WEI ZHAI^1,2, XIANG ZHENG², MENGYUAN LIU², QIURONG ZHAO², YUSHU ZHANG², YUQING LUO³, SHANSHAN FENG³, JINJING WANG³, XUEYING LI^2,*, MINGSONG WU^1,*

BIOCELL, Vol.47, No.8, pp. 1821-1833, 2023, DOI:10.32604/biocell.2023.027175

Abstract Objective: Endoplasmic reticulum-Golgi intermediate compartment 3 (ERGIC3) promotes cell proliferation and metastasis in lung cancer, but its molecular mechanism is unclear. Methods: The GLC-82 cells were randomly divided into the ERGIC3i group and the negative control group. The cells were transfected with ERGIC3 siRNA or control siRNA in the groups, respectively. The ERGIC3-interacting proteins expressed in cells or extracellularly were isolated by the immunoprecipitation method and detected by isobaric tags for relative and absolute quantitation and liquid chromatography-tandem mass spectrometry. The differentially expressed proteins were determined by bioinformatic methods. Results: After ERGIC3 knockdown, 88 extracellular differentially expressed proteins, 41 up-regulated… More >

LIN QIU^1,#, ANQI TAO^1,#, XIAOQIAN SUN^4,5, FEI LIU¹, XIANPENG GE^2,3,*, CUIYING LI^1,*

Oncology Research, Vol.31, No.5, pp. 715-752, 2023, DOI:10.32604/or.2023.029443

Abstract We analyzed RNA-sequencing (RNA-seq) and clinical data from head and neck squamous cell carcinoma (HNSCC) patients in The Cancer Genome Atlas (TCGA) Genomic Data Commons (GDC) portal to investigate the prognostic value of anoikis-related genes (ARGs) in HNSCC and develop new targeted drugs. Differentially expressed ARGs were screened using bioinformatics methods; subsequently, a prognostic model including three ARGs (CDKN2A, BIRC5, and PLAU) was constructed. Our results showed that the model-based risk score was a good prognostic indicator, and the potential of the three ARGs in HNSCC prognosis was validated by the TISCH database, the model’s accuracy was validated in two… More >

DONGJIE SUN^1,2, CHI ZHANG^3,*

Oncology Research, Vol.31, No.5, pp. 753-767, 2023, DOI:10.32604/or.2023.029287

Abstract Lung adenocarcinoma (LUAD) is the leading cause of cancer-related deaths, accounting for over a million deaths worldwide annually. Immunogenic cell death (ICD) elicits an adaptive immune response. However, the role of ICD-related long noncoding RNAs (lncRNAs) in LUAD is unknown. In this study, we investigated the characteristics of the tumor microenvironment in LUAD, the prognostic significance of ICD-related lncRNAs, and the half-maximal inhibitory concentration (IC50) of possible chemotherapeutic drugs. We sorted prognostic lncRNAs using univariate Cox regression and constructed a risk signature based on them. We then confirmed the model’s accuracy and generated a nomogram. Additionally, we performed immune microenvironment… More > Graphic Abstract

BOWEN PENG¹, YUN GE¹, GANG YIN^2,3,*

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 >

Minghui Niu^1,#, Heng Zhang^1,#, Xiangyang Li¹, Zhibao Hu¹, Hongjiao Zhang^2,3, Zhiru Xu^2,3, Chunpu Qu^1,4,*, Guanjun Liu^1,*

Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 2001-2015, 2023, DOI:10.32604/phyton.2023.029350

Abstract KANADI (KAN) is a plant-specific gene that controlled the polarity development of lateral organs. It mainly acted on the abaxial characteristics of plants to make the lateral organs asymmetrical. However, it had been less identified in woody plants. In this study, the members of the KAN gene family in Populus trichocarpa were identified and analyzed using the bioinformatics method. The results showed that a total of 8 KAN family members were screened out, and each member contained the unique GARP domain and conserved region of the family proteins. Phylogenetic analysis and their gene structures revealed that all KAN genes from… More >

JIAHENG XIE^1,#, MENGMENG OU^1,#, PAN YU^1,#, DAN WU^2,#, QIKAI TANG³, YUAN CAO⁴, JING HANG⁵, LU YIN¹, TINGHONG XIANG¹, MING WANG^1,*, JINGPING SHI^1,*

Oncology Research, Vol.31, No.3, pp. 389-403, 2023, DOI:10.32604/or.2023.029274

Abstract Purpose: To screen potential tumor antigens for melanoma vaccine development and identify different immune subtypes. Methods: Transcriptional data (HTSEQ-FPKM) and clinical information of a 472 Melanoma cohort GDC TCGA Melanoma (SKCM) were downloaded from the UCSC XENA website (). Subsequently, transcriptome data and clinical information of 210 melanoma cohort GSE65904 were downloaded from Gene Expression Omnibus (GEO), a large global public database. All the transcriptome expression data matrices were log2 transformed for subsequent analysis. GEPIA, TIMER, and IMMPORT databases are also used for analysis. Cell function experiments were performed to validate the role of the IDO1 gene in melanoma cell… More >

WEI BAO^1,#, QIANGUANG HAN^2,#, XIAO GUAN³, ZIJIE WANG², MIN GU^1,2,*

Oncology Research, Vol.31, No.2, pp. 181-192, 2023, DOI:10.32604/or.2023.028051

Abstract Background: Clear-cell renal cell carcinoma (ccRCC) is the most common malignant kidney cancer. However, the tumor microenvironment and crosstalk involved in metabolic reprogramming in ccRCC are not well-understood. Methods: We used The Cancer Genome Atlas to obtain ccRCC transcriptome data and clinical information. The E-MTAB-1980 cohort was used for external validation. The GENECARDS database contains the first 100 solute carrier (SLC)-related genes. The predictive value of SLC-related genes for ccRCC prognosis and treatment was assessed using univariate Cox regression analysis. An SLC-related predictive signature was developed through Lasso regression analysis and used to determine the risk profiles of patients with… More >

XI YANG^1,5,#, HUIXIAN WU^2,3,#, CHAO XIONG^4,#, BO ZHAO¹, MEILIAN LIU¹, JIE QIN⁶, MEI DENG^1,2,3,*

BIOCELL, Vol.47, No.5, pp. 1021-1037, 2023, DOI:10.32604/biocell.2023.027103

Abstract Background: Cytochrome b561 (CYB561) plays a critical role in neuroendocrine function, cardiovascular regulation, and tumor growth; however, the prognostic value of CYB561 in patients with breast cancer and the relationship between CYB561 expression and immune infiltration in breast cancer remain unclear. Methods: The mRNA expression and clinical data of patients with breast cancer were obtained from The Cancer Genome Atlas database. Functional enrichment analysis was used to explore underlying biological functions associated with CYB561. The methylation status of CYB561 was analyzed using the MethSurv database. The enrichment score of immune cell infiltration for CYB561 in breast cancer was calculated using… More >

Fahriye Gemci^1,*, Turgay Ibrikci², Ulus Cevik³

Computer Systems Science and Engineering, Vol.46, No.3, pp. 3703-3713, 2023, DOI:10.32604/csse.2023.032706

Abstract The study aims to find a successful solution by using computer algorithms to detect remote homologous proteins, which is a significant problem in the bioinformatics field. In this experimental study, structural classification of proteins (SCOP) 1.53, SCOP benchmark, and the newly created SCOP protein database from the structural classification of proteins—extended (SCOPe) 2.07 were used to detect remote homolog proteins. N-gram method and then Term Frequency-Inverse Document Frequency (TF-IDF) weighting were performed to extract features of the protein sequences taken from these databases. Next, a smoothing process on the obtained features was performed to avoid misclassification. Finally, the proteins with… More >

Ahmad M. Al-Omari^1,*, Shefa M. Tawalbeh¹, Yazan H. Akkam², Mohammad Al-Tawalbeh³, Shima’a Younis¹, Abdullah A. Mustafa⁴, Jonathan Arnold⁵

CMC-Computers, Materials & Continua, Vol.75, No.2, pp. 4155-4173, 2023, DOI:10.32604/cmc.2023.036956

Abstract There are quintillions of data on deoxyribonucleic acid (DNA) and protein in publicly accessible data banks, and that number is expanding at an exponential rate. Many scientific fields, such as bioinformatics and drug discovery, rely on such data; nevertheless, gathering and extracting data from these resources is a tough undertaking. This data should go through several processes, including mining, data processing, analysis, and classification. This study proposes software that extracts data from big data repositories automatically and with the particular ability to repeat data extraction phases as many times as needed without human intervention. This software simulates the extraction of… More >