1
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Barbosa LC, Machado GC, Heringer M, Ferrer VP. Identification of established and novel extracellular matrix components in glioblastoma as targets for angiogenesis and prognosis. Neurogenetics 2024; 25:249-262. [PMID: 38775886 DOI: 10.1007/s10048-024-00763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/10/2024] [Indexed: 07/16/2024]
Abstract
Glioblastomas (GBM) are aggressive tumors known for their heterogeneity, rapid proliferation, treatment resistance, and extensive vasculature. Angiogenesis, the formation of new vessels, involves endothelial cell (EC) migration and proliferation. Various extracellular matrix (ECM) molecules regulate EC survival, migration, and proliferation. Culturing human brain EC (HBMEC) on GBM-derived ECM revealed a decrease in EC numbers compared to controls. Through in silico analysis, we explored ECM gene expression differences between GBM and brain normal glia cells and the impact of GBM microenvironment on EC ECM transcripts. ECM molecules such as collagen alpha chains (COL4A1, COL4A2, p < 0.0001); laminin alpha (LAMA4), beta (LAMB2), and gamma (LAMC1) chains (p < 0.0005); neurocan (NCAN), brevican (BCAN) and versican (VCAN) (p < 0.0005); hyaluronan synthase (HAS) 2 and metalloprotease (MMP) 2 (p < 0.005); MMP inhibitors (TIMP1-4, p < 0.0005), transforming growth factor beta-1 (TGFB1) and integrin alpha (ITGA3/5) (p < 0.05) and beta (ITGB1, p < 0.0005) chains showed increased expression in GBM. Additionally, GBM-influenced EC exhibited elevated expression of COL5A3, COL6A1, COL22A1 and COL27A1 (p < 0.01); LAMA1, LAMB1 (p < 0.001); fibulins (FBLN1/2, p < 0.01); MMP9, HAS1, ITGA3, TGFB1, and wingless-related integration site 9B (WNT9B) (p < 0.01) compared to normal EC. Some of these molecules: COL5A1/3, COL6A1, COL22/27A1, FBLN1/2, ITGA3/5, ITGB1 and LAMA1/B1 (p < 0.01); NCAN, HAS1, MMP2/9, TIMP1/2 and TGFB1 (p < 0.05) correlated with GBM patient survival. In conclusion, this study identified both established and novel ECM molecules regulating GBM angiogenesis, suggesting NCAN and COL27A1 are new potential prognostic biomarkers for GBM.
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Affiliation(s)
- Lucas Cunha Barbosa
- Graduation Program of Pathological Anatomy, Faculty of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Cellular and Molecular Biology of Tumors, Department of Cellular and Molecular Biology, Institute of Biology, Fluminense Federal University, Niteroi, Brazil
| | - Gabriel Cardoso Machado
- Graduation Program of Pathological Anatomy, Faculty of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Cellular and Molecular Biology of Tumors, Department of Cellular and Molecular Biology, Institute of Biology, Fluminense Federal University, Niteroi, Brazil
| | - Manoela Heringer
- Brain's Biomedicine Lab, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Brazil
| | - Valéria Pereira Ferrer
- Graduation Program of Pathological Anatomy, Faculty of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
- Laboratory of Cellular and Molecular Biology of Tumors, Department of Cellular and Molecular Biology, Institute of Biology, Fluminense Federal University, Niteroi, Brazil.
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Becker AP, Becker V, McElroy J, Webb A, Han C, Guo Y, Bell EH, Fleming J, Popp I, Staszewski O, Prinz M, Otero JJ, Haque SJ, Grosu AL, Chakravarti A. Proteomic Analysis of Spatial Heterogeneity Identifies HMGB2 as Putative Biomarker of Tumor Progression in Adult-Type Diffuse Astrocytomas. Cancers (Basel) 2024; 16:1516. [PMID: 38672598 PMCID: PMC11049315 DOI: 10.3390/cancers16081516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Although grading is defined by the highest histological grade observed in a glioma, most high-grade gliomas retain areas with histology reminiscent of their low-grade counterparts. We sought to achieve the following: (i) identify proteins and molecular pathways involved in glioma evolution; and (ii) validate the high mobility group protein B2 (HMGB2) as a key player in tumor progression and as a prognostic/predictive biomarker for diffuse astrocytomas. We performed liquid chromatography tandem mass spectrometry (LC-MS/MS) in multiple areas of adult-type astrocytomas and validated our finding in multiplatform-omics studies and high-throughput IHC analysis. LC-MS/MSdetected proteomic signatures characterizing glioma evolution towards higher grades associated with, but not completely dependent, on IDH status. Spatial heterogeneity of diffuse astrocytomas was associated with dysregulation of specific molecular pathways, and HMGB2 was identified as a putative driver of tumor progression, and an early marker of worse overall survival in grades 2 and 3 diffuse gliomas, at least in part regulated by DNA methylation. In grade 4 astrocytomas, HMGB2 expression was strongly associated with proliferative activity and microvascular proliferation. Grounded in proteomic findings, our results showed that HMGB2 expression assessed by IHC detected early signs of tumor progression in grades 2 and 3 astrocytomas, as well as identified GBMs that had a better response to the standard chemoradiation with temozolomide.
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Affiliation(s)
- Aline P. Becker
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
| | - Valesio Becker
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
| | - Joseph McElroy
- Center for Biostatistics, The Ohio State University, Columbus, OH 43210, USA;
| | - Amy Webb
- School of Biomedical Science-Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA;
| | - Chunhua Han
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
| | - Yingshi Guo
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
| | - Erica H. Bell
- Department of Neurology, The Ohio State University, Columbus, OH 43210, USA;
| | - Jessica Fleming
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
| | - Ilinca Popp
- Department of Radiation Oncology, University of Freiburg, 79110 Freiburg, Germany; (I.P.); (A.-L.G.)
| | - Ori Staszewski
- Institute of Neuropathology, Medical Faculty of the Saarland University, 66421 Homburg, Germany;
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany;
- Signalling Research Centres BIOSS & CIBSS, University of Freiburg, 79098 Freiburg, Germany
| | - Jose J. Otero
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA;
| | - Saikh Jaharul Haque
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
| | - Anca-Ligia Grosu
- Department of Radiation Oncology, University of Freiburg, 79110 Freiburg, Germany; (I.P.); (A.-L.G.)
| | - Arnab Chakravarti
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA; (A.P.B.); (V.B.); (C.H.); (Y.G.); (J.F.); (S.J.H.)
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Zolotovskaia M, Kovalenko M, Pugacheva P, Tkachev V, Simonov A, Sorokin M, Seryakov A, Garazha A, Gaifullin N, Sekacheva M, Zakharova G, Buzdin AA. Algorithmically Reconstructed Molecular Pathways as the New Generation of Prognostic Molecular Biomarkers in Human Solid Cancers. Proteomes 2023; 11:26. [PMID: 37755705 PMCID: PMC10535530 DOI: 10.3390/proteomes11030026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/28/2023] Open
Abstract
Individual gene expression and molecular pathway activation profiles were shown to be effective biomarkers in many cancers. Here, we used the human interactome model to algorithmically build 7470 molecular pathways centered around individual gene products. We assessed their associations with tumor type and survival in comparison with the previous generation of molecular pathway biomarkers (3022 "classical" pathways) and with the RNA transcripts or proteomic profiles of individual genes, for 8141 and 1117 samples, respectively. For all analytes in RNA and proteomic data, respectively, we found a total of 7441 and 7343 potential biomarker associations for gene-centric pathways, 3020 and 2950 for classical pathways, and 24,349 and 6742 for individual genes. Overall, the percentage of RNA biomarkers was statistically significantly higher for both types of pathways than for individual genes (p < 0.05). In turn, both types of pathways showed comparable performance. The percentage of cancer-type-specific biomarkers was comparable between proteomic and transcriptomic levels, but the proportion of survival biomarkers was dramatically lower for proteomic data. Thus, we conclude that pathway activation level is the advanced type of biomarker for RNA and proteomic data, and momentary algorithmic computer building of pathways is a new credible alternative to time-consuming hypothesis-driven manual pathway curation and reconstruction.
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Affiliation(s)
- Marianna Zolotovskaia
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- Omicsway Corp., Walnut, CA 91789, USA
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, 119048 Moscow, Russia
| | - Maks Kovalenko
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| | - Polina Pugacheva
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| | | | - Alexander Simonov
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- Omicsway Corp., Walnut, CA 91789, USA
| | - Maxim Sorokin
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, 119048 Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), 1200 Brussels, Belgium
| | | | | | - Nurshat Gaifullin
- Department of Pathology, Faculty of Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Marina Sekacheva
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, 119048 Moscow, Russia
| | - Galina Zakharova
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, 119048 Moscow, Russia
| | - Anton A. Buzdin
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), 1200 Brussels, Belgium
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119048 Moscow, Russia
- Laboratory of Systems Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
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Ahmad A, Imran M, Ahsan H. Biomarkers as Biomedical Bioindicators: Approaches and Techniques for the Detection, Analysis, and Validation of Novel Biomarkers of Diseases. Pharmaceutics 2023; 15:1630. [PMID: 37376078 DOI: 10.3390/pharmaceutics15061630] [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: 03/24/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
A biomarker is any measurable biological moiety that can be assessed and measured as a potential index of either normal or abnormal pathophysiology or pharmacological responses to some treatment regimen. Every tissue in the body has a distinct biomolecular make-up, which is known as its biomarkers, which possess particular features, viz., the levels or activities (the ability of a gene or protein to carry out a particular body function) of a gene, protein, or other biomolecules. A biomarker refers to some feature that can be objectively quantified by various biochemical samples and evaluates the exposure of an organism to normal or pathological procedures or their response to some drug interventions. An in-depth and comprehensive realization of the significance of these biomarkers becomes quite important for the efficient diagnosis of diseases and for providing the appropriate directions in case of multiple drug choices being presently available, which can benefit any patient. Presently, advancements in omics technologies have opened up new possibilities to obtain novel biomarkers of different types, employing genomic strategies, epigenetics, metabolomics, transcriptomics, lipid-based analysis, protein studies, etc. Particular biomarkers for specific diseases, their prognostic capabilities, and responses to therapeutic paradigms have been applied for screening of various normal healthy, as well as diseased, tissue or serum samples, and act as appreciable tools in pharmacology and therapeutics, etc. In this review, we have summarized various biomarker types, their classification, and monitoring and detection methods and strategies. Various analytical techniques and approaches of biomarkers have also been described along with various clinically applicable biomarker sensing techniques which have been developed in the recent past. A section has also been dedicated to the latest trends in the formulation and designing of nanotechnology-based biomarker sensing and detection developments in this field.
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Affiliation(s)
- Anas Ahmad
- Julia McFarlane Diabetes Research Centre (JMDRC), Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Hotchkiss Brain Institute, Cumming School of Medicine, Foothills Medical Centre, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mohammad Imran
- Therapeutics Research Group, Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane 4102, Australia
| | - Haseeb Ahsan
- Department of Biochemistry, Faculty of Dentistry, Jamia Millia Islamia, New Delhi 110025, India
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Editorial to Special Issue "Glioblastoma: Recapitulating the Key Breakthroughs and Future Perspective". Int J Mol Sci 2023; 24:ijms24032548. [PMID: 36768870 PMCID: PMC9917091 DOI: 10.3390/ijms24032548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
Glioblastoma (GBM) remains the most common and aggressive malignant primary brain tumor [...].
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Zakharova G, Efimov V, Raevskiy M, Rumiantsev P, Gudkov A, Belogurova-Ovchinnikova O, Sorokin M, Buzdin A. Reclassification of TCGA Diffuse Glioma Profiles Linked to Transcriptomic, Epigenetic, Genomic and Clinical Data, According to the 2021 WHO CNS Tumor Classification. Int J Mol Sci 2022; 24:ijms24010157. [PMID: 36613601 PMCID: PMC9820617 DOI: 10.3390/ijms24010157] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/25/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
In 2021, the fifth edition of the WHO classification of tumors of the central nervous system (WHO CNS5) was published. Molecular features of tumors were directly incorporated into the diagnostic decision tree, thus affecting both the typing and staging of the tumor. It has changed the traditional approach, based solely on histopathological classification. The Cancer Genome Atlas project (TCGA) is one of the main sources of molecular information about gliomas, including clinically annotated transcriptomic and genomic profiles. Although TCGA itself has played a pivotal role in developing the WHO CNS5 classification, its proprietary databases still retain outdated diagnoses which frequently appear incorrect and misleading according to the WHO CNS5 standards. We aimed to define the up-to-date annotations for gliomas from TCGA's database that other scientists can use in their research. Based on WHO CNS5 guidelines, we developed an algorithm for the reclassification of TCGA glioma samples by molecular features. We updated tumor type and diagnosis for 828 out of a total of 1122 TCGA glioma cases, after which available transcriptomic and methylation data showed clustering features more consistent with the updated grouping. We also observed better stratification by overall survival for the updated diagnoses, yet WHO grade 3 IDH-mutant oligodendrogliomas and astrocytomas are still indistinguishable. We also detected altered performance in the previous diagnostic transcriptomic molecular biomarkers (expression of SPRY1, CRNDE and FREM2 genes and FREM2 molecular pathway) and prognostic gene signature (FN1, ITGA5, OSMR, and NGFR) after reclassification. Thus, we conclude that further efforts are needed to reconsider glioma molecular biomarkers.
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Affiliation(s)
- Galina Zakharova
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119048 Moscow, Russia
| | - Victor Efimov
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119048 Moscow, Russia
| | - Mikhail Raevskiy
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119048 Moscow, Russia
| | - Pavel Rumiantsev
- Multidisciplinary Medical Center, Group of Clinics, 194044 Saint-Petersburg, Russia
| | - Alexander Gudkov
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119048 Moscow, Russia
| | | | - Maksim Sorokin
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119048 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), 1200 Brussels, Belgium
| | - Anton Buzdin
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119048 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), 1200 Brussels, Belgium
- Correspondence:
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