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Patel D, Dabhi AM, Dmello C, Seervi M, Sneha KM, Agrawal P, Sahani MH, Kanojia D. FKBP1A upregulation correlates with poor prognosis and increased metastatic potential of HNSCC. Cell Biol Int 2021; 46:443-453. [PMID: 34882900 DOI: 10.1002/cbin.11741] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/29/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy globally. The etiology of HNSCC is multifactorial, including cellular stress induced by a tobacco smoking, tobacco chewing excess alcohol consumption, and human papillomavirus infection. The induction of stress includes autophagy as one of the response pathways in maintaining homeostatic equilibrium. We evaluated the expression of autophagy-related genes in HNSCC tissues from RNA sequencing datasets and identified 19 genes correlated with poor prognosis and 18 genes correlated with improved prognosis of HNSCC patients. Further analysis of independent gene expression datasets revealed that ATG12, HSP90AB1, and FKBP1A are overexpressed in HNSCC and correlate with poor prognosis, whereas the overexpression of ANXA1, FOS, and ULK3 correlates with improved prognosis. Using independent datasets, we also found that ATG12, HSP90AB1, and FKBP1A expression increased with an increase in the T-stage of HNSCC. Among all the datasets analyzed, FKBP1A was overexpressed in HNSCC and was strongly associated with lymph node metastasis in multiple in silico datasets. In conclusion, our analysis indicates dynamic alterations in autophagy genes during HNSCC and warrants further investigation, specifically on FKBP1A and its role in tumor progression and metastasis.
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Affiliation(s)
- Dhruti Patel
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Aarsh M Dabhi
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Crismita Dmello
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | | | - K M Sneha
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Pavan Agrawal
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Mayurbhai H Sahani
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Deepak Kanojia
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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2
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Mishra SK, Hole A, Reddy BPK, Srivastava R, Chilakapati MK, De A. Raman micro-spectroscopic map estimating in vivo precision of tumor ablative effect achieved by photothermal therapy procedure. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 37:102437. [PMID: 34273597 DOI: 10.1016/j.nano.2021.102437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/04/2021] [Accepted: 06/16/2021] [Indexed: 11/16/2022]
Abstract
Photothermal-therapy (PTT) inculcates near-infrared laser guided local heating effect, where high degree of precision is expected, but not well proven to-date. An ex vivo tissue biochemical map with molecular/biochemical response showing the coverage area out of an optimized PTT procedure can reveal precision information. In this work, Raman-microscopic mapping and linear discriminant analysis of spectra of PTT treated and surrounding tissue areas ex vivo are done, revealing three distinct spectral clusters/zones, with minimal overlap between the core treated and adjacent untreated zone. The core treated zone showed intense nucleic-acid, cytochrome/mitochondria and protein damage, an adjacent zone showed lesser degree of damages and far zone showed minimal/no damage. Immunohistochemistry for γH2AX (DNA damage marker protein) in PTT exposed tissue also revealed similar results. Altogether, this study reveals the utility of Raman-microspectroscopy for fine-tuning safety parameters and precision that can be achieved from PTT mediated tumor ablation in preclinical/clinical application.
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Affiliation(s)
- Sumit K Mishra
- Molecular Functional Imaging Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India; Department of Life Sciences, Homi Bhaba National Institute, Mumbai, India.
| | - Arti Hole
- Chilakapati Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India.
| | - B Pradeep K Reddy
- NanoBios Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
| | - Rohit Srivastava
- NanoBios Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
| | - Murali Krishna Chilakapati
- Chilakapati Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India; Department of Life Sciences, Homi Bhaba National Institute, Mumbai, India.
| | - Abhijit De
- Molecular Functional Imaging Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India; Department of Life Sciences, Homi Bhaba National Institute, Mumbai, India.
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Robert C, Tsiampali J, Fraser-Miller SJ, Neumann S, Maciaczyk D, Young SL, Maciaczyk J, Gordon KC. Molecular monitoring of glioblastoma's immunogenicity using a combination of Raman spectroscopy and chemometrics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 252:119534. [PMID: 33588367 DOI: 10.1016/j.saa.2021.119534] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
Raman spectroscopy (RS) has been used as a powerful diagnostic and non-invasive tool in cancer diagnosis as well as in discrimination of cancer and immune cells. In this study RS in combination with chemometrics was applied to cellular Raman spectral data to distinguish the phenotype of T-cells and monocytes after incubation with media conditioned by glioblastoma stem-cells (GSCs) showing different molecular background. For this purpose, genetic modulations of epithelial-to-mesenchymal transition (EMT) process and expression of immunomodulator CD73 were introduced. Principal component analysis of the Raman spectral data showed that T-cells and monocytes incubated with tumour-conditioned media (TCMs) of GSCs with inhibited EMT activator ZEB1 or CD73 formed distinct clusters compared to controls highlighting their differences. Further discriminatory analysis performed using linear discriminant analysis (LDA) and support vector machine classification (SVM), yielded sensitivities and specificities of over 70 and 67% respectively upon validation against an independent test set. Supporting those results, flow cytometric analysis was performed to test the influence of TCMs on cytokine profile of T-cells and monocytes. We found that ZEB1 and CD73 influence T-cell and monocyte phenotype and promote monocyte differentiation into a population of mixed pro- and anti-tumorigenic macrophages (MΦs) and dendritic cells (DCs) respectively. In conclusion, Raman spectroscopy in combination with chemometrics enabled tracking T-cells and monocytes.
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Affiliation(s)
- Chima Robert
- Dodd-Walls Centre for Photonics and Quantum Technologies, Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Julia Tsiampali
- Neurosurgery Department, University Hospital Duesseldorf, 40225 Duesseldorf, Germany
| | - Sara J Fraser-Miller
- Dodd-Walls Centre for Photonics and Quantum Technologies, Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Silke Neumann
- Department of Pathology, University of Otago, Dunedin, New Zealand
| | - Donata Maciaczyk
- Department of Pathology, University of Otago, Dunedin, New Zealand
| | - Sarah L Young
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Jaroslaw Maciaczyk
- Department of Neurosurgery, University Hospital Bonn, 53179 Bonn, Germany; Department of Surgical Sciences, University of Otago, Dunedin, New Zealand.
| | - Keith C Gordon
- Dodd-Walls Centre for Photonics and Quantum Technologies, Department of Chemistry, University of Otago, Dunedin, New Zealand.
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Pansare K, Pillai D, Parab S, Singh SR, Kannan S, Ludbe M, Hole A, Murali Krishna C, Gera P. Quality assessment of cryopreserved biospecimens reveals presence of intact biomolecules. JOURNAL OF BIOPHOTONICS 2019; 12:e201960048. [PMID: 31569303 DOI: 10.1002/jbio.201960048] [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] [Received: 07/19/2019] [Revised: 09/03/2019] [Accepted: 09/15/2019] [Indexed: 06/10/2023]
Abstract
Recapitulation of tumor features in isolated biomolecules is preeminently dependent on obtaining reliable quality biospecimen. Moreover, quality assessment of biobanked specimens at regular intervals is an essential intervention for carrying out effective translational and clinical research. In the current study, genomic DNA was extracted from 140 fresh frozen tissues of oral, breast and colorectal specimens cryopreserved over a period of 3 to 8 months (short term) and 3 to 4 years (long term). Quantification of genomic DNA by absorption and fluorescence spectroscopy confirmed high concentration while qualitative analysis by gel electrophoresis showed intact bands for 94% and 87% of short- and long-term cohorts, respectively. PC-LDA based classification of Raman spectra showed overlapping groups of both cohorts suggesting the quality of DNA being preserved irrespective of storage period. To the best of our knowledge this is the first Indian biobank study reporting quality analysis of biospecimens cryopreserved at different time periods.
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Affiliation(s)
| | - Divya Pillai
- Department of Biorepository, TMC, ACTREC, Mumbai, India
| | - Saili Parab
- Department of Biorepository, TMC, ACTREC, Mumbai, India
| | | | - Sadhana Kannan
- Clinical Trials Unit, Clinical Research Secretariat, TMC, ACTREC, Mumbai, India
| | - Madan Ludbe
- Department of Biorepository, TMC, ACTREC, Mumbai, India
| | - Arti Hole
- Chilakapati Lab, TMC, ACTREC, Mumbai, India
| | | | - Poonam Gera
- Department of Biorepository, TMC, ACTREC, Mumbai, India
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de Carvalho LFDCES, Saito Nogueira M. New insights of Raman spectroscopy for oral clinical applications. Analyst 2018; 143:6037-6048. [DOI: 10.1039/c8an01363b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Oral injuries are currently diagnosed by histopathological analysis of biopsy, which is an invasive procedure and does not give immediate results.
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