Single-Cell RNA-Sequencing: Opening New Horizons for Breast Cancer Research
Abstract
:1. Introduction
2. The Functional Principle and Workflow of scRNA-Seq
2.1. Single-Cell Isolation
2.2. Reverse Transcription, Amplification, and Sequencing
2.2.1. PCR after polyA Tailing
2.2.2. Template-Switching-Based PCR
2.2.3. In Vitro Transcription (IVT)
2.3. Data Analysis
3. Application of scRNA-Seq in Breast Cancer
3.1. Application of scRNA-Seq in Exploring the Heterogeneity of Breast Cancer
3.2. Application of scRNA-Seq in TME of Breast Cancer
3.3. Application of scRNA-Seq in Therapy of Breast Cancer
3.4. Application of scRNA-Seq in Drug Resistance of Breast Cancer
3.5. Application of scRNA-Seq in Metastasis of Breast Cancer
4. Potential Future Directions of scRNA-Seq in Breast Cancer Research
5. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Method | RNA-Capture | Transcript Coverage | UMI | Amplification Technology |
---|---|---|---|---|
Tang | polyA | full length | No | PCR after polyA tailing |
Quartz-seq | polyA | full length | No | |
Quartz-seq2 | polyA | full length | Yes | |
SUPeR-seq | polyA | full length | No | |
MATQ-seq | polyA | full length | Yes | |
SMART-seq | polyA | full length | No | Template-switching-based PCR |
SMART-seq2 | polyA | full length | No | |
SMART-seq3 | polyA | full length | Yes | |
FLASH-seq | polyA | full length | Yes | |
STRT-seq | polyA | 5′ tag | Yes | |
STRT-seq-2i | polyA | 5′ tag | Yes | |
SCRB-seq | polyA | 3′ tag | Yes | |
Drop-seq | polyA | 3′ tag | Yes | |
CEL-seq | polyA | 3′ tag | Yes | In vitro transcription(IVT) |
CEL-seq2 | polyA | 3′ tag | Yes | |
MARS-seq | polyA | 3′ tag | Yes | |
MARS-seq2.0 | polyA | 3′ tag | Yes | |
In Drops | polyA | 3′ tag | Yes |
Applications | Category | Study | Clinical Significance | References |
---|---|---|---|---|
Heterogeneity | Heterogeneity within normal breast tissues |
|
| [67,68] |
Heterogeneity within breast tumors |
| Offering insights into the refined classification and tailored therapies for breast cancer. | [69,70,71,72] | |
Heterogeneity between breast cancer malignant cells and reference normal epithelial cells | Revealing evolution mimicry during the specification of breast cancer subtype. | Revealing the origin of tumor cells and providing a foundation for accurate prognostic and therapeutic stratification of breast cancer. | [73] | |
Heterogeneity among breast cancer cell lines | Investigation of the functional relationship among different cell subtypes in breast cancer cell lines and how this interdependence contributes to tumor development. | Highlighting the systemic nature of cancer and task stratification of cell populations to maintain tumor hallmarks. | [66] | |
Heterogeneity in gene expression within each tumor | Revealing the phenotypes and biology underlying the genetic evolution and clinical behavior of TNBC. | Highlighting the connection between the functional heterogeneity of TNBC and genomic evolution, and revealing the biological principles that lead to the poor prognosis of TNBC. | [74] | |
TME | Tumor immune microenvironment(T cells, B cells, macrophages, NK cells) |
|
| [76,77,78,79,80,81] |
Tumor interstitial microenvironment (CAFs) |
|
| [83,84,85,86,87] | |
Therapy | Drug sensitivity | Predicting drug sensitivity | Guiding personalized drug treatment for patients. | [88] |
Predictive markers for NAT | Screening for biomarkers associated with the prognostic response to NAT. | Enabling the identification of subgroups of breast cancer patients who are likely to benefit from NAT. | [89,90,91] | |
Chemotherapy combined with immunotherapy | Analyses on the changes in the immune microenvironment and immune cell dynamics of breast cancer resulting from chemotherapy combined with immunotherapy. | Highlighting the role and concerns of specific immune cells in combined therapy, which could potentially provide important clues for individualized treatment. | [92,93] | |
Drug resistance | Drug resistance of TNBC |
|
| [96,97] |
Drug resistance of luminal breast cancer |
|
| [98,99] | |
Drug resistance of HER2-positive breast cancer |
|
| [100,101] | |
Drug resistance of non-inflammatory breast cancer | The role of combined application of MSA-2 and YM101 in immune therapy resistance of non-inflammatory tumors. | Providing a new treatment strategy for non-inflammatory tumors. | [102] | |
Metastasis | Lymph node metastasis in female breast cancer |
|
| [103,104,105,106,107,108] |
Metastasis in male breast cancer | Metastatic characteristics of male breast cancer. | Providing a new perspective for the research and treatment of male breast cancer. | [109] |
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Xiang, L.; Rao, J.; Yuan, J.; Xie, T.; Yan, H. Single-Cell RNA-Sequencing: Opening New Horizons for Breast Cancer Research. Int. J. Mol. Sci. 2024, 25, 9482. https://doi.org/10.3390/ijms25179482
Xiang L, Rao J, Yuan J, Xie T, Yan H. Single-Cell RNA-Sequencing: Opening New Horizons for Breast Cancer Research. International Journal of Molecular Sciences. 2024; 25(17):9482. https://doi.org/10.3390/ijms25179482
Chicago/Turabian StyleXiang, Lingyan, Jie Rao, Jingping Yuan, Ting Xie, and Honglin Yan. 2024. "Single-Cell RNA-Sequencing: Opening New Horizons for Breast Cancer Research" International Journal of Molecular Sciences 25, no. 17: 9482. https://doi.org/10.3390/ijms25179482