Real-time PCR assay based on the differential expression of microRNAs and protein-coding genes for molecular classification of formalin-fixed paraffin embedded medulloblastomas
Medulloblastoma has recently been found to consist of 4 molecularly and clinically distinct subgroups: WNT, Sonce hedgehog (SHH), Group 3, and Group 4. Deregulated microRNA expression is known to contribute to pathogenesis and has been shown to have diagnostic and prognostic potential in the classif...
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Veröffentlicht in: | Neuro-oncology (Charlottesville, Va.) Va.), 2013-12, Vol.15 (12), p.1644-1651 |
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creator | Kunder, Ratika Jalali, Rakesh Sridhar, Epari Moiyadi, Aliasgar Goel, Naina Goel, Atul Gupta, Tejpal Krishnatry, Rahul Kannan, Sadhana Kurkure, Purna Deopujari, Chandrashekhar Shetty, Prakash Biyani, Naresh Korshunov, Andrey Pfister, Stefan M Northcott, Paul A Shirsat, Neelam Vishwanath |
description | Medulloblastoma has recently been found to consist of 4 molecularly and clinically distinct subgroups: WNT, Sonce hedgehog (SHH), Group 3, and Group 4. Deregulated microRNA expression is known to contribute to pathogenesis and has been shown to have diagnostic and prognostic potential in the classification of various cancers.
Molecular subgrouping and microRNA expression analysis of 44 frozen and 59 formalin-fixed paraffin embedded medulloblastomas from an Indian cohort were carried out by real-time RT-PCR assay.
The differential expression of 9 microRNAs in the 4 molecular subgroups was validated in a set of 101 medulloblastomas. The tumors in the WNT subgroup showed significant (P < .0001) overexpression of miR-193a-3p, miR-224, miR-148a, miR-23b, and miR-365. Reliable classification of medulloblastomas into the 4 molecular subgroups was obtained using a set of 12 protein-coding genes and 9 microRNAs as markers in a real-time RT-PCR assay with an accuracy of 97% as judged by the Prediction Analysis of Microarrays. Age at diagnosis, histology, gender-related incidence, and the relative survival rates of the 4 molecular subgroups in the present Indian cohort were found to be similar to those reported for medulloblastomas from the American and European subcontinent. Non-WNT, non-SHH medulloblastomas underexpressing miR-592 or overexpressing miR-182 were found to have significantly inferior survival rates, indicating utility of these miRNAs as markers for risk stratification.
The microRNA based real-time PCR assay is rapid, simple, inexpensive, and useful for molecular classification and risk stratification of medulloblastomas, in particular formalin-fixed paraffin embedded tissues, wherein the expression profile of protein-coding genes is often less reliable due to RNA fragmentation. |
doi_str_mv | 10.1093/neuonc/not123 |
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Molecular subgrouping and microRNA expression analysis of 44 frozen and 59 formalin-fixed paraffin embedded medulloblastomas from an Indian cohort were carried out by real-time RT-PCR assay.
The differential expression of 9 microRNAs in the 4 molecular subgroups was validated in a set of 101 medulloblastomas. The tumors in the WNT subgroup showed significant (P < .0001) overexpression of miR-193a-3p, miR-224, miR-148a, miR-23b, and miR-365. Reliable classification of medulloblastomas into the 4 molecular subgroups was obtained using a set of 12 protein-coding genes and 9 microRNAs as markers in a real-time RT-PCR assay with an accuracy of 97% as judged by the Prediction Analysis of Microarrays. Age at diagnosis, histology, gender-related incidence, and the relative survival rates of the 4 molecular subgroups in the present Indian cohort were found to be similar to those reported for medulloblastomas from the American and European subcontinent. Non-WNT, non-SHH medulloblastomas underexpressing miR-592 or overexpressing miR-182 were found to have significantly inferior survival rates, indicating utility of these miRNAs as markers for risk stratification.
The microRNA based real-time PCR assay is rapid, simple, inexpensive, and useful for molecular classification and risk stratification of medulloblastomas, in particular formalin-fixed paraffin embedded tissues, wherein the expression profile of protein-coding genes is often less reliable due to RNA fragmentation.</description><identifier>ISSN: 1522-8517</identifier><identifier>EISSN: 1523-5866</identifier><identifier>DOI: 10.1093/neuonc/not123</identifier><identifier>PMID: 24203893</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Adolescent ; Adult ; Basic and Translational Investigations ; Case-Control Studies ; Cerebellar Neoplasms - classification ; Cerebellar Neoplasms - genetics ; Cerebellar Neoplasms - mortality ; Cerebellar Neoplasms - pathology ; Cerebellum - metabolism ; Cerebellum - pathology ; Child ; Child, Preschool ; Female ; Follow-Up Studies ; Gene Expression Profiling ; Hedgehog Proteins - genetics ; Hedgehog Proteins - metabolism ; Humans ; Infant ; Male ; Medulloblastoma - classification ; Medulloblastoma - genetics ; Medulloblastoma - mortality ; Medulloblastoma - pathology ; MicroRNAs - genetics ; Middle Aged ; Neoplasm Staging ; Oligonucleotide Array Sequence Analysis ; Paraffin Embedding ; Prognosis ; Real-Time Polymerase Chain Reaction - methods ; Reverse Transcriptase Polymerase Chain Reaction ; RNA, Messenger - genetics ; Survival Rate ; Wnt Proteins - genetics ; Wnt Proteins - metabolism ; Young Adult</subject><ispartof>Neuro-oncology (Charlottesville, Va.), 2013-12, Vol.15 (12), p.1644-1651</ispartof><rights>The Author(s) 2013. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. 2013</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c350t-d21bfe76f9b17c8b8b1be29ed233887bdfc152740c4b7f598bdb58b99b205e2d3</citedby><cites>FETCH-LOGICAL-c350t-d21bfe76f9b17c8b8b1be29ed233887bdfc152740c4b7f598bdb58b99b205e2d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3829591/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3829591/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24203893$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kunder, Ratika</creatorcontrib><creatorcontrib>Jalali, Rakesh</creatorcontrib><creatorcontrib>Sridhar, Epari</creatorcontrib><creatorcontrib>Moiyadi, Aliasgar</creatorcontrib><creatorcontrib>Goel, Naina</creatorcontrib><creatorcontrib>Goel, Atul</creatorcontrib><creatorcontrib>Gupta, Tejpal</creatorcontrib><creatorcontrib>Krishnatry, Rahul</creatorcontrib><creatorcontrib>Kannan, Sadhana</creatorcontrib><creatorcontrib>Kurkure, Purna</creatorcontrib><creatorcontrib>Deopujari, Chandrashekhar</creatorcontrib><creatorcontrib>Shetty, Prakash</creatorcontrib><creatorcontrib>Biyani, Naresh</creatorcontrib><creatorcontrib>Korshunov, Andrey</creatorcontrib><creatorcontrib>Pfister, Stefan M</creatorcontrib><creatorcontrib>Northcott, Paul A</creatorcontrib><creatorcontrib>Shirsat, Neelam Vishwanath</creatorcontrib><title>Real-time PCR assay based on the differential expression of microRNAs and protein-coding genes for molecular classification of formalin-fixed paraffin embedded medulloblastomas</title><title>Neuro-oncology (Charlottesville, Va.)</title><addtitle>Neuro Oncol</addtitle><description>Medulloblastoma has recently been found to consist of 4 molecularly and clinically distinct subgroups: WNT, Sonce hedgehog (SHH), Group 3, and Group 4. Deregulated microRNA expression is known to contribute to pathogenesis and has been shown to have diagnostic and prognostic potential in the classification of various cancers.
Molecular subgrouping and microRNA expression analysis of 44 frozen and 59 formalin-fixed paraffin embedded medulloblastomas from an Indian cohort were carried out by real-time RT-PCR assay.
The differential expression of 9 microRNAs in the 4 molecular subgroups was validated in a set of 101 medulloblastomas. The tumors in the WNT subgroup showed significant (P < .0001) overexpression of miR-193a-3p, miR-224, miR-148a, miR-23b, and miR-365. Reliable classification of medulloblastomas into the 4 molecular subgroups was obtained using a set of 12 protein-coding genes and 9 microRNAs as markers in a real-time RT-PCR assay with an accuracy of 97% as judged by the Prediction Analysis of Microarrays. Age at diagnosis, histology, gender-related incidence, and the relative survival rates of the 4 molecular subgroups in the present Indian cohort were found to be similar to those reported for medulloblastomas from the American and European subcontinent. Non-WNT, non-SHH medulloblastomas underexpressing miR-592 or overexpressing miR-182 were found to have significantly inferior survival rates, indicating utility of these miRNAs as markers for risk stratification.
The microRNA based real-time PCR assay is rapid, simple, inexpensive, and useful for molecular classification and risk stratification of medulloblastomas, in particular formalin-fixed paraffin embedded tissues, wherein the expression profile of protein-coding genes is often less reliable due to RNA fragmentation.</description><subject>Adolescent</subject><subject>Adult</subject><subject>Basic and Translational Investigations</subject><subject>Case-Control Studies</subject><subject>Cerebellar Neoplasms - classification</subject><subject>Cerebellar Neoplasms - genetics</subject><subject>Cerebellar Neoplasms - mortality</subject><subject>Cerebellar Neoplasms - pathology</subject><subject>Cerebellum - metabolism</subject><subject>Cerebellum - pathology</subject><subject>Child</subject><subject>Child, Preschool</subject><subject>Female</subject><subject>Follow-Up Studies</subject><subject>Gene Expression Profiling</subject><subject>Hedgehog Proteins - genetics</subject><subject>Hedgehog Proteins - metabolism</subject><subject>Humans</subject><subject>Infant</subject><subject>Male</subject><subject>Medulloblastoma - classification</subject><subject>Medulloblastoma - genetics</subject><subject>Medulloblastoma - mortality</subject><subject>Medulloblastoma - pathology</subject><subject>MicroRNAs - genetics</subject><subject>Middle Aged</subject><subject>Neoplasm Staging</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Paraffin Embedding</subject><subject>Prognosis</subject><subject>Real-Time Polymerase Chain Reaction - methods</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><subject>RNA, Messenger - genetics</subject><subject>Survival Rate</subject><subject>Wnt Proteins - genetics</subject><subject>Wnt Proteins - metabolism</subject><subject>Young Adult</subject><issn>1522-8517</issn><issn>1523-5866</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFUstuFDEQHCEQCYEjV-QjlyF-jGfsC1K0ggQpArSCs-VHe2PksRd7Jkr-ik_EsEsEJ05tdVVXt0vVdS8JfkOwZOcJ1pzsecoLoexRd0o4ZT0X4_j495v2gpPppHtW6zeMKeEjedqd0IFiJiQ77X5sQcd-CTOgz5st0rXqe2R0BYdyQssNIBe8hwJpCToiuNsXqDU0LHs0B1vy9uNFRTo5tC95gZB6m11IO7SDBBX5XNCcI9g16oJsbAuCD1YvR4mGzzq2KR_u2s69Ltr7kBDMBpxrnRncGmM2bXLJs67PuydexwovjvWs-_r-3ZfNVX_96fLD5uK6t4zjpXeUGA_T6KUhkxVGGGKASnCUMSEm47xt7kwDtoOZPJfCOMOFkdJQzIE6dta9PejuV9NusM2AoqPalzDrcq-yDupfJIUbtcu3igkquSRN4PVRoOTvK9RFzaFaiFEnyGtVhHMyEjFg-n_qwCXnfBpko_YHanO-1gL-4SKC1a9AqEMg1CEQjf_q7288sP8kgP0EaN65xQ</recordid><startdate>201312</startdate><enddate>201312</enddate><creator>Kunder, Ratika</creator><creator>Jalali, Rakesh</creator><creator>Sridhar, Epari</creator><creator>Moiyadi, Aliasgar</creator><creator>Goel, Naina</creator><creator>Goel, Atul</creator><creator>Gupta, Tejpal</creator><creator>Krishnatry, Rahul</creator><creator>Kannan, Sadhana</creator><creator>Kurkure, Purna</creator><creator>Deopujari, Chandrashekhar</creator><creator>Shetty, Prakash</creator><creator>Biyani, Naresh</creator><creator>Korshunov, Andrey</creator><creator>Pfister, Stefan M</creator><creator>Northcott, Paul A</creator><creator>Shirsat, Neelam Vishwanath</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7TK</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope></search><sort><creationdate>201312</creationdate><title>Real-time PCR assay based on the differential expression of microRNAs and protein-coding genes for molecular classification of formalin-fixed paraffin embedded medulloblastomas</title><author>Kunder, Ratika ; Jalali, Rakesh ; Sridhar, Epari ; Moiyadi, Aliasgar ; Goel, Naina ; Goel, Atul ; Gupta, Tejpal ; Krishnatry, Rahul ; Kannan, Sadhana ; Kurkure, Purna ; Deopujari, Chandrashekhar ; Shetty, Prakash ; Biyani, Naresh ; Korshunov, Andrey ; Pfister, Stefan M ; Northcott, Paul A ; Shirsat, Neelam Vishwanath</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c350t-d21bfe76f9b17c8b8b1be29ed233887bdfc152740c4b7f598bdb58b99b205e2d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Adolescent</topic><topic>Adult</topic><topic>Basic and Translational Investigations</topic><topic>Case-Control Studies</topic><topic>Cerebellar Neoplasms - classification</topic><topic>Cerebellar Neoplasms - genetics</topic><topic>Cerebellar Neoplasms - mortality</topic><topic>Cerebellar Neoplasms - pathology</topic><topic>Cerebellum - metabolism</topic><topic>Cerebellum - pathology</topic><topic>Child</topic><topic>Child, Preschool</topic><topic>Female</topic><topic>Follow-Up Studies</topic><topic>Gene Expression Profiling</topic><topic>Hedgehog Proteins - genetics</topic><topic>Hedgehog Proteins - metabolism</topic><topic>Humans</topic><topic>Infant</topic><topic>Male</topic><topic>Medulloblastoma - classification</topic><topic>Medulloblastoma - genetics</topic><topic>Medulloblastoma - mortality</topic><topic>Medulloblastoma - pathology</topic><topic>MicroRNAs - genetics</topic><topic>Middle Aged</topic><topic>Neoplasm Staging</topic><topic>Oligonucleotide Array Sequence Analysis</topic><topic>Paraffin Embedding</topic><topic>Prognosis</topic><topic>Real-Time Polymerase Chain Reaction - methods</topic><topic>Reverse Transcriptase Polymerase Chain Reaction</topic><topic>RNA, Messenger - genetics</topic><topic>Survival Rate</topic><topic>Wnt Proteins - genetics</topic><topic>Wnt Proteins - metabolism</topic><topic>Young Adult</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kunder, Ratika</creatorcontrib><creatorcontrib>Jalali, Rakesh</creatorcontrib><creatorcontrib>Sridhar, Epari</creatorcontrib><creatorcontrib>Moiyadi, Aliasgar</creatorcontrib><creatorcontrib>Goel, Naina</creatorcontrib><creatorcontrib>Goel, Atul</creatorcontrib><creatorcontrib>Gupta, Tejpal</creatorcontrib><creatorcontrib>Krishnatry, Rahul</creatorcontrib><creatorcontrib>Kannan, Sadhana</creatorcontrib><creatorcontrib>Kurkure, Purna</creatorcontrib><creatorcontrib>Deopujari, Chandrashekhar</creatorcontrib><creatorcontrib>Shetty, Prakash</creatorcontrib><creatorcontrib>Biyani, Naresh</creatorcontrib><creatorcontrib>Korshunov, Andrey</creatorcontrib><creatorcontrib>Pfister, Stefan M</creatorcontrib><creatorcontrib>Northcott, Paul A</creatorcontrib><creatorcontrib>Shirsat, Neelam Vishwanath</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Neurosciences Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Neuro-oncology (Charlottesville, Va.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kunder, Ratika</au><au>Jalali, Rakesh</au><au>Sridhar, Epari</au><au>Moiyadi, Aliasgar</au><au>Goel, Naina</au><au>Goel, Atul</au><au>Gupta, Tejpal</au><au>Krishnatry, Rahul</au><au>Kannan, Sadhana</au><au>Kurkure, Purna</au><au>Deopujari, Chandrashekhar</au><au>Shetty, Prakash</au><au>Biyani, Naresh</au><au>Korshunov, Andrey</au><au>Pfister, Stefan M</au><au>Northcott, Paul A</au><au>Shirsat, Neelam Vishwanath</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Real-time PCR assay based on the differential expression of microRNAs and protein-coding genes for molecular classification of formalin-fixed paraffin embedded medulloblastomas</atitle><jtitle>Neuro-oncology (Charlottesville, Va.)</jtitle><addtitle>Neuro Oncol</addtitle><date>2013-12</date><risdate>2013</risdate><volume>15</volume><issue>12</issue><spage>1644</spage><epage>1651</epage><pages>1644-1651</pages><issn>1522-8517</issn><eissn>1523-5866</eissn><abstract>Medulloblastoma has recently been found to consist of 4 molecularly and clinically distinct subgroups: WNT, Sonce hedgehog (SHH), Group 3, and Group 4. Deregulated microRNA expression is known to contribute to pathogenesis and has been shown to have diagnostic and prognostic potential in the classification of various cancers.
Molecular subgrouping and microRNA expression analysis of 44 frozen and 59 formalin-fixed paraffin embedded medulloblastomas from an Indian cohort were carried out by real-time RT-PCR assay.
The differential expression of 9 microRNAs in the 4 molecular subgroups was validated in a set of 101 medulloblastomas. The tumors in the WNT subgroup showed significant (P < .0001) overexpression of miR-193a-3p, miR-224, miR-148a, miR-23b, and miR-365. Reliable classification of medulloblastomas into the 4 molecular subgroups was obtained using a set of 12 protein-coding genes and 9 microRNAs as markers in a real-time RT-PCR assay with an accuracy of 97% as judged by the Prediction Analysis of Microarrays. Age at diagnosis, histology, gender-related incidence, and the relative survival rates of the 4 molecular subgroups in the present Indian cohort were found to be similar to those reported for medulloblastomas from the American and European subcontinent. Non-WNT, non-SHH medulloblastomas underexpressing miR-592 or overexpressing miR-182 were found to have significantly inferior survival rates, indicating utility of these miRNAs as markers for risk stratification.
The microRNA based real-time PCR assay is rapid, simple, inexpensive, and useful for molecular classification and risk stratification of medulloblastomas, in particular formalin-fixed paraffin embedded tissues, wherein the expression profile of protein-coding genes is often less reliable due to RNA fragmentation.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>24203893</pmid><doi>10.1093/neuonc/not123</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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source | MEDLINE; Oxford University Press Journals All Titles (1996-Current); PubMed Central; EZB Electronic Journals Library |
subjects | Adolescent Adult Basic and Translational Investigations Case-Control Studies Cerebellar Neoplasms - classification Cerebellar Neoplasms - genetics Cerebellar Neoplasms - mortality Cerebellar Neoplasms - pathology Cerebellum - metabolism Cerebellum - pathology Child Child, Preschool Female Follow-Up Studies Gene Expression Profiling Hedgehog Proteins - genetics Hedgehog Proteins - metabolism Humans Infant Male Medulloblastoma - classification Medulloblastoma - genetics Medulloblastoma - mortality Medulloblastoma - pathology MicroRNAs - genetics Middle Aged Neoplasm Staging Oligonucleotide Array Sequence Analysis Paraffin Embedding Prognosis Real-Time Polymerase Chain Reaction - methods Reverse Transcriptase Polymerase Chain Reaction RNA, Messenger - genetics Survival Rate Wnt Proteins - genetics Wnt Proteins - metabolism Young Adult |
title | Real-time PCR assay based on the differential expression of microRNAs and protein-coding genes for molecular classification of formalin-fixed paraffin embedded medulloblastomas |
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