1
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Sorokin M, Buzdin AA, Guryanova A, Efimov V, Suntsova MV, Zolotovskaia MA, Koroleva EV, Sekacheva MI, Tkachev VS, Garazha A, Kremenchutckaya K, Drobyshev A, Seryakov A, Gudkov A, Alekseenko IV, Rakitina O, Kostina MB, Vladimirova U, Moisseev A, Bulgin D, Radomskaya E, Shestakov V, Baklaushev VP, Prassolov V, Shegay PV, Li X, Poddubskaya EV, Gaifullin N. Large-scale assessment of pros and cons of autopsy-derived or tumor-matched tissues as the norms for gene expression analysis in cancers. Comput Struct Biotechnol J 2023; 21:3964-3986. [PMID: 37635765 PMCID: PMC10448432 DOI: 10.1016/j.csbj.2023.07.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/17/2023] [Accepted: 07/30/2023] [Indexed: 08/29/2023] Open
Abstract
Normal tissues are essential for studying disease-specific differential gene expression. However, healthy human controls are typically available only in postmortal/autopsy settings. In cancer research, fragments of pathologically normal tissue adjacent to tumor site are frequently used as the controls. However, it is largely underexplored how cancers can systematically influence gene expression of the neighboring tissues. Here we performed a comprehensive pan-cancer comparison of molecular profiles of solid tumor-adjacent and autopsy-derived "healthy" normal tissues. We found a number of systemic molecular differences related to activation of the immune cells, intracellular transport and autophagy, cellular respiration, telomerase activation, p38 signaling, cytoskeleton remodeling, and reorganization of the extracellular matrix. The tumor-adjacent tissues were deficient in apoptotic signaling and negative regulation of cell growth including G2/M cell cycle transition checkpoint. We also detected an extensive rearrangement of the chemical perception network. Molecular targets of 32 and 37 cancer drugs were over- or underexpressed, respectively, in the tumor-adjacent norms. These processes may be driven by molecular events that are correlated between the paired cancer and adjacent normal tissues, that mostly relate to inflammation and regulation of intracellular molecular pathways such as the p38, MAPK, Notch, and IGF1 signaling. However, using a model of macaque postmortal tissues we showed that for the 30 min - 24-hour time frame at 4ºC, an RNA degradation pattern in lung biosamples resulted in an artifact "differential" expression profile for 1140 genes, although no differences could be detected in liver. Thus, such concerns should be addressed in practice.
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Affiliation(s)
- Maksim Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- Omicsway Corp., Walnut, CA 91789, USA
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Anton A. Buzdin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
| | - Anastasia Guryanova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
| | - Victor Efimov
- World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, Moscow, Russia
| | - Maria V. Suntsova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Marianna A. Zolotovskaia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- Omicsway Corp., Walnut, CA 91789, USA
| | - Elena V. Koroleva
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
| | - Marina I. Sekacheva
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Victor S. Tkachev
- Omicsway Corp., Walnut, CA 91789, USA
- Oncobox Ltd., Moscow 121205, Russia
| | - Andrew Garazha
- Omicsway Corp., Walnut, CA 91789, USA
- Oncobox Ltd., Moscow 121205, Russia
| | | | - Aleksey Drobyshev
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | | | - Alexander Gudkov
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Irina V. Alekseenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", 2, Kurchatov Square, Moscow 123182, Russian
- FSBI "National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov" Ministry of Healthcare of the Russian Federation, Moscow 117198, Russia
| | - Olga Rakitina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Maria B. Kostina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Uliana Vladimirova
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Oncobox Ltd., Moscow 121205, Russia
| | - Aleksey Moisseev
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Dmitry Bulgin
- Research Institute of Medical Primatology, 177 Mira str., Veseloye, Sochi 354376, Russia
| | - Elena Radomskaya
- Research Institute of Medical Primatology, 177 Mira str., Veseloye, Sochi 354376, Russia
| | - Viktor Shestakov
- Research Institute of Medical Primatology, 177 Mira str., Veseloye, Sochi 354376, Russia
| | | | - Vladimir Prassolov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str., Moscow 119991, Russia
| | - Petr V. Shegay
- National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, 249036 Obninsk, Russia
| | - Xinmin Li
- UCLA Technology Center for Genomics & Bioinformatics, Department of Pathology & Laboratory Medicine, 650 Charles E Young Dr., Los Angeles, CA 90095, USA
| | | | - Nurshat Gaifullin
- Department of Physiology and General Pathology, Faculty of Medicine, Lomonosov Moscow State University, Moscow 119991, Russia
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2
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Zakharova G, Modestov A, Pugacheva P, Mekic R, Savina E, Guryanova A, Rachkova A, Yakushov S, Alimov A, Kulaeva E, Fedoseeva E, Kleyman A, Vasin K, Tkachev V, Garazha A, Sekacheva M, Suntsova M, Sorokin M, Buzdin A, Zolotovskaia MA. Distinct Traits of Structural and Regulatory Evolutional Conservation of Human Genes with Specific Focus on Major Cancer Molecular Pathways. Cells 2023; 12:cells12091299. [PMID: 37174700 PMCID: PMC10177184 DOI: 10.3390/cells12091299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/24/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
The evolution of protein-coding genes has both structural and regulatory components. The first can be assessed by measuring the ratio of non-synonymous to synonymous nucleotide substitutions. The second component can be measured as the normalized proportion of transposable elements that are used as regulatory elements. For the first time, we characterized in parallel the regulatory and structural evolutionary profiles for 10,890 human genes and 2972 molecular pathways. We observed a ~0.1 correlation between the structural and regulatory metrics at the gene level, which appeared much higher (~0.4) at the pathway level. We deposited the data in the publicly available database RetroSpect. We also analyzed the evolutionary dynamics of six cancer pathways of two major axes: Notch/WNT/Hedgehog and AKT/mTOR/EGFR. The Hedgehog pathway had both components slower, whereas the Akt pathway had clearly accelerated structural evolution. In particular, the major hub nodes Akt and beta-catenin showed both components strongly decreased, whereas two major regulators of Akt TCL1 and CTMP had outstandingly high evolutionary rates. We also noticed structural conservation of serine/threonine kinases and the genes related to guanosine metabolism in cancer signaling: GPCRs, G proteins, and small regulatory GTPases (Src, Rac, Ras); however, this was compensated by the accelerated regulatory evolution.
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Affiliation(s)
- Galina Zakharova
- World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Alexander Modestov
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Polina Pugacheva
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Rijalda Mekic
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ekaterina Savina
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Anastasia Guryanova
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Anastasia Rachkova
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Semyon Yakushov
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Andrei Alimov
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Elizaveta Kulaeva
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Elena Fedoseeva
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Artem Kleyman
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Kirill Vasin
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | | | | | - Marina Sekacheva
- World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Maria Suntsova
- World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Maksim Sorokin
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Laboratory of Systems Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Anton Buzdin
- World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Laboratory of Systems Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), 1200 Brussels, Belgium
| | - Marianna A Zolotovskaia
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Laboratory for Translational Genomic Bioinformatics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
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3
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Zolotovskaia MA, Kovalenko MA, Tkachev VS, Simonov AM, Sorokin MI, Kim E, Kuzmin DV, Karademir-Yilmaz B, Buzdin AA. Next-Generation Grade and Survival Expression Biomarkers of Human Gliomas Based on Algorithmically Reconstructed Molecular Pathways. Int J Mol Sci 2022; 23:ijms23137330. [PMID: 35806337 PMCID: PMC9266372 DOI: 10.3390/ijms23137330] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 02/04/2023] Open
Abstract
In gliomas, expression of certain marker genes is strongly associated with survival and tumor type and often exceeds histological assessments. Using a human interactome model, we algorithmically reconstructed 7494 new-type molecular pathways that are centered each on an individual protein. Each single-gene expression and gene-centric pathway activation was tested as a survival and tumor grade biomarker in gliomas and their diagnostic subgroups (IDH mutant or wild type, IDH mutant with 1p/19q co-deletion, MGMT promoter methylated or unmethylated), including the three major molecular subtypes of glioblastoma (proneural, mesenchymal, classical). We used three datasets from The Cancer Genome Atlas and the Chinese Glioma Genome Atlas, which in total include 527 glioblastoma and 1097 low grade glioma profiles. We identified 2724 such gene and 2418 pathway survival biomarkers out of total 17,717 genes and 7494 pathways analyzed. We then assessed tumor grade and molecular subtype biomarkers and with the threshold of AUC > 0.7 identified 1322/982 gene biomarkers and 472/537 pathway biomarkers. This suggests roughly two times greater efficacy of the reconstructed pathway approach compared to gene biomarkers. Thus, we conclude that activation levels of algorithmically reconstructed gene-centric pathways are a potent class of new-generation diagnostic and prognostic biomarkers for gliomas.
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Affiliation(s)
- Marianna A. Zolotovskaia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (M.A.K.); (A.M.S.); (M.I.S.); (D.V.K.)
- Correspondence: ; Tel.: +7-9165612175
| | - Max A. Kovalenko
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (M.A.K.); (A.M.S.); (M.I.S.); (D.V.K.)
| | | | - Alexander M. Simonov
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (M.A.K.); (A.M.S.); (M.I.S.); (D.V.K.)
- Omicsway Corp., Walnut, CA 91789, USA;
| | - Maxim I. Sorokin
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (M.A.K.); (A.M.S.); (M.I.S.); (D.V.K.)
- Omicsway Corp., Walnut, CA 91789, USA;
- Laboratory of Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia;
| | - Ella Kim
- Clinic for Neurosurgery, Laboratory of Experimental Neurooncology, Johannes Gutenberg University Medical Centre, Langenbeckstrasse 1, 55124 Mainz, Germany;
| | - Denis V. Kuzmin
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (M.A.K.); (A.M.S.); (M.I.S.); (D.V.K.)
| | - Betul Karademir-Yilmaz
- Department of Biochemistry, School of Medicine/Genetic and Metabolic Diseases Research and Investigation Center (GEMHAM), Marmara University, Istanbul 34854, Turkey;
| | - Anton A. Buzdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia;
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), 1200 Brussels, Belgium
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4
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Zolotovskaia MA, Sorokin MI, Petrov IV, Poddubskaya EV, Moiseev AA, Sekacheva MI, Borisov NM, Tkachev VS, Garazha AV, Kaprin AD, Shegay PV, Giese A, Kim E, Roumiantsev SA, Buzdin AA. Disparity between Inter-Patient Molecular Heterogeneity and Repertoires of Target Drugs Used for Different Types of Cancer in Clinical Oncology. Int J Mol Sci 2020; 21:E1580. [PMID: 32111026 PMCID: PMC7084891 DOI: 10.3390/ijms21051580] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 02/07/2023] Open
Abstract
Inter-patient molecular heterogeneity is the major declared driver of an expanding variety of anticancer drugs and personalizing their prescriptions. Here, we compared interpatient molecular heterogeneities of tumors and repertoires of drugs or their molecular targets currently in use in clinical oncology. We estimated molecular heterogeneity using genomic (whole exome sequencing) and transcriptomic (RNA sequencing) data for 4890 tumors taken from The Cancer Genome Atlas database. For thirteen major cancer types, we compared heterogeneities at the levels of mutations and gene expression with the repertoires of targeted therapeutics and their molecular targets accepted by the current guidelines in oncology. Totally, 85 drugs were investigated, collectively covering 82 individual molecular targets. For the first time, we showed that the repertoires of molecular targets of accepted drugs did not correlate with molecular heterogeneities of different cancer types. On the other hand, we found that the clinical recommendations for the available cancer drugs were strongly congruent with the gene expression but not gene mutation patterns. We detected the best match among the drugs usage recommendations and molecular patterns for the kidney, stomach, bladder, ovarian and endometrial cancers. In contrast, brain tumors, prostate and colorectal cancers showed the lowest match. These findings provide a theoretical basis for reconsidering usage of targeted therapeutics and intensifying drug repurposing efforts.
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Affiliation(s)
- Marianna A. Zolotovskaia
- Oncobox ltd., Moscow, 121205, Russia; (I.V.P.); (A.A.B.)
- Department of Oncology, Hematology and Radiotherapy of Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow, 117997, Russia;
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia;
| | - Maxim I. Sorokin
- I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia (E.V.P.); (A.A.M.)
- Omicsway Corp., Walnut, CA, 91789, USA; (V.S.T.); (A.V.G.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Ivan V. Petrov
- Oncobox ltd., Moscow, 121205, Russia; (I.V.P.); (A.A.B.)
| | - Elena V. Poddubskaya
- I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia (E.V.P.); (A.A.M.)
| | - Alexey A. Moiseev
- I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia (E.V.P.); (A.A.M.)
| | - Marina I. Sekacheva
- I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia (E.V.P.); (A.A.M.)
| | - Nicolas M. Borisov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia;
- I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia (E.V.P.); (A.A.M.)
- Omicsway Corp., Walnut, CA, 91789, USA; (V.S.T.); (A.V.G.)
| | | | | | - Andrey D. Kaprin
- National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, Moscow 125284, Russia;
| | - Peter V. Shegay
- Center for Innovative Radiological and Regenerative Technologies of the Ministry of Health of the Russian Federation, Obninsk 249030, Russia;
| | - Alf Giese
- Orthocentrum Hamburg, Hamburg, Germany; or
| | - Ella Kim
- Johannes Gutenberg University Mainz, Mainz, Germany;
| | - Sergey A. Roumiantsev
- Department of Oncology, Hematology and Radiotherapy of Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow, 117997, Russia;
| | - Anton A. Buzdin
- Oncobox ltd., Moscow, 121205, Russia; (I.V.P.); (A.A.B.)
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia;
- I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia (E.V.P.); (A.A.M.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
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5
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Zolotovskaia MA, Sorokin MI, Emelianova AA, Borisov NM, Kuzmin DV, Borger P, Garazha AV, Buzdin AA. Pathway Based Analysis of Mutation Data Is Efficient for Scoring Target Cancer Drugs. Front Pharmacol 2019; 10:1. [PMID: 30728774 PMCID: PMC6351482 DOI: 10.3389/fphar.2019.00001] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/03/2019] [Indexed: 12/20/2022] Open
Abstract
Despite the significant achievements in chemotherapy, cancer remains one of the leading causes of death. Target therapy revolutionized this field, but efficiencies of target drugs show dramatic variation among individual patients. Personalization of target therapies remains, therefore, a challenge in oncology. Here, we proposed molecular pathway-based algorithm for scoring of target drugs using high throughput mutation data to personalize their clinical efficacies. This algorithm was validated on 3,800 exome mutation profiles from The Cancer Genome Atlas (TCGA) project for 128 target drugs. The output values termed Mutational Drug Scores (MDS) showed positive correlation with the published drug efficiencies in clinical trials. We also used MDS approach to simulate all known protein coding genes as the putative drug targets. The model used was built on the basis of 18,273 mutation profiles from COSMIC database for eight cancer types. We found that the MDS algorithm-predicted hits frequently coincide with those already used as targets of the existing cancer drugs, but several novel candidates can be considered promising for further developments. Our results evidence that the MDS is applicable to ranking of anticancer drugs and can be applied for the identification of novel molecular targets.
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Affiliation(s)
- Marianna A Zolotovskaia
- Oncobox Ltd., Moscow, Russia.,Department of Oncology, Hematology and Radiotherapy of Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maxim I Sorokin
- The Laboratory of Clinical Bioinformatics, IM Sechenov First Moscow State Medical University, Moscow, Russia.,Omicsway Corp., Walnut, CA, United States.,Science-Educational Center Department, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna A Emelianova
- Science-Educational Center Department, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay M Borisov
- The Laboratory of Clinical Bioinformatics, IM Sechenov First Moscow State Medical University, Moscow, Russia.,Omicsway Corp., Walnut, CA, United States
| | - Denis V Kuzmin
- Science-Educational Center Department, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Pieter Borger
- Laboratory of the Swiss Hepato-Pancreato-Biliary, Department of Surgery, Transplantation Center, University Hospital Zurich, Zurich, Switzerland
| | | | - Anton A Buzdin
- Oncobox Ltd., Moscow, Russia.,The Laboratory of Clinical Bioinformatics, IM Sechenov First Moscow State Medical University, Moscow, Russia.,Science-Educational Center Department, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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6
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Zolotovskaia MA, Sorokin MI, Roumiantsev SA, Borisov NM, Buzdin AA. Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers. Front Oncol 2019; 8:658. [PMID: 30662873 PMCID: PMC6328788 DOI: 10.3389/fonc.2018.00658] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/12/2018] [Indexed: 01/20/2023] Open
Abstract
DNA mutations play a crucial role in cancer development and progression. Mutation profiles vary dramatically in different cancer types and between individual tumors. Mutations of several individual genes are known as reliable cancer biomarkers, although the number of such genes is tiny and does not enable differential diagnostics for most of the cancers. We report here a technique enabling dramatically increased efficiency of cancer biomarkers development using DNA mutations data. It includes a quantitative metric termed Pathway instability (PI) based on mutations enrichment of intracellular molecular pathways. This method was tested on 5,956 tumor mutation profiles of 15 cancer types from The Cancer Genome Atlas (TCGA) project. Totally, we screened 2,316,670 mutations in 19,872 genes and 1,748 molecular pathways. Our results demonstrated considerable advantage of pathway-based mutation biomarkers over individual gene mutation profiles, as reflected by more than two orders of magnitude greater numbers by high-quality [ROC area-under-curve (AUC)>0.75] biomarkers. For example, the number of such high-quality mutational biomarkers distinguishing between different cancer types was only six for the individual gene mutations, and already 660 for the pathway-based biomarkers. These results evidence that PI value can be used as a new generation of complex cancer biomarkers significantly outperforming the existing gene mutation biomarkers.
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Affiliation(s)
- Marianna A Zolotovskaia
- Department of Oncology, Hematology and Radiotherapy of Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow, Russia.,Oncobox Ltd., Moscow, Russia
| | - Maxim I Sorokin
- The Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.,Omicsway Corp., Walnut, CA, United States
| | - Sergey A Roumiantsev
- Department of Oncology, Hematology and Radiotherapy of Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nikolay M Borisov
- Oncobox Ltd., Moscow, Russia.,The Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anton A Buzdin
- The Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.,Omicsway Corp., Walnut, CA, United States.,The Laboratory of Systems Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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