High-throughput single-сell sequencing in cancer research

Abstract

With advances in sequencing and instrument technology, bioinformatics analysis is being applied to batches of massive cells at single-cell resolution. High-throughput single-cell sequencing can be utilized for multi-omics characterization of tumor cells, stromal cells or infiltrated immune cells to evaluate tumor progression, responses to environmental perturbations, heterogeneous composition of the tumor microenvironment, and complex intercellular interactions between these factors. Particularly, single-cell sequencing of T cell receptors, alone or in combination with single-cell RNA sequencing, is useful in the fields of tumor immunology and immunotherapy. Clinical insights obtained from single-cell analysis are critically important for exploring the biomarkers of disease progression or antitumor treatment, as well as for guiding precise clinical decision-making for patients with malignant tumors. In this review, we summarize the clinical applications of single-cell sequencing in the fields of tumor cell evolution, tumor immunology, and tumor immunotherapy. Additionally, we analyze the tumor cell response to antitumor treatment, heterogeneity of the tumor microenvironment, and response or resistance to immune checkpoint immunotherapy. The limitations of single-cell analysis in cancer research are also discussed.

Construction of a Novel Clinical Stage-Related Gene Signature for Predicting Outcome and Immune Response in Hepatocellular Carcinoma

“…It is becoming increasingly common to use high-throughput sequencing as a critical tool in the biological sciences, such as for cancer early detection and stage prediction and prognosis prediction [ 16 , 17 ]. In this study, we utilized the Edger R tool and the TCGA database to find genes that were differentially expressed according to the stage of HCC.…”

3D single cell migration driven by temporal correlation between oscillating force dipoles

“…In this context, the determination of genetic and proteins networks has been instrumental in identifying the central pathways at play for motility ( Jia et al, 2022 ). These steps in outlining specific partners are important in localizing defects and they open potential perspectives for testing new strategies to act on these situations where cell migration is impaired in vivo and in vitro.…”

Tumor Microenvironment Cellular Crosstalk Predicts Response to Adoptive TIL Therapy in Melanoma

“…Advances in single-cell (sc) technologies enable in-depth characterization of tumor and immune cells in the tumor microenvironment (TME) (9). Although the molecular profiles of CD4 + or CD8 + tumor-specific TILs at the steady state have been recently reported by singlecell (sc) RNAseq (10)(11)(12)(13)(14), those of other leukocytes regulating T-cell function or performance during ACT remain unclear.…”

“…of Andreatta et al(21) as specific markers. We used the prediction from the annotation coming from public studies, namely Yost et al(18), Guo et al(19), Zhang et al(20) and Oliveira et al(9).A cluster displaying elevated levels of CCR7, LTB, SELL and IL7R gene expression, high TCF7 and LEF1 regulon activity, high concordance with Oliveira et al(9) predictions of naive cells was then named CD8 naive-like. Two clusters were displaying signs of stress or apoptosis: one with elevated levels of mitochondrial-related genes (gene names starting by MT-), expression of the MALAT1 gene and lower number of genes expressed per cell was then named CD8 low-quality and another one with overexpression of heat-shock protein (HSP) genes and DNAJ-related genes which we named CD8 HSP.…”