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Kanmalar M, Kamal R, Abdul Sani SF, Pathmanathan D, Bm Said NA, Paramanantham Y, Abd Jamil AH, Mun KS, Kuppusamy S, Almugren KS, Almajid HF, Bradley DA. Spectroscopic diagnosis and metabolite characterization of cisplatin resistance regulated by FDFT1 in bladder cancer tissue. Appl Radiat Isot 2024; 210:111372. [PMID: 38810354 DOI: 10.1016/j.apradiso.2024.111372] [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: 02/08/2023] [Revised: 11/21/2023] [Accepted: 05/24/2024] [Indexed: 05/31/2024]
Abstract
As is the case for most solid tumours, chemotherapy remains the backbone in the management of metastatic disease. However, the occurrence of chemotherapy resistance is a cause to worry, especially in bladder cancer. Extensive evidence indicates molecular changes in bladder cancer cells to be the underlying cause of chemotherapy resistance, including the reduced expression of farnesyl-diphosphate farnesyltransferase 1 (FDFT1) - a gene involved in cholesterol biosynthesis. This can likely be a hallmark in examining the resistance and sensitivity of chemotherapy drugs. This work performs spectroscopic analysis and metabolite characterization on resistant, sensitive, stable-disease and healthy bladder tissues. Raman spectroscopy has detected peaks at around 1003 cm-1 (squalene), 1178 cm-1 (cholesterol), 1258 cm-1 (cholesteryl ester), 1343 cm-1 (collagen), 1525 cm-1 (carotenoid), 1575 cm-1 (DNA bases) and 1608 cm-1 (cytosine). The peak parameters were examined, and statistical analysis was performed on the peak features, attaining significant differences between the sample groups. Small-angle x-ray scattering (SAXS) measurements observed the triglyceride peak together with 6th, 7th and 8th - order collagen peaks; peak parameters were also determined. Neutron activation analysis (NAA) detected seven trace elements. Carbon (Ca), magnesium (Mg), chlorine (Cl) and sodium (Na) have been found to have the greatest concentration in the sample groups, suggestive of a role as a biomarker for cisplatin resistance studies. Results from the present research are suggested to provide an important insight into understanding the development of drug resistance in bladder cancer, opening up the possibility of novel avenues for treatment through personalised interventions.
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Affiliation(s)
- M Kanmalar
- Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Raihan Kamal
- Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - S F Abdul Sani
- Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Dharini Pathmanathan
- Department of Mathematic, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nur Akmarina Bm Said
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | | | - Amira Hajirah Abd Jamil
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - K S Mun
- Department of Pathology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - S Kuppusamy
- Department of Surgery, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - K S Almugren
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia.
| | - Hadeel F Almajid
- Medicine College, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
| | - D A Bradley
- Sunway University, Centre for Applied Physics and Radiation Technologies, Jalan Universiti, 46150, PJ, Malaysia; School of Mathematics and Physics, University of Surrey, Guildford, GU2 7XH, UK
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Denisov S, Blinchevsky B, Friedman J, Gerbelli B, Ajeer A, Adams L, Greenwood C, Rogers K, Mourokh L, Lazarev P. Vitacrystallography: Structural Biomarkers of Breast Cancer Obtained by X-ray Scattering. Cancers (Basel) 2024; 16:2499. [PMID: 39061139 PMCID: PMC11275015 DOI: 10.3390/cancers16142499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/26/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
With breast cancer being one of the most widespread causes of death for women, there is an unmet need for its early detection. For this purpose, we propose a non-invasive approach based on X-ray scattering. We measured samples from 107 unique patients provided by the Breast Cancer Now Tissue Biobank, with the total dataset containing 2958 entries. Two different sample-to-detector distances, 2 and 16 cm, were used to access various structural biomarkers at distinct ranges of momentum transfer values. The biomarkers related to lipid metabolism are consistent with those of previous studies. Machine learning analysis based on the Random Forest Classifier demonstrates excellent performance metrics for cancer/non-cancer binary decisions. The best sensitivity and specificity values are 80% and 92%, respectively, for the sample-to-detector distance of 2 cm and 86% and 83% for the sample-to-detector distance of 16 cm.
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Affiliation(s)
- Sergey Denisov
- Matur UK Ltd., 5 New Street Square, London EC4A 3TW, UK; (S.D.); (B.B.); (P.L.)
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, Bât. 349, 91405 Orsay, France
| | - Benjamin Blinchevsky
- Matur UK Ltd., 5 New Street Square, London EC4A 3TW, UK; (S.D.); (B.B.); (P.L.)
- EosDx, Inc., 1455 Adams Drive, Menlo Park, CA 94025, USA; (J.F.); (C.G.); (K.R.)
| | - Jonathan Friedman
- EosDx, Inc., 1455 Adams Drive, Menlo Park, CA 94025, USA; (J.F.); (C.G.); (K.R.)
- Physics Department, Queens College, City University of New York, 65-30 Kissena Blvd, Flushing, NY 11367, USA
| | - Barbara Gerbelli
- School of Chemical and Physical Sciences, Keele University, Keele ST5 5BG, UK; (B.G.); (A.A.); (L.A.)
| | - Ash Ajeer
- School of Chemical and Physical Sciences, Keele University, Keele ST5 5BG, UK; (B.G.); (A.A.); (L.A.)
| | - Lois Adams
- School of Chemical and Physical Sciences, Keele University, Keele ST5 5BG, UK; (B.G.); (A.A.); (L.A.)
| | - Charlene Greenwood
- EosDx, Inc., 1455 Adams Drive, Menlo Park, CA 94025, USA; (J.F.); (C.G.); (K.R.)
- School of Chemical and Physical Sciences, Keele University, Keele ST5 5BG, UK; (B.G.); (A.A.); (L.A.)
| | - Keith Rogers
- EosDx, Inc., 1455 Adams Drive, Menlo Park, CA 94025, USA; (J.F.); (C.G.); (K.R.)
- Shrivenham Campus, Cranfield University, Swindon SN6 8LA, UK
| | - Lev Mourokh
- EosDx, Inc., 1455 Adams Drive, Menlo Park, CA 94025, USA; (J.F.); (C.G.); (K.R.)
- Physics Department, Queens College, City University of New York, 65-30 Kissena Blvd, Flushing, NY 11367, USA
| | - Pavel Lazarev
- Matur UK Ltd., 5 New Street Square, London EC4A 3TW, UK; (S.D.); (B.B.); (P.L.)
- EosDx, Inc., 1455 Adams Drive, Menlo Park, CA 94025, USA; (J.F.); (C.G.); (K.R.)
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Mohd Nor Ihsan NS, Abdul Sani SF, Looi LM, Cheah PL, Chiew SF, Pathmanathan D, Bradley DA. A review: Exploring the metabolic and structural characterisation of beta pleated amyloid fibril in human tissue using Raman spectrometry and SAXS. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023:S0079-6107(23)00059-7. [PMID: 37307955 DOI: 10.1016/j.pbiomolbio.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/12/2023] [Accepted: 06/09/2023] [Indexed: 06/14/2023]
Abstract
Amyloidosis is a deleterious condition caused by abnormal amyloid fibril build-up in living tissues. To date, 42 proteins that are linked to amyloid fibrils have been discovered. Amyloid fibril structure variation can affect the severity, progression rate, or clinical symptoms of amyloidosis. Since amyloid fibril build-up is the primary pathological basis for various neurodegenerative illnesses, characterization of these deadly proteins, particularly utilising optical techniques have been a focus. Spectroscopy techniques provide significant non-invasive platforms for the investigation of the structure and conformation of amyloid fibrils, offering a wide spectrum of analyses ranging from nanometric to micrometric size scales. Even though this area of study has been intensively explored, there still remain aspects of amyloid fibrillization that are not fully known, a matter hindering progress in treating and curing amyloidosis. This review aims to provide recent updates and comprehensive information on optical techniques for metabolic and proteomic characterization of β-pleated amyloid fibrils found in human tissue with thorough literature analysis of publications. Raman spectroscopy and SAXS are well established experimental methods for study of structural properties of biomaterials. With suitable models, they offer extended information for valid proteomic analysis under physiologically relevant conditions. This review points to evidence that despite limitations, these techniques are able to provide for the necessary output and proteomics indication in order to extrapolate the aetiology of amyloid fibrils for reliable diagnostic purposes. Our metabolic database may also contribute to elucidating the nature and function of the amyloid proteome in development and clearance of amyloid diseases.
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Affiliation(s)
- N S Mohd Nor Ihsan
- Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - S F Abdul Sani
- Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - L M Looi
- Department of Pathology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - P L Cheah
- Department of Pathology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - S F Chiew
- Department of Pathology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Dharini Pathmanathan
- Institute of Mathematical Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - D A Bradley
- Centre for Applied Physics and Radiation Technologies, Sunway University, 46150 PJ, Malaysia; Department of Physics, School of Mathematics & Physics, University of Surrey, Guildford, GU2 7XH, UK
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Proteomics-Based Identification of Dysregulated Proteins in Breast Cancer. Proteomes 2022; 10:proteomes10040035. [PMID: 36278695 PMCID: PMC9590004 DOI: 10.3390/proteomes10040035] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
Immunohistochemistry (IHC) is still widely used as a morphology-based assay for in situ analysis of target proteins as specific tumor antigens. However, as a very heterogeneous collection of neoplastic diseases, breast cancer (BC) requires an accurate identification and characterization of larger panels of candidate biomarkers, beyond ER, PR, and HER2 proteins, for diagnosis and personalized treatment, without the limited availability of antibodies that are required to identify specific proteins. Top-down, middle-down, and bottom-up mass spectrometry (MS)-based proteomics approaches complement traditional histopathological tissue analysis to examine expression, modification, and interaction of hundreds to thousands of proteins simultaneously. In this review, we discuss the proteomics-based identification of dysregulated proteins in BC that are essential for the following issues: discovery and validation of new biomarkers by analysis of solid and liquid/non-invasive biopsies, cell lines, organoids and xenograft models; identification of panels of biomarkers for early detection and accurate discrimination between cancer, benign and normal tissues; identification of subtype-specific and stage-specific protein expression profiles in BC grading and measurement of disease progression; characterization of new subtypes of BC; characterization and quantitation of post-translational modifications (PTMs) and aberrant protein-protein interactions (PPI) involved in tumor development; characterization of the global remodeling of BC tissue homeostasis, diagnosis and prognostic information; and deciphering of molecular functions, biological processes and mechanisms through which the dysregulated proteins cause tumor initiation, invasion, and treatment resistance.
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Niklaus NJ, Tokarchuk I, Zbinden M, Schläfli AM, Maycotte P, Tschan MP. The Multifaceted Functions of Autophagy in Breast Cancer Development and Treatment. Cells 2021; 10:cells10061447. [PMID: 34207792 PMCID: PMC8229352 DOI: 10.3390/cells10061447] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Macroautophagy (herein referred to as autophagy) is a complex catabolic process characterized by the formation of double-membrane vesicles called autophagosomes. During this process, autophagosomes engulf and deliver their intracellular content to lysosomes, where they are degraded by hydrolytic enzymes. Thereby, autophagy provides energy and building blocks to maintain cellular homeostasis and represents a dynamic recycling mechanism. Importantly, the clearance of damaged organelles and aggregated molecules by autophagy in normal cells contributes to cancer prevention. Therefore, the dysfunction of autophagy has a major impact on the cell fate and can contribute to tumorigenesis. Breast cancer is the most common cancer in women and has the highest mortality rate among all cancers in women worldwide. Breast cancer patients often have a good short-term prognosis, but long-term survivors often experience aggressive recurrence. This phenomenon might be explained by the high heterogeneity of breast cancer tumors rendering mammary tumors difficult to target. This review focuses on the mechanisms of autophagy during breast carcinogenesis and sheds light on the role of autophagy in the traits of aggressive breast cancer cells such as migration, invasion, and therapeutic resistance.
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Affiliation(s)
- Nicolas J. Niklaus
- Institute of Pathology, University of Bern, CH-3008 Bern, Switzerland; (N.J.N.); (I.T.); (M.Z.); (A.M.S.)
- Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Igor Tokarchuk
- Institute of Pathology, University of Bern, CH-3008 Bern, Switzerland; (N.J.N.); (I.T.); (M.Z.); (A.M.S.)
- Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Mara Zbinden
- Institute of Pathology, University of Bern, CH-3008 Bern, Switzerland; (N.J.N.); (I.T.); (M.Z.); (A.M.S.)
| | - Anna M. Schläfli
- Institute of Pathology, University of Bern, CH-3008 Bern, Switzerland; (N.J.N.); (I.T.); (M.Z.); (A.M.S.)
| | - Paola Maycotte
- Centro de Investigación Biomédica de Oriente (CIBIOR), Instituto Mexicano del Seguro Social (IMSS), Puebla 74360, Mexico;
| | - Mario P. Tschan
- Institute of Pathology, University of Bern, CH-3008 Bern, Switzerland; (N.J.N.); (I.T.); (M.Z.); (A.M.S.)
- Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
- Correspondence: ; Tel.: +41-31-632-87-80
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Sabtu SN, Sani SFA, Looi LM, Chiew SF, Pathmanathan D, Bradley DA, Osman Z. Indication of high lipid content in epithelial-mesenchymal transitions of breast tissues. Sci Rep 2021; 11:3250. [PMID: 33547362 PMCID: PMC7864999 DOI: 10.1038/s41598-021-81426-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
The epithelial-mesenchymal transition (EMT) is a crucial process in cancer progression and metastasis. Study of metabolic changes during the EMT process is important in seeking to understand the biochemical changes associated with cancer progression, not least in scoping for therapeutic strategies aimed at targeting EMT. Due to the potential for high sensitivity and specificity, Raman spectroscopy was used here to study the metabolic changes associated with EMT in human breast cancer tissue. For Raman spectroscopy measurements, tissue from 23 patients were collected, comprising non-lesional, EMT and non-EMT formalin-fixed and paraffin embedded breast cancer samples. Analysis was made in the fingerprint Raman spectra region (600-1800 cm-1) best associated with cancer progression biochemical changes in lipid, protein and nucleic acids. The ANOVA test followed by the Tukey's multiple comparisons test were conducted to see if there existed differences between non-lesional, EMT and non-EMT breast tissue for Raman spectroscopy measurements. Results revealed that significant differences were evident in terms of intensity between the non-lesional and EMT samples, as well as the EMT and non-EMT samples. Multivariate analysis involving independent component analysis, Principal component analysis and non-negative least square were used to analyse the Raman spectra data. The results show significant differences between EMT and non-EMT cancers in lipid, protein, and nucleic acids. This study demonstrated the capability of Raman spectroscopy supported by multivariate analysis in analysing metabolic changes in EMT breast cancer tissue.
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Affiliation(s)
- Siti Norbaini Sabtu
- Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - S F Abdul Sani
- Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - L M Looi
- Department of Pathology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - S F Chiew
- Department of Pathology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Dharini Pathmanathan
- Institute of Mathematical Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - D A Bradley
- Centre for Biomedical Physics, Sunway University, Jalan Universiti, 46150, Petaling Jaya, Malaysia
- Department of Physics, University of Surrey, Guildford, GU2 7XH, UK
| | - Z Osman
- Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
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