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  • Open Access

    ARTICLE

    In silico Prediction and Analysis of Potential Off-Targets and Off-Target Mutation Detection in StERF3-Gene Edited Potato Plants

    Hafiza Arooj Razzaq1, Siddra Ijaz1,*, Imran Ul Haq2, Faisal Saeed Awan1

    Phyton-International Journal of Experimental Botany, Vol.92, No.8, pp. 2451-2460, 2023, DOI:10.32604/phyton.2023.030501

    Abstract The imperative aspect of the CRISPR/Cas9 system is a short stretch of 20 nucleotides of gRNA that control the overall specificity. Due to the small size, the chance of its multiple occurrences in the genome increases; however, a few mismatches are tolerated by the Cas9 endonuclease activity. An accurate and careful in silico-based off-target prediction while target selection is preferred to address the issue. These predictions are based on a comprehensive set of selectable parameters. Therefore, we investigated the possible off-target prediction and their screening in StERF3 gene-edited potato plants while developing StERF3-loss-of-function mutants using CRISPR/Cas9 approach. The 201 off-targets… More >

  • Open Access

    ARTICLE

    System analysis based on the T cell exhaustion‑related genes identifies CD38 as a novel therapy target for ovarian cancer

    TIANMING SHI1,2,#, RONGRONG YAN1,2,#, MI HAN1,2,*

    Oncology Research, Vol.31, No.4, pp. 591-604, 2023, DOI:10.32604/or.2023.029282

    Abstract Ovarian cancer (OV) is highly heterogeneous tumor with a very poor prognosis. Studies increasingly show that T cell exhaustion is prognostically relevant in OV. The aim of this study was to dissect the heterogeneity of T cell subclusters in OV through single cell transcriptomic analysis. The single RNA-sequencing (scRNA-seq) data of five OV patients were analyzed, and six major cell clusters were identified after threshold screening. Further clustering of T cell-associated clusters revealed four subtypes. Pathways related to oxidative phosphorylation, G2M checkpoint, JAK-STAT and MAPK signaling were significantly activated, while the p53 pathway was inhibited in the CD8+ exhausted T… More > Graphic Abstract

    System analysis based on the T cell exhaustion‑related genes identifies CD38 as a novel therapy target for ovarian cancer

  • Open Access

    ARTICLE

    Targeting LncRNA LLNLR-299G3.1 with antisense oligonucleotide inhibits malignancy of esophageal squamous cell carcinoma cells in vitro and in vivo

    LI TIAN1,#, YONGYI HUANG1,#, BAOZHEN ZHANG2,#, YI SONG1,#, LIN YANG3, QIANQIAN CHEN1, ZHENG WANG3, YILING WANG1, QIHAN HE1, WENHAN YANG1, SHUYONG YU4, TIANYU LU5, ZICHEN LIU1, KAIPING GAO1,*, XIUJUN FAN2,*, JIAN SONG4,*, RIHONG ZHAI1,*

    Oncology Research, Vol.31, No.4, pp. 463-479, 2023, DOI:10.32604/or.2023.028791

    Abstract Accumulating evidence has indicated that long non-coding RNAs (lncRNAs) play critical roles in the development and progression of cancers, including esophageal squamous cell carcinoma (ESCC). However, the mechanisms of lncRNAs in ESCC are still incompletely understood and therapeutic attempts for in vivo targeting cancer-associated lncRNA remain a challenge. By RNA-sequencing analysis, we identified that LLNLR-299G3.1 was a novel ESCC-associated lncRNA. LLNLR-299G3.1 was up-regulated in ESCC tissues and cells and promoted ESCC cell proliferation and invasion. Silencing of LLNLR-299G3.1 with ASO (antisense oligonucleotide) resulted in opposite effects. Mechanistically, LLNLR-299G3.1 bound to cancer-associated RNA binding proteins and regulated the expression of cancer-related… More >

  • Open Access

    REVIEW

    Targeting DNA repair for cancer treatment: Lessons from PARP inhibitor trials

    DHANYA K. NAMBIAR1, DEEPALI MISHRA2, RANA P. SINGH2,3,*

    Oncology Research, Vol.31, No.4, pp. 405-421, 2023, DOI:10.32604/or.2023.028310

    Abstract Ionizing radiation is frequently used to treat solid tumors, as it causes DNA damage and kill cancer cells. However, damaged DNA is repaired involving poly-(ADP-ribose) polymerase-1 (PARP-1) causing resistance to radiation therapy. Thus, PARP-1 represents an important target in multiple cancer types, including prostate cancer. PARP is a nuclear enzyme essential for single-strand DNA breaks repair. Inhibiting PARP-1 is lethal in a wide range of cancer cells that lack the homologous recombination repair (HR) pathway. This article provides a concise and simplified overview of the development of PARP inhibitors in the laboratory and their clinical applications. We focused on the… More > Graphic Abstract

    Targeting DNA repair for cancer treatment: Lessons from PARP inhibitor trials

  • Open Access

    REVIEW

    Targeting the “undruggable” cancer driver genes: Ras, myc, and tp53

    XINGBO WU, DAN PAN, SHOUYI TANG, YINGQIANG SHEN*

    BIOCELL, Vol.47, No.7, pp. 1459-1472, 2023, DOI:10.32604/biocell.2023.028790

    Abstract The term “undruggable” is to describe molecules that are not targetable or at least hard to target pharmacologically. Unfortunately, some targets with potent oncogenic activity fall into this category, and currently little is known about how to solve this problem, which largely hampered drug research on human cancers. Ras, as one of the most common oncogenes, was previously considered “undruggable”, but in recent years, a few small molecules like Sotorasib (AMG-510) have emerged and proved their targeted anti-cancer effects. Further, myc, as one of the most studied oncogenes, and tp53, being the most common tumor suppressor genes, are both considered… More >

  • Open Access

    ARTICLE

    A novel prognostic gene signature, nomogram and immune landscape based on tanshinone IIA drug targets for hepatocellular carcinoma: Comprehensive bioinformatics analysis and in vitro experiments

    BOWEN PENG1, YUN GE1, GANG YIN2,3,*

    BIOCELL, Vol.47, No.7, pp. 1519-1535, 2023, DOI:10.32604/biocell.2023.027026

    Abstract Background: Tanshinone IIA, one of the main ingredients of Danshen, is used to treat hepatocellular carcinoma (HCC). However, potential targets of the molecule in the therapy of HCC are unknown. Methods: In this study, we collected the tanshinone IIA targets from public databases for investigation. We screened differentially expressed genes (DEGs) across HCC and normal tissues using mRNA expression profiles from The Cancer Genome Atlas (TCGA). Univariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) Cox regression models were used to identify and construct the prognostic gene signature. Results: Finally, we discovered common genes across tanshinone IIA… More >

  • Open Access

    ARTICLE

    Zinc alpha 2 glycoprotein (ZAG): A potential novel pharmacological target in diabetic retinopathy

    UMAPATHY PRAKASH1, SUBRAMANIAM RAJESH BHARATHIDEVI1,*, RAMYA R. NADIG2, RAJIV RAMAN2, GIRISH SHIV RAO2, MUNA BHENDE2

    BIOCELL, Vol.47, No.7, pp. 1473-1482, 2023, DOI:10.32604/biocell.2023.027804

    Abstract Zinc alpha 2 glycoprotein (ZAG) is a 41 KDa secretory soluble glycoprotein found in different body fluids like the serum, saliva, sweat, breast milk, and urine. It is also found in tissues like the testis, epididymis, kidney, spleen, liver, lungs, heart, and brain. ZAG is an adipokine with multiple roles, including lipid mobilization, modulating glucose metabolisms, improving insulin sensitivity, inhibiting tumor proliferation through RNAse activity, and suppressing inflammation. Low levels of zinc and ZAG are linked to metabolic syndrome and are also reported as potential biomarkers for diabetic nephropathy. Interestingly zinc has been found to regulate the binding of ZAG… More >

  • Open Access

    ARTICLE

    Exploration of the oxidative-inflammatory potential targets of Coicis Semen in osteoarthritis: Data mining and systematic pharmacology

    QIAO ZHOU2,3,4, JIAN LIU1,2,*, LING XIN1, YANYAN FANG1,2, LEI WAN1,2, DAN HUANG1,2, JIANTING WEN1,2

    BIOCELL, Vol.47, No.7, pp. 1623-1643, 2023, DOI:10.32604/biocell.2023.028331

    Abstract Objective: On the basis of data mining, systematic pharmacology, molecular docking, and experiment validation, the oxidative-inflammatory molecular targets of Coicis Semen in the therapy of osteoarthritis (OA) were explored. Methods: The association rule analysis was effectively applied to highlight the correlation between Coicis Semen and oxidative inflammation indices. The random walk model was subsequently used to evaluate the clinical efficacy of Coicis Semen. Network pharmacology was used to predict network targets. The binding affinity of the active ingredient in Coicis Semen to the key target of OA was also successfully predicted. Results: Coicis Semen showed a significant reduction in oxidative-inflammatory… More >

  • Open Access

    ARTICLE

    Ship Detection and Recognition Based on Improved YOLOv7

    Wei Wu1, Xiulai Li2, Zhuhua Hu1, Xiaozhang Liu3,*

    CMC-Computers, Materials & Continua, Vol.76, No.1, pp. 489-498, 2023, DOI:10.32604/cmc.2023.039929

    Abstract In this paper, an advanced YOLOv7 model is proposed to tackle the challenges associated with ship detection and recognition tasks, such as the irregular shapes and varying sizes of ships. The improved model replaces the fixed anchor boxes utilized in conventional YOLOv7 models with a set of more suitable anchor boxes specifically designed based on the size distribution of ships in the dataset. This paper also introduces a novel multi-scale feature fusion module, which comprises Path Aggregation Network (PAN) modules, enabling the efficient capture of ship features across different scales. Furthermore, data preprocessing is enhanced through the application of data… More >

  • Open Access

    REVIEW

    Targeting triple-negative breast cancer: A clinical perspective

    LAZAR S. POPOVIC1,2,*, GORANA MATOVINA-BRKO1, MAJA POPOVIC1,2, KEVIN PUNIE3, ANA CVETANOVIC4,5, MATTEO LAMBERTINI6,7

    Oncology Research, Vol.31, No.3, pp. 221-238, 2023, DOI:10.32604/or.2023.028525

    Abstract Triple-negative breast cancer (TNBC) is a disease with often an aggressive course and a poor prognosis compared to other subtypes of breast cancer. TNBC accounts for approximately 10%–15% of all diagnosed breast cancer cases and represents a high unmet need in the field. Up to just a few years ago, chemotherapy was the only systemic treatment option for this subtype (1). To date, TNBC is considered a heterogeneous disease. One of the existing classifications is based on the analysis of mRNA expression in 587 TNBC cases, in which Lehman et al. proposed six subtypes of TNBC as follows: two basal-like… More > Graphic Abstract

    Targeting triple-negative breast cancer: A clinical perspective

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