Single-cell RNA sequencing and spatial transcriptomic technologies and applications in exploring gastric cancer

Gastric cancer (GC) remains a significant contributor to global cancer incidence and mortality, particularly in Eastern Europe, Asia, and Central America. Despite advancements in treatment, the prognosis for GC patients, especially those with metastatic disease, remains poor. Metastasis, the primary cause of cancer mortality, poses significant challenges in treatment due to its complex mechanisms. Recently, single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics have emerged as powerful tools to provide insights into the molecular mechanisms underlying GC metastasis.

Methods and Technologies

Single-Cell RNA Sequencing (scRNA-seq)

scRNA-seq enables the analysis of gene expression at the single-cell level, providing unprecedented resolution into cellular heterogeneity within tumors. Two major approaches exist: plate-based and droplet-based scRNA-seq. Plate-based methods, such as SMART-seq2, utilize fluorescence-activated cell sorting to isolate individual cells, allowing for flexible experimental setups. However, they are relatively expensive and have lower cellular throughput compared to droplet-based methods like 10× Genomics. Droplet-based scRNA-seq can generate data for thousands of cells in a single experiment, enabling a more comprehensive exploration of cell types in a tissue.

Spatial Transcriptomics

Spatial transcriptomics technologies, such as NanoString GeoMx DSP and 10× Genomics Visium, enable the analysis of gene expression patterns within the spatial context of tissues. These technologies preserve the spatial organization of cells, allowing researchers to correlate gene expression with cellular location and tissue architecture. NanoString GeoMx DSP focuses on user-defined regions of interest (ROIs), while 10× Genomics Visium utilizes a slide with capture regions containing spatial barcodes for gene expression analysis.

Applications in Gastric Cancer Research

Intratumoral Heterogeneity

scRNA-seq has been successfully applied to assess intratumoral heterogeneity in GC. Studies have revealed distinct tumor cell clusters with different gene expression profiles, indicating a high level of intertumoral and intratumoral heterogeneity. This heterogeneity plays a crucial role in drug resistance and the development of new therapeutic strategies.

Tumor Microenvironment (TME)

The TME, comprising stromal cells, immune cells, and extracellular matrix components, plays a vital role in GC progression and metastasis. scRNA-seq and spatial transcriptomics have provided insights into the complex interactions between tumor cells and their microenvironment. For instance, studies have identified differentially expressed genes in stromal cells, such as cancer-associated fibroblasts (CAFs), which promote tumor growth and metastasis.

Immune Cell Composition and Function

The immune landscape of GC is complex and dynamic, with various immune cell subsets exhibiting distinct functional properties. scRNA-seq has enabled the characterization of immune cell subsets, including T cells, B cells, macrophages, and dendritic cells, within the TME. These studies have revealed the expression of inhibitory receptors and cytokines by immune cells, which can influence their antitumor activity.

Drug Response and Therapeutic Strategies

Understanding the molecular mechanisms underlying drug response is crucial for developing effective therapeutic strategies. scRNA-seq and spatial transcriptomics have been used to study the effects of chemotherapy on the TME, revealing changes in gene expression patterns and immune cell composition. These insights can inform the development of novel therapeutic targets and combination therapies.

Conclusions and Future Perspectives

Advances in scRNA-seq and spatial transcriptomics have significantly enhanced our understanding of the molecular mechanisms underlying GC metastasis. These technologies have provided insights into intratumoral heterogeneity, TME composition, immune cell function, and drug response. However, many questions remain unanswered, and further research is needed to fully elucidate the complex mechanisms of GC metastasis.

Future studies should focus on integrating scRNA-seq and spatial transcriptomics data with other omics data, such as proteomics and metabolomics, to gain a more comprehensive understanding of GC biology. Additionally, the development of novel therapeutic strategies targeting specific cell types and molecular pathways identified through these technologies holds great promise for improving the prognosis of GC patients.

In conclusion, scRNA-seq and spatial transcriptomics are powerful tools that have revolutionized our understanding of GC and will continue to play a critical role in advancing GC research and treatment.

Full text

https://www.xiahepublishing.com/2996-3427/OnA-2023-00039

The study was recently published in the Oncology Advances.

Oncology Advances is dedicated to improving the diagnosis and treatment of human malignancies, advancing the understanding of molecular mechanisms underlying oncogenesis, and promoting translation from bench to bedside of oncological sciences. The aim of Oncology Advances is to publish peer-reviewed, high-quality articles in all aspects of translational and clinical studies on human cancers, as well as cutting-edge preclinical and clinical research of novel cancer therapies.

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