Cell State and Cell Type: Deconvoluting Circulating Tumor Cell Populations in Liquid Biopsies by Multi-Omics
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Patients and Samples
2.2. Blood Sample Collection and Processing
2.3. Cell Culture and Contrived Sample Generation
2.4. Immunofluorescent Staining of Patient Slides
2.5. Rare Cell Identification and Characterization
2.6. Single-Cell Next-Generation Sequencing and Bioinformatic Analysis
2.7. Single-Cell Targeted Proteomics and Data Analysis
2.8. Data Analysis and Visualization
3. Results
3.1. Characterization of Circulating Rare Cells Appearing at Time Points of Progression and Stable Disease of a Metastatic Prostate Cancer Patient
3.2. Inter-Patient Assessment of Circulating Cell Types and Cell States in the Liquid Biopsy
3.3. Targeted Proteomics Identifies Distinct Phenotypes
3.4. Morphometrics and Multi-Omics to Separate Cell Types
3.5. Characterization of CECs
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Patient ID | Cancer Type | Stage | IRB # |
---|---|---|---|
PC 1 | Prostate | Metastatic | UP-16-00691 |
PC 2 | Prostate | Metastatic | UP-16-00643 |
PC 3 | Prostate | Metastatic | UP-16-00691 |
PC 4 | Prostate | Metastatic | UP-16-00691 |
Patient ID | Cancer Type | Stage | Cancer Subtype | IRB # |
---|---|---|---|---|
BC 1 | Breast | Metastatic | ER+/HER2− | UP-14-00592 |
BC 2 | Breast | Metastatic | Triple Negative | UP-16-0070 |
BC 3 | Breast | Metastatic | Triple Negative | UP-16-0070 |
BC 4 | Breast | Metastatic | ER+/HER2− | UP-17-00882 |
BC 5 | Breast | Metastatic | Triple Negative | UP-16-0070 |
BC 6 | Breast | Metastatic | Triple Negative | UP-16-0070 |
BC 7 | Breast | Metastatic | ER+/HER2− | UP-14-00182 |
BC 8 | Breast | Metastatic | ER+/HER2− | UP-14-00523 |
BC 9 | Breast | Metastatic | ER+/HER2− | UP-14-00523 |
Patient ID | Disease Type | IRB # |
---|---|---|
MI 1 | MI | IRB-09-5287 |
MI 2 | MI | IRB-09-5287 |
MI 3 | MI | IRB-09-5287 |
Metal Tag | Target | Antibody Clone | Final Dilution |
---|---|---|---|
Yb174 | CK8/18 | C51 | 1:50 |
Pr141 | EpCAM | 9C4 | 1:100 |
Dy163 | ER | D8H8 | 1:100 |
Tb174 | HER2 | 42c/erbB2-2 | 1:100 |
Nd148 | HER2 | 29D8 | 1:100 |
Y89 | CD45 | HI30 | 1:200 |
Tm169 | PSMA | 460420 | 1:100 |
Gd160 | PSA | TD11B3-4 | 1:100 |
Sm154 | AR | G122-434 | 1:100 |
Ir193 | DNA | ||
In115 | Membrane |
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Welter, L.; Zheng, S.; Setayesh, S.M.; Morikado, M.; Agrawal, A.; Nevarez, R.; Naghdloo, A.; Pore, M.; Higa, N.; Kolatkar, A.; et al. Cell State and Cell Type: Deconvoluting Circulating Tumor Cell Populations in Liquid Biopsies by Multi-Omics. Cancers 2023, 15, 3949. https://doi.org/10.3390/cancers15153949
Welter L, Zheng S, Setayesh SM, Morikado M, Agrawal A, Nevarez R, Naghdloo A, Pore M, Higa N, Kolatkar A, et al. Cell State and Cell Type: Deconvoluting Circulating Tumor Cell Populations in Liquid Biopsies by Multi-Omics. Cancers. 2023; 15(15):3949. https://doi.org/10.3390/cancers15153949
Chicago/Turabian StyleWelter, Lisa, Serena Zheng, Sonia Maryam Setayesh, Michael Morikado, Arushi Agrawal, Rafael Nevarez, Amin Naghdloo, Milind Pore, Nikki Higa, Anand Kolatkar, and et al. 2023. "Cell State and Cell Type: Deconvoluting Circulating Tumor Cell Populations in Liquid Biopsies by Multi-Omics" Cancers 15, no. 15: 3949. https://doi.org/10.3390/cancers15153949
APA StyleWelter, L., Zheng, S., Setayesh, S. M., Morikado, M., Agrawal, A., Nevarez, R., Naghdloo, A., Pore, M., Higa, N., Kolatkar, A., Thiele, J.-A., Sharma, P., Moore, H. C. F., Richer, J. K., Elias, A., Pienta, K. J., Zurita, A. J., Gross, M. E., Shishido, S. N., ... Kuhn, P. (2023). Cell State and Cell Type: Deconvoluting Circulating Tumor Cell Populations in Liquid Biopsies by Multi-Omics. Cancers, 15(15), 3949. https://doi.org/10.3390/cancers15153949