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Modlin IM, Kidd M, Drozdov IA, Boegemann M, Bodei L, Kunikowska J, Malczewska A, Bernemann C, Koduru SV, Rahbar K. Development of a multigenomic liquid biopsy (PROSTest) for prostate cancer in whole blood. Prostate 2024; 84:850-865. [PMID: 38571290 DOI: 10.1002/pros.24704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/04/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
INTRODUCTION We describe the development of a molecular assay from publicly available tumor tissue mRNA databases using machine learning and present preliminary evidence of functionality as a diagnostic and monitoring tool for prostate cancer (PCa) in whole blood. MATERIALS AND METHODS We assessed 1055 PCas (public microarray data sets) to identify putative mRNA biomarkers. Specificity was confirmed against 32 different solid and hematological cancers from The Cancer Genome Atlas (n = 10,990). This defined a 27-gene panel which was validated by qPCR in 50 histologically confirmed PCa surgical specimens and matched blood. An ensemble classifier (Random Forest, Support Vector Machines, XGBoost) was trained in age-matched PCas (n = 294), and in 72 controls and 64 BPH. Classifier performance was validated in two independent sets (n = 263 PCas; n = 99 controls). We assessed the panel as a postoperative disease monitor in a radical prostatectomy cohort (RPC: n = 47). RESULTS A PCa-specific 27-gene panel was identified. Matched blood and tumor gene expression levels were concordant (r = 0.72, p < 0.0001). The ensemble classifier ("PROSTest") was scaled 0%-100% and the industry-standard operating point of ≥50% used to define a PCa. Using this, the PROSTest exhibited an 85% sensitivity and 95% specificity for PCa versus controls. In two independent sets, the metrics were 92%-95% sensitivity and 100% specificity. In the RPCs (n = 47), PROSTest scores decreased from 72% ± 7% to 33% ± 16% (p < 0.0001, Mann-Whitney test). PROSTest was 26% ± 8% in 37 with normal postoperative PSA levels (<0.1 ng/mL). In 10 with elevated postoperative PSA, PROSTest was 60% ± 4%. CONCLUSION A 27-gene whole blood signature for PCa is concordant with tissue mRNA levels. Measuring blood expression provides a minimally invasive genomic tool that may facilitate prostate cancer management.
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Affiliation(s)
- Irvin M Modlin
- Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mark Kidd
- Wren Laboratories LLC, Branford, Connecticut, USA
| | | | - Martin Boegemann
- Department of Urology, Münster University Hospital, Münster, Germany
| | - Lisa Bodei
- Department of Radiology, Molecular Imaging and Therapy Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jolanta Kunikowska
- Department of Nuclear Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Anna Malczewska
- Department of Endocrinology, Medical University of Silesia, Katowice, Poland
| | | | | | - Kambiz Rahbar
- Department of Nuclear Medicine, Münster University Hospital, Münster, Germany
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Hongo H, Kosaka T, Takayama KI, Baba Y, Yasumizu Y, Ueda K, Suzuki Y, Inoue S, Beltran H, Oya M. G-protein signaling of oxytocin receptor as a potential target for cabazitaxel-resistant prostate cancer. PNAS NEXUS 2024; 3:pgae002. [PMID: 38250514 PMCID: PMC10799637 DOI: 10.1093/pnasnexus/pgae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024]
Abstract
Although the treatment armamentarium for patients with metastatic prostate cancer has improved recently, treatment options after progression on cabazitaxel (CBZ) are limited. To identify the mechanisms underlying CBZ resistance and therapeutic targets, we performed single-cell RNA sequencing of circulating tumor cells (CTCs) from patients with CBZ-resistant prostate cancer. Cells were clustered based on gene expression profiles. In silico screening was used to nominate candidate drugs for overcoming CBZ resistance in castration-resistant prostate cancer. CTCs were divided into three to four clusters, reflecting intrapatient tumor heterogeneity in refractory prostate cancer. Pathway analysis revealed that clusters in two cases showed up-regulation of the oxytocin (OXT) receptor-signaling pathway. Spatial gene expression analysis of CBZ-resistant prostate cancer tissues confirmed the heterogeneous expression of OXT-signaling molecules. Cloperastine (CLO) had significant antitumor activity against CBZ-resistant prostate cancer cells. Mass spectrometric phosphoproteome analysis revealed the suppression of OXT signaling specific to CBZ-resistant models. These results support the potential of CLO as a candidate drug for overcoming CBZ-resistant prostate cancer via the inhibition of OXT signaling.
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Affiliation(s)
- Hiroshi Hongo
- Department of Urology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Takeo Kosaka
- Department of Urology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo 173-001, Japan
| | - Yuto Baba
- Department of Urology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yota Yasumizu
- Department of Urology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo 173-001, Japan
- Division of Systems Medicine and Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1298, Japan
| | - Himisha Beltran
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Mototsugu Oya
- Department of Urology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
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Orrapin S, Thongkumkoon P, Udomruk S, Moonmuang S, Sutthitthasakul S, Yongpitakwattana P, Pruksakorn D, Chaiyawat P. Deciphering the Biology of Circulating Tumor Cells through Single-Cell RNA Sequencing: Implications for Precision Medicine in Cancer. Int J Mol Sci 2023; 24:12337. [PMID: 37569711 PMCID: PMC10418766 DOI: 10.3390/ijms241512337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Circulating tumor cells (CTCs) hold unique biological characteristics that directly involve them in hematogenous dissemination. Studying CTCs systematically is technically challenging due to their extreme rarity and heterogeneity and the lack of specific markers to specify metastasis-initiating CTCs. With cutting-edge technology, single-cell RNA sequencing (scRNA-seq) provides insights into the biology of metastatic processes driven by CTCs. Transcriptomics analysis of single CTCs can decipher tumor heterogeneity and phenotypic plasticity for exploring promising novel therapeutic targets. The integrated approach provides a perspective on the mechanisms underlying tumor development and interrogates CTCs interactions with other blood cell types, particularly those of the immune system. This review aims to comprehensively describe the current study on CTC transcriptomic analysis through scRNA-seq technology. We emphasize the workflow for scRNA-seq analysis of CTCs, including enrichment, single cell isolation, and bioinformatic tools applied for this purpose. Furthermore, we elucidated the translational knowledge from the transcriptomic profile of individual CTCs and the biology of cancer metastasis for developing effective therapeutics through targeting key pathways in CTCs.
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Affiliation(s)
- Santhasiri Orrapin
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Patcharawadee Thongkumkoon
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Sasimol Udomruk
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
- Musculoskeletal Science and Translational Research (MSTR) Center, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
| | - Sutpirat Moonmuang
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Songphon Sutthitthasakul
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Petlada Yongpitakwattana
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Dumnoensun Pruksakorn
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
- Musculoskeletal Science and Translational Research (MSTR) Center, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
- Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
| | - Parunya Chaiyawat
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
- Musculoskeletal Science and Translational Research (MSTR) Center, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
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Clack K, Soda N, Kasetsirikul S, Mahmudunnabi RG, Nguyen NT, Shiddiky MJA. Toward Personalized Nanomedicine: The Critical Evaluation of Micro and Nanodevices for Cancer Biomarker Analysis in Liquid Biopsy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205856. [PMID: 36631277 DOI: 10.1002/smll.202205856] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Liquid biopsy for the analysis of circulating cancer biomarkers (CBs) is a major advancement toward the early detection of cancer. In comparison to tissue biopsy techniques, liquid biopsy is relatively painless, offering multiple sampling opportunities across easily accessible bodily fluids such as blood, urine, and saliva. Liquid biopsy is also relatively inexpensive and simple, avoiding the requirement for specialized laboratory equipment or trained medical staff. Major advances in the field of liquid biopsy are attributed largely to developments in nanotechnology and microfabrication that enables the creation of highly precise chip-based platforms. These devices can overcome detection limitations of an individual biomarker by detecting multiple markers simultaneously on the same chip, or by featuring integrated and combined target separation techniques. In this review, the major advances in the field of portable and semi-portable micro, nano, and multiplexed platforms for CB detection for the early diagnosis of cancer are highlighted. A comparative discussion is also provided, noting merits and drawbacks of the platforms, especially in terms of portability. Finally, key challenges toward device portability and possible solutions, as well as discussing the future direction of the field are highlighted.
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Affiliation(s)
- Kimberley Clack
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Narshone Soda
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Surasak Kasetsirikul
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Rabbee G Mahmudunnabi
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
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Negishi R, Yamakawa H, Kobayashi T, Horikawa M, Shimoyama T, Koizumi F, Sawada T, Oboki K, Omuro Y, Funasaka C, Kageyama A, Kanemasa Y, Tanaka T, Matsunaga T, Yoshino T. Transcriptomic profiling of single circulating tumor cells provides insight into human metastatic gastric cancer. Commun Biol 2022; 5:20. [PMID: 35017627 PMCID: PMC8752828 DOI: 10.1038/s42003-021-02937-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 12/01/2021] [Indexed: 12/24/2022] Open
Abstract
Transcriptome analysis of circulating tumor cells (CTCs), which migrate into blood vessels from primary tumor tissues, at the single-cell level offers critical insights into the biology of metastasis and contributes to drug discovery. However, transcriptome analysis of single CTCs has only been reported for a limited number of cancer types, such as multiple myeloma, breast, hepatocellular, and prostate cancer. Herein, we report the transcriptome analysis of gastric cancer single-CTCs. We utilized an antigen-independent strategy for CTC isolation from metastatic gastric cancer patients involving a size-dependent recovery of CTCs and a single cell isolation technique. The transcriptomic profile of single-CTCs revealed that a majority of gastric CTCs had undergone epithelial-mesenchymal transition (EMT), and indicated the contribution of platelet adhesion toward EMT progression and acquisition of chemoresistance. Taken together, this study serves to employ CTC characterization to elucidate the mechanisms of chemoresistance and metastasis in gastric cancer.
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Affiliation(s)
- Ryo Negishi
- Division of Biotechnology and Life science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Hitomi Yamakawa
- Division of Biotechnology and Life science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Takeru Kobayashi
- Division of Biotechnology and Life science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Mayuko Horikawa
- Division of Biotechnology and Life science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tatsu Shimoyama
- Department of Medical Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Fumiaki Koizumi
- Department of Laboratory Medicine, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Takeshi Sawada
- Department of Medical Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Keisuke Oboki
- Center for Medical Research Cooperation, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Japan
| | - Yasushi Omuro
- Department of Medical Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Chikako Funasaka
- Department of Medical Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Akihiko Kageyama
- Department of Medical Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Yusuke Kanemasa
- Department of Medical Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tadashi Matsunaga
- Division of Biotechnology and Life science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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6
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Sun G, Li Z, Rong D, Zhang H, Shi X, Yang W, Zheng W, Sun G, Wu F, Cao H, Tang W, Sun Y. Single-cell RNA sequencing in cancer: Applications, advances, and emerging challenges. Mol Ther Oncolytics 2021; 21:183-206. [PMID: 34027052 PMCID: PMC8131398 DOI: 10.1016/j.omto.2021.04.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cancer has become one of the greatest threats to human health, and new technologies are urgently needed to further clarify the mechanisms of cancer so that better detection and treatment strategies can be developed. At present, extensive genomic analysis and testing of clinical specimens shape the insights into carcinoma. Nevertheless, carcinoma of humans is a complex ecosystem of cells, including carcinoma cells and immunity-related and stroma-related subsets, with accurate characteristics obscured by extensive genome-related approaches. A growing body of research shows that sequencing of single-cell RNA (scRNA-seq) is emerging to be an effective way for dissecting human tumor tissue at single-cell resolution, presenting one prominent way for explaining carcinoma biology. This review summarizes the research progress of scRNA-seq in the field of tumors, focusing on the application of scRNA-seq in tumor circulating cells, tumor stem cells, tumor drug resistance, the tumor microenvironment, and so on, which provides a new perspective for tumor research.
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Affiliation(s)
- Guangshun Sun
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhouxiao Li
- Department of Hand Surgery, Plastic Surgery and Aesthetic Surgery, Ludwig Maximilians University, Munich, Germany
| | - Dawei Rong
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Hao Zhang
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xuesong Shi
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weijun Yang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wubin Zheng
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Guoqiang Sun
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Fan Wu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongyong Cao
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weiwei Tang
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Yangbai Sun
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
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Cell Heterogeneity Analysis in Single-Cell RNA-seq Data Using Mixture Exponential Graph and Markov Random Field Model. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9919080. [PMID: 34095314 PMCID: PMC8164540 DOI: 10.1155/2021/9919080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/30/2021] [Indexed: 11/18/2022]
Abstract
Advanced single-cell profiling technologies promote exploration of cell heterogeneity, and clustering of single-cell RNA (scRNA-seq) data enables discovery of coexpression genes and network relationships between genes. In particular, single-cell profiling of circulating tumor cells (CTCs) can provide unique insights into tumor heterogeneity (including in triple-negative breast cancer (TNBC)), while scRNA-seq leads to better understanding of subclonal architecture and biological function. Despite numerous reports suggesting a direct correlation between circulating tumor cells (CTCs) and poor clinical outcomes, few studies have provided a thorough heterogeneity characterization of CTCs. In addition, TNBC is a disease with not only intertumor but also intratumor heterogeneity and represents various biological distinct subgroups that may have relationships with immune functions that are not clearly established yet. In this article, we introduce a new scheme for detecting genotypic characterization of single-cell heterogeneities and apply it to CTC and TNBC single-cell RNA-seq data. First, we use an existing mixture exponential family graph model to partition the cell-cell network; then, with the Markov random field model, we obtain more flexible network rewiring. Finally, we find the cell heterogeneity and network relationships according to different high coexpression gene modules in different cell subsets. Our results demonstrate that this scheme provides a reasonable and effective way to model different cell clusters and different biological enrichment gene clusters. Thus, using different internal coexpression genes of different cell clusters, we can infer the differences in tumor composition and diversity.
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Rastogi N, Seth P, Bhat R, Sen P. Vortex chip incorporating an orthogonal turn for size-based isolation of circulating cells. Anal Chim Acta 2021; 1159:338423. [PMID: 33867033 DOI: 10.1016/j.aca.2021.338423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/23/2021] [Accepted: 03/15/2021] [Indexed: 12/11/2022]
Abstract
Size-based label-free separation of rare cells such as CTCs is attractive due to its wider applicability, simpler sample preparation, faster turnaround and better efficiency. Amongst such methods, vortex-trapping based techniques offer high throughput but operate at high flow velocities where the resulting hydrodynamic shear stress is likely to damage cells and compromise their viability for subsequent assays. We present here an orthogonal vortex chip which can carry out size-differentiated trapping at significantly lower (38% of previously reported) velocities. Composed of entry-exit channels that couple orthogonally to a trapping chamber, fluid flow in such configuration results in formation of a vortex which selectively traps larger particles above a critical velocity while smaller particles get ejected with the flow. We call this phenomenon the turn-effect. Critical velocities and optimal architectures for trapping of cells and particles of different sizes are characterized. We explain how shear-gradient lift, centrifugal and Dean flow drag forces contribute to the turn-effect by pushing particles into specific vortex orbits in a size- and velocity-dependent fashion. Selective trapping of human breast cancer cells mixed with whole blood at low concentration is demonstrated. The device shows promising results for gentle isolation of rare cells from blood.
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Affiliation(s)
- Navya Rastogi
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
| | - Pranjal Seth
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India; Department of Biomedical Engineering, McGill University, Montreal, H3A 0G4, Canada.
| | - Ramray Bhat
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India.
| | - Prosenjit Sen
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
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Rushton AJ, Nteliopoulos G, Shaw JA, Coombes RC. A Review of Circulating Tumour Cell Enrichment Technologies. Cancers (Basel) 2021; 13:cancers13050970. [PMID: 33652649 PMCID: PMC7956528 DOI: 10.3390/cancers13050970] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Circulating tumour cells (CTCs) are cancer cells shed into the bloodstream from tumours and their analysis can provide important insights into cancer detection and monitoring, with the potential to direct personalised therapies for the patient. These CTCs are rare in the blood, which makes their detection and enrichment challenging and to date, only one technology (the CellSearch) has gained FDA approval for determining the prognosis of patients with advanced breast, prostate and colorectal cancers. Here, we review the wide range of enrichment technologies available to isolate CTCs from other blood components and highlight the important characteristics that new technologies should possess for routine clinical use. Abstract Circulating tumour cells (CTCs) are the precursor cells for the formation of metastatic disease. With a simple blood draw, liquid biopsies enable the non-invasive sampling of CTCs from the blood, which have the potential to provide important insights into cancer detection and monitoring. Since gaining FDA approval in 2004, the CellSearch system has been used to determine the prognosis of patients with metastatic breast, prostate and colorectal cancers. This utilises the cell surface marker Epithelial Cell Adhesion Molecule (EpCAM), to enrich CTCs, and many other technologies have adopted this approach. More recently, the role of mesenchymal-like CTCs in metastasis formation has come to light. It has been suggested that these cells are more aggressive metastatic precursors than their epithelial counterparts; however, mesenchymal CTCs remain undetected by EpCAM-based enrichment methods. This has prompted the development of a variety of ‘label free’ enrichment technologies, which exploit the unique physical properties of CTCs (such as size and deformability) compared to other blood components. Here, we review a wide range of both immunocapture and label free CTC enrichment technologies, summarising the most significant advantages and disadvantages of each. We also highlight the important characteristics that technologies should possess for routine clinical use, since future developments could have important clinical implications, with the potential to direct personalised therapies for patients with cancer.
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Affiliation(s)
- Amelia J. Rushton
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (G.N.); (R.C.C.)
- Correspondence:
| | - Georgios Nteliopoulos
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (G.N.); (R.C.C.)
| | - Jacqueline A. Shaw
- Leicester Cancer Research Centre, University of Leicester, Leicester LE2 7LX, UK;
| | - R. Charles Coombes
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (G.N.); (R.C.C.)
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Casanova-Salas I, Athie A, Boutros PC, Del Re M, Miyamoto DT, Pienta KJ, Posadas EM, Sowalsky AG, Stenzl A, Wyatt AW, Mateo J. Quantitative and Qualitative Analysis of Blood-based Liquid Biopsies to Inform Clinical Decision-making in Prostate Cancer. Eur Urol 2021; 79:762-771. [PMID: 33422353 DOI: 10.1016/j.eururo.2020.12.037] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/23/2020] [Indexed: 12/12/2022]
Abstract
CONTEXT Genomic stratification can impact prostate cancer (PC) care through diagnostic, prognostic, and predictive biomarkers that aid in clinical decision-making. The temporal and spatial genomic heterogeneity of PC together with the challenges of acquiring metastatic tissue biopsies hinder implementation of tissue-based molecular profiling in routine clinical practice. Blood-based liquid biopsies are an attractive, minimally invasive alternative. OBJECTIVE To review the clinical value of blood-based liquid biopsy assays in PC and identify potential applications to accelerate the development of precision medicine. EVIDENCE ACQUISITION A systematic review of PubMed/MEDLINE was performed to identify relevant literature on blood-based circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and extracellular vesicles (EVs) in PC. EVIDENCE SYNTHESIS Liquid biopsy has emerged as a practical tool to profile tumor dynamics over time, elucidating features that evolve (genome, epigenome, transcriptome, and proteome) with tumor progression. Liquid biopsy tests encompass analysis of DNA, RNA, and proteins that can be detected in CTCs, ctDNA, or EVs. Blood-based liquid biopsies have demonstrated promise in the context of localized tumors (diagnostic signatures, risk stratification, and disease monitoring) and advanced disease (response/resistance biomarkers and prognostic markers). CONCLUSIONS Liquid biopsies have value as a source of prognostic, predictive, and response biomarkers in PC. Most clinical applications have been developed in the advanced metastatic setting, where CTC and ctDNA yields are significantly higher. However, standardization of assays and analytical/clinical validation is necessary prior to clinical implementation. PATIENT SUMMARY Traces of tumors can be isolated from blood samples from patients with prostate cancer either as whole cells or as DNA fragments. These traces provide information on tumor features. These minimally invasive tests can guide diagnosis and treatment selection.
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Affiliation(s)
- Irene Casanova-Salas
- Vall d'Hebron Institute of Oncology (VHIO) and Vall d'Hebron University Hospital, Barcelona, Spain
| | - Alejandro Athie
- Vall d'Hebron Institute of Oncology (VHIO) and Vall d'Hebron University Hospital, Barcelona, Spain
| | - Paul C Boutros
- Departments of Human Genetics and Urology, Institute for Precision Health and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
| | - Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - David T Miyamoto
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Edwin M Posadas
- Translational Oncology Program & Urologic Oncology Program, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Adam G Sowalsky
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Arnulf Stenzl
- Department of Urology, University Hospital Tübingen, Tübingen, Germany
| | - Alexander W Wyatt
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Joaquin Mateo
- Vall d'Hebron Institute of Oncology (VHIO) and Vall d'Hebron University Hospital, Barcelona, Spain.
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11
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Liu P, Jonkheijm P, Terstappen LWMM, Stevens M. Magnetic Particles for CTC Enrichment. Cancers (Basel) 2020; 12:cancers12123525. [PMID: 33255978 PMCID: PMC7760229 DOI: 10.3390/cancers12123525] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary For the enrichment of very rare cells, such as Circulating Tumor Cells (CTCs), immunomagnetic enrichment is frequently used. For this purpose, magnetic nanoparticles (MNPs) coated with specific antibodies directed against cancer cells are used. In this review, we look at the properties such a particle needs to have in order to be used successfully, and describe the different methods used in the production of such a particle as well as the methods for their separation. Additionally, an overview is given of the antibodies that could potentially be used for this purpose. Abstract Here, we review the characteristics and synthesis of magnetic nanoparticles (MNPs) and place these in the context of their usage in the immunomagnetic enrichment of Circulating Tumor Cells (CTCs). The importance of the different characteristics is explained, the need for a very specific enrichment is emphasized and different (commercial) magnetic separation techniques are shown. As the specificity of an MNP is in a large part dependent on the antibody coated onto the particle, different strategies in the coupling of specific antibodies as well as an overview of the available antibodies is given.
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Affiliation(s)
- Peng Liu
- Department of Medical Cell BioPhysics, University of Twente, 7522 NB Enschede, The Netherlnds; (P.L.); (L.W.M.M.T.)
- Department of Molecular Nanofabrication, University of Twente, 7522 NB Enschede, The Netherlands;
| | - Pascal Jonkheijm
- Department of Molecular Nanofabrication, University of Twente, 7522 NB Enschede, The Netherlands;
| | - Leon W. M. M. Terstappen
- Department of Medical Cell BioPhysics, University of Twente, 7522 NB Enschede, The Netherlnds; (P.L.); (L.W.M.M.T.)
| | - Michiel Stevens
- Department of Medical Cell BioPhysics, University of Twente, 7522 NB Enschede, The Netherlnds; (P.L.); (L.W.M.M.T.)
- Correspondence: ; Tel.: +31-53-489-4101
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12
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Abstract
Single-cell sequencing (SCS) is a powerful new tool that applies Next Generation Sequencing at the cellular level. SCS has revolutionized our understanding of tumor heterogeneity and the tumor microenvironment, immune infiltration, cancer stem cells (CSCs), circulating tumor cells (CTCs), and clonal evolution. The following chapter highlights the current literature on SCS in genitourinary (GU) malignancies and discusses future applications of SCS technology. The renal cell carcinoma (RCC) section highlights the use of SCS in characterizing the initial cells driving tumorigenesis, the intercellular mutational landscape of RCC, intratumoral heterogeneity (ITH) between primary and metastatic lesions, and genes driving RCC cancer stem cells (CSCs). The bladder cancer section will also illustrate molecular drivers of bladder cancer stem cells (BCSCs), SCS use in reconstructing tumor developmental history and underlying subclones, and understanding the effect of cisplatin on intratumoral heterogeneity in vitro and potential mechanisms behind platinum resistance. The final section featuring prostate cancer will discuss how SCS can be used to identify the cellular origins of benign prostatic hyperplasia and prostate cancer, the plasticity and heterogeneity of prostate cancer cells with regard to androgen dependence, and the use of SCS in CTCs to understand chemotherapy resistance and gene expression changes after androgen deprivation therapy (ADT). The studies listed in this chapter illustrate many translational applications of SCS in GU malignancies, including diagnostic, prognostic, and treatment-related approaches. The ability of SCS to resolve intratumor heterogeneity and better define the genomic landscape of tumors and CTCs will be fundamental in the new era of precision-based care.
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13
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Design, Development, and Multi-Characterization of an Integrated Clinical Transrectal Ultrasound and Photoacoustic Device for Human Prostate Imaging. Diagnostics (Basel) 2020; 10:diagnostics10080566. [PMID: 32784534 PMCID: PMC7460329 DOI: 10.3390/diagnostics10080566] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/30/2020] [Accepted: 08/04/2020] [Indexed: 01/06/2023] Open
Abstract
The standard diagnostic procedure for prostate cancer (PCa) is transrectal ultrasound (TRUS)-guided needle biopsy. However, due to the low sensitivity of TRUS to cancerous tissue in the prostate, small yet clinically significant tumors can be missed. Magnetic resonance imaging (MRI) with TRUS fusion biopsy has recently been introduced as a way to improve the identification of clinically significant PCa in men. However, the spatial errors in coregistering the preprocedural MRI with the real-time TRUS causes false negatives. A real-time and intraprocedural imaging modality that can sensitively detect PCa tumors and, more importantly, differentiate aggressive from nonaggressive tumors could largely improve the guidance of biopsy sampling to improve diagnostic accuracy and patient risk stratification. In this work, we seek to fill this long-standing gap in clinical diagnosis of PCa via the development of a dual-modality imaging device that integrates the emerging photoacoustic imaging (PAI) technique with the established TRUS for improved guidance of PCa needle biopsy. Unlike previously published studies on the integration of TRUS with PAI capabilities, this work introduces a novel approach for integrating a focused light delivery mechanism with a clinical-grade commercial TRUS probe, while assuring much-needed ease of operation in the transrectal space. We further present the clinical potential of our device by (i) performing rigorous characterization studies, (ii) examining the acoustic and optical safety parameters for human prostate imaging, and (iii) demonstrating the structural and functional imaging capabilities using deep-tissue-mimicking phantoms. Our TRUSPA experimental studies demonstrated a field-of-view in the range of 130 to 150 degrees and spatial resolutions in the range of 300 μm to 400 μm at a soft tissue imaging depth of 5 cm.
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14
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Kothapalli SR, Sonn GA, Choe JW, Nikoozadeh A, Bhuyan A, Park KK, Cristman P, Fan R, Moini A, Lee BC, Wu J, Carver TE, Trivedi D, Shiiba L, Steinberg I, Huland DM, Rasmussen MF, Liao JC, Brooks JD, Khuri-Yakub PT, Gambhir SS. Simultaneous transrectal ultrasound and photoacoustic human prostate imaging. Sci Transl Med 2020; 11:11/507/eaav2169. [PMID: 31462508 DOI: 10.1126/scitranslmed.aav2169] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 07/26/2019] [Indexed: 11/02/2022]
Abstract
Imaging technologies that simultaneously provide anatomical, functional, and molecular information are emerging as an attractive choice for disease screening and management. Since the 1980s, transrectal ultrasound (TRUS) has been routinely used to visualize prostatic anatomy and guide needle biopsy, despite limited specificity. Photoacoustic imaging (PAI) provides functional and molecular information at ultrasonic resolution based on optical absorption. Combining the strengths of TRUS and PAI approaches, we report the development and bench-to-bedside translation of an integrated TRUS and photoacoustic (TRUSPA) device. TRUSPA uses a miniaturized capacitive micromachined ultrasonic transducer array for simultaneous imaging of anatomical and molecular optical contrasts [intrinsic: hemoglobin; extrinsic: intravenous indocyanine green (ICG)] of the human prostate. Hemoglobin absorption mapped vascularity of the prostate and surroundings, whereas ICG absorption enhanced the intraprostatic photoacoustic contrast. Future work using the TRUSPA device for biomarker-specific molecular imaging may enable a fundamentally new approach to prostate cancer diagnosis, prognostication, and therapeutic monitoring.
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Affiliation(s)
- Sri-Rajasekhar Kothapalli
- Molecular Imaging Program at Stanford and Bio-X Program, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94305, USA.,Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.,Penn State Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Geoffrey A Sonn
- Department of Urology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Jung Woo Choe
- Department of Electrical Engineering, Stanford University, Palo Alto, CA 94305, USA
| | - Amin Nikoozadeh
- Department of Electrical Engineering, Stanford University, Palo Alto, CA 94305, USA
| | - Anshuman Bhuyan
- Department of Electrical Engineering, Stanford University, Palo Alto, CA 94305, USA
| | - Kwan Kyu Park
- Department of Electrical Engineering, Stanford University, Palo Alto, CA 94305, USA
| | - Paul Cristman
- Department of Electrical Engineering, Stanford University, Palo Alto, CA 94305, USA
| | - Richard Fan
- Department of Urology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Azadeh Moini
- Department of Electrical Engineering, Stanford University, Palo Alto, CA 94305, USA
| | - Byung Chul Lee
- Department of Electrical Engineering, Stanford University, Palo Alto, CA 94305, USA
| | - Jonathan Wu
- Department of Urology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Thomas E Carver
- Edward L. Ginzton Laboratory, Center for Nanoscale Science and Engineering, Stanford University, Palo Alto, CA 94305, USA
| | - Dharati Trivedi
- Department of Urology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Lillian Shiiba
- Department of Urology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Idan Steinberg
- Molecular Imaging Program at Stanford and Bio-X Program, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - David M Huland
- Molecular Imaging Program at Stanford and Bio-X Program, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Morten F Rasmussen
- Department of Electrical Engineering, Stanford University, Palo Alto, CA 94305, USA
| | - Joseph C Liao
- Department of Urology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Pierre T Khuri-Yakub
- Department of Electrical Engineering, Stanford University, Palo Alto, CA 94305, USA
| | - Sanjiv S Gambhir
- Molecular Imaging Program at Stanford and Bio-X Program, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94305, USA. .,Department of Bioengineering and Department of Materials Science & Engineering, Stanford University School of Medicine, Palo Alto, CA 94305, USA
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15
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Winther MD, Kristensen G, Stroomberg HV, Berg KD, Toft BG, Brooks JD, Brasso K, Røder MA. AZGP1 Protein Expression in Hormone-Naïve Advanced Prostate Cancer Treated with Primary Androgen Deprivation Therapy. Diagnostics (Basel) 2020; 10:diagnostics10080520. [PMID: 32726925 PMCID: PMC7460336 DOI: 10.3390/diagnostics10080520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/14/2020] [Accepted: 07/23/2020] [Indexed: 12/14/2022] Open
Abstract
Biomarkers for predicting the risk of castration-resistant prostate cancer (CRPC) in men treated with primary androgen deprivation therapy (ADT) are lacking. We investigated whether Zinc-alpha 2 glycoprotein (AZGP1) expression in the diagnostic biopsies of men with hormone-naïve prostate cancer (PCa) undergoing primary ADT was predictive of the development of CRPC and PCa-specific mortality. The study included 191 patients who commenced ADT from 2000 to 2011. The AZGP1 expression was evaluated using immunohistochemistry and scored as high or low expression. The risks of CRPC and PCa-specific mortality were analyzed using stratified cumulative incidences and a cause-specific COX regression analysis for competing risk assessment. The median follow-up time was 9.8 (IQR: 6.1–12.7) years. In total, 94 and 97 patients presented with low and high AZGP1 expression, respectively. A low AZGP1 expression was found to be associated with a shorter time to CRPC when compared to patients with a high AZGP1 expression (HR: 1.5; 95% CI: 1.0–2.1; p = 0.03). However, the multivariable analysis demonstrated no added benefit by adding the AZGP1 expression to prediction models for CRPC. No differences for PCa-specific mortality between the AZGP1 groups were observed. In conclusion, a low AZGP1 expression was associated with a shorter time to CRPC for PCa patients treated with first-line ADT but did not add any predictive information besides well-established clinicopathological variables.
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Affiliation(s)
- Mads Dochedahl Winther
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark; (M.D.W.); (H.V.S.); (K.D.B.); (K.B.); (M.A.R.)
| | - Gitte Kristensen
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark; (M.D.W.); (H.V.S.); (K.D.B.); (K.B.); (M.A.R.)
- Correspondence: ; Tel.: +45-2243-3688
| | - Hein Vincent Stroomberg
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark; (M.D.W.); (H.V.S.); (K.D.B.); (K.B.); (M.A.R.)
| | - Kasper Drimer Berg
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark; (M.D.W.); (H.V.S.); (K.D.B.); (K.B.); (M.A.R.)
| | - Birgitte Grønkær Toft
- Department of Pathology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - James D. Brooks
- Department of Urology, Stanford University, Stanford, CA 94305, USA;
| | - Klaus Brasso
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark; (M.D.W.); (H.V.S.); (K.D.B.); (K.B.); (M.A.R.)
| | - Martin Andreas Røder
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark; (M.D.W.); (H.V.S.); (K.D.B.); (K.B.); (M.A.R.)
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16
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Kolenčík D, Shishido SN, Pitule P, Mason J, Hicks J, Kuhn P. Liquid Biopsy in Colorectal Carcinoma: Clinical Applications and Challenges. Cancers (Basel) 2020; 12:E1376. [PMID: 32471160 PMCID: PMC7352156 DOI: 10.3390/cancers12061376] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/16/2020] [Accepted: 05/25/2020] [Indexed: 12/24/2022] Open
Abstract
Colorectal carcinoma (CRC) is characterized by wide intratumor heterogeneity with general genomic instability and there is a need for improved diagnostic, prognostic, and therapeutic tools. The liquid biopsy provides a noninvasive route of sample collection for analysis of circulating tumor cells (CTCs) and genomic material, including cell-free DNA (cfDNA), as a complementary biopsy to the solid tumor tissue. The solid biopsy is critical for molecular characterization and diagnosis at the time of collection. The liquid biopsy has the advantage of longitudinal molecular characterization of the disease, which is crucial for precision medicine and patient-oriented treatment. In this review, we provide an overview of CRC and the different methodologies for the detection of CTCs and cfDNA, followed by a discussion on the potential clinical utility of the liquid biopsy in CRC patient care, and lastly, current challenges in the field.
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Affiliation(s)
- Drahomír Kolenčík
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (P.P.)
| | - Stephanie N. Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (J.M.); (J.H.)
| | - Pavel Pitule
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (P.P.)
| | - Jeremy Mason
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (J.M.); (J.H.)
- USC Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (J.M.); (J.H.)
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (J.M.); (J.H.)
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17
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Prospects for Comprehensive Analyses of Circulating Tumor Cells in Tumor Biology. Cancers (Basel) 2020; 12:cancers12051135. [PMID: 32369927 PMCID: PMC7281475 DOI: 10.3390/cancers12051135] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 12/24/2022] Open
Abstract
The comprehensive analysis of biological and clinical aspects of circulating tumor cells (CTCs) has attracted interest as a means of enabling non-invasive, real-time monitoring of cancer patients and enhancing our fundamental understanding of tumor metastasis. However, CTC populations are extremely small when compared to other cell populations in the blood, limiting our comprehension of CTC biology and their clinical utility. Recently developed proteomic and genomic techniques that require only a small amount of sample have attracted much interest and expanded the potential utility of CTCs. Cancer heterogeneity, including specific mutations, greatly impacts disease diagnosis and the choice of available therapeutic strategies. The CTC population consists primarily of cancer stem cells, and CTC subpopulations are thought to undergo epithelial-mesenchymal transition during dissemination. To better characterize tumor cell populations, we demonstrated that changes in genomic profiles identified via next-generation sequencing of liquid biopsy samples could be expanded upon to increase sensitivity without decreasing specificity by using a combination of assays with CTCs and circulating tumor DNA. To enhance our understanding of CTC biology, we developed a metabolome analysis method applicable to single CTCs. Here, we review-omics studies related to CTC analysis and discuss various clinical and biological issues related to CTCs.
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18
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Morrison GJ, Cunha AT, Jojo N, Xu Y, Xu Y, Kwok E, Robinson P, Dorff T, Quinn D, Carpten J, Manojlovic Z, Goldkorn A. Cancer transcriptomic profiling from rapidly enriched circulating tumor cells. Int J Cancer 2020; 146:2845-2854. [PMID: 32037533 DOI: 10.1002/ijc.32915] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 12/26/2022]
Abstract
Transcriptomic profiling of metastatic cancer can illuminate mechanisms of progression and lead to new therapies, but standard biopsy is invasive and reflects only a single metastatic site. In contrast, circulating tumor cell (CTC) profiling is noninvasive and repeatable, reflecting the dynamic and systemic nature of advanced disease. To date, transcriptomic profiling of CTCs has not delivered on its full potential, because white blood cells (WBCs) vastly outnumber CTCs. Current profiling strategies either lack cancer sensitivity and specificity or require specialized CTC capture protocols that are not readily scalable to large patient cohorts. Here, we describe a new strategy for rapid CTC enrichment and transcriptomic profiling using commercially available WBC depletion, microfluidic enrichment and RNA sequencing. When applied to blood samples from patients with advanced prostate cancer (PC), transcriptomes from enriched samples cluster with cancer positive controls and previously undetectable prostate-specific transcripts become readily measurable. Gene set enrichment analysis reveals multiple significantly enriched signaling pathways associated with PC, as well as novel pathways that merit further study. This accessible and scalable approach yields cancer-specific transcriptomic data and can be applied repeatedly and noninvasively in large cancer patient cohorts to discover new therapeutic targets in advanced disease.
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Affiliation(s)
- Gareth J Morrison
- Department of Medicine, University of Southern California (USC), Keck School of Medicine and Norris Comprehensive Cancer Center (NCCC), California, Los Angeles
| | - Alexander T Cunha
- Department of Medicine, University of Southern California (USC), Keck School of Medicine and Norris Comprehensive Cancer Center (NCCC), California, Los Angeles
| | - Nita Jojo
- Department of Medicine, University of Southern California (USC), Keck School of Medicine and Norris Comprehensive Cancer Center (NCCC), California, Los Angeles
| | - Yucheng Xu
- Department of Medicine, University of Southern California (USC), Keck School of Medicine and Norris Comprehensive Cancer Center (NCCC), California, Los Angeles
| | - Yili Xu
- Department of Translational Genomics, USC Keck School of Medicine and NCCC, California, Los Angeles
| | - Eric Kwok
- Department of Translational Genomics, USC Keck School of Medicine and NCCC, California, Los Angeles
| | - Peggy Robinson
- Angle PLC, Surrey, United Kingdom
- Caza Health LLC, Earlysville, Virginia
| | - Tanya Dorff
- Department of Medicine, University of Southern California (USC), Keck School of Medicine and Norris Comprehensive Cancer Center (NCCC), California, Los Angeles
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - David Quinn
- Department of Medicine, University of Southern California (USC), Keck School of Medicine and Norris Comprehensive Cancer Center (NCCC), California, Los Angeles
| | - John Carpten
- Department of Translational Genomics, USC Keck School of Medicine and NCCC, California, Los Angeles
| | - Zarko Manojlovic
- Department of Translational Genomics, USC Keck School of Medicine and NCCC, California, Los Angeles
| | - Amir Goldkorn
- Department of Medicine, University of Southern California (USC), Keck School of Medicine and Norris Comprehensive Cancer Center (NCCC), California, Los Angeles
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Jiménez-Zenteno AK, Cerf A. Liquid Biopsy Based on Circulating Cancer-Associated Cells: Bridging the Gap from an Emerging Concept to a Mainstream Tool in Precision Medicine. ACTA ACUST UNITED AC 2019; 4:e1900164. [PMID: 32293131 DOI: 10.1002/adbi.201900164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/15/2019] [Indexed: 01/01/2023]
Abstract
The concept of liquid biopsy and the isolation and analysis of circulating biomarkers from blood samples is proposed as a surrogate to solid biopsies and can have the potential to revolutionize the management of patients with cancer. The relevance of circulating tumor cells (CTCs) and the importance of the information they carry is acknowledged by the medical community. But what are the barriers to clinical adoption? This review draws a panorama of the biological implications of CTCs, their physical and biochemical properties, and the current technological bottlenecks for their analysis in relation with the medical needs. Keys and considerations to bridge the technological and clinical gaps that still need to be overcome to be able to introduce CTCs in clinical routine are finally synthesized.
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Affiliation(s)
| | - Aline Cerf
- Université de Toulouse, CNRS, 7 Avenue du Colonel Roche, 31400, Toulouse, France
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20
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Abstract
As an alternative target to surgically resected tissue specimens, liquid biopsy has gained much attention over the past decade. Of the various circulating biomarkers, circulating tumor cells (CTCs) have particularly opened new windows into the metastatic cascade, with their functional, biochemical, and biophysical properties. Given the extreme rarity of intact CTCs and the associated technical challenges, however, analyses have been limited to bulk-cell strategies, missing out on clinically significant sources of information from cellular heterogeneity. With recent technological developments, it is now possible to probe genetic material of CTCs at the single-cell resolution to study spatial and temporal dynamics in circulation. Here, we discuss recent transcriptomic profiling efforts that enabled single-cell characterization of patient-derived CTCs spanning diverse cancer types. We further highlight how expression data of these putative biomarkers have advanced our understanding of metastatic spectrum and provided a basis for the development of CTC-based liquid biopsies to track, monitor, and predict the efficacy of therapy and any emergent resistance.
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21
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Vu TN, Wills QF, Kalari KR, Niu N, Wang L, Pawitan Y, Rantalainen M. Isoform-level gene expression patterns in single-cell RNA-sequencing data. Bioinformatics 2019; 34:2392-2400. [PMID: 29490015 PMCID: PMC6041805 DOI: 10.1093/bioinformatics/bty100] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 02/23/2018] [Indexed: 12/22/2022] Open
Abstract
Motivation RNA sequencing of single cells enables characterization of transcriptional heterogeneity in seemingly homogeneous cell populations. Single-cell sequencing has been applied in a wide range of researches fields. However, few studies have focus on characterization of isoform-level expression patterns at the single-cell level. In this study, we propose and apply a novel method, ISOform-Patterns (ISOP), based on mixture modeling, to characterize the expression patterns of isoform pairs from the same gene in single-cell isoform-level expression data. Results We define six principal patterns of isoform expression relationships and describe a method for differential-pattern analysis. We demonstrate ISOP through analysis of single-cell RNA-sequencing data from a breast cancer cell line, with replication in three independent datasets. We assigned the pattern types to each of 16 562 isoform-pairs from 4929 genes. Among those, 26% of the discovered patterns were significant (P<0.05), while remaining patterns are possibly effects of transcriptional bursting, drop-out and stochastic biological heterogeneity. Furthermore, 32% of genes discovered through differential-pattern analysis were not detected by differential-expression analysis. Finally, the effects of drop-out events and expression levels of isoforms on ISOP's performances were investigated through simulated datasets. To conclude, ISOP provides a novel approach for characterization of isoform-level preference, commitment and heterogeneity in single-cell RNA-sequencing data. Availability and implementation The ISOP method has been implemented as a R package and is available at https://github.com/nghiavtr/ISOP under a GPL-3 license. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Trung Nghia Vu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Nifang Niu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mattias Rantalainen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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22
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Lu YT, Delijani K, Mecum A, Goldkorn A. Current status of liquid biopsies for the detection and management of prostate cancer. Cancer Manag Res 2019; 11:5271-5291. [PMID: 31239778 PMCID: PMC6559244 DOI: 10.2147/cmar.s170380] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/18/2019] [Indexed: 12/14/2022] Open
Abstract
In recent years, new therapeutic options have become available for prostate cancer (PC) patients, generating an urgent need for better biomarkers to guide the choice of therapy and monitor treatment response. Liquid biopsies, including circulating tumor cells (CTCs), circulating nucleic acids, and exosomes, have been developed as minimally invasive assays allowing oncologists to monitor PC patients with real-time cellular or molecular information. While CTC counts remain the most extensively validated prognostic biomarker to monitor treatment response, recent advances demonstrate that CTC morphology and androgen receptor characterization can provide additional information to guide the choice of treatment. Characterization of cell-free DNA (cfDNA) is another rapidly emerging field with novel technologies capable of monitoring the evolution of treatment relevant alterations such as those in DNA damage repair genes for poly (ADP-ribose) polymerase (PARP) inhibition. In addition, several new liquid biopsy fields are emerging, including the characterization of heterogeneity, CTC RNA sequencing, the culture and xenografting of CTCs, and the characterization of extracellular vesicles (EVs) and circulating microRNAs. This review describes the clinical utilization of liquid biopsies in the management of PC patients and emerging liquid biopsy technologies with the potential to advance personalized cancer therapy.
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Affiliation(s)
- Yi-Tsung Lu
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Kevin Delijani
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Andrew Mecum
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Amir Goldkorn
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
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23
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Abstract
Precision medicine is emerging as a cornerstone of future cancer care with the objective of providing targeted therapies based on the molecular phenotype of each individual patient. Traditional bulk-level molecular phenotyping of tumours leads to significant information loss, as the molecular profile represents an average phenotype over large numbers of cells, while cancer is a disease with inherent intra-tumour heterogeneity at the cellular level caused by several factors, including clonal evolution, tissue hierarchies, rare cells and dynamic cell states. Single-cell sequencing provides means to characterize heterogeneity in a large population of cells and opens up opportunity to determine key molecular properties that influence clinical outcomes, including prognosis and probability of treatment response. Single-cell sequencing methods are now reliable enough to be used in many research laboratories, and we are starting to see applications of these technologies for characterization of human primary cancer cells. In this review, we provide an overview of studies that have applied single-cell sequencing to characterize human cancers at the single-cell level, and we discuss some of the current challenges in the field.
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Affiliation(s)
- Mattias Rantalainen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels Vag 12A, Stockholm, Sweden
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24
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Abstract
Cell-free circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) can be found in the bloodstream of individuals with cancer and are increasingly being explored as biomarkers in various aspects of cancer management. The application of next-generation sequencing (NGS) technologies to ctDNA and CTC analysis are providing new opportunities to characterize the cancer genome from a simple blood test and can facilitate the ease with which tumor-specific genomic changes can be followed over time. The serial analysis of ctDNA and CTCs has enormous potential to provide insights into intratumor heterogeneity and clonal evolution during disease progression, and may ultimately allow noninvasive molecular disease monitoring to guide therapeutic decisions and improve patient outcomes.
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Affiliation(s)
- Sarah-Jane Dawson
- Divisions of Cancer Medicine and Research, Peter MacCallum Cancer Centre, Melbourne 3000, Australia; Centre for Cancer Research, University of Melbourne, Melbourne 3010, Australia
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25
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Cho H, Kim J, Song H, Sohn KY, Jeon M, Han KH. Microfluidic technologies for circulating tumor cell isolation. Analyst 2019; 143:2936-2970. [PMID: 29796523 DOI: 10.1039/c7an01979c] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Metastasis is the main cause of tumor-related death, and the dispersal of tumor cells through the circulatory system is a critical step in the metastatic process. Early detection and analysis of circulating tumor cells (CTCs) is therefore important for early diagnosis, prognosis, and effective treatment of cancer, enabling favorable clinical outcomes in cancer patients. Accurate and reliable methods for isolating and detecting CTCs are necessary to obtain this clinical information. Over the past two decades, microfluidic technologies have demonstrated great potential for isolating and detecting CTCs from blood. The present paper reviews current advanced microfluidic technologies for isolating CTCs based on various biological and physical principles, and discusses their fundamental advantages and drawbacks for subsequent cellular and molecular assays. Owing to significant genetic heterogeneity among CTCs, microfluidic technologies for isolating individual CTCs have recently been developed. We discuss these single-cell isolation methods, as well as approaches to overcoming the limitations of current microfluidic CTC isolation technologies. Finally, we provide an overview of future innovative microfluidic platforms.
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Affiliation(s)
- Hyungseok Cho
- Department of Nanoscience and Engineering, Center for Nano Manufacturing, Inje University, Gimhae 621-749, Republic of Korea.
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26
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Tellez-Gabriel M, Cochonneau D, Cadé M, Jubellin C, Heymann MF, Heymann D. Circulating Tumor Cell-Derived Pre-Clinical Models for Personalized Medicine. Cancers (Basel) 2018; 11:cancers11010019. [PMID: 30586936 PMCID: PMC6356998 DOI: 10.3390/cancers11010019] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 12/19/2022] Open
Abstract
The main cause of death from cancer is associated with the development of metastases, resulting from the inability of current therapies to cure patients at metastatic stages. Generating preclinical models to better characterize the evolution of the disease is thus of utmost importance, in order to implement effective new cancer biomarkers and therapies. Circulating Tumor Cells (CTCs) are good candidates for generating preclinical models, making it possible to follow up the spatial and temporal heterogeneity of tumor tissues. This method is a non-invasive liquid biopsy that can be obtained at any stage of the disease. It partially summarizes the molecular heterogeneity of the corresponding tumors at a given time. Here, we discuss the CTC-derived models that have been generated so far, from simplified 2D cultures to the most complex CTC-derived explants (CDX models). We highlight the challenges and strengths of these preclinical tools, as well as some of the recent studies published using these models.
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Affiliation(s)
- Marta Tellez-Gabriel
- RNA and Molecular Pathology Research Group, Department of Medical Biology, The Artic University of Norway, N-9037 Tromsø, Norway.
| | - Denis Cochonneau
- LabCT, Institut de Cancérologie de l'Ouest, CRCINA, Université d'Angers, 44805 Saint Herblain CEDEX, France.
| | - Marie Cadé
- INSERM, European Associated Laboratory "Sarcoma Research Unit", University of Nantes, 44035 Nantes, France.
| | - Camille Jubellin
- INSERM, European Associated Laboratory "Sarcoma Research Unit", University of Nantes, 44035 Nantes, France.
| | - Marie-Françoise Heymann
- LabCT, Institut de Cancérologie de l'Ouest, CRCINA, Université d'Angers, 44805 Saint Herblain CEDEX, France.
| | - Dominique Heymann
- LabCT, Institut de Cancérologie de l'Ouest, CRCINA, Université d'Angers, 44805 Saint Herblain CEDEX, France.
- INSERM, European Associated Laboratory "Sarcoma Research Unit", University of Nantes, 44035 Nantes, France.
- Department of Oncology & Metabolism, The Medical School, Beech Hill Road, Sheffield S10 2RX, UK.
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27
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Tinhofer I, Staudte S. Circulating tumor cells as biomarkers in head and neck cancer: recent advances and future outlook. Expert Rev Mol Diagn 2018; 18:897-906. [DOI: 10.1080/14737159.2018.1522251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Ingeborg Tinhofer
- Department of Radiooncology and Radiotherapy, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Research Center (DKFZ), Heidelberg, and German Cancer Consortium (DKTK) partner site Berlin, Berlin, Germany
| | - Stephanie Staudte
- Department of Radiooncology and Radiotherapy, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Research Center (DKFZ), Heidelberg, and German Cancer Consortium (DKTK) partner site Berlin, Berlin, Germany
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28
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D'Avola D, Villacorta-Martin C, Martins-Filho SN, Craig A, Labgaa I, von Felden J, Kimaada A, Bonaccorso A, Tabrizian P, Hartmann BM, Sebra R, Schwartz M, Villanueva A. High-density single cell mRNA sequencing to characterize circulating tumor cells in hepatocellular carcinoma. Sci Rep 2018; 8:11570. [PMID: 30068984 PMCID: PMC6070499 DOI: 10.1038/s41598-018-30047-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/23/2018] [Indexed: 12/15/2022] Open
Abstract
Patients with hepatocellular carcinoma (HCC) release tumor cells to the bloodstream, which can be detected using cell surface markers. Despite numerous reports suggest a direct correlation between the number of circulating tumor cells (CTCs) and poor clinical outcomes, few studies have provided a thorough molecular characterization of CTCs. Due to the limited access to tissue samples in patients at advanced stages of HCC, it is crucial to develop new technologies to identify HCC cancer drivers in routine clinical conditions. Here, we describe a method that sequentially combines image flow cytometry and high density single-cell mRNA sequencing to identify CTCs in HCC patients. Genome wide expression profiling of CTCs using this approach demonstrates CTC heterogeneity and helps detect known oncogenic drivers in HCC such as IGF2. This integrated approach provides a novel tool for biomarker development in HCC using liquid biopsy.
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Affiliation(s)
- Delia D'Avola
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- LiverUnit and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Clínica Universidad de Navarra, Pamplona, Spain
| | - Carlos Villacorta-Martin
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Sebastiao N Martins-Filho
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Amanda Craig
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Ismail Labgaa
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Visceral Surgery, Lausanne University Hospital CHUV, Lausanne, Switzerland
| | - Johann von Felden
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Allette Kimaada
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | | | - Parissa Tabrizian
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Boris M Hartmann
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Robert Sebra
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Sema4, a Mount Sinai Venture, Stamford, CT, USA
| | - Myron Schwartz
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Augusto Villanueva
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA.
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, USA.
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29
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Analyzing Circulating Tumor Cells One at a Time. Trends Cell Biol 2018; 28:764-775. [PMID: 29891227 DOI: 10.1016/j.tcb.2018.05.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/12/2018] [Accepted: 05/16/2018] [Indexed: 11/20/2022]
Abstract
Whole-genome sequencing has made a significant impact on cancer research, but traditional bulk methods fail to detect information from rare cells. Recently developed single-cell sequencing methods have provided new insights and unprecedented details about cancer progression and diversity. These advancements also enable the investigation of rare cells, such as circulating tumor cells (CTCs) derived from cancer patients. In this review, we outline various single-cell sequencing techniques that can elucidate the molecular properties of CTCs. In addition, we explain the drawbacks that need to be overcome for each method.
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30
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Abstract
PURPOSE OF REVIEW Metastatic prostate cancer is a lethal and highly heterogeneous malignancy, associated with a broad spectrum of potentially actionable molecular alterations. In the past decade, disease profiling has expanded to include not only traditional tumor tissue, but also liquid biopsies of cells and genetic material circulating in the blood. These liquid biopsies offer a minimally invasive, repeatable source of tumor material for longitudinal disease profiling but also raise new technical and biological challenges. Here we will summarize recent advances in liquid biopsy strategies and the role they have played in biomarker development and disease management. RECENT FINDINGS Technologies for analysis of circulating tumor cells (CTCs) continue to evolve rapidly, and the latest high content scanning platforms have underscored the phenotypic heterogeneity of CTC populations. Among liquid biopsies, CTC enumeration remains the most extensively validated prognostic marker to date, but other clinically relevant phenotypes like androgen receptor (AR) localization or presence of AR-V7 splice variant are important new predictors of therapy response. Serial genomic profiling of CTCs or circulating tumor DNA (ctDNA) is helping to define primary and acquired resistance mechanisms and helping to guide patient selection for targeted therapies such as poly(adenosine diphosphate [ADP] ribose) polymerase (PARP) inhibition. The era of liquid biopsy-based biomarkers has arrived, driven by powerful new enrichment and analysis techniques. As new blood-based markers are identified, their biological significance as disease drivers must be elucidated to advance new therapeutic strategies, and their clinical impact must be translated through assay standardization, followed by analytical and clinical validation. These efforts, already ongoing on multiple fronts, constitute the critical steps toward more effective precision management of advanced prostate cancer.
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Affiliation(s)
- Gareth J Morrison
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Amir Goldkorn
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
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31
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Sharma S, Zhuang R, Long M, Pavlovic M, Kang Y, Ilyas A, Asghar W. Circulating tumor cell isolation, culture, and downstream molecular analysis. Biotechnol Adv 2018; 36:1063-1078. [PMID: 29559380 DOI: 10.1016/j.biotechadv.2018.03.007] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 12/12/2022]
Abstract
Circulating tumor cells (CTCs) are a major contributor of cancer metastases and hold a promising prognostic significance in cancer detection. Performing functional and molecular characterization of CTCs provides an in-depth knowledge about this lethal disease. Researchers are making efforts to design devices and develop assays for enumeration of CTCs with a high capture and detection efficiency from whole blood of cancer patients. The existing and on-going research on CTC isolation methods has revealed cell characteristics which are helpful in cancer monitoring and designing of targeted cancer treatments. In this review paper, a brief summary of existing CTC isolation methods is presented. We also discuss methods of detaching CTC from functionalized surfaces (functional assays/devices) and their further use for ex-vivo culturing that aid in studies regarding molecular properties that encourage metastatic seeding. In the clinical applications section, we discuss a number of cases that CTCs can play a key role for monitoring metastases, drug treatment response, and heterogeneity profiling regarding biomarkers and gene expression studies that bring treatment design further towards personalized medicine.
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Affiliation(s)
- Sandhya Sharma
- Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA; Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
| | - Rachel Zhuang
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
| | - Marisa Long
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
| | - Mirjana Pavlovic
- Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Yunqing Kang
- Department of Ocean & Mechanical Engineering, College of Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA; Department of Biomedical Science, College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Azhar Ilyas
- Department of Electrical & Computer Engineering, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Waseem Asghar
- Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA; Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA; Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA.
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32
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Magbanua MJM, Rugo HS, Wolf DM, Hauranieh L, Roy R, Pendyala P, Sosa EV, Scott JH, Lee JS, Pitcher B, Hyslop T, Barry WT, Isakoff SJ, Dickler M, Van't Veer L, Park JW. Expanded Genomic Profiling of Circulating Tumor Cells in Metastatic Breast Cancer Patients to Assess Biomarker Status and Biology Over Time (CALGB 40502 and CALGB 40503, Alliance). Clin Cancer Res 2018; 24:1486-1499. [PMID: 29311117 PMCID: PMC5856614 DOI: 10.1158/1078-0432.ccr-17-2312] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/18/2017] [Accepted: 01/02/2018] [Indexed: 11/16/2022]
Abstract
Purpose: We profiled circulating tumor cells (CTCs) to study the biology of blood-borne metastasis and to monitor biomarker status in metastatic breast cancer (MBC).Methods: CTCs were isolated from 105 patients with MBC using EPCAM-based immunomagnetic enrichment and fluorescence-activated cells sorting (IE/FACS), 28 of whom had serial CTC analysis (74 samples, 2-5 time points). CTCs were subjected to microfluidic-based multiplex QPCR array of 64 cancer-related genes (n = 151) and genome-wide copy-number analysis by array comparative genomic hybridization (aCGH; n = 49).Results: Combined transcriptional and genomic profiling showed that CTCs were 26% ESR1-ERBB2-, 48% ESR1+ERBB2-, and 27% ERBB2+ Serial testing showed that ERBB2 status was more stable over time compared with ESR1 and proliferation (MKI67) status. While cell-to-cell heterogeneity was observed at the single-cell level, with increasingly stable expression in larger pools, patient-specific CTC expression "fingerprints" were also observed. CTC copy-number profiles clustered into three groups based on the extent of genomic aberrations and the presence of large chromosomal imbalances. Comparative analysis showed discordance in ESR1/ER (27%) and ERBB2/HER2 (23%) status between CTCs and matched primary tumors. CTCs in 65% of the patients were considered to have low proliferation potential. Patients who harbored CTCs with high proliferation (MKI67) status had significantly reduced progression-free survival (P = 0.0011) and overall survival (P = 0.0095) compared with patients with low proliferative CTCs.Conclusions: We demonstrate an approach for complete isolation of EPCAM-positive CTCs and downstream comprehensive transcriptional/genomic characterization to examine the biology and assess breast cancer biomarkers in these cells over time. Clin Cancer Res; 24(6); 1486-99. ©2018 AACR.
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Affiliation(s)
- Mark Jesus M Magbanua
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California.
| | - Hope S Rugo
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California
| | - Denise M Wolf
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | - Louai Hauranieh
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California
| | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center and Computational Biology and Informatics, University of California at San Francisco, San Francisco, California
| | - Praveen Pendyala
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California
| | - Eduardo V Sosa
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California
| | - Janet H Scott
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California
| | - Jin Sun Lee
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California
| | - Brandelyn Pitcher
- Alliance Statistics and Data Center, Duke University, Durham, North Carolina
| | - Terry Hyslop
- Alliance Statistics and Data Center, Duke University, Durham, North Carolina
| | - William T Barry
- Alliance Statistics and Data Center, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Steven J Isakoff
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Maura Dickler
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura Van't Veer
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | - John W Park
- Division of Hematology/Oncology, University of California at San Francisco, San Francisco, California.
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33
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Zaporozhchenko IA, Ponomaryova AA, Rykova EY, Laktionov PP. The potential of circulating cell-free RNA as a cancer biomarker: challenges and opportunities. Expert Rev Mol Diagn 2018; 18:133-145. [DOI: 10.1080/14737159.2018.1425143] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ivan A. Zaporozhchenko
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia
- Laboratory of Biomedical Technologies, Centre of New Surgical Technologies, E.N. Meshalkin Siberian Federal Biomedical Research Center, Novosibirsk, Russia
| | - Anastasia A. Ponomaryova
- Laboratory of Immunology, Tomsk Cancer Research Institute of SB RAMS, Tomsk, Russia
- Department of Applied Physics, National Research Tomsk Polytechnic University, Tomsk, Russia
| | - Elena Yu Rykova
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia
- Laboratory of Biomedical Technologies, Centre of New Surgical Technologies, E.N. Meshalkin Siberian Federal Biomedical Research Center, Novosibirsk, Russia
| | - Pavel P. Laktionov
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia
- Laboratory of Biomedical Technologies, Centre of New Surgical Technologies, E.N. Meshalkin Siberian Federal Biomedical Research Center, Novosibirsk, Russia
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34
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Chalfin HJ, Glavaris SA, Malihi PD, Sperger JM, Gorin MA, Lu C, Goodwin CR, Chen Y, Caruso EA, Dumpit R, Kuhn P, Lang JM, Nelson PS, Luo J, Pienta KJ. Prostate Cancer Disseminated Tumor Cells are Rarely Detected in the Bone Marrow of Patients with Localized Disease Undergoing Radical Prostatectomy across Multiple Rare Cell Detection Platforms. J Urol 2018; 199:1494-1501. [PMID: 29339080 DOI: 10.1016/j.juro.2018.01.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2018] [Indexed: 01/04/2023]
Abstract
PURPOSE Prostate circulating tumor cells escape into peripheral blood and enter bone marrow as disseminated tumor cells, representing an early step before conventionally detectable metastasis. It is unclear how frequently this occurs in localized disease and existing detection methods rely on epithelial markers with low specificity and sensitivity. We used multiple methodologies of disseminated tumor cell detection in bone marrow harvested at radical prostatectomy. MATERIALS AND METHODS Bone marrow was harvested from 208 clinically localized cases, 16 controls and 5 metastatic cases with peripheral blood obtained from 37 metastatic cases. Samples were evaluated at 4 centers with 4 distinct platforms using antibody enrichment with the AdnaTest (Qiagen®) or VERSA (versatile exclusion based rare sample analysis), or whole sample interrogation with the RareCyte platform (Seattle, Washington) or HD-SCA (high definition single cell assay) using traditional epithelial markers and prostate specific markers. We investigated the sensitivity and specificity of these markers by evaluating expression levels in control and metastatic cases. RESULTS EpCAM, NKX3.1 and AR were nonspecifically expressed in controls and in most samples using AdnaTest with no relation to perioperative variables. Only 1 patient with localized disease showed positive results for the prostate specific marker PSA. With the VERSA platform no localized case demonstrated disseminated tumor cells. With the RareCyte and HD-SCA platforms only a single patient had 1 disseminated tumor cell. CONCLUSIONS Evaluation across multiple platforms revealed that epithelial markers are nonspecific in bone marrow and, thus, not suitable for disseminated tumor cell detection. Using prostate specific markers disseminated tumor cells were typically not detected in patients with localized prostate cancer.
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Affiliation(s)
- Heather J Chalfin
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Stephanie A Glavaris
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Paymaneh D Malihi
- Bridge Institute, University of Southern California, Los Angeles, California
| | - Jamie M Sperger
- Department of Medicine, University of Wisconsin Carbone Cancer Center, Madison, Wisconsin
| | - Michael A Gorin
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Changxue Lu
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - C Rory Goodwin
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yan Chen
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Emily A Caruso
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ruth Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Peter Kuhn
- Bridge Institute, University of Southern California, Los Angeles, California
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin Carbone Cancer Center, Madison, Wisconsin
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jun Luo
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Pal SK, Patel J, He M, Foulk B, Kraft K, Smirnov DA, Twardowski P, Kortylewski M, Bhargava V, Jones JO. Identification of mechanisms of resistance to treatment with abiraterone acetate or enzalutamide in patients with castration-resistant prostate cancer (CRPC). Cancer 2017; 124:1216-1224. [PMID: 29266182 DOI: 10.1002/cncr.31161] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/16/2017] [Accepted: 10/26/2017] [Indexed: 01/25/2023]
Abstract
BACKGROUND Two androgen receptor (AR)-targeted therapies, enzalutamide and abiraterone acetate plus prednisone (abiraterone), have been approved for the treatment of metastatic castration-resistant prostate cancer (CRPC). Many patients respond to these agents, but both de novo and acquired resistance are common. The authors characterized resistant phenotypes that emerge after treatment with abiraterone or enzalutamide. METHODS Patients who received abiraterone or enzalutamide in the course of routine clinical care were consented for serial blood collection. A proprietary system (CellSearch) was used to enumerate and enrich circulating tumor cells (CTCs). RNA-sequencing (RNA-seq) was performed on pools of up to 10 epithelial cell adhesion molecule (EpCAM)-positive/CD45-negative CTCs. The impact of gene expression changes observed in CTCs between patients who responded or were resistant to abiraterone/enzalutamide therapies was further explored in a model cell line system. RESULTS RNA-seq data from CTCs identified mutations commonly associated with CRPC as well as novel mutations, including several in the ligand-binding domain of AR that could facilitate escape from AR-targeted agents. Ingenuity pathway analysis of differentially regulated genes identified the transforming growth factor β (TGFβ) and cyclin D1 (CCND1) signaling pathways as significantly upregulated in drug-resistant CTCs. Transfection experiments using enzalutamide-sensitive and enzalutamide-resistant LNCaP cells confirmed the involvement of SMAD family member 3, a key mediator of the TGFβ pathway, and of CCND1 in resistance to enzalutamide treatment. CONCLUSIONS The current results indicate that RNA-seq of CTCs representing abiraterone and enzalutamide sensitive and resistant states can identify potential mechanisms of resistance. Therapies targeting the downstream signaling mediated by SMAD family member 3 (SMAD3) and CCND1, such as cyclin-dependent kinase 4/cyclin-dependent kinase 6 inhibitors, could provide new therapeutic options for the treatment of antiandrogen-resistant disease. Cancer 2018;124:1216-24. © 2017 American Cancer Society.
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Affiliation(s)
- Sumanta Kumar Pal
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | | | - Miaoling He
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Brad Foulk
- Janssen Pharmaceuticals, Spring House, Pennsylvania
| | | | | | - Przemyslaw Twardowski
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Marcin Kortylewski
- Department of Cancer Immunotherapeutics and Tumor Immunology, City of Hope Comprehensive Cancer Center, Duarte, California
| | | | - Jeremy O Jones
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
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36
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Whole blood stabilization for the microfluidic isolation and molecular characterization of circulating tumor cells. Nat Commun 2017; 8:1733. [PMID: 29170510 PMCID: PMC5700979 DOI: 10.1038/s41467-017-01705-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 10/09/2017] [Indexed: 01/13/2023] Open
Abstract
Precise rare-cell technologies require the blood to be processed immediately or be stabilized with fixatives. Such restrictions limit the translation of circulating tumor cell (CTC)-based liquid biopsy assays that provide accurate molecular data in guiding clinical decisions. Here we describe a method to preserve whole blood in its minimally altered state by combining hypothermic preservation with targeted strategies that counter cooling-induced platelet activation. Using this method, whole blood preserved for up to 72 h can be readily processed for microfluidic sorting without compromising CTC yield and viability. The tumor cells retain high-quality intact RNA suitable for single-cell RT-qPCR as well as RNA-Seq, enabling the reliable detection of cancer-specific transcripts including the androgen-receptor splice variant 7 in a cohort of prostate cancer patients with an overall concordance of 92% between fresh and preserved blood. This work will serve as a springboard for the dissemination of diverse blood-based diagnostics. The current FDA-approved whole blood stabilization method for circulating tumor cell (CTC) isolation suffers from RNA degradation. Here the authors combine hypothermic preservation and antiplatelet strategies to stabilize whole blood up to 72 h without compromising CTC yield and RNA integrity.
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37
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Progress and challenges of sequencing and analyzing circulating tumor cells. Cell Biol Toxicol 2017; 34:405-415. [PMID: 29168077 PMCID: PMC6132989 DOI: 10.1007/s10565-017-9418-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 10/29/2017] [Indexed: 01/09/2023]
Abstract
Circulating tumor cells (CTCs) slough off primary tumor tissues and are swept away by the circulatory system. These CTCs can remain in circulation or colonize new sites, forming metastatic clones in distant organs. Recently, CTC analyses have been successfully used as effective clinical tools to monitor tumor progression and prognosis. With advances in next-generation sequencing (NGS) and single-cell sequencing (SCS) technologies, scientists can obtain the complete genome of a CTC and compare it with corresponding primary and metastatic tumors. CTC sequencing has been successfully applied to monitor genomic variations in metastatic and recurrent tumors, infer tumor evolution during treatment, and examine gene expression as well as the mechanism of the epithelial-mesenchymal transition. However, compared with cancer biopsy sequencing and circulating tumor DNA sequencing, the sequencing of CTC genomes and transcriptomes is more complex and technically difficult. Challenges include enriching pure tumor cells from a background of white blood cells, isolating and collecting cells without damaging or losing DNA and RNA, obtaining unbiased and even whole-genome and transcriptome amplification material, and accurately analyzing CTC sequencing data. Here, we review and summarize recent studies using NGS on CTCs. We mainly focus on CTC genome and transcriptome sequencing and the biological and potential clinical applications of these methodologies. Finally, we discuss challenges and future perspectives of CTC sequencing.
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38
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Galletti G, Worroll D, Nanus DM, Giannakakou P. Using circulating tumor cells to advance precision medicine in prostate cancer. JOURNAL OF CANCER METASTASIS AND TREATMENT 2017; 3:190-205. [PMID: 29707651 PMCID: PMC5913755 DOI: 10.20517/2394-4722.2017.45] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The field of CTC enrichment has seen many emerging technologies in recent years, which have resulted in the identification and monitoring of clinically relevant, CTC-based biomarkers that can be analyzed routinely without invasive procedures. Several molecular platforms have been used to investigate the molecular profile of the disease, from high throughput gene expression analyses down to single cell biological dissection. The established presence of CTC heterogeneity nevertheless constitutes a challenge for cell isolation as the several subpopulations can potentially display different molecular characteristics; in this scenario, careful consideration must be given to the isolation approach, whereas methods that discriminate against certain subpopulations may result in the exclusion of CTCs that carry biological relevance. In the context of prostate cancer (PC), CTC molecular interrogation can enable longitudinal monitoring of key biological features during treatment with substantial clinical impact, as several biomarkers could predict tumor response to AR signaling inhibitors (abiraterone, enzalutamide) or standard chemotherapy (taxanes). Thus, CTCs represent a valuable opportunity to personalize medicine in current clinical practice.
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Affiliation(s)
- Giuseppe Galletti
- Department of Medicine, Hematology/Oncology, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Daniel Worroll
- Department of Medicine, Hematology/Oncology, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - David M Nanus
- Department of Medicine, Hematology/Oncology, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Paraskevi Giannakakou
- Department of Medicine, Hematology/Oncology, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY
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Fachin F, Spuhler P, Martel-Foley JM, Edd JF, Barber TA, Walsh J, Karabacak M, Pai V, Yu M, Smith K, Hwang H, Yang J, Shah S, Yarmush R, Sequist LV, Stott SL, Maheswaran S, Haber DA, Kapur R, Toner M. Monolithic Chip for High-throughput Blood Cell Depletion to Sort Rare Circulating Tumor Cells. Sci Rep 2017; 7:10936. [PMID: 28883519 PMCID: PMC5589885 DOI: 10.1038/s41598-017-11119-x] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 08/18/2017] [Indexed: 01/17/2023] Open
Abstract
Circulating tumor cells (CTCs) are a treasure trove of information regarding the location, type and stage of cancer and are being pursued as both a diagnostic target and a means of guiding personalized treatment. Most isolation technologies utilize properties of the CTCs themselves such as surface antigens (e.g., epithelial cell adhesion molecule or EpCAM) or size to separate them from blood cell populations. We present an automated monolithic chip with 128 multiplexed deterministic lateral displacement devices containing ~1.5 million microfabricated features (12 µm-50 µm) used to first deplete red blood cells and platelets. The outputs from these devices are serially integrated with an inertial focusing system to line up all nucleated cells for multi-stage magnetophoresis to remove magnetically-labeled white blood cells. The monolithic CTC-iChip enables debulking of blood samples at 15-20 million cells per second while yielding an output of highly purified CTCs. We quantified the size and EpCAM expression of over 2,500 CTCs from 38 patient samples obtained from breast, prostate, lung cancers, and melanoma. The results show significant heterogeneity between and within single patients. Unbiased, rapid, and automated isolation of CTCs using monolithic CTC-iChip will enable the detailed measurement of their physicochemical and biological properties and their role in metastasis.
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Affiliation(s)
- Fabio Fachin
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Philipp Spuhler
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Joseph M Martel-Foley
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Jon F Edd
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Thomas A Barber
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - John Walsh
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Murat Karabacak
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Vincent Pai
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Melissa Yu
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Kyle Smith
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Henry Hwang
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Jennifer Yang
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Sahil Shah
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Ruby Yarmush
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Lecia V Sequist
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
| | - Shannon L Stott
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
| | - Shyamala Maheswaran
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
| | - Daniel A Haber
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
| | - Ravi Kapur
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Mehmet Toner
- BioMEMS Resource Center, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, USA.
- Shriners Hospitals for Children, Boston, Massachusetts, 02114, USA.
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40
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Thiele JA, Bethel K, Králíčková M, Kuhn P. Circulating Tumor Cells: Fluid Surrogates of Solid Tumors. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2017; 12:419-447. [PMID: 28135562 DOI: 10.1146/annurev-pathol-052016-100256] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Evaluation of circulating tumor cells (CTCs) has demonstrated clinical validity as a prognostic tool based on enumeration, but since the introduction of this tool to the clinic in 2004, further clinical utility and widespread adoption have been limited. However, immense efforts have been undertaken to further the understanding of the mechanisms behind the biology and kinetics of these rare cells, and progress continues toward better applicability in the clinic. This review describes recent advances within the field, with a particular focus on understanding the biological significance of CTCs, and summarizes emerging methods for identifying, isolating, and interrogating the cells that may provide technical advantages allowing for the discovery of more specific clinical applications. Included is an atlas of high-definition images of CTCs from various cancer types, including uncommon CTCs captured only by broadly inclusive nonenrichment techniques.
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Affiliation(s)
- J-A Thiele
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic
| | - K Bethel
- Scripps Clinic Medical Group, Scripps Clinic, La Jolla, California 92121
| | - M Králíčková
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University in Prague, 301 00 Pilsen, Czech Republic
| | - P Kuhn
- Bridge Institute, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California 90089; .,Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089
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41
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Jackson JM, Witek MA, Kamande JW, Soper SA. Materials and microfluidics: enabling the efficient isolation and analysis of circulating tumour cells. Chem Soc Rev 2017; 46:4245-4280. [PMID: 28632258 PMCID: PMC5576189 DOI: 10.1039/c7cs00016b] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a critical review of microfluidic technologies and material effects on the analyses of circulating tumour cells (CTCs) selected from the peripheral blood of cancer patients. CTCs are a minimally invasive source of clinical information that can be used to prognose patient outcome, monitor minimal residual disease, assess tumour resistance to therapeutic agents, and potentially screen individuals for the early diagnosis of cancer. The performance of CTC isolation technologies depends on microfluidic architectures, the underlying principles of isolation, and the choice of materials. We present a critical review of the fundamental principles used in these technologies and discuss their performance. We also give context to how CTC isolation technologies enable downstream analysis of selected CTCs in terms of detecting genetic mutations and gene expression that could be used to gain information that may affect patient outcome.
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42
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Cuevas-Diaz Duran R, Wei H, Wu JQ. Single-cell RNA-sequencing of the brain. Clin Transl Med 2017; 6:20. [PMID: 28597408 PMCID: PMC5465230 DOI: 10.1186/s40169-017-0150-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) is revolutionizing our understanding of the genomic, transcriptomic and epigenomic landscapes of cells within organs. The mammalian brain is composed of a complex network of millions to billions of diverse cells with either highly specialized functions or support functions. With scRNA-seq it is possible to comprehensively dissect the cellular heterogeneity of brain cells, and elucidate their specific functions and state. In this review, we describe the current experimental methods used for scRNA-seq. We also review bioinformatic tools and algorithms for data analyses and discuss critical challenges. Additionally, we summarized recent mouse brain scRNA-seq studies and systematically compared their main experimental approaches, computational tools implemented, and important findings. scRNA-seq has allowed researchers to identify diverse cell subpopulations within many brain regions, pinpointing gene signatures and novel cell markers, as well as addressing functional differences. Due to the complexity of the brain, a great deal of work remains to be accomplished. Defining specific brain cell types and functions is critical for understanding brain function as a whole in development, health, and diseases.
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Affiliation(s)
- Raquel Cuevas-Diaz Duran
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA
| | - Haichao Wei
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA. .,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA.
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43
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Zhu S, Qing T, Zheng Y, Jin L, Shi L. Advances in single-cell RNA sequencing and its applications in cancer research. Oncotarget 2017; 8:53763-53779. [PMID: 28881849 PMCID: PMC5581148 DOI: 10.18632/oncotarget.17893] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/24/2017] [Indexed: 12/13/2022] Open
Abstract
Unlike population-level approaches, single-cell RNA sequencing enables transcriptomic analysis of an individual cell. Through the combination of high-throughput sequencing and bioinformatic tools, single-cell RNA-seq can detect more than 10,000 transcripts in one cell to distinguish cell subsets and dynamic cellular changes. After several years’ development, single-cell RNA-seq can now achieve massively parallel, full-length mRNA sequencing as well as in situ sequencing and even has potential for multi-omic detection. One appealing area of single-cell RNA-seq is cancer research, and it is regarded as a promising way to enhance prognosis and provide more precise target therapy by identifying druggable subclones. Indeed, progresses have been made regarding solid tumor analysis to reveal intratumoral heterogeneity, correlations between signaling pathways, stemness, drug resistance, and tumor architecture shaping the microenvironment. Furthermore, through investigation into circulating tumor cells, many genes have been shown to promote a propensity toward stemness and the epithelial-mesenchymal transition, to enhance anchoring and adhesion, and to be involved in mechanisms of anoikis resistance and drug resistance. This review focuses on advances and progresses of single-cell RNA-seq with regard to the following aspects: 1. Methodologies of single-cell RNA-seq 2. Single-cell isolation techniques 3. Single-cell RNA-seq in solid tumor research 4. Single-cell RNA-seq in circulating tumor cell research 5. Perspectives
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Affiliation(s)
- Sibo Zhu
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Tao Qing
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Yuanting Zheng
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Li Jin
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Leming Shi
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200438, China
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44
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Wu T, Cheng B, Fu L. Clinical Applications of Circulating Tumor Cells in Pharmacotherapy: Challenges and Perspectives. Mol Pharmacol 2017; 92:232-239. [PMID: 28356334 DOI: 10.1124/mol.116.108142] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 03/22/2017] [Indexed: 12/11/2022] Open
Abstract
Screening for circulating tumor cells (CTCs) has been identified as one approach to ultrasensitive liquid biopsy in real-time monitoring of cancer patients. The detection of CTCs in peripheral blood from cancer patients is promising as a diagnostic tool; however, the application of CTCs in therapeutic treatment still faces serious challenges with respect to specificity and sensitivity. Here, we review the significant roles of CTCs in metastasis and the strengths and weaknesses of the currently available methods for CTC detection and characterization. Moreover, we discuss the clinical application of CTCs as markers for patient prognosis, and we specifically focus on the application of CTCs as indicators in cancer pharmacotherapy. Characterization of the detected CTCs will provide new biologic perspectives and clinical applications for the treatment of cancer patients with metastasis.
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Affiliation(s)
- Tong Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Esophageal Cancer Institute (T.W., L.F.); and Department of Oral Medicine, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China (T.W., B.C.)
| | - Bin Cheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Esophageal Cancer Institute (T.W., L.F.); and Department of Oral Medicine, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China (T.W., B.C.)
| | - Liwu Fu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Esophageal Cancer Institute (T.W., L.F.); and Department of Oral Medicine, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China (T.W., B.C.)
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45
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Yadavalli S, Jayaram S, Manda SS, Madugundu AK, Nayakanti DS, Tan TZ, Bhat R, Rangarajan A, Chatterjee A, Gowda H, Thiery JP, Kumar P. Data-Driven Discovery of Extravasation Pathway in Circulating Tumor Cells. Sci Rep 2017; 7:43710. [PMID: 28262832 PMCID: PMC5337960 DOI: 10.1038/srep43710] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/26/2017] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor cells (CTCs) play a crucial role in cancer dissemination and provide a promising source of blood-based markers. Understanding the spectrum of transcriptional profiles of CTCs and their corresponding regulatory mechanisms will allow for a more robust analysis of CTC phenotypes. The current challenge in CTC research is the acquisition of useful clinical information from the multitude of high-throughput studies. To gain a deeper understanding of CTC heterogeneity and identify genes, pathways and processes that are consistently affected across tumors, we mined the literature for gene expression profiles in CTCs. Through in silico analysis and the integration of CTC-specific genes, we found highly significant biological mechanisms and regulatory processes acting in CTCs across various cancers, with a particular enrichment of the leukocyte extravasation pathway. This pathway appears to play a pivotal role in the migration of CTCs to distant metastatic sites. We find that CTCs from multiple cancers express both epithelial and mesenchymal markers in varying amounts, which is suggestive of dynamic and hybrid states along the epithelial-mesenchymal transition (EMT) spectrum. Targeting the specific molecular nodes to monitor disease and therapeutic control of CTCs in real time will likely improve the clinical management of cancer progression and metastases.
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Affiliation(s)
- S. Yadavalli
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore, 560 066, India
| | - S. Jayaram
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore, 560 066, India
- Manipal University, Madhav Nagar, Manipal, 576104, India
| | - S. S. Manda
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore, 560 066, India
- Center for Bioinformatics, Pondicherry University, Puducherry 605 014, India
| | - A. K. Madugundu
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore, 560 066, India
- Center for Bioinformatics, Pondicherry University, Puducherry 605 014, India
| | - D. S. Nayakanti
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore, 560 066, India
| | - T. Z. Tan
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine NUS Yong Loo Lin School of Medicine, Singapore 117599, Singapore
| | - R. Bhat
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - A. Rangarajan
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - A. Chatterjee
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore, 560 066, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India
| | - H. Gowda
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore, 560 066, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India
| | - J. P. Thiery
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine NUS Yong Loo Lin School of Medicine, Singapore 117599, Singapore
- Comprehensive Cancer Center, Institut Gustave Roussy, 114 Rue Edouard Vaillant, 94805 Villejuif, France
- CNRS UMR 7057, Matter and Complex Systems, Université Paris Diderot, 10 rue Alice Domon et Léonie Duquet 75013 Paris, France
- Department of Biochemistry, National University of Singapore, Singapore 117597, Singapore
| | - P. Kumar
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore, 560 066, India
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46
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Chen J, Suo S, Tam PP, Han JDJ, Peng G, Jing N. Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq. Nat Protoc 2017; 12:566-580. [PMID: 28207000 DOI: 10.1038/nprot.2017.003] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Conventional gene expression studies analyze multiple cells simultaneously or single cells, for which the exact in vivo or in situ position is unknown. Although cellular heterogeneity can be discerned when analyzing single cells, any spatially defined attributes that underpin the heterogeneous nature of the cells cannot be identified. Here, we describe how to use Geo-seq, a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology. The combination of these two methods enables the elucidation of cellular heterogeneity and spatial variance simultaneously. The Geo-seq protocol allows the profiling of transcriptome information from only a small number cells and retains their native spatial information. This protocol has wide potential applications to address biological and pathological questions of cellular properties such as prospective cell fates, biological function and the gene regulatory network. Geo-seq has been applied to investigate the spatial transcriptome of mouse early embryo, mouse brain, and pathological liver and sperm tissues. The entire protocol from tissue collection and microdissection to sequencing requires ∼5 d, Data analysis takes another 1 or 2 weeks, depending on the amount of data and the speed of the processor.
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Affiliation(s)
- Jun Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Shengbao Suo
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Patrick Pl Tam
- Embryology Unit, Children's Medical Research Institute and School of MedicalSciences, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Jing-Dong J Han
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guangdun Peng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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47
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Neu KE, Tang Q, Wilson PC, Khan AA. Single-Cell Genomics: Approaches and Utility in Immunology. Trends Immunol 2017; 38:140-149. [PMID: 28094102 DOI: 10.1016/j.it.2016.12.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/03/2016] [Accepted: 12/05/2016] [Indexed: 12/27/2022]
Abstract
Single-cell genomics offers powerful tools for studying immune cells, which make it possible to observe rare and intermediate cell states that cannot be resolved at the population level. Advances in computer science and single-cell sequencing technology have created a data-driven revolution in immunology. The challenge for immunologists is to harness computing and turn an avalanche of quantitative data into meaningful discovery of immunological principles, predictive models, and strategies for therapeutics. Here, we review the current literature on computational analysis of single-cell RNA-sequencing data and discuss underlying assumptions, methods, and applications in immunology, and highlight important directions for future research.
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Affiliation(s)
- Karlynn E Neu
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Qingming Tang
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Patrick C Wilson
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Aly A Khan
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA.
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48
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Hwang WL, Hwang KL, Miyamoto DT. The promise of circulating tumor cells for precision cancer therapy. Biomark Med 2016; 10:1269-1285. [PMID: 27924634 PMCID: PMC5827810 DOI: 10.2217/bmm-2016-0192] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/27/2016] [Indexed: 12/20/2022] Open
Abstract
The rapidly growing array of therapeutic options in cancer requires informative biomarkers to guide the rational selection and precision application of appropriate therapies. Circulating biomarkers such as circulating tumor cells have immense potential as noninvasive, serial 'liquid biopsies' that may be more representative of the complete spectrum of a patient's individual malignancy than spatially and temporally restricted tumor biopsies. In this review, we discuss the current state-of-the-art in the isolation and molecular characterization of circulating tumor cells as well as their utility in a wide range of clinical applications such as prognostics, treatment monitoring and identification of novel therapeutic targets and resistance mechanisms to enable real-time adjustments in the clinical management of cancer.
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Affiliation(s)
- William L Hwang
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Katie L Hwang
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
- Medical Scientist Training Program, Harvard Medical School, Boston, MA 02115, USA
| | - David T Miyamoto
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
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49
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Gangavarapu KJ, Miller A, Huss WJ. Gene Expression in Single Cells Isolated from the CWR-R1 Prostate Cancer Cell Line and Human Prostate Tissue Based on the Side Population Phenotype. ACTA ACUST UNITED AC 2016; 5. [PMID: 27785389 PMCID: PMC5076885 DOI: 10.4172/2168-9431.1000150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Defining biological signals at the single cell level can identify cancer initiating driver mutations. Techniques to isolate single cells such as microfluidics sorting and magnetic capturing systems have limitations such as: high cost, labor intense, and the requirement of a large number of cells. Therefore, the goal of our current study is to identify a cost and labor effective, reliable, and reproducible technique that allows single cell isolation for analysis to promote regular laboratory use, including standard reverse transcription PCR (RT-PCR). In the current study, we utilized single prostate cells isolated from the CWR-R1 prostate cancer cell line and human prostate clinical specimens, based on the ATP binding cassette (ABC) transporter efflux of dye cycle violet (DCV), side population assay. Expression of four genes: ABCG2; Aldehyde dehydrogenase1A1 (ALDH1A1); androgen receptor (AR); and embryonic stem cell marker, Oct-4, were determined. Results from the current study in the CWR-R1 cell line showed ABCG2 and ALDH1A1 gene expression in 67% of single side population cells and in 17% or 100% of non-side population cells respectively. Studies using single cells isolated from clinical specimens showed that the Oct-4 gene is detected in only 22% of single side population cells and in 78% of single non-side population cells. Whereas, AR gene expression is in 100% single side population and non-side population cells isolated from the same human prostate clinical specimen. These studies show that performing RT-PCR on single cells isolated by FACS can be successfully conducted to determine gene expression in single cells from cell lines and enzymatically digested tissue. While these studies provide a simple yes/no expression readout, the more sensitive quantitative RT-PCR would be able to provide even more information if necessary.
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Affiliation(s)
- Kalyan J Gangavarapu
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY-14263, USA
| | - Austin Miller
- Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY-14263, USA
| | - Wendy J Huss
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY-14263, USA; Department of Urologic Oncology, Roswell Park Cancer Institute, Buffalo, NY-14263, USA
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50
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Fish RN, Bostick M, Lehman A, Farmer A. Transcriptome Analysis at the Single-Cell Level Using SMART Technology. ACTA ACUST UNITED AC 2016; 116:4.26.1-4.26.24. [PMID: 27723086 DOI: 10.1002/cpmb.23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA sequencing (RNA-seq) is a powerful method for analyzing cell state, with minimal bias, and has broad applications within the biological sciences. However, transcriptome analysis of seemingly homogenous cell populations may in fact overlook significant heterogeneity that can be uncovered at the single-cell level. The ultra-low amount of RNA contained in a single cell requires extraordinarily sensitive and reproducible transcriptome analysis methods. As next-generation sequencing (NGS) technologies mature, transcriptome profiling by RNA-seq is increasingly being used to decipher the molecular signature of individual cells. This unit describes an ultra-sensitive and reproducible protocol to generate cDNA and sequencing libraries directly from single cells or RNA inputs ranging from 10 pg to 10 ng. Important considerations for working with minute RNA inputs are given. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Rachel N Fish
- Takara Bio USA, Inc. (formerly Clontech Laboratories, Inc.), Mountain View, California
| | - Magnolia Bostick
- Takara Bio USA, Inc. (formerly Clontech Laboratories, Inc.), Mountain View, California
| | - Alisa Lehman
- Takara Bio USA, Inc. (formerly Clontech Laboratories, Inc.), Mountain View, California.,Current affiliation: 23andMe, Mountain View, California
| | - Andrew Farmer
- Takara Bio USA, Inc. (formerly Clontech Laboratories, Inc.), Mountain View, California
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