1
|
Kelam J, Kelam N, Filipović N, Komić L, Racetin A, Komić D, Kostić S, Kuzmić Prusac I, Vukojević K. Expression of Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) Candidate Genes EDA2R, PCDH9, and TRAF7 in Normal Human Kidney Development and CAKUT. Genes (Basel) 2024; 15:702. [PMID: 38927638 PMCID: PMC11203332 DOI: 10.3390/genes15060702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Approximately half of the cases of chronic kidney disease (CKD) in childhood are caused by congenital anomalies of the kidney and urinary tract (CAKUT). Specific genes were identified as having significant importance in regard to the underlying genetic factors responsible for the CAKUT phenotype, and in our research, we focused on analyzing and comparing the expression levels of ectodysplasin A2 receptor (EDA2R), protocadherin9 (PCDH9), and TNF receptor-associated factor 7 (TRAF7) proteins in the cortex and medulla of healthy control kidneys during developmental phases 2, 3, and 4. We also performed an analysis of the area percentages of the mentioned proteins in the cortical and medullary sections of healthy embryonic and fetal kidneys compared to those affected by CAKUT, including duplex kidneys (DK), horseshoe kidneys (HK), hypoplastic kidneys (HYP), and dysplastic kidneys (DYS). We found that the CAKUT candidate gene proteins EDA2R, PCDH9, and TRAF7 are all expressed during normal human kidney development stages. In DYS, the expression of EDA2R was higher than in normal kidneys, likely due to EDA2R's role in apoptosis, which was upregulated in specific cases and could possibly contribute to the formation of DYS. The expression of PCDH9 was lower in HK, which can be attributed to the possible role of PCDH9 in cell migration suppression. Decreased PCDH9 expression is linked to increased cell migration, potentially contributing to the development of HK. The level of TRAF7 expression was reduced in all examined kidney disorders compared to normal kidneys, suggesting that this reduction might be attributed to the crucial role of TRAF7 in the formation of endothelium and ciliogenesis, both of which are essential for normal kidney development. Further research is required to ascertain the function of these proteins in both the typical development of the kidney and in CAKUT.
Collapse
Affiliation(s)
- Jelena Kelam
- Department of Family Medicine, Split-Dalmatia County Health Center, 21000 Split, Croatia; (J.K.); (L.K.)
| | - Nela Kelam
- Department of Anatomy, Histology and Embryology, University of Split School of Medicine, 21000 Split, Croatia; (N.K.); (N.F.); (A.R.); (D.K.); (S.K.)
| | - Natalija Filipović
- Department of Anatomy, Histology and Embryology, University of Split School of Medicine, 21000 Split, Croatia; (N.K.); (N.F.); (A.R.); (D.K.); (S.K.)
| | - Luka Komić
- Department of Family Medicine, Split-Dalmatia County Health Center, 21000 Split, Croatia; (J.K.); (L.K.)
| | - Anita Racetin
- Department of Anatomy, Histology and Embryology, University of Split School of Medicine, 21000 Split, Croatia; (N.K.); (N.F.); (A.R.); (D.K.); (S.K.)
| | - Dora Komić
- Department of Anatomy, Histology and Embryology, University of Split School of Medicine, 21000 Split, Croatia; (N.K.); (N.F.); (A.R.); (D.K.); (S.K.)
| | - Sandra Kostić
- Department of Anatomy, Histology and Embryology, University of Split School of Medicine, 21000 Split, Croatia; (N.K.); (N.F.); (A.R.); (D.K.); (S.K.)
| | - Ivana Kuzmić Prusac
- Department of Pathology, University Hospital Center Split, 21000 Split, Croatia;
| | - Katarina Vukojević
- Department of Anatomy, Histology and Embryology, University of Split School of Medicine, 21000 Split, Croatia; (N.K.); (N.F.); (A.R.); (D.K.); (S.K.)
- Department of Anatomy, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- Center for Translational Research in Biomedicine, School of Medicine, University of Split, 21000 Split, Croatia
| |
Collapse
|
2
|
Bagratuni T, Aktypi F, Theologi O, Sakkou M, Verrou KM, Mavrianou‐Koutsoukou N, Patseas D, Liacos C, Skourti S, Papadimou A, Taouxi K, Theodorakakou F, Kollias G, Sfikakis P, Terpos E, Dimopoulos MA, Kastritis E. Single-cell analysis of MYD88 L265P and MYD88 WT Waldenström macroglobulinemia patients. Hemasphere 2024; 8:e27. [PMID: 38435423 PMCID: PMC10878187 DOI: 10.1002/hem3.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 11/07/2023] [Indexed: 03/05/2024] Open
Abstract
Waldenström macroglobulinemia (WM) is characterized by the expansion of clonal lymphoplasmacytic cells; the MYD88L265P somatic mutation is found in >90% of patients, but malignant B cells may still display intra-clonal heterogeneity. To assess clonal heterogeneity in WM, we generated and performed single-cell RNA sequencing of CD19+ sorted cells from five patients with MYD88 L265P and two patients with MYD88 WT genotype as well as two healthy donors. We identified distinct transcriptional patterns in the clonal subpopulations not only between the two genetically distinct WM subgroups but also among MYD88 L265P patients, which affected the B cell composition in the different subgroups. Comparison of clonal and normal/polyclonal B cells within each patient sample enabled the identification of patient-specific transcriptional changes. We identified gene signatures active in a subset of MYD88L265P patients, while other signatures were active in MYD88 WT patients. Finally, gene expression analysis showed common transcriptional features between patients compared to the healthy control but also differentially expressed genes between MYD88 L265P and MYD88 WT patients involved in distinct pathways, including NFκΒ, BCL2, and BTK. Overall, our data highlight the intra-tumor clonal heterogeneity in WM with potential prognostic and therapeutic implications.
Collapse
Affiliation(s)
- Tina Bagratuni
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Foteini Aktypi
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Ourania Theologi
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Maria Sakkou
- School of Medicine, Center of New Biotechnologies & Precision MedicineNational and Kapodistrian University of AthensAthensGreece
- Department of PhysiologyNational and Kapodistrian University of Athens Medical SchoolAthensGreece
- Biomedical Sciences Research Center (BSRC) ‘Alexander Fleming’Institute for BioinnovationVariGreece
| | - Kleio Maria Verrou
- School of Medicine, Center of New Biotechnologies & Precision MedicineNational and Kapodistrian University of AthensAthensGreece
- Joint Rheumatology ProgramNational and Kapodistrian University of Athens Medical SchoolAthensGreece
| | - Nefeli Mavrianou‐Koutsoukou
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Dimitrios Patseas
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Christine Liacos
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Stamatia Skourti
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Alexandra Papadimou
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Kostantina Taouxi
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Foteini Theodorakakou
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Georgios Kollias
- School of Medicine, Center of New Biotechnologies & Precision MedicineNational and Kapodistrian University of AthensAthensGreece
- Department of PhysiologyNational and Kapodistrian University of Athens Medical SchoolAthensGreece
- Biomedical Sciences Research Center (BSRC) ‘Alexander Fleming’Institute for BioinnovationVariGreece
| | - Petros Sfikakis
- School of Medicine, Center of New Biotechnologies & Precision MedicineNational and Kapodistrian University of AthensAthensGreece
- Joint Rheumatology ProgramNational and Kapodistrian University of Athens Medical SchoolAthensGreece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Meletios A. Dimopoulos
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| | - Efstathios Kastritis
- Department of Clinical Therapeutics, School of MedicineNational and Kapodistrian University of AthensAthensGreece
| |
Collapse
|
3
|
An integrated analysis of the effects of maternal broccoli sprouts exposure on transcriptome and methylome in prevention of offspring mammary cancer. PLoS One 2022; 17:e0264858. [PMID: 35263365 PMCID: PMC8906608 DOI: 10.1371/journal.pone.0264858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/17/2022] [Indexed: 11/19/2022] Open
Abstract
Broccoli sprouts (BSp), a cruciferous vegetable, has shown promising effects on prevention of many types of cancer including breast cancer (BC). BC has a developmental foundation, and maternal nutrition status may influence an offspring’s risk to BC later in life. What is less understood, however, is the influence of maternal nutrition intervention on reversing epigenomic abnormalities that are essential in BC programming during early development. Our research focused on how maternal exposure to BSp diet prevents offspring BC and investigation of possible epigenetic mechanisms during these processes. Our results showed that maternal feeding of BSp can prevent mammary tumor development in the offspring of a transgenic mouse model. Through comprehensive integrated multi-omics studies on transcriptomic and methylomic analysis, we identified numerous target genes exhibiting significantly differential gene expression and DNA methylation patterns in the offspring mammary tumor. We discovered that maternal exposure to BSp diet can induce both gene and methylation changes in several key genes such as Avpr2, Cyp4a12b, Dpp6, Gria2, Pcdh9 and Tspan11 that are correlated with pivotal biological functions during carcinogenesis. In addition, we found an impact of maternal BSp treatment on DNA methyltransferase and histone deacetylases activity. Our study provides knowledgeable information regarding how maternal BSp diet influences key tumor-related gene expression and the epigenetic changes using a genome-wide perspective. Additionally, these findings provide mechanistic insights into the effectiveness of maternal BSp administration on the prevention of BC in the offspring later in life, which may lead to an early-life BC chemopreventive strategy that benefits the progenies’ long-term health.
Collapse
|
4
|
COP1 Acts as a Ubiquitin Ligase for PCDH9 Ubiquitination and Degradation in Human Glioma. Mol Neurobiol 2022; 59:2378-2388. [PMID: 35084653 DOI: 10.1007/s12035-021-02634-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
Constitutive photomorphogenic 1 (COP1, also known as RFWD2), a ring-finger-type E3 ubiquitin ligase, has been reported to play a pivotal role in the regulation of cell growth, apoptosis, and DNA repair. Accumulating evidence has suggested that COP1 plays a role in tumorigenesis by triggering the ubiquitination and degradation of its substrates, but the potential mechanism remains unclear. In this study, COP1 was used as a bait in a yeast two-hybrid experiment to screen COP1-interacting proteins in a human brain cDNA library, and the results indicated that protocadherin 9 (PCDH9) was a potential binding protein of COP1. The interaction between and colocalization of COP1 and PCDH9 was further confirmed by coimmunoprecipitation (co-IP) assay and immunofluorescent staining. Subsequently, we demonstrated that COP1 acted as an E3 ligase to promote the ubiquitination and degradation of PCDH9 through the proteasome pathway in glioma cells. Furthermore, we identified that the type of COP1 mediated PCDH9 ubiquitination was Lys48-linked polyubiquitination. Finally, we found that the COP1 protein level was inversely correlated with the PCDH9 protein level in human glioma tissues. Taken together, our results suggest that COP1 is an E3 ubiquitin ligase for PCDH9 and reveal an important mechanism for PCDH9 regulation in human glioma.
Collapse
|
5
|
Expression profiles and prognostic significance of WNT family members in glioma via bioinformatic analysis. Biosci Rep 2021; 40:222401. [PMID: 32181818 PMCID: PMC7103590 DOI: 10.1042/bsr20194255] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/13/2020] [Accepted: 03/16/2020] [Indexed: 01/11/2023] Open
Abstract
AIMS The dysregulation and essential role of WNTs in glioma have been widely implicated. However, there is a paucity of literature on the expression status of all the 19 WNTs in glioma. Our study was aimed to evaluate the expression and prognostic values of the 19 WNTs in glioma. METHODS mRNA expression and clinical data were retrieved from the Cancer Genome Atlas (TCGA) database, Chinese Glioma Genome Atlas (CGGA), GTEx and ONCOMINE databases. The 50 frequent neighbor genes of WNT5A and WNT10B were shown with PPI network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. RESULTS We found that the mRNA expression of WNT5A was significantly higher in glioma; however, the WNT10B expression was significantly lower in glioma. Furthermore, the expression of WNT5A and WNT10B was associated with the clinicopathology of glioma. The survival analysis revealed that the higher expressions of WNT5A and WNT16 were associated poor overall survival (OS) in patients with glioma. Conversely, overexpression of WNT3, WNT5B, and WNT10B was associated with better OS. Finally, Go and KEGG analysis revealed WNT5A was associated with multiple signal translations, and crucial oncogenes (EGFR and MDM2) and 2 important tumor suppressors (PTEN and IKN4a/ARF) were found closely correlated with WNT5A in glioma. CONCLUSION Among 19WNTs, WNT5A can serve as a candidate to diagnose and therapy glioma, while WNT10B might be valuable for anti-glioma research. The presumed direction was provided to explore the relation of WNTs signal and multiple pathways in glioma.
Collapse
|
6
|
Jaafar L, Fakhoury I, Saab S, El-Hajjar L, Abou-Kheir W, El-Sibai M. StarD13 differentially regulates migration and invasion in prostate cancer cells. Hum Cell 2021; 34:607-623. [PMID: 33420961 DOI: 10.1007/s13577-020-00479-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/24/2020] [Indexed: 11/26/2022]
Abstract
Prostate cancer is the second most commonly diagnosed cancer in men and one of the main leading causes of cancer deaths among men worldwide. Rapid uncontrolled growth and the ability to metastasize to other sites are key hallmarks in cancer development and progression. The Rho family of GTPases and its activators the GTPase-activating proteins (GAPs) are required for regulating cancer cell proliferation and migration. StarD13 is a GAP for Rho GTPases, specifically for RhoA and Cdc42. We have previously shown that StarD13 acts as a tumor suppressor in astrocytoma as well as breast and colorectal cancer. In this study, we performed a functional comparative analysis of StarD13 targets/and or interacting molecules to understand the general role that StarD13 plays in cancers. Our data highlight the importance of StarD13 in modulating several hallmarks of cancer. Findings from database mining and immunohistochemistry revealed that StarD13 is underexpressed in prostate cancers, in addition knocking down Stard13 increased cancer cell proliferation, consistent with its role as a tumor suppressor. Stard13 depletion, however, led to an increase in cell adhesion, which inhibited 2D cell migration. Most interestingly, StarD13 depletion increases invasion and matrix degradation, at least in part, through its regulation of Cdc42. Altogether, the data presented suggest that StarD13 acts as a tumor suppressor inhibiting prostate cancer cell invasion.
Collapse
Affiliation(s)
- Leila Jaafar
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Chouran, P.O. Box 13-5053, Beirut, 1102 2801, Lebanon
| | - Isabelle Fakhoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Chouran, P.O. Box 13-5053, Beirut, 1102 2801, Lebanon
| | - Sahar Saab
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Chouran, P.O. Box 13-5053, Beirut, 1102 2801, Lebanon
| | - Layal El-Hajjar
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Wassim Abou-Kheir
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Mirvat El-Sibai
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Chouran, P.O. Box 13-5053, Beirut, 1102 2801, Lebanon.
| |
Collapse
|
7
|
Cho SB. Set-Wise Differential Interaction Between Copy Number Alterations and Gene Expressions of Lower-Grade Glioma Reveals Prognosis-Associated Pathways. ENTROPY 2020; 22:e22121434. [PMID: 33353229 PMCID: PMC7765960 DOI: 10.3390/e22121434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/30/2020] [Accepted: 12/16/2020] [Indexed: 12/22/2022]
Abstract
The integrative analysis of copy number alteration (CNA) and gene expression (GE) is an essential part of cancer research considering the impact of CNAs on cancer progression and prognosis. In this research, an integrative analysis was performed with generalized differentially coexpressed gene sets (gdCoxS), which is a modification of dCoxS. In gdCoxS, set-wise interaction is measured using the correlation of sample-wise distances with Renyi’s relative entropy, which requires an estimation of sample density based on omics profiles. To capture correlations between the variables, multivariate density estimation with covariance was applied. In the simulation study, the power of gdCoxS outperformed dCoxS that did not use the correlations in the density estimation explicitly. In the analysis of the lower-grade glioma of the cancer genome atlas program (TCGA-LGG) data, the gdCoxS identified 577 pathway CNAs and GEs pairs that showed significant changes of interaction between the survival and non-survival group, while other benchmark methods detected lower numbers of such pathways. The biological implications of the significant pathways were well consistent with previous reports of the TCGA-LGG. Taken together, the gdCoxS is a useful method for an integrative analysis of CNAs and GEs.
Collapse
Affiliation(s)
- Seong Beom Cho
- Department of Biomedical Informatics, College of Medicine, Gachon University, Seongnam-Daero 1342, Korea
| |
Collapse
|
8
|
Al Haddad M, El-Rif R, Hanna S, Jaafar L, Dennaoui R, Abdellatef S, Miskolci V, Cox D, Hodgson L, El-Sibai M. Differential regulation of rho GTPases during lung adenocarcinoma migration and invasion reveals a novel role of the tumor suppressor StarD13 in invadopodia regulation. Cell Commun Signal 2020; 18:144. [PMID: 32900380 PMCID: PMC7487901 DOI: 10.1186/s12964-020-00635-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/03/2020] [Indexed: 11/11/2022] Open
Abstract
Background Lung cancer is the second most commonly occurring cancer. The ability to metastasize and spread to distant locations renders the tumor more aggressive. Members of the Rho subfamily of small GTP-binding proteins (GTPases) play a central role in the regulation of the actin cytoskeleton and in cancer cell migration and metastasis. In this study we investigated the role of the RhoA/Cdc42 GAP, StarD13, a previously described tumor suppressor, in malignancy, migration and invasion of the lung cancer cells A549. Methods We knocked down StarD13 expression in A549 lung cancer cells and tested the effect on cell migration and invadopodia formation using time lapse imaging and invasion assays. We also performed rescue experiments to determine the signaling pathways downstream of StarD13 and transfected the cells with FRET biosensors for RhoGTPases to identify the proteins involved in invadopodia formation. Results We observed a decrease in the level of expression of StarD13 in lung tumor tissues compared to normal lung tissues through immunohistochemistry. StarD13 also showed a lower expression in the lung adenocarcinoma cell line A549 compared to normal lung cells, WI38. In addition, the depletion of StarD13 increased cell proliferation and viability in WI38 and A549 cells, suggesting that StarD13 might potentially be a tumor suppressor in lung cancer. The depletion of StarD13, however, inhibited cell motility, conversely demonstrating a positive regulatory role in cell migration. This was potentially due to the constitutive activation of RhoA detected by pull down and FRET assays. Surprisingly, StarD13 suppressed cell invasion by inhibiting Cdc42-mediated invadopodia formation. Indeed, TKS4 staining and invadopodia assay revealed that StarD13 depletion increased Cdc42 activation as well as invadopodia formation and matrix degradation. Normal lung cells depleted of StarD13 also produced invadopodia, otherwise a unique hallmark of invasive cancer cells. Cdc42 knock down mimicked the effects of StarD13, while overexpression of a constitutively active Cdc42 mimicked the effects of its depletion. Finally, immunostaining and FRET analysis revealed the absence of StarD13 in invadopodia as compared to Cdc42, which was activated in invadopodia at the sites of matrix degradation. Conclusion In conclusion, StarD13 plays distinct roles in lung cancer cell migration and invasion through its differential regulation of Rho GTPases. Video abstract.
Collapse
Affiliation(s)
- Maria Al Haddad
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, P.O. Box: 13-5053. Chouran, Beirut, 1102 2801, Lebanon
| | - Rayane El-Rif
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, P.O. Box: 13-5053. Chouran, Beirut, 1102 2801, Lebanon
| | - Samer Hanna
- Department of Pediatrics HemeOnc division, Weill Cornell Medicine, Joan & Sanford I. Weill Medical College of Cornell University, New York, USA
| | - Leila Jaafar
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, P.O. Box: 13-5053. Chouran, Beirut, 1102 2801, Lebanon
| | - Rayanne Dennaoui
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, P.O. Box: 13-5053. Chouran, Beirut, 1102 2801, Lebanon
| | - Sandra Abdellatef
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, P.O. Box: 13-5053. Chouran, Beirut, 1102 2801, Lebanon
| | - Veronika Miskolci
- Department of Medical Microbiology and Immunology, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - Dianne Cox
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, USA
| | - Louis Hodgson
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, USA
| | - Mirvat El-Sibai
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, P.O. Box: 13-5053. Chouran, Beirut, 1102 2801, Lebanon.
| |
Collapse
|
9
|
Mishan MA, Tabari MAK, Parnian J, Fallahi J, Mahrooz A, Bagheri A. Functional mechanisms of miR-192 family in cancer. Genes Chromosomes Cancer 2020; 59:722-735. [PMID: 32706406 DOI: 10.1002/gcc.22889] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/14/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022] Open
Abstract
By growing research on the mechanisms and functions of microRNAs (miRNAs, miRs), the role of these noncoding RNAs gained more attention in healthcare. Due to the remarkable regulatory role of miRNAs, any dysregulation in their expression causes cellular functional impairment. In recent years, it has become increasingly apparent that these small molecules contribute to development, cell differentiation, proliferation, apoptosis, and tumor growth. In many studies, the miR-192 family has been suggested as a potential prognostic and diagnostic biomarker and even as a possible therapeutic target for several cancers. However, the mechanistic effects of the miR-192 family on cancer cells are still controversial. Here, we have reviewed each family member of the miR-192 including miR-192, miR-194, and miR-215, and discussed their mechanistic roles in various cancers.
Collapse
Affiliation(s)
- Mohammad Amir Mishan
- Ocular Tissue Engineering Research Center, Research Institute for Ophthalmology and Vision Science, Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Amin Khazeei Tabari
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
- USERN Office, Mazandaran University of Medical Sciences, Sari, Iran
| | - Javad Parnian
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Jafar Fallahi
- Molecular Medicine Department, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abdolkarim Mahrooz
- Department of Clinical Biochemistry and Medical Genetics, Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Abouzar Bagheri
- Department of Clinical Biochemistry and Medical Genetics, Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| |
Collapse
|
10
|
Molecular Characterization of Astrocytoma Progression Towards Secondary Glioblastomas Utilizing Patient-Matched Tumor Pairs. Cancers (Basel) 2020; 12:cancers12061696. [PMID: 32604718 PMCID: PMC7352509 DOI: 10.3390/cancers12061696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/08/2020] [Accepted: 06/21/2020] [Indexed: 12/16/2022] Open
Abstract
Astrocytomas are primary human brain tumors including diffuse or anaplastic astrocytomas that develop towards secondary glioblastomas over time. However, only little is known about molecular alterations that drive this progression. We measured multi-omics profiles of patient-matched astrocytoma pairs of initial and recurrent tumors from 22 patients to identify molecular alterations associated with tumor progression. Gene copy number profiles formed three major subcluters, but more than half of the patient-matched astrocytoma pairs differed in their gene copy number profiles like astrocytomas from different patients. Chromosome 10 deletions were not observed for diffuse astrocytomas, but occurred in corresponding recurrent tumors. Gene expression profiles formed three other major subclusters and patient-matched expression profiles were much more heterogeneous than their copy number profiles. Still, recurrent tumors showed a strong tendency to switch to the mesenchymal subtype. The direct progression of diffuse astrocytomas to secondary glioblastomas showed the largest number of transcriptional changes. Astrocytoma progression groups were further distinguished by signaling pathway expression signatures affecting cell division, interaction and differentiation. As expected, IDH1 was most frequently mutated closely followed by TP53, but also MUC4 involved in the regulation of apoptosis and proliferation was frequently mutated. Astrocytoma progression groups differed in their mutation frequencies of these three genes. Overall, patient-matched astrocytomas can differ substantially within and between patients, but still molecular signatures associated with the progression to secondary glioblastomas exist and should be analyzed for their potential clinical relevance in future studies.
Collapse
|
11
|
Clinical relevance and functional significance of cell-free microRNA-1260b expression profiles in infiltrative myxofibrosarcoma. Sci Rep 2020; 10:9414. [PMID: 32523124 PMCID: PMC7287053 DOI: 10.1038/s41598-020-66120-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 05/13/2020] [Indexed: 12/24/2022] Open
Abstract
Infiltrative tumor growth into adjacent soft tissues is a major cause of the frequent recurrence and tumor-related death of myxofibrosarcoma (MFS), but no useful biomarkers reflecting tumor burden and infiltrative growth are available. While emerging evidence suggests a diagnostic and functional role of extracellular/circulating microRNA (miRNA) in various malignant diseases, their significance in MFS patients remains unknown. Global miRNA profiling identified four upregulated miRNAs in MFS patient sera and culture media of MFS cells. Among these, serum miR-1260b level was significantly upregulated in patient serum discriminating from healthy individuals and closely correlated with clinical status and tumor dynamics in MFS-bearing mice. In addition, high miR-1260b expression in serum was correlated with radiological tail-like patterns, characteristic of the infiltrative MFS. The extracellular miR-1260b was embedded in tumor-derived extracellular vesicles (EVs) and promoted cellular invasion of MFS through the downregulation of PCDH9 in the adjacent normal fibroblasts. Collectively, circulating miR-1260b expression may represent a novel diagnostic target for tumor monitoring of this highly aggressive sarcoma. Moreover, EV-miR-1260b could act as a transfer messenger to adjacent cells and mediate the infiltrative growth of MFS, providing new insights into the mechanism of infiltrative nature via crosstalk between tumor cells and their microenvironment.
Collapse
|
12
|
Ahlstedt J, Konradsson E, Ceberg C, Redebrandt HN. Increased effect of two-fraction radiotherapy in conjunction with IDO1 inhibition in experimental glioblastoma. PLoS One 2020; 15:e0233617. [PMID: 32469935 PMCID: PMC7259656 DOI: 10.1371/journal.pone.0233617] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 05/09/2020] [Indexed: 12/24/2022] Open
Abstract
Objectives The aim of the study was to investigate therapeutic efficacy of single- or two-fraction radiotherapy in conjunction with IDO1-inhibition in a syngeneic rat glioblastoma model. IDO is known to cause immunosuppression through breakdown of tryptophan in the tumor microenvironment. Methods Gene expression analyses of IDO in glioblastoma were performed with data from publicly available datasets. Fractionation studies were done on animals to evaluate tumor size, immune cell infiltration of tumors and serum profile on day 18 after tumor inoculation. Survival analyses were done with animals carrying intracranial glioblastomas comparing two-fraction radiotherapy+IDO1-inhibition to controls. IDO inhibition was achieved by administration of 1-methyl tryptophan (1-MT), and radiotherapy (RT) was delivered in doses of 8Gy. Results The expression of IDO1 was increased on gene level in glioblastoma stem cells. Tumor size was significantly reduced in animals treated with 1-MT+RTx 2 (both long and short intervals, i.e. 7 and 4 days between the treatments) as compared to control animals, animals treated with only 1-MT or animals treated with 1-MT+RTx1. Serum levels of IL-1A were significantly altered in all treated animals as compared to control animals. Survival was significantly increased in the animals treated with 1-MT+RTx2 (7-day interval) compared to control animals. Conclusions Addition of two-fraction RT to IDO1 inhibition with 1-MT significantly reduced tumor size in animals with glioblastoma. Survival was significantly increased in animals treated with two-fractioned RT+1-MT as compared to untreated controls increased significantly. Advances in knowledge The currently used combination of only two fractions of radiotherapy and immune therapy is a promising area of research, increasing efficacy compared to single fraction irradiation, while potentially lowering radiation side effects compared to radiation in current clinical practice.
Collapse
Affiliation(s)
- Jonatan Ahlstedt
- Division of Neurosurgery, Department of Clinical Sciences, The Rausing Laboratory, Lund University, Lund, Sweden
- * E-mail:
| | - Elise Konradsson
- Department of Clinical Sciences, Medical Radiation Physics, Lund University, Lund, Sweden
| | - Crister Ceberg
- Department of Clinical Sciences, Medical Radiation Physics, Lund University, Lund, Sweden
| | - Henrietta Nittby Redebrandt
- Division of Neurosurgery, Department of Clinical Sciences, The Rausing Laboratory, Lund University, Lund, Sweden
| |
Collapse
|
13
|
Jaafar L, Chamseddine Z, El-Sibai M. StarD13: a potential star target for tumor therapeutics. Hum Cell 2020; 33:437-443. [PMID: 32274657 DOI: 10.1007/s13577-020-00358-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 04/03/2020] [Indexed: 12/19/2022]
Abstract
StarD13 is a tumor suppressor and a GTPase activating protein (GAP) for Rho GTPases. Thus, StarD13 regulates cell survival pathways and induces apoptosis in a p53-dependent and independent manners. In tumors, StarD13 is either downregulated or completely inhibited, depending on the tumor type. As such, and through the dysregulation of Rho GTPases, this affects adhesion dynamics, actin dynamics, and leads to an increase or a decrease in tumor metastasis depending on the tumor grade and type. Being a key regulatory protein, StarD13 is a potential promising candidate for therapeutic approaches. This paper reviews the key characteristics of this protein and its role in tumor malignancies.
Collapse
Affiliation(s)
- Leila Jaafar
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Chouran, P.O. Box 13-5053, 1102 2801, Beirut, Lebanon
| | - Zeinab Chamseddine
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Chouran, P.O. Box 13-5053, 1102 2801, Beirut, Lebanon
| | - Mirvat El-Sibai
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Chouran, P.O. Box 13-5053, 1102 2801, Beirut, Lebanon.
| |
Collapse
|
14
|
Richardson TE, Sathe AA, Kanchwala M, Jia G, Habib AA, Xiao G, Snuderl M, Xing C, Hatanpaa KJ. Genetic and Epigenetic Features of Rapidly Progressing IDH-Mutant Astrocytomas. J Neuropathol Exp Neurol 2019; 77:542-548. [PMID: 29741737 DOI: 10.1093/jnen/nly026] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
IDH-mutant astrocytomas are significantly less aggressive than their IDH-wildtype counterparts. We analyzed The Cancer Genome Atlas dataset (TCGA) and identified a small group of IDH-mutant, WHO grade II-III astrocytomas (n = 14) with an unexpectedly poor prognosis characterized by a rapid progression to glioblastoma and death within 3 years of the initial diagnosis. Compared with IDH-mutant tumors with the typical, extended progression-free survival in a control group of age-similar patients, the tumors in the rapidly progressing group were characterized by a markedly increased level of overall copy number alterations ([CNA]; p = 0.006). In contrast, the mutation load was similar, as was the methylation pattern, being consistent with IDH-mutant astrocytoma. Two of the gliomas (14%) in the rapidly progressing, IDH-mutant group but none of the other grade II-III gliomas in the TCGA (n = 283) had pathogenic mutations in genes (FANCB and APC) associated with maintaining chromosomal stability. These results suggest that chromosomal instability can negate the beneficial effect of IDH mutations in WHO II-III astrocytomas. The mechanism of the increased CNA is unknown but in some cases appears to be due to mutations in genes with a role in chromosomal stability. Increased CNA could serve as a biomarker for tumors at risk for rapid progression.
Collapse
Affiliation(s)
- Timothy E Richardson
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Adwait Amod Sathe
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Mohammed Kanchwala
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Gaoxiang Jia
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Amyn A Habib
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, Texas.,North Texas Veterans Affairs Medical Center, Dallas, Texas
| | - Guanghua Xiao
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Matija Snuderl
- Department of Pathology, New York University Langone Medical Center, New York City, New York
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kimmo J Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| |
Collapse
|
15
|
Mirchia K, Sathe AA, Walker JM, Fudym Y, Galbraith K, Viapiano MS, Corona RJ, Snuderl M, Xing C, Hatanpaa KJ, Richardson TE. Total copy number variation as a prognostic factor in adult astrocytoma subtypes. Acta Neuropathol Commun 2019; 7:92. [PMID: 31177992 PMCID: PMC6556960 DOI: 10.1186/s40478-019-0746-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/20/2019] [Indexed: 01/24/2023] Open
Abstract
Since the discovery that IDH1/2 mutations confer a significantly better prognosis in astrocytomas, much work has been done to identify other molecular signatures to help further stratify lower-grade astrocytomas and glioblastomas, with the goal of accurately predicting clinical outcome and identifying potentially targetable mutations. In the present study, we subclassify 135 astrocytomas (67 IDH-wildtype and 68 IDH-mutant) from The Cancer Genome Atlas dataset (TCGA) on the basis of grade, IDH-status, and the previously established prognostic factors, CDK4 amplification and CDKN2A/B deletion, within the IDH-mutant groups. We analyzed these groups for total copy number variation (CNV), total mutation burden, chromothripsis, specific mutations, and amplifications/deletions of specific genes/chromosomal regions. Herein, we demonstrate that across all of these tumor groups, total CNV level is a relatively consistent prognostic factor. We also identified a trend towards increased levels of chromothripsis in tumors with lower progression-free survival (PFS) and overall survival (OS) intervals. While no significant differences were identified in overall mutation load, we did identify a significantly higher number of cases with mutations in genes with functions related to maintaining genomic stability in groups with higher mean CNV and worse PFS and OS intervals, particularly in the IDH-mutant groups. Our data further support the case for total CNV level as a potential prognostic factor in astrocytomas, and suggest mutations in genes responsible for overall genomic instability as a possible underlying mechanism for some astrocytomas with poor clinical outcome.
Collapse
|
16
|
Sun L, Sun J, Song JD. High expression of DLC family proteins predicts better prognosis and inhibits tumor progression in NSCLC. Mol Med Rep 2019; 19:4881-4889. [PMID: 31059015 PMCID: PMC6522875 DOI: 10.3892/mmr.2019.10146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 04/02/2019] [Indexed: 12/11/2022] Open
Abstract
The incidence of primary lung cancer (PLC) is increasing and is becoming a leading cause of cancer‑associated mortality worldwide. Non‑small cell lung cancer (NSCLC) accounts for ~80% of PLC cases and has the worst prognosis among malignant tumors. Deleted in liver cancer (DLC) proteins belong to the RhoGTPase‑activating protein family and are considered to be tumor suppressor genes. However, the role of the proteins, particularly DLC2 and DLC3, in NSCLC, has not been fully elucidated. The present study investigated the expression levels and prognostic values of DLCs in NSCLC using The Cancer Genome Atlas, the Genotype‑Tissue Expression project and Kaplan‑Meier plotter datasets. The current study demonstrated that the three DLCs were downregulated in NSCLC. High expression levels of DLC1 and DLC2 were associated with an improved survival in NSCLC. Additionally, the effects of DLCs on the proliferation and apoptosis of the lung cancer cell line A‑549 were investigated in vitro using a Cell Counting Kit‑8 assay and flow cytometry analysis. DLC2 and DLC3 overexpression inhibited proliferation and induced apoptosis in A549 cells. To the best of our knowledge, the current study was the first to investigate the expression level and prognostic values of DLC2 and DLC3 in NSCLC. The results indicated that DLC1 DLC2 and DLC3 serve specific roles in the occurrence and development of NSCLC, and may be considered as potential prognostic indicators in NSCLC.
Collapse
Affiliation(s)
- Li Sun
- Department of Cardiothoracic Surgery, Zaozhuang Municipal Hospital, Zaozhuang, Shandong 277000, P.R. China
| | - Jing Sun
- Department of Infectious Diseases, Zaozhuang Hospital of Zaozhuang Mining Group, Zaozhuang, Shandong 277101, P.R. China
| | - Jun-Ding Song
- Department of Cardiothoracic Surgery, Zaozhuang Municipal Hospital, Zaozhuang, Shandong 277000, P.R. China
| |
Collapse
|
17
|
He Y, Wang Z, Liu C, Gong Z, Li Y, Lu T, Hu G. Protocadherin 17 is a tumor suppressor and is frequently methylated in nasopharyngeal carcinoma. Cancer Manag Res 2019; 11:1601-1613. [PMID: 30863170 PMCID: PMC6388982 DOI: 10.2147/cmar.s191102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Purpose Several PCDH genes were shown to be downregulated or silenced in carcinomas and act as candidate tumor suppressor genes. However, the functions of PCDH17 in nasopharyngeal carcinoma (NPC) remain unclear. Here, we investigated the PCDH17 promoter methylation status and its impact on the expression and functions of PCDH17 in NPC. Patients and methods To determine the mRNA levels and promoter methylation status of PCDH17 in NPC cell lines as well as 42 NPC patient specimens, we performed reverse transcription PCR, methylation-specific PCR, and bisulfite genome sequencing. The effects of ectopic PCDH17 expression in NPC cell lines were determined by colony formation, cell proliferation, wound healing, in vitro human umbilical vein endothelial cells tube formation, migration, invasion, cell cycle, and apoptosis assays and an in vivo subcutaneous tumor model. Results PCDH17 expression was almost absent or significantly reduced in 100% of the NPC cell lines (5/5). However, 5-aza-2′-deoxycytidine and trichostatin A treatment restored PCDH17 expression. Promoter methylation was involved in PCDH17 silencing. Ectopic expression of PCDH17 in silenced NPC cells reduced colony formation, cell migration, angiogenesis, VEGF secretion, and tumorigenicity. Conclusion PCDH17 plays a tumor suppressor role in NPC. PCDH17 methylation may be a tumor-specific event and can be used as an epigenetic biomarker for NPC.
Collapse
Affiliation(s)
- Ya He
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China, .,Department of Otolaryngology Head and Neck Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Zhihai Wang
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China,
| | - Chuan Liu
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China,
| | - Zhitao Gong
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China,
| | - Yanshi Li
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China,
| | - Tao Lu
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China,
| | - Guohua Hu
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China,
| |
Collapse
|
18
|
Lemée JM, Clavreul A, Aubry M, Com E, de Tayrac M, Mosser J, Menei P. Integration of transcriptome and proteome profiles in glioblastoma: looking for the missing link. BMC Mol Biol 2018; 19:13. [PMID: 30463513 PMCID: PMC6249855 DOI: 10.1186/s12867-018-0115-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 11/09/2018] [Indexed: 12/21/2022] Open
Abstract
Background Glioblastoma (GB) is the most common and aggressive tumor of the brain. Genotype-based approaches and independent analyses of the transcriptome or the proteome have led to progress in understanding the underlying biology of GB. Joint transcriptome and proteome profiling may reveal new biological insights, and identify pathogenic mechanisms or therapeutic targets for GB therapy. We present a comparison of transcriptome and proteome data from five GB biopsies (TZ) vs their corresponding peritumoral brain zone (PBZ). Omic analyses were performed using RNA microarray chips and the isotope-coded protein label method (ICPL). Results As described in other cancers, we found a poor correlation between transcriptome and proteome data in GB. We observed only two commonly deregulated mRNAs/proteins (neurofilament light polypeptide and synapsin 1) and 12 altered biological processes; they are related to cell communication, synaptic transmission and nervous system processes. This poor correlation may be a consequence of the techniques used to produce the omic profiles, the intrinsic properties of mRNA and proteins and/or of cancer- or GB-specific phenomena. Of interest, the analysis of the transcription factor binding sites present upstream from the open reading frames of all altered proteins identified by ICPL method shows a common binding site for the topoisomerase I and p53-binding protein TOPORS. Its expression was observed in 7/11 TZ samples and not in PBZ. Some findings suggest that TOPORS may function as a tumor suppressor; its implication in gliomagenesis should be examined in future studies. Conclusions In this study, we showed a low correlation between transcriptome and proteome data for GB samples as described in other cancer tissues. We observed that NEFL, SYN1 and 12 biological processes were deregulated in both the transcriptome and proteome data. It will be important to analyze more specifically these processes and these two proteins to allow the identification of new theranostic markers or potential therapeutic targets for GB. Electronic supplementary material The online version of this article (10.1186/s12867-018-0115-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jean-Michel Lemée
- Department of Neurosurgery, CHU Angers, University Hospital of Angers, 4, Rue Larrey, 49933, Angers Cedex 09, France. .,CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France.
| | - Anne Clavreul
- Department of Neurosurgery, CHU Angers, University Hospital of Angers, 4, Rue Larrey, 49933, Angers Cedex 09, France.,CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| | - Marc Aubry
- UEB, UMS 3480 Biosit, Faculté de Médecine, Université Rennes 1, Rennes, France.,Plate-forme Génomique Santé Biosit, Université Rennes 1, Rennes, France
| | - Emmanuelle Com
- Inserm U1085 IRSET, Université de Rennes 1, Rennes, France.,Protim, Université de Rennes 1, Rennes, France
| | - Marie de Tayrac
- UEB, UMS 3480 Biosit, Faculté de Médecine, Université Rennes 1, Rennes, France.,Service de Génétique Moléculaire et Génomique, CHU Rennes, Rennes, France.,CNRS, UMR 6290, Institut de Génétique et Développement de Rennes (IGdR), Rennes, France
| | - Jean Mosser
- UEB, UMS 3480 Biosit, Faculté de Médecine, Université Rennes 1, Rennes, France.,Plate-forme Génomique Santé Biosit, Université Rennes 1, Rennes, France.,Service de Génétique Moléculaire et Génomique, CHU Rennes, Rennes, France.,CNRS, UMR 6290, Institut de Génétique et Développement de Rennes (IGdR), Rennes, France
| | - Philippe Menei
- Department of Neurosurgery, CHU Angers, University Hospital of Angers, 4, Rue Larrey, 49933, Angers Cedex 09, France.,CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France
| |
Collapse
|
19
|
Wang C, Chen Q, Li S, Li S, Zhao Z, Gao H, Wang X, Li B, Zhang W, Yuan Y, Ming L, He H, Tao B, Zhong J. Dual inhibition of PCDH9 expression by miR-215-5p up-regulation in gliomas. Oncotarget 2018; 8:10287-10297. [PMID: 28055966 PMCID: PMC5354659 DOI: 10.18632/oncotarget.14396] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 12/12/2016] [Indexed: 12/25/2022] Open
Abstract
The clinical prognosis of malignant gliomas is poor and PCDH9 down-regulation is strongly associated with its poor prognosis. But the mechanism of PCDH9 down-regulation is unknown. Abnormal miRNAs profiles regulate tumor phenotypes through inhibiting their target genes and miRNAs could inhibit target genes more efficiently by binding to both the promoter and 3′UTR of target genes. In this study, to search the dual inhibitory miRNAs which suppress PCDH9 expression in gliomas, we performed an integrative analysis of databases including miRDB, TargetScan, microPIR and miRCancer. We identified three candidate miRNAs which were predicted to bind both the promoter and 3′UTR of PCDH9 and up-regulated in gliomas. Then, we validated miR-215-5p up-regulation and PCDH9 down-regulation in glioma samples and demonstrated that miR-215-5p could inhibit the mRNA and protein levels of PCDH9 in glioma cell lines by targeting its promoter and 3′ UTR at the same time. Moreover, miR-215-5p could increase glioma cell proliferation, clone formation, in-vitro migration and reduce apoptosis via inhibiting PCDH9 expression. Our study provides evidence for a novel dual inhibition of PCDH9 by miR-215-5p in gliomas and suggests that miR-215-5p might be a therapeutic target for the treatment of gliomas.
Collapse
Affiliation(s)
- Chunlin Wang
- Department of Neurosurgery, The 105th Hospital of PLA, Hefei, Anhui 230000, China
| | - Qi Chen
- Department of Anesthesiology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Shu Li
- Department of Pathophysiology, Wannan Medical College, Wuhu 241002, China; Department of Neurosurgery, Wuxi Second People's Hospital, Wuxi, Jiangsu, 214002, China
| | - Shiting Li
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Zhenyu Zhao
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100003, China
| | - Hongliang Gao
- Department of Pathophysiology, Wannan Medical College, Wuhu 241002, China; Department of Neurosurgery, Wuxi Second People's Hospital, Wuxi, Jiangsu, 214002, China
| | - Xiaoqiang Wang
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Bin Li
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Wenchuan Zhang
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Yan Yuan
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Linzhao Ming
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Hua He
- Department of Neurosurgery, Changzheng Hospital, The Second Hospital affiliated with The Second Military Medical University, Shanghai 200003, China
| | - Bangbao Tao
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| | - Jun Zhong
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200003, China
| |
Collapse
|
20
|
Wang D, Qian X, Rajaram M, Durkin ME, Lowy DR. DLC1 is the principal biologically-relevant down-regulated DLC family member in several cancers. Oncotarget 2018; 7:45144-45157. [PMID: 27174913 PMCID: PMC5216712 DOI: 10.18632/oncotarget.9266] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 04/10/2016] [Indexed: 01/12/2023] Open
Abstract
The RHO family of RAS-related GTPases in tumors may be activated by reduced levels of RHO GTPase accelerating proteins (GAPs). One common mechanism is decreased expression of one or more members of the Deleted in Liver Cancer (DLC) family of Rho-GAPs, which comprises three closely related genes (DLC1, DLC2, and DLC3) that are down-regulated in a wide range of malignancies. Here we have studied their comparative biological activity in cultured cells and used publicly available datasets to examine their mRNA expression patterns in normal and cancer tissues, and to explore their relationship to cancer phenotypes and survival outcomes. In The Cancer Genome Atlas (TCGA) database, DLC1 expression predominated in normal lung, breast, and liver, but not in colorectum. Conversely, reduced DLC1 expression predominated in lung squamous cell carcinoma (LSC), lung adenocarcinoma (LAD), breast cancer, and hepatocellular carcinoma (HCC), but not in colorectal cancer. Reduced DLC1 expression was frequently associated with promoter methylation in LSC and LAD, while DLC1 copy number loss was frequent in HCC. DLC1 expression was higher in TCGA LAD patients who remained cancer-free, while low DLC1 had a poorer prognosis than low DLC2 or low DLC3 in a more completely annotated database. The poorest prognosis was associated with low expression of both DLC1 and DLC2 (P < 0.0001). In cultured cells, the three genes induced a similar reduction of Rho-GTP and cell migration. We conclude that DLC1 is the predominant family member expressed in several normal tissues, and its expression is preferentially reduced in common cancers at these sites.
Collapse
Affiliation(s)
- Dunrui Wang
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaolan Qian
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megha Rajaram
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Current address: BioTek Instruments Inc., Winooski, VT 05404, USA
| | - Marian E Durkin
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Douglas R Lowy
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
21
|
Mah KM, Weiner JA. Regulation of Wnt signaling by protocadherins. Semin Cell Dev Biol 2017; 69:158-171. [PMID: 28774578 PMCID: PMC5586504 DOI: 10.1016/j.semcdb.2017.07.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 07/21/2017] [Accepted: 07/28/2017] [Indexed: 12/23/2022]
Abstract
The ∼70 protocadherins comprise the largest group within the cadherin superfamily. Their diversity, the complexity of the mechanisms through which their genes are regulated, and their many critical functions in nervous system development have engendered a growing interest in elucidating the intracellular signaling pathways through which they act. Recently, multiple protocadherins across several subfamilies have been implicated as modulators of Wnt signaling pathways, and through this as potential tumor suppressors. Here, we review the extant data on the regulation by protocadherins of Wnt signaling pathways and components, and highlight some key unanswered questions that could shape future research.
Collapse
Affiliation(s)
- Kar Men Mah
- Department of Biology, The University of Iowa, Iowa City, IA, USA.
| | - Joshua A Weiner
- Department of Biology, The University of Iowa, Iowa City, IA, USA; Department of Psychiatry, The University of Iowa, Iowa City, IA, USA; Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA, USA.
| |
Collapse
|
22
|
Lv J, Zhu P, Zhang X, Zhang L, Chen X, Lu F, Yu Z, Liu S. PCDH9 acts as a tumor suppressor inducing tumor cell arrest at G0/G1 phase and is frequently methylated in hepatocellular carcinoma. Mol Med Rep 2017; 16:4475-4482. [PMID: 28791409 PMCID: PMC5647006 DOI: 10.3892/mmr.2017.7193] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 05/26/2017] [Indexed: 12/17/2022] Open
Abstract
Tumor suppressor genes (TSGs) are frequently involved in the pathogenesis of hepatocellular carcinoma (HCC). The epigenetic and genetic alterations of a novel TSG-protocadherin 9 (PCDH9) and its functions in the pathogenesis of HCC were investigated. The methylation status of the PCDH9 promoter was quantitatively analyzed, and the PCDH9 expression was analyzed in HCC cell lines treated with 5-azacytidine. The effects of PCDH9 re-expression and knockdown on growth, proliferation and tumorigenic potential were determined. The results indicated that expression of PCDH9 mRNA was restored in hypermethylation HCC cells following treatment with the DNA de-methylation reagent 5′-Aza. Methylation of the PCDH9 promoter was observed in 22% primary HCC tissues (24/111 tumors). Among the primary HCC cases, the methylated PCDH9 appeared to be associated with a larger tumor size (≥5 cm; P=0.0139) and a more pronounced intrahepatic dissemination (P=0.0312). In addition, it was observed that restored PCDH9 expression could inhibit tumor cell proliferation and xenograft tumor formation. Furthermore, restored PCDH9 expression could inhibit cell proliferation of HCC cell lines via inducing cell cycle arrest at G0/G1 phase. Thus, it is suggested that PCDH9 may act as a novel tumor suppressor candidate gene in HCC pathogenesis.
Collapse
Affiliation(s)
- Jun Lv
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Pengfei Zhu
- Department of Microbiology & Infectious Disease Center, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Xiaolei Zhang
- Department of Microbiology & Infectious Disease Center, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Ling Zhang
- Department of Hepatobiliary Surgery, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Xiangmei Chen
- Department of Microbiology & Infectious Disease Center, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Fengmin Lu
- Department of Microbiology & Infectious Disease Center, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Zujiang Yu
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Shuang Liu
- Beijing Artificial Liver Treatment & Training Center, Beijing Youan Hospital Capital Medical University, Beijing 100069, P.R. China
| |
Collapse
|
23
|
Integrated genomic analysis of clear cell ovarian cancers identified PRKCI as a potential therapeutic target. Oncotarget 2017; 8:96482-96495. [PMID: 29228547 PMCID: PMC5722499 DOI: 10.18632/oncotarget.19946] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 05/29/2017] [Indexed: 12/22/2022] Open
Abstract
Clear cell ovarian cancer (CCOC) is an epithelial ovarian cancer histotype with unique pathologic, biologic and clinical features. Despite its worse prognosis than serous ovarian cancer (SOC), the genomic landscape of CCOC is less well defined. Integrated genomic analysis of CCOC allows the identification of potential therapeutic targets to improve the treatment of this tumor. Using comparative genomic hybridization and gene expression profiling, we have screened 12 CCOC cell lines and 40 tumors to identify 45 amplified and overexpressed genes. Pathways analysis of these genes identified 19 genes with cancer-related functions. Of these, PRKCI is one of the most frequently amplified and overexpressed genes and its expression induced cancer cell proliferation and migration/invasion in vitro as well as tumor growth in vivo. Targeting PRKCI by small molecule inhibitor, sodium aurothiomalate (ATM), significantly reduced the in vivo tumor growth and may be a new therapeutic strategy to improve the treatment of CCOC.
Collapse
|
24
|
LeBlanc VG, Firme M, Song J, Chan SY, Lee MH, Yip S, Chittaranjan S, Marra MA. Comparative transcriptome analysis of isogenic cell line models and primary cancers links capicua (CIC) loss to activation of the MAPK signalling cascade. J Pathol 2017; 242:206-220. [PMID: 28295365 PMCID: PMC5485162 DOI: 10.1002/path.4894] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 02/27/2017] [Accepted: 03/09/2017] [Indexed: 01/30/2023]
Abstract
CIC encodes a transcriptional repressor, capicua (CIC), whose disrupted activity appears to be involved in several cancer types, including type I low‐grade gliomas (LGGs) and stomach adenocarcinomas (STADs). To explore human CIC's transcriptional network in an isogenic background, we developed novel isogenic CIC knockout cell lines as model systems, and used these in transcriptome analyses to study the consequences of CIC loss. We also compared our results with analyses of transcriptome data from TCGA for type I LGGs and STADs. We identified 39 candidate targets of CIC transcriptional regulation, and confirmed seven of these as direct targets. We showed that, although many CIC targets appear to be context‐specific, the effects of CIC loss converge on the dysregulation of similar biological processes in different cancer types. For example, we found that CIC deficiency was associated with disruptions in the expression of genes involved in cell–cell adhesion, and in the development of several cell and tissue types. We also showed that loss of CIC leads to overexpression of downstream members of the mitogen‐activated protein kinase (MAPK) signalling cascade, indicating that CIC deficiency may present a novel mechanism for activation of this oncogenic pathway. © 2017 The Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Veronique G LeBlanc
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Marlo Firme
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Jungeun Song
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Susanna Y Chan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Min Hye Lee
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, BC, Canada
| | - Suganthi Chittaranjan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
25
|
Uyen TN, Sakashita K, Al-Kzayer LFY, Nakazawa Y, Kurata T, Koike K. Aberrant methylation of protocadherin 17 and its prognostic value in pediatric acute lymphoblastic leukemia. Pediatr Blood Cancer 2017; 64. [PMID: 27643535 DOI: 10.1002/pbc.26259] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 11/12/2022]
Abstract
BACKGROUND The outcome of approximately 20% of patients with acute lymphoblastic leukemia (ALL) remains poor because of disease recurrence. We examined whether DNA methylation of cadherin superfamily genes is a useful biomarker for ALL relapse. PROCEDURE We used Infinium Methylation 450K Arrays to assess genome-wide DNA methylation status. The methylation status of each individual gene was then determined by a combination of bisulfite restriction analysis and genome bisulfite sequencing. mRNA expression was evaluated by reverse-transcriptase PCR (RT-PCR) and quantitative real-time PCR. RESULTS Cadherin superfamily genes including cadherin (CDH) 1, protocadherin (PCDH) 8, and PCDH17 were selected for analysis of methylation status. In 40 patient samples with B-cell precursor (BCP) ALL at diagnosis, the methylation frequencies of CDH1, PCDH8, and PCDH17 were 62.5, 55, and 30%, respectively. CDH1 and PCDH8 methylation was also detected in 80 and 20% of control bone marrow (BM) samples, respectively. On the contrary, PCDH17 was unmethylated in all control BM samples. There was a significant correlation between the methylation status of PCDH17 (but not CDH1 and PCDH8) and event-free survival or overall survival. Univariate and multivariate analyses showed that only PCDH17 methylation was associated with an increased risk for relapse and mortality in patients with BCP ALL. CONCLUSION PCDH17 methylation at diagnosis was closely related to poor prognosis and thus could be used as a new biomarker to predict relapse in patients with BCP ALL.
Collapse
Affiliation(s)
- Thanh Nha Uyen
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Kazuo Sakashita
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan.,Department of Pediatric Hematology and Oncology, Nagano Children's Hospital, Azumino, Nagano, Japan
| | | | - Yozo Nakazawa
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Takashi Kurata
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Kenichi Koike
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| |
Collapse
|
26
|
Cilibrasi C, Riva G, Romano G, Cadamuro M, Bazzoni R, Butta V, Paoletta L, Dalprà L, Strazzabosco M, Lavitrano M, Giovannoni R, Bentivegna A. Resveratrol Impairs Glioma Stem Cells Proliferation and Motility by Modulating the Wnt Signaling Pathway. PLoS One 2017; 12:e0169854. [PMID: 28081224 PMCID: PMC5231344 DOI: 10.1371/journal.pone.0169854] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 12/22/2016] [Indexed: 12/31/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a grade IV astrocytoma and the most common form of malignant brain tumor in adults. GBM remains one of the most fatal and least successfully treated solid tumors: current therapies provide a median survival of 12–15 months after diagnosis, due to the high recurrence rate. Glioma Stem Cells (GSCs) are believed to be the real driving force of tumor initiation, progression and relapse. Therefore, better therapeutic strategies GSCs-targeted are needed. Resveratrol is a polyphenolic phytoalexin found in fruits and vegetables displaying pleiotropic health benefits. Many studies have highlighted its chemo-preventive and chemotherapeutic activities in a wide range of solid tumors. In this work, we analyzed the effects of Resveratrol exposure on cell viability, proliferation and motility in seven GSC lines isolated from GBM patients. For the first time in our knowledge, we investigated Resveratrol impact on Wnt signaling pathway in GSCs, evaluating the expression of seven Wnt signaling pathway-related genes and the protein levels of c-Myc and β-catenin. Finally, we analyzed Twist1 and Snail1 protein levels, two pivotal activators of epithelial-mesenchymal transition (EMT) program. Results showed that although response to Resveratrol exposure was highly heterogeneous among GSC lines, generally it was able to inhibit cell proliferation, increase cell mortality, and strongly decrease cell motility, modulating the Wnt signaling pathway and the EMT activators. Treatment with Resveratrol may represent a new interesting therapeutic approach, in order to affect GSCs proliferation and motility, even if further investigations are needed to deeply understand the GSCs heterogeneous response.
Collapse
Affiliation(s)
- Chiara Cilibrasi
- School of Medicine and Surgery, University of Milano-Bicocca, via Cadore, Monza, Italy
- PhD Program in Neuroscience, University of Milano-Bicocca, via Cadore, Monza, Italy
- NeuroMI, Milan center of Neuroscience, University of Milano Bicocca, Dept. of Neurology and Neuroscience, San Gerardo Hospital, via Pergolesi, Monza, Italy
| | - Gabriele Riva
- School of Medicine and Surgery, University of Milano-Bicocca, via Cadore, Monza, Italy
- PhD Program in Neuroscience, University of Milano-Bicocca, via Cadore, Monza, Italy
- NeuroMI, Milan center of Neuroscience, University of Milano Bicocca, Dept. of Neurology and Neuroscience, San Gerardo Hospital, via Pergolesi, Monza, Italy
| | - Gabriele Romano
- School of Medicine and Surgery, University of Milano-Bicocca, via Cadore, Monza, Italy
- PhD Program in Translational and Molecular Medicine (DIMET), University of Milano-Bicocca, via Cadore, Monza, Italy
| | - Massimiliano Cadamuro
- School of Medicine and Surgery, University of Milano-Bicocca, via Cadore, Monza, Italy
| | - Riccardo Bazzoni
- School of Medicine and Surgery, University of Milano-Bicocca, via Cadore, Monza, Italy
| | - Valentina Butta
- School of Medicine and Surgery, University of Milano-Bicocca, via Cadore, Monza, Italy
- PhD Program in Neuroscience, University of Milano-Bicocca, via Cadore, Monza, Italy
| | - Laura Paoletta
- School of Medicine and Surgery, University of Milano-Bicocca, via Cadore, Monza, Italy
| | - Leda Dalprà
- School of Medicine and Surgery, University of Milano-Bicocca, via Cadore, Monza, Italy
| | - Mario Strazzabosco
- School of Medicine and Surgery, University of Milano-Bicocca, via Cadore, Monza, Italy
| | - Marialuisa Lavitrano
- School of Medicine and Surgery, University of Milano-Bicocca, via Cadore, Monza, Italy
| | - Roberto Giovannoni
- School of Medicine and Surgery, University of Milano-Bicocca, via Cadore, Monza, Italy
| | - Angela Bentivegna
- School of Medicine and Surgery, University of Milano-Bicocca, via Cadore, Monza, Italy
- NeuroMI, Milan center of Neuroscience, University of Milano Bicocca, Dept. of Neurology and Neuroscience, San Gerardo Hospital, via Pergolesi, Monza, Italy
- * E-mail:
| |
Collapse
|
27
|
Zhang X, Takata K, Cui W, Miyata-Takata T, Sato Y, Noujima-Harada M, Yoshino T. Protocadherin γ A3 is expressed in follicular lymphoma irrespective of BCL2 status and is associated with tumor cell growth. Mol Med Rep 2016; 14:4622-4628. [PMID: 27748813 PMCID: PMC5102029 DOI: 10.3892/mmr.2016.5808] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/18/2016] [Indexed: 01/24/2023] Open
Abstract
Protocadherin genes (PCDHs) have been suggested to act as tumor suppressor genes in various tumor types. Previous studies have demonstrated the upregulation of certain PCDH-γ subfamily genes in nodal and duodenal follicular lymphoma (FL) using gene expression analyses. However, the mechanisms and associated molecular function of PCDH-γ subfamily gene upregulation in FL remain to be elucidated. The present study examined the expression of PCDHGA3, an upregulated PCDH-γ gene subfamily member, in B-cell lymphoma 2 (BCL2)-positive and -negative FL, and evaluated its association with tumor cell proliferation in an FL-derived cell line. Immunohistochemical analysis demonstrated that the majority of FL grade 1–2 samples (19/20; 95%) and over half of grade 3A FL samples (5/9; 56%) were PCDHGA3-positive, whereas only 1/17 reactive lymphoid hyperplasia samples was positive. Notably, this positivity was widely observed in samples of BCL2-negative FL (13/15; 87%) and FL with diffuse area (10/10; 100%). The FL-derived cell line FL18 exhibited strong PCDHGA3 expression, similar to the patient samples, and its proliferation was suppressed by PCDHGA3 gene knockdown. Genes expressed concomitantly with PCDHGA3 were selected from gene expression data, and TNFRSF6B, a member of the tumor necrosis factor receptor superfamily, was among the top five most strongly correlated genes. Coexpression of TNFRSF6B and PCDHGA3 was observed immunohistochemically in FL18 cells, suggesting potential cooperation in tumor cell maintenance. In conclusion, the results of the present study indicated that PCDHGA3 was expressed in FL irrespective of BCL2 status and grading and was associated with cell proliferation. Further studies involving molecular genetic analyses are required to elucidate the mechanisms underlying the activity of PCDHGA3 in FL.
Collapse
Affiliation(s)
- Xueyan Zhang
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Katsuyoshi Takata
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Wei Cui
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Tomoko Miyata-Takata
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Yasuharu Sato
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Mai Noujima-Harada
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Tadashi Yoshino
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| |
Collapse
|
28
|
Dickinson PJ, York D, Higgins RJ, LeCouteur RA, Joshi N, Bannasch D. Chromosomal Aberrations in Canine Gliomas Define Candidate Genes and Common Pathways in Dogs and Humans. J Neuropathol Exp Neurol 2016; 75:700-10. [PMID: 27251041 DOI: 10.1093/jnen/nlw042] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 12/16/2022] Open
Abstract
Spontaneous gliomas in dogs occur at a frequency similar to that in humans and may provide a translational model for therapeutic development and comparative biological investigations. Copy number alterations in 38 canine gliomas, including diffuse astrocytomas, glioblastomas, oligodendrogliomas, and mixed oligoastrocytomas, were defined using an Illumina 170K single nucleotide polymorphism array. Highly recurrent alterations were seen in up to 85% of some tumor types, most notably involving chromosomes 13, 22, and 38, and gliomas clustered into 2 major groups consisting of high-grade IV astrocytomas, or oligodendrogliomas and other tumors. Tumor types were characterized by specific broad and focal chromosomal events including focal loss of the INK4A/B locus in glioblastoma and loss of the RB1 gene and amplification of the PDGFRA gene in oligodendrogliomas. Genes associated with the 3 critical pathways in human high-grade gliomas (TP53, RB1, and RTK/RAS/PI3K) were frequently associated with canine aberrations. Analysis of oligodendrogliomas revealed regions of chromosomal losses syntenic to human 1p involving tumor suppressor genes, such as CDKN2C, as well as genes associated with apoptosis, autophagy, and response to chemotherapy and radiation. Analysis of high frequency chromosomal aberrations with respect to human orthologues may provide insight into both novel and common pathways in gliomagenesis and response to therapy.
Collapse
Affiliation(s)
- Peter J Dickinson
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California.
| | - Dan York
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| | - Robert J Higgins
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| | - Richard A LeCouteur
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| | - Nikhil Joshi
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| | - Danika Bannasch
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| |
Collapse
|
29
|
Aubry M, de Tayrac M, Etcheverry A, Clavreul A, Saikali S, Menei P, Mosser J. From the core to beyond the margin: a genomic picture of glioblastoma intratumor heterogeneity. Oncotarget 2016; 6:12094-109. [PMID: 25940437 PMCID: PMC4494925 DOI: 10.18632/oncotarget.3297] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/06/2015] [Indexed: 12/22/2022] Open
Abstract
Glioblastoma (GB) is a highly invasive primary brain tumor that almost systematically recurs despite aggressive therapies. One of the most challenging problems in therapy of GB is its extremely complex and heterogeneous molecular biology. To explore this heterogeneity, we performed a genome-wide integrative screening of three molecular levels: genome, transcriptome, and methylome. We analyzed tumor biopsies obtained by neuro-navigation in four distinct areas for 10 GB patients (necrotic zone, tumor zone, interface, and peripheral brain zone). We classified samples and deciphered a key genes signature of intratumor heterogeneity by Principal Component Analysis and Weighted Gene Co-expression Network Analysis. At the genome level, we identified common GB copy number alterations and but a strong interindividual molecular heterogeneity. Transcriptome analysis highlighted a pronounced intratumor architecture reflecting the surgical sampling plan of the study and identified gene modules associated with hallmarks of cancer. We provide a signature of key cancer-heterogeneity genes highly associated with the intratumor spatial gradient and show that it is enriched in genes with correlation between methylation and expression levels. Our study confirms that GBs are molecularly highly diverse and that a single tumor can harbor different transcriptional GB subtypes depending on its spatial architecture.
Collapse
Affiliation(s)
- Marc Aubry
- Université Rennes1, UEB, UMS 3480 Biosit, Faculté de Médecine, Rennes F-35043, France.,Plate-forme Génomique Santé Biosit, Université Rennes1, Rennes F-35043, France
| | - Marie de Tayrac
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes (IGdR), Rennes F-35043, France.,Université Rennes1, UEB, UMS 3480 Biosit, Faculté de Médecine, Rennes F-35043, France.,CHU Rennes, Service de Génétique Moléculaire et Génomique, Rennes F-35033, France
| | - Amandine Etcheverry
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes (IGdR), Rennes F-35043, France.,Université Rennes1, UEB, UMS 3480 Biosit, Faculté de Médecine, Rennes F-35043, France.,CHU Rennes, Service de Génétique Moléculaire et Génomique, Rennes F-35033, France
| | - Anne Clavreul
- INSERM UMR-1066, Micro et Nano-Médecines Biomimétiques (MINT), Angers F-49933, France
| | - Stéphan Saikali
- CHU Rennes, Service d'Anatomie et Cytologie Pathologiques, Rennes F-35033, France.,Service d'Anatomie Pathologique, Hôpital de l'Enfant-Jésus, Québec, Canada
| | - Philippe Menei
- INSERM UMR-1066, Micro et Nano-Médecines Biomimétiques (MINT), Angers F-49933, France.,CHU Angers, Département de Neurochirurgie, Angers F-49933, France
| | - Jean Mosser
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes (IGdR), Rennes F-35043, France.,Université Rennes1, UEB, UMS 3480 Biosit, Faculté de Médecine, Rennes F-35043, France.,Plate-forme Génomique Santé Biosit, Université Rennes1, Rennes F-35043, France.,CHU Rennes, Service de Génétique Moléculaire et Génomique, Rennes F-35033, France
| |
Collapse
|
30
|
Chen T, Long B, Ren G, Xiang T, Li L, Wang Z, He Y, Zeng Q, Hong S, Hu G. Protocadherin20 Acts as a Tumor Suppressor Gene: Epigenetic Inactivation in Nasopharyngeal Carcinoma. J Cell Biochem 2016; 116:1766-75. [PMID: 25736877 DOI: 10.1002/jcb.25135] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 02/06/2015] [Indexed: 11/12/2022]
Abstract
Genetic alterations of 13q21 (PCDH 8,9,17, and 20) are frequently observed in multiple tumors, suggesting the presence of critical tumor suppressor genes (TSGs). Protocadherin20 (PCDH20), located at 13q21.2, belongs to the δ1-protocadherins, which constitutes one of the largest subgroup within the adherin superfamily. Frequent downregulation/silencing of PCDH20 was found in NPC cell lines using semiquantitative PCR. PCDH20 mRNA was broadly expressed in normal nasopharyngeal tissues and cell lines. Promoter methylation of PCDH20 was observed in 80% (4/5) of NPC cell lines and 78.4% (40 of 51) of primary tumors by methylation-specific PCR, but rarely in normal nasopharygeal tissues and nasopharyngeal epithelial cell line (NP69). The silencing of PCDH20 can be reversed by pharmacological demethylation, indicating an epigenetic mechanism. Restoration of PCDH20 expression in NPC cells strongly suppressed cell numbers and colony formation. Overexpression of PCDH20 antagonized Wnt/β-catenin signaling pathway and promoted β-catenin to translocate from nucleus to cytoplasm and membrane. PCDH20 significantly inhibited the migration and invasion ability of NPC cells. PCDH20 also inhibited epithelial-mesenchymal transition (EMT) through enhanced expression of E-cadherin. Our study identified PCDH20 as a functional tumor suppressor and an important antagonist of Wnt/β-catenin signaling and EMT, with frequent epigenetic inactivation in NPC.
Collapse
Affiliation(s)
- Tao Chen
- Department of Otolaryngology, The first Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, China
| | - Biaoli Long
- Department of Otolaryngology, The first Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, China
| | - Guosheng Ren
- Molecular Oncology and Epigenetics Laboratory, The first Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, China
| | - Tingxiu Xiang
- Molecular Oncology and Epigenetics Laboratory, The first Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, China
| | - Lili Li
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Zhaohui Wang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Ya He
- Department of Otolaryngology, The first Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, China
| | - Quan Zeng
- Department of Otolaryngology, The first Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, China
| | - Suling Hong
- Department of Otolaryngology, The first Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, China
| | - Guohua Hu
- Department of Otolaryngology, The first Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, China
| |
Collapse
|
31
|
Qu LS, Jin F, Guo YM, Liu TT, Xue RY, Huang XW, Xu M, Chen TY, Ni ZP, Shen XZ. Nine susceptibility loci for hepatitis B virus-related hepatocellular carcinoma identified by a pilot two-stage genome-wide association study. Oncol Lett 2015; 11:624-632. [PMID: 26870257 PMCID: PMC4727098 DOI: 10.3892/ol.2015.3958] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 10/26/2015] [Indexed: 12/12/2022] Open
Abstract
Previous studies have indicated that complex interactions among viral, environmental and genetic factors lead to hepatocellular carcinoma (HCC). To identify susceptibility alleles for hepatitis B virus (HBV)-related HCC, the present study conducted a pilot two-phase genome-wide association study (GWAS) in 660 Han Chinese individuals. In phase 1, a total of 500,447 single-nucleotide polymorphisms (SNPs) were genotyped in 50 HCC cases and 50 controls using Affymetrix GeneChip 500k Array Set. In phase 2, 1,152 SNPs were selected from phase 1 and genotyped in 282 cases and 278 controls using the Illumina GoldenGate platform. The prior probability of HCC in control subjects was assigned at 0.01, and false-positive report probability (FPRP) was utilized to evaluate the statistical significance. In phase 1, one SNP (rs2212522) showed a significant association with HCC (Pallele=5.23×10−8; ORallele=4.96; 95% CI, 2.72–9.03). In phase 2, among 27 SNPs with unadjusted Pallele<0.05, 9 SNPs were associated with HCC based on FPRP criteria (FPRP <0.20). The strongest statistical evidence for an association signal was with rs2120243 (combined ORallele=1.76; 95% CI, 1.39–2.22; P=2.00×10−6), which maps within the fourth intron of VEPH1. The second strongest statistical evidence for an association was identified for rs1350171 (combined ORallele=1.66; 95% CI, 1.33–2.07; P=6.48×10−6), which maps to the region downstream of the FZD4 gene. The other potential susceptibility genes included PCDH9, PRMT6, LHX1, KIF2B and L3MBTL4. In conclusion, this pilot two-phase GWAS provides the evidence for the existence of common susceptibility loci for HCC. These genes involved various signaling pathways, including those associated with transforming growth factor β, insulin/phosphoinositide 3 kinase, Wnt and epidermal growth factor receptor. These associations must be replicated and validated in larger studies.
Collapse
Affiliation(s)
- Li-Shuai Qu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Fei Jin
- Department of Gastroenterology, Shanghai Xuhui Central Hospital, Shanghai 200032, P.R. China
| | - Yan-Mei Guo
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Tao-Tao Liu
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Ru-Yi Xue
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Xiao-Wu Huang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Min Xu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Tao-Yang Chen
- Department of Liver Surgery, Qidong Liver Cancer Institute, Qidong, Jiangsu 226200, P.R. China
| | - Zheng-Ping Ni
- Department of Liver Surgery, Qidong Liver Cancer Institute, Qidong, Jiangsu 226200, P.R. China
| | - Xi-Zhong Shen
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| |
Collapse
|
32
|
Lemée JM, Clavreul A, Menei P. Intratumoral heterogeneity in glioblastoma: don't forget the peritumoral brain zone. Neuro Oncol 2015. [PMID: 26203067 DOI: 10.1093/neuonc/nov119] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Glioblastoma (GB) is the most frequent and aggressive primary tumor of the central nervous system. Prognosis remains poor despite ongoing progress. In cases where the gadolinium-enhanced portion of the GB is completely resected, 90% of recurrences occur at the margin of surgical resection in the macroscopically normal peritumoral brain zone (PBZ). Intratumoral heterogeneity in GB is currently a hot topic in neuro-oncology, and the GB PBZ may be involved in this phenomenon. Indeed, this region, which possesses specific properties, has been less studied than the core of the GB tumor. The high rate of local recurrence in the PBZ and the limited success of targeted therapies against GB demonstrate the need for a better understanding of the PBZ. We present here a review of the literature on the GB PBZ, focusing on its radiological, cellular, and molecular characteristics. We discuss how intraoperative analysis of the PBZ is important for the optimization of surgical resection and the development of targeted therapies against GB.
Collapse
Affiliation(s)
- Jean-Michel Lemée
- Department of Neurosurgery, University Hospital of Angers, Angers, France (J.-M.L., A.C., P.M.); INSERM U1066, "Micro- et nano-médecine biomimétiques", Angers, France (J.-M.L., A.C., P.M.)
| | - Anne Clavreul
- Department of Neurosurgery, University Hospital of Angers, Angers, France (J.-M.L., A.C., P.M.); INSERM U1066, "Micro- et nano-médecine biomimétiques", Angers, France (J.-M.L., A.C., P.M.)
| | - Philippe Menei
- Department of Neurosurgery, University Hospital of Angers, Angers, France (J.-M.L., A.C., P.M.); INSERM U1066, "Micro- et nano-médecine biomimétiques", Angers, France (J.-M.L., A.C., P.M.)
| |
Collapse
|
33
|
Cohen A, Sato M, Aldape K, Mason CC, Alfaro-Munoz K, Heathcock L, South ST, Abegglen LM, Schiffman JD, Colman H. DNA copy number analysis of Grade II-III and Grade IV gliomas reveals differences in molecular ontogeny including chromothripsis associated with IDH mutation status. Acta Neuropathol Commun 2015; 3:34. [PMID: 26091668 PMCID: PMC4474351 DOI: 10.1186/s40478-015-0213-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 12/21/2022] Open
Abstract
Introduction Isocitrate dehydrogenase (IDH) mutation status and grade define subgroups of diffuse gliomas differing based on age, tumor location, presentation, and prognosis. While some biologic differences between IDH mutated (IDHmut) and wild-type (IDHwt) gliomas are clear, the distinct alterations associated with progression of the two subtypes to glioblastoma (GBM, Grade IV) have not been well described. We analyzed copy number alterations (CNAs) across grades (Grade II–III and GBM) in both IDHmut and IDHwt infiltrating gliomas using molecular inversion probe arrays. Results Ninety four patient samples were divided into four groups: Grade II–III IDHwt (n = 17), Grade II–III IDHmut (n = 28), GBM IDHwt (n = 25), and GBM IDHmut (n = 24). We validated prior observations that IDHwt GBM have a high frequency of chromosome 7 gain (including EGFR) and chromosome 10 loss (including PTEN) compared with IDHmut GBM. Hierarchical clustering of IDHmut gliomas demonstrated distinct CNA patterns distinguishing lower grade gliomas versus GBM. However, similar hierarchical clustering of IDHwt gliomas demonstrated no CNA distinction between lower grade glioma and GBM. Functional analyses showed that IDHwt gliomas had more chromosome gains in regions containing receptor tyrosine kinase pathways. In contrast, IDHmut gliomas more commonly demonstrated amplification of cyclins and cyclin dependent kinase genes. One of the most common alterations associated with transformation of lower grade to GBM IDHmut gliomas was the loss of chromosomal regions surrounding PTEN. IDHmut GBM tumors demonstrated significantly higher levels of overall CNAs compared to lower grade IDHmut tumors and all grades of IDHwt tumors, and IDHmut GBMs also demonstrated significant increase in incidence of chromothripsis. Conclusions Taken together, these analyses demonstrate distinct molecular ontogeny between IDHwt and IDHmut gliomas. Our data also support the novel findings that malignant progression of IDHmut gliomas to GBM involves increased genomic instability and genomic catastrophe, while IDHwt lower grade tumors are virtually identical to GBMs at the level of DNA copy number alterations. Electronic supplementary material The online version of this article (doi:10.1186/s40478-015-0213-3) contains supplementary material, which is available to authorized users.
Collapse
|
34
|
Common variants at 10p12.31, 10q21.1 and 13q12.13 are associated with sporadic pituitary adenoma. Nat Genet 2015; 47:793-7. [PMID: 26029870 DOI: 10.1038/ng.3322] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/07/2015] [Indexed: 01/02/2023]
Abstract
Pituitary adenoma is one of the most common intracranial neoplasms, and its genetic basis remains largely unknown. To identify genetic susceptibility loci for sporadic pituitary adenoma, we performed a three-stage genome-wide association study (GWAS) in the Han Chinese population. We first analyzed genome-wide SNP data in 771 pituitary adenoma cases and 2,788 controls and then carried forward the promising variants for replication in another 2 independent sets (2,542 cases and 3,620 controls in total). We identified three new susceptibility loci below the genome-wide significance threshold (P < 5 × 10(-8)) in the combined analyses: 10p12.31 (rs2359536, P(meta) = 2.25 × 10(-10) and rs10828088, P(meta) = 6.27 × 10(-10)), 10q21.1 (rs10763170, P(meta) = 6.88 × 10(-10)) and 13q12.13 (rs17083838, P(meta) = 1.89 × 10(-8)). This study is the first GWAS to our knowledge on sporadic pituitary adenoma, and our results provide insight into the genetic basis of this disease.
Collapse
|
35
|
Characterizing the peritumoral brain zone in glioblastoma: a multidisciplinary analysis. J Neurooncol 2015; 122:53-61. [PMID: 25559687 DOI: 10.1007/s11060-014-1695-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/20/2014] [Indexed: 10/24/2022]
Abstract
Glioblastoma (GB) is the most frequent and aggressive type of primary brain tumor. Recurrences are mostly located at the margin of the resection cavity in the peritumoral brain zone (PBZ). Although it is widely believed that infiltrative tumor cells in this zone are responsible for GB recurrence, few studies have examined this zone. In this study, we analyzed PBZ left after surgery with a variety of techniques including radiology, histopathology, flow cytometry, genomic, transcriptomic, proteomic, and primary cell cultures. The resulting PBZ profiles were compared with those of the GB tumor zone and normal brain samples to identify characteristics specific to the PBZ. We found that tumor cell infiltration detected by standard histological analysis was present in almost one third of PBZ taken from an area that was considered normal both on standard MRI and by the neurosurgeon under an operating microscope. The panel of techniques used in this study show that the PBZ, similar to the tumor zone itself, is characterized by substantial inter-patient heterogeneity, which makes it difficult to identify representative markers. Nevertheless, we identified specific alterations in the PBZ such as the presence of selected tumor clones and stromal cells with tumorigenic and angiogenic properties. The study of GB-PBZ is a growing field of interest and this region needs to be characterized further. This will facilitate the development of new, targeted therapies for patients with GB and the development of approaches to refine the per-operative evaluation of the PBZ to optimize the surgical resection of the tumor.
Collapse
|
36
|
Protocadherin 9 inhibits epithelial-mesenchymal transition and cell migration through activating GSK-3β in hepatocellular carcinoma. Biochem Biophys Res Commun 2014; 452:567-74. [PMID: 25172662 DOI: 10.1016/j.bbrc.2014.08.101] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 08/21/2014] [Indexed: 11/21/2022]
Abstract
Protocadherin 9 (PCDH9) was found frequently lost in hepatocellular carcinoma (HCC). Here we investigated the role of PCDH9 in the development of HCC. We confirmed that PCDH9 was down-regulated in HCC tissues and cell lines compared with the adjacent non-tumor tissues. PCDH9 downregulation was significantly associated with malignant portal vein invasion of HCC patients. Gain- and loss-of-function studies revealed that downregulation of PCDH9 facilitated tumor cell migration and epithelial-mesenchymal transition (EMT). We identified PCDH9 as a novel regulator of EMT by increasing the activity of GSK-3β and inhibiting Snail1, indicating its potential therapeutic value for reducing metastasis of HCC.
Collapse
|
37
|
Seifert M, Abou-El-Ardat K, Friedrich B, Klink B, Deutsch A. Autoregressive higher-order hidden Markov models: exploiting local chromosomal dependencies in the analysis of tumor expression profiles. PLoS One 2014; 9:e100295. [PMID: 24955771 PMCID: PMC4067306 DOI: 10.1371/journal.pone.0100295] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 05/22/2014] [Indexed: 12/21/2022] Open
Abstract
Changes in gene expression programs play a central role in cancer. Chromosomal aberrations such as deletions, duplications and translocations of DNA segments can lead to highly significant positive correlations of gene expression levels of neighboring genes. This should be utilized to improve the analysis of tumor expression profiles. Here, we develop a novel model class of autoregressive higher-order Hidden Markov Models (HMMs) that carefully exploit local data-dependent chromosomal dependencies to improve the identification of differentially expressed genes in tumor. Autoregressive higher-order HMMs overcome generally existing limitations of standard first-order HMMs in the modeling of dependencies between genes in close chromosomal proximity by the simultaneous usage of higher-order state-transitions and autoregressive emissions as novel model features. We apply autoregressive higher-order HMMs to the analysis of breast cancer and glioma gene expression data and perform in-depth model evaluation studies. We find that autoregressive higher-order HMMs clearly improve the identification of overexpressed genes with underlying gene copy number duplications in breast cancer in comparison to mixture models, standard first- and higher-order HMMs, and other related methods. The performance benefit is attributed to the simultaneous usage of higher-order state-transitions in combination with autoregressive emissions. This benefit could not be reached by using each of these two features independently. We also find that autoregressive higher-order HMMs are better able to identify differentially expressed genes in tumors independent of the underlying gene copy number status in comparison to the majority of related methods. This is further supported by the identification of well-known and of previously unreported hotspots of differential expression in glioblastomas demonstrating the efficacy of autoregressive higher-order HMMs for the analysis of individual tumor expression profiles. Moreover, we reveal interesting novel details of systematic alterations of gene expression levels in known cancer signaling pathways distinguishing oligodendrogliomas, astrocytomas and glioblastomas. An implementation is available under www.jstacs.de/index.php/ARHMM.
Collapse
Affiliation(s)
- Michael Seifert
- Center for Information Services and High Performance Computing, Dresden University of Technology, Dresden, Germany
| | - Khalil Abou-El-Ardat
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Betty Friedrich
- Center for Information Services and High Performance Computing, Dresden University of Technology, Dresden, Germany
| | - Barbara Klink
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Andreas Deutsch
- Center for Information Services and High Performance Computing, Dresden University of Technology, Dresden, Germany
| |
Collapse
|
38
|
Abstract
Loss of cadherin 1 (CDH1; also known as epithelial cadherin (E-cadherin)) is used for the diagnosis and prognosis of epithelial cancers. However, it should not be ignored that the superfamily of transmembrane cadherin proteins encompasses more than 100 members in humans, including other classical cadherins, numerous protocadherins and cadherin-related proteins. Elucidation of their roles in suppression versus initiation or progression of various tumour types is a young but fascinating field of molecular cancer research. These cadherins are very diverse in both structure and function, and their mutual interactions seem to influence biological responses in complex and versatile ways.
Collapse
Affiliation(s)
- Frans van Roy
- Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium.The Inflammation Research Center, VIB, B-9052 Ghent, Belgium
| |
Collapse
|
39
|
Hirabayashi T, Yagi T. Protocadherins in neurological diseases. ADVANCES IN NEUROBIOLOGY 2014; 8:293-314. [PMID: 25300142 DOI: 10.1007/978-1-4614-8090-7_13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cadherins were originally isolated as calcium-dependent cell adhesion molecules and are characterized by their cadherin motifs in the extracellular domain. In vertebrates, including humans, there are more than 100 different cadherin-related genes, which constitute the cadherin superfamily. The protocadherin (Pcdh) family comprises a large subgroup within the cadherin superfamily. The Pcdhs are divided into clustered and non-clustered Pcdhs, based on their genomic structure. Almost all the Pcdh genes are expressed widely in the brain and play important roles in brain development and in the regulation of brain function. This chapter presents an overview of Pcdh family members with regard to their functions, knockout mouse phenotypes, and association with neurological diseases and tumors.
Collapse
|
40
|
Khalil BD, Hanna S, Saykali BA, El-Sitt S, Nasrallah A, Marston D, El-Sabban M, Hahn KM, Symons M, El-Sibai M. The regulation of RhoA at focal adhesions by StarD13 is important for astrocytoma cell motility. Exp Cell Res 2013; 321:109-22. [PMID: 24333506 DOI: 10.1016/j.yexcr.2013.11.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 11/27/2013] [Accepted: 11/29/2013] [Indexed: 10/25/2022]
Abstract
Malignant astrocytomas are highly invasive into adjacent and distant regions of the normal brain. Rho GTPases are small monomeric G proteins that play important roles in cytoskeleton rearrangement, cell motility, and tumor invasion. In the present study, we show that the knock down of StarD13, a GTPase activating protein (GAP) for RhoA and Cdc42, inhibits astrocytoma cell migration through modulating focal adhesion dynamics and cell adhesion. This effect is mediated by the resulting constitutive activation of RhoA and the subsequent indirect inhibition of Rac. Using Total Internal Reflection Fluorescence (TIRF)-based Förster Resonance Energy Transfer (FRET), we show that RhoA activity localizes with focal adhesions at the basal surface of astrocytoma cells. Moreover, the knock down of StarD13 inhibits the cycling of RhoA activation at the rear edge of cells, which makes them defective in retracting their tail. This study highlights the importance of the regulation of RhoA activity in focal adhesions of astrocytoma cells and establishes StarD13 as a GAP playing a major role in this process.
Collapse
Affiliation(s)
- Bassem D Khalil
- Department of Natural Sciences, The Lebanese American University, P.O. Box: 13-5053, Chouran, Beirut 1102 2801, Lebanon
| | - Samer Hanna
- Department of Natural Sciences, The Lebanese American University, P.O. Box: 13-5053, Chouran, Beirut 1102 2801, Lebanon
| | - Bechara A Saykali
- Department of Natural Sciences, The Lebanese American University, P.O. Box: 13-5053, Chouran, Beirut 1102 2801, Lebanon
| | - Sally El-Sitt
- Department of Natural Sciences, The Lebanese American University, P.O. Box: 13-5053, Chouran, Beirut 1102 2801, Lebanon
| | - Anita Nasrallah
- Department of Natural Sciences, The Lebanese American University, P.O. Box: 13-5053, Chouran, Beirut 1102 2801, Lebanon
| | - Daniel Marston
- Department of Pharmacology, University of North Carolina School of Medicine, CB7365, Chapel Hill, NC27599, USA
| | - Marwan El-Sabban
- Department of Human Morphology, Faculty of Medicine, The American University of Beirut, Beirut, Lebanon
| | - Klaus M Hahn
- Department of Pharmacology, University of North Carolina School of Medicine, CB7365, Chapel Hill, NC27599, USA
| | - Marc Symons
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research at North Shore-LIJ, North Shore University Hospital, Manhasset, NY 11030, USA
| | - Mirvat El-Sibai
- Department of Natural Sciences, The Lebanese American University, P.O. Box: 13-5053, Chouran, Beirut 1102 2801, Lebanon.
| |
Collapse
|
41
|
Characterizing the role of PCDH9 in the regulation of glioma cell apoptosis and invasion. J Mol Neurosci 2013; 52:250-60. [PMID: 24214103 DOI: 10.1007/s12031-013-0133-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 09/30/2013] [Indexed: 01/09/2023]
Abstract
PCDH9, a member of the protocadherin superfamily, is frequently lost in many different cancer types. This study aimed to detect PCDH9 expression in glioma tissues. This study also assessed the effects of PCDH9 expression in two different glioma cell lines. This was accomplished by manipulating PCDH9 expression in these glioma cell lines. The data showed that the expression of PCDH9 mRNA and protein was significantly decreased in gliomas compared to normal brain tissues. Lentivirus carrying PCDH9 cDNA restored PCDH9 expression in the U87 and U251 glioma cell lines. PCDH9 restoration in these cell lines reduced tumor cell viability, induced apoptosis, and caused G0/G1 cell cycle arrest. PCDH9 expression also suppressed the colony formation ability and invasion capacity of U87 and U251 cells. Molecularly, the restoration of PCDH9 expression upregulated Bax protein expression, but downregulated Bcl-2 and cyclin D1 expression. These data from the current study suggest that the loss of PCDH9 expression could contribute to glioma development and/or progression. Further studies will evaluate PCDH9 expression as a biomarker for the early detection of gliomas and as a prognostic indicator for this cancer type.
Collapse
|
42
|
Mu Y, Chen Y, Zhang G, Zhan X, Li Y, Liu T, Li G, Li M, Xiao Z, Gong X, Chen Z. Identification of stromal differentially expressed proteins in the colon carcinoma by quantitative proteomics. Electrophoresis 2013; 34:1679-92. [PMID: 23737015 DOI: 10.1002/elps.201200596] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/28/2013] [Accepted: 02/07/2013] [Indexed: 12/18/2022]
Abstract
Tumor microenvironment plays very important roles in the carcinogenesis. A variety of stromal cells in the microenvironment have been modified to support the unique needs of the malignant state. This study was to discover stromal differentially expressed proteins (DEPs) that were involved in colon carcinoma carcinogenesis. Laser capture microdissection (LCM) was captured and isolated the stromal cells from colon adenocarcinoma (CAC) and non-neoplastic colon mucosa (NNCM) tissues, respectively. Seventy DEPs were identified between the pooled LCM-enriched CAC and NNCM stroma samples by iTRAQ-based quantitative proteomics. Gene Ontology (GO) relationship analysis revealed that DEPs were hierarchically grouped into 10 clusters, and were involved in multiple biological functions that were altered during carcinogenesis, including extracellular matrix organization, cytoskeleton, transport, metabolism, inflammatory response, protein polymerization, and cell motility. Pathway network analysis revealed 6 networks and 56 network eligible proteins with Ingenuity pathway analysis. Four significant networks functioned in digestive system development and its function, inflammatory disease, and developmental disorder. Eight DEPs (DCN, FN1, PKM2, HSP90B1, S100A9, MYH9, TUBB, and YWHAZ) were validated by Western blotting, and four DEPs (DCN, FN1, PKM2, and HSP90B1) were validated by immunohistochemical analysis. It is the first report of stromal DEPs between CAC and NNCM tissues. It will be helpful to recognize the roles of stromas in the colon carcinoma microenvironment, and improve the understanding of carcinogenesis in colon carcinoma. The present data suggest that DCN, FN1, PKM2, HSP90B1, S100A9, MYH9, TUBB, and YWHAZ might be the potential targets for colon cancer prevention and therapy.
Collapse
Affiliation(s)
- Yibing Mu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, P. R. China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Guo P, Nie Q, Lan J, Ge J, Qiu Y, Mao Q. C-Myc negatively controls the tumor suppressor PTEN by upregulating miR-26a in glioblastoma multiforme cells. Biochem Biophys Res Commun 2013; 441:186-90. [PMID: 24140063 DOI: 10.1016/j.bbrc.2013.10.034] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 10/08/2013] [Indexed: 12/22/2022]
Abstract
The c-Myc oncogene is amplified in many tumor types. It is an important regulator of cell proliferation and has been linked to altered miRNA expression, suggesting that c-Myc-regulated miRNAs might contribute to tumor progression. Although miR-26a has been reported to be upregulated in glioblastoma multiforme (GBM), the mechanism has not been established. We have shown that ectopic expression of miR-26a influenced cell proliferation by targeting PTEN, a tumor suppressor gene that is inactivated in many common malignancies, including GBM. Our findings suggest that c-Myc modulates genes associated with oncogenesis in GBM through deregulation of miRNAs via the c-Myc-miR-26a-PTEN signaling pathway. This may be of clinical relevance.
Collapse
Affiliation(s)
- Pin Guo
- Department of Neurosurgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | | | | | | | | | | |
Collapse
|
44
|
Baronchelli S, Bentivegna A, Redaelli S, Riva G, Butta V, Paoletta L, Isimbaldi G, Miozzo M, Tabano S, Daga A, Marubbi D, Cattaneo M, Biunno I, Dalprà L. Delineating the cytogenomic and epigenomic landscapes of glioma stem cell lines. PLoS One 2013; 8:e57462. [PMID: 23468990 PMCID: PMC3585345 DOI: 10.1371/journal.pone.0057462] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 01/24/2013] [Indexed: 12/18/2022] Open
Abstract
Glioblastoma multiforme (GBM), the most common and malignant type of glioma, is characterized by a poor prognosis and the lack of an effective treatment, which are due to a small sub-population of cells with stem-like properties, termed glioma stem cells (GSCs). The term "multiforme" describes the histological features of this tumor, that is, the cellular and morphological heterogeneity. At the molecular level multiple layers of alterations may reflect this heterogeneity providing together the driving force for tumor initiation and development. In order to decipher the common "signature" of the ancestral GSC population, we examined six already characterized GSC lines evaluating their cytogenomic and epigenomic profiles through a multilevel approach (conventional cytogenetic, FISH, aCGH, MeDIP-Chip and functional bioinformatic analysis). We found several canonical cytogenetic alterations associated with GBM and a common minimal deleted region (MDR) at 1p36.31, including CAMTA1 gene, a putative tumor suppressor gene, specific for the GSC population. Therefore, on one hand our data confirm a role of driver mutations for copy number alterations (CNAs) included in the GBM genomic-signature (gain of chromosome 7- EGFR gene, loss of chromosome 13- RB1 gene, loss of chromosome 10-PTEN gene); on the other, it is not obvious that the new identified CNAs are passenger mutations, as they may be necessary for tumor progression specific for the individual patient. Through our approach, we were able to demonstrate that not only individual genes into a pathway can be perturbed through multiple mechanisms and at different levels, but also that different combinations of perturbed genes can incapacitate functional modules within a cellular networks. Therefore, beyond the differences that can create apparent heterogeneity of alterations among GSC lines, there's a sort of selective force acting on them in order to converge towards the impairment of cell development and differentiation processes. This new overview could have a huge importance in therapy.
Collapse
Affiliation(s)
- Simona Baronchelli
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
- Science and Technology Park, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
| | - Angela Bentivegna
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | - Serena Redaelli
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | - Gabriele Riva
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | - Valentina Butta
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | - Laura Paoletta
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | | | - Monica Miozzo
- Department of Pathophysiology and Organ Transplant, University of Milan, Milan, Italy
- Pathology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Silvia Tabano
- Department of Pathophysiology and Organ Transplant, University of Milan, Milan, Italy
- Pathology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonio Daga
- Department of Hematology-Oncology, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria San Martino- Istituto Scientifico Tumori (IST) Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Daniela Marubbi
- Department of Hematology-Oncology, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria San Martino- Istituto Scientifico Tumori (IST) Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Monica Cattaneo
- Science and Technology Park, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
| | - Ida Biunno
- Institute of Genetics and Biomedical Research-National Research Council, Milan, Italy
| | - Leda Dalprà
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
- Department of Surgical Pathology, S. Gerardo Hospital, Monza, Italy
- * E-mail:
| |
Collapse
|
45
|
Distinct genomic aberrations between low-grade and high-grade gliomas of Chinese patients. PLoS One 2013; 8:e57168. [PMID: 23451178 PMCID: PMC3579804 DOI: 10.1371/journal.pone.0057168] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 01/17/2013] [Indexed: 11/19/2022] Open
Abstract
Background Glioma is a type of tumor that develops in the central nerve system, mainly the brain. Alterations of genomic sequence and sequence segments (such as copy number variations or CNV and copy neutral loss of heterozygosities or cnLOH) are thought to be a major determinant of the tumor grade. Methods We mapped genomic variations between low-grade and high-grade gliomas (LGG and HGG) in Chinese population based on Illumina’s Beadchip and validated the results using real-time qPCR. Results At the cytoband level, we discovered: (1) unique losses in LGG on 5q, 8p and 11q, and in HGG on 6q, 11p, 13q and 19q; (2) unique gains in the LGG on 1p and in HGG at 5p, 7p, 7q and 20q; and (3) cnLOH in HGG only on 3q, 8q, 10p, 14q, 15q, 17p, 17q, 18q and 21q. Subsequently, we confirmed well-characterized oncogenes among tumor-related loci (such as EGFR and KIT) and detected novel genes that gained chromosome sequences (such as AASS, HYAL4, NDUFA5 and SPAM1) in both LGG and HGG. In addition, we found gains, losses, and cnLOH in several genes, including VN1R2, VN1R4, and ZNF677, in multiple samples. Mapping grade-associated pathways and their related gene ontology (GO) terms, we classified LGG-associated functions as “arachidonic acid metabolism”, “DNA binding” and “regulation of DNA-dependent transcription” and the HGG-associated as “neuroactive ligand-receptor interaction”, “neuronal cell body” and “defense response to bacterium”. Conclusion LGG and HGG appear to have different molecular signatures in genomic variations and our results provide invaluable information for the diagnosis and treatment of gliomas in patients with variable duration or diverse tumor differentiation.
Collapse
|
46
|
Abstract
RhoGTPases are defined as a family of 20 small G proteins playing important roles in almost every cellular process. RhoGTPases are guanine nucleotide-binding proteins existing in two forms: the active form which is GTP bound and the inactive one that being GDP bound. RhoGTPase-activating proteins known as RhoGAPs constitute one of the major classes of regulators of RhoGTPases. They act as negative regulators of the RhoGTPases by enhancing their slow intrinsic GTPase activity. STARD13, a GTPase activating protein (GAP) for RhoGTPases, has been described as a tumor suppressor in hepatocellular carcinoma. In the present review, we discuss the family of RhoGTPases, their regulation and their RhoGAPs, focusing mainly on STARD13.
Collapse
Affiliation(s)
- Sally El-Sitt
- Department of Natural Sciences, Lebanese American University, Beirut Campus, Beirut, Lebanon
| | | |
Collapse
|
47
|
Kahr I, Vandepoele K, van Roy F. Delta-protocadherins in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 116:169-92. [PMID: 23481195 DOI: 10.1016/b978-0-12-394311-8.00008-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The protocadherin family comprises clustered and nonclustered protocadherin genes. The nonclustered genes encode mainly δ-protocadherins, which deviate markedly from classical cadherins. They can be subdivided phylogenetically into δ0-protocadherins (protocadherin-20), δ1-protocadherins (protocadherin-1, -7, -9, and -11X/Y), and δ2-protocadherins (protocadherin-8, -10, -17, -18, and -19). δ-Protocadherins share a similar gene structure and are expressed as multiple alternative splice forms differing mostly in their cytoplasmic domains (CDs). Some δ-protocadherins reportedly show cell-cell adhesion properties. Individual δ-protocadherins appear to be involved in specific signaling pathways, as they interact with proteins such as TAF1/Set, TAO2β, Nap1, and the Frizzled-7 receptor. The spatiotemporally restricted expression of δ-protocadherins in various tissues and species and their functional analysis suggest that they play multiple, tightly regulated roles in vertebrate development. Furthermore, several δ-protocadherins have been implicated in neurological disorders and in cancers, highlighting the importance of scrutinizing their properties and their dysregulation in various pathologies.
Collapse
Affiliation(s)
- Irene Kahr
- Department for Molecular Biomedical Research, VIB, Ghent, Belgium
| | | | | |
Collapse
|
48
|
Wastowski IJ, Simões RT, Yaghi L, Donadi EA, Pancoto JT, Poras I, Lechapt-Zalcman E, Bernaudin M, Valable S, Carlotti CG, Flajollet S, Jensen SS, Ferrone S, Carosella ED, Kristensen BW, Moreau P. Human leukocyte antigen-G is frequently expressed in glioblastoma and may be induced in vitro by combined 5-aza-2'-deoxycytidine and interferon-γ treatments: results from a multicentric study. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 182:540-52. [PMID: 23219427 DOI: 10.1016/j.ajpath.2012.10.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 10/22/2012] [Accepted: 10/25/2012] [Indexed: 12/31/2022]
Abstract
Human leukocyte antigen-G (HLA-G) is a nonclassical major histocompatibility complex (MHC) class I molecule involved in immune tolerance processes, playing an important role in the maintenance of the semi-allogeneic fetus. Although HLA-G expression is restricted in normal tissues, it is broadly expressed in malignant tumors and may favor tumor immune escape. We analyzed HLA-G protein and mRNA expression in tumor samples from patients with glioblastoma collected in France, Denmark, and Brazil. We found HLA-G protein expression in 65 of 108 samples and mRNA in 20 of 21 samples. The absence of HLA-G protein expression was associated with a better long-term survival rate. The mechanisms underlying HLA-G gene expression were investigated in glioma cell lines U251MG, D247MG, and U138MG. Induction of HLA-G transcriptional activity was dependent of 5-aza-2'-deoxycytidine treatment and enhanced by interferon-γ. HLA-G protein expression was observed in U251MG cells only. These cells exhibited a permissive chromatin state at the HLA-G gene promoter and the highest levels of induced HLA-G transcriptional activity following 5-aza-2'-deoxycytidine treatment. Several antigen-presenting machinery components were up-regulated in U251MG cells after demethylating and IFN-γ treatments, suggesting an effect on the up-regulation of HLA-G cell surface expression. Therefore, because of its role in tumor tolerance, HLA-G found to be expressed in glioblastoma samples should be taken into consideration in clinical studies on the pathology and in the design of therapeutic strategies to prevent its expression in HLA-G-negative tumors.
Collapse
Affiliation(s)
- Isabela J Wastowski
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut des Maladies Emergentes et des Thérapies Innovantes, Service de Recherches en Hémato-Immunologie, Hôpital Saint-Louis, Paris, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Fontanillo C, Aibar S, Sanchez-Santos JM, De Las Rivas J. Combined analysis of genome-wide expression and copy number profiles to identify key altered genomic regions in cancer. BMC Genomics 2012; 13 Suppl 5:S5. [PMID: 23095915 PMCID: PMC3476997 DOI: 10.1186/1471-2164-13-s5-s5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Analysis of DNA copy number alterations and gene expression changes in human samples have been used to find potential target genes in complex diseases. Recent studies have combined these two types of data using different strategies, but focusing on finding gene-based relationships. However, it has been proposed that these data can be used to identify key genomic regions, which may enclose causal genes under the assumption that disease-associated gene expression changes are caused by genomic alterations.
Collapse
Affiliation(s)
- Celia Fontanillo
- Cancer Research Center, Consejo Superior de Investigaciones Cientificas, Campus Miguel de Unamuno, Salamanca, Spain.
| | | | | | | |
Collapse
|
50
|
Jiang Y, Ma Y, Cheng Y. Transcriptome and Coexpression Network Analysis of the Human Glioma Cell Line Hs683 Exposed to Candoxin. J Int Med Res 2012; 40:887-98. [PMID: 22906261 DOI: 10.1177/147323001204000307] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE: Gliomas are the most common primary tumours of the central nervous system. Snake venom, such as candoxin (CDX) isolated from Bungarus candidus, inhibits glioma cell proliferation. This study explored the gene regulation profile of CDX-treated human glioma Hs683 cells. METHODS: Using microarray technology and bioinformatics analyses the underlying molecular mechanism of action of CDX was evaluated by constructing gene regulation and protein—protein interaction coexpression networks. RESULTS: CDX treatment induced a large number of related genes at the transcriptional level. The MYC gene (v-myc myelocytomatosis viral oncogene homologue [avian]) had a key role in the response of Hs683 cells to CDX treatment. Activation of MYC upregulated NDRG1 (N-myc downstream regulated 1), WNT10B (wingless-type mouse mammary tumour virus integration site family, member 10B), CASP9 (caspase 9, apoptosis-related cysteine peptidase) and CDKN2A (cyclin-dependent kinase inhibitor 2A), and downregulated ID3 (inhibitor of DNA binding 3, dominant negative helix—loop—helix protein) and SLC1A4 (solute carrier family 1 [glutamate/neutral amino acid transporter], member 4). In addition, a subnetwork was constructed among SPP1 (secreted phosphoprotein 1), SDC1 (syndecan 1) and CD44 based on protein—protein interactions, and these genes were predicted to be involved in glioma cell invasion. CONCLUSION: These findings might provide novel therapeutic targets for glioma chemotherapy.
Collapse
Affiliation(s)
- Yx Jiang
- Department of Neurosurgery, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Y Ma
- Department of Neurosurgery, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Y Cheng
- Department of Neurosurgery, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| |
Collapse
|