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Primak A, Bozov K, Rubina K, Dzhauari S, Neyfeld E, Illarionova M, Semina E, Sheleg D, Tkachuk V, Karagyaur M. Morphogenetic theory of mental and cognitive disorders: the role of neurotrophic and guidance molecules. Front Mol Neurosci 2024; 17:1361764. [PMID: 38646100 PMCID: PMC11027769 DOI: 10.3389/fnmol.2024.1361764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/04/2024] [Indexed: 04/23/2024] Open
Abstract
Mental illness and cognitive disorders represent a serious problem for the modern society. Many studies indicate that mental disorders are polygenic and that impaired brain development may lay the ground for their manifestation. Neural tissue development is a complex and multistage process that involves a large number of distant and contact molecules. In this review, we have considered the key steps of brain morphogenesis, and the major molecule families involved in these process. The review provides many indications of the important contribution of the brain development process and correct functioning of certain genes to human mental health. To our knowledge, this comprehensive review is one of the first in this field. We suppose that this review may be useful to novice researchers and clinicians wishing to navigate the field.
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Affiliation(s)
- Alexandra Primak
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Kirill Bozov
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Kseniya Rubina
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Stalik Dzhauari
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Elena Neyfeld
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
- Federal State Budgetary Educational Institution of the Higher Education “A.I. Yevdokimov Moscow State University of Medicine and Dentistry” of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Maria Illarionova
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Semina
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitriy Sheleg
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
- Federal State Budgetary Educational Institution of the Higher Education “A.I. Yevdokimov Moscow State University of Medicine and Dentistry” of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Vsevolod Tkachuk
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim Karagyaur
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Moscow, Russia
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2
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Dai L, Shen KF, Zhang CQ. Plexin-mediated neuronal development and neuroinflammatory responses in the nervous system. Histol Histopathol 2023; 38:1239-1248. [PMID: 37170703 DOI: 10.14670/hh-18-625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Plexins are a large family of single-pass transmembrane proteins that mediate semaphorin signaling in multiple systems. Plexins were originally characterized for their role modulating cytoskeletal activity to regulate axon guidance during nervous system development. Thereafter, different semaphorin-plexin complexes were identified in the nervous system that have diverse functions in neurons, astrocytes, glia, oligodendrocytes, and brain derived-tumor cells, providing unexpected but meaningful insights into the biological activities of this protein family. Here, we review the overall structure and relevant downstream signaling cascades of plexins. We consider the current knowledge regarding the function of semaphorin-plexin cascades in the nervous system, including the most recent data regarding their roles in neuronal development, neuroinflammation, and glioma.
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Affiliation(s)
- Lu Dai
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
| | - Kai-Feng Shen
- Department of Neurosurgery, Epilepsy Research Center of PLA, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Chun-Qing Zhang
- Department of Neurosurgery, Epilepsy Research Center of PLA, Xinqiao Hospital, Army Medical University, Chongqing, China.
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3
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Demirci Y, Heger G, Katkat E, Papatheodorou I, Brazma A, Ozhan G. Brain Regeneration Resembles Brain Cancer at Its Early Wound Healing Stage and Diverges From Cancer Later at Its Proliferation and Differentiation Stages. Front Cell Dev Biol 2022; 10:813314. [PMID: 35223842 PMCID: PMC8868567 DOI: 10.3389/fcell.2022.813314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/18/2022] [Indexed: 12/15/2022] Open
Abstract
Gliomas are the most frequent type of brain cancers and characterized by continuous proliferation, inflammation, angiogenesis, invasion and dedifferentiation, which are also among the initiator and sustaining factors of brain regeneration during restoration of tissue integrity and function. Thus, brain regeneration and brain cancer should share more molecular mechanisms at early stages of regeneration where cell proliferation dominates. However, the mechanisms could diverge later when the regenerative response terminates, while cancer cells sustain proliferation. To test this hypothesis, we exploited the adult zebrafish that, in contrast to the mammals, can efficiently regenerate the brain in response to injury. By comparing transcriptome profiles of the regenerating zebrafish telencephalon at its three different stages, i.e., 1 day post-lesion (dpl)-early wound healing stage, 3 dpl-early proliferative stage and 14 dpl-differentiation stage, to those of two brain cancers, i.e., low-grade glioma (LGG) and glioblastoma (GBM), we reveal the common and distinct molecular mechanisms of brain regeneration and brain cancer. While the transcriptomes of 1 dpl and 3 dpl harbor unique gene modules and gene expression profiles that are more divergent from the control, the transcriptome of 14 dpl converges to that of the control. Next, by functional analysis of the transcriptomes of brain regeneration stages to LGG and GBM, we reveal the common and distinct molecular pathways in regeneration and cancer. 1 dpl and LGG and GBM resemble with regard to signaling pathways related to metabolism and neurogenesis, while 3 dpl and LGG and GBM share pathways that control cell proliferation and differentiation. On the other hand, 14 dpl and LGG and GBM converge with respect to developmental and morphogenetic processes. Finally, our global comparison of gene expression profiles of three brain regeneration stages, LGG and GBM exhibit that 1 dpl is the most similar stage to LGG and GBM while 14 dpl is the most distant stage to both brain cancers. Therefore, early convergence and later divergence of brain regeneration and brain cancer constitutes a key starting point in comparative understanding of cellular and molecular events between the two phenomena and development of relevant targeted therapies for brain cancers.
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Affiliation(s)
- Yeliz Demirci
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, Izmir, Turkey
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Esra Katkat
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, Izmir, Turkey
| | - Irene Papatheodorou
- European Molecular Biology Laboratory–European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Alvis Brazma
- European Molecular Biology Laboratory–European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Gunes Ozhan
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Inciralti-Balcova, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Inciralti-Balcova, Izmir, Turkey
- *Correspondence: Gunes Ozhan,
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4
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Cho H, Park HJ, Seo YK. Induction of PLXNA4 Gene during Neural Differentiation in Human Umbilical-Cord-Derived Mesenchymal Stem Cells by Low-Intensity Sub-Sonic Vibration. Int J Mol Sci 2022; 23:ijms23031522. [PMID: 35163445 PMCID: PMC8835879 DOI: 10.3390/ijms23031522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/22/2022] [Accepted: 01/27/2022] [Indexed: 02/01/2023] Open
Abstract
Human umbilical-cord-derived mesenchymal stem cells (hUC-MSC) are a type of mesenchymal stem cells and are more primitive than other MSCs. In this study, we identify novel genes and signal-activating proteins involved in the neural differentiation of hUC-MSCs induced by Low-Intensity Sub-Sonic Vibration (LISSV). RNA sequencing was used to find genes involved in the differentiation process by LISSV. The changes in hUC-MSCs caused by LISSV were confirmed by PLXNA4 overexpression and gene knockdown through small interfering RNA experiments. The six genes were increased among genes related to neurons and the nervous system. One of them, the PLXNA4 gene, is known to play a role as a guide for axons in the development of the nervous system. When the PLXNA4 recombinant protein was added, neuron-related genes were increased. In the PLXNA4 gene knockdown experiment, the expression of neuron-related genes was not changed by LISSV exposure. The PLXNA4 gene is activated by sema family ligands. The expression of SEMA3A was increased by LISSV, and its downstream signaling molecule, FYN, was also activated. We suggest that the PLXNA4 gene plays an important role in hUC-MSC neuronal differentiation through exposure to LISSV. The differentiation process depends on SEMA3A-PLXNA4-dependent FYN activation in hUC-MSCs.
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Affiliation(s)
- Hyunjin Cho
- Research Institute of Integrative Life Sciences, Dongguk University, Goyang-si 10326, Korea;
| | - Hee-Jung Park
- Department of Medical Biotechnology (BK21 Plus Team), Dongguk University, Goyang-si 10326, Korea;
| | - Young-Kwon Seo
- Department of Medical Biotechnology (BK21 Plus Team), Dongguk University, Goyang-si 10326, Korea;
- Correspondence:
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5
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Chen CH, Lin YJ, Lin YY, Lin CH, Feng LY, Chang IYF, Wei KC, Huang CY. Glioblastoma Primary Cells Retain the Most Copy Number Alterations That Predict Poor Survival in Glioma Patients. Front Oncol 2021; 11:621432. [PMID: 33981597 PMCID: PMC8108987 DOI: 10.3389/fonc.2021.621432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/06/2021] [Indexed: 11/16/2022] Open
Abstract
Gliomas are solid tumors that originate from glial cells in the brain or spine and account for 74.6% of malignant primary central nervous system tumors worldwide. As patient-derived primary cells are important tools for drug screening and new therapy development in glioma, we aim to understand the genomic similarity of the primary cells to their parental tumors by comparing their whole-genome copy number variations and expression profile of glioma clinicopathologic factors. We found that the primary cells from grade II/III gliomas lost most of the gene copy number alterations (CNAs), which were mainly located on chromosome 1p and 19q in their parental tumors. The glioblastoma (GBM) primary cells preserved 83.7% of the gene CNAs in the parental GBM tumors, including chromosome 7 gain and 10q loss. The CNA gains of LINC00226 and ADAM6 and the chromosome 16p11 loss were reconstituted in primary cells from both grade II/III gliomas and GBMs. Interestingly, we found these CNAs were correlated to overall survival (OS) in glioma patients using the Merged Cohort LGG and GBM dataset from cBioPortal. The gene CNAs preserved in glioma primary cells often predicted poor survival, whereas the gene CNAs lost in grade II/III primary cells were mainly associated to better prognosis in glioma patients. Glioma prognostic factors that predict better survival, such as IDH mutations and 1p/19q codeletion in grade II/III gliomas, were lost in their primary cells, whereas methylated MGMT promoters as well as TERT promoter mutations were preserved in GBM primary cells while lost in grade II/III primary cells. Our results suggest that GBM primary cells tend to preserve CNAs in their parental tumors, and these CNAs are correlated to poor OS and predict worse prognosis in glioma patients.
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Affiliation(s)
- Chia-Hua Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Ya-Jui Lin
- Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,The Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - You-Yu Lin
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chang-Hung Lin
- Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Li-Ying Feng
- School of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Kuo-Chen Wei
- Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,School of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan
| | - Chiung-Yin Huang
- School of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan
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6
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Kääriäinen A, Pesola V, Dittmann A, Kontio J, Koivunen J, Pihlajaniemi T, Izzi V. Machine Learning Identifies Robust Matrisome Markers and Regulatory Mechanisms in Cancer. Int J Mol Sci 2020; 21:E8837. [PMID: 33266472 PMCID: PMC7700160 DOI: 10.3390/ijms21228837] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
The expression and regulation of matrisome genes-the ensemble of extracellular matrix, ECM, ECM-associated proteins and regulators as well as cytokines, chemokines and growth factors-is of paramount importance for many biological processes and signals within the tumor microenvironment. The availability of large and diverse multi-omics data enables mapping and understanding of the regulatory circuitry governing the tumor matrisome to an unprecedented level, though such a volume of information requires robust approaches to data analysis and integration. In this study, we show that combining Pan-Cancer expression data from The Cancer Genome Atlas (TCGA) with genomics, epigenomics and microenvironmental features from TCGA and other sources enables the identification of "landmark" matrisome genes and machine learning-based reconstruction of their regulatory networks in 74 clinical and molecular subtypes of human cancers and approx. 6700 patients. These results, enriched for prognostic genes and cross-validated markers at the protein level, unravel the role of genetic and epigenetic programs in governing the tumor matrisome and allow the prioritization of tumor-specific matrisome genes (and their regulators) for the development of novel therapeutic approaches.
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Affiliation(s)
- Anni Kääriäinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
| | - Vilma Pesola
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
| | - Annalena Dittmann
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
| | - Juho Kontio
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
| | - Jarkko Koivunen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
| | - Taina Pihlajaniemi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
| | - Valerio Izzi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland; (A.K.); (V.P.); (A.D.); (J.K.); (J.K.); (T.P.)
- Faculty of Medicine, University of Oulu, P.O. BOX 8000, FI-90014 Oulu, Finland
- Finnish Cancer Institute, 00130 Helsinki, Finland
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Shin K, Shin H, Cho HJ, Kang H, Lee JK, Seo YJ, Shin YJ, Kim D, Koo H, Kong DS, Seol HJ, Lee JI, Lee HW, Nam DH. Sphere-Forming Culture for Expanding Genetically Distinct Patient-Derived Glioma Stem Cells by Cellular Growth Rate Screening. Cancers (Basel) 2020; 12:cancers12030549. [PMID: 32120790 PMCID: PMC7139415 DOI: 10.3390/cancers12030549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
Diffusely infiltrating gliomas (DIGs) are difficult to completely resect and are associated with a high rate of tumor relapse and progression from low- to high-grade glioma. In particular, optimized short-term culture-enriching patient-derived glioma stem cells (GSCs) are essential for customizing the therapeutic strategy based on clinically feasible in vitro drug screening for a wide range of DIGs, owing to the high inter-tumoral heterogeneity. Herein, we constructed a novel high-throughput culture condition screening platform called ‘GFSCAN’, which evaluated the cellular growth rates of GSCs for each DIG sample in 132 serum-free combinations, using 13 previously reported growth factors closely associated with glioma aggressiveness. In total, 72 patient-derived GSCs with available genomic profiles were tested in GFSCAN to explore the association between cellular growth rates in specific growth factor combinations and genomic/molecular backgrounds, including isocitrate dehydrogenase 1 (IDH1) mutation, chromosome arm 1p and 19q co-deletion, ATRX chromatin remodeler alteration, and transcriptional subtype. GSCs were clustered according to the dependency on epidermal growth factor and basic fibroblast growth factor (E&F), and isocitrate dehydrogenase 1 (IDH1) wild-type GSCs showed higher E&F dependencies than IDH1 mutant GSCs. More importantly, we elucidated optimal combinations for IDH1 mutant glioblastoma and lower grade glioma GSCs with low dependencies on E&F, which could be an aid in clinical decision-making for these DIGs. Thus, we demonstrated the utility of GFSCAN in personalizing in vitro cultivation to nominate personalized therapeutic options, in a clinically relevant time frame, for individual DIG patients, where standard clinical options have been exhausted.
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Affiliation(s)
- Kayoung Shin
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul 06531, Korea; (K.S.); (H.K.)
- Research Institute for Future Medicine, Samsung Medical Center, Seoul 06351, Korea; (H.S.); (H.J.C.); (Y.J.S.); (Y.J.S.); (D.K.)
| | - Hyemi Shin
- Research Institute for Future Medicine, Samsung Medical Center, Seoul 06351, Korea; (H.S.); (H.J.C.); (Y.J.S.); (Y.J.S.); (D.K.)
- Precision Medicine Research Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Hee Jin Cho
- Research Institute for Future Medicine, Samsung Medical Center, Seoul 06351, Korea; (H.S.); (H.J.C.); (Y.J.S.); (Y.J.S.); (D.K.)
- Precision Medicine Research Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Hyunju Kang
- Graduate School of Biomedical Science, Ajou University School of Medicine, Suwon 16499, Korea; (H.K.); (J.-K.L.)
| | - Jin-Ku Lee
- Graduate School of Biomedical Science, Ajou University School of Medicine, Suwon 16499, Korea; (H.K.); (J.-K.L.)
| | - Yun Jee Seo
- Research Institute for Future Medicine, Samsung Medical Center, Seoul 06351, Korea; (H.S.); (H.J.C.); (Y.J.S.); (Y.J.S.); (D.K.)
| | - Yong Jae Shin
- Research Institute for Future Medicine, Samsung Medical Center, Seoul 06351, Korea; (H.S.); (H.J.C.); (Y.J.S.); (Y.J.S.); (D.K.)
| | - Donggeon Kim
- Research Institute for Future Medicine, Samsung Medical Center, Seoul 06351, Korea; (H.S.); (H.J.C.); (Y.J.S.); (Y.J.S.); (D.K.)
| | - Harim Koo
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul 06531, Korea; (K.S.); (H.K.)
- Research Institute for Future Medicine, Samsung Medical Center, Seoul 06351, Korea; (H.S.); (H.J.C.); (Y.J.S.); (Y.J.S.); (D.K.)
| | - Doo-Sik Kong
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06531, Korea; (D.-S.K.); (H.J.S.); (J.-I.L.)
| | - Ho Jun Seol
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06531, Korea; (D.-S.K.); (H.J.S.); (J.-I.L.)
| | - Jung-Il Lee
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06531, Korea; (D.-S.K.); (H.J.S.); (J.-I.L.)
| | - Hye Won Lee
- Department of Hospital Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
- Correspondence: (H.W.L.); (D.-H.N.); Tel.: +82-31-5189-8531 (H.W.L.); +82-2-2148-3497 (D.-H.N.); Fax: +82-2-2148-9829 (H.W.L.); +82-2-2149-9829 (D.-H.N.)
| | - Do-Hyun Nam
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University, Seoul 06531, Korea; (K.S.); (H.K.)
- Research Institute for Future Medicine, Samsung Medical Center, Seoul 06351, Korea; (H.S.); (H.J.C.); (Y.J.S.); (Y.J.S.); (D.K.)
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06531, Korea; (D.-S.K.); (H.J.S.); (J.-I.L.)
- Correspondence: (H.W.L.); (D.-H.N.); Tel.: +82-31-5189-8531 (H.W.L.); +82-2-2148-3497 (D.-H.N.); Fax: +82-2-2148-9829 (H.W.L.); +82-2-2149-9829 (D.-H.N.)
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8
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Zeng Z, Vo AH, Mao C, Clare SE, Khan SA, Luo Y. Cancer classification and pathway discovery using non-negative matrix factorization. J Biomed Inform 2019; 96:103247. [PMID: 31271844 PMCID: PMC6697569 DOI: 10.1016/j.jbi.2019.103247] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/23/2019] [Accepted: 07/01/2019] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Extracting genetic information from a full range of sequencing data is important for understanding disease. We propose a novel method to effectively explore the landscape of genetic mutations and aggregate them to predict cancer type. DESIGN We applied non-smooth non-negative matrix factorization (nsNMF) and support vector machine (SVM) to utilize the full range of sequencing data, aiming to better aggregate genetic mutations and improve their power to predict disease type. More specifically, we introduce a novel classifier to distinguish cancer types using somatic mutations obtained from whole-exome sequencing data. Mutations were identified from multiple cancers and scored using SIFT, PP2, and CADD, and collapsed at the individual gene level. nsNMF was then applied to reduce dimensionality and obtain coefficient and basis matrices. A feature matrix was derived from the obtained matrices to train a classifier for cancer type classification with the SVM model. RESULTS We have demonstrated that the classifier was able to distinguish four cancer types with reasonable accuracy. In five-fold cross-validations using mutation counts as features, the average prediction accuracy was 80% (SEM = 0.1%), significantly outperforming baselines and outperforming models using mutation scores as features. CONCLUSION Using the factor matrices derived from the nsNMF, we identified multiple genes and pathways that are significantly associated with each cancer type. This study presents a generic and complete pipeline to study the associations between somatic mutations and cancers. The proposed method can be adapted to other studies for disease status classification and pathway discovery.
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Affiliation(s)
- Zexian Zeng
- Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Andy H Vo
- Committee on Developmental Biology and Regenerative Medicine, The University of Chicago, Chicago, IL, USA
| | - Chengsheng Mao
- Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Susan E Clare
- Department of Surgery, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
| | - Seema A Khan
- Department of Surgery, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
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9
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Multifaceted Functional Role of Semaphorins in Glioblastoma. Int J Mol Sci 2019; 20:ijms20092144. [PMID: 31052281 PMCID: PMC6539029 DOI: 10.3390/ijms20092144] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/19/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023] Open
Abstract
Glioblastoma (GBM) is the most malignant tumor type affecting the adult central nervous system. Despite advances in therapy, the prognosis for patients with GBM remains poor, with a median survival of about 15 months. To date, few treatment options are available and recent trials based on the molecular targeting of some of the GBM hallmark pathways (e.g., angiogenesis) have not produced any significant improvement in overall survival. The urgent need to develop more efficacious targeted therapies has led to a better molecular characterization of GBM, revealing an emerging role of semaphorins in GBM progression. Semphorins are a wide group of membrane-bound and secreted proteins, originally identified as axon guidance cues, signaling through their receptors, neuropilins, and plexins. A number of semaphorin signals involved in the control of axonal growth and navigation during development have been found to furthermore participate in crosstalk with different dysfunctional GBM pathways, controlling tumor cell proliferation, migration, and invasion, as well as tumor angiogenesis or immune response. In this review, we summarize the regulatory activities mediated by semaphorins and their receptors on the oncogenic pathways implicated in GBM growth and invasive/metastatic progression.
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10
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The Expression of Key Guidance Genes at a Forebrain Axon Turning Point Is Maintained by Distinct Fgfr Isoforms but a Common Downstream Signal Transduction Mechanism. eNeuro 2019; 6:eN-NWR-0086-19. [PMID: 30993182 PMCID: PMC6464512 DOI: 10.1523/eneuro.0086-19.2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/24/2022] Open
Abstract
During development the axons of neurons grow toward and locate their synaptic partners to form functional neural circuits. Axons do so by reading a map of guidance cues expressed by surrounding tissues. Guidance cues are expressed at a precise space and time, but how guidance cue expression is regulated, and in a coordinated manner, is poorly understood. Semaphorins (Semas) and Slits are families of molecular ligands that guide axons. We showed previously that fibroblast growth factor (Fgf) signaling maintains sema3a and slit1 forebrain expression in Xenopus laevis, and these two repellents cooperate to guide retinal ganglion cell (RGC) axons away from the mid-diencephalon and on towards the optic tectum. Here, we investigate whether there are common features of the regulatory pathways that control the expression of these two guidance cues at this single axon guidance decision point. We isolated the sema3a proximal promoter and confirmed its responsiveness to Fgf signaling. Through misexpression of truncated Fgf receptors (Fgfrs), we found that sema3a forebrain expression is dependent on Fgfr2-4 but not Fgfr1. This is in contrast to slit1, whose expression we showed previously depends on Fgfr1 but not Fgfr2-4. Using pharmacological inhibitors and misexpression of constitutively active (CA) and dominant negative (DN) signaling intermediates, we find that while distinct Fgfrs regulate these two guidance genes, intracellular signaling downstream of Fgfrs appears to converge along the phosphoinositol 3-kinase (PI3K)-Akt signaling pathway. A common PI3K-Akt signaling pathway may allow for the coordinated expression of guidance cues that cooperate to direct axons at a guidance choice point.
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Garcia S. Role of Semaphorins in Immunopathologies and Rheumatic Diseases. Int J Mol Sci 2019; 20:ijms20020374. [PMID: 30654587 PMCID: PMC6359241 DOI: 10.3390/ijms20020374] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 12/17/2022] Open
Abstract
Rheumatic diseases are disorders characterized by joint inflammation, in which other organs are also affected. There are more than two hundred rheumatic diseases, the most studied so far are rheumatoid arthritis, osteoarthritis, spondyloarthritis, systemic lupus erythematosus, and systemic sclerosis. The semaphorin family is a large group of proteins initially described as axon guidance molecules involved in nervous system development. Studies have demonstrated that semaphorins play a role in other processes such as the regulation of immunity, angiogenesis, bone remodeling, apoptosis, and cell migration and invasion. Moreover, semaphorins have been related to the pathogenesis of multiple sclerosis, asthma, Alzheimer, myocarditis, atherosclerosis, fibrotic diseases, osteopetrosis, and cancer. The aim of this review is to summarize current knowledge regarding the role of semaphorins in rheumatic diseases, and discuss their potential applications as therapeutic targets to treat these disorders.
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Affiliation(s)
- Samuel Garcia
- Department of Rheumatology and Clinical Immunology and Laboratory of Translational Immunology, University Medical Center Utrecht, University of Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands.
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Ferrer VP, Moura Neto V, Mentlein R. Glioma infiltration and extracellular matrix: key players and modulators. Glia 2018; 66:1542-1565. [DOI: 10.1002/glia.23309] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 01/18/2018] [Accepted: 01/29/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | | | - Rolf Mentlein
- Department of Anatomy; University of Kiel; Kiel Germany
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Angelopoulou E, Piperi C. Emerging role of plexins signaling in glioma progression and therapy. Cancer Lett 2018; 414:81-87. [DOI: 10.1016/j.canlet.2017.11.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 12/14/2022]
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Pathological and functional significance of Semaphorin-5A in pancreatic cancer progression and metastasis. Oncotarget 2017; 9:5931-5943. [PMID: 29464045 PMCID: PMC5814185 DOI: 10.18632/oncotarget.23644] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/11/2017] [Indexed: 01/23/2023] Open
Abstract
Semaphorin-5A (SEMA5A) has differential cell surface expression between normal and cancer cells and represents an attractive target for therapeutic intervention in pancreatic cancer (PC). In this study, we delineated the pathological expression and significance of SEMA5A during PC progression and metastasis. We utilized human tissue microarrays and different PC mouse models (Pdx1-cre; LSL- Kras(G12D), Pdx1-Cre; LSL-Kras(G12D); LSL-p53(R172H) and RIP1-Tag2) to analyze SEMA5A expression during PC progression. Using human patients and different mouse models, we demonstrated that SEMA5A expression was highest in liver metastases, followed by primary pancreatic tumors, and the lowest expression was found in the normal pancreas. SEMA5A expression was localized on tumor cells with no staining in the surrounding stroma. To understand the functional significance of SEMA5A, we treated PC cell lines with recombinant SEMA5A. We observed an increase in migration, chemotaxis, and scattering of PC cells. To delineate the signaling axis of SEMA5A, we generated SEMA5A receptor-Plexin-B3 knockdown in T3M-4 and CD18/HPAF PC cell lines and observed that the effect of SEMA5A treatment was absent in the Plexin-B3 knockdown counterparts of T3M-4 and CD18/HPAF cells. SEMA5A treatment leads to phosphorylation of cMET in Plexin-B3 dependent manner. Our data demonstrate that there is an increase in SEMA5A expression during PC progression and the elevation of this expression takes place at metastatic sites especially the liver in both exocrine and endocrine tumors. SEMA5A can elicit a migratory response in cells by activating cMET through the Plexin-B3 receptor. In conclusion, SEMA5A signaling represents a potential molecule for targeting metastasis in pancreatic cancer.
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Iwadate Y, Fukuda K, Matsutani T, Saeki N. Intrinsic protective mechanisms of the neuron-glia network against glioma invasion. J Clin Neurosci 2016; 26:19-25. [DOI: 10.1016/j.jocn.2015.07.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/02/2015] [Accepted: 07/03/2015] [Indexed: 10/25/2022]
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Moriarity BS, Otto GM, Rahrmann EP, Rathe SK, Wolf NK, Weg MT, Manlove LA, LaRue RS, Temiz NA, Molyneux SD, Choi K, Holly KJ, Sarver AL, Scott MC, Forster CL, Modiano JF, Khanna C, Hewitt SM, Khokha R, Yang Y, Gorlick R, Dyer MA, Largaespada DA. A Sleeping Beauty forward genetic screen identifies new genes and pathways driving osteosarcoma development and metastasis. Nat Genet 2015; 47:615-24. [PMID: 25961939 DOI: 10.1038/ng.3293] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/07/2015] [Indexed: 12/13/2022]
Abstract
Osteosarcomas are sarcomas of the bone, derived from osteoblasts or their precursors, with a high propensity to metastasize. Osteosarcoma is associated with massive genomic instability, making it problematic to identify driver genes using human tumors or prototypical mouse models, many of which involve loss of Trp53 function. To identify the genes driving osteosarcoma development and metastasis, we performed a Sleeping Beauty (SB) transposon-based forward genetic screen in mice with and without somatic loss of Trp53. Common insertion site (CIS) analysis of 119 primary tumors and 134 metastatic nodules identified 232 sites associated with osteosarcoma development and 43 sites associated with metastasis, respectively. Analysis of CIS-associated genes identified numerous known and new osteosarcoma-associated genes enriched in the ErbB, PI3K-AKT-mTOR and MAPK signaling pathways. Lastly, we identified several oncogenes involved in axon guidance, including Sema4d and Sema6d, which we functionally validated as oncogenes in human osteosarcoma.
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Affiliation(s)
- Branden S Moriarity
- 1] Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA. [2] Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA. [3] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - George M Otto
- 1] Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA. [2] Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA. [3] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [4] Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Eric P Rahrmann
- 1] Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA. [2] Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA. [3] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [4] Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Susan K Rathe
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Natalie K Wolf
- 1] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [2] Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Madison T Weg
- 1] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [2] Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Luke A Manlove
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rebecca S LaRue
- 1] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [2] Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Nuri A Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Kwangmin Choi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Kevin J Holly
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Aaron L Sarver
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Milcah C Scott
- 1] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [2] Department of Veterinary Clinical Sciences, University of Minnesota, St. Paul, Minnesota, USA
| | - Colleen L Forster
- BioNet, Academic Health Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jaime F Modiano
- 1] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [2] Department of Veterinary Clinical Sciences, University of Minnesota, St. Paul, Minnesota, USA. [3] Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Chand Khanna
- Tumor and Metastasis Biology Section, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephen M Hewitt
- Tissue Array Research Program (TARP), Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland, USA
| | - Rama Khokha
- Ontario Cancer Institute, Toronto, Ontario, Canada
| | - Yi Yang
- Department of Orthopedic Surgery, Musculoskeletal Tumor Center, People's Hospital, Peking University, Beijing, China
| | - Richard Gorlick
- 1] Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, New York, USA. [2] Department of Molecular Pharmacology, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, New York, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David A Largaespada
- 1] Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA. [2] Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA. [3] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [4] Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
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Man J, Shoemake J, Zhou W, Fang X, Wu Q, Rizzo A, Prayson R, Bao S, Rich JN, Yu JS. Sema3C promotes the survival and tumorigenicity of glioma stem cells through Rac1 activation. Cell Rep 2014; 9:1812-1826. [PMID: 25464848 DOI: 10.1016/j.celrep.2014.10.055] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/30/2014] [Accepted: 10/21/2014] [Indexed: 12/15/2022] Open
Abstract
Different cancer cell compartments often communicate through soluble factors to facilitate tumor growth. Glioma stem cells (GSCs) are a subset of tumor cells that resist standard therapy to contribute to disease progression. How GSCs employ a distinct secretory program to communicate with and nurture each other over the nonstem tumor cell (NSTC) population is not well defined. Here, we show that GSCs preferentially secrete Sema3C and coordinately express PlexinA2/D1 receptors to activate Rac1/nuclear factor (NF)-κB signaling in an autocrine/paracrine loop to promote their own survival. Importantly, Sema3C is not expressed in neural progenitor cells (NPCs) or NSTCs. Disruption of Sema3C induced apoptosis of GSCs, but not NPCs or NSTCs, and suppressed tumor growth in orthotopic models of glioblastoma. Introduction of activated Rac1 rescued the Sema3C knockdown phenotype in vivo. Our study supports the targeting of Sema3C to break this GSC-specific autocrine/paracrine loop in order to improve glioblastoma treatment, potentially with a high therapeutic index.
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Affiliation(s)
- Jianghong Man
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Jocelyn Shoemake
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Wenchao Zhou
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Xiaoguang Fang
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Qiulian Wu
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Anthony Rizzo
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Richard Prayson
- Department of Anatomic Pathology, Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA; Burkhardt Brain Tumor and Neuro-Oncology Center, Neurological Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Shideng Bao
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA; Burkhardt Brain Tumor and Neuro-Oncology Center, Neurological Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Jeremy N Rich
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA; Burkhardt Brain Tumor and Neuro-Oncology Center, Neurological Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Jennifer S Yu
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA; Burkhardt Brain Tumor and Neuro-Oncology Center, Neurological Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA; Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA.
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Brown KJ, Seol H, Pillai DK, Sankoorikal BJ, Formolo CA, Mac J, Edwards NJ, Rose MC, Hathout Y. The human secretome atlas initiative: implications in health and disease conditions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2454-61. [PMID: 23603790 DOI: 10.1016/j.bbapap.2013.04.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/26/2013] [Accepted: 04/11/2013] [Indexed: 01/24/2023]
Abstract
Proteomic analysis of human body fluids is highly challenging, therefore many researchers are redirecting efforts toward secretome profiling. The goal is to define potential biomarkers and therapeutic targets in the secretome that can be traced back in accessible human body fluids. However, currently there is a lack of secretome profiles of normal human primary cells making it difficult to assess the biological meaning of current findings. In this study we sought to establish secretome profiles of human primary cells obtained from healthy donors with the goal of building a human secretome atlas. Such an atlas can be used as a reference for discovery of potential disease associated biomarkers and eventually novel therapeutic targets. As a preliminary study, secretome profiles were established for six different types of human primary cell cultures and checked for overlaps with the three major human body fluids including plasma, cerebrospinal fluid and urine. About 67% of the 1054 identified proteins in the secretome of these primary cells occurred in at least one body fluid. Furthermore, comparison of the secretome profiles of two human glioblastoma cell lines to this new human secretome atlas enabled unambiguous identification of potential brain tumor biomarkers. These biomarkers can be easily monitored in different body fluids using stable isotope labeled standard proteins. The long term goal of this study is to establish a comprehensive online human secretome atlas for future use as a reference for any disease related secretome study. This article is part of a Special Issue entitled: An Updated Secretome.
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Affiliation(s)
- Kristy J Brown
- Center for Genetic Medicine Research, Children's National Medical Center, Washington DC 20010, USA
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