1
|
KAŠTELAN SNJEŽANA, PAVIČIĆ ANADIDOVIĆ, PAŠALIĆ DARIA, NIKUŠEVA-MARTIĆ TAMARA, ČANOVIĆ SAMIR, KOVAČEVIĆ PETRA, KONJEVODA SUZANA. Biological characteristics and clinical management of uveal and conjunctival melanoma. Oncol Res 2024; 32:1265-1285. [PMID: 39055896 PMCID: PMC11267116 DOI: 10.32604/or.2024.048437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/23/2024] [Indexed: 07/28/2024] Open
Abstract
Uveal and conjunctival melanomas are relatively rare tumors; nonetheless, they pose a significant risk of mortality for a large number of affected individuals. The pathogenesis of melanoma at different sites is very similar, however, the prognosis for patients with ocular melanoma remains unfavourable, primarily due to its distinctive genetic profile and tumor microenvironment. Regardless of considerable advances in understanding the genetic characteristics and biological behaviour, the treatment of uveal and conjunctival melanoma remains a formidable challenge. To enhance the prospect of success, collaborative efforts involving medical professionals and researchers in the fields of ocular biology and oncology are essential. Current data show a lack of well-designed randomized clinical trials and limited benefits in current forms of treatment for these tumors. Despite advancements in the development of effective melanoma therapeutic strategies, all current treatments for uveal melanoma (UM) and conjunctival melanoma (CoM) remain unsatisfactory, resulting in a poor long-term prognosis. Ongoing trials offer hope for positive outcomes in advanced and metastatic tumors. A more comprehensive understanding of the genetic and molecular abnormalities involved in the development and progression of ocular melanomas opens the way for the development of personalized therapy, with various potential therapeutic targets currently under consideration. Increased comprehension of the molecular pathogenesis of UM and CoM and their specificities may aid in the development of new and more effective systemic therapeutic agents, with the hope of improving the prognosis for patients with metastatic disease.
Collapse
Affiliation(s)
- SNJEŽANA KAŠTELAN
- School of Medicine, University of Zagreb, Zagreb, 10000, Croatia
- Department of Ophthalmology, Clinical Hospital Dubrava, Zagreb, 10000, Croatia
| | | | - DARIA PAŠALIĆ
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, School of Medicine, University of Zagreb, Zagreb, 10000, Croatia
| | - TAMARA NIKUŠEVA-MARTIĆ
- Department of Biology and Genetics, School of Medicine, University of Zagreb, Zagreb, 10000, Croatia
| | - SAMIR ČANOVIĆ
- Department of Ophthalmology, Zadar General Hospital, Zadar, 23000, Croatia
- Department of Health Studies, University of Zadar, Zadar, 23000, Croatia
| | - PETRA KOVAČEVIĆ
- School of Medicine, University of Zagreb, Zagreb, 10000, Croatia
- School of Medicine, University of Split, Split, 21000, Croatia
| | - SUZANA KONJEVODA
- Department of Ophthalmology, Zadar General Hospital, Zadar, 23000, Croatia
- Department of Health Studies, University of Zadar, Zadar, 23000, Croatia
| |
Collapse
|
2
|
Hu Q, Xu L, Yi Q, Yuan J, Wu G, Wang Y. miR-204 suppresses uveal melanoma cell migration and invasion through negative regulation of RAB22A. Funct Integr Genomics 2023; 23:49. [PMID: 36705739 DOI: 10.1007/s10142-022-00953-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 01/28/2023]
Abstract
Uveal melanoma (UM), a frequently seen adulthood primary ocular malignancy, shows high aggressiveness. Accumulating studies have revealed the crucial effects of microRNAs (miRNAs) on tumorigenesis and development in various human tumors. miR-204, the cancer-associated miRNA, shows dysregulation and is related to several human malignancies, but its effect on UM remains unknown. The present work focused on exploring miR-204's effect on UM and elucidating its possible molecular mechanisms. According to our results, miR-204 expression markedly increased within both UM tissues and cell lines. As revealed by functional analysis, miR-204 suppressed UM cell invasion and migration. Besides, RAB22A expression decreased through directly binding miR-204 into the corresponding 3' untranslated region (3'UTR) in UM cells. Furthermore, the RAB22A mRNA level increased, which was negatively related to the miR-204 level within UM samples. As revealed by mechanical research, miR-204 exerted its inhibition on the invasion and migration of UM cells via RAB22A. Taken together, this study suggested the tumor-suppressing effect of miR-204 on UM through down-regulating RAB22A. Thus, miR-204 may serve as the new anti-UM therapeutic target.
Collapse
Affiliation(s)
- Qidi Hu
- Department of Ophthalmology, The Affiliated Ningbo Eye Hospital of Wenzhou Medical University, No. 599 Beimingcheng Road, Ningbo, 315040, China
| | - Lingli Xu
- Department of Ophthalmology, The Affiliated Ningbo Eye Hospital of Wenzhou Medical University, No. 599 Beimingcheng Road, Ningbo, 315040, China
| | - Quanyong Yi
- Department of Ophthalmology, The Affiliated Ningbo Eye Hospital of Wenzhou Medical University, No. 599 Beimingcheng Road, Ningbo, 315040, China
| | - Jianshu Yuan
- Department of Ophthalmology, The Affiliated Ningbo Eye Hospital of Wenzhou Medical University, No. 599 Beimingcheng Road, Ningbo, 315040, China
| | - Guohai Wu
- Department of Ophthalmology, The Affiliated Ningbo Eye Hospital of Wenzhou Medical University, No. 599 Beimingcheng Road, Ningbo, 315040, China
| | - Yuwen Wang
- Department of Ophthalmology, The Affiliated Ningbo Eye Hospital of Wenzhou Medical University, No. 599 Beimingcheng Road, Ningbo, 315040, China.
| |
Collapse
|
3
|
Lactate Rewrites the Metabolic Reprogramming of Uveal Melanoma Cells and Induces Quiescence Phenotype. Int J Mol Sci 2022; 24:ijms24010024. [PMID: 36613471 PMCID: PMC9820521 DOI: 10.3390/ijms24010024] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Uveal melanoma (UM), the most common primary intraocular cancer in adults, is among the tumors with poorer prognosis. Recently, the role of the oncometabolite lactate has become attractive due to its role as hydroxycarboxylic acid receptor 1 (HCAR1) activator, as an epigenetic modulator inducing lysine residues lactylation and, of course, as a glycolysis end-product, bridging the gap between glycolysis and oxidative phosphorylation. The aim of the present study was to dissect in UM cell line (92.1) the role of lactate as either a metabolite or a signaling molecule, using the known modulators of HCAR1 and of lactate transporters. Our results show that lactate (20 mM) resulted in a significant decrease in cell proliferation and migration, acting and switching cell metabolism toward oxidative phosphorylation. These results were coupled with increased euchromatin content and quiescence in UM cells. We further showed, in a clinical setting, that an increase in lactate transporters MCT4 and HCAR1 is associated with a spindle-shape histological type in UM. In conclusion, our results suggest that lactate metabolism may serve as a prognostic marker of UM progression and may be exploited as a potential therapeutic target.
Collapse
|
4
|
Genome-wide CRISPR knockout screening identified G protein pathway suppressor 2 as a novel tumor suppressor for uveal melanoma metastasis. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04160-5. [PMID: 35941228 DOI: 10.1007/s00432-022-04160-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/16/2022] [Indexed: 10/15/2022]
Abstract
PURPOSE Uveal melanoma (UM) is the most common intraocular malignant tumor in adults. Due to the lack of effective treatments for metastatic UM, the survival of UM has not changed over the past 3 decades. Therefore, it is important to identify essential genes regulating the metastasis of UM. METHODS In this study, a genome-wide CRISPR knockout screen in an orthotopic mouse model of UM was performed to identify the regulatory genes conferring the metastatic phenotype. Loss-of-function analyses were performed to explore the function of G protein pathway suppressor 2 (GPS2) in UM metastasis in vitro and in vivo. RNA sequencing was performed to investigate the molecular mechanism underlying the function of GPS2 as a tumor suppressor in UM. RESULTS Among the highest-ranking genes, we found several validated tumor suppressors, such as SHPRH, GPS2, PRPH2, and hsa-mir-1229; GPS2 was chosen as the candidate gene for further studies. GPS2 was lower expressed in the tumor tissues of UM patients. Furthermore, knocking-down GPS2 promoted the proliferation and metastatic abilities of UM cells both in vivo and in vitro. Finally, analysis of the transcriptome data revealed that silencing GPS2 upregulates oncogenic signaling pathways MAPK and PI3K-Akt, and in the meantime downregulates tumor suppressor signaling pathway Slit/Robo in UM cells. CONCLUSION Altogether, our study proved that the GPS2 gene functions as a tumor suppressor and might be a novel potential therapeutic target for UM treatment.
Collapse
|
5
|
Wang T, Bai J, Zhang Y, Xue Y, Peng Q. N6-Methyladenosine regulator RBM15B acts as an independent prognostic biomarker and its clinical significance in uveal melanoma. Front Immunol 2022; 13:918522. [PMID: 36003405 PMCID: PMC9393712 DOI: 10.3389/fimmu.2022.918522] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Uveal melanoma (UM) is the most frequent intraocular malignant tumor in adults. N6-Methyladenosine (m6A) methylation is recognized as the most critical epigenetic change and is implicated in the development of many malignancies. However, its prognostic value in UM is poorly understood. RNA-seq and clinical data from The Cancer Genome Atlas (TCGA) help us better understand the relationship between m6A regulators and UM patients. Herein, four UM groups established by consensus clustering were shown to have different immune cell infiltrations and prognostic survival. Five m6A regulators, including RBM15B, IGF2BP1, IGF2BP2, YTHDF3, and YTHDF1, were associated with the prognosis of UM patients. Intriguingly, RBM15B was confirmed to be the only independent prognostic factor for UM and it was significantly correlated with clinicopathologic characteristics of UM. Notably, RBM15B expression was significantly negatively correlated with immune checkpoints. Furthermore, LINC00665/hsa-let-7b-5p/RBM15B axis and LINC00638/hsa-miR-103a-3p/RBM15B axis were found to be potential prognostic biomarkers in UM. In a nutshell, this work, through bioinformatics analysis, systematically described the gene signatures and prognostic values of m6A regulators. RBM15B is an independent protective prognostic factor, which may help us better understand the crosstalk within UM.
Collapse
|
6
|
Albaradei S, Albaradei A, Alsaedi A, Uludag M, Thafar MA, Gojobori T, Essack M, Gao X. MetastaSite: Predicting metastasis to different sites using deep learning with gene expression data. Front Mol Biosci 2022; 9:913602. [PMID: 35936793 PMCID: PMC9353773 DOI: 10.3389/fmolb.2022.913602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/29/2022] [Indexed: 12/03/2022] Open
Abstract
Deep learning has massive potential in predicting phenotype from different omics profiles. However, deep neural networks are viewed as black boxes, providing predictions without explanation. Therefore, the requirements for these models to become interpretable are increasing, especially in the medical field. Here we propose a computational framework that takes the gene expression profile of any primary cancer sample and predicts whether patients' samples are primary (localized) or metastasized to the brain, bone, lung, or liver based on deep learning architecture. Specifically, we first constructed an AutoEncoder framework to learn the non-linear relationship between genes, and then DeepLIFT was applied to calculate genes' importance scores. Next, to mine the top essential genes that can distinguish the primary and metastasized tumors, we iteratively added ten top-ranked genes based upon their importance score to train a DNN model. Then we trained a final multi-class DNN that uses the output from the previous part as an input and predicts whether samples are primary or metastasized to the brain, bone, lung, or liver. The prediction performances ranged from AUC of 0.93-0.82. We further designed the model's workflow to provide a second functionality beyond metastasis site prediction, i.e., to identify the biological functions that the DL model uses to perform the prediction. To our knowledge, this is the first multi-class DNN model developed for the generic prediction of metastasis to various sites.
Collapse
Affiliation(s)
- Somayah Albaradei
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Asim Alsaedi
- King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Mahmut Uludag
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maha A. Thafar
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- College of Computers and Information Technology, Taif University, Taif, Saudi Arabia
| | - Takashi Gojobori
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Magbubah Essack
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xin Gao
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| |
Collapse
|
7
|
Tollis S, Rizzotto A, Pham NT, Koivukoski S, Sivakumar A, Shave S, Wildenhain J, Zuleger N, Keys JT, Culley J, Zheng Y, Lammerding J, Carragher NO, Brunton VG, Latonen L, Auer M, Tyers M, Schirmer EC. Chemical Interrogation of Nuclear Size Identifies Compounds with Cancer Cell Line-Specific Effects on Migration and Invasion. ACS Chem Biol 2022; 17:680-700. [PMID: 35199530 PMCID: PMC8938924 DOI: 10.1021/acschembio.2c00004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Background: Lower survival rates for many cancer
types correlate with changes in nuclear size/scaling in a tumor-type/tissue-specific
manner. Hypothesizing that such changes might confer an advantage
to tumor cells, we aimed at the identification of commercially available
compounds to guide further mechanistic studies. We therefore screened
for Food and Drug Administration (FDA)/European Medicines Agency (EMA)-approved
compounds that reverse the direction of characteristic tumor nuclear
size changes in PC3, HCT116, and H1299 cell lines reflecting, respectively,
prostate adenocarcinoma, colonic adenocarcinoma, and small-cell squamous
lung cancer. Results: We found distinct, largely
nonoverlapping sets of compounds that rectify nuclear size changes
for each tumor cell line. Several classes of compounds including,
e.g., serotonin uptake inhibitors, cyclo-oxygenase inhibitors, β-adrenergic
receptor agonists, and Na+/K+ ATPase inhibitors,
displayed coherent nuclear size phenotypes focused on a particular
cell line or across cell lines and treatment conditions. Several compounds
from classes far afield from current chemotherapy regimens were also
identified. Seven nuclear size-rectifying compounds selected for further
investigation all inhibited cell migration and/or invasion. Conclusions: Our study provides (a) proof of concept that
nuclear size might be a valuable target to reduce cell migration/invasion
in cancer treatment and (b) the most thorough collection of tool compounds
to date reversing nuclear size changes specific to individual cancer-type
cell lines. Although these compounds still need to be tested in primary
cancer cells, the cell line-specific nuclear size and migration/invasion
responses to particular drug classes suggest that cancer type-specific
nuclear size rectifiers may help reduce metastatic spread.
Collapse
Affiliation(s)
- Sylvain Tollis
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Andrea Rizzotto
- The Institute of Cell Biology, University of Edinburgh, Kings Buildings, Michael Swann Buildings, Max Born Crescent, Edinburgh EH9 3BF, U.K
| | - Nhan T. Pham
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, U.K
| | - Sonja Koivukoski
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Aishwarya Sivakumar
- The Institute of Cell Biology, University of Edinburgh, Kings Buildings, Michael Swann Buildings, Max Born Crescent, Edinburgh EH9 3BF, U.K
| | - Steven Shave
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, U.K
| | - Jan Wildenhain
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, U.K
| | - Nikolaj Zuleger
- The Institute of Cell Biology, University of Edinburgh, Kings Buildings, Michael Swann Buildings, Max Born Crescent, Edinburgh EH9 3BF, U.K
| | - Jeremy T. Keys
- Nancy E. and Peter C. Meinig School of Biomedical Engineering & Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jayne Culley
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, U.K
| | - Yijing Zheng
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, U.K
| | - Jan Lammerding
- Nancy E. and Peter C. Meinig School of Biomedical Engineering & Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Neil O. Carragher
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, U.K
| | - Valerie G. Brunton
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, U.K
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Manfred Auer
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, U.K
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Eric C. Schirmer
- The Institute of Cell Biology, University of Edinburgh, Kings Buildings, Michael Swann Buildings, Max Born Crescent, Edinburgh EH9 3BF, U.K
| |
Collapse
|
8
|
Drabarek W, van Riet J, Nguyen JQN, Smit KN, van Poppelen NM, Jansen R, Medico-Salsench E, Vaarwater J, Magielsen FJ, Brands T, Eussen B, van den Bosch TPP, Verdijk RM, Naus NC, Paridaens D, de Klein A, Brosens E, van de Werken HJG, Kilic E. Identification of Early-Onset Metastasis in SF3B1 Mutated Uveal Melanoma. Cancers (Basel) 2022; 14:cancers14030846. [PMID: 35159112 PMCID: PMC8834136 DOI: 10.3390/cancers14030846] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/31/2022] Open
Abstract
Simple Summary This study describes clinical and genetic characteristics of the largest aggregated cohort of Splicing Factor 3 Subunit B1 (SF3B1)-mutated Uveal Melanoma (UM) in the literature (n = 146). Missense mutations in the spliceosome gene SF3B1 result in an altered splice site recognition and aberrant mRNA transcripts. The SF3B1-mutated UM show early- and late-onset of metastatic disease for which, currently, no distinguishing biomarkers exist. Using a cutoff of 60 months for stratification, we found that a largest basal tumor diameter was more prevalent in the early-onset metastatic disease group. Furthermore, using differential gene expression and the detection of aberrant transcripts, we found that the expression of alpha/beta-Hydrolase domain containing 6 (ABHD6) is associated with early-onset metastatic SF3B1 and aberrant transcripts that are associated with early-onset SF3B1-mutated UM. Our results provide more accurate prognostication and targets for future functional studies in an effort to elucidate pathogenesis of SF3B1-mutated UM. Abstract Approximately 25% of all uveal melanoma (UM) contain driver mutations in the gene encoding the spliceosome factor SF3B1, and whilst patients with such SF3B1 mutations generally have an intermediate risk on developing metastatic disease, a third of these patients develop early metastasis within 5 years after diagnosis. We therefore investigated whether clinical and/or genetic variables could be indicative of short progression-free survival (PFS < 60 months) or long PFS (PFS ≥ 60 months) for SF3B1-mutated (SF3B1mut) UM patients. We collected 146 SF3B1mut UM from our Rotterdam Ocular Melanoma Studygroup (ROMS) database and external published datasets. After stratification of all SF3B1mut UM using short PFS vs. long PFS, only largest tumor diameter (LTD) was significantly larger (mean: 17.7 mm (±2.8 SD) in the short PFS SF3B1mut group vs. the long PFS group (mean: 14.7 (±3.7 SD, p = 0.001). Combined ROMS and The Cancer Genome Atlas (TCGA) transcriptomic data were evaluated, and we identified SF3B1mut-specific canonical transcripts (e.g., a low expression of ABHD6 indicative for early-onset metastatic disease) or distinct expression of SF3B1mut UM aberrant transcripts, indicative of early- or late-onset or no metastatic SF3B1mut UM.
Collapse
Affiliation(s)
- Wojtek Drabarek
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Job van Riet
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands;
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, 3000 CA, Rotterdam, The Netherlands;
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Josephine Q. N. Nguyen
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Kyra N. Smit
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Natasha M. van Poppelen
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Rick Jansen
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, 3000 CA, Rotterdam, The Netherlands;
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Eva Medico-Salsench
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Jolanda Vaarwater
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
| | - Frank J. Magielsen
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Tom Brands
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Bert Eussen
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Thierry. P. P. van den Bosch
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (T.P.P.v.d.B.); (R.M.V.)
| | - Robert M. Verdijk
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (T.P.P.v.d.B.); (R.M.V.)
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
| | - Dion Paridaens
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Harmen J. G. van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, 3000 CA, Rotterdam, The Netherlands;
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands
- Department of Immunology, Erasmus MC Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands
- Correspondence: (H.J.G.v.d.W.); (E.K.); Tel.: +31-107044467 (H.J.G.v.d.W.); +31-107044272 (E.K.)
| | - Emine Kilic
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- Correspondence: (H.J.G.v.d.W.); (E.K.); Tel.: +31-107044467 (H.J.G.v.d.W.); +31-107044272 (E.K.)
| | | |
Collapse
|
9
|
Establishment and validation of five autophagy-related signatures for predicting survival and immune microenvironment in glioma. Genes Genomics 2021; 44:79-95. [PMID: 34609723 DOI: 10.1007/s13258-021-01172-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 09/23/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Gliomas, especially Glioblastoma multiforme, are the most frequent type of primary tumors in central nervous system. Increasing researches have revealed the relationship between autophagy and tumor, while the molecular mechanism of autophagy in glioma is still rarely reported. OBJECTIVE Our research aims to conform the autophagy-related genes (ARGs) implicated in the development and progression of glioma and improve our understanding of autophagy in glioma. METHODS 20 candidate ARGs were screened through the protein-protein interaction network. We also downloaded the publicly accessible glioma data for 665 individuals from TCGA and 970 individuals from CGGA with RNA sequences and clinicopathological information. Subsequently, univariate and multivariate Cox regression analysis identified 5 key ARGs among the 20 candidate genes as key prognostic genes for survival, GSEA and immune response analysis. RESULTS ATG5, BCL2L1, CASP3, CASP8, GAPDH were identified as key ARGs in our research. Further studies showed that the high-risk population was linked to a dismal prognosis and suggested an immune-inhibitory microenvironment. GSEA results demonstrated that high risk population was closely related to DNA repair, hypoxia pathways, implicated in immunosuppression and carcinogenesis. Through CMap, we finally identified 14 candidate drugs for the ARG high risk population. CONCLUSIONS This study established and verified an ARG risk model, which can serve as an independent predictor for prognosis, reflect on the strength of the immune response and predict the potential drugs in glioma. Our findings offer new understandings of ARG molecular mechanism and promising therapeutic targets for glioma treatment.
Collapse
|
10
|
Liao CL, Hu N, Sun XY, Zhou Q, Tian M, Cao Y, Lyu HB. Identification and validation of tumor microenvironment-related lncRNA prognostic signature for uveal melanoma. Int J Ophthalmol 2021; 14:1151-1159. [PMID: 34414077 DOI: 10.18240/ijo.2021.08.03] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/16/2021] [Indexed: 12/11/2022] Open
Abstract
AIM To investigate the role of tumor microenvironment (TME)-related long non-coding RNA (lncRNA) in uveal melanoma (UM), probable prognostic signature and potential small molecule drugs using bioinformatics analysis. METHODS UM expression profile data were downloaded from the Cancer Genome Atlas (TCGA) and bioinformatics methods were used to find prognostic lncRNAs related to UM immune cell infiltration. The gene expression profile data of 80 TCGA specimens were analyzed using the single sample Gene Set Enrichment Analysis (ssGSEA) method, and the immune cell infiltration of a single specimen was evaluated. Finally, the specimens were divided into high and low infiltration groups. The differential expression between the two groups was analyzed using the R package 'edgeR'. Univariate, multivariate and Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression analyses were performed to explore the prognostic value of TME-related lncRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses were also performed. The Connectivity Map (CMap) data set was used to screen molecular drugs that may treat UM. RESULTS A total of 2393 differentially expressed genes were identified and met the criteria for the low and high immune cell infiltration groups. Univariate Cox analysis of lncRNA genes with differential expression identified 186 genes associated with prognosis. Eight prognostic markers of TME-included lncRNA genes were established as potentially independent prognostic elements. Among 269 differentially expressed lncRNAs, 69 were up-regulated and 200 were down-regulated. Univariate Cox regression analysis of the risk indicators and clinical characteristics of the 8 lncRNA gene constructs showed that age, TNM stage, tumor base diameter, and low and high risk indices had significant prognostic value. We screened the potential small-molecule drugs for UM, including W-13, AH-6809 and Imatinib. CONCLUSION The prognostic markers identified in this study are reliable biomarkers of UM. This study expands our current understanding of the role of TME-related lncRNAs in UM genesis, which may lay the foundations for future treatment of this disease.
Collapse
Affiliation(s)
- Chen-Lu Liao
- Department of Ophthalmology, Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Nan Hu
- Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Xing-Yu Sun
- Department of Gynecology, Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Qi Zhou
- Department of Ophthalmology, Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Min Tian
- Department of Ophthalmology, Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Yang Cao
- Department of Ophthalmology, Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Hong-Bin Lyu
- Department of Ophthalmology, Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan Province, China
| |
Collapse
|
11
|
Shi L, Huang R, Lai Y. Identification and validation of signal recognition particle 14 as a prognostic biomarker predicting overall survival in patients with acute myeloid leukemia. BMC Med Genomics 2021; 14:127. [PMID: 33985510 PMCID: PMC8120815 DOI: 10.1186/s12920-021-00975-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND This study aimed to determine and verify the prognostic value and potential functional mechanism of signal recognition particle 14 (SRP14) in acute myeloid leukemia (AML) using a genome-wide expression profile dataset. METHODS We obtained an AML genome-wide expression profile dataset and clinical prognostic data from The Cancer Genome Atlas (TCGA) and GSE12417 databases, and explored the prognostic value and functional mechanism of SRP14 in AML using survival analysis and various online tools. RESULTS Survival analysis showed that AML patients with high SRP14 expression had poorer overall survival than patients with low SRP14 expression. Time-dependent receiver operating characteristic curves indicated that SRP14 had good accuracy for predicting the prognosis in patients with AML. Genome-wide co-expression analysis suggested that SRP14 may play a role in AML by participating in the regulation of biological processes and signaling pathways, such as cell cycle, cell adhesion, mitogen-activated protein kinase, tumor necrosis factor, T cell receptor, DNA damage response, and nuclear factor-kappa B (NF-κB) signaling. Gene set enrichment analysis indicated that SRP14 was significantly enriched in biological processes and signaling pathways including regulation of hematopoietic progenitor cell differentiation and stem cell differentiation, intrinsic apoptotic signaling pathway by p53 class mediator, interleukin-1, T cell mediated cytotoxicity, and NF-κB-inducing kinase/NF-κB signaling. Using the TCGA AML dataset, we also identified four drugs (phenazone, benzydamine, cinnarizine, antazoline) that may serve as SRP14-targeted drugs in AML. CONCLUSION The current results revealed that high SRP14 expression was significantly related to a poor prognosis and may serve as a prognostic biomarker in patients with AML.
Collapse
Affiliation(s)
- Lingling Shi
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6, Nanning, 530021 Guangxi People’s Republic of China
| | - Rui Huang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6, Nanning, 530021 Guangxi People’s Republic of China
| | - Yongrong Lai
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6, Nanning, 530021 Guangxi People’s Republic of China
| |
Collapse
|
12
|
Andrade RC, Boroni M, Amazonas MK, Vargas FR. New drug candidates for osteosarcoma: Drug repurposing based on gene expression signature. Comput Biol Med 2021; 134:104470. [PMID: 34004576 DOI: 10.1016/j.compbiomed.2021.104470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/01/2021] [Accepted: 05/02/2021] [Indexed: 02/03/2023]
Abstract
Osteosarcoma (OS) is an aggressive bone malignancy and the third most common cancer in adolescence. Since the late 1970s, OS therapy and prognosis had only modest improvements, making it appealing to explore new tools that could help ameliorate the treatment. We present a meta-analysis of the gene expression signature of primary OS, and propose small molecules that could reverse this signature. The meta-analysis was performed using GEO microarray series. We first compared gene expression from eleven primary OS against osteoblasts to obtain the differentially expressed genes (DEGs). We later filtered those DEGs by verifying which ones had a concordant direction of differential expression in a validation group of 82 OS samples versus 30 bone marrow mesenchymal stem cells (BM-MSC) samples. A final gene expression signature of 266 genes (98 up and 168 down regulated) was obtained. The L1000CDS2 engine was used for drug repurposing. The top molecules predicted to reverse the signature were afatinib (PubChem CID 10184653), BRD-K95196255 (PubChem CID 3242434), DG-041 (PubChem CID 11296282) and CA-074 Me (PubChem CID 23760717). Afatinib (Gilotrif™) is currently used for metastatic non-small-cell lung cancer with EGFR mutations, and in vitro evidence shows antineoplastic potential in OS cells. The other three molecules have reports of antineoplastic effects, but are not currently FDA-approved. Further studies are necessary to establish the potential of these drugs in OS treatment. We believe our results can be an important contribution for the investigation of new therapeutic genetic targets and for selecting new drugs to be tested for OS.
Collapse
Affiliation(s)
- Raissa Coelho Andrade
- Birth Defects Epidemiology Laboratory, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil; Genetics and Molecular Biology Department, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
| | - Mariana Boroni
- Bioinformatics and Computational Biology Lab, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil; Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Fernando Regla Vargas
- Birth Defects Epidemiology Laboratory, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil; Genetics and Molecular Biology Department, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil.
| |
Collapse
|
13
|
Additive Role of Immune System Infiltration and Angiogenesis in Uveal Melanoma Progression. Int J Mol Sci 2021; 22:ijms22052669. [PMID: 33800878 PMCID: PMC7961481 DOI: 10.3390/ijms22052669] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 12/17/2022] Open
Abstract
Uveal melanoma (UM) is a malignant tumor that arises in the melanocytes of the uveal tract. It is the most frequent eye cancer, and despite new therapeutic approaches, prognosis is still poor, with up to 50% of patients developing metastasis with no efficient treatment options available. In contrast to cutaneous melanoma, UM is considered an “immune-cold” tumor due to the low mutational burden and the unique immunosuppressive microenvironment. To gain insight into the role of the UM microenvironment in regard to prognosis and metastatic progression, we have performed a pool analysis characterizing the UM microenvironment by using a bioinformatic approach. A variety of scores based on gene expression measuring stromal infiltration were calculated and used to assess association with prognosis. As a result, the highest immune and stromal scores were associated with poor prognosis. Specifically, stromal cells (fibroblasts and endothelial cells), T cells CD8+, natural killer (NK) cells, and macrophages M1 and M2 infiltration were associated with poor prognosis. Contrary to other tumors, lymphocytic infiltration is related to poor prognosis. Only B cells were associated with more favorable prognosis. UM samples scoring high in both angiogenesis (Angio) and antigen presentation (AP) pathways showed a poor prognosis suggesting an additive role of both functions. Almost all these tumors exhibited a chromosome 3 monosomy. Finally, an enrichment analysis showed that tumors classified as high Angio-high AP also activated metabolic pathways such as glycolysis or PI3K-AKT-MTOR. In summary, our pool analysis identified a cluster of samples with angiogenic and inflammatory phenotypes exhibiting poor prognosis and metabolic activation. Our analysis showed robust results replicated in a pool analysis merging different datasets from different analytic platforms.
Collapse
|
14
|
Vivarelli S, Falzone L, Basile MS, Candido S, Libra M. Nitric Oxide in Hematological Cancers: Partner or Rival? Antioxid Redox Signal 2021; 34:383-401. [PMID: 32027171 DOI: 10.1089/ars.2019.7958] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Significance: Hematological malignancies represent the fourth most diagnosed cancer. Relapse and acquired resistance to anticancer therapy constitute two actual issues that need to be overcome. Nitric oxide (NO) plays a pivotal role in regulating cancer progression. At present, many studies are attempting to uncover the potentials of modulating NO levels to improve the efficacy of currently available treatments against lymphoma, leukemia, and myeloma. Recent Advances: It is becoming progressively clear that NO modulation may help hematological cancer management, either by targeting directly tumor cells or by driving the immune system to eliminate cancer cells. Critical Issues: NO is a dual molecule that can have a tumor-protecting or stimulating effect, depending on its local concentration. Moreover, NO is able to target a wide range of molecules involved in both cancer genesis and evolution. In this review, an overview of the recent findings regarding the pivotal role played by NO and nitric oxide synthase in cancer progression and anticancer therapy is presented, with particular focus on hematological malignancies. Future Directions: It is critical to establish the cancer-specific function of NO and critically drive its modulation to improve cancer management toward a personalized approach. This has a special importance in hematological tumors, where the urgency of finding eradicative therapies is constant. Antioxid. Redox Signal. 34, 383-401.
Collapse
Affiliation(s)
- Silvia Vivarelli
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Luca Falzone
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", Napoli, Italy
| | - Maria Sofia Basile
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy.,Research Centre for Prevention, Diagnosis and Treatment of Cancer, University of Catania, Catania, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy.,Research Centre for Prevention, Diagnosis and Treatment of Cancer, University of Catania, Catania, Italy
| |
Collapse
|
15
|
Lombardo SD, Bramanti A, Ciurleo R, Basile MS, Pennisi M, Bella R, Mangano K, Bramanti P, Nicoletti F, Fagone P. Profiling of inhibitory immune checkpoints in glioblastoma: Potential pathogenetic players. Oncol Lett 2020; 20:332. [PMID: 33123243 PMCID: PMC7583708 DOI: 10.3892/ol.2020.12195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/06/2020] [Indexed: 12/27/2022] Open
Abstract
Glioblastoma (GBM) represents the most frequent glial tumor, with almost 3 new cases per 100,000 people per year. Despite treatment, the prognosis for GBM patients remains extremely poor, with a median survival of 14.6 months, and a 5-year survival less than 5%. It is generally believed that GBM creates a highly immunosuppressive microenvironment, sustained by the expression of immune-regulatory factors, including inhibitory immune checkpoints, on both infiltrating cells and tumor cells. However, the trials assessing the efficacy of current immune checkpoint inhibitors in GBM are still disappointing. In the present study, the expression levels of several inhibitory immune checkpoints in GBM (CD276, VTCN1, CD47, PVR, TNFRSF14, CD200, LGALS9, NECTIN2 and CD48) were characterized in order to evaluate their potential as prognostic and eventually, therapeutic targets. Among the investigated immune checkpoints, TNFRSF14 and NECTIN2 were identified as the most promising targets in GBM. In particular, a higher TNFRSF14 expression was associated with worse overall survival and disease-free survival, and with a lower Th1 response.
Collapse
Affiliation(s)
- Salvo Danilo Lombardo
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria
| | | | - Rosella Ciurleo
- IRCCS Centro Neurolesi Bonino Pulejo, I-98124 Messina, Italy
| | | | - Manuela Pennisi
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Rita Bella
- Department of Medical Sciences, Surgery and Advanced Technologies, University of Catania, I-95123 Catania, Italy
| | - Katia Mangano
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | | | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| |
Collapse
|
16
|
Mallone F, Sacchetti M, Lambiase A, Moramarco A. Molecular Insights and Emerging Strategies for Treatment of Metastatic Uveal Melanoma. Cancers (Basel) 2020; 12:E2761. [PMID: 32992823 PMCID: PMC7600598 DOI: 10.3390/cancers12102761] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
Uveal melanoma (UM) is the most common intraocular cancer. In recent decades, major advances have been achieved in the diagnosis and prognosis of UM allowing for tailored treatments. However, nearly 50% of patients still develop metastatic disease with survival rates of less than 1 year. There is currently no standard of adjuvant and metastatic treatment in UM, and available therapies are ineffective resulting from cutaneous melanoma protocols. Advances and novel treatment options including liver-directed therapies, immunotherapy, and targeted-therapy have been investigated in UM-dedicated clinical trials on single compounds or combinational therapies, with promising results. Therapies aimed at prolonging or targeting metastatic tumor dormancy provided encouraging results in other cancers, and need to be explored in UM. In this review, the latest progress in the diagnosis, prognosis, and treatment of UM in adjuvant and metastatic settings are discussed. In addition, novel insights into tumor genetics, biology and immunology, and the mechanisms underlying metastatic dormancy are discussed. As evident from the numerous studies discussed in this review, the increasing knowledge of this disease and the promising results from testing of novel individualized therapies could offer future perspectives for translating in clinical use.
Collapse
Affiliation(s)
| | | | - Alessandro Lambiase
- Department of Sense Organs, Sapienza University of Rome, 00161 Rome, Italy; (F.M.); (M.S.); (A.M.)
| | | |
Collapse
|
17
|
Pesce A, Ciurleo R, Bramanti A, Armeli Iapichino EC, Petralia MC, Magro GG, Fagone P, Bramanti P, Nicoletti F, Mangano K. Effects of Combined Admistration of Imatinib and Sorafenib in a Murine Model of Liver Fibrosis. Molecules 2020; 25:molecules25184310. [PMID: 32962198 PMCID: PMC7571085 DOI: 10.3390/molecules25184310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/17/2020] [Accepted: 09/19/2020] [Indexed: 02/06/2023] Open
Abstract
Liver fibrosis is defined as excessive extracellular matrix deposition in the hepatic parenchyma as a consequence of complex interactions among matrix-producing hepatic stellate cells (HSCs) and liver-resident and infiltrating cells. In addition to the liver, the process of fibrosis may represent end-stage disease of several diseases including kidneys, lungs, spleens, heart, muscles and at certain extent, the central nervous system and the peripheral nerves. To date, antifibrotic treatment of fibrosis represents an unconquered area for drug development. The aim of the present study was to test the efficacy of a new drug combination for the treatment of hepatic fibrosis in order to provide a proof-of-concept for the use of therapeutic agents in clinical practice. For this purpose, we have studied the effects of the PDGF inhibitor imatinib and the angiogenesis inhibitor sorafenib, administered alone or in combination, in reducing the progression of the fibrogenetic process in a pre-clinical model of liver damage induced in mice by repeated administration of Concanavalin A (ConA), resembling long-tern autoimmune hepatitis. Our results suggest that treatments with imatinib and sorafenib can modulate potently and, in a superimposable fashion, the fibrinogenic process when administered alone. However, and in agreement with the computational data presently generated, they only exert partial overlapping antifibrotic effects in modulating the main pathways involved in the process of liver fibrosis, without significant additive or synergist effects, when administered in combination.
Collapse
Affiliation(s)
- Antonio Pesce
- Department of Medical and Surgical Sciences and Advanced Technology G.F. Ingrassia, University of Catania, Via Santa Sofia 86, 95123 Catania, Italy; (A.P.); (G.G.M.)
| | - Rosella Ciurleo
- IRCCS Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124 Messina, Italy; (R.C.); (A.B.); (P.B.)
| | - Alessia Bramanti
- IRCCS Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124 Messina, Italy; (R.C.); (A.B.); (P.B.)
| | | | - Maria Cristina Petralia
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (M.C.P.); (P.F.); (K.M.)
| | - Gaetano Giuseppe Magro
- Department of Medical and Surgical Sciences and Advanced Technology G.F. Ingrassia, University of Catania, Via Santa Sofia 86, 95123 Catania, Italy; (A.P.); (G.G.M.)
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (M.C.P.); (P.F.); (K.M.)
| | - Placido Bramanti
- IRCCS Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124 Messina, Italy; (R.C.); (A.B.); (P.B.)
| | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (M.C.P.); (P.F.); (K.M.)
- Correspondence:
| | - Katia Mangano
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (M.C.P.); (P.F.); (K.M.)
| |
Collapse
|
18
|
Fritz I, Wagner P, Bottai M, Eriksson H, Ingvar C, Krakowski I, Nielsen K, Olsson H. Desloratadine and loratadine use associated with improved melanoma survival. Allergy 2020; 75:2096-2099. [PMID: 32171023 DOI: 10.1111/all.14273] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/10/2020] [Accepted: 03/01/2020] [Indexed: 02/03/2023]
Affiliation(s)
- Ildikó Fritz
- Department of Cancer Epidemiology Clinical Sciences Lund University Lund Sweden
| | - Philippe Wagner
- Department of Cancer Epidemiology Clinical Sciences Lund University Lund Sweden
| | - Matteo Bottai
- Division of Biostatistics Institute of Environmental Medicine Karolinska Institute Solna Sweden
| | - Hanna Eriksson
- Department of Oncology and Pathology Karolinska Institute Solna Sweden
- Skin Cancer Center/Theme Cancer Karolinska University Hospital Solna Sweden
- Department of Oncology/Theme Cancer Karolinska University Hospital Solna Sweden
| | - Christian Ingvar
- Department of Surgery Clinical Sciences Lund University Lund Sweden
| | - Isabelle Krakowski
- Department of Oncology and Pathology Karolinska Institute Solna Sweden
- Department of Dermatology/Theme Inflammation Karolinska University Hospital Solna Sweden
| | - Kari Nielsen
- Department of Dermatology Clinical Sciences Lund University Lund Sweden
| | - Håkan Olsson
- Department of Cancer Epidemiology Clinical Sciences Lund University Lund Sweden
- Department of Oncology Clinical Sciences Lund University Lund Sweden
| |
Collapse
|
19
|
Lazarević M, Battaglia G, Jevtić B, Đedović N, Bruno V, Cavalli E, Miljković Đ, Nicoletti F, Momčilović M, Fagone P. Upregulation of Tolerogenic Pathways by the Hydrogen Sulfide Donor GYY4137 and Impaired Expression of H 2S-Producing Enzymes in Multiple Sclerosis. Antioxidants (Basel) 2020; 9:E608. [PMID: 32664399 PMCID: PMC7402185 DOI: 10.3390/antiox9070608] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/22/2020] [Accepted: 07/08/2020] [Indexed: 12/16/2022] Open
Abstract
The aim of this study was to examine the in vitro effects of the slow-releasing H2S donor GYY4137 on the immune cells involved in the pathogenesis of the central nervous system (CNS) autoimmune disease, multiple sclerosis (MS). GYY4137 specifically potentiated TGF-β expression and production in dendritic cells and significantly reduced IFN-γ and IL-17 production in the lymph node and spinal cord T cells obtained from mice immunized with CNS antigens. Both the proportion of FoxP3+ regulatory CD4+ T cells in the lymph node cells, and the percentage of IL-17+ CD4+ T cells in the spinal cord cells were reduced upon culturing with GYY4137. Interestingly, the peripheral blood mononuclear cells obtained from the MS patients had a lower expression of the H2S-producing enzyme, 3-mercaptopyruvate-sulfurtransferase (MPST), in comparison to those obtained from healthy donors. A significant inverse correlation between the expression of MPST and several pro-inflammatory factors was also observed. Further studies on the relevance of the observed results for the pathogenesis and therapy of MS are warranted.
Collapse
Affiliation(s)
- Milica Lazarević
- Department of Immunology, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | - Giuseppe Battaglia
- Department of Physiology and Pharmacology, Sapienza University, Piazzale A. Moro, 5, 00185 Rome, Italy
- IRCCS Neuromed, Località Camerelle, 86077 Pozzilli, Italy
| | - Bojan Jevtić
- Department of Immunology, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | - Neda Đedović
- Department of Immunology, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | - Valeria Bruno
- Department of Physiology and Pharmacology, Sapienza University, Piazzale A. Moro, 5, 00185 Rome, Italy
- IRCCS Neuromed, Località Camerelle, 86077 Pozzilli, Italy
| | - Eugenio Cavalli
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy
| | - Đorđe Miljković
- Department of Immunology, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy
| | - Miljana Momčilović
- Department of Immunology, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy
| |
Collapse
|
20
|
Transcriptional landscape of SARS-CoV-2 infection dismantles pathogenic pathways activated by the virus, proposes unique sex-specific differences and predicts tailored therapeutic strategies. Autoimmun Rev 2020; 19:102571. [PMID: 32376402 PMCID: PMC7252184 DOI: 10.1016/j.autrev.2020.102571] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/11/2020] [Indexed: 12/21/2022]
Abstract
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19) has posed a serious threat to global health. As no specific therapeutics are yet available to control disease evolution, more in-depth understanding of the pathogenic mechanisms induced by SARS-CoV-2 will help to characterize new targets for the management of COVID-19. The present study identified a specific set of biological pathways altered in primary human lung epithelium upon SARS-CoV-2 infection, and a comparison with SARS-CoV from the 2003 pandemic was studied. The transcriptomic profiles were also exploited as possible novel therapeutic targets, and anti-signature perturbation analysis predicted potential drugs to control disease progression. Among them, Mitogen-activated protein kinase kinase (MEK), serine-threonine kinase (AKT), mammalian target of rapamycin (mTOR) and I kappa B Kinase (IKK) inhibitors emerged as candidate drugs. Finally, sex-specific differences that may underlie the higher COVID-19 mortality in men are proposed.
Collapse
|
21
|
Kaštelan S, Antunica AG, Oresković LB, Pelčić G, Kasun E, Hat K. Immunotherapy for Uveal Melanoma - Current Knowledge and Perspectives. Curr Med Chem 2020; 27:1350-1366. [DOI: 10.2174/0929867326666190704141444] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 06/09/2019] [Accepted: 06/14/2019] [Indexed: 12/17/2022]
Abstract
Uveal melanoma is the most prevalent primary intraocular tumour in adults with
the incidence between five and six cases per million people in the United States and Europe.
The prognosis of patients with uveal melanoma is unfavourable with a 5-year survival rate of
50-70% despite significant advances in local tumour treatment using radiotherapy or surgical
resection. Approximately 50% of the patients develop metastases within 15 years from initial
diagnosis, mostly in the liver. The median survival rate after the onset of metastases is 6
months. Potential treatment options for metastatic uveal melanoma are chemotherapy, targeted
therapy, and immunotherapy but no method showed satisfactory results. Immunotherapy
with checkpoint inhibition showed promising results in the treatment of cutaneous melanoma;
however, it did not appear to be equally effective with uveal melanoma. This may be
due to differences in mutational burden, expression of neoantigens between these two types of
tumour, immunosuppressive tumour microenvironment, and low immunogenicity and immune
privilege of uveal melanoma. Considering the disappointing results of treatment with
anti-CTLA-4 and PD-1/PD-L1 blockade in patients with advanced uveal melanoma several
new forms of therapies are being developed. This may include immunotherapy with
IMCgp100, glembatumumab vedotin and the infusion of autologous TILs, targeted therapy
with selective MEK inhibitors, epigenetic therapy, and nanotherapy. Better insight into the
molecular and genetic profile of uveal melanoma will facilitate detection of new prognostic
biomarkers and thus enable a better modification of the existing immunotherapy methods and
development of new forms of treatment specifically designed for uveal melanoma patients.
Collapse
Affiliation(s)
- Snježana Kaštelan
- Department of Ophthalmology, University Hospital Dubrava, Zagreb, Croatia
| | | | | | - Goran Pelčić
- Department of Ophthalmology, Faculty of Medicine, University of Rijeka and Clinical Hospital Center Rijeka, Rijeka, Croatia
| | - Ema Kasun
- School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Koraljka Hat
- Department of Maxillofacial Surgery, University Hospital Dubrava, Zagreb, Croatia
| |
Collapse
|
22
|
Mangano K, Lanteri R, Basile MS, Bellavia N, Latino R, Messina D, Fagone P, Colletti G, Nania R, Caltabiano R, Di Marco R, Di Cataldo A. Effects of GIT-27NO, a NO-donating compound, on hepatic ischemia/reperfusion injury. Int J Immunopathol Pharmacol 2020; 33:2058738419862736. [PMID: 31298048 PMCID: PMC6628530 DOI: 10.1177/2058738419862736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Hepatic ischemia/reperfusion injury (IRI) is a clinical condition that may lead
to cellular injury and organ dysfunction that can be observed in different
conditions, such as trauma, shock, liver resection, and transplantation.
Moderate levels of nitric oxide (NO) produced by the endothelial isoform of the
NO synthase protect against liver IRI. GIT-27NO is a NO-derivative of the
toll-like receptor 4 antagonist VGX-1027 that has been shown to possess both
antineoplastic and immunomodulatory properties in vitro and in vivo. In this
study, we have investigated the effects of this compound in vitro, in a model of
oxidative stress induced in HepG2 cells by hydrogen peroxide
(H2O2), and in vivo, in a rat model of IRI of the
liver. GIT-27NO significantly counteracted the toxic effects induced by the
H2O2 on the HepG2 cells and in vivo, GIT-27NO reduced
the transaminase levels and the histological liver injury by reducing necrotic
areas with preservation of viable tissue. These effects were almost similar to
that of the positive control drug dimethyl fumarate. These data suggest that the
beneficial effect of GIT-27NO in the hepatic IRI can be secondary to
anti-oxidative effects and hepatocyte necrosis reduction probably mediated by NO
release.
Collapse
Affiliation(s)
- Katia Mangano
- 1 Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Raffaele Lanteri
- 2 Department of General Surgery and Medical-Surgical Specialties, University of Catania, Catania, Italy
| | - Maria Sofia Basile
- 1 Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Noemi Bellavia
- 2 Department of General Surgery and Medical-Surgical Specialties, University of Catania, Catania, Italy
| | - Rosalia Latino
- 2 Department of General Surgery and Medical-Surgical Specialties, University of Catania, Catania, Italy
| | - Domenico Messina
- 1 Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Paolo Fagone
- 1 Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Giuseppe Colletti
- 1 Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Riccardo Nania
- 1 Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Rosario Caltabiano
- 3 Department of Surgical Sciences, Organ Transplantation and Advanced Technologies, G.F. Ingrassia, University of Catania, Catania, Italy
| | - Roberto Di Marco
- 4 Department of Medicine and Health Sciences "Vincenzo Tiberio," University of Molise, Campobasso, Italy
| | - Antonio Di Cataldo
- 2 Department of General Surgery and Medical-Surgical Specialties, University of Catania, Catania, Italy
| |
Collapse
|
23
|
Petralia MC, Mazzon E, Mangano K, Fagone P, Di Marco R, Falzone L, Basile MS, Nicoletti F, Cavalli E. Transcriptomic analysis reveals moderate modulation of macrophage migration inhibitory factor superfamily genes in alcohol use disorders. Exp Ther Med 2020; 19:1755-1762. [PMID: 32104230 PMCID: PMC7026954 DOI: 10.3892/etm.2020.8410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/14/2019] [Indexed: 12/20/2022] Open
Abstract
Alcohol use disorder (AUD) is a primary, chronic and relapsing disease of brain reward, motivation and memory, which is associated with several comorbidities, including major depression and post-traumatic stress disorder. It has been revealed that Ibudilast (IBUD), a dual inhibitor of phosphodiesterase-4 and −10 and of macrophage migration inhibitory factor (MIF), exerts beneficial effects on AUD in rodent models and human patients. Therefore, IBUD has attracted increasing interest, with research focusing on the elucidation of the pathogenic role of MIF and its homologue, D-dopachrome tautomerase (DDT), in the pathogenesis and maintenance of AUD. By using DNA microarray analysis, the current study performed a transcriptomic expression analysis of MIF, DDT and their co-receptors, including CD74, C-X-C chemokine receptor (CXCR)2, CXCR4 and CXCR7 in patients with AUD. The results revealed that the transcriptomic levels of MIF, DDT and their receptors were superimposable in the prefrontal cortex of rodents and patients with AUD and human patients. Furthermore, peripheral blood cells from heavy drinkers exhibited a moderate increase in MIF and DDT levels, both at the baseline and following exposure to alcohol-associated cues, based on individual situations that included alcohol-related stimuli resulting in subsequent alcohol use (buying alcohol and being at a bar, watching others drink alcohol). Considering the overlapping effects of MIF and DDT, the inverse Fisher's χ2 test was performed on unadjusted P-values to evaluate the combined effect of MIF and DDT. The results revealed a significant increase in these cytokines in heavy drinkers compared with controls (moderate drinkers). To the best of our knowledge, the present study demonstrated for the first time that MIF and DDT expression was upregulated in the blood of patients with AUD. These results therefore warrant further study to evaluate the role of MIF and DDT in the development and maintenance of AUD, to evaluate their use as biomarkers to predict the psychotherapeutic and pharmacological response of patients with AUD and for use as therapeutic targets.
Collapse
Affiliation(s)
- Maria Cristina Petralia
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Emanuela Mazzon
- IRCCS (Scientific Institute for Research, Hospitalization and Healthcare) Centro Neurolesi 'Bonino-Pulejo', I-98124 Messina, Italy
| | - Katia Mangano
- IRCCS (Scientific Institute for Research, Hospitalization and Healthcare) Centro Neurolesi 'Bonino-Pulejo', I-98124 Messina, Italy
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Roberto Di Marco
- Department of Medicine and Health Sciences 'Vincenzo Tiberio', University of Molise, I-86100 Campobasso, Italy
| | - Luca Falzone
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Maria Sofia Basile
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Eugenio Cavalli
- IRCCS (Scientific Institute for Research, Hospitalization and Healthcare) Centro Neurolesi 'Bonino-Pulejo', I-98124 Messina, Italy
| |
Collapse
|
24
|
Wang X, Dong Y, Wu Q, Lu T, Wang Y, Liu W, Liu C, Xu W. Analysis of circular RNA-associated competing endogenous RNA network in breast cancer. Oncol Lett 2020; 19:1619-1634. [PMID: 32002039 PMCID: PMC6960389 DOI: 10.3892/ol.2020.11247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 10/16/2019] [Indexed: 02/07/2023] Open
Abstract
As the most common type of cancer in female patients, the morbidity and mortality rates of breast cancer (BC) are high, and its incidence is gradually increasing worldwide. However, the underlying molecular and genetic mechanisms involved in the etiopathogenesis of BC remain unclear. Circular RNAs (circRNAs) are a novel type of non-coding RNAs that have been verified to serve a crucial role in tumorigenesis. However, the majority of functions and mechanisms of circRNAs remain unknown. The present study identified 47 differentially expressed circRNAs in a dataset from Gene Expression Omnibus. Using the cancer-specific circRNA database, the potential microRNA (miRNA) response elements, RNA-binding proteins and open reading frames of the candidate circRNAs were predicted. Combing the predictions of miRNAs and target mRNAs, a competing endogenous RNA network was constructed, which may serve as the theoretical basis for further research. Furthermore, the analyses conducted using Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways indicated that candidate circRNAs may serve a role in transcriptional regulation. Moreover, 20 BC tissue specimens and their paired adjacent normal tissue specimens were used to evaluate the expression levels of the screened circRNAs. Thus, the analyses of the raw microarray data conducted in the present study offer perspectives on the exploration of mechanisms associated with BC tumorigenesis with regard to the circRNA-miRNA-mRNA network.
Collapse
Affiliation(s)
- Xuekang Wang
- Department of Inspection, Medical Faculty of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Yanhan Dong
- Center for Developmental Cardiology, Institute of Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Qiong Wu
- Clinical Laboratory, Qingdao Hiser Medical Center, Qingdao, Shandong 266034, P.R. China
| | - Tong Lu
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Yuanyong Wang
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Wenchao Liu
- Clinical Laboratory Blood Transfusion Service, Qingdao Municipal Hospital, Qingdao, Shandong 266011, P.R. China
| | - Chengyu Liu
- Department of Inspection, Medical Faculty of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Wenhua Xu
- Department of Inspection, Medical Faculty of Qingdao University, Qingdao, Shandong 266003, P.R. China
| |
Collapse
|
25
|
Cavalli E, Mazzon E, Basile MS, Mammana S, Pennisi M, Fagone P, Kalfin R, Martinovic V, Ivanovic J, Andabaka M, Mesaros S, Pekmezovic T, Drulovic J, Nicoletti F, Petralia MC. In Silico and In Vivo Analysis of IL37 in Multiple Sclerosis Reveals Its Probable Homeostatic Role on the Clinical Activity, Disability, and Treatment with Fingolimod. Molecules 2019; 25:molecules25010020. [PMID: 31861585 PMCID: PMC6982851 DOI: 10.3390/molecules25010020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
We evaluated the in silico expression and circulating levels of interleukin (IL)37 in patients with different forms of multiple sclerosis (MS) and also upon treatment with different disease-modifying drugs. The combined interpretation of the resulting data strengthens and extends the current emerging concept that endogenous IL37 plays an important role in determining onset and progression of MS. The in silico analysis revealed that production of IL37 from cluster of differentiation (CD)4+ T cells from MS patients was reduced in vitro as compared to healthy controls. The analysis of the datasets also demonstrated that “higher” levels of IL37 production from PBMC entailed significant protection from MS relapses. In addition, the in vivo part of the study showed that IL37 was selectively augmented in the sera of MS patients during a relapse and that treatment with the high potency disease-modifying drug fingolimod significantly increased the frequency of patients with circulating blood levels of IL37 (6/9, 66%) as compared to patients receiving no treatment (n = 48) or platform therapy (n = 59) who had levels of IL37 below the limit of the sensitivity of the assay. This finding therefore anticipates that fingolimod may at least partially exert its beneficial effects in MS by upregulating the production of IL37.
Collapse
Affiliation(s)
- Eugenio Cavalli
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Contrada Casazza, 98124 Messina, Italy; (E.C.); (E.M.); (S.M.); (M.C.P.)
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Contrada Casazza, 98124 Messina, Italy; (E.C.); (E.M.); (S.M.); (M.C.P.)
| | - Maria Sofia Basile
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (M.S.B.); (M.P.); (P.F.)
| | - Santa Mammana
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Contrada Casazza, 98124 Messina, Italy; (E.C.); (E.M.); (S.M.); (M.C.P.)
| | - Manuela Pennisi
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (M.S.B.); (M.P.); (P.F.)
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (M.S.B.); (M.P.); (P.F.)
| | - Reni Kalfin
- Institute of Neurobiology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 23 1113 Sofia, Bulgaria;
| | - Vanja Martinovic
- Clinic of Neurology, Clinical Center of Serbia, Dr Subotica 6, 11000 Belgrade, Serbia; (V.M.); (J.I.); (M.A.); (S.M.); (T.P.); (J.D.)
| | - Jovana Ivanovic
- Clinic of Neurology, Clinical Center of Serbia, Dr Subotica 6, 11000 Belgrade, Serbia; (V.M.); (J.I.); (M.A.); (S.M.); (T.P.); (J.D.)
| | - Marko Andabaka
- Clinic of Neurology, Clinical Center of Serbia, Dr Subotica 6, 11000 Belgrade, Serbia; (V.M.); (J.I.); (M.A.); (S.M.); (T.P.); (J.D.)
| | - Sarlota Mesaros
- Clinic of Neurology, Clinical Center of Serbia, Dr Subotica 6, 11000 Belgrade, Serbia; (V.M.); (J.I.); (M.A.); (S.M.); (T.P.); (J.D.)
| | - Tatjana Pekmezovic
- Clinic of Neurology, Clinical Center of Serbia, Dr Subotica 6, 11000 Belgrade, Serbia; (V.M.); (J.I.); (M.A.); (S.M.); (T.P.); (J.D.)
| | - Jelena Drulovic
- Clinic of Neurology, Clinical Center of Serbia, Dr Subotica 6, 11000 Belgrade, Serbia; (V.M.); (J.I.); (M.A.); (S.M.); (T.P.); (J.D.)
| | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (M.S.B.); (M.P.); (P.F.)
- Correspondence: ; Tel.: +39-095-478-1270
| | - Maria Cristina Petralia
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Contrada Casazza, 98124 Messina, Italy; (E.C.); (E.M.); (S.M.); (M.C.P.)
| |
Collapse
|
26
|
Tsantoulis P, Delorenzi M, Bièche I, Vacher S, Mariani P, Cassoux N, Houy A, Stern MH, Roman-Roman S, Dietrich PY, Roth A, Cacheux W. Prospective validation in epithelial tumors of a gene expression predictor of liver metastasis derived from uveal melanoma. Sci Rep 2019; 9:17178. [PMID: 31748560 PMCID: PMC6868129 DOI: 10.1038/s41598-019-52841-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
Predicting the risk of liver metastasis can have important prognostic and therapeutic implications, given the availability of liver-directed therapy. Uveal melanoma has a striking predisposition for liver metastasis despite the absence of anatomical proximity. Understanding its biology may uncover factors promoting liver metastasis in other malignancies. We quantified gene expression by RNAseq in 76 uveal melanomas and combined with public data in a meta-analysis of 196 patients. The meta-analysis of uveal melanoma gene expression identified 63 genes which remained prognostic after adjustment for chromosome 3 status. Two genes, PTP4A3 and JPH1, were selected by L1-penalized regression and combined in a prognostic score. The score predicted liver-specific relapse in a public pan-cancer dataset and in two public colorectal cancer datasets. The score varied between colorectal consensus molecular subtypes (CMS), as did the risk of liver relapse, which was lowest in CMS1. Additional prospective validation was done by real-time PCR in 463 breast cancer patients. The score was significantly correlated with liver relapse in hormone receptor positive tumors. In conclusion, the expression of PTP4A3 and JPH1 correlates with risk of liver metastasis in colorectal cancer and breast cancer. The underlying biological mechanism is an interesting area for further research.
Collapse
Affiliation(s)
- Petros Tsantoulis
- Hôpitaux Universitaires de Genève, Service d'Oncologie, Geneva, Switzerland. .,University of Geneva, Geneva, Switzerland. .,SIB Swiss Institute of Bioinformatics, Bioinformatics Core Facility, Lausanne, Switzerland.
| | - Mauro Delorenzi
- SIB Swiss Institute of Bioinformatics, Bioinformatics Core Facility, Lausanne, Switzerland.,University Lausanne, Department of Fundamental Oncology, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, Epalinges, Switzerland
| | - Ivan Bièche
- Institut Curie, Département de génétique, Paris, France
| | - Sophie Vacher
- Institut Curie, Département de génétique, Paris, France
| | | | | | - Alexandre Houy
- Institut Curie, Département de génétique, Paris, France.,Institut Curie, PSL Research University, INSERM U830, Paris, France
| | - Marc-Henri Stern
- Institut Curie, Département de génétique, Paris, France.,Institut Curie, PSL Research University, INSERM U830, Paris, France
| | - Sergio Roman-Roman
- Institut Curie, PSL Research University, Translational Research Department, Paris, France
| | - Pierre-Yves Dietrich
- Hôpitaux Universitaires de Genève, Service d'Oncologie, Geneva, Switzerland.,University of Geneva, Geneva, Switzerland
| | - Arnaud Roth
- Hôpitaux Universitaires de Genève, Service d'Oncologie, Geneva, Switzerland.,University of Geneva, Geneva, Switzerland
| | - Wulfran Cacheux
- Hôpitaux Universitaires de Genève, Service d'Oncologie, Geneva, Switzerland.,Institut Curie, Département de génétique, Paris, France.,Hôpital Privé - Pays de Savoie, Oncology department, Annemasse, France
| |
Collapse
|
27
|
Transcriptomic Analysis Reveals Involvement of the Macrophage Migration Inhibitory Factor Gene Network in Duchenne Muscular Dystrophy. Genes (Basel) 2019; 10:genes10110939. [PMID: 31752120 PMCID: PMC6896047 DOI: 10.3390/genes10110939] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/11/2019] [Accepted: 11/15/2019] [Indexed: 01/04/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a progressive hereditary muscular disease with X-linked recessive inheritance, that leads patients to premature death. The loss of dystrophin determines membrane instability, causing cell damage and inflammatory response. Macrophage migration inhibitory factor (MIF) is a cytokine that exerts pleiotropic properties and is implicated in the pathogenesis of a variety of diseases. Recently, converging data from independent studies have pointed to a possible role of MIF in dystrophic muscle disorders, including DMD. In the present study, we have investigated the modulation of MIF and MIF-related genes in degenerative muscle disorders, by making use of publicly available whole-genome expression datasets. We show here a significant enrichment of MIF and related genes in muscle samples from DMD patients, as well as from patients suffering from Becker’s disease and limb-girdle muscular dystrophy type 2B. On the other hand, transcriptomic analysis of in vitro differentiated myotubes from healthy controls and DMD patients revealed no significant alteration in the expression levels of MIF-related genes. Finally, by analyzing DMD samples as a time series, we show that the modulation of the genes belonging to the MIF network is an early event in the DMD muscle and does not change with the increasing age of the patients, Overall, our analysis suggests that MIF may play a role in vivo during muscle degeneration, likely promoting inflammation and local microenvironment reaction.
Collapse
|
28
|
Basile MS, Mazzon E, Fagone P, Longo A, Russo A, Fallico M, Bonfiglio V, Nicoletti F, Avitabile T, Reibaldi M. Immunobiology of Uveal Melanoma: State of the Art and Therapeutic Targets. Front Oncol 2019; 9:1145. [PMID: 31750244 PMCID: PMC6848265 DOI: 10.3389/fonc.2019.01145] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 10/15/2019] [Indexed: 12/16/2022] Open
Abstract
Uveal Melanoma (UM) represents the most common primary intraocular malignant tumor in adults. Although it originates from melanocytes as cutaneous melanoma, it shows significant clinical and biological differences with the latter, including high resistance to immune therapy. Indeed, UM can evade immune surveillance via multiple mechanisms, such as the expression of inhibitory checkpoints (e.g., PD-L1, CD47, CD200) and the production of IDO-1 and soluble FasL, among others. More in-depth understanding of these mechanisms will suggest potential targets for the design of novel and more effective management strategies for UM patients.
Collapse
Affiliation(s)
- Maria Sofia Basile
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi Bonino Pulejo, C.da Casazza, Messina, Italy
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Antonio Longo
- Department of Ophthalmology, University of Catania, Catania, Italy
| | - Andrea Russo
- Department of Ophthalmology, University of Catania, Catania, Italy
| | - Matteo Fallico
- Department of Ophthalmology, University of Catania, Catania, Italy
| | | | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | | | - Michele Reibaldi
- Department of Ophthalmology, University of Catania, Catania, Italy
| |
Collapse
|
29
|
Cavalli E, Mazzon E, Mammana S, Basile MS, Lombardo SD, Mangano K, Bramanti P, Nicoletti F, Fagone P, Petralia MC. Overexpression of Macrophage Migration Inhibitory Factor and Its Homologue D-Dopachrome Tautomerase as Negative Prognostic Factor in Neuroblastoma. Brain Sci 2019; 9:brainsci9100284. [PMID: 31635049 PMCID: PMC6826588 DOI: 10.3390/brainsci9100284] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/01/2019] [Accepted: 10/18/2019] [Indexed: 01/09/2023] Open
Abstract
Neuroblastoma (NB) represents one of the most frequent pediatric solid tumors. Macrophage migration inhibitory factor (MIF) is a cytokine exerting multiple biological functions. More recently, a second member of the MIF family of cytokine has been identified, the D-dopachrome tautomerase (DDT), that exerts several overlapping functions with MIF. Growing evidence suggests a key role for MIF and DDT in the development of cancer. The aim of this study is to characterize the prognostic value of MIF and DDT in NB. We show that higher expression levels of MIF and DDT in Stage 4 NB samples are associated with a poorer prognosis, independently of the presence of MYCN amplification. Moreover, higher levels of MIF are mostly enriched by Th1 cells, while lower levels of MIF are associated with an increased proportion of B cells, Cytotoxic T cells, Dendritic cells and Natural Killer T cells. We also show that treatment with the histone deacetylase (HDAC) inhibitor, vorinostat, of the NB cell line, SH-SY5Y, determines a significant reduction in the expression of both MIF and DDT. Finally, MIF and DDT inhibition by short interfering RNA is able to revert vincristine sensitivity in vitro. Overall, our data suggest that MIF exert pro-tumorigenic properties in NB, likely by dampening antigen presentation and cytotoxic immune responses, and we propose the HDAC inhibitors as a potential therapeutic strategy for NB patients.
Collapse
Affiliation(s)
- Eugenio Cavalli
- IRCCS Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124 Messina, Italy.
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124 Messina, Italy.
| | - Santa Mammana
- IRCCS Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124 Messina, Italy.
| | - Maria Sofia Basile
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy.
| | - Salvo Danilo Lombardo
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy.
| | - Katia Mangano
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy.
| | - Placido Bramanti
- IRCCS Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124 Messina, Italy.
| | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy.
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy.
| | | |
Collapse
|
30
|
Lombardo SD, Mazzon E, Basile MS, Campo G, Corsico F, Presti M, Bramanti P, Mangano K, Petralia MC, Nicoletti F, Fagone P. Modulation of Tetraspanin 32 (TSPAN32) Expression in T Cell-Mediated Immune Responses and in Multiple Sclerosis. Int J Mol Sci 2019; 20:ijms20184323. [PMID: 31487788 PMCID: PMC6770290 DOI: 10.3390/ijms20184323] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/30/2019] [Indexed: 01/25/2023] Open
Abstract
Tetraspanins are a conserved family of proteins involved in a number of biological processes including, cell–cell interactions, fertility, cancer metastasis and immune responses. It has previously been shown that TSPAN32 knockout mice have normal hemopoiesis and B-cell responses, but hyperproliferative T cells. Here, we show that TSPAN32 is expressed at higher levels in the lymphoid lineage as compared to myeloid cells. In vitro activation of T helper cells via anti-CD3/CD28 is associated with a significant downregulation of TSPAN32. Interestingly, engagement of CD3 is sufficient to modulate TSPAN32 expression, and its effect is potentiated by costimulation with anti-CD28, but not anti-CTLA4, -ICOS nor -PD1. Accordingly, we measured the transcriptomic levels of TSPAN32 in polarized T cells under Th1 and Th2 conditions and TSPAN32 resulted significantly reduced as compared with unstimulated cells. On the other hand, in Treg cells, TSPAN32 underwent minor changes upon activation. The in vitro data were finally translated into the context of multiple sclerosis (MS). Encephalitogenic T cells from Myelin Oligodendrocyte Glycoprotein (MOG)-Induced Experimental Autoimmune Encephalomyelitis (EAE) mice showed significantly lower levels of TSPAN32 and increased levels of CD9, CD53, CD82 and CD151. Similarly, in vitro-activated circulating CD4 T cells from MS patients showed lower levels of TSPAN32 as compared with cells from healthy donors. Overall, these data suggest an immunoregulatory role for TSPAN32 in T helper immune response and may represent a target of future immunoregulatory therapies for T cell-mediated autoimmune diseases.
Collapse
Affiliation(s)
- Salvo Danilo Lombardo
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124 Messina, Italy
| | - Maria Sofia Basile
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Giorgia Campo
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Federica Corsico
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Mario Presti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Placido Bramanti
- IRCCS Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124 Messina, Italy
| | - Katia Mangano
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | | | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy.
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| |
Collapse
|
31
|
Lombardo SD, Presti M, Mangano K, Petralia MC, Basile MS, Libra M, Candido S, Fagone P, Mazzon E, Nicoletti F, Bramanti A. Prediction of PD-L1 Expression in Neuroblastoma via Computational Modeling. Brain Sci 2019; 9:E221. [PMID: 31480495 PMCID: PMC6770763 DOI: 10.3390/brainsci9090221] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/26/2019] [Accepted: 08/31/2019] [Indexed: 12/21/2022] Open
Abstract
Immunotherapy is a promising new therapeutic approach for neuroblastoma (NBM): an anti-GD2 vaccine combined with orally administered soluble beta-glucan is undergoing a phase II clinical trial and nivolumab and ipilimumab are being tested in recurrent and refractory tumors. Unfortunately, predictive biomarkers of response to immunotherapy are currently not available for NBM patients. The aim of this study was to create a computational network model simulating the different intracellular pathways involved in NBM, in order to predict how the tumor phenotype may be influenced to increase the sensitivity to anti-programmed cell death-ligand-1 (PD-L1)/programmed cell death-1 (PD-1) immunotherapy. The model runs on COPASI software. In order to determine the influence of intracellular signaling pathways on the expression of PD-L1 in NBM, we first developed an integrated network of protein kinase cascades. Michaelis-Menten kinetics were associated to each reaction in order to tailor the different enzymes kinetics, creating a system of ordinary differential equations (ODEs). The data of this study offers a first tool to be considered in the therapeutic management of the NBM patient undergoing immunotherapeutic treatment.
Collapse
Affiliation(s)
- Salvo Danilo Lombardo
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123- Catania, Italy
| | - Mario Presti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123- Catania, Italy
| | - Katia Mangano
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123- Catania, Italy
| | - Maria Cristina Petralia
- IRCCS (Istituti di Ricovero e Cura a Carattere Scientifico) Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124- Messina, Italy
| | - Maria Sofia Basile
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123- Catania, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123- Catania, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123- Catania, Italy
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123- Catania, Italy.
| | - Emanuela Mazzon
- IRCCS (Istituti di Ricovero e Cura a Carattere Scientifico) Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124- Messina, Italy
| | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123- Catania, Italy
| | - Alessia Bramanti
- IRCCS (Istituti di Ricovero e Cura a Carattere Scientifico) Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124- Messina, Italy
| |
Collapse
|
32
|
Keenan AB, Wojciechowicz ML, Wang Z, Jagodnik KM, Jenkins SL, Lachmann A, Ma'ayan A. Connectivity Mapping: Methods and Applications. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-072018-021211] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Connectivity mapping resources consist of signatures representing changes in cellular state following systematic small-molecule, disease, gene, or other form of perturbations. Such resources enable the characterization of signatures from novel perturbations based on similarity; provide a global view of the space of many themed perturbations; and allow the ability to predict cellular, tissue, and organismal phenotypes for perturbagens. A signature search engine enables hypothesis generation by finding connections between query signatures and the database of signatures. This framework has been used to identify connections between small molecules and their targets, to discover cell-specific responses to perturbations and ways to reverse disease expression states with small molecules, and to predict small-molecule mimickers for existing drugs. This review provides a historical perspective and the current state of connectivity mapping resources with a focus on both methodology and community implementations.
Collapse
Affiliation(s)
- Alexandra B. Keenan
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan L. Wojciechowicz
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zichen Wang
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kathleen M. Jagodnik
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sherry L. Jenkins
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
33
|
Lombardo SD, Mazzon E, Basile MS, Cavalli E, Bramanti P, Nania R, Fagone P, Nicoletti F, Petralia MC. Upregulation of IL-1 Receptor Antagonist in a Mouse Model of Migraine. Brain Sci 2019; 9:E172. [PMID: 31331109 PMCID: PMC6680509 DOI: 10.3390/brainsci9070172] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 07/18/2019] [Indexed: 02/07/2023] Open
Abstract
Migraine is a disorder characterized by attacks of monolateral headaches, often accompanied by nausea, vomiting, and photophobia. Around 30% of patients also report aura symptoms. The cause of the aura is believed to be related to the cortical spreading depression (CSD), a wave of neuronal and glial depolarization originating in the occipital cortex, followed by temporary neuronal silencing. During a migraine attack, increased expression of inflammatory mediators, along with a decrease in the expression of anti-inflammatory genes, have been observed. The aim of this study was to evaluate the expression of inflammatory genes, in particular that of IL-1 receptor antagonist (IL-1RN), following CSD in a mouse model of familial hemiplegic migraine type 1 (FHM-1). We show here that the expression of IL-1RN was upregulated after the CSD, suggesting a possible attempt to modulate the inflammatory response. This study allows researchers to better understand the development of the disease and aids in the search for new therapeutic strategies in migraine.
Collapse
Affiliation(s)
- Salvo Danilo Lombardo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi Bonino Pulejo, Strada Statale 113, C.da Casazza, 98124 Messina, Italy
| | - Maria Sofia Basile
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy
| | - Eugenio Cavalli
- IRCCS Centro Neurolesi Bonino Pulejo, Strada Statale 113, C.da Casazza, 98124 Messina, Italy
| | - Placido Bramanti
- IRCCS Centro Neurolesi Bonino Pulejo, Strada Statale 113, C.da Casazza, 98124 Messina, Italy
| | - Riccardo Nania
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy
| | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy.
| | - Maria Cristina Petralia
- IRCCS Centro Neurolesi Bonino Pulejo, Strada Statale 113, C.da Casazza, 98124 Messina, Italy
| |
Collapse
|
34
|
Petralia MC, Mazzon E, Fagone P, Falzone L, Bramanti P, Nicoletti F, Basile MS. Retrospective follow-up analysis of the transcriptomic patterns of cytokines, cytokine receptors and chemokines at preconception and during pregnancy, in women with post-partum depression. Exp Ther Med 2019; 18:2055-2062. [PMID: 31410161 PMCID: PMC6676209 DOI: 10.3892/etm.2019.7774] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 07/08/2019] [Indexed: 12/29/2022] Open
Abstract
Post-partum depression (PPD) occurs in approximately 20% of women usually early following child delivery. PPD represents an important unmet medical need as it is frequently underdiagnosed and, as the neurobiology of the disease is limitedly known, no pathogenic-tailored approach is available and only symptomatic medications are used. In the present study, we carried out a DNA microarray analysis to evaluate the fluctuation of cytokines, cytokine receptors and chemokines during the preconception period, the 1st and 3th trimester of pregnancy and the early post-partum period. The data demonstrated that, as compared to always-depressed patients and euthymic controls, women who developed PPD exhibited significant fluctuations in the levels of different cytokines and cytokine receptors, primarily related to tumor necrosis factor (TNF) and interleukin (IL)18. These data emphasize the role of the immune system in PPD. However, additional studies aimed at evaluating if and how these functional modifications of the immune system during pregnancy are related to the development of PPD warranted to confirm our findings.
Collapse
Affiliation(s)
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi 'Bonino-Pulejo', I-98124 Messina, Italy
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Luca Falzone
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | | | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Maria Sofia Basile
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| |
Collapse
|
35
|
Characterization of the Pathophysiological Role of CD47 in Uveal Melanoma. Molecules 2019; 24:molecules24132450. [PMID: 31277366 PMCID: PMC6651482 DOI: 10.3390/molecules24132450] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/28/2019] [Accepted: 07/03/2019] [Indexed: 02/08/2023] Open
Abstract
Uveal melanoma (UM) represents the most frequent primary intraocular tumor, however, limited therapeutic options are still available. We have previously shown that cluster of differentiation 47 (CD47) is significantly upregulated in UM cells following inflammatory stimuli and that it represents a predictor of disease progression. Here, we aimed to better characterize the pathophysiological role of CD47 in UM. We show that CD47 is not modulated at different cancer stages, although patients with the lowest expression of CD47 show significant better progression-free survival, after correcting for the presence of BAP1, GNAQ, and GNA11 mutations. By stratifying patients based on the expression of CD47 in the tumor, we observed that patients with high levels of CD47 have a significant increase in immune score as compared to patients with low levels of CD47. In particular, deconvolution analysis of infiltrating immune cell populations revealed that a significantly higher number of CD4+ and CD8+ T cells can be found in patients with high CD47 levels, with the most enriched populations being the Th2, Treg, and CD8+ Tcm cells. We also show that a large number of transcripts are significantly modulated between the groups of patients with high and low levels of CD47, with a significant enrichment of interferon IFN-alpha regulated genes. The results from this study may propel the development of anti-CD47 therapies for UM patients.
Collapse
|
36
|
Uveal melanoma: physiopathology and new in situ-specific therapies. Cancer Chemother Pharmacol 2019; 84:15-32. [DOI: 10.1007/s00280-019-03860-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/02/2019] [Indexed: 12/12/2022]
|
37
|
Bowlt Blacklock KL, Birand Z, Selmic LE, Nelissen P, Murphy S, Blackwood L, Bass J, McKay J, Fox R, Beaver S, Starkey M. Genome-wide analysis of canine oral malignant melanoma metastasis-associated gene expression. Sci Rep 2019; 9:6511. [PMID: 31019223 PMCID: PMC6482147 DOI: 10.1038/s41598-019-42839-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 04/04/2019] [Indexed: 12/12/2022] Open
Abstract
Oral malignant melanoma (OMM) is the most common canine melanocytic neoplasm. Overlap between the somatic mutation profiles of canine OMM and human mucosal melanomas suggest a shared UV-independent molecular aetiology. In common with human mucosal melanomas, most canine OMM metastasise. There is no reliable means of predicting canine OMM metastasis, and systemic therapies for metastatic disease are largely palliative. Herein, we employed exon microarrays for comparative expression profiling of FFPE biopsies of 18 primary canine OMM that metastasised and 10 primary OMM that did not metastasise. Genes displaying metastasis-associated expression may be targets for anti-metastasis treatments, and biomarkers of OMM metastasis. Reduced expression of CXCL12 in the metastasising OMMs implies that the CXCR4/CXCL12 axis may be involved in OMM metastasis. Increased expression of APOBEC3A in the metastasising OMMs may indicate APOBEC3A-induced double-strand DNA breaks and pro-metastatic hypermutation. DNA double strand breakage triggers the DNA damage response network and two Fanconi anaemia DNA repair pathway members showed elevated expression in the metastasising OMMs. Cross-validation was employed to test a Linear Discriminant Analysis classifier based upon the RT-qPCR-measured expression levels of CXCL12, APOBEC3A and RPL29. Classification accuracies of 94% (metastasising OMMs) and 86% (non-metastasising OMMs) were estimated.
Collapse
Affiliation(s)
| | - Z Birand
- Animal Health Trust, Newmarket, Suffolk, UK
| | - L E Selmic
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, USA
| | - P Nelissen
- Dick White Referrals, Newmarket, Suffolk, UK
| | - S Murphy
- Animal Health Trust, Newmarket, Suffolk, UK
- The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - L Blackwood
- Institute of Veterinary Science, University of Liverpool, Liverpool, UK
| | - J Bass
- Animal Health Trust, Newmarket, Suffolk, UK
- Finn Pathologists, Harleston, UK
| | - J McKay
- IDEXX Laboratories, Ltd, Wetherby, UK
| | - R Fox
- Finn Pathologists, Harleston, UK
| | - S Beaver
- Nationwide Laboratory Services, Poulton-le-Fylde, UK
| | - M Starkey
- Animal Health Trust, Newmarket, Suffolk, UK.
| |
Collapse
|
38
|
Differential modulation and prognostic values of immune-escape genes in uveal melanoma. PLoS One 2019; 14:e0210276. [PMID: 30653520 PMCID: PMC6336329 DOI: 10.1371/journal.pone.0210276] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/19/2018] [Indexed: 02/07/2023] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular cancer in adults. In the present study, we aimed to characterize the immunological features of primary UM cancer and to provide an association with prognostic markers and outcome. Also, we assessed the influence of the microenvironment on the expression of inhibitory immune checkpoints in UM. Genes of interest included MHC Class I and Class II molecules, as well as inhibitory immune-checkpoints, i.e. PDL1, PDL2, B7-H3, B7-H4, TBFRSF6B, CD47, CD155, GAL9, HVEM and CD200. We observed significant lower levels of MHC genes in UM cells as compared to normal uveal melanocytes. Unexpectedly however, the expression levels of most of the analyzed inhibitory immune-checkpoint genes were not different in cancer cells as compared to normal melanocytes, with the exception of CD200 and HVEM, that resulted significantly reduced. On the other hand, PDL1 inversely correlated with OS, PFS and thickness of the tumor. Also, PDL1, along with PDL2, expression significantly increased under inflammatory conditions. Finally, for the first time, we propose a possible role for CD47 in the immune evasive properties of UM. We show here that CD47 is significantly upregulated by UM cells following inflammatory stimuli and that it represents a good independent predictor of disease progression. The results from this study may propel advances in the development of immune-based therapies for UM patients.
Collapse
|
39
|
Longhitano L, Castracani CC, Tibullo D, Avola R, Viola M, Russo G, Prezzavento O, Marrazzo A, Amata E, Reibaldi M, Longo A, Russo A, Parrinello NL, Volti GL. Sigma-1 and Sigma-2 receptor ligands induce apoptosis and autophagy but have opposite effect on cell proliferation in uveal melanoma. Oncotarget 2017; 8:91099-91111. [PMID: 29207628 PMCID: PMC5710909 DOI: 10.18632/oncotarget.19556] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/13/2017] [Indexed: 01/30/2023] Open
Abstract
Uveal melanoma is the most common primary intraocular tumor in adults, with about 1200-1500 new cases occurring per year in the United States. Metastasis is a frequent occurrence in uveal melanoma, and outcomes are poor once distant spread occurs and no clinically significant chemotherapeutic protocol is so far available. The aim of the present study was to test the effect of various σ1 and σ2 receptor ligands as a possible pharmacological strategy for this rare tumor. Human uveal melanoma cells (92.1) were treated with various concentrations of different σ2 ligands (haloperidol and haloperidol metabolite II) and σ1 ligand ((+)-pentazocine) at various concentrations (1, 10 and 25 μM) and time points (0, 4 h, 8 h, 24 h and 48 h). Cell proliferation and migration were evaluated respectively by continuous cell monitoring by xCELLigence analysis, clonogenic assay and wound healing. Apoptosis and autophagy were also measured by cytofluorimetric and microscopy analysis. Our results showed that σ2 receptor ligands significantly reduced cell proliferation whereas (+)-pentazocine exhibited opposite results. All tested ligands showed significant decrease in cell migration. Interestingly, both σ1 and σ2 receptor ligands showed significant increase of autophagy and apoptosis at all concentrations. Taken all together these results suggest that sigma receptors mediates opposite biological effects but they also share common pharmacological effect on apoptosis and autophagy in uveal melanoma. In conclusion, these data provide the first evidence that sigma receptors may represent a "druggable" target to develop new chemotherapic agent for uveal melanoma.
Collapse
Affiliation(s)
- Lucia Longhitano
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | | | - Daniele Tibullo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Roberto Avola
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Maria Viola
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Giuliano Russo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | | | | | - Emanuele Amata
- Department of Drug Sciences, University of Catania, Catania, Italy
| | - Michele Reibaldi
- Department of Ophthalmology, University of Catania, Catania, Italy
| | - Antonio Longo
- Department of Ophthalmology, University of Catania, Catania, Italy
| | - Andrea Russo
- Department of Ophthalmology, University of Catania, Catania, Italy
| | - Nunziatina Laura Parrinello
- Regional Reference Center for Rare Diseases, Clinical Division of Hematology and Transplantation, PO Ferrarotto Hospital, Azienda Ospedaliera-Universitaria Policlinico-Vittorio Emanuele, Via Citelli, Catania, Italy
| | - Giovanni Li Volti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- Euromediterranean Institute of Science and Technology, Palermo, Italy
| |
Collapse
|