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

2022 ◽  
Vol 12 ◽  
Author(s):  
Shuaibing Yang ◽  
Qianqian Zhao ◽  
Lihua Tang ◽  
Zejia Chen ◽  
Zhaoting Wu ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Cell Line ◽  
Genomic Sequence ◽  
Cancer Tissue ◽  
Whole Genome ◽  
Nanopore Sequencing ◽  
Caski Cell ◽  
Physical Status ◽  
Long Reads ◽  
Caski Cell Line

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.

scholarly journals Human Papillomavirus and the Development of Different Cancers

2016 ◽  
Vol 150 (3-4) ◽  
pp. 185-193 ◽  
Author(s):  
Ge Gao ◽  
David I. Smith
Keyword(s):  
Cervical Cancer ◽  
Squamous Cell Carcinomas ◽  
Human Papillomaviruses ◽  
Whole Genome ◽  
Physical Status ◽  
Cervical Cancers ◽  
Mate Pair ◽  
Almost All ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Human papillomaviruses (HPV) are responsible for the development of almost all cervical cancers. HPV is also found in 85% of anal cancer and in 50% of penile, vulvar, and vaginal cancers, and they are increasingly found in a subset of head and neck cancers, i.e., oropharyngeal squamous cell carcinomas (OPSCC). The model for how HPV causes cancer is derived from several decades of study on cervical cancer, and it is just presumed that this model is not only completely valid for cervical cancer but for all other HPV-driven cancers as well. Next-generation sequencing (NGS) has now provided the necessary tools to characterize genomic alterations in cancer cells and can precisely determine the physical status of HPV in those cells as well. We discuss recent discoveries from different applications of NGS in both cervical cancer and OPSCCs, including whole-genome sequencing and mate-pair NGS. We also discuss what NGS studies have revealed about the different ways that HPV can be involved in cancer formation, specifically comparing cervical cancer and OPSCC.

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

2020 ◽  
Vol 8 (1) ◽  
pp. 12 ◽  
Author(s):  
Sachin Bhoora ◽  
Yuvelia Pather ◽  
Sumari Marais ◽  
Rivak Punchoo
Keyword(s):  
Cell Cycle ◽  
Vitamin D ◽  
Cell Death ◽  
Cell Count ◽  
Cell Line ◽  
Cervical Cancer Cell Line ◽  
High Dose ◽  
Caski Cell ◽  
Anti Cancer ◽  
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.

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

2014 ◽  
Vol 18 (03) ◽  
pp. 182-187 ◽  
Author(s):  
Pankaj Kumar Chaturvedi ◽  
Yong-Wan Kim ◽  
Sang Soo Kim ◽  
Woong Shick Ahn
Keyword(s):  
Cell Line ◽  
Chlorophyll A ◽  
Palliative Treatment ◽  
Caski Cell ◽  
Blue Green Algae ◽  
Naturally Occurring ◽  
Caski Cell Line ◽  
Cervical Cancer Cells ◽  
Pyropheophorbide A

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.

Cisplatin sensitivity and mechanisms of anti-HPV16 E6-ribozyme on cervical carcinoma CaSKi cell line

2012 ◽  
Vol 11 (4) ◽  
pp. 237-242 ◽  
Author(s):  
Zhiguo Rao ◽  
Jianfei Gao ◽  
Bicheng Zhang ◽  
Bo Yang ◽  
Jiren Zhang
Keyword(s):  
Cell Line ◽  
Cervical Carcinoma ◽  
Caski Cell ◽  
Hpv16 E6 ◽  
Caski Cell Line ◽  
Cisplatin Sensitivity

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

2019 ◽  
Vol 3 (5) ◽  
Author(s):  
Dr. Reena Rani ◽  
Dr. Anupam Kumar Singh ◽  
Dr. Samreen Khan ◽  
Prof. Najmul Islam
Keyword(s):  
Cell Viability ◽  
Cell Line ◽  
Dose Dependence ◽  
Time Dependent ◽  
Dependent Manner ◽  
Cancer Cell Proliferation ◽  
Caski Cell ◽  
Papilloma Virus ◽  
Caski Cell Line ◽  
Apoptotic Effect

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

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

2021 ◽  
Author(s):  
Serena Judith DSouza ◽  
Arati Mane ◽  
Linata Patil ◽  
Aazam Shaikh ◽  
Madhuri Thakar ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Progression ◽  
Statistical Significance ◽  
Caski Cell ◽  
Notch 1 ◽  
Hpv 16 ◽  
Cancer Phenotype ◽  
Hiv 1

Abstract 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.

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