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Molecular markers related to patient outcome in patients with IDH-mutant astrocytomas grade 2 to 4: A systematic review. Eur J Cancer 2022; 175:214-223. [PMID: 36152406 DOI: 10.1016/j.ejca.2022.08.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND Grading and classification of IDH-mutant astrocytomas has shifted from solely histology towards histology combined with molecular diagnostics. In this systematic review, we give an overview of all currently known clinically relevant molecular markers within IDH-mutant astrocytomas grade 2 to 4. METHODS A literature search was performed in five electronic databases for English original papers on patient outcome with respect to a molecular marker as determined by DNA/RNA sequencing, micro-arrays, or DNA methylation profiling in IDH-mutant astrocytomas grade 2 to 4. Papers were included if molecular diagnostics were performed on tumour tissue of at least 15 IDH-mutant astrocytoma patients, and if the investigated molecular markers were not limited to the diagnostic markers MGMT, ATRX, TERT, and/or TP53. RESULTS The literature search identified 4508 unique articles, published between August 2012 and December 2021, of which ultimately 44 articles were included. Numerous molecular markers from these papers were significantly correlated to patient outcome. The associations between patient outcome and non-canonical IDH mutations, PI3K mutations, high expression of MSH2, high expression of RAD18, homozygous deletion of CDKN2A/B, amplification of PDGFRA, copy number neutral loss of chromosomal arm 17p, loss of chromosomal arm 19q, the G-CIMP-low DNA methylation cluster, high total CNV, and high tumour mutation burden were confirmed in multiple studies. CONCLUSIONS Multiple genetic and epigenetic markers are associated with survival in IDH-mutant astrocytoma patients. Commonly affected are the RB signalling pathway, the RTK-PI3K-mTOR signalling pathway, genomic stability markers, and (epigenetic) gene regulation.
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2
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Boziki M, Grigoriadis N, Papaefthymiou A, Doulberis M, Polyzos SA, Gavalas E, Deretzi G, Karafoulidou E, Kesidou E, Taloumtzis C, Theotokis P, Sofou E, Katsinelos P, Vardaka E, Fludaras I, Touloumtzi M, Koukoufiki A, Simeonidou C, Liatsos C, Kountouras J. The trimebutine effect on Helicobacter pylori-related gastrointestinal tract and brain disorders: A hypothesis. Neurochem Int 2021; 144:104938. [PMID: 33535070 DOI: 10.1016/j.neuint.2020.104938] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/17/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023]
Abstract
The localization of bacterial components and/or metabolites in the central nervous system may elicit neuroinflammation and/or neurodegeneration. Helicobacter pylori (a non-commensal symbiotic gastrointestinal pathogen) infection and its related metabolic syndrome have been implicated in the pathogenesis of gastrointestinal tract and central nervous system disorders, thus medications affecting the nervous system - gastrointestinal tract may shape the potential of Helicobacter pylori infection to trigger these pathologies. Helicobacter pylori associated metabolic syndrome, by impairing gut motility and promoting bacterial overgrowth and translocation, might lead to brain pathologies. Trimebutine maleate is a prokinetic drug that hastens gastric emptying, by inducing the release of gastrointestinal agents such as motilin and gastrin. Likewise, it appears to protect against inflammatory signal pathways, involved in inflammatory disorders including brain pathologies. Trimebutine maleate also acts as an antimicrobial agent and exerts opioid agonist effect. This study aimed to investigate a hypothesis regarding the recent advances in exploring the potential role of gastrointestinal tract microbiota dysbiosis-related metabolic syndrome and Helicobacter pylori in the pathogenesis of gastrointestinal tract and brain diseases. We hereby proposed a possible neuroprotective role for trimebutine maleate by altering the dynamics of the gut-brain axis interaction, thus suggesting an additional effect of trimebutine maleate on Helicobacter pylori eradication regimens against these pathologies.
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Affiliation(s)
- Marina Boziki
- Second Neurological Department, Aristotle University of Thessaloniki, AHEPA University General Hospital of Thessaloniki, Thessaloniki, 54636, Macedonia, Greece
| | - Nikolaos Grigoriadis
- Second Neurological Department, Aristotle University of Thessaloniki, AHEPA University General Hospital of Thessaloniki, Thessaloniki, 54636, Macedonia, Greece
| | - Apostolis Papaefthymiou
- Department of Gastroenterology, University Hospital of Larissa, Larissa, 41110, Greece; Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 546 42, Macedonia, Greece; First Laboratory of Pharmacology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | - Michael Doulberis
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 546 42, Macedonia, Greece; First Laboratory of Pharmacology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece; Division of Gastroenterology and Hepatology, Medical University Department, Kantonsspital Aarau, Aarau, 5001, Switzerland
| | - Stergios A Polyzos
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 546 42, Macedonia, Greece; First Laboratory of Pharmacology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | - Emmanuel Gavalas
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 546 42, Macedonia, Greece
| | - Georgia Deretzi
- Department of Neurology, Papageorgiou General Hospital, Thessaloniki, 56429, Macedonia, Greece
| | - Eleni Karafoulidou
- Second Neurological Department, Aristotle University of Thessaloniki, AHEPA University General Hospital of Thessaloniki, Thessaloniki, 54636, Macedonia, Greece
| | - Evangelia Kesidou
- Second Neurological Department, Aristotle University of Thessaloniki, AHEPA University General Hospital of Thessaloniki, Thessaloniki, 54636, Macedonia, Greece
| | - Charilaos Taloumtzis
- Second Neurological Department, Aristotle University of Thessaloniki, AHEPA University General Hospital of Thessaloniki, Thessaloniki, 54636, Macedonia, Greece; 424 General Military Hospital of Thessaloniki, Department of Gastroenterology, Thessaloniki, 56429, Macedonia, Greece
| | - Paschalis Theotokis
- Second Neurological Department, Aristotle University of Thessaloniki, AHEPA University General Hospital of Thessaloniki, Thessaloniki, 54636, Macedonia, Greece
| | - Electra Sofou
- Second Neurological Department, Aristotle University of Thessaloniki, AHEPA University General Hospital of Thessaloniki, Thessaloniki, 54636, Macedonia, Greece
| | - Panagiotis Katsinelos
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 546 42, Macedonia, Greece
| | - Elisabeth Vardaka
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 546 42, Macedonia, Greece; Department of Nutritional Sciences and Dietetics, School of Health Sciences, International Hellenic University, Alexander Campus, 574 00, Thessaloniki, Macedonia, Greece
| | - Ioannis Fludaras
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 546 42, Macedonia, Greece
| | - Maria Touloumtzi
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 546 42, Macedonia, Greece
| | - Argiro Koukoufiki
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 546 42, Macedonia, Greece
| | - Constantina Simeonidou
- Laboratory of Experimental Physiology, Department of Physiology and Pharmacology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, 54124, Macedonia, Greece
| | - Christos Liatsos
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 546 42, Macedonia, Greece; Department of Gastroenterology, 401 Army General Hospital of Athens, Athens, 115 25, Greece
| | - Jannis Kountouras
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 546 42, Macedonia, Greece.
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3
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Panagopoulos I, Brunetti M, Stoltenberg M, Strandabø RAU, Staurseth J, Andersen K, Kostolomov I, Hveem TS, Lorenz S, Nystad TA, Flægstad T, Micci F, Heim S. Novel GTF2I- PDGFRB and IKZF1- TYW1 fusions in pediatric leukemia with normal karyotype. Exp Hematol Oncol 2019; 8:12. [PMID: 31161074 PMCID: PMC6542082 DOI: 10.1186/s40164-019-0136-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/23/2019] [Indexed: 11/25/2022] Open
Abstract
Background Many cases of acute lymphoblastic leukemia (ALL) carry visible acquired chromosomal changes of pathogenetic, diagnostic, and prognostic importance. Nevertheless, from one-fourth to half of newly diagnosed ALL patients have no visible chromosomal changes detectable by G-banding analysis at diagnosis. The introduction of powerful molecular methodologies has shown that many karyotypically normal ALLs carry clinically important submicroscopic aberrations. Case presentation We used fluorescence in situ hybridization (FISH), array comparative genomic hybridization (aCGH), RNA sequencing, reverse transcription (RT) and genomic polymerase chain reaction (PCR), as well as Sanger sequencing to investigate a case of pediatric ALL with a normal karyotype. FISH with a commercial PDGFRB breakapart probe showed loss of the distal part of the probe suggesting a breakpoint within the PDGFRB locus. aCGH revealed submicroscopic deletions in chromosome bands 5q32q35.3 (about 30 Mb long, starting within PDGFRB and finishing in the CANX locus), 7q34 (within TCRB), 9p13 (PAX5), 10q26.13 (DMBT1), 14q11.2 (TRAC), and 14q32.33 (within the IGH locus). RNA sequencing detected an in-frame GTF2I–PDGFRB and an out-of-frame IKZF1–TYW1 fusion transcript. Both fusion transcripts were verified by RT-PCR together with Sanger sequencing and interphase FISH. The GTF2I–PDGFRB fusion was also verified by genomic PCR and FISH. The corresponding GTF2I–PDGFRB fusion protein would consist of almost the entire GTF2I and that part of PDGFRB which harbors the catalytic domain of the tyrosine kinase. It would therefore seem to lead to abnormal tyrosine kinase activity in a manner similar to what has been seen for other PDGFRB fusion proteins. Conclusions The examined pediatric leukemia is a Ph-like ALL which carries novel GTF2I–PDGFRB and IKZF1–TYW1 fusion genes together with additional submicroscopic deletions. Because hematologic neoplasms with PDGFRB-fusion genes can be treated with tyrosine kinase inhibitors, the detection of such novel fusions may be clinically important. Since the GTF2I–PDGFRB could be detected only after molecular studies of the leukemic cells, further investigations of ALL-cases, perhaps especially but not exclusively with a normal karyotype, are needed in order to determine the frequency of GTF2I–PDGFRB in leukemia, and also to find out which clinical impact the fusion may have.
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Affiliation(s)
- Ioannis Panagopoulos
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Marta Brunetti
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Margrethe Stoltenberg
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Rønnaug A U Strandabø
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Julie Staurseth
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Kristin Andersen
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Ilyá Kostolomov
- 2Section for Applied Informatics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Tarjei S Hveem
- 2Section for Applied Informatics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Susanne Lorenz
- 3Genomics Core Facility, Department of Core Facilities, Oslo University Hospital, Oslo, Norway
| | - Tove Anita Nystad
- 4Department of Pediatrics, Division of Child and Adolescent Health, University Hospital of North-Norway, 9038 Tromsø, Norway
| | - Trond Flægstad
- 4Department of Pediatrics, Division of Child and Adolescent Health, University Hospital of North-Norway, 9038 Tromsø, Norway.,5Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway-UiT, 9037 Tromsø, Norway
| | - Francesca Micci
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway
| | - Sverre Heim
- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Nydalen, PO Box 49534, 0424 Oslo, Norway.,6Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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The landscape of postsurgical recurrence patterns in diffuse low-grade gliomas. Crit Rev Oncol Hematol 2019; 138:148-155. [PMID: 31092371 DOI: 10.1016/j.critrevonc.2019.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/02/2019] [Accepted: 04/08/2019] [Indexed: 12/20/2022] Open
Abstract
Early and maximal safe surgical resection optionally followed by adjuvant treatment is currently recommended in diffuse low-grade glioma (DLGG). Although this management delays malignant transformation (MT), recurrence will most often occur. Because this relapse usually arises locally, reoperation can be considered, with possible further chemotherapy/radiotherapy. However, due to a prolonged overall survival, a large spectrum of unusual recurrence patterns begins to emerge during long-term follow-up, beyond the classical slow and local tumor re-growth. We review various atypical patterns of DLGG relapse, we discuss their pathophysiological mechanisms and how to adapt the treatment(s). Those patterns include very diffuse, ipsi- or bilateral gliomatosis-like progression, multicentric recurrence with emergence of remote low-grade or high-grade glioma, leptomeningeal dissemination, acute (early or delayed) local MT or bulky relapse into the operating cavity. This landscape of recurrence patterns may allow physicians to elaborate new tailored therapeutic strategies and scientists to develop original hypotheses for basic research.
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5
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Wood MD, Halfpenny AM, Moore SR. Applications of molecular neuro-oncology - a review of diffuse glioma integrated diagnosis and emerging molecular entities. Diagn Pathol 2019; 14:29. [PMID: 30967140 PMCID: PMC6457044 DOI: 10.1186/s13000-019-0802-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/12/2019] [Indexed: 11/10/2022] Open
Abstract
Insights into the molecular underpinnings of primary central nervous system tumors have radically changed the approach to tumor diagnosis and classification. Diagnostic emphasis has shifted from the morphology of a tumor under the microscope to an integrated approach based on morphologic and molecular features, including gene mutations, chromosomal copy number alterations, and gene rearrangements. In 2016, the World Health Organization provided guidelines for making an integrated diagnosis that incorporates both morphologic and molecular features in a subset of brain tumors. The integrated diagnosis now applies to infiltrating gliomas, a category that includes diffusely infiltrating astrocytoma grades II, III, and IV, and oligodendroglioma, grades II and III, thereby encompassing the most common primary intra-axial central nervous system tumors. Other neoplasms such as medulloblastoma, embryonal tumor with multilayered rosettes, certain supratentorial ependymomas, and atypical teratoid/rhabdoid tumor are also eligible for integrated diagnosis, which can sometimes be aided by characteristic immunohistochemical markers. Since 2016, advances in molecular neuro-oncology have resulted in periodic updates and clarifications to the integrated diagnostic approach. These advances reflect expanding knowledge on the molecular pathology of brain tumors, but raise a challenge in rapidly incorporating new molecular findings into diagnostic practice. This review provides a background on the molecular characteristics of primary brain tumors, emphasizing the molecular basis for classification of infiltrating gliomas, the most common entities that are eligible for an integrated diagnosis. We then discuss entities within the diffuse gliomas that do not receive an integrated diagnosis by WHO 2016 criteria, but have distinctive molecular features that are important to recognize because their clinical behavior can influence clinical management and prognosis. Particular attention is given to the histone H3 G34R/G34V mutant astrocytomas, an entity to consider when faced with an infiltrating glioma in the cerebral hemisphere of children and young adults, and to the group of histologically lower grade diffuse astrocytic gliomas with molecular features of glioblastoma, an important category of tumors to recognize due to their aggressive clinical behavior.
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Affiliation(s)
- Matthew D Wood
- OHSU Department of Pathology, Division of Anatomic Pathology, Section of Neuropathology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97213, USA.
| | - Aaron M Halfpenny
- OHSU Department of Pathology, Division of Anatomic Pathology, Section of Neuropathology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97213, USA
| | - Stephen R Moore
- Knight Diagnostic Laboratories and Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, USA
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6
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Du Z, Xia Q, Wu B, Ding J, Zhao Y, Lin L, Chen M, Cai Z, Wang S, Xu L, Li E, Wu Z, Li Y, Xu H, Yin D. The analyses of SRCR genes based on protein-protein interaction network in esophageal squamous cell carcinoma. Am J Transl Res 2019; 11:2683-2705. [PMID: 31217847 PMCID: PMC6556668 DOI: pmid/31217847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/29/2019] [Indexed: 02/05/2023]
Abstract
The scavenger receptor cysteine-rich (SRCR) proteins, with one to several SRCR domains, play important roles in human diseases. A full view of their functions in esophageal squamous cell carcinoma (ESCC) remain unclear. Sequence alignment and phylogenetic tree for all human SRCR domains were performed. Differentially-expressed SRCR genes were identified in ESCC, followed by protein-protein interaction (PPI) network construction, topological parameters, subcellular distribution, functional enrichment and survival analyses. The variation of conserved cysteines in each SRCR domain suggested a requirement for new classification of the SRCR family. Six genes (LGALS3BP, MSR1, CD163, LOXL2, LOXL3 and LOXL4) were upregulated, and four genes (DMBT1, PRSS12, TMPRSS2 and SCARA5) were downregulated in ESCC. These 10 SRCR genes form a unique biological network. Functional enrichment analyses provided important clues to investigate the biological functions for SRCR gene network in ESCC, such as extracellular structure organization and the PI3K-Akt signaling pathway. Kaplan-Meier curves confirmed that high expression of SCARA5, LOXL2, LOXL3, LOXL4 were related to poor survival, whereas high expression of DMBTI and PRSS12 showed the opposite result. SRCR genes promote the development of ESCC through its network and could serve as potential prognostic factors and therapy targets of ESCC.
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Affiliation(s)
- Zepeng Du
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Genes Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen UniversityShantou 515041, China
| | - Qiaoxi Xia
- Department of Biochemistry and Molecular Biology, Shantou University Medical CollegeShantou 515041, China
| | - Bingli Wu
- Department of Biochemistry and Molecular Biology, Shantou University Medical CollegeShantou 515041, China
| | - Jiyu Ding
- Department of Biochemistry and Molecular Biology, Shantou University Medical CollegeShantou 515041, China
| | - Yan Zhao
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen UniversityShantou 515041, China
| | - Ling Lin
- Department of Biochemistry and Molecular Biology, Shantou University Medical CollegeShantou 515041, China
| | - Mantong Chen
- Department of Biochemistry and Molecular Biology, Shantou University Medical CollegeShantou 515041, China
| | - Zhixiong Cai
- Department of Cardiology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen UniversityShantou 515041, China
| | - Shaohong Wang
- Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen UniversityShantou 515041, China
| | - Liyan Xu
- Institute of Oncologic Pathology, Shantou University Medical CollegeShantou 515041, China
| | - Enmin Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical CollegeShantou 515041, China
| | - Zhiyong Wu
- Department of Surgical Oncology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen UniversityShantou 515041, China
| | - Yun Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Genes Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Haixiong Xu
- Department of Neurosurgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen UniversityShantou 515041, China
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Genes Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
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7
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Valero A, Roldán ML, Ruiz MF, Teijeiro JM, Marquez SB, Marini PE. Deleted in Malignant Brain Tumor 1 (DMBT1) Expression Pattern in Normal Cervix and at Different Stages of Squamous Intraepithelial Lesions. ACTA ACUST UNITED AC 2018. [DOI: 10.2174/1875318301808010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background:
Cervical cancer is one of the most frequently occurring malignancies in women worldwide, with high mortality rates. Cervical Squamous Cell Carcinoma (SCC) presents previous states of non-invasive precursor lesions, and early stage Low-Grade Squamous Intraepithelial Lesions (LSIL) regress to normal or Atypical Squamous Cells of Undetermined Significance (ASCUS) in approximately 50% of cases. Deleted in Malignant Brain Tumors 1 (DMBT1) is a tumour suppression glycoprotein, which absence is considered a malignancy marker in many epithelial cancers.
Objective:
To analyse DMBT1’s presence and localization in SCC and precursor lesions.
Method:
Immunohistochemistry for DMBT1 was performed in cervix biopsies classified as normal, LSIL, HSIL and SCC.
Results:
DMBT1 was detected at the supranuclear and sometimes infranuclear regions of the endocervix monolayer epithelial cells in normal and HSIL biopsies. In LSIL samples the detection of DMBT1 in endocervix was variable between patients. Also variable was DMBT1 staining in cells of glandular epithelium. The glycoprotein was not detected in the stratified epithelium of the exocervix, regardless of the lesion grade; nor in dysplastic cells.
Conclusion:
The absence of DMBT1 from endocervix only in some samples of LSIL is promising as a candidate for possible lesion regression potential marker.
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8
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Naba A, Clauser KR, Mani DR, Carr SA, Hynes RO. Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression. Sci Rep 2017; 7:40495. [PMID: 28071719 PMCID: PMC5223159 DOI: 10.1038/srep40495] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/07/2016] [Indexed: 02/07/2023] Open
Abstract
The angiogenic switch, the time at which a tumor becomes vascularized, is a critical step in tumor progression. Indeed, without blood supply, tumors will fail to grow beyond 1 mm3 and are unlikely to disseminate. The extracellular matrix (ECM), a major component of the tumor microenvironment, is known to undergo significant changes during angiogenesis and tumor progression. However the extent of these changes remains unknown. In this study, we used quantitative proteomics to profile the composition of the ECM of pancreatic islets in a mouse model of insulinoma characterized by a precisely timed angiogenic switch. Out of the 120 ECM proteins quantified, 35 were detected in significantly different abundance as pancreatic islets progressed from being hyperplastic to angiogenic to insulinomas. Among these, the core ECM proteins, EFEMP1, fibrillin 1, and periostin were found in higher abundance, and decorin, Dmbt1, hemicentin, and Vwa5 in lower abundance. The angiogenic switch being a common feature of solid tumors, we propose that some of the proteins identified represent potential novel anti-angiogenic targets. In addition, we report the characterization of the ECM composition of normal pancreatic islets and propose that this could be of interest for the design of tissue-engineering strategies for treatment of diabetes.
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Affiliation(s)
- Alexandra Naba
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, U.S.A
| | - Karl R Clauser
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, U.S.A
| | - D R Mani
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, U.S.A
| | - Steven A Carr
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, U.S.A
| | - Richard O Hynes
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, U.S.A.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, U.S.A
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9
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Leiserson MDM, Wu HT, Vandin F, Raphael BJ. CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer. Genome Biol 2015; 16:160. [PMID: 26253137 PMCID: PMC4531541 DOI: 10.1186/s13059-015-0700-7] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/22/2015] [Indexed: 12/11/2022] Open
Abstract
Cancer is a heterogeneous disease with different combinations of genetic alterations driving its development in different individuals. We introduce CoMEt, an algorithm to identify combinations of alterations that exhibit a pattern of mutual exclusivity across individuals, often observed for alterations in the same pathway. CoMEt includes an exact statistical test for mutual exclusivity and techniques to perform simultaneous analysis of multiple sets of mutually exclusive and subtype-specific alterations. We demonstrate that CoMEt outperforms existing approaches on simulated and real data. We apply CoMEt to five different cancer types, identifying both known cancer genes and pathways, and novel putative cancer genes.
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Affiliation(s)
- Mark D M Leiserson
- Department of Computer Science, Brown University, 115 Waterman Street, Providence, 02912, RI, USA.
- Center for Computational Molecular Biology, Brown University, Providence, Box 1910, 02912, RI, USA.
| | - Hsin-Ta Wu
- Department of Computer Science, Brown University, 115 Waterman Street, Providence, 02912, RI, USA.
- Center for Computational Molecular Biology, Brown University, Providence, Box 1910, 02912, RI, USA.
| | - Fabio Vandin
- Department of Computer Science, Brown University, 115 Waterman Street, Providence, 02912, RI, USA.
- Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, Odense M, Denmark.
| | - Benjamin J Raphael
- Department of Computer Science, Brown University, 115 Waterman Street, Providence, 02912, RI, USA.
- Center for Computational Molecular Biology, Brown University, Providence, Box 1910, 02912, RI, USA.
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10
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Doloff JC, Waxman DJ. Transcriptional profiling provides insights into metronomic cyclophosphamide-activated, innate immune-dependent regression of brain tumor xenografts. BMC Cancer 2015; 15:375. [PMID: 25952672 PMCID: PMC4523019 DOI: 10.1186/s12885-015-1358-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/23/2015] [Indexed: 02/07/2023] Open
Abstract
Background Cyclophosphamide treatment on a six-day repeating metronomic schedule induces a dramatic, innate immune cell-dependent regression of implanted gliomas. However, little is known about the underlying mechanisms whereby metronomic cyclophosphamide induces innate immune cell mobilization and recruitment, or about the role of DNA damage and cell stress response pathways in eliciting the immune responses linked to tumor regression. Methods Untreated and metronomic cyclophosphamide-treated human U251 glioblastoma xenografts were analyzed on human microarrays at two treatment time points to identify responsive tumor cell-specific factors and their upstream regulators. Mouse microarray analysis across two glioma models (human U251, rat 9L) was used to identify host factors and gene networks that contribute to the observed immune and tumor regression responses. Results Metronomic cyclophosphamide increased expression of tumor cell-derived DNA damage, cell stress, and cell death genes, which may facilitate innate immune activation. Increased expression of many host (mouse) immune networks was also seen in both tumor models, including complement components, toll-like receptors, interferons, and cytolysis pathways. Key upstream regulators activated by metronomic cyclophosphamide include members of the interferon, toll-like receptor, inflammatory response, and PPAR signaling pathways, whose activation may contribute to anti-tumor immunity. Many upstream regulators inhibited by metronomic cyclophosphamide, including hypoxia-inducible factors and MAP kinases, have glioma-promoting activity; their inhibition may contribute to the therapeutic effectiveness of the six-day repeating metronomic cyclophosphamide schedule. Conclusions Large numbers of responsive cytokines, chemokines and immune regulatory genes linked to innate immune cell recruitment and tumor regression were identified, as were several immunosuppressive factors that may contribute to the observed escape of some tumors from metronomic CPA-induced, immune-based regression. These factors may include useful biomarkers that facilitate discovery of clinically effective immunogenic metronomic drugs and treatment schedules, and the selection of patients most likely to be responsive to immunogenic drug scheduling. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1358-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joshua C Doloff
- Department of Biology, Division of Cell and Molecular Biology, Boston University, Boston, USA.
| | - David J Waxman
- Department of Biology, Division of Cell and Molecular Biology, Boston University, Boston, USA.
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Li Y, Wang Y, Yu L, Sun C, Cheng D, Yu S, Wang Q, Yan Y, Kang C, Jin S, An T, Shi C, Xu J, Wei C, Liu J, Sun J, Wen Y, Zhao S, Kong Y. miR-146b-5p inhibits glioma migration and invasion by targeting MMP16. Cancer Lett 2013; 339:260-9. [PMID: 23796692 DOI: 10.1016/j.canlet.2013.06.018] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 04/10/2013] [Accepted: 06/17/2013] [Indexed: 01/05/2023]
Abstract
miR-146b-5p is frequently down-regulated in solid tumours, including prostate cancer, pancreatic cancer, and glioblastoma. However, the tumour-suppressive effects of miR-146b-5p in malignant gliomas have not been investigated thoroughly. Here, we found that decreased miR-146b-5p expression was strongly correlated with chromosome 10q loss in gliomas, especially glioblastomas. The overexpression of miR-146b-5p in glioblastoma cell lines led to MMP16 mRNA silencing, MMP2 inactivation, and the inhibition of tumour cell migration and invasion. Our results suggest that the restoration of miR-146b-5p expression may be a feasible approach for inhibiting the migration and invasion of malignant gliomas.
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Affiliation(s)
- Yanyan Li
- Dept. of Neuropathology, Tianjin Neurologic Institute, Tianjin Medical University General Hospital, Tianjin 300052, China; Tianjin Key Laboratory of Injuries, Variations and Regeneration of the Nervous System, Tianjin 300052, China; Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin 300052, China
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12
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Abstract
Glioblastomas with a proneural expression signature are characterized by frequent IDH1 mutations (i.e. genetic hallmarks of secondary glioblastomas) and PDGFRA (platelet-derived growth factor receptor-α) amplification. Mutations in IDH1/2 are frequent and early genetic events in diffuse astrocytomas (World Health Organization grade II), precursor to secondary glioblastomas, but little is known about the role and timing of PDGFRA amplification in these tumors. We assessed PDGFRA gain in 342 low-grade diffuse gliomas by quantitative polymerase chain reaction. Gain in PDGFRA was detected in 27 (16.3%) of 166 diffuse astrocytomas, significantly more frequent than in oligodendrogliomas (3 [2.6%] of 115, p < 0.0001). Analyses using previously published data from our laboratory showed an inverse correlation between PDGFRA gain and IDH1/2 mutations (p = 0.018) or 1p/19q loss (p < 0.0001). The vast majority of diffuse astrocytomas showed IDH1/2 mutations and/or PDGFRA gain (154 [93%] of 166). Mean survival of diffuse astrocytoma patients with PDGFRA gain was 8.8 ± 1.6 years, similar to that with IDH1/2 mutations (7.8 ± 0.5 years) or TP53 mutations (7.6 ± 0.6 years) but significantly longer than those with MET gain (4.4 ± 0.7 years). Dual-color fluorescence in situ hybridization in 6 diffuse astrocytomas with PDGFRA/MET co-gain identified by quantitative polymerase chain reaction revealed that PDGFRA and MET were typically amplified in different tumor cell populations. Tumor cells with coamplification were also focally observed, suggesting intratumoral heterogeneity, even in diffuse astrocytomas.
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Codispoti KET, Mosier S, Ramsey R, Lin MT, Rodriguez FJ. Genetic and pathologic evolution of early secondary gliosarcoma. Brain Tumor Pathol 2013; 31:40-6. [PMID: 23324827 DOI: 10.1007/s10014-012-0132-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 12/23/2012] [Indexed: 12/18/2022]
Abstract
Gliosarcoma is a subset of glioblastoma with glial and mesenchymal components. True secondary gliosarcomas (i.e. progressing from lower-grade precursors) in the absence of radiation therapy are very rare. We report the unique case of a 61-year-old male who developed a fibrillary astrocytoma (WHO grade II). In the absence of adjuvant therapy the tumor recurred 3 years later as a gliosarcoma comprising an infiltrating glial component and a curious, early high-grade sarcomatous component surrounding intratumoral vessels. DNA was extracted from formalin fixed paraffin-embedded tissues from the precursor low-grade glioma and from the glioma and sarcomatous components at progression. Samples were hybridized separately to a 300 k Illumina SNP array. IDH1(R132H) mutant protein immunohistochemistry was positive in all tissue components. Alterations identified in all samples included dup(1)(q21q41), del(1)(q41qter), del(2)(q31.1), del(2)(q36.3qter), del(4)(q35.1qter), dup(7)(q22.2q36.3), del(7)(q36.3qter), del(9)(p21.3pter), dup(10)(p13pter), del(10)(q26.13q26.3), dup(17) (q12qter), and copy neutral LOH(20)(p11.23p11.21). The recurrent tumor had additional alterations, including del(3)(p21.31q13.31), del(18)(q21.2qter), and a homozygous del(9)(p21.3)(CDKN2A locus) and the sarcoma component had, in addition, del(4)(p14pter), del(6)(q12qter), del(11)(q24.3qter), and del(16)(p11.2pter). In conclusion, unique copy number alterations were identified during tumor progression from a low-grade glioma to gliosarcoma. A subset of alterations developed specifically in the sarcomatous component.
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Comparative analysis of methods for identifying recurrent copy number alterations in cancer. PLoS One 2012; 7:e52516. [PMID: 23285074 PMCID: PMC3527554 DOI: 10.1371/journal.pone.0052516] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 11/14/2012] [Indexed: 11/19/2022] Open
Abstract
Recurrent copy number alterations (CNAs) play an important role in cancer genesis. While a number of computational methods have been proposed for identifying such CNAs, their relative merits remain largely unknown in practice since very few efforts have been focused on comparative analysis of the methods. To facilitate studies of recurrent CNA identification in cancer genome, it is imperative to conduct a comprehensive comparison of performance and limitations among existing methods. In this paper, six representative methods proposed in the latest six years are compared. These include one-stage and two-stage approaches, working with raw intensity ratio data and discretized data respectively. They are based on various techniques such as kernel regression, correlation matrix diagonal segmentation, semi-parametric permutation and cyclic permutation schemes. We explore multiple criteria including type I error rate, detection power, Receiver Operating Characteristics (ROC) curve and the area under curve (AUC), and computational complexity, to evaluate performance of the methods under multiple simulation scenarios. We also characterize their abilities on applications to two real datasets obtained from cancers with lung adenocarcinoma and glioblastoma. This comparison study reveals general characteristics of the existing methods for identifying recurrent CNAs, and further provides new insights into their strengths and weaknesses. It is believed helpful to accelerate the development of novel and improved methods.
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Abstract
Glioblastoma is the most frequent and malignant brain tumor. The vast majority of glioblastomas (~90%) develop rapidly de novo in elderly patients, without clinical or histologic evidence of a less malignant precursor lesion (primary glioblastomas). Secondary glioblastomas progress from low-grade diffuse astrocytoma or anaplastic astrocytoma. They manifest in younger patients, have a lesser degree of necrosis, are preferentially located in the frontal lobe, and carry a significantly better prognosis. Histologically, primary and secondary glioblastomas are largely indistinguishable, but they differ in their genetic and epigenetic profiles. Decisive genetic signposts of secondary glioblastoma are IDH1 mutations, which are absent in primary glioblastomas and which are associated with a hypermethylation phenotype. IDH1 mutations are the earliest detectable genetic alteration in precursor low-grade diffuse astrocytomas and in oligodendrogliomas, indicating that these tumors are derived from neural precursor cells that differ from those of primary glioblastomas. In this review, we summarize epidemiologic, clinical, histopathologic, genetic, and expression features of primary and secondary glioblastomas and the biologic consequences of IDH1 mutations. We conclude that this genetic alteration is a definitive diagnostic molecular marker of secondary glioblastomas and more reliable and objective than clinical criteria. Despite a similar histologic appearance, primary and secondary glioblastomas are distinct tumor entities that originate from different precursor cells and may require different therapeutic approaches.
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Affiliation(s)
- Hiroko Ohgaki
- Molecular Pathology Section, International Agency for Research on Cancer, Lyon, France.
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