Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions

Genetic diseases are driven by aberrations of the human genome. Identification of such aberrations including structural variations (SVs) is key to our understanding. Conventional short-reads whole genome sequencing (cWGS) can identify SVs to base-pair resolution, but utilizes only short-range information and suffers from high false discovery rate (FDR). Linked-reads sequencing (10XWGS) utilizes long-range information by linkage of short-reads originating from the same large DNA molecule. This can mitigate alignment-based artefacts especially in repetitive regions and should enable better prediction of SVs. However, an unbiased evaluation of this technology is not available. In this study, we performed a comprehensive analysis of different types and sizes of SVs predicted by both the technologies and validated with an independent PCR based approach. The SVs commonly identified by both the technologies were highly specific, while validation rate dropped for uncommon events. A particularly high FDR was observed for SVs only found by 10XWGS. To improve FDR and sensitivity, statistical models for both the technologies were trained. Using our approach, we characterized SVs from the MCF7 cell line and a primary breast cancer tumor with high precision. This approach improves SV prediction and can therefore help in understanding the underlying genetics in various diseases.

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Direct Read and Quantify Damage Nucleotide from an Oligonucleotide Using a Single Molecule Interface

10.26434/chemrxiv.10080638.v2 ◽

2019 ◽

Author(s):

Jiajun Wang ◽

Meng-Yin Li ◽

Jie Yang ◽

Ya-Qian Wang ◽

Xue-Yuan Wu ◽

...

Keyword(s):

Dna Sequencing ◽

Single Molecule ◽

Genetic Diseases ◽

High Sensitivity ◽

Dna Lesions ◽

Lesion Detection ◽

The Novel ◽

Structural Variations ◽

Dna Lesion ◽

Base Lesion

DNA lesion such as metholcytosine(mC), 8-OXO-guanine(OG), inosine(I) etc could cause the genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remain challenge due to the massive varieties and less distinguishable readouts for minor structural variations. Moreover, standard amplification and labelling hardly works in DNA lesions detection. Herein, we designed a single molecule interface from the mutant K238Q Aerolysin, whose confined sensing region shows the high compatible to capture and then directly convert each base lesion into distinguishable current readouts. Compared with previous single molecule sensing interface, the resolution of the K238Q Aerolysin nanopore is enhanced by 2-order. The novel K238Q could direct discriminate at least 3 types (mC, OG, I) lesions without lableing and quantify modification sites under mixed hetero-composition condition of oligonucleotide. Such nanopore could be further applied to diagnose genetic diseases at high sensitivity.

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Methoxy and bromo scans on N-(5-methoxyphenyl) methoxybenzenesulphonamides reveal potent cytotoxic compounds, especially against the human breast adenocarcinoma MCF7 cell line

Journal of Enzyme Inhibition and Medicinal Chemistry ◽

10.1080/14756366.2021.1925265 ◽

2021 ◽

Vol 36 (1) ◽

pp. 1029-1047

Author(s):

Myriam González ◽

María Ovejero-Sánchez ◽

Alba Vicente-Blázquez ◽

Manuel Medarde ◽

Rogelio González-Sarmiento ◽

...

Keyword(s):

Cell Line ◽

Mcf7 Cell ◽

Breast Adenocarcinoma ◽

Human Breast ◽

Human Breast Adenocarcinoma ◽

Cytotoxic Compounds ◽

Mcf7 Cell Line

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Bioassay Development for Bispecific Antibodies—Challenges and Opportunities

International Journal of Molecular Sciences ◽

10.3390/ijms22105350 ◽

2021 ◽

Vol 22 (10) ◽

pp. 5350

Author(s):

Ames C. Register ◽

Somayeh S. Tarighat ◽

Ho Young Lee

Keyword(s):

Mechanism Of Action ◽

Bispecific Antibodies ◽

Structural Variations ◽

Antibody Therapeutics ◽

Regulatory Guidelines ◽

Different Types ◽

Challenges And Opportunities ◽

Target Binding ◽

Monospecific Antibodies ◽

Complicated Mechanism

Antibody therapeutics are expanding with promising clinical outcomes, and diverse formats of antibodies are further developed and available for patients of the most challenging disease areas. Bispecific antibodies (BsAbs) have several significant advantages over monospecific antibodies by engaging two antigen targets. Due to the complicated mechanism of action, diverse structural variations, and dual-target binding, developing bioassays and other types of assays to characterize BsAbs is challenging. Developing bioassays for BsAbs requires a good understanding of the mechanism of action of the molecule, principles and applications of different bioanalytical methods, and phase-appropriate considerations per regulatory guidelines. Here, we review recent advances and case studies to provide strategies and insights for bioassay development for different types of bispecific molecules.

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Eryngium billardieri Extract and Fractions Induces Apoptosis in Cancerous Cells

Anti-Cancer Agents in Medicinal Chemistry ◽

10.2174/1871520621666211201151736 ◽

2021 ◽

Vol 21 ◽

Author(s):

Samira Hasanbeiglu ◽

Kamran Hosseini ◽

Ommoleila Molavi ◽

Parina Asgharian ◽

Vahideh Tarhriz

Keyword(s):

Cell Lines ◽

Mcf7 Cell ◽

Inhibitory Effect ◽

P Value ◽

Breast Cancers ◽

Natural Habitats ◽

Cytotoxic Effects ◽

Soxhlet Apparatus ◽

Mcf7 Cell Line ◽

Cancerous Cells

Background: Eryngium is genus flowering plants in the Umbelliferae family having pharmacological properties such as anti-inflammatory and anti-diabetic. Given the nature of melanoma and breast cancers in recent years and the fact that the anti-cancer properties of Eryngium billardieri on mentioned cell lines have not been studied, the present study conducted to explore these properties. Objective: The mechanisms of cytotoxicity and apoptosis of aerial parts of various extracts and fractions of E. billardieri on cancerous cells and normal cells were investigated. Methods: Samples were collected from natural habitats, dried and then extracted by Soxhlet apparatus with solvents of n-Hex, DCM and methanol, respectively. The cytotoxic effects of the extracts were investigated by MTT method on MCF7, B16 and HFF-2 classes for 24 and 48 hours. Flowcytometry, was also used to investigate the mechanism of cytotoxicity and confirming by Real-time PCR of p53 and Bax genes, which codes apoptosis regulator proteins. Meanwhile, volatile compounds of extracts were identified by GC-MS method. Results: The obtained data showed that the n-Hex extract of E. billardieri on B-16 and MCF7 cell lines and dichromethane extract on MCF7 cell line had the most significant cytotoxic effect compared to DMSO control (p value <0.001). Our finding showed that the mechanism of n-Hex extract with 80% and 100% vlc fractions on B16 induced apoptotic compared to HFF-2 control cells, moreover, n-Hex extract and 80% vlc fraction on MCF7 was apoptotic. The major compounds of n-Hex, DCM and 80% and 100% fractions of n-Hex extract obtained from GC-MS are non-terpenoid. Conclusion: Non-terpenoids compounds of E. billardieri can be the responsible for showing the most cytotoxic effects on MCF7 and B16 cell lines with apoptotic mechanism and n-Hex extract had the most significant inhibitory effect on cancerous cells compared to the HFF-2 control cells by the mechanism of apoptosis.

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Novel 1,8-Naphthyridine Derivatives: Design, Synthesis and in vitro screening of their cytotoxic activity against MCF7 cell line

Open Chemistry ◽

10.1515/chem-2019-0097 ◽

2019 ◽

Vol 17 (1) ◽

pp. 943-954

Author(s):

Abeer N. Al-romaizan ◽

Thoraya S. Jaber ◽

Nesreen S. Ahmed

Keyword(s):

Cell Line ◽

Human Breast Cancer ◽

Mcf7 Cell ◽

Cancer Cell Line ◽

Human Breast Cancer Cell ◽

The Other ◽

Human Breast ◽

Design Synthesis ◽

Mcf7 Cell Line

AbstractA series of new 2-phenyl-7-methyl-1,8-naphthyridine derivatives with variable substituents at C3 were synthesized for an in vitro evaluation of their anticancer activity against human breast cancer cell line (MCF7). On one hand, compounds 3f, 6f, 8c, and 10b showed IC50 values (6.53, 7.88, 7.89, 7.79 μM, respectively) compared to that of the mentioned drug staurosparine (IC50 = 4.51 μM). On the other hand, derivatives 10c, 8d, 4d, 10f and 8b displayed better activity than staurosporin with IC50 values (1.47, 1.62, 1.68, 2.30, 3.19 μM, respectively).

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The Role of Sumoylation in the Response to Hypoxia: An Overview

Cells ◽

10.3390/cells9112359 ◽

2020 ◽

Vol 9 (11) ◽

pp. 2359 ◽

Cited By ~ 1

Author(s):

Chrysa Filippopoulou ◽

George Simos ◽

Georgia Chachami

Keyword(s):

Cellular Response ◽

Therapeutic Interventions ◽

Covalent Attachment ◽

Glucose And Lipid Metabolism ◽

Different Types ◽

Cancer Tumor ◽

Molecular Therapeutic ◽

And Oxidative Stress ◽

The Way

Sumoylation is the covalent attachment of the small ubiquitin-related modifier (SUMO) to a vast variety of proteins in order to modulate their function. Sumoylation has emerged as an important modification with a regulatory role in the cellular response to different types of stress including osmotic, hypoxic and oxidative stress. Hypoxia can occur under physiological or pathological conditions, such as ischemia and cancer, as a result of an oxygen imbalance caused by low supply and/or increased consumption. The hypoxia inducible factors (HIFs), and the proteins that regulate their fate, are critical molecular mediators of the response to hypoxia and modulate procedures such as glucose and lipid metabolism, angiogenesis, erythropoiesis and, in the case of cancer, tumor progression and metastasis. Here, we provide an overview of the sumoylation-dependent mechanisms that are activated under hypoxia and the way they influence key players of the hypoxic response pathway. As hypoxia is a hallmark of many diseases, understanding the interrelated connections between the SUMO and the hypoxic signaling pathways can open the way for future molecular therapeutic interventions.

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