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Gisina A, Kim Y, Yarygin K, Lupatov A. Can CD133 Be Regarded as a Prognostic Biomarker in Oncology: Pros and Cons. Int J Mol Sci 2023; 24:17398. [PMID: 38139228 PMCID: PMC10744290 DOI: 10.3390/ijms242417398] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The CD133 cell membrane glycoprotein, also termed prominin-1, is expressed on some of the tumor cells of both solid and blood malignancies. The CD133-positive tumor cells were shown to exhibit higher proliferative activity, greater chemo- and radioresistance, and enhanced tumorigenicity compared to their CD133-negative counterparts. For this reason, CD133 is regarded as a potential prognostic biomarker in oncology. The CD133-positive cells are related to the cancer stem cell subpopulation in many types of cancer. Recent studies demonstrated the involvement of CD133 in the regulation of proliferation, autophagy, and apoptosis in cancer cells. There is also evidence of its participation in the epithelial-mesenchymal transition associated with tumor progression. For a number of malignant tumor types, high CD133 expression is associated with poor prognosis, and the prognostic significance of CD133 has been confirmed in a number of meta-analyses. However, some published papers suggest that CD133 has no prognostic significance or even demonstrate a certain correlation between high CD133 levels and a positive prognosis. This review summarizes and discusses the existing evidence for and against the prognostic significance of CD133 in cancer. We also consider possible reasons for conflicting findings from the studies of the clinical significance of CD133.
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Affiliation(s)
- Alisa Gisina
- Laboratory of Cell Biology, V. N. Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia
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Cherkashova E, Namestnikova D, Leonov G, Gubskiy I, Sukhinich K, Melnikov P, Chekhonin V, Yarygin K, Goldshtein D, Salikhova D. Comparative study of the efficacy of intra-arterial and intravenous transplantation of human induced pluripotent stem cells-derived neural progenitor cells in experimental stroke. PeerJ 2023; 11:e16358. [PMID: 38025691 PMCID: PMC10640846 DOI: 10.7717/peerj.16358] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Background Cell therapy using neural progenitor cells (NPCs) is a promising approach for ischemic stroke treatment according to the results of multiple preclinical studies in animal stroke models. In the vast majority of conducted animal studies, the therapeutic efficacy of NPCs was estimated after intracerebral transplantation, while the information of the effectiveness of systemic administration is limited. Nowadays, several clinical trials aimed to estimate the safety and efficacy of NPCs transplantation in stroke patients were also conducted. In these studies, NPCs were transplanted intracerebrally in the subacute/chronic phase of stroke. The results of clinical trials confirmed the safety of the approach, however, the degree of functional improvement (the primary efficacy endpoint) was not sufficient in the majority of the studies. Therefore, more studies are needed in order to investigate the optimal transplantation parameters, especially the timing of cell transplantation after the stroke onset. This study aimed to evaluate the therapeutic effects of intra-arterial (IA) and intravenous (IV) administration of NPCs derived from induced pluripotent stem cells (iNPCs) in the acute phase of experimental stroke in rats. Induced pluripotent stem cells were chosen as the source of NPCs as this technology is perspective, has no ethical concerns and provides the access to personalized medicine. Methods Human iNPCs were transplanted IA or IV into male Wistar rats 24 h after the middle cerebral artery occlusion stroke modeling. Therapeutic efficacy was monitored for 14 days and evaluated in comparison with the cell transplantation-free control group. Additionally, cell distribution in the brain was assessed. Results The obtained results show that both routes of systemic transplantation (IV and IA) significantly reduced the mortality and improved the neurological deficit of experimental animals compared to the control group. At the same time, according to the MRI data, only IA administration led to faster and prominent reduction of the stroke volume. After IA administration, iNPCs transiently trapped in the brain and were not detected on day 7 after the transplantation. In case of IV injection, transplanted cells were not visualized in the brain. The obtained data demonstrated that the systemic transplantation of human iNPCs in the acute phase of ischemic stroke can be a promising therapeutic strategy.
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Affiliation(s)
- Elvira Cherkashova
- Pirogov Russian National Research Medical University of the Ministry of Healthcare of Russian Federation, Moscow, Russian Federation
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency of Russian Federation, Moscow, Russian Federation
| | - Daria Namestnikova
- Pirogov Russian National Research Medical University of the Ministry of Healthcare of Russian Federation, Moscow, Russian Federation
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency of Russian Federation, Moscow, Russian Federation
| | - Georgiy Leonov
- Orekhovich Research Institute of Biomedical Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Ilya Gubskiy
- Pirogov Russian National Research Medical University of the Ministry of Healthcare of Russian Federation, Moscow, Russian Federation
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency of Russian Federation, Moscow, Russian Federation
| | - Kirill Sukhinich
- Orekhovich Research Institute of Biomedical Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Pavel Melnikov
- Serbsky Federal Medical Research Centre of Psychiatry and Narcology of the Ministry of Healthcare of Russian Federation, Moscow, Russian Federation
| | - Vladimir Chekhonin
- Pirogov Russian National Research Medical University of the Ministry of Healthcare of Russian Federation, Moscow, Russian Federation
- Serbsky Federal Medical Research Centre of Psychiatry and Narcology of the Ministry of Healthcare of Russian Federation, Moscow, Russian Federation
| | - Konstantin Yarygin
- Orekhovich Research Institute of Biomedical Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare of the Russian Federation, Moscow, Russian Federation
| | | | - Diana Salikhova
- Institute of Molecular and Cellular Medicine, Medical Institute, RUDN University, Moscow, Russian Federation
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Gisina A, Novikova S, Kim Y, Sidorov D, Bykasov S, Volchenko N, Kaprin A, Zgoda V, Yarygin K, Lupatov A. CEACAM5 overexpression is a reliable characteristic of CD133-positive colorectal cancer stem cells. Cancer Biomark 2021; 32:85-98. [PMID: 34092615 DOI: 10.3233/cbm-203187] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND CD133 (prominin-1) is the most commonly used molecular marker of the cancer stem cells (CSCs) that maintain tumor progression and recurrence in colorectal cancer. However, the proteome of CSCs directly isolated from colorectal tumors based on CD133 expression has never been investigated. OBJECTIVE To reveal biomarkers of CD133-positive colorectal CSCs. METHODS Thirty colorectal tumor samples were collected from patients undergoing bowel resection. CD133-positive and CD133-negative cells were isolated by FACS. Comparative proteomic profiling was performed by LC-MS/MS analysis combined with label-free quantification. Verification of differentially expressed proteins was performed by flow cytometry or ELISA. CD133-knockout Caco-2 and HT-29 cell lines were generated using CRISPR-Cas9 gene editing. RESULTS LC-MS/MS analysis identified 29 proteins with at least 2.5-fold higher expression in CD133-positive cells versus CD133-negative cells. Flow cytometry confirmed CEACAM5 overexpression in CD133-positive cells in all clinical samples analyzed. S100A8, S100A9, and DEFA1 were differentially expressed in only a proportion of the samples. CD133 knockout in the colon cancer cell lines Caco-2 and HT-29 did not affect the median level of CEACAM5 expression, but led to higher variance of the percentage of CEACAM5-positive cells. CONCLUSIONS High CEACAM5 expression in colorectal cancer cells is firmly associated with the CD133-positive colorectal CSC phenotype, but it is unlikely that CD133 directly regulates CEACAM5 expression.
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Affiliation(s)
- Alisa Gisina
- Laboratory of Cell Biology, Institute of Biomedical Chemistry, Moscow, Russia
| | - Svetlana Novikova
- Laboratory of Systems Biology, Institute of Biomedical Chemistry, Moscow, Russia
| | - Yan Kim
- Laboratory of Cell Biology, Institute of Biomedical Chemistry, Moscow, Russia
| | - Dmitry Sidorov
- Department of Abdominal Surgery, P. Hertsen Moscow Oncology Research Institute, Moscow, Russia
| | - Stanislav Bykasov
- Department of Abdominal Surgery, P. Hertsen Moscow Oncology Research Institute, Moscow, Russia
| | - Nadezhda Volchenko
- Department of Oncomorphology, P. Hertsen Moscow Oncology Research Institute, Moscow, Russia
| | - Andrey Kaprin
- P. Hertsen Moscow Oncology Research Institute, Moscow, Russia
| | - Victor Zgoda
- Laboratory of Systems Biology, Institute of Biomedical Chemistry, Moscow, Russia
| | - Konstantin Yarygin
- Laboratory of Cell Biology, Institute of Biomedical Chemistry, Moscow, Russia
| | - Alexey Lupatov
- Laboratory of Cell Biology, Institute of Biomedical Chemistry, Moscow, Russia
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Novikova S, Tikhonova O, Kurbatov L, Farafonova T, Vakhrushev I, Lupatov A, Yarygin K, Zgoda V. Omics Technologies to Decipher Regulatory Networks in Granulocytic Cell Differentiation. Biomolecules 2021; 11:biom11060907. [PMID: 34207065 PMCID: PMC8233756 DOI: 10.3390/biom11060907] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 01/01/2023] Open
Abstract
Induced granulocytic differentiation of human leukemic cells under all-trans-retinoid acid (ATRA) treatment underlies differentiation therapy of acute myeloid leukemia. Knowing the regulation of this process it is possible to identify potential targets for antileukemic drugs and develop novel approaches to differentiation therapy. In this study, we have performed transcriptomic and proteomic profiling to reveal up- and down-regulated transcripts and proteins during time-course experiments. Using data on differentially expressed transcripts and proteins we have applied upstream regulator search and obtained transcriptome- and proteome-based regulatory networks of induced granulocytic differentiation that cover both up-regulated (HIC1, NFKBIA, and CASP9) and down-regulated (PARP1, VDR, and RXRA) elements. To verify the designed network we measured HIC1 and PARP1 protein abundance during granulocytic differentiation by selected reaction monitoring (SRM) using stable isotopically labeled peptide standards. We also revealed that transcription factor CEBPB and LYN kinase were involved in differentiation onset, and evaluated their protein levels by SRM technique. Obtained results indicate that the omics data reflect involvement of the DNA repair system and the MAPK kinase cascade as well as show the balance between the processes of the cell survival and apoptosis in a p53-independent manner. The differentially expressed transcripts and proteins, predicted transcriptional factors, and key molecules such as HIC1, CEBPB, LYN, and PARP1 may be considered as potential targets for differentiation therapy of acute myeloid leukemia.
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Salikhova D, Bukharova T, Cherkashova E, Namestnikova D, Leonov G, Nikitina M, Gubskiy I, Akopyan G, Elchaninov A, Midiber K, Bulatenco N, Mokrousova V, Makarov A, Yarygin K, Chekhonin V, Mikhaleva L, Fatkhudinov T, Goldshtein D. Therapeutic Effects of hiPSC-Derived Glial and Neuronal Progenitor Cells-Conditioned Medium in Experimental Ischemic Stroke in Rats. Int J Mol Sci 2021; 22:ijms22094694. [PMID: 33946667 PMCID: PMC8125106 DOI: 10.3390/ijms22094694] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 03/09/2021] [Revised: 04/12/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
Transplantation of various types of stem cells as a possible therapy for stroke has been tested for years, and the results are promising. Recent investigations have shown that the administration of the conditioned media obtained after stem cell cultivation can also be effective in the therapy of the central nervous system pathology (hypothesis of their paracrine action). The aim of this study was to evaluate the therapeutic effects of the conditioned medium of hiPSC-derived glial and neuronal progenitor cells in the rat middle cerebral artery occlusion model of the ischemic stroke. Secretory activity of the cultured neuronal and glial progenitor cells was evaluated by proteomic and immunosorbent-based approaches. Therapeutic effects were assessed by overall survival, neurologic deficit and infarct volume dynamics, as well as by the end-point values of the apoptosis- and inflammation-related gene expression levels, the extent of microglia/macrophage infiltration and the numbers of formed blood vessels in the affected area of the brain. As a result, 31% of the protein species discovered in glial progenitor cells-conditioned medium and 45% in neuronal progenitor cells-conditioned medium were cell type specific. The glial progenitor cell-conditioned media showed a higher content of neurotrophins (BDNF, GDNF, CNTF and NGF). We showed that intra-arterial administration of glial progenitor cells-conditioned medium promoted a faster decrease in neurological deficit compared to the control group, reduced microglia/macrophage infiltration, reduced expression of pro-apoptotic gene Bax and pro-inflammatory cytokine gene Tnf, increased expression of anti-inflammatory cytokine genes (Il4, Il10, Il13) and promoted the formation of blood vessels within the damaged area. None of these effects were exerted by the neuronal progenitor cell-conditioned media. The results indicate pronounced cytoprotective, anti-inflammatory and angiogenic properties of soluble factors secreted by glial progenitor cells.
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Affiliation(s)
- Diana Salikhova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.B.); (G.L.); (N.B.); (V.M.); (D.G.)
- Research Institute of Human Morphology, 117418 Moscow, Russia; (M.N.); (A.E.); (K.M.); (L.M.); (T.F.)
- Correspondence:
| | - Tatiana Bukharova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.B.); (G.L.); (N.B.); (V.M.); (D.G.)
| | - Elvira Cherkashova
- Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (E.C.); (D.N.); (I.G.); (A.M.); (V.C.)
- Radiology and Clinical Physiology Scientific Research Center, Federal State Budgetary Institution “Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency”, 117997 Moscow, Russia;
| | - Daria Namestnikova
- Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (E.C.); (D.N.); (I.G.); (A.M.); (V.C.)
- Radiology and Clinical Physiology Scientific Research Center, Federal State Budgetary Institution “Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency”, 117997 Moscow, Russia;
| | - Georgy Leonov
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.B.); (G.L.); (N.B.); (V.M.); (D.G.)
| | - Maria Nikitina
- Research Institute of Human Morphology, 117418 Moscow, Russia; (M.N.); (A.E.); (K.M.); (L.M.); (T.F.)
| | - Ilya Gubskiy
- Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (E.C.); (D.N.); (I.G.); (A.M.); (V.C.)
- Radiology and Clinical Physiology Scientific Research Center, Federal State Budgetary Institution “Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency”, 117997 Moscow, Russia;
| | - Gevorg Akopyan
- Radiology and Clinical Physiology Scientific Research Center, Federal State Budgetary Institution “Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency”, 117997 Moscow, Russia;
| | - Andrey Elchaninov
- Research Institute of Human Morphology, 117418 Moscow, Russia; (M.N.); (A.E.); (K.M.); (L.M.); (T.F.)
| | - Konstantin Midiber
- Research Institute of Human Morphology, 117418 Moscow, Russia; (M.N.); (A.E.); (K.M.); (L.M.); (T.F.)
| | - Natalia Bulatenco
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.B.); (G.L.); (N.B.); (V.M.); (D.G.)
| | - Victoria Mokrousova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.B.); (G.L.); (N.B.); (V.M.); (D.G.)
| | - Andrey Makarov
- Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (E.C.); (D.N.); (I.G.); (A.M.); (V.C.)
| | - Konstantin Yarygin
- Institute of Biomedical Chemistry, 119121 Moscow, Russia;
- Russian Medical Academy of Continuous Professional Education, 125993 Moscow, Russia
| | - Vladimir Chekhonin
- Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (E.C.); (D.N.); (I.G.); (A.M.); (V.C.)
| | - Liudmila Mikhaleva
- Research Institute of Human Morphology, 117418 Moscow, Russia; (M.N.); (A.E.); (K.M.); (L.M.); (T.F.)
| | - Timur Fatkhudinov
- Research Institute of Human Morphology, 117418 Moscow, Russia; (M.N.); (A.E.); (K.M.); (L.M.); (T.F.)
- Department of Histology, Cytology and Embryology, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
| | - Dmitry Goldshtein
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.B.); (G.L.); (N.B.); (V.M.); (D.G.)
- Department of Histology, Cytology and Embryology, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
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Namestnikova D, Gubskiy I, Kholodenko I, Melnikov P, Sukhinich K, Gabashvili A, Vishnevskiy D, Soloveva A, Abakumov M, Vakhrushev I, Lupatov A, Chekhonin V, Gubsky L, Yarygin K. Methodological aspects of MRI of transplanted superparamagnetic iron oxide-labeled mesenchymal stem cells in live rat brain. PLoS One 2017; 12:e0186717. [PMID: 29049361 PMCID: PMC5648235 DOI: 10.1371/journal.pone.0186717] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 10/08/2017] [Indexed: 12/22/2022] Open
Abstract
In vivo tracking of transplanted mesenchymal stem cells (MSCs) migration and homing is vital for understanding the mechanisms of beneficial effects of MSCs transplantation in animal models of diseases and in clinical trials. Transplanted cells can be labeled with superparamagnetic iron oxide (SPIO) particles and visualized in vivo using a number of iron sensitive MRI techniques. However, the applicability of those techniques for SPIO-labeled MSCs tracking in live brain has not been sufficiently investigated. The goal of this study was to estimate the efficiency of various MRI techniques of SPIO-labeled cell tracing in the brain. To achieve that goal, the precision and specificity of T2WI, T2*WI and SWI (Susceptibility-Weighted Imaging) techniques of SPIO-labeled MSCs tracing in vitro and in live rat brain were for the first time compared in the same experiment. We have shown that SWI presents the most sensitive pulse sequence for SPIO-labeled MSCs MR visualization. After intracerebral administration due to limitations caused by local micro-hemorrhages the visualization threshold was 102 cells, while after intra-arterial transplantation SWI permitted detection of several cells or even single cells. There is just one publication claiming detection of individual SPIO-labeled MSCs in live brain, while the other state much lower sensitivity, describe detection of different cell types or high resolution tracing of MSCs in other tissues. This study confirms the possibility of single cell tracing in live brain and outlines the necessary conditions. SWI is a method convenient for the detection of single SPIO labeled MSCs and small groups of SPIO labeled MSCs in brain tissue and can be appropriate for monitoring migration and homing of transplanted cells in basic and translational neuroscience.
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Affiliation(s)
| | - Ilya Gubskiy
- Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Pavel Melnikov
- Pirogov Russian National Research Medical University, Moscow, Russia.,Serbsky Federal Medical Research Centre of Psychiatry and Narcology, Moscow, Russia
| | | | | | | | | | - Maxim Abakumov
- Pirogov Russian National Research Medical University, Moscow, Russia.,National University of Science and Technology, Moscow, Russia
| | | | | | - Vladimir Chekhonin
- Pirogov Russian National Research Medical University, Moscow, Russia.,Serbsky Federal Medical Research Centre of Psychiatry and Narcology, Moscow, Russia
| | - Leonid Gubsky
- Pirogov Russian National Research Medical University, Moscow, Russia
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Namestnikova D, Gubskiy I, Gabashvili A, Sukhinich K, Melnikov P, Vishnevskiy D, Soloveva A, Vitushev E, Chekhonin V, Gubsky L, Yarygin K. MRI evaluation of frequent complications after intra-arterial transplantation of mesenchymal stem cells in rats. ACTA ACUST UNITED AC 2017. [DOI: 10.1088/1742-6596/886/1/012012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Yarygin K, Tyakht A, Larin A, Kostryukova E, Kolchenko S, Bitner V, Alexeev D. Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses. PLoS One 2017; 12:e0176154. [PMID: 28448616 PMCID: PMC5407692 DOI: 10.1371/journal.pone.0176154] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 04/06/2017] [Indexed: 12/21/2022] Open
Abstract
The gut microbiota is essentially a multifunctional bioreactor within a human being. The exploration of its enormous metabolic potential provides insights into the mechanisms underlying microbial ecology and interactions with the host. The data obtained using “shotgun” metagenomics capture information about the whole spectrum of microbial functions. However, each new study presenting new sequencing data tends to extract only a little of the information concerning the metabolic potential and often omits specific functions. A meta-analysis of the available data with an emphasis on biomedically relevant gene groups can unveil new global trends in the gut microbiota. As a step toward the reuse of metagenomic data, we developed a method for the quantitative profiling of user-defined groups of genes in human gut metagenomes. This method is based on the quick analysis of a gene coverage matrix obtained by pre-mapping the metagenomic reads to a global gut microbial catalogue. The method was applied to profile the abundance of several gene groups related to antibiotic resistance, phages, biosynthesis clusters and carbohydrate degradation in 784 metagenomes from healthy populations worldwide and patients with inflammatory bowel diseases and obesity. We discovered country-wise functional specifics in gut resistome and virome compositions. The most distinct features of the disease microbiota were found for Crohn’s disease, followed by ulcerative colitis and obesity. Profiling of the genes belonging to crAssphage showed that its abundance varied across the world populations and was not associated with clinical status. We demonstrated temporal resilience of crAssphage and the influence of the sample preparation protocol on its detected abundance. Our approach offers a convenient method to add value to accumulated “shotgun” metagenomic data by helping researchers state and assess novel biological hypotheses.
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Affiliation(s)
- Konstantin Yarygin
- Federal Research and Clinical Centre of Physical-Chemical Medicine (FRCC CPM), Malaya Pirogovskaya 1a, Moscow 119435, Russia
- Moscow Institute of Physics and Technology, Institutsky lane 9, Dolgoprudny, Moscow Region, 141700, Russia
- * E-mail:
| | - Alexander Tyakht
- Federal Research and Clinical Centre of Physical-Chemical Medicine (FRCC CPM), Malaya Pirogovskaya 1a, Moscow 119435, Russia
- Moscow Institute of Physics and Technology, Institutsky lane 9, Dolgoprudny, Moscow Region, 141700, Russia
| | - Andrey Larin
- Federal Research and Clinical Centre of Physical-Chemical Medicine (FRCC CPM), Malaya Pirogovskaya 1a, Moscow 119435, Russia
| | - Elena Kostryukova
- Federal Research and Clinical Centre of Physical-Chemical Medicine (FRCC CPM), Malaya Pirogovskaya 1a, Moscow 119435, Russia
- Moscow Institute of Physics and Technology, Institutsky lane 9, Dolgoprudny, Moscow Region, 141700, Russia
| | - Sergei Kolchenko
- Moscow Institute of Physics and Technology, Institutsky lane 9, Dolgoprudny, Moscow Region, 141700, Russia
- HPC HUB LLC, Prospect Mira 112, Bld.12, Moscow 129626, Russia
| | - Vilgelm Bitner
- Moscow Institute of Physics and Technology, Institutsky lane 9, Dolgoprudny, Moscow Region, 141700, Russia
- HPC HUB LLC, Prospect Mira 112, Bld.12, Moscow 129626, Russia
| | - Dmitry Alexeev
- Federal Research and Clinical Centre of Physical-Chemical Medicine (FRCC CPM), Malaya Pirogovskaya 1a, Moscow 119435, Russia
- Moscow Institute of Physics and Technology, Institutsky lane 9, Dolgoprudny, Moscow Region, 141700, Russia
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