Single-cell sequencing technology in tumor research

2021 ◽  
Author(s):  
Xue Bai ◽  
Yuxuan Li ◽  
Xuemei Zeng ◽  
Qiang Zhao ◽  
Zhiwei Zhang
Keyword(s):  
Single Cell ◽  
Sequencing Technology ◽  
Single Cell Sequencing ◽  
Tumor Research

scholarly journals Using single-cell sequencing technology to detect circulating tumor cells in solid tumors

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Jiasheng Xu ◽  
Kaili Liao ◽  
Xi Yang ◽  
Chengfeng Wu ◽  
Wei Wu ◽  
...  
Keyword(s):  
Single Cell ◽  
Solid Tumors ◽  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Peripheral Blood ◽  
High Throughput Sequencing ◽  
Metastatic Potential ◽  
Sequencing Analysis ◽  
Sequencing Technology ◽  
Single Cell Sequencing

AbstractCirculating tumor cells are tumor cells with high vitality and high metastatic potential that invade and shed into the peripheral blood from primary solid tumors or metastatic foci. Due to the heterogeneity of tumors, it is difficult for high-throughput sequencing analysis of tumor tissues to find the genomic characteristics of low-abundance tumor stem cells. Single-cell sequencing of circulating tumor cells avoids interference from tumor heterogeneity by comparing the differences between single-cell genomes, transcriptomes, and epigenetic groups among circulating tumor cells, primary and metastatic tumors, and metastatic lymph nodes in patients' peripheral blood, providing a new perspective for understanding the biological process of tumors. This article describes the identification, biological characteristics, and single-cell genome-wide variation in circulating tumor cells and summarizes the application of single-cell sequencing technology to tumor typing, metastasis analysis, progression detection, and adjuvant therapy.

scholarly journals Application of single-cell sequencing technologies in pancreatic cancer

2021 ◽  
Author(s):  
Mastan Mannarapu ◽  
Begum Dariya ◽  
Obul Reddy Bandapalli
Keyword(s):  
Pancreatic Cancer ◽  
Single Cell ◽  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Single Cells ◽  
Evolutionary Relationship ◽  
Intratumor Heterogeneity ◽  
Sequencing Technology ◽  
Single Cell Sequencing ◽  
Sequencing Technologies

AbstractPancreatic cancer (PC) is the third lethal disease for cancer-related mortalities globally. This is mainly because of the aggressive nature and heterogeneity of the disease that is diagnosed only in their advanced stages. Thus, it is challenging for researchers and clinicians to study the molecular mechanism involved in the development of this aggressive disease. The single-cell sequencing technology enables researchers to study each and every individual cell in a single tumor. It can be used to detect genome, transcriptome, and multi-omics of single cells. The current single-cell sequencing technology is now becoming an important tool for the biological analysis of cells, to find evolutionary relationship between multiple cells and unmask the heterogeneity present in the tumor cells. Moreover, its sensitivity nature is found progressive enabling to detect rare cancer cells, circulating tumor cells, metastatic cells, and analyze the intratumor heterogeneity. Furthermore, these single-cell sequencing technologies also promoted personalized treatment strategies and next-generation sequencing to predict the disease. In this review, we have focused on the applications of single-cell sequencing technology in identifying cancer-associated cells like cancer-associated fibroblast via detecting circulating tumor cells. We also included advanced technologies involved in single-cell sequencing and their advantages. The future research indeed brings the single-cell sequencing into the clinical arena and thus could be beneficial for diagnosis and therapy of PC patients.

scholarly journals Cell “hashing” with barcoded antibodies enables multiplexing and doublet detection for single cell genomics

2017 ◽  
Author(s):  
Marlon Stoeckius ◽  
Shiwei Zheng ◽  
Brian Houck-Loomis ◽  
Stephanie Hao ◽  
Bertrand Z. Yeung ◽  
...  
Keyword(s):  
Single Cell ◽  
Surface Proteins ◽  
Batch Effects ◽  
Sequencing Technology ◽  
Massive Datasets ◽  
Human Pbmc ◽  
Single Cell Sequencing ◽  
The Cost ◽  
Multiple Samples ◽  
Cellular Transcriptome

ABSTRACTDespite rapid developments in single cell sequencing technology, sample-specific batch effects, detection of cell doublets, and the cost of generating massive datasets remain outstanding challenges. Here, we introduce cell “hashing”, where oligo-tagged antibodies against ubiquitously expressed surface proteins are used to uniquely label cells from distinct samples, which can be subsequently pooled. By sequencing these tags alongside the cellular transcriptome, we can assign each cell to its sample of origin, and robustly identify doublets originating from multiple samples. We demonstrate our approach by pooling eight human PBMC samples on a single run of the 10x Chromium system, substantially reducing our per-cell costs for library generation. Cell “hashing” is inspired by, and complementary to, elegant multiplexing strategies based on genetic variation, which we also leverage to validate our results. We therefore envision that our approach will help to generalize the benefits of single cell multiplexing to diverse samples and experimental designs.

scholarly journals Single-cell Sequencing in the Field of Stem Cells

2020 ◽  
Vol 21 (8) ◽  
pp. 576-584
Author(s):  
Tian Chen ◽  
Jiawei Li ◽  
Yichen Jia ◽  
Jiyan Wang ◽  
Ruirui Sang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Single Cell ◽  
High Throughput Sequencing ◽  
Acid Extraction ◽  
Sequencing Analysis ◽  
Sequencing Technology ◽  
Single Cell Sequencing ◽  
Continuous Progress ◽  
Basic Characteristics ◽  
Cover Up

Variation and heterogeneity between cells are the basic characteristics of stem cells. Traditional sequencing analysis methods often cover up this difference. Single-cell sequencing technology refers to the technology of high-throughput sequencing analysis of genomes at the single-cell level. It can effectively analyze cell heterogeneity and identify a small number of cell populations. With the continuous progress of cell sorting, nucleic acid extraction and other technologies, single-cell sequencing technology has also made great progress. Encouraging new discoveries have been made in stem cell research, including pluripotent stem cells, tissue-specific stem cells and cancer stem cells. In this review, we discuss the latest progress and future prospects of single-cell sequencing technology in the field of stem cells.

scholarly journals PNOC Expressed by B Cells in Cholangiocarcinoma Was Survival Related and LAIR2 Could Be a T Cell Exhaustion Biomarker in Tumor Microenvironment: Characterization of Immune Microenvironment Combining Single-Cell and Bulk Sequencing Technology

2021 ◽  
Vol 12 ◽  
Author(s):  
Zheng Chen ◽  
Mincheng Yu ◽  
Jiuliang Yan ◽  
Lei Guo ◽  
Bo Zhang ◽  
...  
Keyword(s):  
T Cell ◽  
B Cells ◽  
Tumor Microenvironment ◽  
Single Cell ◽  
Malignant Cell ◽  
Cell Populations ◽  
Sequencing Data ◽  
Sequencing Technology ◽  
Immune Infiltration ◽  
Single Cell Sequencing

BackgroundCholangiocarcinoma was a highly malignant liver cancer with poor prognosis, and immune infiltration status was considered an important factor in response to immunotherapy. In this investigation, we tried to locate immune infiltration related genes of cholangiocarcinoma through combination of bulk-sequencing and single-cell sequencing technology.MethodsSingle sample gene set enrichment analysis was used to annotate immune infiltration status in datasets of TCGA CHOL, GSE32225, and GSE26566. Differentially expressed genes between high- and low-infiltrated groups in TCGA dataset were yielded and further compressed in other two datasets through backward stepwise regression in R environment. Single-cell sequencing data of GSE138709 was loaded by Seurat software and was used to examined the expression of infiltration-related gene set. Pathway changes in malignant cell populations were analyzed through scTPA web tool.ResultsThere were 43 genes differentially expressed between high- and low-immune infiltrated patients, and after further compression, PNOC and LAIR2 were significantly correlated with high immune infiltration status in cholangiocarcinoma. Through analysis of single-cell sequencing data, PNOC was mainly expressed by infiltrated B cells in tumor microenvironment, while LAIR2 was expressed by Treg cells and partial GZMB+ CD8 T cells, which were survival related and increased in tumor tissues. High B cell infiltration levels were related to better overall survival. Also, malignant cell populations demonstrated functionally different roles in tumor progression.ConclusionPNOC and LAIR2 were biomarkers for immune infiltration evaluation in cholangiocarcinoma. PNOC, expressed by B cells, could predict better survival of patients, while LAIR2 was a potential marker for exhaustive T cell populations, correlating with worse survival of patients.

Characterization of BMSC subpopulations by using novel single cell sequencing technology

Cytotherapy ◽  
2018 ◽  
Vol 20 (5) ◽  
pp. S41-S42
Author(s):  
P. Jin ◽  
S. Liu ◽  
H. Bae ◽  
Y. Zhao ◽  
R. Shi ◽  
...  
Keyword(s):  
Single Cell ◽  
Sequencing Technology ◽  
Single Cell Sequencing

scholarly journals Advances in Single-Cell Sequencing Technology and its Applications in Triple-Negative Breast Cancer

2021 ◽  
Author(s):  
Meng Li ◽  
Miaozhou Wang ◽  
Yanlin Xie ◽  
Tingting Yan ◽  
Yanfang Li
Keyword(s):  
Breast Cancer ◽  
Single Cell ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Current Knowledge ◽  
Resistance Mechanisms ◽  
Sequencing Technology ◽  
Single Cell Sequencing ◽  
Aggressive Subtype

Abstract Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer and is mainly treated with chemotherapy-based combination therapy. In recent years, the increasing development of single-cell sequencing (SCS) has become one of the most promising technologies in the field of biotechnology. The study of the heterogeneity of TNBC tumor cells using SCS will expand our current knowledge of metastasis, drug resistance mechanisms, mutations, and cloning in these cells; this will further guide clinical chemotherapy, targeted therapy, and immunotherapy. Relevant studies shown that SCS exactly plays an important role in clinical diagnosis and treatment. To highlight the role of SCS in the study of TNBC, we elaborate on the progress of research and the applications of SCS in TNBC.

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