 in an independent series of 71 patients with primary GIST (validation set).ResultsUsing whole exome sequencing we found significant enrichment of genomic aberrations in cell cycle-associated genes (Fisher’s Exact p = 0.001), most commonly affecting CDKN2A/B, RB1, and TP53 in our discovery set. We found a low mutational tumor burden in these 29 advanced GIST samples, a finding with significant implications for the development of immunotherapy for GIST. In addition, we found mutation of spliceosome genes in a minority of cases, implicating dysregulation of splicing as a potential cancer promoting mechanism in GIST. We next assessed the prognostic significance of CDKN2A, RB1 or TP53 mutation/copy loss in an independent cohort of 71 patients with primary GIST. Genetic events (mutation, deletion, and/or LOH) involving at least one of the three genes examined were found in 17% of the very low-risk, 36% of the low-risk, 42% of the intermediate risk, 67% of the high-risk/low mitotic-count, and in 86% of the high-risk/high mitotic-count group. The presence of cell cycle-related events was associated with a significantly shorter relapse-free survival (median 67 months versus not reached; p < 0.0001) and overall survival (Log Rank, p = 0.042).ConclusionOur results demonstrate that genomic events targeting cell cycle-related genes are associated with GIST progression to malignant disease. Based on this data, we propose a model for molecular pathogenesis of malignant GIST.

Abstract P3-10-08: Markers of response to CDK4 &amp; 6 inhibition from neoMONARCH: A phase II neoadjuvant study of abemaciclib in postmenopausal women with hormone receptor positive, HER2 negative breast cancer

Abstract Background: Combination treatments of endocrine therapy (ET) with CDK4 &amp; 6 inhibitors have improved outcomes in patients with HR+ advanced breast cancer, both as initial therapy and after progression on ET. Abemaciclib is a selective inhibitor of CDK4 &amp; 6 approved on a continuous dosing schedule for the treatment of HR+, HER2- MBC patients (pts), alone or in combination with ET. However, biomarkers that predict benefit from this class of agents remain elusive. We previously reported in the phase II neoadjuvant neoMONARCH study (NCT02441946), after 2 weeks of treatment, abemaciclib, alone or in combination with anastrozole (ANZ), led to a significantly higher rate of complete cell cycle arrest (CCCA, defined as Ki67 ≤2.7%) compared to ANZ alone in early stage HR+, HER2- breast cancer (Martin et al. SABCS 2017). As an exploratory aim of this trial, we evaluated the gene expression analyses in order to determine markers of sensitivity and resistance to therapy. Methods: Serial biopsies were collected at 3 time points: Baseline (BL) - prior to treatment, Early – after 2 weeks of therapy with abemaciclib, ANZ, or abemaciclib+ANZ, and Late – after 2 weeks of initial therapy followed by 14 weeks of abemaciclib+ANZ. RNA was extracted from FFPE tumor biopsies at each timepoint and subjected to a Cell Cycle Associated Gene (CCAG) expression panel using the Modaplex® platform and whole transcriptome RNA sequencing. Ki67 was measured at each time point by immunohistochemistry (IHC). Tumors were categorized by the post-treatment Ki67 expression as either sensitive (Ki67 ≤2.7) or resistant (Ki67 ≥7.4), based upon the IMPACT and POETIC studies. Additionally, tumors intrinsically resistant/sensitive to therapy were also identified. Results: ANZ-treated tumors that did not achieve CCCA at 2 weeks (N= 8) displayed higher expression of the cell cycle associated genes FOXM1, E2F1, TOPO2A, and RRM2. The addition of abemaciclib to ANZ decreased gene expression in a majority of the tumors (N=5, 62.5%). Tumors intrinsically resistant to treatment with abemaciclib+ANZ displayed persistently elevated levels of cell cycle associated genes compared to sensitive tumors. Finally, gene expression signature of Rb loss-of-function (Rbsig) and RB1 gene expression levels were associated with sensitivity to abemaciclib. Conclusion: On-treatment Ki67 indicated treatment sensitivity and correlated with cell cycle associated gene expression in sensitive and resistant tumors. These exploratory analyses suggest that gene expression analyses may identify genomic markers for abemaciclib and ET treatment sensitivity and may help inform in which tumors to use abemaciclib. Citation Format: Hurvitz S, Martin M, Wijayawardana S, Brahmachary M, Ebert PJ, Young S, Jansen V, Slamon D. Markers of response to CDK4 &amp; 6 inhibition from neoMONARCH: A phase II neoadjuvant study of abemaciclib in postmenopausal women with hormone receptor positive, HER2 negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-10-08.

Dark-colored maple syrup treatment induces S-phase cell cycle arrest via reduced proliferating cell nuclear antigen expression in colorectal cancer cells.

Maple syrup is a natural sweetener that is consumed worldwide. It has been previously reported that dark-colored maple syrup exerts an inhibitory effect on colorectal cancer (CRC) proliferation and invasion. In the present study, the underlying mechanism of CRC cell growth inhibition was examined with dark-colored maple syrup treatment using a shotgun liquid chromatography-tandem mass spectrometry-based global proteomic approach. Applying a semi-quantitative method based on spectral counting, 388 proteins were identified with expression changes of >1.5-fold following dark-colored maple syrup treatment. Gene Ontology analysis revealed that these proteins possessed cell cycle-associated functions. It was also indicated that CRC cells treated with dark-colored maple syrup exhibited decreased proliferating cell nuclear antigen (PCNA) expression and S-phase cell cycle arrest. Dark-colored maple syrup treatment also resulted in altered expression of cell cycle-associated genes, including cyclin-dependent kinase (CDK)4 and CDK6. In conclusion, these data suggested that dark-colored maple syrup induced S-phase cell cycle arrest in CRC cells by reducing the expression of PCNA and regulating cell cycle-associated genes. These findings suggest that dark-colored maple syrup may be a source of compounds for the development of novel drugs for colorectal cancer treatment.

Assembly of a parts list of the human mitotic cell cycle machinery.

The set of proteins required for mitotic division remains poorly characterized. Here, an extensive series of correlation analyses of human and mouse transcriptomics data were performed to identify genes strongly and reproducibly associated with cells undergoing S/G2-M phases of the cell cycle. In so doing, 701 cell cycle-associated genes were defined and while it was shown that many are only expressed during these phases, the expression of others is also driven by alternative promoters. Of this list, 496 genes have known cell cycle functions, whereas 205 were assigned as putative cell cycle genes, 53 of which are functionally uncharacterized. Among these, 27 were screened for subcellular localization revealing many to be nuclear localized and at least three to be novel centrosomal proteins. Furthermore, 10 others inhibited cell proliferation upon siRNA knockdown. This study presents the first comprehensive list of human cell cycle proteins, identifying many new candidate proteins.

MiR-483 inhibits bovine myoblast cell proliferation and differentiation via IGF1/PI3K/AKT signal pathway.

MicroRNAs (miRNAs) have been established to regulate skeletal muscle development in mammals. However, few studies have been conducted on the regulation of proliferation and differentiation of bovine myoblast cells by miRNAs. The aim of our study was to explore the function of miR-483 in cell proliferation and differentiation of bovine myoblast. Here, we found that miR-483 declined in both proliferation and differentiation stages of bovine myoblast cells. During the proliferation phase, the overexpression of miR-483 downregulated the cell cycle-associated genes cyclin-dependent kinase 2 (CDK2), proliferating cell nuclear antigen (PCNA) messenger RNA (mRNA), and the protein levels. At the cellular level, cell cycle, cell counting kit-8, and 5-ethynyl-2´-deoxyuridine results indicated that the overexpression of miR-483 block cell proliferation. During differentiation, the overexpression of miR-483 led to a decrease in the levels of the myogenic marker genes MyoD1 and MyoG mRNA and protein. Furthermore, the immunofluorescence analysis results showed that the number of MyHC-positive myotubes was reduced. In contrast, the opposite experimental results were obtained concerning both proliferation and differentiation after the inhibition of miR-483. Mechanistically, we demonstrated that miR-483 targetinsulin-like growth factor 1 (IGF1) and downregulated the expression of key proteins in the PI3K/AKT signaling pathway. Altogether, our findings indicate that miR-483 acts as a negative regulator of bovine myoblast cell proliferation and differentiation.

Integrated genomic analyses in PDX model reveal a cyclin-dependent kinase inhibitor Palbociclib as a novel candidate drug for nasopharyngeal carcinoma

BackgroundPatient-derived xenograft (PDX) tumor model has become a new approach in identifying druggable tumor mutations, screening and evaluating personalized cancer drugs based on the mutated targets.MethodsWe established five nasopharyngeal carcinoma (NPC) PDXs in mouse model. Subsequently, whole-exome sequencing (WES) and genomic mutation analyses were performed to search for genetic alterations for new drug targets. Potential drugs were applied in two NPC PDX mice model to assess their anti-cancer activities. RNA sequencing and transcriptomic analysis were performed in one NPC PDX mice to correlate with the efficacy of the anti-cancer drugs.ResultsA relative high incident rate of copy number variations (CNVs) of cell cycle-associated genes. Among the five NPC-PDXs, three had cyclin D1 (CCND1) amplification while four had cyclin-dependent kinase inhibitor CDKN2A deletion. Furthermore, CCND1 overexpression was observed in > 90% FFPE clinical metastatic NPC tumors (87/91) and was associated with poor outcomes. CNV analysis disclosed that plasma CCND1/CDKN2A ratio is correlated with EBV DNA load in NPC patients’ plasma and could serve as a screening test to select potential CDK4/6 inhibitor treatment candidates. Based on our NPC PDX model and RNA sequencing, Palbociclib, a cyclin-dependent kinase inhibitor, proved to have anti-tumor effects by inducing G1 arrest. One NPC patient with liver metastatic was treated with Palbociclib, had stable disease response and a drop in Epstein Barr virus (EBV) EBV titer.ConclusionsOur integrated information of sequencing-based genomic studies and tumor transcriptomes with drug treatment in NPC-PDX models provided guidelines for personalized precision treatments and revealed a cyclin-dependent kinase inhibitor Palbociclib as a novel candidate drug for NPC.

KT2 and RT2 modified antimicrobial peptides derived from Crocodylus siamensis Leucrocin I show activity against human colon cancer HCT-116 cells

Conventional colon cancer treatments have been associated with side effects. Consequently, the discovery of novel effective and safe therapies is urgently needed. Hence, cationic antimicrobial peptides KT2 and RT2 were evaluated towards human colon cancer HCT-116 cells. The MTT assay indicated that both KT2 and RT2 exhibited anticancer activity with good therapeutic indices, and were found to be non-toxic to non-cancerous Vero cells. The IC50 values of KT2 were determined as 111.96 and 90.25 μg/mL while RT2 showed IC50 as 104.07 and 87.84 μg/mL after 12 and 24 h treatments, respectively. Moreover, KT2 and RT2 treatment caused a significant reduction in PI3K, AKT1 and mTOR mRNA expression levels, which resulted in suppression either of HCT-116 proliferation or migration. The mechanism involved in apoptosis induction were due to decreased Bcl-2 and XIAP and increased p53, cytochrome c, caspase-2, caspase-3, caspase-8, and caspase-9 mRNA expression levels. These effects increased the level of cell cycle associated gene p21 and decreased cyclin B1 and cyclin D1 expression.

MAPK/AP-1 pathway regulates benzidine-induced cell proliferation through the control of cell cycle in human normal bladder epithelial cells.

Bladder cancer is the most common malignancy of the urinary tract. Long-term exposure to benzidine is one of the major causes of bladder cancer. However, the mechanism of benzidine-induced bladder cancer is not yet sufficiently characterized. Dysregulated cell proliferation serves a critical role in cancer initiation and development; whether benzidine promotes cell proliferation, and the role of MAPKs in this process, have not previously been investigated. The present study aimed to investigate the benzidine-induced modulation of intracellular mitogen-activated protein kinases (MAPKs) and activator protein-1 (AP-1) signaling cascades on cell proliferation in SV-40 immortalized human uroepithelial cells (SV-HUC-1). It was identified that benzidine exposure enhanced the proliferation of SV-HUC-1 cells, promoted the transition of cells from G1 to S phase and altered the expression level of cell cycle-associated genes at the mRNA and protein levels. Furthermore, exposure of the SV-HUC-1 cells to benzidine was associated with the activation of MAPKs, including extracellular regulated protein kinases 1 and 2, p38 and Jun N-terminal kinase. The downstream target of MAPKs, AP-1 monomers, was also activated. Benzidine-induced proliferation was reversed by MAPK-specific inhibitors. Thus, the present study demonstrated that benzidine enhances the proliferation of bladder cells via activating the MAPK/AP-1 pathway, which may provide novel insights into the molecular mechanisms of benzidine-initiated bladder tumorigenesis, as well as cancer prevention.

PO-345 The role of the deubiquitinase USP11 in endocrine-driven breast cancer

IntroductionApproximately 80% of breast cancers overexpress the oestrogen receptor α (ERα) and depend on this key transcriptional regulator for growth. The discovery of novel mechanisms controlling ERα function represent major advances in our understanding of breast cancer progression and potentially offer new therapeutic opportunities. Here, we investigated the role of deubiquitinating enzymes (DUBs), which remove ubiquitin moieties from proteins, in regulating ERα activity in breast cancer.Material and methodsTo identify DUBs involved in ERα transcriptional activity, we performed an RNAi loss-of-function screen using a library of shRNA vectors targeting all 108 known or putative human DUB genes. We found that suppression of the BRCA-associated DUB, USP11, downregulated ERα transcriptional activity in ZR-75–1 cells. Dual luciferase reporter assays and qRT-PCR were used to determine ERα activity in stable ZR-75–1 USP11 knockdown cell lines. PTMScan technology, which allows for enrichment of ubiquitinated proteins and quantitative profiling by mass spectrometry, was used to reveal the ubiquitinome in these cells and results are pending. RNA sequencing (RNA-seq) technology was carried out in estrogen-independent LCC1 USP11 knockdown cells, were USP11 was hypothesised to play a vital role. Finally, immunohistochemistry (IHC) was used to investigate the prognostic relevance of USP11 in breast cancer patients.Results and discussionsKnockdown of USP11 in ZR-75–1 cells decreased ERα transcriptional activity and mRNA expression of ERα target genes. These results were further validated in a HEK293T USP11 CRISPR knockout model with ectopic ERα expression. Interestingly, USP11 expression was upregulated in LCC1 cells, an isogenic, estrogen-independent model derived from MCF-7 cells. Knockdown of USP11 in LCC1 cells decreased the expression of multiple ERα target genes and cell cycle-associated genes, as determined by RNA-seq. IHC staining of a breast cancer tissue microarray (103 ER +patients) and subsequent Kaplan-Meier analysis of this cohort revealed a significant association between high USP11 expression and poor overall (p=0.030) and breast cancer-specific survival (p=0.041). In silico analysis of publically available breast cancer gene expression datasets further supported an association between high USP11 expression and poor prognosis.ConclusionThese results suggest a role for USP11 in ERα transcriptional activity and reveal a novel mechanism as to how this receptor is regulated in breast cancer.

Abstract 343: Targeting DNA replication as a therapeutic strategy for acute myeloid leukemia with DNMT3A mutations

Abstract Acute Myeloid Leukemia (AML) is an aggressive malignancy of the blood system, wherein somatic mutations in epigenetic modifier and chromatin remodeling genes are common. Recurrent somatic mutations in the DNA methyltransferase 3 alpha (DNMT3A) gene are detected in about 30% of AML cases, and predict poor outcomes in patients treated with anthracycline-based induction chemotherapy, due to suboptimal response to therapy and subsequent early disease relapse. DNA methylation profiling in both primary AML samples and in animal models carrying a DNMT3A mutation detected modest DNA hypomethylation that did not fully explain how mutant DNMT3A contributed to AML pathogenesis. Recent studies have uncovered disordered nucleosome remodeling in response to DNA topological stress in DNMT3A-mutant cells, which was most pronounced during DNA replication. These changes were accompanied by negative enrichment of the cell cycle-associated gene expression signatures and attenuated CHK1 signaling, implicated in DNA damage response and replication fork integrity. Therefore, we hypothesized that targeting the S-phase in leukemic cells with DNMT3A mutations by pharmacologic agents that stall replication may offer enhanced therapeutic benefit. Indeed, our studies show increased sensitivity to replication stalling pharmacological treatments such as nucleoside analogues cytarabine and fludarabine in different cellular systems harboring DNMT3A mutations. This was accompanied by increased apoptosis as measured by PARP cleavage and annexin V binding.Analysis of the DNA damage signaling revealed elevated CHK1 phosphorylation signaling and accumulation of the DNA damage marker gammaH2A.X. A similar drug sensitivity trend was observed in murine Dnmt3a-mutant bone marrow cells treated with cytarabine, using clonogenic survival in MethoCult as readout. In order to examine this, we are developing isogenic cellular systems with differing DNMT3A mutational status via the CRISPR-Cas9 gene-editing approach. Further, these isogenic cell lines will be used as a tool to characterize the effect of mutant DNMT3A on replication progression, arrest, and resolution under pharmacologically induced replication stress. This will include analysis of the chromatin remodeling at the replication forks, proficiency of DNA damage repair, and dynamic localization of wild-type and mutant DNMT3A within the cells throughout the cell cycle. Finally, we will test the efficacy of replication stress inducing therapies in vivo in a genetically accurate mouse model of Dnmt3a-mutant AML. These studies will shed light on the mechanism of a potential vulnerability in DNMT3A-mutant leukemia cells and may lead to a more effective treatment strategy for this common subtype of AML. Citation Format: Kartika Venugopal, Daphné Dupéré-Richer, Jonathan Licht, Olga Guryanova. Targeting DNA replication as a therapeutic strategy for acute myeloid leukemia with DNMT3A mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 343.