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Sarić A, Rajić J, Tolić A, Dučić T, Vidaković M. Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 302:123090. [PMID: 37413921 DOI: 10.1016/j.saa.2023.123090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive and label-free technique for identifying subtle changes in all bio-macromolecules, and has been used as a method of choice for studying DNA conformation, secondary DNA structure transition and DNA damage. In addition, the specific level of chromatin complexity is introduced via epigenetic modifications forcing the technological upgrade in the analysis of such an intricacy. As the most studied epigenetic mechanism, DNA methylation is a major regulator of transcriptional activity, involved in the suppression of a broad spectrum of genes and its deregulation is involved in all non-communicable diseases. The present study was designed to explore the use of synchrotron-based FTIR analysis to monitor the subtle changes in molecule bases regarding the DNA methylation status of cytosine in the whole genome. In order to reveal the conformation-related best sample for FTIR-based DNA methylation analysis in situ, we used methodology for nuclear HALO preparations and slightly modified it to isolated DNA in HALO formations. Nuclear DNA-HALOs represent samples with preserved higher-order chromatin structure liberated of any protein residues that are closer to native DNA conformation than genomic DNA (gDNA) isolated by the standard batch procedure. Using FTIR spectroscopy we analyzed the DNA methylation profile of isolated gDNA and compared it with the DNA-HALOs. This study demonstrated the potential of FTIR microspectroscopy to detect DNA methylation marks in analyzed DNA-HALO specimens more precisely in comparison with classical DNA extraction procedures that yield unstructured whole genomic DNA. In addition, we used different cell types to assess their global DNA methylation profile, as well as defined specific infrared peaks that can be used for screening DNA methylation.
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Affiliation(s)
- Ana Sarić
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia.
| | - Jovana Rajić
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia.
| | - Anja Tolić
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia.
| | - Tanja Dučić
- ALBA CELLS Synchrotron, Carrer de la Llum 2-26, Cerdanyola del Valles, 08290 Barcelona, Spain.
| | - Melita Vidaković
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia.
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Qin X, Zhang M, Zhou C, Ran T, Pan Y, Deng Y, Xie X, Zhang Y, Gong T, Zhang B, Zhang L, Wang Y, Li Q, Wang D, Gao L, Zou D. A deep learning model using hyperspectral image for EUS-FNA cytology diagnosis in pancreatic ductal adenocarcinoma. Cancer Med 2023; 12:17005-17017. [PMID: 37455599 PMCID: PMC10501295 DOI: 10.1002/cam4.6335] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 06/12/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND AND AIMS Endoscopic ultrasonography-guided fine-needle aspiration/biopsy (EUS-FNA/B) is considered to be a first-line procedure for the pathological diagnosis of pancreatic cancer owing to its high accuracy and low complication rate. The number of new cases of pancreatic ductal adenocarcinoma (PDAC) is increasing, and its accurate pathological diagnosis poses a challenge for cytopathologists. Our aim was to develop a hyperspectral imaging (HSI)-based convolution neural network (CNN) algorithm to aid in the diagnosis of pancreatic EUS-FNA cytology specimens. METHODS HSI images were captured of pancreatic EUS-FNA cytological specimens from benign pancreatic tissues (n = 33) and PDAC (n = 39) prepared using a liquid-based cytology method. A CNN was established to test the diagnostic performance, and Attribution Guided Factorization Visualization (AGF-Visualization) was used to visualize the regions of important classification features identified by the model. RESULTS A total of 1913 HSI images were obtained. Our ResNet18-SimSiam model achieved an accuracy of 0.9204, sensitivity of 0.9310 and specificity of 0.9123 (area under the curve of 0.9625) when trained on HSI images for the differentiation of PDAC cytological specimens from benign pancreatic cells. AGF-Visualization confirmed that the diagnoses were based on the features of tumor cell nuclei. CONCLUSIONS An HSI-based model was developed to diagnose cytological PDAC specimens obtained using EUS-guided sampling. Under the supervision of experienced cytopathologists, we performed multi-staged consecutive in-depth learning of the model. Its superior diagnostic performance could be of value for cytologists when diagnosing PDAC.
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Affiliation(s)
- Xianzheng Qin
- Department of GastroenterologyRuijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Minmin Zhang
- Department of GastroenterologyRuijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Chunhua Zhou
- Department of GastroenterologyRuijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Taojing Ran
- Department of GastroenterologyRuijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Yundi Pan
- Department of GastroenterologyRuijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Yingjiao Deng
- Shanghai Key Laboratory of Multidimensional Information ProcessingEast China Normal UniversityShanghaiChina
| | - Xingran Xie
- Shanghai Key Laboratory of Multidimensional Information ProcessingEast China Normal UniversityShanghaiChina
| | - Yao Zhang
- Department of GastroenterologyRuijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Tingting Gong
- Department of GastroenterologyRuijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Benyan Zhang
- Department of PathologyRuijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Ling Zhang
- Department of GastroenterologyRuijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Yan Wang
- Shanghai Key Laboratory of Multidimensional Information ProcessingEast China Normal UniversityShanghaiChina
| | - Qingli Li
- Shanghai Key Laboratory of Multidimensional Information ProcessingEast China Normal UniversityShanghaiChina
| | - Dong Wang
- Department of GastroenterologyRuijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Lili Gao
- Department of PathologyRuijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
| | - Duowu Zou
- Department of GastroenterologyRuijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
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Agrawal T, Paul D, Saroj S, Ali A, Choubey V, Mukherjee D, Pal S, Rakshit T. Label-Free Physical-Analytical Techniques Reveal Epigenetic Modifications of Breast Cancer Chromosomes. J Phys Chem B 2023; 127:3534-3542. [PMID: 37036757 DOI: 10.1021/acs.jpcb.3c00147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Epigenetic dysregulation including DNA methylation and histone modifications is being increasingly recognized as a promising biomarker for the diagnosis and prognosis of cancer. Herein, we devised a label-free analytical toolbox comprising IR, UV-vis, CD spectroscopy, and cyclic voltammetry, which is capable to differentiate significantly hyper-methylated breast cancer chromosomes from the normal breast epithelial counterparts.
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Affiliation(s)
- Tanya Agrawal
- Department of Chemistry, Shiv Nadar IoE, Delhi-NCR, Uttar Pradesh 201314, India
| | - Debashish Paul
- Department of Chemistry, Shiv Nadar IoE, Delhi-NCR, Uttar Pradesh 201314, India
| | - Saroj Saroj
- Department of Chemistry, Shiv Nadar IoE, Delhi-NCR, Uttar Pradesh 201314, India
| | - Akbar Ali
- Department of Chemistry, Indian Institute of Technology, Bhilai, Chhattisgarh 492015, India
| | - Vivekanand Choubey
- Department of Chemistry, Shiv Nadar IoE, Delhi-NCR, Uttar Pradesh 201314, India
| | - Dipanjan Mukherjee
- Laboratory of Bioimaging and Pathologies, University of Strasbourg, F-67081 Strasbourg CEDEX, France
| | - Suchetan Pal
- Department of Chemistry, Indian Institute of Technology, Bhilai, Chhattisgarh 492015, India
| | - Tatini Rakshit
- Department of Chemistry, Shiv Nadar IoE, Delhi-NCR, Uttar Pradesh 201314, India
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Szymoński K, Chmura Ł, Lipiec E, Adamek D. Vibrational spectroscopy – are we close to finding a solution for early pancreatic cancer diagnosis? World J Gastroenterol 2023; 29:96-109. [PMID: 36683712 PMCID: PMC9850953 DOI: 10.3748/wjg.v29.i1.96] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/03/2022] [Accepted: 10/31/2022] [Indexed: 01/04/2023] Open
Abstract
Pancreatic cancer (PC) is an aggressive and lethal neoplasm, ranking seventh in the world for cancer deaths, with an overall 5-year survival rate of below 10%. The knowledge about PC pathogenesis is rapidly expanding. New aspects of tumor biology, including its molecular and morphological heterogeneity, have been reported to explain the complicated “cross-talk” that occurs between the cancer cells and the tumor stroma or the nature of pancreatic ductal adenocarcinoma-associated neural remodeling. Nevertheless, currently, there are no specific and sensitive diagnosis options for PC. Vibrational spectroscopy (VS) shows a promising role in the development of early diagnosis technology. In this review, we summarize recent reports about improvements in spectroscopic methodologies, briefly explain and highlight the drawbacks of each of them, and discuss available solutions. The important aspects of spectroscopic data evaluation with multivariate analysis and a convolutional neural network methodology are depicted. We conclude by presenting a study design for systemic verification of the VS-based methods in the diagnosis of PC.
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Affiliation(s)
- Krzysztof Szymoński
- Department of Pathomorphology, Jagiellonian University Medical College, Cracow 33-332, Poland
- Department of Pathomorphology, University Hospital in Cracow, Cracow 31-501, Poland
| | - Łukasz Chmura
- Department of Pathomorphology, Jagiellonian University Medical College, Cracow 33-332, Poland
- Department of Pathomorphology, University Hospital in Cracow, Cracow 31-501, Poland
| | - Ewelina Lipiec
- M. Smoluchowski Institute of Physics, Jagiellonian University, Cracow 30-348, Poland
| | - Dariusz Adamek
- Department of Pathomorphology, University Hospital in Cracow, Cracow 31-501, Poland
- Department of Neuropathology, Jagiellonian University Medical College, Cracow 33-332, Poland
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Mello MLS. Sodium Valproate-Induced Chromatin Remodeling. Front Cell Dev Biol 2021; 9:645518. [PMID: 33959607 PMCID: PMC8093769 DOI: 10.3389/fcell.2021.645518] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
Valproic acid/sodium valproate (VPA), a drug originally prescribed as an anticonvulsant, has been widely reported to act on epigenetic marks by inducing histone acetylation, affecting the DNA and histone methylation status, and altering the expression of transcription factors, thus leading to modulation of gene expression. All these epigenetic changes have been associated with chromatin remodeling effects. The present minireview briefly reports the main effects of VPA on chromatin and image analysis and Fourier transform infrared (FTIR) microspectroscopy in association with molecular biology methodological approaches to investigate the VPA-induced changes in chromatin structure and at the higher-order supraorganizational level.
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Affiliation(s)
- Maria Luiza S. Mello
- Department of Structural and Functional Biology, University of Campinas (Unicamp), Campinas, Brazil
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Veronezi GMB, Felisbino MB, Gatti MSV, Mello MLS, Vidal BDC. DNA Methylation Changes in Valproic Acid-Treated HeLa Cells as Assessed by Image Analysis, Immunofluorescence and Vibrational Microspectroscopy. PLoS One 2017; 12:e0170740. [PMID: 28114349 PMCID: PMC5256918 DOI: 10.1371/journal.pone.0170740] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 01/10/2017] [Indexed: 12/18/2022] Open
Abstract
Valproic acid (VPA), a well-known histone deacetylase inhibitor, has been reported to affect the DNA methylation status in addition to inducing histone hyperacetylation in several cell types. In HeLa cells, VPA promotes histone acetylation and chromatin remodeling. However, DNA demethylation was not checked in this cell model for standing effects longer than those provided by histone acetylation, which is a rapid and transient phenomenon. Demonstration of VPA-induced DNA demethylation in HeLa cells would contribute to understanding the effect of VPA on an aggressive tumor cell line. In the present work, DNA demethylation in VPA-treated HeLa cells was assessed by image analysis of chromatin texture, the abundance of 5-methylcytosine (5mC) immunofluorescence signals and Fourier transform-infrared (FT-IR) microspectroscopy centered on spectral regions related to the vibration of–CH3 groups. Image analysis indicated that increased chromatin unpacking promoted by a 4-h-treatment with 1.0 mM VPA persisted for 24 h in the absence of the drug, suggesting the occurrence of DNA demethylation that was confirmed by decreased 5mC immunofluorescence signals. FT-IR spectra of DNA samples from 1 mM or 20 mM VPA-treated cells subjected to a peak fitting analysis of the spectral window for–CH3 stretching vibrations showed decreased vibrations and energy of these groups as a function of the decreased abundance of 5mC induced by increased VPA concentrations. Only the 20 mM-VPA treatment caused an increase in the ratio of -CH3 bending vibrations evaluated at 1375 cm-1 in relation to in-plane vibrations of overall cytosines evaluated at 1492 cm-1. CH3 stretching vibrations showed to be more sensitive than–CH3 bending vibrations, as detected with FT-IR microspectroscopy, for studies aiming to associate vibrational spectroscopy and changes in DNA 5mC abundance.
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Affiliation(s)
- Giovana M. B. Veronezi
- Department of Structural and Functional Biology and, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Marina Barreto Felisbino
- Department of Structural and Functional Biology and, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Maria Sílvia V. Gatti
- Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Maria Luiza S. Mello
- Department of Structural and Functional Biology and, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
- * E-mail:
| | - Benedicto de Campos Vidal
- Department of Structural and Functional Biology and, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
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Dong W, Yin X, Sun L, Wang J, Sun S, Zhu G, Wu S, Bao W. Age-associated methylation change of TAP1 promoter in piglet. Gene 2015; 573:70-4. [PMID: 26169022 DOI: 10.1016/j.gene.2015.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/29/2015] [Accepted: 07/09/2015] [Indexed: 01/01/2023]
Abstract
Diarrhea and edematous disease are two major causes of mortality in postweaning piglets. These conditions lead to huge economic losses in the swine industry. Escherichia coli F18 is the primary causative agent of these two diseases. Transported associated with antigen processing (TAP) plays an important role in the immune response and the TAP1 gene could be an effective anti-E. coli F18 molecular marker in pigs. The aim of this study was to determine the correlation between TAP1 gene promoter CpG island methylation status and mRNA expression in piglets. In this study, bisulfite sequencing PCR (BSP) was used to detect the methylation status of the TAP1 gene promoter CpG islands and fluorescence quantitative PCR was used to detect TAP1 expression in the jejunum of Sutai piglets from birth to weaning age. The fragment of the TAP1 gene promoter region under investigation has no mutation, has 13 putative transcription factor binding sites containing 19 CpG sites, and may be important for regulation of gene expression. With increasing age, the overall methylation levels decreased, while the TAP1 expression levels increased, indicating a negative correlation between TAP1 expression and promoter methylation levels. Variance analysis showed significant differences in the methylation status of CpG_4, CpG_13 and CpG_15 among the different age groups (P<0.05). Our data indicate that TAP1 expression is increased by demethylation of promoter CpG islands, with CpG_4, CpG_13 and CpG_15 implicated as the critical regulatory sites.
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Affiliation(s)
- Wenhua Dong
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Xuemei Yin
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Li Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Jing Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Shouyong Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China.
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Vidal BDC. Fluorescence, aggregation properties and FT-IR microspectroscopy of elastin and collagen fibers. Acta Histochem 2014; 116:1359-66. [PMID: 25213809 DOI: 10.1016/j.acthis.2014.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 12/31/2022]
Abstract
Histological and histochemical observations support the hypothesis that collagen fibers can link to elastic fibers. However, the resulting organization of elastin and collagen type complexes and differences between these materials in terms of macromolecular orientation and frequencies of their chemical vibrational groups have not yet been solved. This study aimed to investigate the macromolecular organization of pure elastin, collagen type I and elastin-collagen complexes using polarized light DIC-microscopy. Additionally, differences and similarities between pure elastin and collagen bundles (CB) were investigated by Fourier transform-infrared (FT-IR) microspectroscopy. Although elastin exhibited a faint birefringence, the elastin-collagen complex aggregates formed in solution exhibited a deep birefringence and formation of an ordered-supramolecular complex typical of collagen chiral structure. The FT-IR study revealed elastin and CB peptide NH groups involved in different types of H-bonding. More energy is absorbed in the vibrational transitions corresponding to CH, CH2 and CH3 groups (probably associated with the hydrophobicity demonstrated by 8-anilino-1-naphtalene sulfonic acid sodium salt [ANS] fluorescence), and to νCN, δNH and ωCH2 groups of elastin compared to CB. It is assumed that the α-helix contribution to the pure elastin amide I profile is 46.8%, whereas that of the B-sheet is 20% and that unordered structures contribute to the remaining percentage. An FT-IR profile library reveals that the elastin signature within the 1360-1189cm(-1) spectral range resembles that of Conex-Toray aramid fibers.
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Affiliation(s)
- Benedicto de Campos Vidal
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), Rua Monteiro Lobato 255, CEP 013083-862 Campinas, SP, Brazil.
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