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Zamora-Fuentes JM, Hernández-Lemus E, Espinal-Enríquez J. Methylation-related genes involved in renal carcinoma progression. Front Genet 2023; 14:1225158. [PMID: 37693315 PMCID: PMC10486271 DOI: 10.3389/fgene.2023.1225158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/25/2023] [Indexed: 09/12/2023] Open
Abstract
Renal carcinomas are a group of malignant tumors often originating in the cells lining the small tubes in the kidney responsible for filtering waste from the blood and urine production. Kidney tumors arise from the uncontrolled growth of cells in the kidneys and are responsible for a large share of global cancer-related morbidity and mortality. Understanding the molecular mechanisms driving renal carcinoma progression results crucial for the development of targeted therapies leading to an improvement of patient outcomes. Epigenetic mechanisms such as DNA methylation are known factors underlying the development of several cancer types. There is solid experimental evidence of relevant biological functions modulated by methylation-related genes, associated with the progression of different carcinomas. Those mechanisms can often be associated to different epigenetic marks, such as DNA methylation sites or chromatin conformation patterns. Currently, there is no definitive method to establish clear relations between genetic and epigenetic factors that influence the progression of cancer. Here, we developed a data-driven method to find methylation-related genes, so we could find relevant bonds between gene co-expression and methylation-wide-genome regulation patterns able to drive biological processes during the progression of clear cell renal carcinoma (ccRC). With this approach, we found out genes such as ITK oncogene that appear hypomethylated during all four stages of ccRC progression and are strongly involved in immune response functions. Also, we found out relevant tumor suppressor genes such as RAB25 hypermethylated, thus potentially avoiding repressed functions in the AKT signaling pathway during the evolution of ccRC. Our results have relevant implications to further understand some epigenetic-genetic-affected roles underlying the progression of renal cancer.
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Affiliation(s)
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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2
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Wu M, Lo TH, Li L, Sun J, Deng C, Chan KY, Li X, Yeh STY, Lee JTH, Lui PPY, Xu A, Wong CM. Amelioration of non-alcoholic fatty liver disease by targeting adhesion G protein-coupled receptor F1 ( Adgrf1). eLife 2023; 12:e85131. [PMID: 37580962 PMCID: PMC10427146 DOI: 10.7554/elife.85131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/28/2023] [Indexed: 08/16/2023] Open
Abstract
Background Recent research has shown that the adhesion G protein-coupled receptor F1 (Adgrf1; also known as GPR110; PGR19; KPG_012; hGPCR36) is an oncogene. The evidence is mainly based on high expression of Adgrf1 in numerous cancer types, and knockdown Adgrf1 can reduce the cell migration, invasion, and proliferation. Adgrf1 is, however, mostly expressed in the liver of healthy individuals. The function of Adgrf1 in liver has not been revealed. Interestingly, expression level of hepatic Adgrf1 is dramatically decreased in obese subjects. Here, the research examined whether Adgrf1 has a role in liver metabolism. Methods We used recombinant adeno-associated virus-mediated gene delivery system, and antisense oligonucleotide was used to manipulate the hepatic Adgrf1 expression level in diet-induced obese mice to investigate the role of Adgrf1 in hepatic steatosis. The clinical relevance was examined using transcriptome profiling and archived biopsy specimens of liver tissues from non-alcoholic fatty liver disease (NAFLD) patients with different degree of fatty liver. Results The expression of Adgrf1 in the liver was directly correlated to fat content in the livers of both obese mice and NAFLD patients. Stearoyl-coA desaturase 1 (Scd1), a crucial enzyme in hepatic de novo lipogenesis, was identified as a downstream target of Adgrf1 by RNA-sequencing analysis. Treatment with the liver-specific Scd1 inhibitor MK8245 and specific shRNAs against Scd1 in primary hepatocytes improved the hepatic steatosis of Adgrf1-overexpressing mice and lipid profile of hepatocytes, respectively. Conclusions These results indicate Adgrf1 regulates hepatic lipid metabolism through controlling the expression of Scd1. Downregulation of Adgrf1 expression can potentially serve as a protective mechanism to stop the overaccumulation of fat in the liver in obese subjects. Overall, the above findings not only reveal a new mechanism regulating the progression of NAFLD, but also proposed a novel therapeutic approach to combat NAFLD by targeting Adgrf1. Funding This work was supported by the National Natural Science Foundation of China (81870586), Area of Excellence (AoE/M-707/18), and General Research Fund (15101520) to CMW, and the National Natural Science Foundation of China (82270941, 81974117) to SJ.
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Affiliation(s)
- Mengyao Wu
- Department of Chemistry and Chemical Engineering, Guangzhou UniversityGuangzhouChina
| | - Tak-Ho Lo
- Department of Health Technology and Informatics, Hong Kong Polytechnic UniversityHong KongHong Kong
| | - Liping Li
- Zhujiang Hospital, Southern Medical UniversityChinaChina
| | - Jia Sun
- Zhujiang Hospital, Southern Medical UniversityChinaChina
| | - Chujun Deng
- Department of Health Technology and Informatics, Hong Kong Polytechnic UniversityHong KongHong Kong
| | - Ka-Ying Chan
- Department of Health Technology and Informatics, Hong Kong Polytechnic UniversityHong KongHong Kong
| | - Xiang Li
- Department of Health Technology and Informatics, Hong Kong Polytechnic UniversityHong KongHong Kong
| | | | - Jimmy Tsz Hang Lee
- Department of Medicine, University of Hong KongHong KongHong Kong
- State Key Laboratory of Pharmaceutical Biotechnology, University of Hong KongHong KongChina
| | - Pauline Po Yee Lui
- Department of Orthopaedics and Traumatology, Chinese University of Hong KongHong KongHong Kong
| | - Aimin Xu
- Department of Medicine, University of Hong KongHong KongHong Kong
- State Key Laboratory of Pharmaceutical Biotechnology, University of Hong KongHong KongChina
| | - Chi-Ming Wong
- Department of Health Technology and Informatics, Hong Kong Polytechnic UniversityHong KongHong Kong
- State Key Laboratory of Pharmaceutical Biotechnology, University of Hong KongHong KongChina
- Hong Kong Polytechnic University, Shenzhen Research InstituteHong KongChina
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3
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Chiari D, Pirali B, Perano V, Leone R, Mantovani A, Bottazzi B. The crossroad between autoimmune disorder, tissue remodeling and cancer of the thyroid: The long pentraxin 3 (PTX3). Front Endocrinol (Lausanne) 2023; 14:1146017. [PMID: 37025408 PMCID: PMC10070760 DOI: 10.3389/fendo.2023.1146017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/07/2023] [Indexed: 04/08/2023] Open
Abstract
Thyroid is at the crossroads of immune dysregulation, tissue remodeling and oncogenesis. Autoimmune disorders, nodular disease and cancer of the thyroid affect a large amount of general population, mainly women. We wondered if there could be a common factor behind three processes (immune dysregulation, tissue remodeling and oncogenesis) that frequently affect, sometimes coexisting, the thyroid gland. The long pentraxin 3 (PTX3) is an essential component of the humoral arm of the innate immune system acting as soluble pattern recognition molecule. The protein is found expressed in a variety of cell types during tissue injury and stress. In addition, PTX3 is produced by neutrophils during maturation in the bone-marrow and is stored in lactoferrin-granules. PTX3 is a regulator of the complement cascade and orchestrates tissue remodeling and repair. Preclinical data and studies in human tumors indicate that PTX3 can act both as an extrinsic oncosuppressor by modulating complement-dependent tumor-promoting inflammation, or as a tumor-promoter molecule, regulating cell invasion and proliferation and epithelial to mesenchymal transition, thus suggesting that this molecule may have different functions on carcinogenesis. The involvement of PTX3 in the regulation of immune responses, tissue remodeling and oncosuppressive processes led us to explore its potential role in the development of thyroid disorders. In this review, we aimed to highlight what is known, at the state of the art, regarding the connection between the long pentraxin 3 and the main thyroid diseases i.e., nodular thyroid disease, thyroid cancer and autoimmune thyroid disorders.
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Affiliation(s)
- Damiano Chiari
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
- General Surgery Department, Humanitas Mater Domini Clinical Institute, Castellanza, Italy
- *Correspondence: Barbara Pirali, ; Damiano Chiari,
| | - Barbara Pirali
- Endocrinology Clinic, Internal Medicine Department, Humanitas Mater Domini Clinical Institute, Castellanza, Italy
- *Correspondence: Barbara Pirali, ; Damiano Chiari,
| | - Vittoria Perano
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | | | - Alberto Mantovani
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
- IRCCS Humanitas Research Hospital, Rozzano, Italy
- Harvey Research Institute, Queen Mary University of London Charterhouse Square, London, United Kingdom
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Luo Y, Yang YC, Ma B, Xu WB, Liao T, Wang Y. Integrated analysis of novel macrophage related signature in anaplastic thyroid cancer. Endocrine 2022; 78:517-530. [PMID: 36070052 DOI: 10.1007/s12020-022-03179-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/22/2022] [Indexed: 11/26/2022]
Abstract
PURPOSE Patients with anaplastic thyroid cancer (ATC) have a very poor prognosis. Immunotherapy is a potential treatment, while the current outcome is limited which may be due to the complicated tumor microenvironment (TME). Tumor associated macrophages (TAMs) is the most abundant cell in the TME of ATC. We aimed to clarify the novel indicators based on TAM in ATC. METHODS Transcriptome files were downloaded from the Gene Expression Omnibus (GEO) dataset. Weighted gene co-expression network analysis, cox regression, support vector machine, and random forest were utilized to identify TAM-related prognostic genes. Consensus clustering and principal component analysis were performed for integrated analysis. Moreover, external validation (Fudan University Shanghai Cancer Center cohort) was conducted in 23 ATC samples via immunohistochemistry. RESULTS ATC patients with an abundance of TAMs had a poorer prognosis. Four TAM related genes (FZD6, RBBP8, PREX1, HSD3B7) were identified and a TAM-related prognostic index (TAMRPI) was constructed with high area under the curve (AUC). Next, high TAMRPI was related to the higher level of TAM infiltration and upregulation of several pathways, such as E2F targets, IL6-JAK-STAT3, and G2M checkpoint. Immune checkpoint TIM-3 and CSF1R were positively associated with TAMRPI, and dysfunction of T cells was increased in high TAMRPI subset. Moreover, in the external validation of protein level, strong expression of TAM related genes was related to poorer prognosis, which was further supported by time-dependent AUC analysis. CONCLUSION TAM is negatively correlated to the prognosis of ATC. FZD6, RBBP8, PREX1, and HSD3B7 are potential biomarkers of ATC.
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Affiliation(s)
- Yi Luo
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Head and Neck Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yi-Chen Yang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Head and Neck Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ben Ma
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Head and Neck Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wei-Bo Xu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Head and Neck Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Tian Liao
- Department of Head and Neck Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yu Wang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Department of Head and Neck Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China.
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Thind AS, Ashford B, Strbenac D, Mitchell J, Lee J, Mueller SA, Minaei E, Perry JR, Ch’ng S, Iyer NG, Clark JR, Gupta R, Ranson M. Whole genome analysis reveals the genomic complexity in metastatic cutaneous squamous cell carcinoma. Front Oncol 2022; 12:919118. [PMID: 35982973 PMCID: PMC9379253 DOI: 10.3389/fonc.2022.919118] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
Metastatic cutaneous squamous cell carcinoma (CSCC) is a highly morbid disease requiring radical surgery and adjuvant therapy, which is associated with a poor prognosis. Yet, compared to other advanced malignancies, relatively little is known of the genomic landscape of metastatic CSCC. We have previously reported the mutational signatures and mutational patterns of CCCTC-binding factor (CTCF) regions in metastatic CSCC. However, many other genomic components (indel signatures, non-coding drivers, and structural variants) of metastatic CSCC have not been reported. To this end, we performed whole genome sequencing on lymph node metastases and blood DNA from 25 CSCC patients with regional metastases of the head and neck. We designed a multifaceted computational analysis at the whole genome level to provide a more comprehensive perspective of the genomic landscape of metastatic CSCC. In the non-coding genome, 3′ untranslated region (3′UTR) regions of EVC (48% of specimens), PPP1R1A (48% of specimens), and ABCA4 (20% of specimens) along with the tumor-suppressing long non-coding RNA (lncRNA) LINC01003 (64% of specimens) were significantly functionally altered (Q-value < 0.05) and represent potential non-coding biomarkers of CSCC. Recurrent copy number loss in the tumor suppressor gene PTPRD was observed. Gene amplification was much less frequent, and few genes were recurrently amplified. Single nucleotide variants driver analyses from three tools confirmed TP53 and CDKN2A as recurrently mutated genes but also identified C9 as a potential novel driver in this disease. Furthermore, indel signature analysis highlighted the dominance of ID signature 13 (ID13) followed by ID8 and ID9. ID9 has previously been shown to have no association with skin melanoma, unlike ID13 and ID8, suggesting a novel pattern of indel variation in metastatic CSCC. The enrichment analysis of various genetically altered candidates shows enrichment of “TGF-beta regulation of extracellular matrix” and “cell cycle G1 to S check points.” These enriched terms are associated with genetic instability, cell proliferation, and migration as mechanisms of genomic drivers of metastatic CSCC.
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Affiliation(s)
- Amarinder Singh Thind
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Bruce Ashford
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- Illawarra Shoalhaven Local Health District, Wollongong, NSW, Australia
- *Correspondence: Bruce Ashford,
| | - Dario Strbenac
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Jenny Mitchell
- Illawarra Shoalhaven Local Health District, Wollongong, NSW, Australia
| | - Jenny Lee
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Department of Clinical Medicine, Macquarie University, Sydney, NSW, Australia
| | - Simon A. Mueller
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Department of Otorhinolaryngology, Head and Neck Surgery, Zurich University Hospital and University of Zurich, Zurich, Switzerland
| | - Elahe Minaei
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Jay R. Perry
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Sydney Ch’ng
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
| | - N. Gopalakrishna Iyer
- Department of Head and Neck Surgery, National Cancer Center, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Jonathan R. Clark
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Royal Prince Alfred Institute of Academic Surgery, Sydney Local Health District, Sydney, NSW, Australia
| | - Ruta Gupta
- Anatomical Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Marie Ranson
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
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Zheng H, Liu H, Li H, Dou W, Wang J, Zhang J, Liu T, Wu Y, Liu Y, Wang X. Characterization of stem cell landscape and identification of stemness-relevant prognostic gene signature to aid immunotherapy in colorectal cancer. Stem Cell Res Ther 2022; 13:244. [PMID: 35681225 PMCID: PMC9185878 DOI: 10.1186/s13287-022-02913-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/22/2022] [Indexed: 02/08/2023] Open
Abstract
Background It is generally accepted that colorectal cancer (CRC) originates from cancer stem cells (CSCs), which are responsible for CRC progression, metastasis and therapy resistance. The high heterogeneity of CSCs has precluded clinical application of CSC-targeting therapy. Here, we aimed to characterize the stemness landscapes and screen for certain patients more responsive to immunotherapy. Methods Twenty-six stem cell gene sets were acquired from StemChecker database. Consensus clustering algorithm was applied for stemness subtypes identification on 1,467 CRC samples from TCGA and GEO databases. The differences in prognosis, tumor microenvironment (TME) components, therapy responses were evaluated among subtypes. Then, the stemness-risk model was constructed by weighted gene correlation network analysis (WGCNA), Cox regression and random survival forest analyses, and the most important marker was experimentally verified. Results Based on single-sample gene set enrichment analysis (ssGSEA) enrichments scores, CRC patients were classified into three subtypes (C1, C2 and C3). C3 subtype exhibited the worst prognosis, highest macrophages M0 and M2 infiltrations, immune and stromal scores, and minimum sensitivity to immunotherapies, but was more sensitive to drugs like Bosutinib, Docetaxel, Elesclomol, Gefitinib, Lenalidomide, Methotrexate and Sunitinib. The turquoise module was identified by WGCNA that it was most positively correlated with C3 but most negatively with C2, and five hub genes in turquoise module were identified for stemness model construction. CRC patients with higher stemness scores exhibited worse prognosis, more immunosuppressive components in TME and lower immunotherapeutic responses. Additionally, the model’s immunotherapeutic prediction efficacy was further confirmed from two immunotherapy cohorts (anti-PD-L1 in IMvigor210 cohort and anti-PD-1 in GSE78220 cohort). Mechanistically, Gene Set Enrichment Analysis (GSEA) results revealed high stemness score group was enriched in interferon gamma response, interferon alpha response, P53 pathway, coagulation, apoptosis, KRAS signaling upregulation, complement, epithelial–mesenchymal transition (EMT) and IL6-mediated JAK-STAT signaling gene sets. Conclusions Our study characterized three stemness-related subtypes with distinct prognosis and TME patterns in CRC patients, and a 5-gene stemness-risk model was constructed by comprehensive bioinformatic analyses. We suggest our stemness model has prospective clinical implications for prognosis evaluation and might facilitate physicians selecting prospective responders for preferential use of current immune checkpoint inhibitors. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02913-0.
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Affiliation(s)
- Hang Zheng
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Heshu Liu
- Department of Oncology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Huayu Li
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Weidong Dou
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Jingui Wang
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Junling Zhang
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Tao Liu
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Yingchao Wu
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Yucun Liu
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Xin Wang
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China.
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Liu L, Shi Y, Lai Q, Huang Y, Jiang X, Liu Q, Huang Y, Xia Y, Xu D, Jiang Z, Tu W. Construction of a Signature Model to Predict the Radioactive Iodine Response of Papillary Thyroid Cancer. Front Endocrinol (Lausanne) 2022; 13:865909. [PMID: 35634509 PMCID: PMC9132198 DOI: 10.3389/fendo.2022.865909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/28/2022] [Indexed: 12/04/2022] Open
Abstract
Papillary thyroid cancer (PTC) accounts for about 90% of thyroid cancer. There are approximately 20%-30% of PTC patients showing disease persistence/recurrence and resistance to radioactive iodine (RAI) treatment. For these PTC patients with RAI refractoriness, the prognosis is poor. In this study, we aimed to establish a comprehensive prognostic model covering multiple signatures to increase the predictive accuracy for progression-free survival (PFS) of PTC patients with RAI treatment. The expression profiles of mRNAs and miRNAs as well as the clinical information of PTC patients were extracted from TCGA and GEO databases. A series of bioinformatics methods were successfully applied to filtrate a two-RNA model (IPCEF1 and hsa-mir-486-5p) associated with the prognosis of RAI-therapy. Finally, the RNA-based risk score was calculated based on the Cox coefficient of the individual RNA, which achieved good performances by the time-dependent receiver operating characteristic (tROC) curve and PFS analyses. Furthermore, the predictive power of the nomogram, integrated with the risk score and clinical parameters (age at diagnosis and tumor stage), was assessed by tROC curves. Collectively, our study demonstrated high precision in predicting the RAI response of PTC patients.
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Affiliation(s)
- Lina Liu
- Department of Nuclear Medicine, the Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Yuhong Shi
- Department of Nuclear Medicine, the Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Qian Lai
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Yuan Huang
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Xue Jiang
- Department of Nuclear Medicine, the Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Qian Liu
- Department of Nuclear Medicine, the Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Ying Huang
- Department of Nuclear Medicine, the Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Yuxiao Xia
- Department of Nuclear Medicine, the Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Dongkun Xu
- Department of Nuclear Medicine, the Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Zhiqiang Jiang
- Department of General Surgery, the Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Wenling Tu
- Department of Nuclear Medicine, the Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
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Baldini E, Presutti D, Favoriti P, Santini S, Papoff G, Tuccilli C, Carletti R, Di Gioia C, Lori E, Ferent IC, Gagliardi F, Catania A, Pironi D, Tripodi D, D’Andrea V, Sorrenti S, Ruberti G, Ulisse S. In Vitro and In Vivo Effects of the Urokinase Plasminogen Activator Inhibitor WX-340 on Anaplastic Thyroid Cancer Cell Lines. Int J Mol Sci 2022; 23:ijms23073724. [PMID: 35409084 PMCID: PMC8999125 DOI: 10.3390/ijms23073724] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 12/19/2022] Open
Abstract
Increased expression of the urokinase-type plasminogen activator (uPA) system is associated with tumor invasion, neo-angiogenesis, and metastatic spread, and has been shown to positively correlate with a poor prognosis in several cancer types, including thyroid carcinomas. In recent years, several uPA inhibitors were found to have anticancer effects in preclinical studies and in some phase II clinical trials, which prompted us to evaluate uPA as a potential therapeutic target for the treatment of patients affected by the most aggressive form of thyroid cancer, the anaplastic thyroid carcinoma (ATC). In this study, we evaluated the in vitro and in vivo effects of WX-340, a highly specific and selective uPA inhibitor, on two ATC-derived cell lines, CAL-62 and BHT-101. The results obtained indicated that WX-340 was able to reduce cell adhesion and invasiveness in a dose-dependent manner in both cell lines. In addition, WX-340 increased uPA receptor (uPAR) protein levels without affecting its plasma membrane concentration. However, this compound was unable to significantly reduce ATC growth in a xenograft model, indicating that uPA inhibition alone may not have the expected therapeutic effects.
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Affiliation(s)
- Enke Baldini
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (E.B.); (P.F.); (C.T.); (E.L.); (I.C.F.); (F.G.); (A.C.); (D.P.); (D.T.); (V.D.); (S.S.)
| | - Dario Presutti
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Monterotondo, 00015 Rome, Italy; (D.P.); (S.S.); (G.P.); (G.R.)
| | - Pasqualino Favoriti
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (E.B.); (P.F.); (C.T.); (E.L.); (I.C.F.); (F.G.); (A.C.); (D.P.); (D.T.); (V.D.); (S.S.)
| | - Simonetta Santini
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Monterotondo, 00015 Rome, Italy; (D.P.); (S.S.); (G.P.); (G.R.)
| | - Giuliana Papoff
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Monterotondo, 00015 Rome, Italy; (D.P.); (S.S.); (G.P.); (G.R.)
| | - Chiara Tuccilli
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (E.B.); (P.F.); (C.T.); (E.L.); (I.C.F.); (F.G.); (A.C.); (D.P.); (D.T.); (V.D.); (S.S.)
| | - Raffaella Carletti
- Department of Radiological, Oncological and Pathological Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (R.C.); (C.D.G.)
| | - Cira Di Gioia
- Department of Radiological, Oncological and Pathological Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (R.C.); (C.D.G.)
| | - Eleonora Lori
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (E.B.); (P.F.); (C.T.); (E.L.); (I.C.F.); (F.G.); (A.C.); (D.P.); (D.T.); (V.D.); (S.S.)
| | - Iulia Catalina Ferent
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (E.B.); (P.F.); (C.T.); (E.L.); (I.C.F.); (F.G.); (A.C.); (D.P.); (D.T.); (V.D.); (S.S.)
| | - Federica Gagliardi
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (E.B.); (P.F.); (C.T.); (E.L.); (I.C.F.); (F.G.); (A.C.); (D.P.); (D.T.); (V.D.); (S.S.)
| | - Antonio Catania
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (E.B.); (P.F.); (C.T.); (E.L.); (I.C.F.); (F.G.); (A.C.); (D.P.); (D.T.); (V.D.); (S.S.)
| | - Daniele Pironi
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (E.B.); (P.F.); (C.T.); (E.L.); (I.C.F.); (F.G.); (A.C.); (D.P.); (D.T.); (V.D.); (S.S.)
| | - Domenico Tripodi
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (E.B.); (P.F.); (C.T.); (E.L.); (I.C.F.); (F.G.); (A.C.); (D.P.); (D.T.); (V.D.); (S.S.)
| | - Vito D’Andrea
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (E.B.); (P.F.); (C.T.); (E.L.); (I.C.F.); (F.G.); (A.C.); (D.P.); (D.T.); (V.D.); (S.S.)
| | - Salvatore Sorrenti
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (E.B.); (P.F.); (C.T.); (E.L.); (I.C.F.); (F.G.); (A.C.); (D.P.); (D.T.); (V.D.); (S.S.)
| | - Giovina Ruberti
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Monterotondo, 00015 Rome, Italy; (D.P.); (S.S.); (G.P.); (G.R.)
| | - Salvatore Ulisse
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy; (E.B.); (P.F.); (C.T.); (E.L.); (I.C.F.); (F.G.); (A.C.); (D.P.); (D.T.); (V.D.); (S.S.)
- Correspondence:
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9
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Yang F, Lian M, Ma H, Feng L, Shen X, Chen J, Fang J. Identification of key genes associated with papillary thyroid microcarcinoma characteristics by integrating transcriptome sequencing and weighted gene co-expression network analysis. Gene 2022; 811:146086. [PMID: 34856364 DOI: 10.1016/j.gene.2021.146086] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/01/2021] [Accepted: 11/23/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Papillary thyroid microcarcinoma (PTMC) is the most prevalent histological type of thyroid carcinoma. Despite the overall favorable prognosis of PTMC, some cases exhibit aggressive phenotypes. The identification of robust biomarkers may improve early PTMC diagnosis. In this study, we integrated high-throughput transcriptome sequencing, bioinformatic analyses and experimental validation to identify key genes associated with the malignant characteristics of PTMC. METHODS Total RNA was extracted from 24 PTMC samples and 7 non-malignant thyroid tissue samples, followed by RNA sequencing. The differentially expressed genes (DEGs) were identified and used to construct co-expression networks by weighted gene co-expression network analysis (WGCNA). Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed, and protein-protein interaction networks were constructed. Key modules and hub genes showing a strong correlation with the malignant characteristics of PTMC were identified and validated. RESULTS The green-yellow and turquoise modules generated by WGCNA were strongly associated with the malignant characteristics of PTMC. Functional enrichment analysis revealed that genes in the green-yellow module participated in cell motility and metabolism, whereas those in the turquoise module participated in several oncogenic biological processes. Nine real hub genes (FHL1, NDRG2, NEXN, SYNM, COL1A1, FN1, LAMC2, POSTN, and TGFBI) were identified and validated at the transcriptional and translational levels. Our preliminary results indicated their diagnostic potentials in PTMC. CONCLUSIONS In this study, we identified key co-expression modules and nine malignancy-related genes with potential diagnostic value in PTMC.
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Affiliation(s)
- Fan Yang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, China, 100029.
| | - Meng Lian
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Hongzhi Ma
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Ling Feng
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Xixi Shen
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Jiaming Chen
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Jugao Fang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730; Department of Thyroid Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730.
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10
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He L, Zhang T, Sun W, Qin Y, Wang Z, Dong W, Zhang H. The DPP-IV inhibitor saxagliptin promotes the migration and invasion of papillary thyroid carcinoma cells via the NRF2/HO1 pathway. Med Oncol 2020; 37:97. [PMID: 33001278 DOI: 10.1007/s12032-020-01419-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022]
Abstract
Dipeptidyl peptidase-IV (DPP-IV) inhibitors are used to control blood glucose levels in patients with type 2 diabetes. However, the influence of DPP-IV inhibitors on malignant tumors remains unknown. The present study aimed to investigate the effect of the DPP-IV inhibitor saxagliptin on thyroid carcinoma cells. Transwell assays and a nude mouse lung metastasis model were used to evaluate the invasion and metastasis of thyroid carcinoma cells. Western blotting was used to determine the protein levels of migration and invasion-related molecules. We tested the expression and distribution of nuclear factor, erythroid 2 like 2 (NRF2) in thyroid carcinoma cells with and without saxagliptin. Furthermore, we silenced NRF2 and observed saxagliptin's effect on migration and invasion. Quantitative real-time reverse transcription PCR (qRT-PCR) and western blotting were then used to measure the expression of NFR2's downstream molecules (heme oxygenase 1 (HO1), matrix metalloproteinase 2 (MMP2), and vascular endothelial growth factor (VEGF)). A luciferase reporter assay was used to validate whether NRF2 could regulate the transcriptional activity of the HO1 promoter. Saxagliptin enhanced the migratory and invasive ability of thyroid carcinoma cells. MMP2 and VEGF levels were also elevated by saxagliptin treatment. We found that saxagliptin treatment increases the nuclear and cytoplasmic accumulation NRF2. Silencing NRF2 abolished the effect of saxagliptin on migration and invasion. Accordingly, NRF2 silencing downregulated HO1, MMP2, and VEGF levels. The luciferase assay showed that NRF2 activated transcription from the HO1 promoter. Saxagliptin could promote this transcriptional activity by upregulating NRF2. Saxagliptin enhanced the migratory and invasive ability of human thyroid carcinoma cells, as well as the expression of MMP2 and VEGF, by activating the NRF2/HO1 pathway.
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Affiliation(s)
- Liang He
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ting Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wei Sun
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuan Qin
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhihong Wang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wenwu Dong
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Hao Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China.
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11
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Netti GS, Lucarelli G, Spadaccino F, Castellano G, Gigante M, Divella C, Rocchetti MT, Rascio F, Mancini V, Stallone G, Carrieri G, Gesualdo L, Battaglia M, Ranieri E. PTX3 modulates the immunoflogosis in tumor microenvironment and is a prognostic factor for patients with clear cell renal cell carcinoma. Aging (Albany NY) 2020; 12:7585-7602. [PMID: 32345771 PMCID: PMC7202504 DOI: 10.18632/aging.103169] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/31/2020] [Indexed: 01/05/2023]
Abstract
Pentraxin-3 (PTX3) belongs to the pentraxine family, innate immune regulators involved in angiogenesis, proliferation and immune escape in cancer. Here, we evaluated PTX3 tissue expression and serum levels as biomarkers of clear cell renal cell carcinoma (ccRCC) and analyzed the possible role of complement system activation on tumor site. A 10-year retrospective cohort study including patients undergoing nephrectomy for ccRCC was also performed. PTX3 expression was elevated in both neoplastic renal cell lines and tissues, while it was absent in both normal renal proximal tubular cells (HK2) and normal renal tissues. Analysis of complement system activation on tumor tissues showed the co-expression of PTX3 with C1q, C3aR, C5R1 and CD59, but not with C5b-9 terminal complex. RCC patients showed higher serum PTX3 levels as compared to non-neoplastic patients (p<0.0001). Higher PTX3 serum levels were observed in patients with higher Fuhrman grade (p<0.01), lymph node (p<0.0001), and visceral metastases (p<0.001). Patients with higher PTX3 levels also showed significantly lower survival rates (p=0.002). Our results suggest that expression of PTX3 can affect the immunoflogosis in the ccRCC microenvironment, by activating the classical pathway of CS (C1q) and releasing pro-angiogenic factors (C3a, C5a). The up-regulation of CD59 also inhibits the complement-mediated cellular lysis.
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Affiliation(s)
- Giuseppe Stefano Netti
- Clinical Pathology Unit and Center of Molecular Medicine, Department of Medical and Surgical Sciences, University of Foggia, Viale Luigi Pinto 71122, Foggia, Italy
| | - Giuseppe Lucarelli
- Urology and Renal Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, Bari 70124, Italy
| | - Federica Spadaccino
- Clinical Pathology Unit and Center of Molecular Medicine, Department of Medical and Surgical Sciences, University of Foggia, Viale Luigi Pinto 71122, Foggia, Italy
| | - Giuseppe Castellano
- Nephrology Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, Bari 70124, Italy
| | - Margherita Gigante
- Clinical Pathology Unit and Center of Molecular Medicine, Department of Medical and Surgical Sciences, University of Foggia, Viale Luigi Pinto 71122, Foggia, Italy
| | - Chiara Divella
- Nephrology Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, Bari 70124, Italy
| | - Maria Teresa Rocchetti
- Clinical Pathology Unit and Center of Molecular Medicine, Department of Medical and Surgical Sciences, University of Foggia, Viale Luigi Pinto 71122, Foggia, Italy
| | - Federica Rascio
- Nephrology Dialysis and Transplantation Unit, Department of Medical and Surgical Sciences, University of Foggia, Viale Luigi Pinto 71122, Foggia, Italy
| | - Vito Mancini
- Urology and Renal Transplantation Unit, Department of Medical and Surgical Sciences, University of Foggia, Viale Luigi Pinto 71122, Foggia, Italy
| | - Giovanni Stallone
- Nephrology Dialysis and Transplantation Unit, Department of Medical and Surgical Sciences, University of Foggia, Viale Luigi Pinto 71122, Foggia, Italy
| | - Giuseppe Carrieri
- Urology and Renal Transplantation Unit, Department of Medical and Surgical Sciences, University of Foggia, Viale Luigi Pinto 71122, Foggia, Italy
| | - Loreto Gesualdo
- Nephrology Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, Bari 70124, Italy
| | - Michele Battaglia
- Urology and Renal Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, Bari 70124, Italy
| | - Elena Ranieri
- Clinical Pathology Unit and Center of Molecular Medicine, Department of Medical and Surgical Sciences, University of Foggia, Viale Luigi Pinto 71122, Foggia, Italy
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12
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Gad AA, Balenga N. The Emerging Role of Adhesion GPCRs in Cancer. ACS Pharmacol Transl Sci 2020; 3:29-42. [PMID: 32259086 DOI: 10.1021/acsptsci.9b00093] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Indexed: 02/08/2023]
Abstract
Aberrant expression, function, and mutation of G protein-coupled receptors (GPCRs) and their signaling partners, G proteins, have been well documented in many forms of cancer. These cell surface receptors and their endogenous ligands are implicated in all aspects of cancer including proliferation, angiogenesis, invasion, and metastasis. Adhesion GPCRs (aGPCRs) form the second largest family of GPCRs, most of which are orphan receptors with unknown physiological functions. This is mainly due to our limited insight into their structure, natural ligands, signaling pathways, and tissue expression profiles. Nevertheless, recent studies show that aGPCRs play important roles in cell adhesion to the extracellular matrix and cell-cell communication, processes that are dysregulated in cancer. Emerging evidence suggests that aGPCRs are implicated in migration, proliferation, and survival of tumor cells. We here review the role of aGPCRs in the five most common types of cancer (lung, breast, colorectal, prostate, and gastric) and emphasize the importance of further translational studies in this field.
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Affiliation(s)
- Abanoub A Gad
- Graduate Program in Life Sciences, University of Maryland, Baltimore, Maryland 20201, United States.,Division of General & Oncologic Surgery, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland 20201, United States
| | - Nariman Balenga
- Division of General & Oncologic Surgery, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland 20201, United States.,Molecular and Structural Biology program at University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland 20201, United States
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13
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Doni A, Stravalaci M, Inforzato A, Magrini E, Mantovani A, Garlanda C, Bottazzi B. The Long Pentraxin PTX3 as a Link Between Innate Immunity, Tissue Remodeling, and Cancer. Front Immunol 2019; 10:712. [PMID: 31019517 PMCID: PMC6459138 DOI: 10.3389/fimmu.2019.00712] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/15/2019] [Indexed: 12/20/2022] Open
Abstract
The innate immune system comprises a cellular and a humoral arm. Humoral pattern recognition molecules include complement components, collectins, ficolins, and pentraxins. These molecules are involved in innate immune responses by recognizing microbial moieties and damaged tissues, activating complement, exerting opsonic activity and facilitating phagocytosis, and regulating inflammation. The long pentraxin PTX3 is a prototypic humoral pattern recognition molecule that, in addition to providing defense against infectious agents, plays several functions in tissue repair and regulation of cancer-related inflammation. Characterization of the PTX3 molecular structure and biochemical properties, and insights into its interactome and multiple roles in tissue damage and remodeling support the view that microbial and matrix recognition are evolutionarily conserved functions of humoral innate immunity molecules.
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Affiliation(s)
- Andrea Doni
- Humanitas Clinical and Research Institute-IRCCS, Milan, Italy
| | - Matteo Stravalaci
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Antonio Inforzato
- Humanitas Clinical and Research Institute-IRCCS, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Elena Magrini
- Humanitas Clinical and Research Institute-IRCCS, Milan, Italy
| | - Alberto Mantovani
- Humanitas Clinical and Research Institute-IRCCS, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy.,The William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Cecilia Garlanda
- Humanitas Clinical and Research Institute-IRCCS, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
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14
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Li S, Yin Y, Yu H. Genetic expression profile-based screening of genes and pathways associated with papillary thyroid carcinoma. Oncol Lett 2018; 16:5723-5732. [PMID: 30344727 PMCID: PMC6176351 DOI: 10.3892/ol.2018.9342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 07/27/2018] [Indexed: 12/11/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common subtype of thyroid cancer; however, the specific genes and signaling pathways involved in this cancer remain largely unclear. The present study analyzed three profile datasets, GSE6004, GSE29265 and GSE60542, which were comprised of 47 PTC and 41 normal thyroid tissue samples, to identify key genes and pathways associated with PTC. Initially, differentially-expressed genes (DEGs) between PTC and normal thyroid tissue were screened using R 3.4.0 (2017-04-21, R Foundation, Vienna, Austria, http://www.R-project.org/). These DEGs were then clustered by gene ontology functional terms and representative signaling pathways. Additionally, specific key gene nodes were filtered out from a constructed protein-protein interaction (PPI) network. The results identified a total of 423 shared DEGs associated with PTC, including 211 upregulated and 212 downregulated genes. These 423 genes were primarily enriched in glycosaminoglycan binding, sulfur compound binding, heparin binding, enzyme activator activity, peptidase activator activity and hsa04512: Extracellular matrix (ECM)-receptor interaction. A total of 21 central node genes were identified as key genes in the PTC disease process including complement factor D (CFD), Collagen Type I α 1 Chain (COL1A1), Extracellular Matrix Protein 1 (ECM1) and Fibronectin 1 (FN1). These genes are involved in protease binding, G-protein coupled receptor binding, extracellular matrix structural constituent and peptidase regulator activity. To conclude, using bioinformatics analysis, the present study identified candidate DEGs and critical pathways in PTC that may improve the current understanding regarding the underlying mechanisms of PTC. These genes and pathways may be used as potential therapeutic targets of PTC in the future.
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Affiliation(s)
- Shubin Li
- Department of Internal Medicine, Southern Branch of Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 102600, P.R. China
| | - Yihang Yin
- School of Computer Science and Engineering, Beihang University, Beijing 100191, P.R. China
| | - Hong Yu
- Cell Biology Laboratory, Jilin Province Institute of Cancer Prevention and Treatment, Jilin Cancer Hospital, Changchun, Jilin 130012, P.R. China
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15
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Alcalá-Corona SA, de Anda-Jáuregui G, Espinal-Enríquez J, Hernández-Lemus E. Network Modularity in Breast Cancer Molecular Subtypes. Front Physiol 2017; 8:915. [PMID: 29204123 PMCID: PMC5699328 DOI: 10.3389/fphys.2017.00915] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/30/2017] [Indexed: 01/20/2023] Open
Abstract
Breast cancer is a heterogeneous and complex disease, a clear manifestation of this is its classification into different molecular subtypes. On the other hand, gene transcriptional networks may exhibit different modular structures that can be related to known biological processes. Thus, modular structures in transcriptional networks may be seen as manifestations of regulatory structures that tightly controls biological processes. In this work, we identify modular structures on gene transcriptional networks previously inferred from microarray data of molecular subtypes of breast cancer: luminal A, luminal B, basal, and HER2-enriched. We analyzed the modules (communities) found in each network to identify particular biological functions (described in the Gene Ontology database) associated to them. We further explored these modules and their associated functions to identify common and unique features that could allow a better level of description of breast cancer, particularly in the basal-like subtype, the most aggressive and poor prognosis manifestation. Our findings related to the immune system and a decrease in cell death-related processes in basal subtype could help to understand it and design strategies for its treatment.
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Affiliation(s)
- Sergio Antonio Alcalá-Corona
- Computational Genomics, National Institute of Genomic Medicine, México City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, México City, Mexico
| | - Guillermo de Anda-Jáuregui
- Computational Genomics, National Institute of Genomic Medicine, México City, Mexico.,School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, United States
| | - Jesús Espinal-Enríquez
- Computational Genomics, National Institute of Genomic Medicine, México City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, México City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics, National Institute of Genomic Medicine, México City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, México City, Mexico
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16
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Durand S, Trillet K, Uguen A, Saint-Pierre A, Le Jossic-Corcos C, Corcos L. A transcriptome-based protein network that identifies new therapeutic targets in colorectal cancer. BMC Genomics 2017; 18:758. [PMID: 28962550 PMCID: PMC5622428 DOI: 10.1186/s12864-017-4139-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 09/13/2017] [Indexed: 01/22/2023] Open
Abstract
Background Colon cancer occurrence is increasing worldwide, making it the third most frequent cancer. Although many therapeutic options are available and quite efficient at the early stages, survival is strongly decreased when the disease has spread to other organs. The identification of molecular markers of colon cancer is likely to help understanding its course and, eventually, to uncover novel genes to be targeted by drugs. In this study, we compared gene expression in a set of 95 human colon cancer samples to that in 19 normal colon mucosae, focusing on 401 genes from 5 selected pathways (Apoptosis, Cancer, Cholesterol metabolism and lipoprotein signaling, Drug metabolism, Wnt/beta-catenin). Deregulation of mRNA levels largely matched that of proteins, leading us to build in silico protein networks, starting from mRNA levels, to identify key proteins central to network activity. Results Among the analyzed genes, 10.5% (42) had no reported link with colon cancer, including the SFRP1, IGF1 and ADH1B (down), and MYC and IL8 (up), whose encoded proteins were most interacting with other proteins from the same or even distinct networks. Analyzing all pathways globally led us to uncover novel functional links between a priori unrelated or rather remotely connected pathways, such as the Drug metabolism and the Cancer pathways or, even more strikingly, between the Cholesterol metabolism and lipoprotein signaling and the Cancer pathways. In addition, we analyzed the responsiveness of some of the deregulated genes essential to network activities, to chemotherapeutic agents used alone or in presence of Lovastatin, a lipid-lowering drug. Some of these treatments could oppose the deregulations occurring in cancer samples, including those of the CHECK2, CYP51A1, HMGCS1, ITGA2, NME1 or VEGFA genes. Conclusions Our network-based approach allowed discovering genes not previously known to play regulatory roles in colon cancer. Our results also showed that selected drug treatments might revert the cancer-specific deregulation of genes playing prominent roles within the networks operating to maintain colon homeostasis. Among those genes, some could constitute novel testable targets to eliminate colon cancer cells, either directly or, potentially, through the use of lipid-lowering drugs such as statins, in association with selected anticancer drugs. Electronic supplementary material The online version of this article (10.1186/s12864-017-4139-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stéphanie Durand
- INSERM 1078 Unit, "Cancérologie appliquée et épissage alternatif" team, Brest Institute of Health, Agronomy and Material (IBSAM), Faculty of medicine, University of Western Brittany (UBO), 22 avenue Camille Desmoulins, F-29200, Brest, France
| | - Killian Trillet
- INSERM 1078 Unit, "Cancérologie appliquée et épissage alternatif" team, Brest Institute of Health, Agronomy and Material (IBSAM), Faculty of medicine, University of Western Brittany (UBO), 22 avenue Camille Desmoulins, F-29200, Brest, France
| | - Arnaud Uguen
- INSERM 1078 Unit, "Cancérologie appliquée et épissage alternatif" team, Brest Institute of Health, Agronomy and Material (IBSAM), Faculty of medicine, University of Western Brittany (UBO), 22 avenue Camille Desmoulins, F-29200, Brest, France.,Department of Pathology, Brest University Hospital, F-29200, Brest, France
| | - Aude Saint-Pierre
- INSERM 1078 Unit, "Epidemiology, genetic Epidemiology and population genetics" team, 46 rue Félix Le Dantec, F-29200, Brest, France
| | - Catherine Le Jossic-Corcos
- INSERM 1078 Unit, "Cancérologie appliquée et épissage alternatif" team, Brest Institute of Health, Agronomy and Material (IBSAM), Faculty of medicine, University of Western Brittany (UBO), 22 avenue Camille Desmoulins, F-29200, Brest, France
| | - Laurent Corcos
- INSERM 1078 Unit, "Cancérologie appliquée et épissage alternatif" team, Brest Institute of Health, Agronomy and Material (IBSAM), Faculty of medicine, University of Western Brittany (UBO), 22 avenue Camille Desmoulins, F-29200, Brest, France. .,INSERM 1078 Unit, "Cancérologie appliquée et épissage alternatif" laboratory, University of Western Brittany (UBO), Faculty of medicine, 22, rue Camille Desmoulins, 29200, Brest, France.
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17
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Lu JY, Cheng WC, Chen KY, Lin CC, Chang CC, Kuo KT, Chen PL. Using Ion Torrent sequencing to study genetic mutation profiles of fatal thyroid cancers. J Formos Med Assoc 2017; 117:488-496. [PMID: 28757314 DOI: 10.1016/j.jfma.2017.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 05/05/2017] [Accepted: 05/10/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND/PURPOSE Surgery followed by radioiodine is a mainstay of treatment for thyroid cancers of follicular origins. However, about 5% of the thyroid cancers are non-operable and/or radioiodine-refractory diseases, which are either locally advanced or metastatic and result in a survival of less than 5 years. How to treat this population of thyroid cancer patients becomes a critical issue requiring further understanding of the tumor's genetic information. METHODS We used formalin-fixed paraffin-embedded specimens of 22 fatal thyroid cancers and their corresponding non-tumor parts, if available, to yield genomic DNA, and applied the Ion Torrent™ Personal Genome Machine (IT-PGM) System (Life Technologies), a next generation sequencing technology, to interrogate 740 mutational hotspots in 46 oncogenes. We further validated the results by conventional direct sequencing. RESULTS We confirmed 21 mutations of 11 oncogenes in the 22 fatal thyroid cancer samples. Among them, the MET p.N375S and MLH1 p.V384D mutations, each was detected in two cases, and has rarely been found to be involved in thyroid cancer pathogenesis before. We also identified homozygous PDGFRA p.V824V mutation in eight out of the 22 cases, while the non-tumor counterparts carried heterozygous PDGFRA p.V824V mutation. We noted that the Ion Torrent technique unfortunately showed high false positive rates for detecting EGFR mutations in thyroid cancers. CONCLUSION The extensive genetic studies provide new insights to future targeted therapy in these patients. IT-PGM proved to be valuable for comprehensively searching genetic mutations in potentially fatal thyroid cancers.
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Affiliation(s)
- Jin-Ying Lu
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| | - Wern-Cherng Cheng
- Department of Laboratory Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Kuen-Yuan Chen
- Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Chia-Chi Lin
- Department of Oncology, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Ching-Chung Chang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, China Medical University Hospital, Taichung 404, Taiwan; Department of Internal Medicine, China Medical University, Taichung 404, Taiwan
| | - Kuan-Ting Kuo
- Department of Pathology, College of Medicine, National Taiwan University, Taipei 100, Taiwan.
| | - Pei-Lung Chen
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan; Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei 100, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University, Taipei 100, Taiwan.
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18
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Espinal-Enríquez J, Fresno C, Anda-Jáuregui G, Hernández-Lemus E. RNA-Seq based genome-wide analysis reveals loss of inter-chromosomal regulation in breast cancer. Sci Rep 2017; 7:1760. [PMID: 28496157 PMCID: PMC5431987 DOI: 10.1038/s41598-017-01314-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 03/27/2017] [Indexed: 12/21/2022] Open
Abstract
Breast cancer is a complex heterogeneous disease. Common hallmark features of cancer can be found. Their origin may be traced back to their intricate relationships governing regulatory programs during the development of this disease. To unveil distinctive features of the transcriptional regulation program in breast cancer, a pipeline for RNA-seq analysis in 780 breast cancer and 101 healthy breast samples, at gene expression and network level, was implemented. Inter-chromosomal relationships between genes resulted strikingly scarce in a cancer network, in comparison to its healthy counterpart. We suggest that inter-chromosomal regulation loss may be a novel feature in breast cancer. Additional evidence was obtained by independent validation in microarray and Hi-C data as well as supplementary computational analyses. Functional analysis showed upregulation in processes related to cell cycle and division; while migration, adhesion and cell-to-cell communication, were downregulated. Both the BRCA1 DNA repairing signalling and the Estrogen-mediated G1/S phase entry pathways were found upregulated. In addition, a synergistic underexpression of the γ-protocadherin complex, located at Chr5q31 is also shown. This region has previously been reported to be hypermethylated in breast cancer. These findings altogether provide further evidence for the central role of transcriptional regulatory programs in shaping malignant phenotypes.
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Affiliation(s)
- Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine (INMEGEN), 14610, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (UNAM), 04510, Mexico City, Mexico
| | - Cristóbal Fresno
- Computational Genomics Division, National Institute of Genomic Medicine (INMEGEN), 14610, Mexico City, Mexico
- UA AREA CS. AGR. ING. BIO Y S, CONICET - Universidad Católica de Córdoba, Córdoba, Argentina
| | - Guillermo Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine (INMEGEN), 14610, Mexico City, Mexico
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Rd Stop 9061, Grand Forks, ND, 58203, USA
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine (INMEGEN), 14610, Mexico City, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (UNAM), 04510, Mexico City, Mexico.
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19
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Weinberger P, Ponny SR, Xu H, Bai S, Smallridge R, Copland J, Sharma A. Cell Cycle M-Phase Genes Are Highly Upregulated in Anaplastic Thyroid Carcinoma. Thyroid 2017; 27:236-252. [PMID: 27796151 PMCID: PMC5314727 DOI: 10.1089/thy.2016.0285] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Anaplastic thyroid carcinoma (ATC) accounts for only 3% of thyroid cancers, yet strikingly, it accounts for almost 40% of thyroid cancer deaths. Currently, no effective therapies exist. In an effort to identify ATC-specific therapeutic targets, we analyzed global gene expression data from multiple studies to identify ATC-specific dysregulated genes. METHODS The National Center for Biotechnology Information Gene Expression Omnibus database was searched for high-throughput gene expression microarray studies from human ATC tissue along with normal thyroid and/or papillary thyroid cancer (PTC) tissue. Gene expression levels in ATC were compared with normal thyroid or PTC using seven separate comparisons, and an ATC-specific gene set common in all seven comparisons was identified. We investigated these genes for their biological functions and pathways. RESULTS There were three studies meeting inclusion criteria, (including 32 ATC patients, 69 PTC, and 75 normal). There were 259 upregulated genes and 286 downregulated genes in ATC with at least two-fold change in all seven comparisons. Using a five-fold filter, 36 genes were upregulated in ATC, while 40 genes were downregulated. Of the 10 top globally upregulated genes in ATC, 4/10 (MMP1, ANLN, CEP55, and TFPI2) are known to play a role in ATC progression; however, 6/10 genes (TMEM158, CXCL5, E2F7, DLGAP5, MME, and ASPM) had not been specifically implicated in ATC. Similarly, 3/10 (SFTA3, LMO3, and C2orf40) of the most globally downregulated genes were novel in this context, while 7/10 genes (SLC26A7, TG, TSHR, DUOX2, CDH1, PDE8B, and FOXE1) have been previously identified in ATC. We experimentally validated a significant correlation for seven transcription factors (KLF16, SP3, ETV6, FOXC1, SP1, EGFR1, and MAFK) with the ATC-specific genes using microarray analysis of ATC cell lines. Ontology clustering of globally altered genes revealed that "mitotic cell cycle" is highly enriched in the globally upregulated gene set (44% of top upregulated genes, p-value <10-30). CONCLUSIONS By focusing on globally altered genes, we have identified a set of consistently altered biological processes and pathways in ATC. Our data are consistent with an important role for M-phase cell cycle genes in ATC, and may provide direction for future studies to identify novel therapeutic targets for this disease.
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Affiliation(s)
- Paul Weinberger
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia
- Department of Otolaryngology, Medical College of Georgia at Augusta University, Augusta, Georgia
- Augusta University Cancer Center, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Sithara Raju Ponny
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Hongyan Xu
- Department of Biostatistics and Epidemiology, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Shan Bai
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia
| | | | - John Copland
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia
- Department of Biostatistics and Epidemiology, Medical College of Georgia at Augusta University, Augusta, Georgia
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20
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Pietrowska M, Diehl HC, Mrukwa G, Kalinowska-Herok M, Gawin M, Chekan M, Elm J, Drazek G, Krawczyk A, Lange D, Meyer HE, Polanska J, Henkel C, Widlak P. Molecular profiles of thyroid cancer subtypes: Classification based on features of tissue revealed by mass spectrometry imaging. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:837-845. [PMID: 27760391 DOI: 10.1016/j.bbapap.2016.10.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/07/2016] [Accepted: 10/11/2016] [Indexed: 02/08/2023]
Abstract
Determination of the specific type of thyroid cancer is crucial for the prognosis and selection of treatment of this malignancy. However, in some cases appropriate classification is not possible based on histopathological features only, and it might be supported by molecular biomarkers. Here we aimed to characterize molecular profiles of different thyroid malignancies using mass spectrometry imaging (MSI) which enables the direct annotation of molecular features with morphological pictures of an analyzed tissue. Fifteen formalin-fixed paraffin-embedded tissue specimens corresponding to five major types of thyroid cancer were analyzed by MALDI-MSI after in-situ trypsin digestion, and the possibility of classification based on the results of unsupervised segmentation of MALDI images was tested. Novel method of semi-supervised detection of the cancer region of interest (ROI) was implemented. We found strong separation of medullary cancer from malignancies derived from thyroid epithelium, and separation of anaplastic cancer from differentiated cancers. Reliable classification of medullary and anaplastic cancers using an approach based on automated detection of cancer ROI was validated with independent samples. Moreover, extraction of spectra from tumor areas allowed the detection of molecular components that differentiated follicular cancer and two variants of papillary cancer (classical and follicular). We concluded that MALDI-MSI approach is a promising strategy in the search for biomarkers supporting classification of thyroid malignant tumors. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Monika Pietrowska
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch, ul. Wybrzeze Armii Krajowej 15, 44101 Gliwice, Poland
| | - Hanna C Diehl
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Grzegorz Mrukwa
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, ul. Akademicka 16, 44100 Gliwice, Poland
| | - Magdalena Kalinowska-Herok
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch, ul. Wybrzeze Armii Krajowej 15, 44101 Gliwice, Poland
| | - Marta Gawin
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch, ul. Wybrzeze Armii Krajowej 15, 44101 Gliwice, Poland
| | - Mykola Chekan
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch, ul. Wybrzeze Armii Krajowej 15, 44101 Gliwice, Poland
| | - Julian Elm
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Grzegorz Drazek
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, ul. Akademicka 16, 44100 Gliwice, Poland
| | - Anna Krawczyk
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, ul. Akademicka 16, 44100 Gliwice, Poland
| | - Dariusz Lange
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch, ul. Wybrzeze Armii Krajowej 15, 44101 Gliwice, Poland
| | - Helmut E Meyer
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany; Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany
| | - Joanna Polanska
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, ul. Akademicka 16, 44100 Gliwice, Poland.
| | - Corinna Henkel
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany; Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany.
| | - Piotr Widlak
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch, ul. Wybrzeze Armii Krajowej 15, 44101 Gliwice, Poland.
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21
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The collectins CL-L1, CL-K1 and CL-P1, and their roles in complement and innate immunity. Immunobiology 2016; 221:1058-67. [DOI: 10.1016/j.imbio.2016.05.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 05/21/2016] [Accepted: 05/23/2016] [Indexed: 12/11/2022]
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22
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Sandhu V, Wedge DC, Bowitz Lothe IM, Labori KJ, Dentro SC, Buanes T, Skrede ML, Dalsgaard AM, Munthe E, Myklebost O, Lingjærde OC, Børresen-Dale AL, Ikdahl T, Van Loo P, Nord S, Kure EH. The Genomic Landscape of Pancreatic and Periampullary Adenocarcinoma. Cancer Res 2016; 76:5092-102. [PMID: 27488532 DOI: 10.1158/0008-5472.can-16-0658] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/21/2016] [Indexed: 02/05/2023]
Abstract
Despite advances in diagnostics, less than 5% of patients with periampullary tumors experience an overall survival of five years or more. Periampullary tumors are neoplasms that arise in the vicinity of the ampulla of Vater, an enlargement of liver and pancreas ducts where they join and enter the small intestine. In this study, we analyzed copy number aberrations using Affymetrix SNP 6.0 arrays in 60 periampullary adenocarcinomas from Oslo University Hospital to identify genome-wide copy number aberrations, putative driver genes, deregulated pathways, and potential prognostic markers. Results were validated in a separate cohort derived from The Cancer Genome Atlas Consortium (n = 127). In contrast to many other solid tumors, periampullary adenocarcinomas exhibited more frequent genomic deletions than gains. Genes in the frequently codeleted region 17p13 and 18q21/22 were associated with cell cycle, apoptosis, and p53 and Wnt signaling. By integrating genomics and transcriptomics data from the same patients, we identified CCNE1 and ERBB2 as candidate driver genes. Morphologic subtypes of periampullary adenocarcinomas (i.e., pancreatobiliary or intestinal) harbor many common genomic aberrations. However, gain of 13q and 3q, and deletions of 5q were found specific to the intestinal subtype. Our study also implicated the use of the PAM50 classifier in identifying a subgroup of patients with a high proliferation rate, which had impaired survival. Furthermore, gain of 18p11 (18p11.21-23, 18p11.31-32) and 19q13 (19q13.2, 19q13.31-32) and subsequent overexpression of the genes in these loci were associated with impaired survival. Our work identifies potential prognostic markers for periampullary tumors, the genetic characterization of which has lagged. Cancer Res; 76(17); 5092-102. ©2016 AACR.
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Affiliation(s)
- Vandana Sandhu
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway. Department for Environmental Health and Science, University College of Southeast Norway, Bø, Norway
| | - David C Wedge
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom. Department of Cancer Genomics, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Inger Marie Bowitz Lothe
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway. Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Knut Jørgen Labori
- Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Oslo, Norway
| | - Stefan C Dentro
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom. Department of Cancer Genomics, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Trond Buanes
- Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Oslo, Norway. Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Martina L Skrede
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Astrid M Dalsgaard
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Else Munthe
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ola Myklebost
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway. Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tone Ikdahl
- Department of Oncology, Oslo University Hospital, Oslo, Norway. Akershus University Hospital, Nordbyhagen, Norway
| | - Peter Van Loo
- The Francis Crick Institute, London, United Kingdom. Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Silje Nord
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Elin H Kure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway. Department for Environmental Health and Science, University College of Southeast Norway, Bø, Norway.
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23
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Hima S, Sreeja S. Modulatory role of 17β-estradiol in the tumor microenvironment of thyroid cancer. IUBMB Life 2015; 68:85-96. [DOI: 10.1002/iub.1462] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/24/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Sithul Hima
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology; Thycaud Thiruvananthapuram Kerala India
| | - Sreeharshan Sreeja
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology; Thycaud Thiruvananthapuram Kerala India
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24
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Veronese N, Luchini C, Nottegar A, Kaneko T, Sergi G, Manzato E, Solmi M, Scarpa A. Prognostic impact of extra-nodal extension in thyroid cancer: A meta-analysis. J Surg Oncol 2015; 112:828-33. [DOI: 10.1002/jso.24070] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/01/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Nicola Veronese
- Geriatrics Division; Department of Medicine; University of Padova; Padova Italy
| | - Claudio Luchini
- Department of Pathology and Diagnostics; University and Hospital Trust of Verona; Verona Italy
| | - Alessia Nottegar
- Department of Pathology and Diagnostics; University and Hospital Trust of Verona; Verona Italy
| | - Takuma Kaneko
- Department of Molecular Pathology; Tohoku University School of Medicine; Sendai Japan
| | - Giuseppe Sergi
- Geriatrics Division; Department of Medicine; University of Padova; Padova Italy
| | - Enzo Manzato
- Geriatrics Division; Department of Medicine; University of Padova; Padova Italy
| | - Marco Solmi
- Department of Neurosciences; University of Padova; Padova Italy
| | - Aldo Scarpa
- Department of Pathology and Diagnostics; University and Hospital Trust of Verona; Verona Italy
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25
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Transcriptional master regulator analysis in breast cancer genetic networks. Comput Biol Chem 2015; 59 Pt B:67-77. [PMID: 26362298 DOI: 10.1016/j.compbiolchem.2015.08.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 08/17/2015] [Accepted: 08/17/2015] [Indexed: 01/05/2023]
Abstract
Gene regulatory networks account for the delicate mechanisms that control gene expression. Under certain circumstances, gene regulatory programs may give rise to amplification cascades. Such transcriptional cascades are events in which activation of key-responsive transcription factors called master regulators trigger a series of gene expression events. The action of transcriptional master regulators is then important for the establishment of certain programs like cell development and differentiation. However, such cascades have also been related with the onset and maintenance of cancer phenotypes. Here we present a systematic implementation of a series of algorithms aimed at the inference of a gene regulatory network and analysis of transcriptional master regulators in the context of primary breast cancer cells. Such studies were performed in a highly curated database of 880 microarray gene expression experiments on biopsy-captured tissue corresponding to primary breast cancer and healthy controls. Biological function and biochemical pathway enrichment analyses were also performed to study the role that the processes controlled - at the transcriptional level - by such master regulators may have in relation to primary breast cancer. We found that transcription factors such as AGTR2, ZNF132, TFDP3 and others are master regulators in this gene regulatory network. Sets of genes controlled by these regulators are involved in processes that are well-known hallmarks of cancer. This kind of analyses may help to understand the most upstream events in the development of phenotypes, in particular, those regarding cancer biology.
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