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Lippitt WL, Maier LA, Fingerlin TE, Lynch DA, Yadav R, Rieck J, Hill AC, Liao SY, Mroz MM, Barkes BQ, Chae KJ, Hwang HJ, Carlson NE. The textures of sarcoidosis: quantifying lung disease through variograms. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.20.24307618. [PMID: 38826353 PMCID: PMC11142277 DOI: 10.1101/2024.05.20.24307618] [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
Objective Sarcoidosis is a granulomatous disease affecting the lungs in over 90% of patients. Qualitative assessment of chest CT by radiologists is standard clinical practice and reliable quantification of disease from CT would support ongoing efforts to identify sarcoidosis phenotypes. Standard imaging feature engineering techniques such as radiomics suffer from extreme sensitivity to image acquisition and processing, potentially impeding generalizability of research to clinical populations. In this work, we instead investigate approaches to engineering variogram-based features with the intent to identify a robust, generalizable pipeline for image quantification in the study of sarcoidosis. Approach For a cohort of more than 300 individuals with sarcoidosis, we investigated 24 feature engineering pipelines differing by decisions for image registration to a template lung, empirical and model variogram estimation methods, and feature harmonization for CT scanner model, and subsequently 48 sets of phenotypes produced through unsupervised clustering. We then assessed sensitivity of engineered features, phenotypes produced through unsupervised clustering, and sarcoidosis disease signal strength to pipeline. Main results We found that variogram features had low to mild association with scanner model and associations were reduced by image registration. For each feature type, features were also typically robust to all pipeline decisions except image registration. Strength of disease signal as measured by association with pulmonary function testing and some radiologist visual assessments was strong (optimistic AUC ≈ 0.9, p ≪ 0.0001 in models for architectural distortion, conglomerate mass, fibrotic abnormality, and traction bronchiectasis) and fairly consistent across engineering approaches regardless of registration and harmonization for CT scanner. Significance Variogram-based features appear to be a suitable approach to image quantification in support of generalizable research in pulmonary sarcoidosis.
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Affiliation(s)
- William L Lippitt
- Dept of Biostatistics and Informatics, Uni. of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lisa A Maier
- Dept of Medicine, National Jewish Health, Denver, CO, USA
- Dept of Medicine, Uni. of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Environmental and Occupational Health, Uni. of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tasha E Fingerlin
- Dept of Biostatistics and Informatics, Uni. of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
| | - David A Lynch
- Dept of Radiology, National Jewish Health, Denver, CO, USA
| | - Ruchi Yadav
- Dept of Diagnostic Radiology, Cleveland Clinic, Cleveland, OH, USA
| | - Jared Rieck
- Dept of Biostatistics and Informatics, Uni. of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew C Hill
- Dept of Biostatistics and Informatics, Uni. of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Shu-Yi Liao
- Dept of Medicine, National Jewish Health, Denver, CO, USA
- Dept of Medicine, Uni. of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | | | - Kum Ju Chae
- Dept of Radiology, Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Jeollabuk-do, Korea
| | - Hye Jeon Hwang
- Dept of Radiology and Research Institute of Radiology, University of Ulsan College of Medicine, Asan Medical Center, 86 Asanbyeongwon-Gil, Songpa-Gu, Seoul, Korea
| | - Nichole E Carlson
- Dept of Biostatistics and Informatics, Uni. of Colorado Anschutz Medical Campus, Aurora, CO, USA
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Nanoscale Prognosis of Colorectal Cancer Metastasis from AFM Image Processing of Histological Sections. Cancers (Basel) 2023; 15:cancers15041220. [PMID: 36831563 PMCID: PMC9953928 DOI: 10.3390/cancers15041220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/05/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Early ascertainment of metastatic tumour phases is crucial to improve cancer survival, formulate an accurate prognostic report of disease advancement, and, most importantly, quantify the metastatic progression and malignancy state of primary cancer cells with a universal numerical indexing system. This work proposes an early improvement to metastatic cancer detection with 97.7 nm spatial resolution by indexing the metastatic cancer phases from the analysis of atomic force microscopy images of human colorectal cancer histological sections. The procedure applies variograms of residuals of Gaussian filtering and theta statistics of colorectal cancer tissue image settings. This methodology elucidates the early metastatic progression at the nanoscale level by setting metastatic indexes and critical thresholds based on relatively large histological sections and categorising the malignancy state of a few suspicious cells not identified with optical image analysis. In addition, we sought to detect early tiny morphological differentiations indicating potential cell transition from epithelial cell phenotypes of low metastatic potential to those of high metastatic potential. This metastatic differentiation, which is also identified in higher moments of variograms, sets different hierarchical levels for metastatic progression dynamics.
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Karri S, Aviel-Ronen S, Firer MA. Fractal and textural imaging identify new subgroups of patients with colorectal cancer based on biophysical properties of the cancer cells. Pathol Res Pract 2022; 238:154040. [PMID: 36057191 DOI: 10.1016/j.prp.2022.154040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/19/2022] [Accepted: 07/26/2022] [Indexed: 10/16/2022]
Abstract
Colorectal cancer (CRC) can been sub-divided, based on the generation of tertiary lymphoid structures (TLS), into CRC with a Crohn's like lymphoid reaction (CLR) representing de novo formation of TLSs or CRC lacking TLSs that show Diffuse Inflammatory infiltration (DII). The association between TLS, early treatment initiation and longer survival highlights the need for deeper patient stratification that could lead to more targeted therapies. We hypothesized that such stratification might be achieved by using digital image analyses. Here we retrospectively analyzed 35 CRC patient samples classified as CLR or DII by digital analysis, focusing on the parameters Fractal dimension, Lacunarity and the textural features Angular second momentum, Correlation, Inverse difference momentum and Entropy. Significant differences in the grades of these parameters between the two patient groups provided preliminary data that additional biophysical information can divide CRC into at least 3 subgroups which encompass CLR and DII. Additional studies are needed to test if this sub-classification aids in the selection of targeted therapy for patients with CRC.
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Affiliation(s)
- Sirish Karri
- Department of Chemical Engineering, Ariel University, Ariel 40700, Israel
| | | | - Michael A Firer
- Department of Chemical Engineering, Ariel University, Ariel 40700, Israel; Adelson School of Medicine, Ariel University, Ariel 40700, Israel; Ariel Center for Applied Cancer Research, Ariel University, Ariel 40700, Israel.
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Lobo J, See EYS, Biggs M, Pandit A. An insight into morphometric descriptors of cell shape that pertain to regenerative medicine. J Tissue Eng Regen Med 2015; 10:539-53. [DOI: 10.1002/term.1994] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/25/2014] [Accepted: 12/09/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Joana Lobo
- Network of Excellence for Functional Biomaterials (NFB); National University of Ireland; Galway Ireland
| | - Eugene Yong-Shun See
- Network of Excellence for Functional Biomaterials (NFB); National University of Ireland; Galway Ireland
| | - Manus Biggs
- Network of Excellence for Functional Biomaterials (NFB); National University of Ireland; Galway Ireland
| | - Abhay Pandit
- Network of Excellence for Functional Biomaterials (NFB); National University of Ireland; Galway Ireland
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Abstract
Fractal characteristics of chromatin, revealed by light or electron microscopy, have been reported during the last 20 years. Fractal features can easily be estimated in digitalized microscopic images and are helpful for diagnosis and prognosis of neoplasias. During carcinogenesis and tumor progression, an increase of the fractal dimension (FD) of stained nuclei has been shown in intraepithelial lesions of the uterine cervix and the anus, oral squamous cell carcinomas or adenocarcinomas of the pancreas. Furthermore, an increased FD of chromatin is an unfavorable prognostic factor in squamous cell carcinomas of the oral cavity and the larynx, melanomas and multiple myelomas. High goodness-of-fit of the regression line of the FD is a favorable prognostic factor in acute leukemias and multiple myelomas. The nucleus has fractal and power-law organization in several different levels, which might in part be interrelated. Some possible relations between modifications of the chromatin organization during carcinogenesis and tumor progression and an increase of the FD of stained chromatin are suggested. Furthermore, increased complexity of the chromatin structure, loss of heterochromatin and a less-perfect self-organization of the nucleus in aggressive neoplasias are discussed.
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Affiliation(s)
- Konradin Metze
- Department of Pathology, Faculty of Medical Sciences Research Group, 'Analytical Cellular Pathology' and National Institute of Photonics Applied to Cell Biology, University of Campinas, Campinas, Brazil +55 19 32893897 kmetze.at.fcm.unicamp.br
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Pantic I, Harhaji-Trajkovic L, Pantovic A, Milosevic NT, Trajkovic V. Changes in fractal dimension and lacunarity as early markers of UV-induced apoptosis. J Theor Biol 2012; 303:87-92. [PMID: 22763132 DOI: 10.1016/j.jtbi.2012.03.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 03/08/2012] [Accepted: 03/13/2012] [Indexed: 12/30/2022]
Abstract
The aim of our study was to employ fractal analysis for evaluation of ultrastructural changes during early stages of apoptosis. Apoptosis was induced in U251 human glioma cell line by exposure to UVB light. The cells were visualized by optical phase-contrast microscopy and photographed before the UV treatment, immediately after the treatment, as well as at 30 min intervals during 5h observation period. For each of the 32 cells analyzed, cellular and nuclear fractal dimension, as well as nuclear lacunarity, were determined at each time point. Our data demonstrate that cellular ultrastructural complexity determined by fractal dimension and lacunarity significantly decreases after the UV irradiation, with the nuclear lacunarity being a particularly sensitive parameter in detecting early apoptosis. Importantly, fractal analysis was able to detect cellular apoptotic changes earlier than conventional flow cytometric analysis of phosphatidylserine exposure, DNA fragmentation and cell membrane permeabilization. These results indicate that fractal analysis might be a powerful and affordable method for non-invasive early identification of apoptosis in cell cultures.
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Affiliation(s)
- Igor Pantic
- Institute of Medical Physiology, School of Medicine, University of Belgrade, Visegradska 26/II, 11000 Belgrade, Serbia.
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Mitręga K, Zorniak M, Varghese B, Lange D, Nożynski J, Porc M, Białka S, Krzemiński TF. Beneficial effects of l-leucine and l-valine on arrhythmias, hemodynamics and myocardial morphology in rats. Pharmacol Res 2011; 64:218-25. [PMID: 21605982 DOI: 10.1016/j.phrs.2011.04.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 04/14/2011] [Accepted: 04/26/2011] [Indexed: 01/19/2023]
Abstract
Branched chain amino acids (BCAA) have been shown to have a general protective effect on the heart in different animal models as well as in humans. However, so far no attempt has been made to specifically elucidate their influence on arrhythmias. Our study was performed to evaluate whether an infusion of either l-leucine or l-valine in a dose of 1mgkg(-1)h(-1) 10min before a 7-min period of left anterior descending artery occlusion followed by 15min of reperfusion, had an effect on arrhythmias measured during the reperfusion phase in the ischemia- and reperfusion-induced arrhythmias model in rats in vivo. The effect of the infusion of these substances on mean arterial blood pressure was monitored throughout the experiment. Both of the tested amino acids exhibited significant antiarrhythmic properties. l-Leucine reduced the duration of ventricular fibrillation (P<0.05) and l-valine decreased the duration of ventricular fibrillation (P<0.001) and ventricular tachycardia (P<0.05). The two amino acids were generally hypotensive. l-Valine lowered blood pressure in all phases of the experiment (P<0.05) while l-leucine lowered this parameter mainly towards the end of occlusion and reperfusion (P<0.05). In addition, 30min infusion of the amino acids in the used dose did not produce any apparent adverse histological changes that were remarkably different from control. In summary, the results of our study suggest that l-leucine and l-valine in the dose that was used attenuates arrhythmias and are hypotensive in their influence. Our findings lend support to the many ongoing investigations into the benefit of the application of l-leucine and l-valine in cardiology like their addition to cardioplegic solutions.
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Affiliation(s)
- Katarzyna Mitręga
- Chair and Department of Pharmacology, Medical University of Silesia, ul. Jordana 19, 41-808 Zabrze, Poland.
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