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Shin S, Yun HG, Chung H, Cho H, Choi S. Automation of 3D digital rolling circle amplification using a 3D-printed liquid handler. Biosens Bioelectron 2024; 261:116503. [PMID: 38905856 DOI: 10.1016/j.bios.2024.116503] [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: 03/19/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/23/2024]
Abstract
Automation of liquid handling is indispensable to improve throughput and reproducibility in biochemical assays. However, the incorporation of automated systems into laboratory workflows is often hindered by the high cost and complexity associated with building robotic liquid handlers. Here, we report a 3D-printed liquid handler based on a fluidic manifold, thereby obviating the need for complex robotic mechanisms. The fluidic manifold, termed a dispensing and aspirating (DA) device, comprises parallelized multi-pipette structures connected by distribution and aspiration channels, enabling the precise supply and removal of reagents, respectively. Leveraging the versatility of 3D printing, the DA device can be custom-designed and printed to fit specific applications. As a proof-of-principle, we engineered a 3D-printed liquid handler dedicated for 3D digital rolling circle amplification (4DRCA), an advanced biochemical assay involving multiple sample preparation steps such as antibody incubation, cell fixation, nucleic acid amplification, probe hybridization, and extensive washing. We demonstrate the efficacy of the 3D-printed liquid handler to automate the preparation of clinical samples for the simultaneous, in situ analysis of oncogenic protein and transcript markers in B-cell acute lymphoblastic leukemia cells using 4DRCA. This approach provides an effective and accessible solution for liquid handling automation, offering high throughput and reproducibility in biochemical assays.
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Affiliation(s)
- Suyeon Shin
- Department of Electronic Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Hyo Geun Yun
- Department of Electronic Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Haerim Chung
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Hyunsoo Cho
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - Sungyoung Choi
- Department of Electronic Engineering, Hanyang University, Seoul, 04763, Republic of Korea; Department of Biomedical Engineering, Hanyang University, Seoul, 04763, Republic of Korea; Department of Healthcare Digital Engineering, Hanyang University, Seoul, 04763, Republic of Korea.
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Abou Dalle I, Moukalled N, El Cheikh J, Mohty M, Bazarbachi A. Philadelphia-chromosome positive acute lymphoblastic leukemia: ten frequently asked questions. Leukemia 2024:10.1038/s41375-024-02319-2. [PMID: 38902471 DOI: 10.1038/s41375-024-02319-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 06/22/2024]
Abstract
Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ ALL) constitutes a distinctive cytogenetic entity associated with challenging outcomes, particularly in adult patients. Current upfront chemotherapy-tyrosine kinase inhibitor (TKI)-based therapies include first, second and third-generation TKIs that have revolutionized patient outcomes including molecular remission and overall survival. Chemotherapy-free regimens such as blinatumomab-dasatinib or blinatumomab-ponatinib offer exciting possibilities, yet challenges arise, particularly in preventing central nervous system relapse. Monitoring measurable residual disease is now a cornerstone particularly using next-generation sequencing (NGS)-Clonoseq for accurate assessment. Controversy regarding the ability to omit consolidation with allogeneic stem cell transplantation, specifically for patients achieving early molecular remission, is related to the excellent survival achieved with novel combinations in the upfront setting, however challenged by the lower disease control when transplant is utilized beyond first remission. Post-transplant maintenance introduces new dilemmas: the optimal TKI, dosing, and duration of therapy are open questions. Meanwhile, a myriad of new combinations and cellular therapies are used for relapsed Ph+ ALL, prompting us to unravel the optimal sequencing of these promising regimen. In this review, we delve into the breakthroughs and controversies in Ph+ ALL with ten commonly asked questions.
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Affiliation(s)
- Iman Abou Dalle
- Hematology-Oncology Division, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Nour Moukalled
- Hematology-Oncology Division, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Jean El Cheikh
- Hematology-Oncology Division, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Mohamad Mohty
- Sorbonne University, Department of Clinical Hematology and Cellular Therapy, Saint-Antoine Hospital, AP-HP, INSERM UMRs 938, Paris, France
| | - Ali Bazarbachi
- Hematology-Oncology Division, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon.
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Shin S, Kim YJ, Yun HG, Chung H, Cho H, Choi S. 3D Amplified Single-Cell RNA and Protein Imaging Identifies Oncogenic Transcript Subtypes in B-Cell Acute Lymphoblastic Leukemia. ACS NANO 2024. [PMID: 38320154 DOI: 10.1021/acsnano.3c10421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Simultaneous in situ detection of transcript and protein markers at the single-cell level is essential for gaining a better understanding of tumor heterogeneity and for predicting and monitoring treatment responses. However, the limited accessibility to advanced 3D imaging techniques has hindered their rapid implementation. Here, we present a 3D single-cell imaging technique, termed 3D digital rolling circle amplification (4DRCA), capable of the multiplexed and amplified simultaneous digital quantification of single-cell RNAs and proteins using standard fluorescence microscopy and off-the-shelf reagents. We generated spectrally distinguishable DNA amplicons from molecular markers through an integrative protocol combining single-cell RNA and protein assays and directly enumerated the amplicons by leveraging an open-source algorithm for 3D deconvolution with a custom-built automatic gating algorithm. With 4DRCA, we were able to simultaneously quantify surface protein markers and cytokine transcripts in T-lymphocytes. We also show that 4DRCA can distinguish BCR-ABL1 fusion transcript positive B-cell acute lymphoblastic leukemia cells with or without CD19 protein expression. The accessibility and extensibility of 4DRCA render it broadly applicable to other cell-based diagnostic workflows, enabling sensitive and accurate single-cell RNA and protein profiling.
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Affiliation(s)
- Suyeon Shin
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Yoon-Jin Kim
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Hyo Geun Yun
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Haerim Chung
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyunsoo Cho
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Sungyoung Choi
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Republic of Korea
- Department of Biomedical Engineering, Hanyang University, Seoul 04763, Republic of Korea
- Department of Healthcare Digital Engineering, Hanyang University, Seoul 04763, Republic of Korea
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Wieduwilt MJ. Ph+ ALL in 2022: is there an optimal approach? HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2022; 2022:206-212. [PMID: 36485090 PMCID: PMC9820632 DOI: 10.1182/hematology.2022000338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukemia (ALL) carried a very poor prognosis prior to the advent of tyrosine kinase inhibitors (TKIs) that block the activity of the BCR-ABL1 oncoprotein. With improvements in TKI efficacy and allogeneic hematopoietic cell transplantation (HCT), survival has improved over the past 3 decades, and the role of chemotherapy and allogeneic HCT is now changing. Better risk stratification, the application of the third-generation TKI ponatinib, and the use of immunotherapy with the CD19-CD3 bifunctional T-cell engaging antibody blinatumomab in place of chemotherapy has made therapy for Ph+ ALL more tolerable and arguably more efficacious, especially for older patients who comprise most patients with Ph+ ALL.
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Affiliation(s)
- Matthew J. Wieduwilt
- Correspondence Matthew J. Wieduwilt, 1 Medical Center Blvd #3rd, Winston- Salem, NC 27157, USA; e-mail:
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Yu G, Lu W, Chen X, Li Y, Long J, Zheng Z, Yin C, Xu D. Single-cell RNA sequencing to explore composition of peripheral blood NK cells in patients with chronic myeloid leukemia in treatment-free remission. Leuk Lymphoma 2022; 63:2604-2615. [PMID: 35695125 DOI: 10.1080/10428194.2022.2086243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This study was to explore the role of NK cell subsets and gene expression in maintaining TFR status. We identified six types of NK cells in the PBMCs over both groups (healthy controls and patients with TFR). Gene Oncology analysis showed that up regulated genes were enriched in the categories of "immune response," "reaction to tumor cells," and "cytolysis." In addition, we found that the three NK cell subsets, mature and terminal NK cells, CD56 bright NK cells, and transitional NK cells, contained many significantly up regulated genes in both groups, and that CD56 bright NK cells and transitional NK cells in patients with CML-TFR were in a proliferating and activated state. Through single-cell RNA sequencing analysis, we confirmed that the mature and terminal, CD56 bright, and transitional subsets of NK cells play an indispensable role in maintaining TFR in patients with CML.
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Affiliation(s)
- Guopan Yu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Weixiang Lu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaofan Chen
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanlin Li
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiaxin Long
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhongxin Zheng
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Changxin Yin
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dan Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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