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Sun J, Xie X, Song Y, Sun T, Liu X, Yuan H, Shen C. Selenomethionine in gelatin methacryloyl hydrogels: Modulating ferroptosis to attenuate skin aging. Bioact Mater 2024; 35:495-516. [PMID: 38404642 PMCID: PMC10885793 DOI: 10.1016/j.bioactmat.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/27/2024] Open
Abstract
During skin aging, the degeneration of epidermal stem cells (EpiSCs) leads to diminished wound healing capabilities and epidermal disintegration. This study tackles this issue through a comprehensive analysis combining transcriptomics and untargeted metabolomics, revealing age-dependent alterations in the Gpx gene family and arachidonic acid (AA) metabolic networks, resulting in enhanced ferroptosis. Selenomethionine (Se-Met) could enhance GPX4 expression, thereby assisting EpiSCs in countering AA-induced mitochondrial damage and ferroptosis. Additionally, Se-Met demonstrates antioxidative characteristics and extensive ultraviolet absorption. For the sustained and controllable release of Se-Met, it was covalently grafted to UV-responsive GelMA hydrogels via AC-PEG-NHS tethers. The Se-Met@GelMA hydrogel effectively accelerated wound healing in a chronological aging mice model, by inhibiting lipid peroxidation and ferroptosis with augmented GPX4 expression. Moreover, in a photoaging model, this hydrogel significantly mitigated inflammatory responses, extracellular matrix remodeling, and ferroptosis in UV-exposed mice. These characteristics render Se-Met@GelMA hydrogel valuable in practical clinical applications.
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Affiliation(s)
- Jiachen Sun
- Department of Burns and Plastic Surgery, Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100048, China
| | - Xiaoye Xie
- Department of Burns and Plastic Surgery, Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100048, China
| | - Yaoyao Song
- Department of Burns and Plastic Surgery, Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100048, China
| | - Tianjun Sun
- Department of Burns and Plastic Surgery, Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100048, China
| | - Xinzhu Liu
- Department of Burns and Plastic Surgery, Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100048, China
| | - Huageng Yuan
- Department of Burns and Plastic Surgery, Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100048, China
| | - Chuanan Shen
- Department of Burns and Plastic Surgery, Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100048, China
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2
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Meng YW, Liu JY. Pathological and pharmacological functions of the metabolites of polyunsaturated fatty acids mediated by cyclooxygenases, lipoxygenases, and cytochrome P450s in cancers. Pharmacol Ther 2024; 256:108612. [PMID: 38369063 DOI: 10.1016/j.pharmthera.2024.108612] [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: 10/30/2023] [Revised: 01/19/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024]
Abstract
Oxylipins have garnered increasing attention because they were consistently shown to play pathological and/or pharmacological roles in the development of multiple cancers. Oxylipins are the metabolites of polyunsaturated fatty acids via both enzymatic and nonenzymatic pathways. The enzymes mediating the metabolism of PUFAs include but not limited to lipoxygenases (LOXs), cyclooxygenases (COXs), and cytochrome P450s (CYPs) pathways, as well as the down-stream enzymes. Here, we systematically summarized the pleiotropic effects of oxylipins in different cancers through pathological and pharmacological aspects, with specific reference to the enzyme-mediated oxylipins. We discussed the specific roles of oxylipins on cancer onset, growth, invasion, and metastasis, as well as the expression changes in the associated metabolic enzymes and the associated underlying mechanisms. In addition, we also discussed the clinical application and potential of oxylipins and related metabolic enzymes as the targets for cancer prevention and treatment. We found the specific function of most oxylipins in cancers, especially the underlying mechanisms and clinic applications, deserves and needs further investigation. We believe that research on oxylipins will provide not only more therapeutic targets for various cancers but also dietary guidance for both cancer patients and healthy humans.
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Affiliation(s)
- Yi-Wen Meng
- CNTTI of the Institute of Life Sciences & Department of Anesthesia of the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China; Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Chongqing 400016, China
| | - Jun-Yan Liu
- CNTTI of the Institute of Life Sciences & Department of Anesthesia of the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China; Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Chongqing 400016, China; College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
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3
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Huang X, Su B, Li M, Zhou Y, He X. Multiomics characterization of fatty acid metabolism for the clinical management of hepatocellular carcinoma. Sci Rep 2023; 13:22472. [PMID: 38110715 PMCID: PMC10728109 DOI: 10.1038/s41598-023-50156-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a prevalent malignancy and there is a lack of effective biomarkers for HCC diagnosis. Living organisms are complex, and different omics molecules interact with each other to implement various biological functions. Genomics and metabolomics, which are the top and bottom of systems biology, play an important role in HCC clinical management. Fatty acid metabolism is associated with malignancy, prognosis, and immune phenotype in cancer, which is a potential hallmark in malignant tumors. In this study, the genes and metabolites related to fatty acid metabolism were thoroughly investigated by a dynamic network construction algorithm named EWS-DDA for the early diagnosis and prognosis of HCC. Three gene ratios and eight metabolite ratios were identified by EWS-DDA as potential biomarkers for HCC clinical management. Further analysis using biological analysis, statistical analysis and document validation in the discovery and validation sets suggested that the selected potential biomarkers had great clinical prognostic value and helped to achieve effective early diagnosis of HCC. Experimental results suggested that in-depth evaluation of fatty acid metabolism from different omics viewpoints can facilitate the further understanding of pathological alterations associated with HCC characteristics, improving the performance of early diagnosis and clinical prognosis.
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Affiliation(s)
- Xin Huang
- School of Artificial Intelligence, Anshan Normal University, Pingan Street, Anshan, 114007, Liaoning, China.
- Biomedical Engineering Postdoctoral Research Station, Dalian University of Technology, Dalian, Liaoning, China.
- Postdoctoral Workstation of Dalian Yongjia Electronic Technology Co., Ltd, Dalian, Liaoning, China.
| | - Benzhe Su
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China
| | - Mengjun Li
- School of Artificial Intelligence, Anshan Normal University, Pingan Street, Anshan, 114007, Liaoning, China
| | - Yang Zhou
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo Medical Center Li Huili Hospital, Ningbo, Zhejiang, China
| | - Xinyu He
- School of Computer and Information Technology, Liaoning Normal University, Dalian, Liaoning, China
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4
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Kothapalli KSD, Park HG, Kothapalli NSL, Brenna JT. FADS2 function at the major cancer hotspot 11q13 locus alters fatty acid metabolism in cancer. Prog Lipid Res 2023; 92:101242. [PMID: 37597812 DOI: 10.1016/j.plipres.2023.101242] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/31/2023] [Accepted: 08/15/2023] [Indexed: 08/21/2023]
Abstract
Dysregulation of fatty acid metabolism and de novo lipogenesis is a key driver of several cancer types through highly unsaturated fatty acid (HUFA) signaling precursors such as arachidonic acid. The human chromosome 11q13 locus has long been established as the most frequently amplified in a variety of human cancers. The fatty acid desaturase genes (FADS1, FADS2 and FADS3) responsible for HUFA biosynthesis localize to the 11q12-13.1 region. FADS2 activity is promiscuous, catalyzing biosynthesis of several unsaturated fatty acids by Δ6, Δ8, and Δ4 desaturation. Our main aim here is to review known and putative consequences of FADS2 dysregulation due to effects on the 11q13 locus potentially driving various cancer types. FADS2 silencing causes synthesis of sciadonic acid (5Z,11Z,14Z-20:3) in MCF7 cells and breast cancer in vivo. 5Z,11Z,14Z-20:3 is structurally identical to arachidonic acid (5Z,8Z,11Z,14Z-20:4) except it lacks the internal Δ8 double bond required for prostaglandin and leukotriene synthesis, among other eicosanoids. Palmitic acid has substrate specificity for both SCD and FADS2. Melanoma, prostate, liver and lung cancer cells insensitive to SCD inhibition show increased FADS2 activity and sapienic acid biosynthesis. Elevated serum mead acid levels found in hepatocellular carcinoma patients suggest an unsatisfied demand for arachidonic acid. FADS2 circular RNAs are at high levels in colorectal and lung cancer tissues. FADS2 circular RNAs are associated with shorter overall survival in colorectal cancer patients. The evidence thusfar supports an effort for future research on the role of FADS2 as a tumor suppressor in a range of neoplastic disorders.
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Affiliation(s)
- Kumar S D Kothapalli
- Dell Pediatric Research Institute, Dell Medical School and Department of Nutritional Sciences, The University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX 78723, USA.
| | - Hui Gyu Park
- Dell Pediatric Research Institute, Dell Medical School and Department of Nutritional Sciences, The University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX 78723, USA
| | | | - J Thomas Brenna
- Dell Pediatric Research Institute, Dell Medical School and Department of Nutritional Sciences, The University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX 78723, USA.
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Whitlock NC, White ME, Capaldo BJ, Ku AT, Agarwal S, Fang L, Wilkinson S, Trostel SY, Shi ZD, Basuli F, Wong K, Jagoda EM, Kelly K, Choyke PL, Sowalsky AG. Progression of prostate cancer reprograms MYC-mediated lipid metabolism via lysine methyltransferase 2A. Discov Oncol 2022; 13:97. [PMID: 36181613 PMCID: PMC9526773 DOI: 10.1007/s12672-022-00565-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/27/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The activities of MYC, the androgen receptor, and its associated pioneer factors demonstrate substantial reprogramming between early and advanced prostate cancer. Although previous studies have shown a shift in cellular metabolic requirements associated with prostate cancer progression, the epigenetic regulation of these processes is incompletely described. Here, we have integrated chromatin immunoprecipitation sequencing (ChIP-seq) and whole-transcriptome sequencing to identify novel regulators of metabolism in advanced prostate tumors characterized by elevated MYC activity. RESULTS Using ChIP-seq against MYC, HOXB13, and AR in LNCaP cells, we observed redistribution of co-bound sites suggestive of differential KMT2A activity as a function of MYC expression. In a cohort of 177 laser-capture microdissected foci of prostate tumors, KMT2A expression was positively correlated with MYC activity, AR activity, and HOXB13 expression, but decreased with tumor grade severity. However, KMT2A expression was negatively correlated with these factors in 25 LuCaP patient-derived xenograft models of advanced prostate cancer and 99 laser-capture microdissected foci of metastatic castration-resistant prostate cancer. Stratified by KMT2A expression, ChIP-seq against AR and HOXB13 in 15 LuCaP patient-derived xenografts showed an inverse association with sites involving genes implicated in lipid metabolism, including the arachidonic acid metabolic enzyme PLA2G4F. LuCaP patient-derived xenograft models grown as organoids recapitulated the inverse association between KMT2A expression and fluorine-18 labeled arachidonic acid uptake in vitro. CONCLUSIONS Our study demonstrates that the epigenetic activity of transcription factor oncogenes exhibits a shift during prostate cancer progression with distinctive phenotypic effects on metabolism. These epigenetically driven changes in lipid metabolism may serve as novel targets for the development of novel imaging agents and therapeutics.
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Affiliation(s)
- Nichelle C Whitlock
- Laboratory of Genitourinary Cancer Pathogenesis, National Cancer Institute, NIH, 37 Convent Drive, Bethesda, MD, 20892, USA
| | - Margaret E White
- Laboratory of Genitourinary Cancer Pathogenesis, National Cancer Institute, NIH, 37 Convent Drive, Bethesda, MD, 20892, USA
- Molecular Imaging Branch, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Brian J Capaldo
- Laboratory of Genitourinary Cancer Pathogenesis, National Cancer Institute, NIH, 37 Convent Drive, Bethesda, MD, 20892, USA
| | - Anson T Ku
- Laboratory of Genitourinary Cancer Pathogenesis, National Cancer Institute, NIH, 37 Convent Drive, Bethesda, MD, 20892, USA
| | - Supreet Agarwal
- Laboratory of Genitourinary Cancer Pathogenesis, National Cancer Institute, NIH, 37 Convent Drive, Bethesda, MD, 20892, USA
| | - Lei Fang
- Laboratory of Genitourinary Cancer Pathogenesis, National Cancer Institute, NIH, 37 Convent Drive, Bethesda, MD, 20892, USA
| | - Scott Wilkinson
- Laboratory of Genitourinary Cancer Pathogenesis, National Cancer Institute, NIH, 37 Convent Drive, Bethesda, MD, 20892, USA
| | - Shana Y Trostel
- Laboratory of Genitourinary Cancer Pathogenesis, National Cancer Institute, NIH, 37 Convent Drive, Bethesda, MD, 20892, USA
| | - Zhen-Dan Shi
- Chemistry and Synthesis Center, National Heart, Lung and Blood Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Falguni Basuli
- Chemistry and Synthesis Center, National Heart, Lung and Blood Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Karen Wong
- Molecular Imaging Branch, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Elaine M Jagoda
- Molecular Imaging Branch, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Kathleen Kelly
- Laboratory of Genitourinary Cancer Pathogenesis, National Cancer Institute, NIH, 37 Convent Drive, Bethesda, MD, 20892, USA
| | - Peter L Choyke
- Molecular Imaging Branch, National Cancer Institute, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Adam G Sowalsky
- Laboratory of Genitourinary Cancer Pathogenesis, National Cancer Institute, NIH, 37 Convent Drive, Bethesda, MD, 20892, USA.
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Dey S, Singh AK, Singh AK, Rawat K, Banerjee J, Agnihotri V, Upadhaya D. Critical pathways of oral squamous cell carcinoma: molecular biomarker and therapeutic intervention. Med Oncol 2022; 39:30. [DOI: 10.1007/s12032-021-01633-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022]
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7
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Pansare K, Mohanty B, Dhotre R, Pettiwala AM, Parab S, Gupta N, Gera P, Gardi N, Dugge R, Sahu P, Alhans R, Kowtal P, Chaudhari P, Sarin R. Aspirin Inhibition of Group VI Phospholipase A2 Induces Synthetic Lethality in AAM Pathway Down-Regulated Gingivobuccal Squamous Carcinoma. Cells 2021; 11:cells11010123. [PMID: 35011685 PMCID: PMC8750243 DOI: 10.3390/cells11010123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022] Open
Abstract
Background: To elucidate the role of iPLA2/PLA2G6 in gingivobuccal squamous cell carcinoma (GB-SCC) and to ascertain the synthetic lethality-based chemoprevention role of aspirin in arachidonic acid metabolism (AAM) pathway down-regulated GB-SCC. Methods: The in vitro efficacy of aspirin on GB-SCC cells (ITOC-03 and ITOC-04) was assessed by cell proliferation, colony formation, apoptosis, cell migration, cell cycle assay and RNA-seq, while inhibition of PLA2G6 and AAM pathway components was affirmed by qPCR, Western blot and immunofluorescence staining. The in vivo effect of aspirin was evaluated using NOD-SCID mice xenografts and immunohistochemical analysis. Results: We found that aspirin, which has been reported to act through the COX pathway, is inhibiting PLA2G6, and thereby the COX and LOX components of the AAM pathway. The findings were validated using PLA2G6 siRNA and immunohistochemical marker panel. Moreover, a pronounced effect in ITOC-04 cells and xenografts implied aspirin-induced synthetic lethality in the AAM pathway down-regulated GB-SCC. Conclusions: This study reveals that aspirin induces the anti-tumor effect by a previously unrecognized mechanism of PLA2G6 inhibition. In addition, the effect of aspirin is influenced by the baseline AAM pathway status and could guide precision prevention clinical trials of AAM pathway inhibitors.
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Affiliation(s)
- Kshama Pansare
- ICGC Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; (K.P.); (R.D.); (A.M.P.); (N.G.); (P.G.); (R.D.); (P.S.); (R.A.); (P.K.)
| | - Bhabani Mohanty
- Small Animal Imaging Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; (B.M.); (P.C.)
| | - Ranjeeta Dhotre
- ICGC Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; (K.P.); (R.D.); (A.M.P.); (N.G.); (P.G.); (R.D.); (P.S.); (R.A.); (P.K.)
| | - Aafrin M. Pettiwala
- ICGC Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; (K.P.); (R.D.); (A.M.P.); (N.G.); (P.G.); (R.D.); (P.S.); (R.A.); (P.K.)
| | - Saili Parab
- Biorepository, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India;
| | - Neha Gupta
- ICGC Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; (K.P.); (R.D.); (A.M.P.); (N.G.); (P.G.); (R.D.); (P.S.); (R.A.); (P.K.)
| | - Poonam Gera
- ICGC Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; (K.P.); (R.D.); (A.M.P.); (N.G.); (P.G.); (R.D.); (P.S.); (R.A.); (P.K.)
- Biorepository, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India;
| | - Nilesh Gardi
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, India;
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, India
| | - Rucha Dugge
- ICGC Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; (K.P.); (R.D.); (A.M.P.); (N.G.); (P.G.); (R.D.); (P.S.); (R.A.); (P.K.)
| | - Priyanka Sahu
- ICGC Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; (K.P.); (R.D.); (A.M.P.); (N.G.); (P.G.); (R.D.); (P.S.); (R.A.); (P.K.)
| | - Ruby Alhans
- ICGC Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; (K.P.); (R.D.); (A.M.P.); (N.G.); (P.G.); (R.D.); (P.S.); (R.A.); (P.K.)
| | - Pradnya Kowtal
- ICGC Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; (K.P.); (R.D.); (A.M.P.); (N.G.); (P.G.); (R.D.); (P.S.); (R.A.); (P.K.)
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, India
- Sarin Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India
| | - Pradip Chaudhari
- Small Animal Imaging Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; (B.M.); (P.C.)
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, India
| | - Rajiv Sarin
- ICGC Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; (K.P.); (R.D.); (A.M.P.); (N.G.); (P.G.); (R.D.); (P.S.); (R.A.); (P.K.)
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, India
- Sarin Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India
- Correspondence: ; Fax: +91-22-2740-5085
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Inhibition of PLA2G4E/cPLA2 promotes survival of random skin flaps by alleviating Lysosomal membrane permeabilization-Induced necroptosis. Autophagy 2021; 18:1841-1863. [PMID: 34872436 PMCID: PMC9450981 DOI: 10.1080/15548627.2021.2002109] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Necrosis that appears at the ischemic distal end of random-pattern skin flaps increases the pain and economic burden of patients. Necroptosis is thought to contribute to flap necrosis. Lysosomal membrane permeabilization (LMP) plays an indispensable role in the regulation of necroptosis. Nonetheless, the mechanisms by which lysosomal membranes become leaky and the relationship between necroptosis and lysosomes are still unclear in ischemic flaps. Based on Western blotting, immunofluorescence, enzyme-linked immunosorbent assay, and liquid chromatography-mass spectrometry (LC-MS) analysis results, we found that LMP was presented in the ischemic distal portion of random-pattern skin flaps, which leads to disruption of lysosomal function and macroautophagic/autophagic flux, increased necroptosis, and aggravated necrosis of the ischemic flaps. Moreover, bioinformatics analysis of the LC-MS results enabled us to focus on the role of PLA2G4E/cPLA2 (phospholipase A2, group IVE) in LMP of the ischemic flaps. In vivo inhibition of PLA2G4E with an adeno-associated virus vector attenuated LMP and necroptosis, and promoted flap survival. In addition, microRNA-seq helped us determine that Mir504-5p was differentially expressed in ischemic flaps. A string of in vitro and in vivo tests was employed to verify the inhibitory effect of Mir504-5p on PLA2G4E, LMP and necroptosis. Finally, we concluded that the inhibition of PLA2G4E by Mir504-5p reduced LMP-induced necroptosis, thereby promoting the survival of random-pattern skin flaps.
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9
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Shenoy SR, Dey B. Funding for cancer research by an Indian funding agency, DBT. J Biosci 2021. [DOI: 10.1007/s12038-020-00121-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Gao L, Chen R, Sugimoto M, Mizuta M, Kishimoto Y, Omori K. The Impact of m1A Methylation Modification Patterns on Tumor Immune Microenvironment and Prognosis in Oral Squamous Cell Carcinoma. Int J Mol Sci 2021; 22:ijms221910302. [PMID: 34638642 PMCID: PMC8508946 DOI: 10.3390/ijms221910302] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 02/07/2023] Open
Abstract
N1-methyladenosine (m1A) modification widely participates in the occurrence and progression of numerous diseases. Nevertheless, the potential roles of m1A in the tumor immune microenvironment (TIME) are still not fully understood. Based on 10 m1A methylation regulators, we comprehensively explored the m1A modification patterns in 502 patients with oral squamous cell carcinoma (OSCC). The m1A modification patterns were correlated with TIME characteristics and the m1A score was established to evaluate the effect of the m1A modification patterns on individual OSCC patients. The TIME characteristics and survival outcomes under the three m1A modification patterns were significantly distinct. OSCC patients in the high m1A score group were characterized by poorer prognosis, lower immune infiltration, lower ssGSEA score, lower expression levels of immune checkpoint molecules, and higher tumor mutation loads. The present study revealed that m1A modification might be associated with the TIME in OSCC, and has potential predictive ability for the prognosis of OSCC.
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Affiliation(s)
- Li Gao
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (L.G.); (M.M.); (K.O.)
| | - Ru Chen
- Matsusaka City Hospital, Matsusaka 515-8544, Japan;
| | - Masahiro Sugimoto
- Center for Minimally Invasive Therapies, Institute of Medical Science Research and Development, Tokyo Medical University, Tokyo 160-8402, Japan;
| | - Masanobu Mizuta
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (L.G.); (M.M.); (K.O.)
| | - Yo Kishimoto
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (L.G.); (M.M.); (K.O.)
- Correspondence: ; Tel.: +81-75-751-3346
| | - Koichi Omori
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan; (L.G.); (M.M.); (K.O.)
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11
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Li S, Mai Z, Gu W, Ogbuehi AC, Acharya A, Pelekos G, Ning W, Liu X, Deng Y, Li H, Lethaus B, Savkovic V, Zimmerer R, Ziebolz D, Schmalz G, Wang H, Xiao H, Zhao J. Molecular Subtypes of Oral Squamous Cell Carcinoma Based on Immunosuppression Genes Using a Deep Learning Approach. Front Cell Dev Biol 2021; 9:687245. [PMID: 34422810 PMCID: PMC8375681 DOI: 10.3389/fcell.2021.687245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/04/2021] [Indexed: 12/21/2022] Open
Abstract
Background: The mechanisms through which immunosuppressed patients bear increased risk and worse survival in oral squamous cell carcinoma (OSCC) are unclear. Here, we used deep learning to investigate the genetic mechanisms underlying immunosuppression in the survival of OSCC patients, especially from the aspect of various survival-related subtypes. Materials and methods: OSCC samples data were obtained from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and OSCC-related genetic datasets with survival data in the National Center for Biotechnology Information (NCBI). Immunosuppression genes (ISGs) were obtained from the HisgAtlas and DisGeNET databases. Survival analyses were performed to identify the ISGs with significant prognostic values in OSCC. A deep learning (DL)-based model was established for robustly differentiating the survival subpopulations of OSCC samples. In order to understand the characteristics of the different survival-risk subtypes of OSCC samples, differential expression analysis and functional enrichment analysis were performed. Results: A total of 317 OSCC samples were divided into one inferring cohort (TCGA) and four confirmation cohorts (ICGC set, GSE41613, GSE42743, and GSE75538). Eleven ISGs (i.e., BGLAP, CALCA, CTLA4, CXCL8, FGFR3, HPRT1, IL22, ORMDL3, TLR3, SPHK1, and INHBB) showed prognostic value in OSCC. The DL-based model provided two optimal subgroups of TCGA-OSCC samples with significant differences (p = 4.91E-22) and good model fitness [concordance index (C-index) = 0.77]. The DL model was validated by using four external confirmation cohorts: ICGC cohort (n = 40, C-index = 0.39), GSE41613 dataset (n = 97, C-index = 0.86), GSE42743 dataset (n = 71, C-index = 0.87), and GSE75538 dataset (n = 14, C-index = 0.48). Importantly, subtype Sub1 demonstrated a lower probability of survival and thus a more aggressive nature compared with subtype Sub2. ISGs in subtype Sub1 were enriched in the tumor-infiltrating immune cells-related pathways and cancer progression-related pathways, while those in subtype Sub2 were enriched in the metabolism-related pathways. Conclusion: The two survival subtypes of OSCC identified by deep learning can benefit clinical practitioners to divide immunocompromised patients with oral cancer into two subpopulations and give them target drugs and thus might be helpful for improving the survival of these patients and providing novel therapeutic strategies in the precision medicine area.
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Affiliation(s)
- Simin Li
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Zhaoyi Mai
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Wenli Gu
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | | | - Aneesha Acharya
- Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pune, India
| | - George Pelekos
- Faculty of Dentistry, University of Hong Kong, Hong Kong, China
| | - Wanchen Ning
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Xiangqiong Liu
- Laboratory of Molecular Cell Biology, Beijing Tibetan Hospital, China Tibetology Research Center, Beijing, China
| | - Yupei Deng
- Laboratory of Molecular Cell Biology, Beijing Tibetan Hospital, China Tibetology Research Center, Beijing, China
| | - Hanluo Li
- Department of Cranio Maxillofacial Surgery, University Clinic Leipzig, Leipzig, Germany
| | - Bernd Lethaus
- Department of Cranio Maxillofacial Surgery, University Clinic Leipzig, Leipzig, Germany
| | - Vuk Savkovic
- Department of Cranio Maxillofacial Surgery, University Clinic Leipzig, Leipzig, Germany
| | - Rüdiger Zimmerer
- Department of Cranio Maxillofacial Surgery, University Clinic Leipzig, Leipzig, Germany
| | - Dirk Ziebolz
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
| | - Gerhard Schmalz
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
| | - Hao Wang
- Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
| | - Hui Xiao
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Jianjiang Zhao
- Shenzhen Stomatological Hospital, Southern Medical University, Shenzhen, China
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12
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Ding Q, Sun Y, Shang J, Li F, Zhang Y, Liu JX. NMFNA: A Non-negative Matrix Factorization Network Analysis Method for Identifying Modules and Characteristic Genes of Pancreatic Cancer. Front Genet 2021; 12:678642. [PMID: 34367241 PMCID: PMC8340025 DOI: 10.3389/fgene.2021.678642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/03/2021] [Indexed: 01/15/2023] Open
Abstract
Pancreatic cancer (PC) is a highly fatal disease, yet its causes remain unclear. Comprehensive analysis of different types of PC genetic data plays a crucial role in understanding its pathogenic mechanisms. Currently, non-negative matrix factorization (NMF)-based methods are widely used for genetic data analysis. Nevertheless, it is a challenge for them to integrate and decompose different types of genetic data simultaneously. In this paper, a non-NMF network analysis method, NMFNA, is proposed, which introduces a graph-regularized constraint to the NMF, for identifying modules and characteristic genes from two-type PC data of methylation (ME) and copy number variation (CNV). Firstly, three PC networks, i.e., ME network, CNV network, and ME-CNV network, are constructed using the Pearson correlation coefficient (PCC). Then, modules are detected from these three PC networks effectively due to the introduced graph-regularized constraint, which is the highlight of the NMFNA. Finally, both gene ontology (GO) and pathway enrichment analyses are performed, and characteristic genes are detected by the multimeasure score, to deeply understand biological functions of PC core modules. Experimental results demonstrated that the NMFNA facilitates the integration and decomposition of two types of PC data simultaneously and can further serve as an alternative method for detecting modules and characteristic genes from multiple genetic data of complex diseases.
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Affiliation(s)
- Qian Ding
- School of Computer Science, Qufu Normal University, Rizhao, China
| | - Yan Sun
- School of Computer Science, Qufu Normal University, Rizhao, China
| | - Junliang Shang
- School of Computer Science, Qufu Normal University, Rizhao, China
| | - Feng Li
- School of Computer Science, Qufu Normal University, Rizhao, China
| | - Yuanyuan Zhang
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao, China
| | - Jin-Xing Liu
- School of Computer Science, Qufu Normal University, Rizhao, China
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13
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Moura ACD, Assad DX, Amorim Dos Santos J, Porto de Toledo I, Barra GB, Castilho RM, Squarize CH, Guerra ENS. Worldwide prevalence of PI3K-AKT-mTOR pathway mutations in head and neck cancer: A systematic review and meta-analysis. Crit Rev Oncol Hematol 2021; 160:103284. [PMID: 33675910 DOI: 10.1016/j.critrevonc.2021.103284] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 02/03/2021] [Accepted: 02/27/2021] [Indexed: 02/07/2023] Open
Abstract
A systematic review (SR) and meta-analysis were conducted to determine the prevalence of PI3K-AKT-mTOR signaling pathway mutations in patients with head and neck cancer (HNC). Overall, 105 studies comprising 8630 patients and 1306 mutations were selected. The estimated mutations prevalence was 13 % for PIK3CA (95 % confidence interval [CI] = 11-14; I2 = 82 %; p < 0.0001), 4% for PTEN (95 % CI = 3-5; I2 = 55 %; p < 0.0001), 3% for MTOR (95 % CI = 2-4; I2 = 5%; p = 0.40), and 2% for AKT (95 % CI = 1-2; I2 = 50 %; p = 0.0001). We further stratified the available data of the participants according to risk factors and tumor characteristics, including HPV infection, tobacco use, alcohol exposure, TNM stage, and histological tumor differentiation, and performed subgroup analysis. We identified significant associations between PI3K-AKT-mTOR pathway-associated mutations and advanced TNM stage (odds ratio [OR] = 0.20; 95 % CI = 0.09-0.44; I² = 71 %; p = 0.0001) and oropharyngeal HPV-positive tumors and PIK3CA mutations (OR = 17.48; 95 % CI = 4.20-72.76; I² = 69 %; p < 0.0002). No associations were found between alcohol and tobacco exposure, and tumor differentiation grade. This SR demonstrated that the PI3K-AKT-mTOR pathway emerges as a potential prognostic factor and could offer a molecular basis for future studies on therapeutic targeting in HNC patients.
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Affiliation(s)
- Adriana Castelo de Moura
- Laboratory of Oral Histopathology, Health Sciences Faculty, University of Brasília, Brasília, Brazil; Hospital Universitário de Brasília (HUB-UnB/Ebserh), Brasília, DF, Brazil; Hospital Santa Lúcia, Brasília, DF, Brazil
| | - Daniele Xavier Assad
- Laboratory of Oral Histopathology, Health Sciences Faculty, University of Brasília, Brasília, Brazil; Medical Oncology Department, Hospital Sírio-Libanês, Brasília, DF, Brazil
| | - Juliana Amorim Dos Santos
- Laboratory of Oral Histopathology, Health Sciences Faculty, University of Brasília, Brasília, Brazil
| | - Isabela Porto de Toledo
- Laboratory of Oral Histopathology, Health Sciences Faculty, University of Brasília, Brasília, Brazil
| | - Gustavo Barcelos Barra
- Sabin Medicina Diagnóstica, SAAN Quadra 03 Lotes 145/185, Brasília, 70632-340, DF, Brazil
| | - Rogerio Moraes Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, Division of Oral Pathology, Radiology and Medicine, University of Michigan School of Dentistry. Ann Arbor, 48109-1078, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Cristiane Helena Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, Division of Oral Pathology, Radiology and Medicine, University of Michigan School of Dentistry. Ann Arbor, 48109-1078, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Eliete Neves Silva Guerra
- Laboratory of Oral Histopathology, Health Sciences Faculty, University of Brasília, Brasília, Brazil; Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, Division of Oral Pathology, Radiology and Medicine, University of Michigan School of Dentistry. Ann Arbor, 48109-1078, MI, USA.
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14
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Heslin C, Boehm D, Gilmore BF, Megaw J, Freeman TA, Hickok NJ, Cullen PJ, Bourke P. Biomolecules as Model Indicators of In Vitro and In Vivo Cold Plasma Safety. FRONTIERS IN PHYSICS 2021; 8:613046. [PMID: 37124146 PMCID: PMC10136044 DOI: 10.3389/fphy.2020.613046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The potential applications for cold plasma in medicine are extensive, from microbial inactivation and induction of apoptosis in cancer cells to stimulating wound healing and enhancing the blood coagulation cascade. The safe bio-medical application of cold plasma and subsequent effect on complex biological pathways requires precision and a distinct understanding of how physiological redox chemistry is manipulated. Chemical modification of biomolecules such as carbohydrates, proteins, and lipids treated with cold plasma have been characterized, however, the context of how alterations of these molecules affect cell behavior or in vivo functionality has not been determined. Thus, this study examines the cytotoxic and mutagenic effects of plasma-treated molecules in vitro using CHO-K1 cells and in vivo in Galleria mellonella larvae. Specifically, albumin, glucose, cholesterol, and arachidonic acid were chosen as representative biomolecules, with established involvement in diverse bioprocesses including; cellular respiration, intracellular transport, cell signaling or membrane structure. Long- and short-term effects depended strongly on the molecule type and the treatment milieu indicating the impact of chemical and physical modifications on downstream biological pathways. Importantly, absence of short-term toxicity did not always correlate with absence of longer-term effects, indicating the need to comprehensively assess ongoing effects for diverse biological applications.
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Affiliation(s)
- Caitlin Heslin
- School of Food Science and Environmental Health, Technological University Dublin, Dublin, Ireland
| | - Daniela Boehm
- School of Food Science and Environmental Health, Technological University Dublin, Dublin, Ireland
| | | | - Julianne Megaw
- School of Pharmacy, Queens University Belfast, Belfast, United Kingdom
| | - Theresa A. Freeman
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Jefferson University, Philadelphia, PA, United States
| | - Noreen J. Hickok
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Jefferson University, Philadelphia, PA, United States
| | - P. J. Cullen
- School of Food Science and Environmental Health, Technological University Dublin, Dublin, Ireland
- School of Chemical and Biomolecular Engineering, University of Sydney, Sydney, NSW, Australia
| | - Paula Bourke
- School of Food Science and Environmental Health, Technological University Dublin, Dublin, Ireland
- School of Biological Sciences, Queens University Belfast, Belfast, United Kingdom
- Plasma Research Group, School of Biosystems and Food Engineering, University College Dublin, Dublin, Ireland
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15
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Huang GJ, Yang BB. Identification of core miRNA prognostic markers in patients with laryngeal cancer using bioinformatics analysis. Eur Arch Otorhinolaryngol 2020; 278:1613-1626. [PMID: 32789639 DOI: 10.1007/s00405-020-06275-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 08/04/2020] [Indexed: 12/19/2022]
Abstract
PURPOSE Lots of studies indicated that many microRNAs (miRNAs) are associated with the prognosis of patients with laryngeal cancer (LC). The objective of our study is to identify potential core miRNAs associated with the pathogenesis and prognosis of LC. METHODS Using the Cancer Genome Atlast database, we identified 70 differentially expressed miRNAs between LC tumor specimens and non-tumor specimens. Then Cox regression analyses and the least absolute shrinkage and selection operator regression signature were performed to detect miRNA prognostic markers. A nomogram integrating miRNA prognostic markers was constructed to predict overall survival (OS) for LC patients. The potential target genes of the key miRNA were predicted by miRTarBase and miRDB databases. Subsequently, their potential functions were revealed by gene ontology annotation and kyoto encyclopedia of genes and genomes pathway enrichment analysis. Related biological pathways of the key target gene involved in LC were detected through gene set enrichment analysis (GSEA). RESULTS A prognostic miRNA signature was constructed. The up-regulated miR-105-1 was related to a worse OS (p = 0.043), which suggested that miR-105-1 may likely be the key miRNA prognostic marker. Survival analyses and paired expression analyses of target genes indicated that ENDOU may be the key target gene. Finally, we conducted GSEA to elucidate the pathways enriched between low- and high-ENDOU expression datasets. CONCLUSION Our findings might bring some new light on the pathogenesis of LC. Then, it might facilitate doctors to predict the prognosis and improve treatment outcomes for LC patients. However, the behaviors of LC are relatively heterogeneous, and the TCGA database cannot provide detailed information about the subsites and treatment modalities of LC. Further molecular biological experiments and clinical investigations would be required to confirm this conclusion.
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Affiliation(s)
- Guan-Jiang Huang
- Department of Otorhinolaryngology, School of Medicine, The Second Affiliated Hospital, Zhejiang University, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China
| | - Bei-Bei Yang
- Department of Otorhinolaryngology, School of Medicine, The Second Affiliated Hospital, Zhejiang University, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China.
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16
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Luo B, Chen C, Wu X, Yan D, Chen F, Yu X, Yuan J. Cytochrome P450 2U1 Is a Novel Independent Prognostic Biomarker in Breast Cancer Patients. Front Oncol 2020; 10:1379. [PMID: 32850442 PMCID: PMC7419690 DOI: 10.3389/fonc.2020.01379] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/30/2020] [Indexed: 12/14/2022] Open
Abstract
Background: The susceptibility of breast cancer is largely affected by the metabolic capacity of breast tissue. This ability depends in part on the expression profile of cytochrome P450 (CYPs). CYPs are a superfamily of enzymes with related catalysis to endogenous and exogenous bioactive substances, including xenobiotic metabolism, drugs, and some endogenous substances metabolism which activate cells and stimulate cell signaling pathways, such as arachidonic acid metabolism, steroid metabolism, fatty acid metabolism. Interestingly, CYP was electively expressed in different tumors, and mediated the metabolic activation of multiple carcinogens and participated in the activation and deactivation of tumor therapeutic drugs. However, the biological action of cytochrome P450 2U1 (CYP2U1) in breast carcinoma is little understood so far. Methods: To investigate the biological value of CYP2U1 in breast carcinoma, we performed immunohistochemical (IHC) analysis and survival analysis based on clinico-pathological data of breast cancer. Results: IHC analysis showed that the abundance of CYP2U1 protein was inversely proportional to the state of estrogen receptor(ER) (P < 0.05), and the lower the degree of tumor differentiation, the higher the protein abundance (P < 0.001). Additionally, compared with luminal tumors, the CYP2U1 protein content was more abundant in triple negative breast cancer (P < 0.05). Importantly, survival analysis showed that higher CYP2U1 protein levels predicted poor 5-year overall survival rate (P < 0.01), 5-year disease-free survival rate (P < 0.05), and 5-year metastatic-free survival rate (P < 0.01) for the entire enrolled breast cancer patients. Conclusions: CYP2U1 is generally closely related to the clinicopathological characteristics and is also an adverse prognostic factor for breast carcinoma patients, indicating that CYP2U1 is engaged in the malignant progression of breast carcinoma.
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Affiliation(s)
- Bin Luo
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chuang Chen
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiaoyan Wu
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Dandan Yan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fangfang Chen
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xinxin Yu
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
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17
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Bai K, He S, Shu L, Wang W, Lin S, Zhang Q, Li L, Cheng L, Dai Y. Identification of cancer stem cell characteristics in liver hepatocellular carcinoma by WGCNA analysis of transcriptome stemness index. Cancer Med 2020; 9:4290-4298. [PMID: 32311840 PMCID: PMC7300398 DOI: 10.1002/cam4.3047] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/07/2020] [Accepted: 03/24/2020] [Indexed: 12/16/2022] Open
Abstract
Cancer stem cells (CSCs) are characterized by self-renewal and -differential potential as compared to common cancer cells and play an important role in the development and therapeutic resistance of liver hepatocellular carcinoma (LIHC). However, the specific pathogenesis of LIHC stem cells is still unclear, and the genes involved in the stemness of LIHC stem cells are currently unknown. In this study, we investigated novel biomarkers associated with LIHC and explored the expression characteristics of stem cell-related genes in LIHC. We found that mRNA expression-based stemness index (mRNAsi) was significantly overexpressed in liver cancer tissues. Further, mRNAsi expression in LIHC increased with the tumor pathological grade, with grade 4 tumors harboring the greatest stem cell features. Upon establishing mRNAsi scores based on mRNA expression of every gene, we found an association with poor overall survival in LIHC. Moreover, modules of interest were determined based on weighted gene co-expression network analysis (WGCNA) inclusion criteria, and three significant modules (red, green, and brown) and 21 key genes (DCN, ECM1, HAND2, PTGIS, SFRP1, SRPX, COLEC10, GRP182, ADAMTS7, CD200, CDH11, COL8A1, FAP, LZTS1, MAP1B, NAV1, NOTCH3, OLFML2A, PRR16, TMEM119, and VCAN) were identified. Functional analysis of these 21 genes demonstrated their enrichment in pathways involved in angiogenesis, negative regulation of DNA-binding transcription factor activity, apoptosis, and autophagy. Causal relationship with proteins indicated that the Wnt, Notch, and Hypoxia pathways are closely related to LIHC tumorigenesis. To our knowledge, this is the first report of a novel CSC biomarker, mRNAsi, to predict the prognosis of LIHC. Further, we identified 21 key genes through mRNA expression network analysis, which could be potential therapeutic targets to inhibit the stemness of cancer cells in LIHC.
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Affiliation(s)
- Kun‐Hao Bai
- Department of EndoscopySun Yat‐Sen University Cancer CenterGuangzhouChina
- State Key Laboratory of Oncology in South ChinaGuangzhouChina
- Collaborative Innovation Center for Cancer MedicineGuangzhouChina
| | - Si‐Yuan He
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical SciencesHoustonTXUSA
| | - Ling‐Ling Shu
- State Key Laboratory of Oncology in South ChinaGuangzhouChina
- Collaborative Innovation Center for Cancer MedicineGuangzhouChina
- Department of Hematological OncologySun Yat‐Sen University Cancer CenterGuangzhouChina
| | - Wei‐Da Wang
- State Key Laboratory of Oncology in South ChinaGuangzhouChina
- Collaborative Innovation Center for Cancer MedicineGuangzhouChina
- Department of Hematological OncologySun Yat‐Sen University Cancer CenterGuangzhouChina
| | - Shi‐Yong Lin
- Department of EndoscopySun Yat‐Sen University Cancer CenterGuangzhouChina
- State Key Laboratory of Oncology in South ChinaGuangzhouChina
- Collaborative Innovation Center for Cancer MedicineGuangzhouChina
| | - Qian‐Yi Zhang
- State Key Laboratory of Oncology in South ChinaGuangzhouChina
- Collaborative Innovation Center for Cancer MedicineGuangzhouChina
- Department of Hematological OncologySun Yat‐Sen University Cancer CenterGuangzhouChina
| | - Liang Li
- State Key Laboratory of Oncology in South ChinaGuangzhouChina
- Collaborative Innovation Center for Cancer MedicineGuangzhouChina
- Department of Hematological OncologySun Yat‐Sen University Cancer CenterGuangzhouChina
| | - Lei Cheng
- Collaborative Innovation Center for Cancer MedicineCancer InstituteFudan University Shanghai Cancer CenterShanghaiChina
| | - Yu‐Jun Dai
- State Key Laboratory of Oncology in South ChinaGuangzhouChina
- Collaborative Innovation Center for Cancer MedicineGuangzhouChina
- Department of Hematological OncologySun Yat‐Sen University Cancer CenterGuangzhouChina
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18
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Das D, Ghosh S, Maitra A, Biswas NK, Panda CK, Roy B, Sarin R, Majumder PP. Epigenomic dysregulation-mediated alterations of key biological pathways and tumor immune evasion are hallmarks of gingivo-buccal oral cancer. Clin Epigenetics 2019; 11:178. [PMID: 31796082 PMCID: PMC6889354 DOI: 10.1186/s13148-019-0782-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/17/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Gingivo-buccal oral squamous cell carcinoma (OSCC-GB) is the most common cancer among men in India and is associated with high mortality. Although OSCC-GB is known to be quite different from tongue cancer in its genomic presentation and its clinical behavior, it is treated identically as tongue cancer. Predictive markers of prognosis and therapy that are specific to OSCC-GB are, therefore, required. Although genomic drivers of OSCC-GB have been identified by whole exome and whole genome sequencing, no epigenome-wide study has been conducted in OSCC-GB; our study has filled this gap, and has discovered and validated epigenomic hallmarks of gingivobuccal oral cancer. METHODS We have carried out integrative analysis of epigenomic (n = 87) and transcriptomic (n = 72) profiles of paired tumor-normal tissues collected from OSCC-GB patients from India. Genome-wide DNA methylation assays and RNA-sequencing were performed on high-throughput platforms (Illumina) using a half-sample of randomly selected patients to discover significantly differentially methylated probes (DMPs), which were validated on the remaining half-sample of patients. RESULTS About 200 genes showed significant inverse correlation between promoter methylation and expression, of which the most significant genes included genes that act as transcription factors and genes associated with other cancer types. Novel findings of this study include identification of (a) potential immunosuppressive effect in OSCC-GB due to significant promoter hypomethylation driven upregulation of CD274 and CD80, (b) significant dysregulation by epigenetic modification of DNMT3B (upregulation) and TET1 (downregulation); and (c) known drugs that can reverse the direction of dysregulation of gene expression caused by promoter methylation. CONCLUSIONS In OSCC-GB patients, there are significant alterations in expression of key genes that (a) regulate normal cell division by maintenance of balanced DNA methylation and transcription process, (b) maintain normal physiological signaling (PPAR, B cell receptor) and metabolism (arachidonic acid) pathways, and (c) provide immune protection against antigens, including tumor cells. These findings indicate novel therapeutic targets, including immunotherapeutic, for treatment of OSCC-GB.
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Affiliation(s)
- Debodipta Das
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India
| | - Sahana Ghosh
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India
| | - Nidhan K Biswas
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India
| | | | - Bidyut Roy
- Indian Statistical Institute, Kolkata, India
| | - Rajiv Sarin
- Advanced Centre for Treatment Research and Education in Cancer, Mumbai, India
| | - Partha P Majumder
- National Institute of Biomedical Genomics, P.O.: N.S.S, Kalyani, 741251, India. .,Indian Statistical Institute, Kolkata, India.
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19
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Halczy-Kowalik L, Drozd A, Stachowska E, Drozd R, Żabski T, Domagała W. Fatty acids distribution and content in oral squamous cell carcinoma tissue and its adjacent microenvironment. PLoS One 2019; 14:e0218246. [PMID: 31242216 PMCID: PMC6594603 DOI: 10.1371/journal.pone.0218246] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 05/29/2019] [Indexed: 12/25/2022] Open
Abstract
Squamous cell carcinoma of the oral cavity mucosa grows under conditions of poor oxygenation and nutrient scarcity. Reprogramming of lipid biosynthesis accompanies tumor growth, but the conditions under which it occurs are not fully understood. The fatty acid content of the serum, tumor tissue and adjacent tumor microenvironment was measured by gas chromatography in 30 patients with squamous cell carcinoma grade 1-3. Twenty-five fatty acids were identified; their frequencies and percentages in each of the environments were assessed. Nineteen of the twenty-five fatty acids were found in tumor tissue, tumor adjacent tissue and blood serum. Of them, 8 were found in all thirty patients. Percentages of C16:0 and C18:1n9 were highest in the tumor, C18:1n9 and C16:0 were highest in tumor adjacent tissue, and C16:0 and C18:0 were highest in blood serum. The frequencies and amounts of C22:1n13, C22:4n6, C22:5n3 and C24:1 in tumor adjacent tissues were higher than those in blood serum, independent of the tumor grade. The correlations between the amount of fatty acid and tumor grade were the strongest in tumor adjacent tissues. The correlations between particular fatty acids were most prevalent for grade 1+2 tumors and were strongest for grade 3 tumors. In the adjacent tumor microenvironment, lipogenesis was controlled by C22:6w3. In blood serum, C18:1trans11 limited the synthesis of long-chain fatty acids. Our research reveals intensive lipid changes in oral cavity SCC adjacent to the tumor microenvironment and blood serum of the patients. Increase in percentage of some of the FAs in the path: blood serum-tumor adjacent microenvironment-tumor, and it is dependent on tumor grade. This dependency is the most visible in the tumor adjacent environment.
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Affiliation(s)
- Ludmiła Halczy-Kowalik
- Clinic of Maxillofacial Surgery, Pomeranian Medical University, Szczecin, Poland
- * E-mail:
| | - Arleta Drozd
- Department of Biochemistry and Human Nutrition, Pomeranian Medical University, Szczecin, Poland
| | - Ewa Stachowska
- Department of Biochemistry and Human Nutrition, Pomeranian Medical University, Szczecin, Poland
| | - Radosław Drozd
- Department of Immunology, Microbiology and Physiological Chemistry, West Pomeranian University of Technology, Szczecin, Poland
| | - Tomasz Żabski
- Clinic of Maxillofacial Surgery, Pomeranian Medical University, Szczecin, Poland
| | - Wenancjusz Domagała
- Department of Pathomorphology, Pomeranian Medical University, Szczecin, Poland
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Establishment and genomic characterization of gingivobuccal carcinoma cell lines with smokeless tobacco associated genetic alterations and oncogenic PIK3CA mutation. Sci Rep 2019; 9:8272. [PMID: 31164688 PMCID: PMC6547758 DOI: 10.1038/s41598-019-44143-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 05/07/2019] [Indexed: 12/15/2022] Open
Abstract
Smokeless tobacco associated Gingivobuccal squamous cell carcinoma (GB-SCC) is a major public health problem but available oral cancer cell lines are mostly from smoking associated tongue SCC raising the need for pertinent GB-SCC cell line models. As part of the International Cancer Genome Consortium (ICGC) Project, 4 novel cell lines, namely, Indian Tata Memorial Centre Oral Cancer (ITOC) -01 to -04 were established and characterized with conventional methods, karyotyping, ultrastructure, in vivo tumourigenicity, Whole exome sequencing (WES) and RNA sequencing. These hyperploid cell lines form xenografts in mice and show metabolically active and necrotic areas on fluorodeoxyglucose-positron emission tomography (FDG-PET) imaging. WES of ITOC cell lines recapitulate the genomic tumor profile of ICGC GB-SCC database. We further identified smokeless tobacco associated genetic alterations (PCLO, FAT3 and SYNE2) and oncogenic PIK3CA mutation in GB-SCC cell lines. Transcriptome profiling identified deregulation of pathways commonly altered in cancer and down-regulation of arachidonic acid metabolism pathway, implying its possible role in GB-SCC. Clinical application of high throughput sequencing data depends on relevant cell line models to validate potential targets. Extensively characterized, these oral SCC cell lines are particularly suited for mechanistic studies and pre-clinical drug development for smokeless tobacco associated oral cancer.
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Sundar S, Khetrapal-Singh P, Frampton J, Trimble E, Rajaraman P, Mehrotra R, Hariprasad R, Maitra A, Gill P, Suri V, Srinivasan R, Singh G, Thakur JS, Dhillon P, Cazier JB. Harnessing genomics to improve outcomes for women with cancer in India: key priorities for research. Lancet Oncol 2019; 19:e102-e112. [PMID: 29413464 DOI: 10.1016/s1470-2045(17)30726-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 08/03/2017] [Accepted: 09/11/2017] [Indexed: 02/08/2023]
Abstract
Cumulatively, breast, cervical, ovarian, and uterine cancer account for more than 70% of cancers in women in India. Distinct differences in the clinical presentation of women with cancer suggest underlying differences in cancer biology and genetics. The peak age of onset of breast and ovarian cancer appears to be a decade earlier in India (age 45-50 years) than in high-income countries (age >60 years). Understanding these differences through research to develop diagnosis, screening, prevention, and treatment frameworks that ar e specific to the Indian population are critical and essential to improving women's health in India. Since the sequencing of the human genome in 2001, applications of advanced technologies, such as massively parallel sequencing, have transformed the understanding of the genetic and environmental drivers of cancer. How can advanced technologies be harnessed to provide health-care solutions at a scale and to a budget suitable for a country of 1·2 billion people? What research programmes are necessary to answer questions specific to India, and to build capacity for innovative solutions using these technologies? In order to answer these questions, we convened a workshop with key stakeholders to address these issues. In this Series paper, we highlight challenges in tackling the growing cancer burden in India, discuss ongoing genomics research and developments in infrastructure, and suggest key priorities for future research in cancer in India.
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Affiliation(s)
- Sudha Sundar
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
| | | | - Jon Frampton
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | | | - Ravi Mehrotra
- National Institute of Cancer Prevention and Research, Noida, Uttar Pradesh, India
| | - Roopa Hariprasad
- National Institute of Cancer Prevention and Research, Noida, Uttar Pradesh, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics, Kolkata, West Bengal, India
| | - Paramjit Gill
- Institute of Applied Health, University of Birmingham, Birmingham, UK
| | - Vanita Suri
- Department of Obstetrics and Gynaecology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Radhika Srinivasan
- Department of Pathology and Cytology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Gurpreet Singh
- Department of Surgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - J S Thakur
- Department of Public Health, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Jean-Baptiste Cazier
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK; Centre for Computational Biology, University of Birmingham, Birmingham, UK
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Hanna GJ, Kofman ER, Shazib MA, Woo SB, Reardon B, Treister NS, Haddad RI, Cutler CS, Antin JH, Van Allen EM, Uppaluri R, Soiffer RJ. Integrated genomic characterization of oral carcinomas in post-hematopoietic stem cell transplantation survivors. Oral Oncol 2018; 81:1-9. [DOI: 10.1016/j.oraloncology.2018.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/15/2018] [Accepted: 04/07/2018] [Indexed: 02/07/2023]
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Yang Y, Zhang Y, Qu X, Xia J, Li D, Li X, Wang Y, He Z, Li S, Zhou Y, Xie L, Yang Z. Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq. Oncotarget 2018; 7:87194-87205. [PMID: 27888627 PMCID: PMC5349981 DOI: 10.18632/oncotarget.13554] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/07/2016] [Indexed: 12/26/2022] Open
Abstract
Objective Osteosarcoma (OS) is a malignant bone tumor with high morbidity in young adults and adolescents. This study aimed to discover potential early diagnosis biomarkers in OS. Results In total, 111 differentially expressed genes (DEGs) were identified in primary OS compared with normal controls and 235 DEGs were identified in metastatic OS compared with primary OS. AURKB and PPP2R2B were the significantly up-regulated and down-regulated hub proteins, respectively, in the PPI protein-protein network (PPI) network of primary OS. ISG15 and BTRC were the significantly up-regulated and down-regulated hub proteins, respectively, in the network of metastatic OS. The DEGs in metastatic OS compared with primary OS were significantly enriched in the arachidonic acid metabolism, malaria, and chemokine signaling pathways. Finally, we employed quantitative real-time polymerase chain reaction (qRT-PCR) to validate the expression levels of candidate DEGs and the results indicated that our bioinformatics approach was acceptable. Materials and Methods The mRNA expression profiling of 20 subjects was obtained through high-throughput RNA-sequencing. DEGs were identified between primary OS and normal Control, and between primary OS and metastatic OS, respectively. Functional annotation and PPI networks were used to obtain insights into the functions of DEGs. qRT-PCR was performed to detect the expression levels of dysregulated genes in OS. Conclusions Our work might provide groundwork for the further exploration of tumorigenesis and metastasis mechanisms of OS.
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Affiliation(s)
- Yihao Yang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, China
| | - Ya Zhang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, China
| | - Xin Qu
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, China
| | - Junfeng Xia
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, China
| | - Dongqi Li
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, China
| | - Xiaojuan Li
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, China
| | - Yu Wang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, China
| | - Zewei He
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, China
| | - Su Li
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, China
| | - Yonghong Zhou
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, China
| | - Lin Xie
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, China
| | - Zuozhang Yang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan 650118, China
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Upadhyay P, Gardi N, Desai S, Chandrani P, Joshi A, Dharavath B, Arora P, Bal M, Nair S, Dutt A. Genomic characterization of tobacco/nut chewing HPV-negative early stage tongue tumors identify MMP10 asa candidate to predict metastases. Oral Oncol 2017; 73:56-64. [PMID: 28939077 PMCID: PMC5628952 DOI: 10.1016/j.oraloncology.2017.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 07/27/2017] [Accepted: 08/06/2017] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Nodal metastases status among early stage tongue squamous cell cancer patients plays a decisive role in the choice of treatment, wherein about 70% patients can be spared from surgery with an accurate prediction of negative pathological lymph node status. This underscores an unmet need for prognostic biomarkers to stratify the patients who are likely to develop metastases. MATERIALS AND METHODS We performed high throughput sequencing of fifty four samples derived from HPV negative early stage tongue cancer patients habitual of chewing betel nuts, areca nuts, lime or tobacco using whole exome (n=47) and transcriptome (n=17) sequencing that were analyzed using in-house computational tools. Additionally, gene expression meta-analyses were carried out for 253 tongue cancer samples. The candidate genes were validated using qPCR and immuno-histochemical analysis in an extended set of 50 early primary tongue cancer samples. RESULTS AND CONCLUSION Somatic analysis revealed a classical tobacco mutational signature C:G>A:T transversion in 53% patients that were mutated in TP53, NOTCH1, CDKN2A, HRAS, USP6, PIK3CA, CASP8, FAT1, APC, and JAK1. Similarly, significant gains at genomic locus 11q13.3 (CCND1, FGF19, ORAOV1, FADD), 5p15.33 (SHANK2, MMP16, TERT), and 8q24.3 (BOP1); and, losses at 5q22.2 (APC), 6q25.3 (GTF2H2) and 5q13.2 (SMN1) were observed in these samples. Furthermore, an integrated gene-expression analysis of 253 tongue tumors suggested an upregulation of metastases-related pathways and over-expression of MMP10 in 48% tumors that may be crucial to predict nodal metastases in early tongue cancer patients. In overall, we present the first descriptive portrait of somatic alterations underlying the genome of tobacco/nut chewing HPV-negative early tongue cancer, and identify MMP10 asa potential prognostic biomarker to stratify those likely to develop metastases.
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Affiliation(s)
- Pawan Upadhyay
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Nilesh Gardi
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India
| | - Sanket Desai
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Pratik Chandrani
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Asim Joshi
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Bhaskar Dharavath
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Priyanca Arora
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, India
| | - Munita Bal
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, India
| | - Sudhir Nair
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, India
| | - Amit Dutt
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
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Singh R, De Sarkar N, Sarkar S, Roy R, Chattopadhyay E, Ray A, Biswas NK, Maitra A, Roy B. Analysis of the whole transcriptome from gingivo-buccal squamous cell carcinoma reveals deregulated immune landscape and suggests targets for immunotherapy. PLoS One 2017; 12:e0183606. [PMID: 28886030 PMCID: PMC5590820 DOI: 10.1371/journal.pone.0183606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/08/2017] [Indexed: 01/19/2023] Open
Abstract
Background Gingivo-buccal squamous cell carcinoma (GBSCC) is one of the most common oral cavity cancers in India with less than 50% patients surviving past 5 years. Here, we report a whole transcriptome profile on a batch of GBSCC tumours with diverse tobacco usage habits. The study provides an entire landscape of altered expression with an emphasis on searching for targets with therapeutic potential. Methods Whole transcriptomes of 12 GBSCC tumours and adjacent normal tissues were sequenced and analysed to explore differential expression of genes. Expression changes were further compared with those in TCGA head and neck cohort (n = 263) data base and validated in an independent set of 10GBSCC samples. Results Differentially expressed genes (n = 2176) were used to cluster the patients based on their tobacco habits, resulting in 3 subgroups. Immune response was observed to be significantly aberrant, along with cell adhesion and lipid metabolism processes. Different modes of immune evasion were seen across 12 tumours with up-regulation or consistent expression of CD47, unlike other immune evasion genes such as PDL1, FUT4, CTLA4 and BTLA which were downregulated in a few samples. Variation in infiltrating immune cell signatures across tumours also indicates heterogeneity in immune evasion strategies. A few actionable genes such as ITGA4, TGFB1 and PTGS1/COX1 were over expressed in most samples. Conclusion This study found expression deregulation of key immune evasion genes, such as CD47 and PDL1, and reasserts their potential as effective immunotherapeutic targets for GBSCC, which requires further clinical studies. Present findings reiterate the idea of using transcriptome profiling to guide precision therapeutic strategies.
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Affiliation(s)
- Richa Singh
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
| | | | - Sumanta Sarkar
- National Institute of Biomedical Genomics, Kalyani, India
| | - Roshni Roy
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
| | | | - Anindita Ray
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
| | | | - Arindam Maitra
- National Institute of Biomedical Genomics, Kalyani, India
| | - Bidyut Roy
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
- * E-mail:
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Dhers L, Ducassou L, Boucher JL, Mansuy D. Cytochrome P450 2U1, a very peculiar member of the human P450s family. Cell Mol Life Sci 2017; 74:1859-1869. [PMID: 28083596 PMCID: PMC11107762 DOI: 10.1007/s00018-016-2443-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 12/14/2022]
Abstract
Cytochrome P450 2U1 (CYP2U1) exhibits several distinctive characteristics among the 57 human CYPs, such as its presence in almost all living organisms with a highly conserved sequence, its particular gene organization with only five exons, its major location in thymus and brain, and its protein sequence involving an unusually long N-terminal region containing 8 proline residues and an insert of about 20 amino acids containing 5 arginine residues after the transmembrane helix. Few substrates, including fatty acids, N-arachidonoylserotonin (AS), and some drugs, have been reported so far. However, its biological roles remain largely unknown, even though CYP2U1 mutations have been involved in some pathological situations, such as complicated forms of hereditary spastic paraplegia. These data together with its ability to hydroxylate some fatty acids and AS suggest its possible role in lipid metabolism.
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Affiliation(s)
- L Dhers
- UMR 8601 CNRS, Université Paris Descartes, Paris Sorbonne Cité, 45 rue des Saints Pères, 75006, Paris, France
| | - L Ducassou
- UMR 8601 CNRS, Université Paris Descartes, Paris Sorbonne Cité, 45 rue des Saints Pères, 75006, Paris, France
| | - J-L Boucher
- UMR 8601 CNRS, Université Paris Descartes, Paris Sorbonne Cité, 45 rue des Saints Pères, 75006, Paris, France.
| | - D Mansuy
- UMR 8601 CNRS, Université Paris Descartes, Paris Sorbonne Cité, 45 rue des Saints Pères, 75006, Paris, France
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Sun Y, Sang Z, Jiang Q, Ding X, Yu Y. Transcriptomic characterization of differential gene expression in oral squamous cell carcinoma: a meta-analysis of publicly available microarray data sets. Tumour Biol 2016; 37:10.1007/s13277-016-5439-6. [PMID: 27704359 DOI: 10.1007/s13277-016-5439-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/23/2016] [Indexed: 01/04/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a highly prevalent cancer worldwide, and OSCC often goes undiagnosed until advanced disease is present, which contributes to a low survival rate for OSCC patients. The identification of biomarkers for the early detection OSCC and novel therapeutic targets for OSCC treatment is an important research objective. We performed bioinformatics analyses of the gene expression profile of OSCC using microarray data to identify genes that contribute to the development of OSCC. We also predicted the transcription factors involved in the regulation of differential gene expression in OSCC. Our results showed that PI3K, EGFR, STAT1, and CPBP are important contributors to the changes in cellular physiology that occur during the development of OSCC. Therefore, these genes represent potential diagnostic biomarkers and therapeutic targets for OSCC.
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Affiliation(s)
- Yang Sun
- Department of Stomatology, Zhongshan Hospital, Fudan University, 111 Yixueyuan Road, Shanghai, 200032, China
| | - Zhijian Sang
- Department of Stomatology, Zhongshan Hospital, Fudan University, 111 Yixueyuan Road, Shanghai, 200032, China
| | - Qian Jiang
- Department of Stomatology, Zhongshan Hospital, Fudan University, 111 Yixueyuan Road, Shanghai, 200032, China
| | - Xiaojun Ding
- Department of Stomatology, Zhongshan Hospital, Fudan University, 111 Yixueyuan Road, Shanghai, 200032, China.
| | - Youcheng Yu
- Department of Stomatology, Zhongshan Hospital, Fudan University, 111 Yixueyuan Road, Shanghai, 200032, China
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