REZA YADOLLAHVANDMIANDOAB^1,#, MEHRSA JALALIZADEH^1,#, FRANCIELE APARECIDA VECHIA DIONATO¹, KEINI BUOSI¹, PATRÍCIA A. F. LEME¹, LUCIANA S. B. DAL COL¹, CRISTIANE F. GIACOMELLI¹, ALEX DIAS ASSIS¹, NASIM BASHIRICHELKASARI¹, LEONARDO OLIVEIRA REIS^1,2,*

Oncology Research, Vol.32, No.4, pp. 597-605, 2024, DOI:10.32604/or.2024.045442

Abstract Bladder cancer (BC) is the 10th most common cancer worldwide, with about 0.5 million reported new cases and about 0.2 million deaths per year. In this scoping review, we summarize the current evidence regarding the clinical implications of single-cell sequencing for bladder cancer based on PRISMA guidelines. We searched PubMed, CENTRAL, Embase, and supplemented with manual searches through the Scopus, and Web of Science for published studies until February 2023. We included original studies that used at least one single-cell technology to study bladder cancer. Forty-one publications were included in the review. Twenty-nine studies showed that this technology can identify… More > Graphic Abstract

YANG ZHANG^1,2,#, NANNAN QIN^5,#, XIJUN WANG^6,#, RUI LIANG⁷, QUAN LIU⁴, RUOYI GENG⁸, TIANXIAO JIANG⁸, YUNFEI LIU^8,*, JINWEI LI^3,4,*

Oncology Research, Vol.32, No.3, pp. 563-576, 2024, DOI:10.32604/or.2023.029697

Abstract Glycogen metabolism plays a key role in the development of hepatocellular carcinoma (HCC), but the function of glycogen metabolism genes in the tumor microenvironment (TME) is still to be elucidated. Single-cell RNA-seq data were obtained from ten HCC tumor samples totaling 64,545 cells, and 65 glycogen metabolism genes were analyzed by a nonnegative matrix factorization (NMF). The prognosis and immune response of new glycogen TME cell clusters were predicted by using HCC and immunotherapy cohorts from public databases. HCC single-cell analysis was divided into fibroblasts, NT T cells, macrophages, endothelial cells, and B cells, which were separately divided into new… More >

Aisa Zulibiya^1,2,#, Jing Wen^3,#, Huiqing Yu^3,#, Xiaoming Chen³, Lei Xu³, Xiao Ma^1,2, Baojian Zhang^1,2,*

Congenital Heart Disease, Vol.18, No.6, pp. 611-625, 2023, DOI:10.32604/chd.2023.047689

Abstract Background: Tetralogy of Fallot (TOF) is a very common cyanotic congenital heart disease. Endothelial-to-mesenchymal transition (EndoMT) is recognized as a physiological mechanism involved in embryonic heart development and endothelial formation. However, there is still a gap in the reports related to the mechanism of EndoMT development in TOF. Methods: First, transcriptomic data of single cell nuclei of TOF and Donor were obtained based on the Gene Expression Omnibus (GEO) database, and the data were normalized and clustered by dimensionality reduction using the Seurat package. Subsequently, differentially expressed genes (DEGs) between TOF and Donor were screened using the “FindMarkers” function, and… More >

XUEFENG WANG^1,#, SICONG JIANG^2,#, XINHONG ZHOU³, XIAOFENG WANG⁴, LAN LI⁵, JIANJUN TANG^1,*

Oncology Research, Vol.31, No.5, pp. 697-714, 2023, DOI:10.32604/or.2023.029458

Abstract Background: Pancreatic cancer is associated with high mortality and is one of the most aggressive of malignancies, but studies have not fully evaluated its molecular subtypes, prognosis and response to immunotherapy of different subtypes. The purpose of this study was to explore the molecular subtypes and the key genes associated with the prognosis of pancreas cancer patients and study the clinical phenotype, prognosis and response to immunotherapy using single-cell seq data and bulk RNA seq data, and data retrieved from GEO and TCGA databases. Methods: Single-cell seq data and bioinformatics methods were used in this study. Pancreatic cancer data were… More >

WUYAO LIU, CHANGBAO QU, XIAOLU WANG^*

Oncology Research, Vol.31, No.4, pp. 543-567, 2023, DOI:10.32604/or.2023.029563

Abstract The high immune infiltration and heterogeneity of the microenvironment in clear cell renal cell carcinoma (ccRCC) result in the variability of prognosis and clinical response. While PANoptosis has strong immunogenicity and is worthy of further study. In this study, data from The Cancer Genome Atlas database was used to obtain immune-related PANoptosis lncRNAs with prognostic value. Subsequently, the role of these lncRNAs in cancer immunity, progression and the therapeutic response was analyzed, and a new prediction model was constructed. Additionally, we further explored the biological value of PANoptosis-related lncRNAs using single-cell data from the Gene Expression Omnibus database. PANoptosis-associated lncRNAs… More >

XINRUI SHI¹, XIA GAO¹, WENCONG LIU², XUEJIAO TANG¹, JIAYI LIU¹, DONGCHEN PAN¹, XUEQING DUAN¹, YUQING JIN¹, WEIYAN REN¹, LEI YANG^1,*, WENXUAN LIU^1,*

Oncology Research, Vol.31, No.4, pp. 569-590, 2023, DOI:10.32604/or.2023.028964

Abstract Hepatocellular carcinoma (HCC) is the most common fatal cancer worldwide, patients with HCC have a high mortality rate and poor prognosis. PANoptosis is a novel discovery of programmed cell death associated with cancer development. However, the role of PANoptosis in HCC remains obscure. In this study, we enrolled 274 PANoptosisrelated genes (PANRGs) and screened 8 genes to set up a prognostic model. A previous scoring system calculated PANscore was utilized to quantify the individual risk level of each HCC patient, and the reliability of the prognostic model has been validated in an external cohort. Nomogram constructed with PANscore and clinical… More >

YIFAN XU^1,#, DONGMEI CHENG^1,#, LEI HU¹, XIN DONG², LIYING LV², CHEN ZHANG², JIAN ZHOU^1,3,4,*

BIOCELL, Vol.47, No.4, pp. 825-836, 2023, DOI:10.32604/biocell.2023.026122

Abstract The Wnt/β-catenin signaling pathway is the main target of tooth regeneration regulation. Treatment of cells with AZD2858 stimulates the Wnt/β-catenin signaling pathway, yet the function of this pathway in tooth regeneration remains unclear. Here, we found that AZD2858 promotes the accumulation of β-catenin in the nuclei of stem cells from the apical papilla (SCAPs) and enhances cell proliferation. Single-cell sequencing was performed on SCAPs treated with AZD2858. Eight clusters were identified, namely SCAPs-CNTNAP2, SCAPs-DTL, SCAPs-MYH11, SCAPs-MKI67, SCAPs-CXCL8, SCAPs-TPM2, SCAPs-IFIT2 and SCAPs-NEK10. The pseudo-time trajectory analysis showed that AZD2858 enhanced the evolution of SCAPs from SCAPs-TMP2 clusters to SCAPs-MYH11, SCAPs-CNTNAPs and… More >

Lina Tang^1,2, Haiyan Hu², Yan Zhou², Yujing Huang², Yonggang Wang², Yawen Zhang², Jinrong Liang², Zhenxin Wang^1,*

Oncologie, Vol.24, No.4, pp. 913-925, 2022, DOI:10.32604/oncologie.2022.026296

Abstract Objective: To investigate the expression of alpha–smooth muscle actin (ACTA2) in osteosarcoma tissues and its relationship with prognosis. Methods: Prognostic analysis of lung metastasis–related genes in osteosarcoma using the TCGA database. Single-cell sequencing detected the expression of ACTA2 in 11 osteosarcoma tissues. Paraf- fin-embedded tissues of 74 osteosarcoma patients treated at the Sixth People’s Hospital of Shanghai Jiao Tong University from 2014 to 2019 were collected, and tissue microarrays were prepared. ACTA2 expression was detected and scored by immunohistochemistry. According to the median value of the ACTA2 histochemical score, 74 patients were divided into two groups, the high-expression group and… More >

Preeti Agarwal^*, Priyaranjan Pal, Pradeep Kumar Mehta

Sound & Vibration, Vol.56, No.2, pp. 105-125, 2022, DOI:10.32604/sv.2022.014874

Abstract The free vibration analysis of simply supported box-girder bridges is carried out using the finite element method. The fundamental frequency is determined in straight, skew, curved and skew-curved box-girder bridges. It is important to analyse the combined effect of skewness and curvature because skew-curved box-girder bridge behaviour cannot be predicted by simply adding the individual effects of skewness and curvature. At first, an existing model is considered to validate the present approach. A convergence study is carried out to decide the mesh size in the finite element method. An exhaustive parametric study is conducted to determine the fundamental frequency of… More >

YUKI MATSUSHITA, WANIDA ONO, NORIAKI ONO^*

BIOCELL, Vol.46, No.5, pp. 1157-1162, 2022, DOI:10.32604/biocell.2022.018960

Abstract Single-cell sequencing technologies have rapidly progressed in recent years, and been applied to characterize stem cells in a number of organs. Somatic (postnatal) stem cells are generally identified using combinations of cell surface markers and transcription factors. However, it has been challenging to define micro-heterogeneity within “stem cell” populations, each of which stands at a different level of differentiation. As stem cells become defined at a single-cell level, their differentiation path becomes clearly defined. Here, this viewpoint discusses the potential synergy of single-cell sequencing analyses with in vivo lineage-tracing approaches, with an emphasis on practical considerations in stem cell biology. More >