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With the development of high-throughput sequencing technology, it has been possible to accurately detect genetic mutations and gene expression of tumor cells at single-cell level. In particular, with the emergence and development of single cell sequencing (scSeq), comprehensive and accurate research on genomics, transcriptomics, and epigenomics of tumor single cells can be carried out. Empowered by extensive experiences in single cell solutions, SingleX can provide you with comprehensive and complete program execution and data analysis.

Studying Invasion in Early Stage Cancers

Ductal carcinoma in situ (DCIS) is early-stage breast cancer that easily evolves into invasive breast cancer over time. Although DCIS is the most common form of early breast cancer and is often detected by mammography, 10% to 30% of this cancer progresses to invasive ductal carcinoma (IDC). Given the technical challenges of tissue analysis, how DCIS accurately produces invasiveness is still not well understood in the genome. Scientists use topographic single cell sequencing (TSCS) analysis methods to accurately measure and characterize the specific characteristics of individual tumor cells. Studies have revealed a direct genomic lineage between DCIS and IDC, and further confirm that most mutations and DNA copy number abnormalities have evolved in the milk duct before invasiveness.

Graphical abstract of multiclonal invasion in breast cancer via single cell DNA sequencing. Fig.1 Graphical abstract of multiclonal invasion in breast cancer via single cell DNA sequencing. (Casasent, 2018)

Investigating Mutation Rates and Mutator Phenotypes

CD4+ regulatory T cells (Tregs) play a key role in maintaining immune balance in vivo, and their phenotypic heterogeneity reflects environmental diversity and the diversity of target cells they regulate. To investigate the phenotype of mutants, scientists explored the expression profiles of regulatory T cells and traditional CD4+FoxP3 T cells by using single-cell transcriptome, activation assays, and TCR analysis. The study found that TCR signal levels did not affect the proportion of activated Treg cells in the physiological environment and without inflammatory stimuli, but significantly distort their phenotypic selection.

Biclustering expression heatmap for 2 independent splenic Treg scRNAseq datasets. Fig.2 Biclustering expression heatmap for 2 independent splenic Treg scRNAseq datasets. (Zemmour, 2018)

Studying Cell Plasticity and the Epithelial-to-mesenchymal Transition

Neural stem cells (NSCs) contribute to the plasticity and repair of the adult brain. Small habitats containing NSCs regulate stem cell self-renewal and differentiation. Scientists use comprehensive and non-targeted single-cell RNA analysis to generate molecular cell maps of the largest germinal region of the adult mouse brain, the subventricular zone (SVZ). The study characterized >20 neuronal and non-neuronal cell types and predicted future cellular states through computational analysis based on RNA dynamics, gaining insights into neural remodeling dynamics. In addition, the study used a single-cell approach to demonstrate that in mice lacking LRP2 (the endocytic receptor required for SVZ maintenance), the number of NSCs decreased, progenitor cell proliferation activity decreased, and Wnt and BMP signaling pathways were disordered.

Single-cell RNA sequencing explores cell types in the subventricular zone. Fig.3 Single-cell RNA sequencing explores cell types in the subventricular zone. (Zywitza, 2018)

Tracing Metastatic Dissemination

Micro-metastases are metastasis of non-hematological malignancies that are present in lymph nodes, bone marrow, and blood circulation, but cannot be detected by conventional clinicopathological and imaging methods. They are generally defined as occultists in the form of individual cells or tiny cell clusters. Micrometastatic cells in the bone marrow are called diffuse tumor cells and have independent prognostic value for breast cancer patients. Scientists used single-cell sequencing to analyze cells that were suspected of having micrometastases isolated from the bone marrow of breast cancer patients. Studies have found that diffuse tumor cells can be undetected for many years before being reactivated and producing new tumors or metastases, and are usually resistant to treatment.

Genotyping of single nucleotide variants from bulk tumor exome sequences in the single-cell sequences. Fig.4 Genotyping of single nucleotide variants from bulk tumor exome sequences in the single-cell sequences. (Demeulemeester, 2016)

Highlights

  • Extensive experience in preparation of single cell suspensions for different sample types
  • Mature single-cell sequencing library construction technology
  • Complete single cell sequencing and experimental quality control process
  • Personalized, customized data analysis services

With extensive experience in single cell analysis, tumor research, SingleX is able to conduct end-to-end single cell omics solutions as per your specific requirements. We are dedicated to being a full-service CRO focused on the single-cell data-driven future. Please contact us to learn how we can help with your single cell program.

References

  1. Casasent, A.K.; et al. Multiclonal invasion in breast tumors identified by topographic single cell sequencing. Cell. 2018, 172(1): 205-217.
  2. Zemmour, D.; et al. Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR. Nature immunology. 2018, 19(3): 291-301.
  3. Zywitza, V.; et al. Single-Cell tranomics characterizes cell types in the subventricular zone and uncovers molecular defects impairing adult neurogenesis. Cell reports. 2018, 25(9): 2457-2469.
  4. Demeulemeester, J.; et al. Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing. Genome biology. 2016, 17: 250.

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