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An automated system for nucleic acid extraction from formalin-fixed paraffin-embedded samples using high intensity focused ultrasound technology. Anal Bioanal Chem 2022; 414:8201-8213. [PMID: 36260128 DOI: 10.1007/s00216-022-04360-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/01/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue samples are routinely used in prospective and retrospective studies. It is crucial to obtain high-quality nucleic acid (NA) from FFPE samples for downstream molecular analysis, such as quantitative polymerase chain reaction (PCR), Sanger sequencing, next-generation sequencing, and microarray, in both clinical diagnosis and basic research. The current NA extraction methods from FFPE samples using chemical solvent are tedious, environmentally unfriendly, and unamenable to automation or field deployment. We present a tool for NA extraction from FFPE samples using a high-intensity focused ultrasound (HIFU) technology. A cartridge strip containing reagents for FFPE sample deparaffinization and NA extraction and purification is operated by an automation tool consisting of a HIFU module, a liquid handling robot unit, and accessories including a thermal block and magnets. The HIFU module is a single concaved piezoelectric ceramic plate driven by a current-mode class-D power amplifier. Based on the ultrasonic cavitation effects, the HIFU module provides highly concentrated energy introducing paraffin emulsification and disintegration. The high quantity and quality of NA extracted using the reported system are evaluated by PCR and compared with the quantity and quality of NA extracted using the current standard methods.
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Cho CH, Cho M, Park JK. Biomarker barcodes: multiplexed microfluidic immunohistochemistry enables high-throughput analysis of tissue microarray. LAB ON A CHIP 2021; 21:3471-3482. [PMID: 34263282 DOI: 10.1039/d1lc00375e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We present a multiplexed microfluidic immunohistochemistry (IHC) technology that enables high-throughput analysis of tissue microarrays (TMAs) using the patterns of biomarker barcodes, which consist of a series of expressed linear patterns of specific biomarkers. A multichannel poly(dimethylsiloxane) microfluidic device was reversibly assembled by the pressure of simple equipment for multiplexed IHC on each core of TMA or cell microarray (CMA) section slides. By injecting primary antibodies from different biomarkers independently into each channel, multiplexed immunostaining can be performed on each core of TMA. We confirmed the equal immunostaining quality regardless of the channel orders and core positions in the slide. Four different biomarkers (ER, PR, HER2, and Ki67) were used for the demonstration of distinctive expression patterns on CMAs which consist of six different breast cancer cell lines, and it was confirmed that these bar-like signals could be a biomarker barcode for the TMA core. A biomarker barcode of breast cancer patient-derived TMA was quickly scanned by a slide scanner and compared to the conventional method for breast cancer diagnosis. This "barcode-IHC" concept, which has been verified by performing multiplexed microfluidic IHC on CMA and TMA samples, provides high reproducibility and the potential of high-throughput screening with molecular diagnostic capability.
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Affiliation(s)
- Chang Hyun Cho
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Minkyung Cho
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Je-Kyun Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Delamarche E, Pereiro I, Kashyap A, Kaigala GV. Biopatterning: The Art of Patterning Biomolecules on Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9637-9651. [PMID: 34347483 DOI: 10.1021/acs.langmuir.1c00867] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Patterning biomolecules on surfaces provides numerous opportunities for miniaturizing biological assays; biosensing; studying proteins, cells, and tissue sections; and engineering surfaces that include biological components. In this Feature Article, we summarize the themes presented in our recent Langmuir Lecture on patterning biomolecules on surfaces, miniaturizing surface assays, and interacting with biointerfaces using three key technologies: microcontact printing, microfluidic networks, and microfluidic probes.
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Affiliation(s)
- Emmanuel Delamarche
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| | - Iago Pereiro
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| | - Aditya Kashyap
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| | - Govind V Kaigala
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
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de Hoyos-Vega JM, Gonzalez-Suarez AM, Garcia-Cordero JL. A versatile microfluidic device for multiple ex vivo/in vitro tissue assays unrestrained from tissue topography. MICROSYSTEMS & NANOENGINEERING 2020; 6:40. [PMID: 34567653 PMCID: PMC8433291 DOI: 10.1038/s41378-020-0156-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 03/04/2020] [Accepted: 03/12/2020] [Indexed: 05/28/2023]
Abstract
Precision-cut tissue slices are an important in vitro system to study organ function because they preserve most of the native cellular microenvironments of organs, including complex intercellular connections. However, during sample manipulation or slicing, some of the natural surface topology and structure of these tissues is lost or damaged. Here, we introduce a microfluidic platform to perform multiple assays on the surface of a tissue section, unhindered by surface topography. The device consists of a valve on one side and eight open microchannels located on the opposite side, with the tissue section sandwiched between these two structures. When the valve is actuated, eight independent microfluidic channels are formed over a tissue section. This strategy prevents cross-contamination when performing assays and enables parallelization. Using irregular tissues such as an aorta, we conducted multiple in vitro and ex vivo assays on tissue sections, including short-term culturing, a drug toxicity assay, a fluorescence immunohistochemistry staining assay, and an immune cell assay, in which we observed the interaction of neutrophils with lipopolysaccharide (LPS)-stimulated endothelium. Our microfluidic platform can be employed in other disciplines, such as tissue physiology and pathophysiology, morphogenesis, drug toxicity and efficiency, metabolism studies, and diagnostics, enabling the conduction of several assays with a single biopsy sample.
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Affiliation(s)
- Jose M. de Hoyos-Vega
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del IPN, Via del conocimiento 201, Parque PIIT, Apodaca, NL 66628 Mexico
| | - Alan M. Gonzalez-Suarez
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del IPN, Via del conocimiento 201, Parque PIIT, Apodaca, NL 66628 Mexico
| | - Jose L. Garcia-Cordero
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del IPN, Via del conocimiento 201, Parque PIIT, Apodaca, NL 66628 Mexico
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Lovchik RD, Taylor D, Kaigala G. Rapid micro-immunohistochemistry. MICROSYSTEMS & NANOENGINEERING 2020; 6:94. [PMID: 34567704 PMCID: PMC8433409 DOI: 10.1038/s41378-020-00205-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 05/04/2023]
Abstract
We present a new and versatile implementation of rapid and localized immunohistochemical staining of tissue sections. Immunohistochemistry (IHC) comprises a sequence of specific biochemical reactions and allows the detection of specific proteins in tissue sections. For the rapid implementation of IHC, we fabricated horizontally oriented microfluidic probes (MFPs) with functionally designed apertures to enable square and circular footprints, which we employ to locally expose a tissue to time-optimized sequences of different biochemicals. We show that the two main incubation steps of IHC protocols can be performed on MDAMB468-1510A cell block sections in less than 30 min, compared to incubation times of an hour or more in standard protocols. IHC analysis on the timescale of tens of minutes could potentially be applied during surgery, enabling clinicians to react in more dynamically and efficiently. Furthermore, this rapid IHC implementation along with conservative tissue usage has strong potential for the implementation of multiplexed assays, allowing the exploration of optimal assay conditions with a small amount of tissue to ensure high-quality staining results for the remainder of the sample.
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Affiliation(s)
- Robert D. Lovchik
- IBM Research Europe, Saeumerstrasse 4, 8803 Rueschlikon, Switzerland
| | - David Taylor
- IBM Research Europe, Saeumerstrasse 4, 8803 Rueschlikon, Switzerland
- Present Address: Eidgenössische Technische Hochschule Zürich, Department of Mechanical and Process Engineering, Sonneggstrasse 3, 8092 Zurich, Switzerland
| | - Govind Kaigala
- IBM Research Europe, Saeumerstrasse 4, 8803 Rueschlikon, Switzerland
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Feng D, Yuan J, Liu Q, Liu L, Zhang X, Wu Y, Qian Y, Chen L, Shi Y, Gu M. UPLC‑MS/MS‑based metabolomic characterization and comparison of pancreatic adenocarcinoma tissues using formalin‑fixed, paraffin‑embedded and optimal cutting temperature‑embedded materials. Int J Oncol 2019; 55:1249-1260. [PMID: 31638165 PMCID: PMC6831194 DOI: 10.3892/ijo.2019.4898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/09/2019] [Indexed: 12/04/2022] Open
Abstract
The purpose of the present study was to compare metabolites from formalin-fixed and paraffin-embedded (FFPE) pancreatic tissue blocks with those identified in optimal cutting temperature (OCT)-embedded pancreatic tissue blocks. Thus, ultra-performance liquid chromatograph-mass spectrometry/mass spectrometry-based metabolic profiling was performed in paired frozen (n=13) and FFPE (n=13) human pancreatic adenocarcinoma tissue samples, in addition to their benign counterparts. A total of 206 metabolites were identified in both OCT-embedded and FFPE tissue samples. The method feasibility was confirmed through reproducibility and a consistency assessment. Partial least-squares discriminant analysis and heatmap analysis reliably distinguished tumor and normal tissue phenotypes. The expression of 10 compounds, including N-acetylaspartate and creatinine, was significantly different in both OCT-embedded and FFPE tumor samples. These ten compounds may be viable candidate biomarkers of malignant pancreatic tissues. The super-categories to which they belonged exhibited no significant differences between FFPE and OCT-embedded samples. Furthermore, purine, arginine and proline, and pyrimidine metabolism used a shared pathway found in both OCT-embedded and FFPE tissue samples. These results supported the notion that metabolomic data acquired from FFPE pancreatic cancer specimens are reliable for use in retrospective and clinical studies.
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Affiliation(s)
- Di Feng
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 311402, P.R. China
| | - Jing Yuan
- Department of Pathology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Qi Liu
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Li Liu
- Department of Epidemiology and Biostatistics, Ministry of Education Key Lab of Environment and Health, School of Public Health, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Xu Zhang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 311402, P.R. China
| | - Yali Wu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 311402, P.R. China
| | - Yifan Qian
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 311402, P.R. China
| | - Liping Chen
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 311402, P.R. China
| | - Yan Shi
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Mancang Gu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 311402, P.R. China
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Taylor DP, Kaigala GV. Fluidic Bypass Structures for Improving the Robustness of Liquid Scanning Probes. IEEE Trans Biomed Eng 2019; 66:2491-2498. [DOI: 10.1109/tbme.2018.2890602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Dixit C, Kadimisetty K, Rusling J. 3D-printed miniaturized fluidic tools in chemistry and biology. Trends Analyt Chem 2018; 106:37-52. [PMID: 32296252 PMCID: PMC7158885 DOI: 10.1016/j.trac.2018.06.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
3D printing (3DP), an additive manufacturing (AM) approach allowing for rapid prototyping and decentralized fabrication on-demand, has become a common method for creating parts or whole devices. The wide scope of the AM extends from organized sectors of construction, ornament, medical, and R&D industries to individual explorers attributed to the low cost, high quality printers along with revolutionary tools and polymers. While progress is being made but big manufacturing challenges are still there. Considering the quickly shifting narrative towards miniaturized analytical systems (MAS) we focus on the development/rapid prototyping and manufacturing of MAS with 3DP, and application dependent challenges in engineering designs and choice of the polymeric materials and provide an exhaustive background to the applications of 3DP in biology and chemistry. This will allow readers to perceive the most important features of AM in creating (i) various individual and modular components, and (ii) complete integrated tools.
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Affiliation(s)
- C.K. Dixit
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060, United States
| | - K. Kadimisetty
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060, United States
| | - J. Rusling
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060, United States
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269-3136, United States
- Department of Surgery and Neag Cancer Centre, UConn Health, Farmington, CT 06030, United States
- School of Chemistry, National University of Ireland at Galway, Galway, Ireland
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Abstract
In this work, we fabricate microfluidic probes (MFPs) in a single step by stereolithographic 3D printing and benchmark their performance with standard MFPs fabricated via glass or silicon micromachining. Two research teams join forces to introduce two independent designs and fabrication protocols, using different equipment. Both strategies adopted are inexpensive and simple (they only require a stereolithography printer) and are highly customizable. Flow characterization is performed by reproducing previously published microfluidic dipolar and microfluidic quadrupolar reagent delivery profiles which are compared to the expected results from numerical simulations and scaling laws. Results show that, for most MFP applications, printer resolution artifacts have negligible impact on probe operation, reagent pattern formation, and cell staining results. Thus, any research group with a moderate resolution (≤100 µm) stereolithography printer will be able to fabricate the MFPs and use them for processing cells, or generating microfluidic concentration gradients. MFP fabrication involved glass and/or silicon micromachining, or polymer micromolding, in every previously published article on the topic. We therefore believe that 3D printed MFPs is poised to democratize this technology. We contribute to initiate this trend by making our CAD files available for the readers to test our "print & probe" approach using their own stereolithographic 3D printers.
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Cho CH, Kwon S, Kim S, Hong Y, Kim P, Lee ES, Park JK. Microfluidic on-chip immunohistochemistry directly from a paraffin-embedded section. BIOMICROFLUIDICS 2018; 12:044110. [PMID: 30079122 PMCID: PMC6053317 DOI: 10.1063/1.5042347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/09/2018] [Indexed: 05/06/2023]
Abstract
We present here a novel microfluidic platform that can perform microfluidic on-chip immunohistochemistry (IHC) processes on a formalin-fixed paraffin-embedded section slide. Unlike previous microfluidic IHC studies, our microfluidic chip made of organic solvent-resistant polyurethane acrylate (PUA) is capable of conducting on-chip IHC processes consecutively. A narrow channel wall structure of the PUA chip shows effective sealing by pressure-based reversible assembly with a section slide. We performed both on-chip IHC and conventional IHC processes and compared the IHC results based on the immunostaining intensity. The result showed that the effects of the on-chip deparaffinization, antigen retrieval, and immunoreaction processes on the IHC result were equivalent to conventional methods while reducing the total process time to less than 1/2. The experiment with breast cancer tissue shows that human epidermal growth factor receptor 2 (HER2) classification can be performed by obtaining a clearly distinguishable immunostaining intensity according to the HER2 expression level. We expect our on-chip microfluidic platform to provide a facile technique suitable for miniaturized, automated, and precise diagnostic devices, including a point-of-care device.
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Affiliation(s)
- Chang Hyun Cho
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seyong Kwon
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Segi Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yoonmi Hong
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Pilnam Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Eun Sook Lee
- Center for Breast Cancer, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Je-Kyun Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Author to whom correspondence should be addressed: . Tel.: +82-42-350-4315. Fax: +82-42-350-4310
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