Whole Genome Assembly of Human Papillomavirus by Nanopore Long-Read Sequencing

Human papillomavirus (HPV) is a causal agent for most cervical cancers. The physical status of the HPV genome in these cancers could be episomal, integrated, or both. HPV integration could serve as a biomarker for clinical diagnosis, treatment, and prognosis. Although whole-genome sequencing by next-generation sequencing (NGS) technologies, such as the Illumina sequencing platform, have been used for detecting integrated HPV genome in cervical cancer, it faces challenges of analyzing long repeats and translocated sequences. In contrast, Oxford nanopore sequencing technology can generate ultra-long reads, which could be a very useful tool for determining HPV genome sequence and its physical status in cervical cancer. As a proof of concept, in this study, we completed whole genome sequencing from a cervical cancer tissue and a CaSki cell line with Oxford Nanopore Technologies. From the cervical cancer tissue, a 7,894 bp-long HPV35 genomic sequence was assembled from 678 reads at 97-fold coverage of HPV genome, sharing 99.96% identity with the HPV sequence obtained by Sanger sequencing. A 7904 bp-long HPV16 genomic sequence was assembled from data generated from the CaSki cell line at 3857-fold coverage, sharing 99.99% identity with the reference genome (NCBI: U89348). Intriguingly, long reads generated by nanopore sequencing directly revealed chimeric cellular–viral sequences and concatemeric genomic sequences, leading to the discovery of 448 unique integration breakpoints in the CaSki cell line and 60 breakpoints in the cervical cancer sample. Taken together, nanopore sequencing is a unique tool to identify HPV sequences and would shed light on the physical status of HPV genome in its associated cancers.

HIV-1 Suppresses Notch-1 Expression in HPV-16+ CaSki Cells for Cancer Progression

Background High Risk Human Papilloma Viruses (HR-HPV) recurrently infect women having Human Immunodeficiency Virus − 1 (HIV-1)infection. Transforming HPV E6 and E7 genes promote invasive cancers and interact with Notch-1receptor. Concomitantly, HIV-1 Tat binds to EGF motifs within the Notch-1extracellular domain. HR-HPV infection activates Notch-1 signalling. Permissive HIV-1entry into the cervix is allowed. Notch-1 inhibitors may offer solace to the aggressive cancer phenotype in HIV-1 positive women. Still, the molecular cross talk between different oncogenes within the Notch-1pathway during HIV-1/HPV-16 + co-infections has not been elucidated. Methods Adherent cervical tumor derived cell lines-CaSki cell line (with inherent HPV16+ sequence and endogenous Notch-1 activity) and C33A cell line (cervical cancer phenotype, HPV -ve for HPV DNA and RNA) were used. Plasmids (pLEGFPN1 encoding HIV-1 Tat and pNL 4 − 3 encoding HIV-1(full HIV-1 genome), were transfected at 600 ng/mL into the above mentioned cell lines, in order to examine independent effects of HIV-1 Tat and HIV-1 transfection in HPV-16+ cervical cancer cells. We performed western blotting, cell cycle analysis and RT-qPCR post transfection. Three sets of independent experiments were analyzed by Graph Pad Prism 5. Statistical significance was calculated using Student t -test. Data expressed as mean ± standard deviation (SD). p values ≤ 0.05* were considered statistically significant. Results HIV-1 Tat and HIV-1 inhibited Notch-1expression, with differential effects on EGFR when comparing C33A and CaSki cell lines. CDK2 induction in Tat transfected CaSki cells, showed concomitant G0/G1 phase accumulation favouring cancer progression. Notch-1 inhibition shut off significant Cyclin D expression with a significant p21 induction and increased G2-M cell population in CaSki cells. On the contrary, HIV-1 infection utilized Hes-1-EGFR-CyclinD-p21axis, G2-M arrest, DDR response and cancer progression. Conclusion Our study highlights for the first time that HIV-1 Tat and/or HIV-1 driven cancers in HPV-16+ CaSki cells, show Notch-1 suppression and CDK2 dependent activity. HIV-1 Tat activates Hes-1 amplifying the EGFR gene which improves the aggressive state possibly through irreversible oxidative-stress induced senescence. HIV-1, favours cancer progression through its CXCR4 receptor, responsible for unbridled mitosis, G2-M arrest and damaged DNA response (DDR). Treatment of CaSki cells with a Notch-1 inhibitor, DAPT showed marginal recovery in p21expression with Go/G1 and S phase recovery.

Antioxidant, Antibacterial and Cytotoxic Activity of the Dillenia suffrutico sa Leaves against the Lung (A549) and Cervical (CaSki) Cancer Cell Lines

Background: Dillenia suffruticosa (Griff.) Mart. has been traditionally used to promote wound healing, relieve rheumatism, fever and some cancerous growths. The leaves of the local variety of D. suffruticosa lack scientific studies on its biological applications in the context of antibacterial, antioxidant and cytotoxic activities. Objective: To evaluate the antioxidant, antibacterial and cytotoxic properties of the leaves of D. suffruticosa from Brunei Darussalam. Methods: The leaves were extracted using 80% (v/v) methanol, 80% (v/v) ethanol and aqueous. The antioxidant capacities were determined using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, 2,2’-azino-bis(3-ethylbenzothia zoline-6-sulfonic acid) (ABTS) radical scavenging and ferric ion reducing antioxidant power (FRAP) assays. The FolinCiocalteu and aluminium chloride colorimetric assays were also used to evaluate the total phenolic and flavonoid contents. The antibacterial and cytotoxic activities of the extracts were determined using the Kirby-Bauer disc diffusion and MTT (3- (4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) cell proliferation assays. Results: The methanolic extract of the D. suffruticosa leaves displayed the highest antioxidant activity despite having comparable phenol content when extracted using the ethanol extraction solvent. The methanolic extract also demonstrated antibacterial activity on Staphylococcus aureus at a concentration of 50 mg/mL or above. The cytotoxicity of the methanolic extract was higher against the CaSki cell line than the A549 lung cancer cell line in the first 24 h but became more cytotoxic against A549 than CaSki at 48 h and 72 h. Conclusion: Our findings suggest that the methanolic extract of the leaves of D. suffruticosa from Brunei Darussalam has significant antioxidant and antibacterial activity against S. aureus and moderate cytotoxicity against A549 and CaSki cell lines.

MicroRNA-128 Confers Anti-Endothelial Adhesion and Anti-Migration Properties to Counteract Highly Metastatic Cervical Cancer Cells’ Migration in a Parallel-Plate Flow Chamber

Despite the distant metastasis of cervical cancer cells being a prominent cause of mortality, neither the metastasis capacity nor the in vitro conditions mimicking adhesion of cervical cancer cells to endothelial cells have been fully elucidated. Circulating metastatic cancer cells undergo transendothelial migration and invade normal organs in distant metastasis; however, the putative molecular mechanism remains largely uncertain. In this study, we describe the use of an in vitro parallel-plate flow chamber to simulate the dynamic circulation stress on cervical cancer cells and elucidate their vascular adhesion and metastasis. We isolate the viable and shear stress-resistant (SSR) cervical cancer cells for mechanistic studies. Remarkably, the identified SSR-HeLa and SSR-CaSki exhibited high in vitro adhesive and metastatic activities. Hence, a consistently suppressed miR-128 level was revealed in SSR cell clones compared to those of parental wild-type (WT) cells. Overexpressed miR-128 attenuated SSR-HeLa cells’ adherence to human umbilical cord vein endothelial cells (HUVECs); in contrast, suppressed miR-128 efficiently augmented the static adhesion capacity in WT-HeLa and WT-CaSki cells. Hence, amplified miR-128 modestly abolished in vitro SSR-augmented HeLa and CaSki cell movement, whereas reduced miR-128 aggravated the migration speed in a time-lapse recording assay in WT groups. Consistently, the force expression of miR-128 alleviated the SSR-enhanced HeLa and CaSki cell mobility in a wound healing assay. Notably, miR-128 mediated SSR-enhanced HeLa and CaSki cells’ adhesion and metastasis through suppressed ITGA5, ITGB5, sLex, CEACAM-6, MMP9, and MMP23 transcript levels. Our data provide evidence suggesting that miR-128 is a promising microRNA that prevented endothelial cells’ adhesion and transendothelial migration to contribute to the SSR-enhanced adhesion and metastasis progression under a parallel-plate flow chamber system. This indicates that the nucleoid-based miR-128 strategy may be an attractive therapeutic strategy to eliminate tumor cells resistant to circulation shear flow, prevent vascular adhesion, and preclude subsequent transendothelial metastasis.

miR-4454 up-regulated by HPV16 E6/E7 promotes invasion and migration by targeting ABHD2/NUDT21 in cervical cancer

The abnormal expression of HPV16 E6/E7 activates oncogenes and/or inactivates tumor suppressor genes, resulting in the selective growth and malignant transformation of cancer cells. miR-4454 was selected by sequencing due to its abnormal high expression in HPV16 E6/E7 positive CaSki cell compared with HPV16 E6/E7 negative C33A cell. Overexpression of miR-4454 enhances cervical cancer cell invasion and migration. ABHD2 and NUDT21 are identified as a target gene of miR-4454.The effects of ABHD2 and NUDT21 on migration and invasion of CaSki and C33A cells were determined. The dual luciferase and RT-qPCR assays confirmed that miR-4454 might regulate its targets ABHD2 and NUDT21 to promote the proliferation, invasion and migration, whereas, inhibit the apoptosis in CaSki and C33A cells.

Cholecalciferol Inhibits Cell Growth and Induces Apoptosis in the CaSki Cell Line

Vitamin D has displayed anti-cancer actions in numerous in vitro studies. Here, we investigated the anti-cancer actions of cholecalciferol, a vitamin D precursor, on a metastatic cervical cancer cell line, namely, CaSki. Experimental cultures were incubated for 72 h and treated with cholecalciferol (10–1000 ng/mL). In the present study, cell count, viability, proliferation and cell cycle were analyzed by a crystal violet assay, trypan blue assay, Ki67 proliferation, and a cell cycle assay, respectively. Biomarkers of apoptosis, necrosis, and autophagic cell death were measured by the Caspase 3/7 and Annexin V/7-AAD Muse™ assays, a LC3-II assay, and a lactate dehydrogenase release assay, respectively. The ultrastructural features of cell death were assessed by transmission electron microscopy. A statistical analysis was performed using a one-way ANOVA and Bonferroni’s post-hoc analysis test, and p < 0.05 is considered statistically significant here. The results identify statistical decreases in cell count and viability at high-dose treatments (100 and 1000 ng/mL). In addition, significant increases in apoptotic biochemical markers and apoptotic ultrastructure are shown to be present at high-dose treatments. In conclusion, high-dose cholecalciferol treatments inhibit cell count and viability, which are both mediated by apoptotic induction in the CaSki cell line.

THE APOPTOTIC EFFECT OF RESVERATROL ON HUMAN PAPILLOMA VIRUS POSITIVE CASKI CELL-LINE: A TIME AND DOSE DEPENDENCE STUDY.

Background & objectives: Resveratrol (trans-3,4,5’ –trihydroxystilbene) is an active compound in food, such as redgrapes, peanuts, and berries. A body of evidence shows that resveratrol is able to inhibit thegrowth of many cancers such as leukemia, breast cancer and primary brain tumors. The objective of the present study was to demonstrate the dose and time dependent apoptotic effect of Resveratrol on Human Caski cell line. Methods: We used cell viability assays like MTT and Trypan blue assays to demonstrate the inhibition of cancer cell proliferation in a dose and time dependent manner. Results: Our results have shown that Resveratrol inhibited proliferation of Caski cells in a concentration and time dependent manner in 48 hr cultures. No significant effect was observed in 24 hour cultures of cell viability assays. Interpretation & conclusions: The results indicated that Resveratrol and NAC inhibited cell growth in Caski cells as a function of dose and time. Keywords: Resveratrol , Cervical cancer, apoptosis

miR-4454 up-regulated by HPV16 E6/E7 promotes invasion and migration by targeting ABHD2/NUDT21 in cervical cancer

The abnormal expression of HPV16 E6/E7 activates oncogenes and/or inactivates tumor suppressor genes, resulting in the selective growth and malignant transformation of cancer cells. miR-4454 was selected by sequencing due to its abnormal high expression in HPV16 E6/E7 positive CaSki cell compared with HPV16 E6/E7 negative C33A cell. Overexpression of miR-4454 enhances cervical cancer cell invasion and migration. ABHD2 and NUDT21 is identified as a target gene of miR-4454.The effects of ABHD2 and NUDT21 on migration and invasion of CaSki and C33A cells were determined. The dual luciferase and RT-qPCR assays confirmed that miR-4454 might regulate its targets ABHD2 and NUDT21 to promote the proliferation, invasion and migration, whereas, inhibit the apoptosis in CaSki and C33A cells.

Phototoxic effects of pyropheophorbide-a from chlorophyll-a on cervical cancer cells

Photodynamic therapy (PDT) is a promising modality in both the curative and palliative treatment against a variety of experimental and naturally occurring human cancers. At present, chlorophyll a derivatives are extensively used for the synthesis of photosensitizers (PSs) for PDT of tumors. In the present study, chlorophyll-a was extracted from the blue-green algae Spirulina platensis by refluxing with acetone. The extract was further acid treated to obtain methylpheophorbide-a (MPa), which was then refluxed in collidine and methylpyropheophorbide-a (Mppa) was obtained. After that, Mppa was converted to pyropheophorbide-a (Ppa) by treatment with 50% sulfuric acid. Finally, phototoxicity and dark toxicity of purified Ppa in two different cell lines, TC-1 and CaSki, were examined by MTT assay. The results suggest that Ppa is more toxic to TC-1 cell line than CaSki cell line. In vivo, the photosensitizing efficiency of Ppa was also higher than those of unloaded PS. These results indicate the potential of Ppa in PDT.

Alkaloids from Penicillium oxalicum, a Fungus Residing in Acrida cinerea

Five alkaloids, (Z)-N-(4-hydroxystyryl) formamide (1), (E)-N-(4-hydroxystyryl) formamide (2), 2-(4-hydroxybenzyl) quinazolin-4(3H)-one (3), penipanoid A (4), asperazine (5), were isolated from cultures of Penicillium oxalicum, a fungus residing in Acrida cinerea. Their chemical structures were determined on the basis of spectroscopic data and chemical evidence. Compounds 1-5 were evaluated for their cytotoxic activity against the HepG2 and CaSki cell lines.