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Joshi H, Singh BP, Butola A, Surya V, Mishra D, Agarwal K, Mehta DS. Compact Linnik-type hyperspectral quantitative phase microscope for advanced classification of cellular components. JOURNAL OF BIOPHOTONICS 2024:e202400088. [PMID: 38899690 DOI: 10.1002/jbio.202400088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/14/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
Hyperspectral quantitative phase microscopy (HS-QPM) involves the acquisition of phase images across narrow spectral bands, which enables wavelength-dependent study of different biological samples. In the present work, a compact Linnik-type HS-QPM system is developed to reduce the instability and complexity associated with conventional HS-QPM techniques. The use of a single objective lens for both reference and sample arms makes the setup compact. The capabilities of the system are demonstrated by evaluating the HS phase map of both industrial and biological specimens. Phase maps of exfoliated cheek cells at different wavelengths are stacked to form a HS phase cube, adding spectral dimensionality to spatial phase distribution. Analysis of wavelength response of different cellular components are performed using principal component analysis to identify dominant spectral features present in the HS phase dataset. Findings of the study emphasize on the efficiency and effectiveness of HS-QPM for advancing cellular characterization in biomedical research and clinical applications.
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Affiliation(s)
- Himanshu Joshi
- Bio-photonics and Green-photonics Laboratory, Department of Physics, Indian Institute of Technology Delhi, New Delhi, India
| | - Bhanu Pratap Singh
- Bio-photonics and Green-photonics Laboratory, Department of Physics, Indian Institute of Technology Delhi, New Delhi, India
| | - Ankit Butola
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Varun Surya
- Department of Oral Pathology and Microbiology, Center for Dental Education & Research, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Deepika Mishra
- Department of Oral Pathology and Microbiology, Center for Dental Education & Research, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Krishna Agarwal
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Dalip Singh Mehta
- Bio-photonics and Green-photonics Laboratory, Department of Physics, Indian Institute of Technology Delhi, New Delhi, India
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Liu Y, Uttam S. Perspective on quantitative phase imaging to improve precision cancer medicine. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:S22705. [PMID: 38584967 PMCID: PMC10996848 DOI: 10.1117/1.jbo.29.s2.s22705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/03/2024] [Accepted: 03/15/2024] [Indexed: 04/09/2024]
Abstract
Significance Quantitative phase imaging (QPI) offers a label-free approach to non-invasively characterize cellular processes by exploiting their refractive index based intrinsic contrast. QPI captures this contrast by translating refractive index associated phase shifts into intensity-based quantifiable data with nanoscale sensitivity. It holds significant potential for advancing precision cancer medicine by providing quantitative characterization of the biophysical properties of cells and tissue in their natural states. Aim This perspective aims to discuss the potential of QPI to increase our understanding of cancer development and its response to therapeutics. It also explores new developments in QPI methods towards advancing personalized cancer therapy and early detection. Approach We begin by detailing the technical advancements of QPI, examining its implementations across transmission and reflection geometries and phase retrieval methods, both interferometric and non-interferometric. The focus then shifts to QPI's applications in cancer research, including dynamic cell mass imaging for drug response assessment, cancer risk stratification, and in-vivo tissue imaging. Results QPI has emerged as a crucial tool in precision cancer medicine, offering insights into tumor biology and treatment efficacy. Its sensitivity to detecting nanoscale changes holds promise for enhancing cancer diagnostics, risk assessment, and prognostication. The future of QPI is envisioned in its integration with artificial intelligence, morpho-dynamics, and spatial biology, broadening its impact in cancer research. Conclusions QPI presents significant potential in advancing precision cancer medicine and redefining our approach to cancer diagnosis, monitoring, and treatment. Future directions include harnessing high-throughput dynamic imaging, 3D QPI for realistic tumor models, and combining artificial intelligence with multi-omics data to extend QPI's capabilities. As a result, QPI stands at the forefront of cancer research and clinical application in cancer care.
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Affiliation(s)
- Yang Liu
- University of Illinois Urbana-Champaign, Beckman Institute for Advanced Science and Technology, Cancer Center at Illinois, Department of Bioengineering, Department of Electrical and Computer Engineering, Urbana, Illinois, United States
- University of Pittsburgh, Departments of Medicine and Bioengineering, Pittsburgh, Pennsylvania, United States
| | - Shikhar Uttam
- University of Pittsburgh, Department of Computational and Systems Biology, Pittsburgh, Pennsylvania, United States
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Kaczara P, Czyzynska-Cichon I, Kus E, Kurpinska A, Olkowicz M, Wojnar-Lason K, Pacia MZ, Lytvynenko O, Baes M, Chlopicki S. Liver sinusoidal endothelial cells rely on oxidative phosphorylation but avoid processing long-chain fatty acids in their mitochondria. Cell Mol Biol Lett 2024; 29:67. [PMID: 38724891 PMCID: PMC11084093 DOI: 10.1186/s11658-024-00584-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND It is generally accepted that endothelial cells (ECs), primarily rely on glycolysis for ATP production, despite having functional mitochondria. However, it is also known that ECs are heterogeneous, and their phenotypic features depend on the vascular bed. Emerging evidence suggests that liver sinusoidal ECs (LSECs), located in the metabolically rich environment of the liver, show high metabolic plasticity. However, the substrate preference for energy metabolism in LSECs remains unclear. METHODS Investigations were conducted in primary murine LSECs in vitro using the Seahorse XF technique for functional bioenergetic assays, untargeted mass spectrometry-based proteomics to analyse the LSEC proteome involved in energy metabolism pathways, liquid chromatography-tandem mass spectrometry-based analysis of acyl-carnitine species and Raman spectroscopy imaging to track intracellular palmitic acid. RESULTS This study comprehensively characterized the energy metabolism of LSECs, which were found to depend on oxidative phosphorylation, efficiently fuelled by glucose-derived pyruvate, short- and medium-chain fatty acids and glutamine. Furthermore, despite its high availability, palmitic acid was not directly oxidized in LSEC mitochondria, as evidenced by the acylcarnitine profile and etomoxir's lack of effect on oxygen consumption. However, together with L-carnitine, palmitic acid supported mitochondrial respiration, which is compatible with the chain-shortening role of peroxisomal β-oxidation of long-chain fatty acids before further degradation and energy generation in mitochondria. CONCLUSIONS LSECs show a unique bioenergetic profile of highly metabolically plastic ECs adapted to the liver environment. The functional reliance of LSECs on oxidative phosphorylation, which is not a typical feature of ECs, remains to be determined.
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Affiliation(s)
- Patrycja Kaczara
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland.
| | - Izabela Czyzynska-Cichon
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Edyta Kus
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Anna Kurpinska
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Mariola Olkowicz
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Kamila Wojnar-Lason
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
- Jagiellonian University Medical College, Department of Pharmacology, Grzegorzecka 16, 31-531, Krakow, Poland
| | - Marta Z Pacia
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Olena Lytvynenko
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Myriam Baes
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Laboratory of Cell Metabolism, 3000, Leuven, Belgium
| | - Stefan Chlopicki
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
- Jagiellonian University Medical College, Department of Pharmacology, Grzegorzecka 16, 31-531, Krakow, Poland
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Bhatt S, Butola A, Kumar A, Thapa P, Joshi A, Jadhav S, Singh N, Prasad DK, Agarwal K, Mehta DS. Single-shot multispectral quantitative phase imaging of biological samples using deep learning. APPLIED OPTICS 2023; 62:3989-3999. [PMID: 37706710 DOI: 10.1364/ao.482788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/18/2023] [Indexed: 09/15/2023]
Abstract
Multispectral quantitative phase imaging (MS-QPI) is a high-contrast label-free technique for morphological imaging of the specimens. The aim of the present study is to extract spectral dependent quantitative information in single-shot using a highly spatially sensitive digital holographic microscope assisted by a deep neural network. There are three different wavelengths used in our method: λ=532, 633, and 808 nm. The first step is to get the interferometric data for each wavelength. The acquired datasets are used to train a generative adversarial network to generate multispectral (MS) quantitative phase maps from a single input interferogram. The network was trained and validated on two different samples: the optical waveguide and MG63 osteosarcoma cells. Validation of the present approach is performed by comparing the predicted MS phase maps with numerically reconstructed (F T+T I E) phase maps and quantifying with different image quality assessment metrices.
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Butola A, Acuna S, Hansen DH, Agarwal K. Scalable-resolution structured illumination microscopy. OPTICS EXPRESS 2022; 30:43752-43767. [PMID: 36523067 DOI: 10.1364/oe.465303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/12/2022] [Indexed: 06/17/2023]
Abstract
Structured illumination microscopy suffers from the need of sophisticated instrumentation and precise calibration. This makes structured illumination microscopes costly and skill-dependent. We present a novel approach to realize super-resolution structured illumination microscopy using an alignment non-critical illumination system and a reconstruction algorithm that does not need illumination information. The optical system is designed to encode higher order frequency components of the specimen by projecting PSF-modulated binary patterns for illuminating the sample plane, which do not have clean Fourier peaks conventionally used in structured illumination microscopy. These patterns fold high frequency content of sample into the measurements in an obfuscated manner, which are de-obfuscated using multiple signal classification algorithm. This algorithm eliminates the need of clean peaks in illumination and the knowledge of illumination patterns, which makes instrumentation simple and flexible for use with a variety of microscope objective lenses. We present a variety of experimental results on beads and cell samples to demonstrate resolution enhancement by a factor of 2.6 to 3.4 times, which is better than the enhancement supported by the conventional linear structure illumination microscopy where the same objective lens is used for structured illumination as well as collection of light. We show that the same system can be used in SIM configuration with different collection objective lenses without any careful re-calibration or realignment, thereby supporting a range of resolutions with the same system.
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Tuning of Liver Sieve: The Interplay between Actin and Myosin Regulatory Light Chain Regulates Fenestration Size and Number in Murine Liver Sinusoidal Endothelial Cells. Int J Mol Sci 2022; 23:ijms23179850. [PMID: 36077249 PMCID: PMC9456121 DOI: 10.3390/ijms23179850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 12/02/2022] Open
Abstract
Liver sinusoidal endothelial cells (LSECs) facilitate the efficient transport of macromolecules and solutes between the blood and hepatocytes. The efficiency of this transport is realized via transcellular nanopores, called fenestrations. The mean fenestration size is 140 ± 20 nm, with the range from 50 nm to 350 nm being mostly below the limits of diffraction of visible light. The cellular mechanisms controlling fenestrations are still poorly understood. In this study, we tested a hypothesis that both Rho kinase (ROCK) and myosin light chain (MLC) kinase (MLCK)-dependent phosphorylation of MLC regulates fenestrations. We verified the hypothesis using a combination of several molecular inhibitors and by applying two high-resolution microscopy modalities: structured illumination microscopy (SIM) and scanning electron microscopy (SEM). We demonstrated precise, dose-dependent, and reversible regulation of the mean fenestration diameter within a wide range from 120 nm to 220 nm and the fine-tuning of the porosity in a range from ~0% up to 12% using the ROCK pathway. Moreover, our findings indicate that MLCK is involved in the formation of new fenestrations—after inhibiting MLCK, closed fenestrations cannot be reopened with other agents. We, therefore, conclude that the Rho-ROCK pathway is responsible for the control of the fenestration diameter, while the inhibition of MLCK prevents the formation of new fenestrations.
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Butola A, Coucheron DA, Szafranska K, Ahmad A, Mao H, Tinguely JC, McCourt P, Senthilkumaran P, Mehta DS, Agarwal K, Ahluwalia BS. Multimodal on-chip nanoscopy and quantitative phase imaging reveals the nanoscale morphology of liver sinusoidal endothelial cells. Proc Natl Acad Sci U S A 2021; 118:e2115323118. [PMID: 34782474 PMCID: PMC8617407 DOI: 10.1073/pnas.2115323118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 12/26/2022] Open
Abstract
Visualization of three-dimensional (3D) morphological changes in the subcellular structures of a biological specimen is a major challenge in life science. Here, we present an integrated chip-based optical nanoscopy combined with quantitative phase microscopy (QPM) to obtain 3D morphology of liver sinusoidal endothelial cells (LSEC). LSEC have unique morphology with small nanopores (50-300 nm in diameter) in the plasma membrane, called fenestrations. The fenestrations are grouped in discrete clusters, which are around 100 to 200 nm thick. Thus, imaging and quantification of fenestrations and sieve plate thickness require resolution and sensitivity of sub-100 nm along both the lateral and the axial directions, respectively. In chip-based nanoscopy, the optical waveguides are used both for hosting and illuminating the sample. The fluorescence signal is captured by an upright microscope, which is converted into a Linnik-type interferometer to sequentially acquire both superresolved images and phase information of the sample. The multimodal microscope provided an estimate of the fenestration diameter of 119 ± 53 nm and average thickness of the sieve plates of 136.6 ± 42.4 nm, assuming the constant refractive index of cell membrane to be 1.38. Further, LSEC were treated with cytochalasin B to demonstrate the possibility of precise detection in the cell height. The mean phase value of the fenestrated area in normal and treated cells was found to be 161 ± 50 mrad and 109 ± 49 mrad, respectively. The proposed multimodal technique offers nanoscale visualization of both the lateral size and the thickness map, which would be of broader interest in the fields of cell biology and bioimaging.
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Affiliation(s)
- Ankit Butola
- Department of Physics and Technology, Universitetet i Tromsø (UiT) The Arctic University of Norway, 9037 Tromsø, Norway
- Bio-photonics and Green Photonics Laboratory, Department of Physics, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - David A Coucheron
- Department of Physics and Technology, Universitetet i Tromsø (UiT) The Arctic University of Norway, 9037 Tromsø, Norway
| | - Karolina Szafranska
- Faculty of Health Sciences, Department of Medical Biology, Vascular Biology Research Group, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Azeem Ahmad
- Department of Physics and Technology, Universitetet i Tromsø (UiT) The Arctic University of Norway, 9037 Tromsø, Norway
| | - Hong Mao
- Department of Physics and Technology, Universitetet i Tromsø (UiT) The Arctic University of Norway, 9037 Tromsø, Norway
| | - Jean-Claude Tinguely
- Department of Physics and Technology, Universitetet i Tromsø (UiT) The Arctic University of Norway, 9037 Tromsø, Norway
| | - Peter McCourt
- Faculty of Health Sciences, Department of Medical Biology, Vascular Biology Research Group, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Paramasivam Senthilkumaran
- Bio-photonics and Green Photonics Laboratory, Department of Physics, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Dalip Singh Mehta
- Bio-photonics and Green Photonics Laboratory, Department of Physics, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Krishna Agarwal
- Department of Physics and Technology, Universitetet i Tromsø (UiT) The Arctic University of Norway, 9037 Tromsø, Norway
| | - Balpreet Singh Ahluwalia
- Department of Physics and Technology, Universitetet i Tromsø (UiT) The Arctic University of Norway, 9037 Tromsø, Norway;
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17177 Stockholm, Sweden
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