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Tang W, Lo CWS, Ma W, Chu ATW, Tong AHY, Chung BHY. Revealing the role of SPP1 + macrophages in glioma prognosis and therapeutic targeting by investigating tumor-associated macrophage landscape in grade 2 and 3 gliomas. Cell Biosci 2024; 14:37. [PMID: 38515213 PMCID: PMC10956315 DOI: 10.1186/s13578-024-01218-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Glioma is a highly heterogeneous brain tumor categorized into World Health Organization (WHO) grades 1-4 based on its malignancy. The suppressive immune microenvironment of glioma contributes significantly to unfavourable patient outcomes. However, the cellular composition and their complex interplays within the glioma environment remain poorly understood, and reliable prognostic markers remain elusive. Therefore, in-depth exploration of the tumor microenvironment (TME) and identification of predictive markers are crucial for improving the clinical management of glioma patients. RESULTS Our analysis of single-cell RNA-sequencing data from glioma samples unveiled the immunosuppressive role of tumor-associated macrophages (TAMs), mediated through intricate interactions with tumor cells and lymphocytes. We also discovered the heterogeneity within TAMs, among which a group of suppressive TAMs named TAM-SPP1 demonstrated a significant association with Epidermal Growth Factor Receptor (EGFR) amplification, impaired T cell response and unfavourable patient survival outcomes. Furthermore, by leveraging genomic and transcriptomic data from The Cancer Genome Atlas (TCGA) dataset, two distinct molecular subtypes with a different constitution of TAMs, EGFR status and clinical outcomes were identified. Exploiting the molecular differences between these two subtypes, we developed a four-gene-based prognostic model. This model displayed strong associations with an elevated level of suppressive TAMs and could be used to predict anti-tumor immune response and prognosis in glioma patients. CONCLUSION Our findings illuminated the molecular and cellular mechanisms that shape the immunosuppressive microenvironment in gliomas, providing novel insights into potential therapeutic targets. Furthermore, the developed prognostic model holds promise for predicting immunotherapy response and assisting in more precise risk stratification for glioma patients.
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Affiliation(s)
- Wenshu Tang
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Cario W S Lo
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Wei Ma
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Annie T W Chu
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Amy H Y Tong
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Brian H Y Chung
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China.
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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Oprescu SN, Baumann N, Chen X, Sun Q, Zhao Y, Yue F, Wang H, Kuang S. Sox11 is enriched in myogenic progenitors but dispensable for development and regeneration of the skeletal muscle. Skelet Muscle 2023; 13:15. [PMID: 37705115 PMCID: PMC10498607 DOI: 10.1186/s13395-023-00324-0] [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: 03/09/2023] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
Transcription factors (TFs) play key roles in regulating differentiation and function of stem cells, including muscle satellite cells (MuSCs), a resident stem cell population responsible for postnatal regeneration of the skeletal muscle. Sox11 belongs to the Sry-related HMG-box (SOX) family of TFs that play diverse roles in stem cell behavior and tissue specification. Analysis of single-cell RNA-sequencing (scRNA-seq) datasets identify a specific enrichment of Sox11 mRNA in differentiating but not quiescent MuSCs. Consistent with the scRNA-seq data, Sox11 levels increase during differentiation of murine primary myoblasts in vitro. scRNA-seq data comparing muscle regeneration in young and old mice further demonstrate that Sox11 expression is reduced in aged MuSCs. Age-related decline of Sox11 expression is associated with reduced chromatin contacts within the topologically associating domains. Unexpectedly, Myod1Cre-driven deletion of Sox11 in embryonic myoblasts has no effects on muscle development and growth, resulting in apparently healthy muscles that regenerate normally. Pax7CreER- or Rosa26CreER- driven (MuSC-specific or global) deletion of Sox11 in adult mice similarly has no effects on MuSC differentiation or muscle regeneration. These results identify Sox11 as a novel myogenic differentiation marker with reduced expression in quiescent and aged MuSCs, but the specific function of Sox11 in myogenesis remains to be elucidated.
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Affiliation(s)
- Stephanie N Oprescu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Nick Baumann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Xiyue Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Qiang Sun
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong, China
| | - Yu Zhao
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong, China
| | - Feng Yue
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Huating Wang
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong, China
| | - Shihuan Kuang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA.
- Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.
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Hamilton DJ, Hein AE, Wuttke DS, Batey RT. The DNA binding high mobility group box protein family functionally binds RNA. Wiley Interdiscip Rev RNA 2023; 14:e1778. [PMID: 36646476 PMCID: PMC10349909 DOI: 10.1002/wrna.1778] [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] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023]
Abstract
Nucleic acid binding proteins regulate transcription, splicing, RNA stability, RNA localization, and translation, together tailoring gene expression in response to stimuli. Upon discovery, these proteins are typically classified as either DNA or RNA binding as defined by their in vivo functions; however, recent evidence suggests dual DNA and RNA binding by many of these proteins. High mobility group box (HMGB) proteins have a DNA binding HMGB domain, act as transcription factors and chromatin remodeling proteins, and are increasingly understood to interact with RNA as means to regulate gene expression. Herein, multiple layers of evidence that the HMGB family are dual DNA and RNA binding proteins is comprehensively reviewed. For example, HMGB proteins directly interact with RNA in vitro and in vivo, are localized to RNP granules involved in RNA processing, and their protein interactors are enriched in RNA binding proteins involved in RNA metabolism. Importantly, in cell-based systems, HMGB-RNA interactions facilitate protein-protein interactions, impact splicing outcomes, and modify HMGB protein genomic or cellular localization. Misregulation of these HMGB-RNA interactions are also likely involved in human disease. This review brings to light that as a family, HMGB proteins are likely to bind RNA which is essential to HMGB protein biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Ravikumar V, Xu T, Al-Holou WN, Fattahi S, Rao A. Efficient Inference of Spatially-Varying Gaussian Markov Random Fields With Applications in Gene Regulatory Networks. IEEE/ACM Trans Comput Biol Bioinform 2023; 20:2920-2932. [PMID: 37276119 PMCID: PMC10623339 DOI: 10.1109/tcbb.2023.3282028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this paper, we study the problem of inferring spatially-varying Gaussian Markov random fields (SV-GMRF) where the goal is to learn a network of sparse, context-specific GMRFs representing network relationships between genes. An important application of SV-GMRFs is in inference of gene regulatory networks from spatially-resolved transcriptomics datasets. The current work on inference of SV-GMRFs are based on the regularized maximum likelihood estimation (MLE) and suffer from overwhelmingly high computational cost due to their highly nonlinear nature. To alleviate this challenge, we propose a simple and efficient optimization problem in lieu of MLE that comes equipped with strong statistical and computational guarantees. Our proposed optimization problem is extremely efficient in practice: we can solve instances of SV-GMRFs with more than 2 million variables in less than 2 minutes. We apply the developed framework to study how gene regulatory networks in Glioblastoma are spatially rewired within tissue, and identify prominent activity of the transcription factor HES4 and ribosomal proteins as characterizing the gene expression network in the tumor peri-vascular niche that is known to harbor treatment resistant stem cells.
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Elshaer SS, Abulsoud AI, Fathi D, Abdelmaksoud NM, Zaki MB, El-Mahdy HA, Ismail A, Elsakka EGE, Abd-Elmawla MA, Abulsoud LA, Doghish AS. miRNAs role in glioblastoma pathogenesis and targeted therapy: Signaling pathways interplay. Pathol Res Pract 2023; 246:154511. [PMID: 37178618 DOI: 10.1016/j.prp.2023.154511] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
High mortality and morbidity rates and variable clinical behavior are hallmarks of glioblastoma (GBM), the most common and aggressive primary malignant brain tumor. Patients with GBM often have a dismal outlook, even after undergoing surgery, postoperative radiation, and chemotherapy, which has fueled the search for specific targets to provide new insights into the development of contemporary therapies. The ability of microRNAs (miRNAs/miRs) to posttranscriptionally regulate the expression of various genes and silence many target genes involved in cell proliferation, cell cycle, apoptosis, invasion, angiogenesis, stem cell behavior and chemo- and radiotherapy resistance makes them promising candidates as prognostic biomarkers and therapeutic targets or factors to advance GBM therapeutics. Hence, this review is like a crash course in GBM and how miRNAs related to GBM. Here, we will outline the miRNAs whose role in the development of GBM has been established by recent in vitro or in vivo research. Moreover, we will provide a summary of the state of knowledge regarding oncomiRs and tumor suppressor (TS) miRNAs in relation to GBM with an emphasis on their potential applications as prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Shereen Saeid Elshaer
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City, Cairo 11823, Egypt; Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Ahmed I Abulsoud
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Doaa Fathi
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Nourhan M Abdelmaksoud
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Mohamed Bakr Zaki
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Menoufia 32897, Egypt
| | - Hesham A El-Mahdy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt.
| | - Ahmed Ismail
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Elsayed G E Elsakka
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Mai A Abd-Elmawla
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Logyna A Abulsoud
- Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt.
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Oprescu SN, Baumann N, Chen X, Sun Q, Zhao Y, Yue F, Wang H, Kuang S. Sox11 is enriched in myogenic progenitors but dispensable for development and regeneration of skeletal muscle. bioRxiv 2023:2023.03.30.534956. [PMID: 37034612 PMCID: PMC10081271 DOI: 10.1101/2023.03.30.534956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Transcription factors (TFs) play key roles in regulating the differentiation and function of stem cells, including muscle satellite cells (MuSCs), a resident stem cell population responsible for postnatal regeneration of the skeletal muscle. Sox11 belongs to the Sry-related HMG-box (SOX) family of TFs that play diverse roles in stem cell behavior and tissue specification. Analysis of single-cell RNA-sequencing (scRNA-seq) datasets identify a specific enrichment of Sox11 mRNA in differentiating but not quiescent MuSCs. Consistent with the scRNA-seq data, Sox11 levels increase during differentiation of murine primary myoblasts in vitro. scRNA-seq data comparing muscle regeneration in young and old mice further demonstrate that Sox11 expression is reduced in aged MuSCs. Age-related decline of Sox11 expression is associated with reduced chromatin contacts within the topologically associated domains. Unexpectedly, Myod1 Cre -driven deletion of Sox11 in embryonic myoblasts has no effects on muscle development and growth, resulting in apparently healthy muscles that regenerate normally. Pax7 CreER or Rosa26 CreER driven (MuSC-specific or global) deletion of Sox11 in adult mice similarly has no effects on MuSC differentiation or muscle regeneration. These results identify Sox11 as a novel myogenic differentiation marker with reduced expression in quiescent and aged MuSCs, but the specific function of Sox11 in myogenesis remain to be elucidated.
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Regal JA, Guerra García ME, Jain V, Chandramohan V, Ashley DM, Gregory SG, Thompson EM, López GY, Reitman ZJ. Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population. Acta Neuropathol Commun 2023; 11:50. [PMID: 36966348 PMCID: PMC10039537 DOI: 10.1186/s40478-023-01548-3] [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: 12/18/2022] [Accepted: 03/06/2023] [Indexed: 03/27/2023] Open
Abstract
Gangliogliomas are brain tumors composed of neuron-like and macroglia-like components that occur in children and young adults. Gangliogliomas are often characterized by a rare population of immature astrocyte-appearing cells expressing CD34, a marker expressed in the neuroectoderm (neural precursor cells) during embryogenesis. New insights are needed to refine tumor classification and to identify therapeutic approaches. We evaluated five gangliogliomas with single nucleus RNA-seq, cellular indexing of transcriptomes and epitopes by sequencing, and/or spatially-resolved RNA-seq. We uncovered a population of CD34+ neoplastic cells with mixed neuroectodermal, immature astrocyte, and neuronal markers. Gene regulatory network interrogation in these neuroectoderm-like cells revealed control of transcriptional programming by TCF7L2/MEIS1-PAX6 and SOX2, similar to that found during neuroectodermal/neural development. Developmental trajectory analyses place neuroectoderm-like tumor cells as precursor cells that give rise to neuron-like and macroglia-like neoplastic cells. Spatially-resolved transcriptomics revealed a neuroectoderm-like tumor cell niche with relative lack of vascular and immune cells. We used these high resolution results to deconvolute clinically-annotated transcriptomic data, confirming that CD34+ cell-associated gene programs associate with gangliogliomas compared to other glial brain tumors. Together, these deep transcriptomic approaches characterized a ganglioglioma cellular hierarchy-confirming CD34+ neuroectoderm-like tumor precursor cells, controlling transcription programs, cell signaling, and associated immune cell states. These findings may guide tumor classification, diagnosis, prognostication, and therapeutic investigations.
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Affiliation(s)
- Joshua A Regal
- Department of Radiation Oncology, Duke University, Durham, NC, 27710, USA
| | | | - Vaibhav Jain
- Duke Molecular Physiology Institute, Duke University, Durham, NC, 27710, USA
| | | | - David M Ashley
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, NC, 27710, USA
| | - Eric M Thompson
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
| | - Giselle Y López
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
- Department of Pathology, Duke University, Durham, NC, 27710, USA
| | - Zachary J Reitman
- Department of Radiation Oncology, Duke University, Durham, NC, 27710, USA.
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA.
- Department of Pathology, Duke University, Durham, NC, 27710, USA.
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He Y, Døssing KBV, Sloth AB, He X, Rossing M, Kjaer A. Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets. Cancers (Basel) 2023; 15. [PMID: 36900348 DOI: 10.3390/cancers15051557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/17/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Targeting glioblastoma (GBM) stem-like cells (GSCs) is a common interest in both the laboratory investigation and clinical treatment of GBM. Most of the currently applied GBM stem-like markers lack validation and comparison with common standards regarding their efficiency and feasibility in various targeting methods. Using single-cell RNA sequencing datasets from 37 GBM patients, we obtained a large pool of 2173 GBM stem-like marker candidates. To evaluate and select these candidates quantitatively, we characterized the efficiency of the candidate markers in targeting the GBM stem-like cells by their frequencies and significance of being the stem-like cluster markers. This was followed by further selection based on either their differential expression in GBM stem-like cells compared with normal brain cells or their relative expression level compared with other expressed genes. The cellular location of the translated protein was also considered. Different combinations of selection criteria highlight different markers for different application scenarios. By comparing the commonly used GSCs marker CD133 (PROM1) with markers selected by our method regarding their universality, significance, and abundance, we revealed the limitations of CD133 as a GBM stem-like marker. Overall, we propose BCAN, PTPRZ1, SOX4, etc. for laboratory-based assays with samples free of normal cells. For in vivo targeting applications that require high efficiency in targeting the stem-like subtype, the ability to distinguish GSCs from normal brain cells, and a high expression level, we recommend the intracellular marker TUBB3 and the surface markers PTPRS and GPR56.
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Vaidya M, Sreerama S, Gonzalez-Vega M, Smith J, Field M, Sugaya K. Coculture with Neural Stem Cells May Shift the Transcription Profile of Glioblastoma Multiforme towards Cancer-Specific Stemness. Int J Mol Sci 2023; 24:ijms24043242. [PMID: 36834653 PMCID: PMC9962301 DOI: 10.3390/ijms24043242] [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: 01/04/2023] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/09/2023] Open
Abstract
Glioblastoma multiforme (GBM) possesses a small but significant population of cancer stem cells (CSCs) thought to play a role in its invasiveness, recurrence, and metastasis. The CSCs display transcriptional profiles for multipotency, self-renewal, tumorigenesis, and therapy resistance. There are two possible theories regarding the origin of CSCs in the context of neural stem cells (NSCs); i.e., NSCs modify cancer cells by conferring them with cancer-specific stemness, or NSCs themselves are transformed into CSCs due to the tumor environment created by cancer cells. To test the theories and to investigate the transcriptional regulation of the genes involved in CSC formation, we cocultured NSC and GBM cell lines together. Where genes related to cancer stemness, drug efflux, and DNA modification were upregulated in GBM, they were downregulated in NSCs upon coculture. These results indicate that cancer cells shift the transcriptional profile towards stemness and drug resistance in the presence of NSCs. Concurrently, GBM triggers NSCs differentiation. Because the cell lines were separated by a membrane (0.4 µm pore size) to prevent direct contact between GBM and NSCs, cell-secreted signaling molecules and extracellular vesicles (EVs) are likely involved in reciprocal communication between NSCs and GBM, causing transcription modification. Understanding the mechanism of CSC creation will aid in the identification of precise molecular targets within the CSCs to exterminate them, which, in turn, will increase the efficacy of chemo-radiation treatment.
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Affiliation(s)
- Manjusha Vaidya
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Sandeep Sreerama
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Maxine Gonzalez-Vega
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Jonhoi Smith
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Melvin Field
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
- Orlando Neurosurgery, AdventHealth Neuroscience Institute, Orlando, FL 32803, USA
| | - Kiminobu Sugaya
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
- Correspondence:
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Sharpe MA, Baskin DS, Johnson RD, Baskin AM. Acquisition of Immune Privilege in GBM Tumors: Role of Prostaglandins and Bile Salts. Int J Mol Sci 2023; 24. [PMID: 36834607 DOI: 10.3390/ijms24043198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Based on the postulate that glioblastoma (GBM) tumors generate anti-inflammatory prostaglandins and bile salts to gain immune privilege, we analyzed 712 tumors in-silico from three GBM transcriptome databases for prostaglandin and bile synthesis/signaling enzyme-transcript markers. A pan-database correlation analysis was performed to identify cell-specific signal generation and downstream effects. The tumors were stratified by their ability to generate prostaglandins, their competency in bile salt synthesis, and the presence of bile acid receptors nuclear receptor subfamily 1, group H, member 4 (NR1H4) and G protein-coupled bile acid receptor 1 (GPBAR1). The survival analysis indicates that tumors capable of prostaglandin and/or bile salt synthesis are linked to poor outcomes. Tumor prostaglandin D2 and F2 syntheses are derived from infiltrating microglia, whereas prostaglandin E2 synthesis is derived from neutrophils. GBMs drive the microglial synthesis of PGD2/F2 by releasing/activating complement system component C3a. GBM expression of sperm-associated heat-shock proteins appears to stimulate neutrophilic PGE2 synthesis. The tumors that generate bile and express high levels of bile receptor NR1H4 have a fetal liver phenotype and a RORC-Treg infiltration signature. The bile-generating tumors that express high levels of GPBAR1 are infiltrated with immunosuppressive microglia/macrophage/myeloid-derived suppressor cells. These findings provide insight into how GBMs generate immune privilege and may explain the failure of checkpoint inhibitor therapy and provide novel targets for treatment.
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Stevanovic M, Lazic A, Schwirtlich M, Stanisavljevic Ninkovic D. The Role of SOX Transcription Factors in Ageing and Age-Related Diseases. Int J Mol Sci 2023; 24. [PMID: 36614288 DOI: 10.3390/ijms24010851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023] Open
Abstract
The quest for eternal youth and immortality is as old as humankind. Ageing is an inevitable physiological process accompanied by many functional declines that are driving factors for age-related diseases. Stem cell exhaustion is one of the major hallmarks of ageing. The SOX transcription factors play well-known roles in self-renewal and differentiation of both embryonic and adult stem cells. As a consequence of ageing, the repertoire of adult stem cells present in various organs steadily declines, and their dysfunction/death could lead to reduced regenerative potential and development of age-related diseases. Thus, restoring the function of aged stem cells, inducing their regenerative potential, and slowing down the ageing process are critical for improving the health span and, consequently, the lifespan of humans. Reprograming factors, including SOX family members, emerge as crucial players in rejuvenation. This review focuses on the roles of SOX transcription factors in stem cell exhaustion and age-related diseases, including neurodegenerative diseases, visual deterioration, chronic obstructive pulmonary disease, osteoporosis, and age-related cancers. A better understanding of the molecular mechanisms of ageing and the roles of SOX transcription factors in this process could open new avenues for developing novel strategies that will delay ageing and prevent age-related diseases.
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Nasrolahi A, Azizidoost S, Radoszkiewicz K, Najafi S, Ghaedrahmati F, Anbiyaee O, Khoshnam SE, Farzaneh M, Uddin S. Signaling pathways governing glioma cancer stem cells behavior. Cell Signal 2023; 101:110493. [PMID: 36228964 DOI: 10.1016/j.cellsig.2022.110493] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/30/2022]
Abstract
Glioma is the most common malignant brain tumor that develops in the glial tissue. Several studies have identified that glioma cancer stem cells (GCSCs) play important roles in tumor-initiating features in malignant gliomas. GCSCs are a small population in the brain that presents an essential role in the metastasis of glioma cells to other organs. These cells can self-renew and differentiate, which are thought to be involved in the pathogenesis of glioma. Therefore, targeting GCSCs might be a novel strategy for the treatment of glioma. Accumulating evidence revealed that several signaling pathways, including Notch, TGF-β, Wnt, STAT3, AKT, and EGFR mediated GCSC growth, proliferation, migration, and invasion. Besides, non-coding RNAs (ncRNAs), including miRNAs, circular RNAs, and long ncRNAs have been found to play pivotal roles in the regulation of GCSC pathogenesis and drug resistance. Therefore, targeting these pathways could open a new avenue for glioma management. In this review, we summarized critical signaling pathways involved in the stimulation or prevention of GCSCs tumorigenesis and invasiveness.
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Affiliation(s)
- Ava Nasrolahi
- Infectious Ophthalmologic Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Klaudia Radoszkiewicz
- Translational Platform for Regenerative Medicine, Mossakowski Medical Research Institute, Polish Academy of Sciences, Poland
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farhoodeh Ghaedrahmati
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Omid Anbiyaee
- Cardiovascular Research Center, Nemazi Hospital, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar.
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Abstract
Suspension and imaging cytometry techniques that simultaneously measure hundreds of cellular features are powering a new era of cell biology and transforming our understanding of human tissues and tumors. However, a central challenge remains in learning the identities of unexpected or novel cell types. Cell identification rubrics that could assist trainees, whether human or machine, are not always rigorously defined, vary greatly by field, and differentially rely on cell intrinsic measurements, cell extrinsic tissue measurements, or external contextual information such as clinical outcomes. This challenge is especially acute in the context of tumors, where cells aberrantly express developmental programs that are normally time, location, or cell-type restricted. Well-established fields have contrasting practices for cell identity that have emerged from convention and convenience as much as design. For example, early immunology focused on identifying minimal sets of protein features that mark individual, functionally distinct cells. In neuroscience, features including morphology, development, and anatomical location were typical starting points for defining cell types. Both immunology and neuroscience now aim to link standardized measurements of protein or RNA to informative cell functions such as electrophysiology, connectivity, lineage potential, phospho-protein signaling, cell suppression, and tumor cell killing ability. The expansion of automated, machine-driven methods for learning cell identity has further created an urgent need for a harmonized framework for distinguishing cell identity across fields and technology platforms. Here, we compare practices in the fields of immunology and neuroscience, highlight concepts from each that might work well in the other, and propose ways to implement these ideas to study neural and immune cell interactions in brain tumors and associated model systems.
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Affiliation(s)
- Stephanie Medina
- grid.152326.10000 0001 2264 7217Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Rebecca A. Ihrie
- grid.152326.10000 0001 2264 7217Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
| | - Jonathan M. Irish
- grid.152326.10000 0001 2264 7217Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
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14
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Xiao G, Wang K, Wang Z, Dai Z, Liang X, Ye W, Luo P, Zhang J, Liu Z, Cheng Q, Peng R. Machine learning-based identification of SOX10 as an immune regulator of macrophage in gliomas. Front Immunol 2022; 13:1007461. [PMID: 36524115 PMCID: PMC9745112 DOI: 10.3389/fimmu.2022.1007461] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/04/2022] [Indexed: 12/03/2022] Open
Abstract
Gliomas, originating from the glial cells, are the most lethal type of primary tumors in the central nervous system. Standard treatments like surgery have not significantly improved the prognosis of glioblastoma patients. Recently, immune therapy has become a novel and effective option. As a conserved group of transcriptional regulators, the Sry-type HMG box (SOX) family has been proved to have a correlation with numerous diseases. Based on the large-scale machine learning, we found that the SOX family, with significant immune characteristics and genomic profiles, can be divided into two distinct clusters in gliomas, among which SOX10 was identified as an excellent immune regulator of macrophage in gliomas. The high expression of SOX10 is related to a shorter OS in LGG, HGG, and pan-cancer groups but benefited from the immunotherapy. It turned out in single-cell sequencing that SOX10 is high in neurons, M1 macrophages, and neural stem cells. Also, macrophages are found to be elevated in the SOX10 high-expression group. SOX10 has a positive correlation with macrophage cytokine production and negative regulation of macrophages' chemotaxis and migration. In conclusion, our study demonstrates the outstanding cluster ability of the SOX family, indicating that SOX10 is an immune regulator of macrophage in gliomas, which can be an effective target for glioma immunotherapy.
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Affiliation(s)
- Gelei Xiao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China,Diagnosis and Treatment Center for Hydrocephalus, Xiangya Hospital, Central South University, Changsha, China,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Kaiyue Wang
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China,MRC Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xisong Liang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Weijie Ye
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Quan Cheng, ; Renjun Peng,
| | - Renjun Peng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Quan Cheng, ; Renjun Peng,
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15
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Xu Z, Jiang J, Wang S. The Critical Role of RNA m6A Methylation in Gliomas: Targeting the Hallmarks of Cancer. Cell Mol Neurobiol. [DOI: 10.1007/s10571-022-01283-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/04/2022] [Indexed: 11/03/2022]
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Drakulic D, Schwirtlich M, Petrovic I, Mojsin M, Milivojevic M, Kovacevic-grujicic N, Stevanovic M. Current Opportunities for Targeting Dysregulated Neurodevelopmental Signaling Pathways in Glioblastoma. Cells 2022; 11:2530. [PMID: 36010607 PMCID: PMC9406959 DOI: 10.3390/cells11162530] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022] Open
Abstract
Glioblastoma (GBM) is the most common and highly lethal type of brain tumor, with poor survival despite advances in understanding its complexity. After current standard therapeutic treatment, including tumor resection, radiotherapy and concomitant chemotherapy with temozolomide, the median overall survival of patients with this type of tumor is less than 15 months. Thus, there is an urgent need for new insights into GBM molecular characteristics and progress in targeted therapy in order to improve clinical outcomes. The literature data revealed that a number of different signaling pathways are dysregulated in GBM. In this review, we intended to summarize and discuss current literature data and therapeutic modalities focused on targeting dysregulated signaling pathways in GBM. A better understanding of opportunities for targeting signaling pathways that influences malignant behavior of GBM cells might open the way for the development of novel GBM-targeted therapies.
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Mercurio S, Serra L, Pagin M, Nicolis SK. Deconstructing Sox2 Function in Brain Development and Disease. Cells 2022; 11:cells11101604. [PMID: 35626641 PMCID: PMC9139651 DOI: 10.3390/cells11101604] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023] Open
Abstract
SOX2 is a transcription factor conserved throughout vertebrate evolution, whose expression marks the central nervous system from the earliest developmental stages. In humans, SOX2 mutation leads to a spectrum of CNS defects, including vision and hippocampus impairments, intellectual disability, and motor control problems. Here, we review how conditional Sox2 knockout (cKO) in mouse with different Cre recombinases leads to very diverse phenotypes in different regions of the developing and postnatal brain. Surprisingly, despite the widespread expression of Sox2 in neural stem/progenitor cells of the developing neural tube, some regions (hippocampus, ventral forebrain) appear much more vulnerable than others to Sox2 deletion. Furthermore, the stage of Sox2 deletion is also a critical determinant of the resulting defects, pointing to a stage-specificity of SOX2 function. Finally, cKOs illuminate the importance of SOX2 function in different cell types according to the different affected brain regions (neural precursors, GABAergic interneurons, glutamatergic projection neurons, Bergmann glia). We also review human genetics data regarding the brain defects identified in patients carrying mutations within human SOX2 and examine the parallels with mouse mutants. Functional genomics approaches have started to identify SOX2 molecular targets, and their relevance for SOX2 function in brain development and disease will be discussed.
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Rodriguez SMB, Staicu GA, Sevastre AS, Baloi C, Ciubotaru V, Dricu A, Tataranu LG. Glioblastoma Stem Cells-Useful Tools in the Battle against Cancer. Int J Mol Sci 2022; 23:ijms23094602. [PMID: 35562993 PMCID: PMC9100635 DOI: 10.3390/ijms23094602] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 03/07/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 02/01/2023] Open
Abstract
Glioblastoma stem cells (GSCs) are cells with a self-renewal ability and capacity to initiate tumors upon serial transplantation that have been linked to tumor cell heterogeneity. Most standard treatments fail to completely eradicate GSCs, causing the recurrence of the disease. GSCs could represent one reason for the low efficacy of cancer therapy and for the short relapse time. Nonetheless, experimental data suggest that the presence of therapy-resistant GSCs could explain tumor recurrence. Therefore, to effectively target GSCs, a comprehensive understanding of their biology and the survival and developing mechanisms during treatment is mandatory. This review provides an overview of the molecular features, microenvironment, detection, and targeting strategies of GSCs, an essential information required for an efficient therapy. Despite the outstanding results in oncology, researchers are still developing novel strategies, of which one could be targeting the GSCs present in the hypoxic regions and invasive edge of the glioblastoma.
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Affiliation(s)
- Silvia Mara Baez Rodriguez
- Neurosurgical Department, Clinical Hospital “Bagdasar-Arseni”, 041915 Bucharest, Romania; (S.M.B.R.); (V.C.); (L.G.T.)
| | - Georgiana-Adeline Staicu
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy, 200349 Craiova, Romania; (G.-A.S.); (C.B.)
| | - Ani-Simona Sevastre
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Medicine and Pharmacy, 200349 Craiova, Romania;
| | - Carina Baloi
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy, 200349 Craiova, Romania; (G.-A.S.); (C.B.)
| | - Vasile Ciubotaru
- Neurosurgical Department, Clinical Hospital “Bagdasar-Arseni”, 041915 Bucharest, Romania; (S.M.B.R.); (V.C.); (L.G.T.)
| | - Anica Dricu
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy, 200349 Craiova, Romania; (G.-A.S.); (C.B.)
- Correspondence:
| | - Ligia Gabriela Tataranu
- Neurosurgical Department, Clinical Hospital “Bagdasar-Arseni”, 041915 Bucharest, Romania; (S.M.B.R.); (V.C.); (L.G.T.)
- Department 6—Clinical Neurosciences, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
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Qin S, Liu G, Jin H, Chen X, He J, Xiao J, Qin Y, Mao Y, Zhao L, Falzone L. The Dysregulation of SOX Family Correlates with DNA Methylation and Immune Microenvironment Characteristics to Predict Prognosis in Hepatocellular Carcinoma. Disease Markers 2022; 2022:1-21. [PMID: 35465267 PMCID: PMC9020970 DOI: 10.1155/2022/2676114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/23/2022] [Indexed: 12/24/2022]
Abstract
Background Due to the molecular heterogeneity of hepatocellular carcinoma (HCC), majority of patients respond poorly among various of therapy. This study is aimed at conducting a comprehensive analysis about roles of SOX family in HCC for obtaining more therapeutic targets and biomarkers which may bring new ideas for the treatment of HCC. Methods UALCAN, Kaplan Meier plotter, cBioPortal, STRING, WebGestalt, Metascape, TIMER 2.0, DiseaseMeth, MethSurv, HPA, CCLE database, and Cytoscape software were used to comprehensively analyze the bioinformatic data. Results SOX2, SOX4, SOX8, SOX10, SOX11, SOX12, SOX17, and SOX18 were significantly differentially expressed in HCC and normal tissues and were valuable for the grade and survival of HCC patients. In addition, the gene alterations of SOX family happened frequently, and SOX4 and SOX17 had the highest mutation rate. The function of SOX family on HCC may be closely correlated with the regulation of angiogenesis-related signaling pathways. Moreover, SOX4, SOX8, SOX11, SOX12, SOX17, and SOX18 were correlation with 8 types of immune cells (including CD8+ T cell, CD4+ T cell, B cell, Tregs, neutrophil, macrophage, myeloid DC, and NK cell), and we found that most types of immune cells had a positive correlation with SOX family. Notably, CD4+ T cell and macrophage were positively related with all these SOX family. NK cells were negatively related with most SOX family genes. DNA methylation levels in promoter area of SOX2, SOX4, and SOX10 were lower in HCC than normal tissues, while SOX8, SOX11, SOX17, and SOX18 had higher DNA methylation levels than normal tissues. Moreover, higher DNA methylation level of SOX12 and SOX18 demonstrated worse survival rates in patients with HCC. Conclusion SOX family genes could predict the prognosis of HCC. In addition, the regulation of angiogenesis-related signaling pathways may participate in the development of HCC. DNA methylation level and immune microenvironment characteristics (especially CD4+ T cell and macrophage immune cell infiltration) could be a novel insight for predicting prognosis in HCC.
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Abstract
Many cells are capable of maintaining viability in a non-dividing state with minimal metabolism under unfavorable conditions. These are germ cells, adult stem cells, and microorganisms. Unfortunately, a resting state, or dormancy, is possible for tuberculosis bacilli in a latent form of the disease and cancer cells, which may later form secondary tumors (metastases) in different parts of the body. These cells are resistant to therapy that can destroy intensely dividing cells and to the host immune system. A cascade of reactions that allows cells to enter and exit dormancy is triggered by regulatory factors from the microenvironment in niches that harbor the cells. A ratio of forbidding and permitting signals dictates whether the cells become dormant or start proliferation. The only difference between the cell dormancy regulation in normal and pathological conditions is that pathogens, mycobacteria, and cancer cells can influence their own fate by changing their microenvironment. Certain mechanisms of these processes are considered in the review.
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Affiliation(s)
- E. S. Pshennikova
- Bakh Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - A. S. Voronina
- Bakh Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
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