1
|
Adi W, Rubio Perez BE, Liu Y, Runkle S, Eliceiri KW, Yesilkoy F. Machine learning-assisted mid-infrared spectrochemical fibrillar collagen imaging in clinical tissues. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:093511. [PMID: 39364328 PMCID: PMC11448345 DOI: 10.1117/1.jbo.29.9.093511] [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: 05/22/2024] [Revised: 09/04/2024] [Accepted: 09/05/2024] [Indexed: 10/05/2024]
Abstract
Significance Label-free multimodal imaging methods that can provide complementary structural and chemical information from the same sample are critical for comprehensive tissue analyses. These methods are specifically needed to study the complex tumor-microenvironment where fibrillar collagen's architectural changes are associated with cancer progression. To address this need, we present a multimodal computational imaging method where mid-infrared spectral imaging (MIRSI) is employed with second harmonic generation (SHG) microscopy to identify fibrillar collagen in biological tissues. Aim To demonstrate a multimodal approach where a morphology-specific contrast mechanism guides an MIRSI method to detect fibrillar collagen based on its chemical signatures. Approach We trained a supervised machine learning (ML) model using SHG images as ground truth collagen labels to classify fibrillar collagen in biological tissues based on their mid-infrared hyperspectral images. Five human pancreatic tissue samples (sizes are in the order of millimeters) were imaged by both MIRSI and SHG microscopes. In total, 2.8 million MIRSI spectra were used to train a random forest (RF) model. The other 68 million spectra were used to validate the collagen images generated by the RF-MIRSI model in terms of collagen segmentation, orientation, and alignment. Results Compared with the SHG ground truth, the generated RF-MIRSI collagen images achieved a high average boundary F -score (0.8 at 4-pixel thresholds) in the collagen distribution, high correlation (Pearson's R 0.82) in the collagen orientation, and similarly high correlation (Pearson's R 0.66) in the collagen alignment. Conclusions We showed the potential of ML-aided label-free mid-infrared hyperspectral imaging for collagen fiber and tumor microenvironment analysis in tumor pathology samples.
Collapse
Affiliation(s)
- Wihan Adi
- University of Wisconsin-Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | - Bryan E. Rubio Perez
- University of Wisconsin-Madison, Department of Electrical and Computer Engineering, Madison, Wisconsin, United States
| | - Yuming Liu
- University of Wisconsin-Madison, Center for Quantitative Cell Imaging, Madison, Wisconsin, United States
| | - Sydney Runkle
- University of Wisconsin-Madison, Department of Computer Science, Madison, Wisconsin, United States
| | - Kevin W. Eliceiri
- University of Wisconsin-Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
- University of Wisconsin-Madison, Center for Quantitative Cell Imaging, Madison, Wisconsin, United States
- Morgridge Institute for Research, Madison, Wisconsin, United States
| | - Filiz Yesilkoy
- University of Wisconsin-Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| |
Collapse
|
2
|
Adi W, Perez BER, Liu Y, Runkle S, Eliceiri KW, Yesilkoy F. Machine learning assisted mid-infrared spectrochemical fibrillar collagen imaging in clinical tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595393. [PMID: 38826188 PMCID: PMC11142197 DOI: 10.1101/2024.05.22.595393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Significance Label-free multimodal imaging methods that can provide complementary structural and chemical information from the same sample are critical for comprehensive tissue analyses. These methods are specifically needed to study the complex tumor-microenvironment where fibrillar collagen's architectural changes are associated with cancer progression. To address this need, we present a multimodal computational imaging method where mid-infrared spectral imaging (MIRSI) is employed with second harmonic generation (SHG) microscopy to identify fibrillar collagen in biological tissues. Aim To demonstrate a multimodal approach where a morphology-specific contrast mechanism guides a mid-infrared spectral imaging method to detect fibrillar collagen based on its chemical signatures. Approach We trained a supervised machine learning (ML) model using SHG images as ground truth collagen labels to classify fibrillar collagen in biological tissues based on their mid-infrared hyperspectral images. Five human pancreatic tissue samples (sizes are in the order of millimeters) were imaged by both MIRSI and SHG microscopes. In total, 2.8 million MIRSI spectra were used to train a random forest (RF) model. The remaining 68 million spectra were used to validate the collagen images generated by the RF-MIRSI model in terms of collagen segmentation, orientation, and alignment. Results Compared to the SHG ground truth, the generated MIRSI collagen images achieved a high average boundary F-score (0.8 at 4 pixels threshold) in the collagen distribution, high correlation (Pearson's R 0.82) in the collagen orientation, and similarly high correlation (Pearson's R 0.66) in the collagen alignment. Conclusions We showed the potential of ML-aided label-free mid-infrared hyperspectral imaging for collagen fiber and tumor microenvironment analysis in tumor pathology samples.
Collapse
Affiliation(s)
- Wihan Adi
- Department of Biomedical Engineering University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Bryan E. Rubio Perez
- Department of Electrical and Computer Engineering University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Yuming Liu
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sydney Runkle
- Department of Computer Science University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Kevin W. Eliceiri
- Department of Biomedical Engineering University of Wisconsin-Madison, Madison, WI, 53705, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53706, USA
| | - Filiz Yesilkoy
- Department of Biomedical Engineering University of Wisconsin-Madison, Madison, WI, 53705, USA
| |
Collapse
|
3
|
Guillard J, Untereiner V, Garnotel R, Boulagnon-Rombi C, Gobinet C, Proult I, Sockalingum GD, Thiéfin G. Longitudinal Study of Cirrhosis Development in STAM and carbon tetrachloride Mouse Models Using Fourier Transform Infrared Spectral Imaging. J Transl Med 2023; 103:100231. [PMID: 37544611 DOI: 10.1016/j.labinv.2023.100231] [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: 10/07/2022] [Revised: 07/31/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023] Open
Abstract
Animal models of cirrhosis are of great interest to investigate the pathological process leading to the final stage of cirrhosis. The aim of this study was to analyze the different steps involved in the progressive development of cirrhosis using Fourier transform infrared spectral histology in 2 mouse models of cirrhosis, the STAM model of metabolic cirrhosis, and the carbon tetrachloride-induced cirrhosis model. Formalin-fixed, paraffin-embedded liver samples were obtained from 3 mice at 5 time points in each model to analyze the course of hepatic lesions up to the formation of cirrhosis. For each time point, adjacent 3-μm-thick liver sections were obtained for histologic stains and spectral histology. Fourier transform infrared acquisitions of liver sections were performed at projected pixel sizes of 25 μm × 25 μm and 6.25 μm × 6.25 μm. Spectral images were then preprocessed with an extended multiplicative signal correction and analyzed with common k-means clustering, including all stages in each model. In both models, the 2- and 4-class common k-means clustering in the 1000 to 1350 cm-1 range showed that spectral classes characterized by higher absorbance peaks of glycogen were predominant at baseline, then decreased markedly in early stages of hepatic damage, and almost disappeared in cirrhotic tissues. Concomitantly, spectral classes characterized by higher absorbance peaks of nucleic acids became progressively predominant during the course of hepatic lesions. These results were confirmed using k-means clustering on the peaks of interest identified for glycogen and nucleic acid content. Our study showed that the glycogen depletion previously described at the stage of cirrhosis is an early event in the pathological process, independently of the cause of cirrhosis. In addition, there was a progressive increase in the nucleic acid content, which may be linked to increased proliferation and polyploidy in response to cellular lesions.
Collapse
Affiliation(s)
- Julien Guillard
- Université de Reims Champagne-Ardenne, BioSpecT, Reims, France
| | - Valérie Untereiner
- Université de Reims Champagne-Ardenne, Plateforme en Imagerie Cellulaire et Tissulaire, Reims, France
| | - Roselyne Garnotel
- Université de Reims Champagne-Ardenne, BioSpecT, Reims, France; Laboratoire de Biochimie-Pharmacologie-Toxicologie, Pôle de Biologie Territoriale, Centre Hospitalo-Universitaire de Reims, Reims, France
| | - Camille Boulagnon-Rombi
- Laboratoire de Biopathologie, Pôle de Biologie Territoriale, Centre Hospitalo-Universitaire de Reims, Reims, France
| | - Cyril Gobinet
- Université de Reims Champagne-Ardenne, BioSpecT, Reims, France
| | - Isabelle Proult
- Université de Reims Champagne-Ardenne, Centre National de la Recherche Scientifique, MEDyC, Reims, France
| | | | - Gérard Thiéfin
- Université de Reims Champagne-Ardenne, BioSpecT, Reims, France; Service d'Hépato-Gastroentérologie et de Cancérologie Digestive, Centre Hospitalo-Universitaire de Reims, Reims, France.
| |
Collapse
|
4
|
Rai C, Priyadarshini P. Whey protein hydrolysates improve high-fat-diet-induced obesity by modulating the brain-peripheral axis of GLP-1 through inhibition of DPP-4 function in mice. Eur J Nutr 2023; 62:2489-2507. [PMID: 37154934 DOI: 10.1007/s00394-023-03162-4] [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: 01/12/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023]
Abstract
PURPOSE Obesity is a growing global health concern. Recent literature indicates a prominent role of glucagon-like peptide-1 (GLP-1) in glucose metabolism and food intake. The synergistic action of GLP-1 in the gut and brain is responsible for its satiety-inducing effect, suggesting that upregulation of active GLP-1 levels could be an alternative strategy to combat obesity. Dipeptidyl peptidase-4 (DPP-4) is an exopeptidase known to inactivate GLP-1, suggesting that its inhibition could be a crucial strategy for effectively extending the half-life of endogenous GLP-1. Peptides derived from partial hydrolysis of dietary proteins are gaining traction due to their inhibitory activity on DPP-4. METHODS Whey protein hydrolysate from bovine milk (bmWPH) was produced using simulated in situ digestion, purified using RP-HPLC, and characterized for DPP-4 inhibition. The antiadipogenic and antiobesity activity of bmWPH was then studied in 3T3-L1 preadipocytes and high-fat diet-induced obesity (HFD) mice model, respectively. RESULTS The dose-dependent inhibitory effect of bmWPH on the catalytic activity of DPP-4 was observed. Additionally, bmWPH suppressed adipogenic transcription factors and DPP-4 protein levels, leading to a negative effect on preadipocyte differentiation. In an HFD mice model, co-administration of WPH for 20 weeks downregulated adipogenic transcription factors, resulting in a concomitant reduction in whole body weight and adipose tissues. Mice fed with bmWPH also showed a marked reduction in DPP-4 levels in WAT, liver, and serum. Furthermore, HFD mice fed with bmWPH exhibited increased serum and brain GLP levels, which led to a significant decrease in food intake. CONCLUSION In conclusion, bmWPH reduces body weight in HFD mice by suppressing appetite through GLP-1, a satiety-inducing hormone, in both the brain and peripheral circulation. This effect is achieved through modulation of both the catalytic and non-catalytic activity of DPP-4.
Collapse
Affiliation(s)
- Chaitra Rai
- Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, 570020, Karnataka, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Poornima Priyadarshini
- Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, 570020, Karnataka, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
5
|
Mittal S, Kim J, Bhargava R. Statistical Considerations and Tools to Improve Histopathologic Protocols with Spectroscopic Imaging. APPLIED SPECTROSCOPY 2022; 76:428-438. [PMID: 35296146 PMCID: PMC9202564 DOI: 10.1177/00037028211066327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Advances in infrared (IR) spectroscopic imaging instrumentation and data science now present unique opportunities for large validation studies of the concept of histopathology using spectral data. In this study, we examine the discrimination potential of IR metrics for different histologic classes to estimate the sample size needed for designing validation studies to achieve a given statistical power and statistical significance. Next, we present an automated annotation transfer tool that can allow large-scale training/validation, overcoming the limitations of sparse ground truth data with current manual approaches by providing a tool to transfer pathologist annotations from stained images to IR images across diagnostic categories. Finally, the results of a combination of supervised and unsupervised analysis provide a scheme to identify diagnostic groups/patterns and isolating pure chemical pixels for each class to better train complex histopathological models. Together, these methods provide essential tools to take advantage of the emerging capabilities to record and utilize large spectroscopic imaging datasets.
Collapse
Affiliation(s)
- Shachi Mittal
- Department of Bioengineering and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Jonathan Kim
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Rohit Bhargava
- Department of Bioengineering and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, USA
- Departments of Mechanical Science and Engineering, Electrical and Computer Engineering, Chemical and Biomolecular Engineering, and Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois at Urbana–Champaign, Urbana, IL, USA
| |
Collapse
|
6
|
Goertzen N, Pappesch R, Fassunke J, Brüning T, Ko YD, Schmidt J, Großerueschkamp F, Buettner R, Gerwert K. Quantum Cascade Laser-Based Infrared Imaging as a Label-Free and Automated Approach to Determine Mutations in Lung Adenocarcinoma. THE AMERICAN JOURNAL OF PATHOLOGY 2021; 191:1269-1280. [PMID: 34004158 DOI: 10.1016/j.ajpath.2021.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/09/2021] [Accepted: 04/22/2021] [Indexed: 12/28/2022]
Abstract
Therapeutic decisions in lung cancer critically depend on the determination of histologic types and oncogene mutations. Therefore, tumor samples are subjected to standard histologic and immunohistochemical analyses and examined for relevant mutations using comprehensive molecular diagnostics. In this study, an alternative diagnostic approach for automatic and label-free detection of mutations in lung adenocarcinoma tissue using quantum cascade laser-based infrared imaging is presented. For this purpose, a five-step supervised classification algorithm was developed, which was not only able to detect tissue types and tumor lesions, but also the tumor type and mutation status of adenocarcinomas. Tumor detection was verified on a data set of 214 patient samples with a specificity of 97% and a sensitivity of 95%. Furthermore, histology typing was verified on samples from 203 of the 214 patients with a specificity of 97% and a sensitivity of 94% for adenocarcinoma. The most frequently occurring mutations in adenocarcinoma (KRAS, EGFR, and TP53) were differentiated by this technique. Detection of mutations was verified in 60 patient samples from the data set with a sensitivity and specificity of 95% for each mutation. This demonstrates that quantum cascade laser infrared imaging can be used to analyze morphologic differences as well as molecular changes. Therefore, this single, one-step measurement provides comprehensive diagnostics of lung cancer histology types and most frequent mutations.
Collapse
Affiliation(s)
- Nina Goertzen
- Center for Protein Diagnostics, Biospectroscopy, Germany; Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | | | - Jana Fassunke
- Institut für Pathologie, Universitätsklinikum Köln, Germany
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum, Bochum, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Johanniter-Kliniken Bonn GmbH, Johanniter Krankenhaus, Bonn, Germany
| | - Joachim Schmidt
- Lung Cancer Center Bonn, Department of Thoracic Surgery, Helios Klinikum Bonn/Rhein-Sieg and Department of Surgery, Division of Thoracic Surgery, Universitätsklinikum Bonn, Germany
| | - Frederik Großerueschkamp
- Center for Protein Diagnostics, Biospectroscopy, Germany; Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | | | - Klaus Gerwert
- Center for Protein Diagnostics, Biospectroscopy, Germany; Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany.
| |
Collapse
|
7
|
Moreau J, Bouzy P, Guillard J, Untereiner V, Garnotel R, Marchal A, Gobinet C, Terryn C, Sockalingum GD, Thiéfin G. Analysis of Hepatic Fibrosis Characteristics in Cirrhotic Patients with and without Hepatocellular Carcinoma by FTIR Spectral Imaging. Molecules 2020; 25:molecules25184092. [PMID: 32906799 PMCID: PMC7570752 DOI: 10.3390/molecules25184092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/31/2020] [Accepted: 09/04/2020] [Indexed: 12/12/2022] Open
Abstract
The evolution of cirrhosis is marked by quantitative and qualitative modifications of the fibrosis tissue and an increasing risk of complications such as hepatocellular carcinoma (HCC). Our purpose was to identify by FTIR imaging the spectral characteristics of hepatic fibrosis in cirrhotic patients with and without HCC. FTIR images were collected at projected pixel sizes of 25 and 2.7 μm from paraffinized hepatic tissues of five patients with uncomplicated cirrhosis and five cirrhotic patients with HCC and analyzed by k-means clustering. When compared to the adjacent histological section, the spectral clusters corresponding to hepatic fibrosis and regeneration nodules were easily identified. The fibrosis area estimated by FTIR imaging was correlated to that evaluated by digital image analysis of histological sections and was higher in patients with HCC compared to those without complications. Qualitative differences were also observed when fibrosis areas were specifically targeted at higher resolution. The partition in two clusters of the fibrosis tissue highlighted subtle differences in the spectral characteristics of the two groups of patients. These data show that the quantitative and qualitative changes of fibrosis tissue occurring during the course of cirrhosis are detectable by FTIR imaging, suggesting the possibility of subclassifying cirrhosis into different steps of severity.
Collapse
Affiliation(s)
- Johanna Moreau
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
- Service d’Hépato-Gastroentérologie et de Cancérologie Digestive, Centre Hospitalier Universitaire de Reims, 51092 Reims, France
| | - Pascaline Bouzy
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
| | - Julien Guillard
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
| | - Valérie Untereiner
- Université de Reims Champagne-Ardenne, Plateforme en Imagerie Cellulaire et Tissulaire (PICT), 51097 Reims Cedex, France; (V.U.); (C.T.)
| | - Roselyne Garnotel
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
- Laboratoire de Biochimie-Pharmacologie-Toxicologie, Centre Hospitalier Universitaire de Reims, 51092 Reims, France
| | - Aude Marchal
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
- Service d’Anatomie et Cytologie Pathologique, Centre Hospitalier Universitaire de Reims, 51100 Reims, France
| | - Cyril Gobinet
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
| | - Christine Terryn
- Université de Reims Champagne-Ardenne, Plateforme en Imagerie Cellulaire et Tissulaire (PICT), 51097 Reims Cedex, France; (V.U.); (C.T.)
| | - Ganesh D. Sockalingum
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
| | - Gérard Thiéfin
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
- Service d’Hépato-Gastroentérologie et de Cancérologie Digestive, Centre Hospitalier Universitaire de Reims, 51092 Reims, France
- Correspondence: ; Tel.: +33-6-87517-344; Fax: +33-3-26788-836
| |
Collapse
|
8
|
Suryadevara V, Nazeer SS, Sreedhar H, Adelaja O, Kajdacsy-Balla A, Natarajan V, Walsh MJ. Infrared spectral microscopy as a tool to monitor lung fibrosis development in a model system. BIOMEDICAL OPTICS EXPRESS 2020; 11:3996-4007. [PMID: 33014581 PMCID: PMC7510888 DOI: 10.1364/boe.394730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
Tissue fibrosis is a progressive and destructive disease process that can occur in many different organs including the liver, kidney, skin, and lungs. Fibrosis is typically initiated by inflammation as a result of chronic insults such as infection, chemicals and autoimmune diseases. Current approaches to examine organ fibrosis are limited to radiological and histological analyses. Infrared spectroscopic imaging offers a potential alternative approach to gain insight into biochemical changes associated with fibrosis progression. In this study, we demonstrate that IR imaging of a mouse model of pulmonary fibrosis can identify biochemical changes observed with fibrosis progression and the beginning of resolution using K-means analysis, spectral ratios and multivariate data analysis. This study demonstrates that IR imaging may be a useful approach to understand the biochemical events associated with fibrosis initiation, progression and resolution for both the clinical setting and for assessing novel anti-fibrotic drugs in a model system.
Collapse
Affiliation(s)
- Vidyani Suryadevara
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Shaiju S. Nazeer
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Hari Sreedhar
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Oluwatobi Adelaja
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - André Kajdacsy-Balla
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Viswanathan Natarajan
- Department of Pharmacology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Contributed equally as senior co-authors
| | - Michael J. Walsh
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Contributed equally as senior co-authors
| |
Collapse
|
9
|
Mittal S, Bhargava R. A comparison of mid-infrared spectral regions on accuracy of tissue classification. Analyst 2019; 144:2635-2642. [PMID: 30839958 DOI: 10.1039/c8an01782d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Infrared (IR) spectroscopic imaging, utilizing both the molecular and structural disease signatures, enables extensive profiling of tumors and their microenvironments. Here, we examine the relative merits of using either the fingerprint or the high frequency regions of the IR spectrum for tissue histopathology. We selected a complex model as a test case, evaluating both stromal and epithelial segmentation for various breast pathologies. IR spectral classification in each of these spectral windows is quantitatively assessed by estimating area under the curve (AUC) of the receiver operating characteristic curve (ROC) for pixel level accuracy and images for diagnostic ability. We found only small differences, though some that may be sufficiently important in diagnostic tasks to be clinically significant, between the two regions with the fingerprint region-based classifiers consistently emerging as more accurate. The work provides added evidence and comparison with fingerprint region, complex models, and previously untested tissue type (breast) - that the use of restricted spectral regions can provide high accuracy. Our study indicates that the fingerprint region is ideal for epithelial and stromal models to obtain high pixel level accuracies. Glass slides provide a limited spectral feature set but provides accurate information at the patient level.
Collapse
Affiliation(s)
- Shachi Mittal
- Department of Bioengineering and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
| | | |
Collapse
|
10
|
Byrne HJ, Bonnier F, Farhane Z. Two-dimensional correlation analysis of Raman microspectroscopy of subcellular interactions of drugs in vitro. JOURNAL OF BIOPHOTONICS 2019; 12:e201800328. [PMID: 30414254 DOI: 10.1002/jbio.201800328] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/06/2018] [Accepted: 11/06/2018] [Indexed: 05/24/2023]
Abstract
Two-dimensional (2D) correlation analysis is explored to data mine the time evolution of the characteristic Raman microspectroscopic signatures of the subcellular responses of the nucleoli of human lung cancer cells to the uptake of doxorubicin. A simulated dataset of experimental control spectra, perturbed with systematically time-dependent spectral changes, constituted by a short-term response which represents the initial binding of the drug in the nucleolus, followed by a longer term response of the organelle metabolism, is used to validate the analysis protocol. Applying 2D correlation analysis, the in phase, synchronous correlation coefficients are seen to contain contributions of both response profiles, whereas they can be independently extracted from the out of phase, asynchronous correlation coefficients. The methodology is applied to experimental data of the uptake of doxorubicin in human lung cell lines to differentiate the signatures of chemical binding and subsequent cellular response.
Collapse
Affiliation(s)
- Hugh J Byrne
- FOCAS Research Institute, Dublin Institute of Technology, Dublin, Ireland
| | - Franck Bonnier
- Université François-Rabelais de Tours, Faculty of Pharmacy, EA 6295 Nanomédicaments et Nanosondes, Tours, France
| | - Zeineb Farhane
- FOCAS Research Institute, Dublin Institute of Technology, Dublin, Ireland
- School of Physics and Clinical & Optometric Sciences, Dublin Institute of Technology, Dublin, Ireland
| |
Collapse
|
11
|
Isensee K, Kröger-Lui N, Petrich W. Biomedical applications of mid-infrared quantum cascade lasers - a review. Analyst 2019; 143:5888-5911. [PMID: 30444222 DOI: 10.1039/c8an01306c] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mid-infrared spectroscopy has been applied to research in biology and medicine for more than 20 years and conceivable applications have been identified. More recently, these applications have been shown to benefit from the use of quantum cascade lasers due to their specific properties, namely high spectral power density, small beam parameter product, narrow emission spectrum and, if needed, tuning capabilities. This review provides an overview of the achievements and illustrates some applications which benefit from the key characteristics of quantum cascade laser-based mid-infrared spectroscopy using examples such as breath analysis, the investigation of serum, non-invasive glucose monitoring in bulk tissue and the combination of spectroscopy and microscopy of tissue thin sections for rapid histopathology.
Collapse
Affiliation(s)
- Katharina Isensee
- Kirchhoff-Institute for Physics, Heidelberg University, INF 277, 69120 Heidelberg, Germany.
| | | | | |
Collapse
|
12
|
Neagu AN. Proteome Imaging: From Classic to Modern Mass Spectrometry-Based Molecular Histology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:55-98. [PMID: 31347042 DOI: 10.1007/978-3-030-15950-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In order to overcome the limitations of classic imaging in Histology during the actually era of multiomics, the multi-color "molecular microscope" by its emerging "molecular pictures" offers quantitative and spatial information about thousands of molecular profiles without labeling of potential targets. Healthy and diseased human tissues, as well as those of diverse invertebrate and vertebrate animal models, including genetically engineered species and cultured cells, can be easily analyzed by histology-directed MALDI imaging mass spectrometry. The aims of this review are to discuss a range of proteomic information emerging from MALDI mass spectrometry imaging comparative to classic histology, histochemistry and immunohistochemistry, with applications in biology and medicine, concerning the detection and distribution of structural proteins and biological active molecules, such as antimicrobial peptides and proteins, allergens, neurotransmitters and hormones, enzymes, growth factors, toxins and others. The molecular imaging is very well suited for discovery and validation of candidate protein biomarkers in neuroproteomics, oncoproteomics, aging and age-related diseases, parasitoproteomics, forensic, and ecotoxicology. Additionally, in situ proteome imaging may help to elucidate the physiological and pathological mechanisms involved in developmental biology, reproductive research, amyloidogenesis, tumorigenesis, wound healing, neural network regeneration, matrix mineralization, apoptosis and oxidative stress, pain tolerance, cell cycle and transformation under oncogenic stress, tumor heterogeneity, behavior and aggressiveness, drugs bioaccumulation and biotransformation, organism's reaction against environmental penetrating xenobiotics, immune signaling, assessment of integrity and functionality of tissue barriers, behavioral biology, and molecular origins of diseases. MALDI MSI is certainly a valuable tool for personalized medicine and "Eco-Evo-Devo" integrative biology in the current context of global environmental challenges.
Collapse
Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania.
| |
Collapse
|
13
|
Ali MH, Rakib F, Al-Saad K, Al-Saady R, Lyng FM, Goormaghtigh E. A simple model for cell type recognition using 2D-correlation analysis of FTIR images from breast cancer tissue. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.03.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
14
|
Quantum Cascade Laser-Based Infrared Microscopy for Label-Free and Automated Cancer Classification in Tissue Sections. Sci Rep 2018; 8:7717. [PMID: 29769696 PMCID: PMC5955970 DOI: 10.1038/s41598-018-26098-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/02/2018] [Indexed: 02/01/2023] Open
Abstract
A feasibility study using a quantum cascade laser-based infrared microscope for the rapid and label-free classification of colorectal cancer tissues is presented. Infrared imaging is a reliable, robust, automated, and operator-independent tissue classification method that has been used for differential classification of tissue thin sections identifying tumorous regions. However, long acquisition time by the so far used FT-IR-based microscopes hampered the clinical translation of this technique. Here, the used quantum cascade laser-based microscope provides now infrared images for precise tissue classification within few minutes. We analyzed 110 patients with UICC-Stage II and III colorectal cancer, showing 96% sensitivity and 100% specificity of this label-free method as compared to histopathology, the gold standard in routine clinical diagnostics. The main hurdle for the clinical translation of IR-Imaging is overcome now by the short acquisition time for high quality diagnostic images, which is in the same time range as frozen sections by pathologists.
Collapse
|
15
|
Pucetaite M, Velicka M, Urboniene V, Ceponkus J, Bandzeviciute R, Jankevicius F, Zelvys A, Sablinskas V, Steiner G. Rapid intra-operative diagnosis of kidney cancer by attenuated total reflection infrared spectroscopy of tissue smears. JOURNAL OF BIOPHOTONICS 2018; 11:e201700260. [PMID: 29316381 DOI: 10.1002/jbio.201700260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/06/2018] [Indexed: 05/13/2023]
Abstract
Herein, a technique to analyze air-dried kidney tissue impression smears by means of attenuated total reflection infrared (ATR-IR) spectroscopy is presented. Spectral tumor markers-absorption bands of glycogen-are identified in the ATR-IR spectra of the kidney tissue smear samples. Thin kidney tissue cryo-sections currently used for IR spectroscopic analysis lack such spectral markers as the sample preparation causes irreversible molecular changes in the tissue. In particular, freeze-thaw cycle results in degradation of the glycogen and reduction or complete dissolution of its content. Supervised spectral classification was applied to the recorded spectra of the smears and the test spectra were classified with a high accuracy of 92% for normal tissue and 94% for tumor tissue, respectively. For further development, we propose that combination of the method with optical fiber ATR probes could potentially be used for rapid real-time intra-operative tissue analysis without interfering with either the established protocols of pathological examination or the ordinary workflow of operating surgeon. Such approach could ensure easier transition of the method to clinical applications where it may complement the results of gold standard histopathology examination and aid in more precise resection of kidney tumors.
Collapse
Affiliation(s)
- Milda Pucetaite
- Department of General Physics and Spectroscopy, Vilnius University, Vilnius, Lithuania
| | - Martynas Velicka
- Department of General Physics and Spectroscopy, Vilnius University, Vilnius, Lithuania
| | - Vidita Urboniene
- Department of General Physics and Spectroscopy, Vilnius University, Vilnius, Lithuania
| | - Justinas Ceponkus
- Department of General Physics and Spectroscopy, Vilnius University, Vilnius, Lithuania
| | - Rimante Bandzeviciute
- Department of General Physics and Spectroscopy, Vilnius University, Vilnius, Lithuania
| | - Feliksas Jankevicius
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania
- Lithuanian National Cancer Institute, Vilnius, Lithuania
| | - Arunas Zelvys
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Valdas Sablinskas
- Department of General Physics and Spectroscopy, Vilnius University, Vilnius, Lithuania
| | - Gerald Steiner
- Department of General Physics and Spectroscopy, Vilnius University, Vilnius, Lithuania
- Faculty of Medicine Carl Gustav Carus, Clinical Sensoring and Monitoring, Dresden University of Technology, Dresden, Germany
| |
Collapse
|
16
|
Wrobel TP, Bhargava R. Infrared Spectroscopic Imaging Advances as an Analytical Technology for Biomedical Sciences. Anal Chem 2018; 90:1444-1463. [PMID: 29281255 PMCID: PMC6421863 DOI: 10.1021/acs.analchem.7b05330] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Tomasz P. Wrobel
- Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801, United States
| | - Rohit Bhargava
- Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801, United States
- Departments of Bioengineering, Electrical and Computer Engineering, Mechanical Science and Engineering, Chemical and Biomolecular Engineering, and Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
17
|
Predicting Fibrosis Progression in Renal Transplant Recipients Using Laser-Based Infrared Spectroscopic Imaging. Sci Rep 2018; 8:686. [PMID: 29330374 PMCID: PMC5766495 DOI: 10.1038/s41598-017-19006-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/20/2017] [Indexed: 12/22/2022] Open
Abstract
Renal transplants have not seen a significant improvement in their 10-year graft life. Chronic damage accumulation often leads to interstitial fibrosis and tubular atrophy (IF/TA) and thus graft function loss over time. For this reason, IF/TA has been the chief suspect for a potential prognostic marker for long term outcomes. In this study, we have used infrared spectroscopic (IR) imaging to interrogate the biochemistry of regions of fibrosis from renal transplant biopsies to identify a biochemical signature that can predict rapid progression of fibrosis. IR imaging represents an approach that permits label-free biochemical imaging of human tissues towards identifying novel biomarkers for disease diagnosis or prognosis. Two cohorts were identified as progressors (n = 5, > 50% fibrosis increase between time points) and non-progressors (n = 5, < 5% increase between time points). Each patient had an early time point and late time point biopsy. Collagen associated carbohydrate moieties (ν(C–O), 1035 cm−1 and ν(C–O–C),1079 cm−1) spectral ratios demonstrated good separation between the two cohorts (p = 0.001). This was true for late and early time point biopsies suggesting the regions of fibrosis are biochemically altered in cases undergoing progressive fibrosis. Thus, IR imaging can potentially predict rapid progression of fibrosis using histologically normal early time point biopsies.
Collapse
|
18
|
Nazeer SS, Sreedhar H, Varma VK, Martinez-Marin D, Massie C, Walsh MJ. Infrared spectroscopic imaging: Label-free biochemical analysis of stroma and tissue fibrosis. Int J Biochem Cell Biol 2017; 92:14-17. [PMID: 28888785 DOI: 10.1016/j.biocel.2017.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
Infrared spectroscopic tissue imaging is a potentially powerful adjunct tool to current histopathology techniques. By coupling the biochemical signature obtained through infrared spectroscopy to the spatial information offered by microscopy, this technique can selectively analyze the chemical composition of different features of unlabeled, unstained tissue sections. In the past, the tissue features that have received the most interest were parenchymal and epithelial cells, chiefly due to their involvement in dysplasia and progression to carcinoma; however, the field has recently turned its focus toward stroma and areas of fibrotic change. These components of tissue present an untapped source of biochemical information that can shed light on many diverse disease processes, and potentially hold useful predictive markers for these same pathologies. Here we review the recent applications of infrared spectroscopic imaging to stromal and fibrotic regions of diseased tissue, and explore the potential of this technique to advance current capabilities for tissue analysis.
Collapse
Affiliation(s)
- Shaiju S Nazeer
- Department of Pathology, University of Illinois at Chicago, 840 S Wood St. 130 CSN, Chicago, IL 60612, USA
| | - Hari Sreedhar
- Department of Pathology, University of Illinois at Chicago, 840 S Wood St. 130 CSN, Chicago, IL 60612, USA
| | - Vishal K Varma
- Department of Bioengineering, University of Illinois at Chicago, 851 S. Morgan St. 218 SEO, Chicago, IL 60607, USA
| | - David Martinez-Marin
- Department of Pathology, University of Illinois at Chicago, 840 S Wood St. 130 CSN, Chicago, IL 60612, USA
| | - Christine Massie
- Department of Pathology, University of Illinois at Chicago, 840 S Wood St. 130 CSN, Chicago, IL 60612, USA
| | - Michael J Walsh
- Department of Pathology, University of Illinois at Chicago, 840 S Wood St. 130 CSN, Chicago, IL 60612, USA; Department of Bioengineering, University of Illinois at Chicago, 851 S. Morgan St. 218 SEO, Chicago, IL 60607, USA.
| |
Collapse
|
19
|
Spectroscopic imaging of biomaterials and biological systems with FTIR microscopy or with quantum cascade lasers. Anal Bioanal Chem 2017; 409:5813-5820. [PMID: 28852781 PMCID: PMC5602084 DOI: 10.1007/s00216-017-0574-5] [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: 06/06/2017] [Revised: 07/26/2017] [Accepted: 08/07/2017] [Indexed: 12/22/2022]
Abstract
Spectroscopic imaging of biomaterials and biological systems has received increased interest within the last decade because of its potential to aid in the detection of disease using biomaterials/biopsy samples and to probe the states of live cells in a label-free manner. The factors behind this increased attention include the availability of improved infrared microscopes and systems that do not require the use of a synchrotron as a light source, as well as the decreasing costs of these systems. This article highlights the current technical challenges and future directions of mid-infrared spectroscopic imaging within this field. Specifically, these are improvements in spatial resolution and spectral quality through the use of novel added lenses and computational algorithms, as well as quantum cascade laser imaging systems, which offer advantages over traditional Fourier transform infrared systems with respect to the speed of acquisition and field of view. Overcoming these challenges will push forward spectroscopic imaging as a viable tool for disease diagnostics and medical research. Absorbance images of a biopsy obtained using an FTIR imaging microscope with and without an added lens, and also using a QCL microscope with high-NA objective. ![]()
Collapse
|