Validation and Selection of New Reference Genes for RT-qPCR Analysis in Pediatric Glioma of Different Grades
Gliomas are heterogeneous, solid, and intracranial tumors that originate from glial cells. Malignant cells from the tumor undergo metabolic alterations to obtain the energy required for proliferation and the invasion of the cerebral parenchyma. The alterations in the expression of the genes related...
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| Veröffentlicht in: | Genes 2021-08, Vol.12 (9), p.1335 |
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| creator | Hernández-Ochoa, Beatriz Fernández-Rosario, Fabiola Castillo-Rodríguez, Rosa Angelica Marhx-Bracho, Alfonso Cárdenas-Rodríguez, Noemí Martínez-Rosas, Víctor Morales-Luna, Laura González-Valdez, Abigail Calderón-Jaimes, Ernesto Pérez de la Cruz, Verónica Rivera-Gutiérrez, Sandra Meza-Toledo, Sergio Wong-Baeza, Carlos Baeza-Ramírez, Isabel Gómez-Manzo, Saúl |
| description | Gliomas are heterogeneous, solid, and intracranial tumors that originate from glial cells. Malignant cells from the tumor undergo metabolic alterations to obtain the energy required for proliferation and the invasion of the cerebral parenchyma. The alterations in the expression of the genes related to the metabolic pathways can be detected in biopsies of gliomas of different CNS WHO grades. In this study, we evaluated the expression of 16 candidate reference genes in the HMC3 microglia cell line. Then, statistical algorithms such as BestKeeper, the comparative ΔC
method, geNorm, NormFinder, and RefFinder were applied to obtain the genes most suitable to be considered as references for measuring the levels of expression in glioma samples. The results show that
and
are two novel genes suitable for genic expression studies on gliomas. Finally, we analyzed the expression of genes involved in metabolic pathways in clinical samples of brain gliomas of different CNS WHO grades. RT-qPCR analysis showed that in CNS WHO grade 3 and 4 gliomas, the expression levels of
,
,
,
,
,
,
,
, and
were higher than those of CNS WHO grade 1 and 2 glioma biopsies. Hence, our results suggest that reference genes from metabolic pathways have different expression profiles depending on the stratification of gliomas and constitute a potential model for studying the development of this type of tumor and the search for molecular targets to treat gliomas. |
| doi_str_mv | 10.3390/genes12091335 |
| format | Article |
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method, geNorm, NormFinder, and RefFinder were applied to obtain the genes most suitable to be considered as references for measuring the levels of expression in glioma samples. The results show that
and
are two novel genes suitable for genic expression studies on gliomas. Finally, we analyzed the expression of genes involved in metabolic pathways in clinical samples of brain gliomas of different CNS WHO grades. RT-qPCR analysis showed that in CNS WHO grade 3 and 4 gliomas, the expression levels of
,
,
,
,
,
,
,
, and
were higher than those of CNS WHO grade 1 and 2 glioma biopsies. Hence, our results suggest that reference genes from metabolic pathways have different expression profiles depending on the stratification of gliomas and constitute a potential model for studying the development of this type of tumor and the search for molecular targets to treat gliomas.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes12091335</identifier><identifier>PMID: 34573317</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Adolescent ; Algorithms ; Biopsy ; Brain cancer ; Brain Neoplasms - genetics ; Brain Neoplasms - pathology ; Brain tumors ; Cell cycle ; Cell Line, Tumor ; Child ; Child, Preschool ; Dehydrogenases ; Fatty acids ; Female ; Gene expression ; Gene Expression Profiling - methods ; Gene Expression Profiling - standards ; Gene Expression Regulation, Neoplastic ; Glial cells ; Glioma ; Glioma - genetics ; Glioma - pathology ; Glucosephosphate dehydrogenase ; Glyceraldehyde-3-phosphate dehydrogenase ; Humans ; Kinases ; Male ; Medical prognosis ; Metabolic pathways ; Metabolism ; Microglia ; Neoplasm Grading ; Parenchyma ; Pediatrics ; Proteins ; Real-Time Polymerase Chain Reaction - standards ; Reference Standards ; Tumors</subject><ispartof>Genes, 2021-08, Vol.12 (9), p.1335</ispartof><rights>2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 by the authors. 2021</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c415t-79ef162b6a2a56e2f78dc395e08b5669d6172f3a089784a0b030908da91e893a3</citedby><cites>FETCH-LOGICAL-c415t-79ef162b6a2a56e2f78dc395e08b5669d6172f3a089784a0b030908da91e893a3</cites><orcidid>0000-0002-6262-8106 ; 0000-0001-6137-6499 ; 0000-0003-2095-9182 ; 0000-0002-6580-3440 ; 0000-0003-4117-6689 ; 0000-0003-3939-6930 ; 0000-0002-1451-8754 ; 0000-0003-1556-9956</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8468898/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8468898/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34573317$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hernández-Ochoa, Beatriz</creatorcontrib><creatorcontrib>Fernández-Rosario, Fabiola</creatorcontrib><creatorcontrib>Castillo-Rodríguez, Rosa Angelica</creatorcontrib><creatorcontrib>Marhx-Bracho, Alfonso</creatorcontrib><creatorcontrib>Cárdenas-Rodríguez, Noemí</creatorcontrib><creatorcontrib>Martínez-Rosas, Víctor</creatorcontrib><creatorcontrib>Morales-Luna, Laura</creatorcontrib><creatorcontrib>González-Valdez, Abigail</creatorcontrib><creatorcontrib>Calderón-Jaimes, Ernesto</creatorcontrib><creatorcontrib>Pérez de la Cruz, Verónica</creatorcontrib><creatorcontrib>Rivera-Gutiérrez, Sandra</creatorcontrib><creatorcontrib>Meza-Toledo, Sergio</creatorcontrib><creatorcontrib>Wong-Baeza, Carlos</creatorcontrib><creatorcontrib>Baeza-Ramírez, Isabel</creatorcontrib><creatorcontrib>Gómez-Manzo, Saúl</creatorcontrib><title>Validation and Selection of New Reference Genes for RT-qPCR Analysis in Pediatric Glioma of Different Grades</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>Gliomas are heterogeneous, solid, and intracranial tumors that originate from glial cells. Malignant cells from the tumor undergo metabolic alterations to obtain the energy required for proliferation and the invasion of the cerebral parenchyma. The alterations in the expression of the genes related to the metabolic pathways can be detected in biopsies of gliomas of different CNS WHO grades. In this study, we evaluated the expression of 16 candidate reference genes in the HMC3 microglia cell line. Then, statistical algorithms such as BestKeeper, the comparative ΔC
method, geNorm, NormFinder, and RefFinder were applied to obtain the genes most suitable to be considered as references for measuring the levels of expression in glioma samples. The results show that
and
are two novel genes suitable for genic expression studies on gliomas. Finally, we analyzed the expression of genes involved in metabolic pathways in clinical samples of brain gliomas of different CNS WHO grades. RT-qPCR analysis showed that in CNS WHO grade 3 and 4 gliomas, the expression levels of
,
,
,
,
,
,
,
, and
were higher than those of CNS WHO grade 1 and 2 glioma biopsies. Hence, our results suggest that reference genes from metabolic pathways have different expression profiles depending on the stratification of gliomas and constitute a potential model for studying the development of this type of tumor and the search for molecular targets to treat gliomas.</description><subject>Adolescent</subject><subject>Algorithms</subject><subject>Biopsy</subject><subject>Brain cancer</subject><subject>Brain Neoplasms - genetics</subject><subject>Brain Neoplasms - pathology</subject><subject>Brain tumors</subject><subject>Cell cycle</subject><subject>Cell Line, Tumor</subject><subject>Child</subject><subject>Child, Preschool</subject><subject>Dehydrogenases</subject><subject>Fatty acids</subject><subject>Female</subject><subject>Gene expression</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene Expression Profiling - standards</subject><subject>Gene Expression Regulation, Neoplastic</subject><subject>Glial cells</subject><subject>Glioma</subject><subject>Glioma - genetics</subject><subject>Glioma - pathology</subject><subject>Glucosephosphate dehydrogenase</subject><subject>Glyceraldehyde-3-phosphate dehydrogenase</subject><subject>Humans</subject><subject>Kinases</subject><subject>Male</subject><subject>Medical prognosis</subject><subject>Metabolic pathways</subject><subject>Metabolism</subject><subject>Microglia</subject><subject>Neoplasm Grading</subject><subject>Parenchyma</subject><subject>Pediatrics</subject><subject>Proteins</subject><subject>Real-Time Polymerase Chain Reaction - standards</subject><subject>Reference Standards</subject><subject>Tumors</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNpdkU1vFDEMhiMEolXpkSuKxIXLQL4_LkjVAgtSBdVSuEbeGaekyk7aZBbUf8_stlQtvsRWHr928hLykrO3Unr27gJHbFwwz6XUT8ihYFZ2Sgn99EF-QI5bu2RzKCYY08_JgVTaSsntIck_IacBplRGCuNAv2PGfl-VSL_iH7rCiBXHHulyN4zGUunqvLs-W6zoyQj5pqVG00jPcEgw1dTTZU5lA7v-Dynumye6rDBge0GeRcgNj-_OI_Lj08fzxefu9Nvyy-LktOsV11NnPUZuxNqAAG1QROuGXnqNzK21MX4w3IoogTlvnQK2ZpJ55gbwHJ2XII_I-1vdq-16g0M_b1Ahh6uaNlBvQoEUHt-M6Ve4KL-DU8Y572aBN3cCtVxvsU1hk1qPOcOIZduC0NYqI7XiM_r6P_SybOv8MXvKKM6NszPV3VJ9La1VjPfLcBZ2VoZHVs78q4cvuKf_GSf_AnNemVo</recordid><startdate>20210827</startdate><enddate>20210827</enddate><creator>Hernández-Ochoa, Beatriz</creator><creator>Fernández-Rosario, Fabiola</creator><creator>Castillo-Rodríguez, Rosa Angelica</creator><creator>Marhx-Bracho, Alfonso</creator><creator>Cárdenas-Rodríguez, Noemí</creator><creator>Martínez-Rosas, Víctor</creator><creator>Morales-Luna, Laura</creator><creator>González-Valdez, Abigail</creator><creator>Calderón-Jaimes, Ernesto</creator><creator>Pérez de la Cruz, Verónica</creator><creator>Rivera-Gutiérrez, Sandra</creator><creator>Meza-Toledo, Sergio</creator><creator>Wong-Baeza, Carlos</creator><creator>Baeza-Ramírez, Isabel</creator><creator>Gómez-Manzo, Saúl</creator><general>MDPI AG</general><general>MDPI</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>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-6262-8106</orcidid><orcidid>https://orcid.org/0000-0001-6137-6499</orcidid><orcidid>https://orcid.org/0000-0003-2095-9182</orcidid><orcidid>https://orcid.org/0000-0002-6580-3440</orcidid><orcidid>https://orcid.org/0000-0003-4117-6689</orcidid><orcidid>https://orcid.org/0000-0003-3939-6930</orcidid><orcidid>https://orcid.org/0000-0002-1451-8754</orcidid><orcidid>https://orcid.org/0000-0003-1556-9956</orcidid></search><sort><creationdate>20210827</creationdate><title>Validation and Selection of New Reference Genes for RT-qPCR Analysis in Pediatric Glioma of Different Grades</title><author>Hernández-Ochoa, Beatriz ; Fernández-Rosario, Fabiola ; Castillo-Rodríguez, Rosa Angelica ; Marhx-Bracho, Alfonso ; Cárdenas-Rodríguez, Noemí ; Martínez-Rosas, Víctor ; Morales-Luna, Laura ; González-Valdez, Abigail ; Calderón-Jaimes, Ernesto ; Pérez de la Cruz, Verónica ; Rivera-Gutiérrez, Sandra ; Meza-Toledo, Sergio ; Wong-Baeza, Carlos ; Baeza-Ramírez, Isabel ; Gómez-Manzo, Saúl</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c415t-79ef162b6a2a56e2f78dc395e08b5669d6172f3a089784a0b030908da91e893a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Adolescent</topic><topic>Algorithms</topic><topic>Biopsy</topic><topic>Brain cancer</topic><topic>Brain Neoplasms - genetics</topic><topic>Brain Neoplasms - pathology</topic><topic>Brain tumors</topic><topic>Cell cycle</topic><topic>Cell Line, Tumor</topic><topic>Child</topic><topic>Child, Preschool</topic><topic>Dehydrogenases</topic><topic>Fatty acids</topic><topic>Female</topic><topic>Gene expression</topic><topic>Gene Expression Profiling - methods</topic><topic>Gene Expression Profiling - standards</topic><topic>Gene Expression Regulation, Neoplastic</topic><topic>Glial cells</topic><topic>Glioma</topic><topic>Glioma - genetics</topic><topic>Glioma - pathology</topic><topic>Glucosephosphate dehydrogenase</topic><topic>Glyceraldehyde-3-phosphate dehydrogenase</topic><topic>Humans</topic><topic>Kinases</topic><topic>Male</topic><topic>Medical prognosis</topic><topic>Metabolic pathways</topic><topic>Metabolism</topic><topic>Microglia</topic><topic>Neoplasm Grading</topic><topic>Parenchyma</topic><topic>Pediatrics</topic><topic>Proteins</topic><topic>Real-Time Polymerase Chain Reaction - standards</topic><topic>Reference Standards</topic><topic>Tumors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hernández-Ochoa, Beatriz</creatorcontrib><creatorcontrib>Fernández-Rosario, Fabiola</creatorcontrib><creatorcontrib>Castillo-Rodríguez, Rosa Angelica</creatorcontrib><creatorcontrib>Marhx-Bracho, Alfonso</creatorcontrib><creatorcontrib>Cárdenas-Rodríguez, Noemí</creatorcontrib><creatorcontrib>Martínez-Rosas, Víctor</creatorcontrib><creatorcontrib>Morales-Luna, Laura</creatorcontrib><creatorcontrib>González-Valdez, Abigail</creatorcontrib><creatorcontrib>Calderón-Jaimes, Ernesto</creatorcontrib><creatorcontrib>Pérez de la Cruz, Verónica</creatorcontrib><creatorcontrib>Rivera-Gutiérrez, Sandra</creatorcontrib><creatorcontrib>Meza-Toledo, Sergio</creatorcontrib><creatorcontrib>Wong-Baeza, Carlos</creatorcontrib><creatorcontrib>Baeza-Ramírez, Isabel</creatorcontrib><creatorcontrib>Gómez-Manzo, Saúl</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hernández-Ochoa, Beatriz</au><au>Fernández-Rosario, Fabiola</au><au>Castillo-Rodríguez, Rosa Angelica</au><au>Marhx-Bracho, Alfonso</au><au>Cárdenas-Rodríguez, Noemí</au><au>Martínez-Rosas, Víctor</au><au>Morales-Luna, Laura</au><au>González-Valdez, Abigail</au><au>Calderón-Jaimes, Ernesto</au><au>Pérez de la Cruz, Verónica</au><au>Rivera-Gutiérrez, Sandra</au><au>Meza-Toledo, Sergio</au><au>Wong-Baeza, Carlos</au><au>Baeza-Ramírez, Isabel</au><au>Gómez-Manzo, Saúl</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Validation and Selection of New Reference Genes for RT-qPCR Analysis in Pediatric Glioma of Different Grades</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2021-08-27</date><risdate>2021</risdate><volume>12</volume><issue>9</issue><spage>1335</spage><pages>1335-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>Gliomas are heterogeneous, solid, and intracranial tumors that originate from glial cells. Malignant cells from the tumor undergo metabolic alterations to obtain the energy required for proliferation and the invasion of the cerebral parenchyma. The alterations in the expression of the genes related to the metabolic pathways can be detected in biopsies of gliomas of different CNS WHO grades. In this study, we evaluated the expression of 16 candidate reference genes in the HMC3 microglia cell line. Then, statistical algorithms such as BestKeeper, the comparative ΔC
method, geNorm, NormFinder, and RefFinder were applied to obtain the genes most suitable to be considered as references for measuring the levels of expression in glioma samples. The results show that
and
are two novel genes suitable for genic expression studies on gliomas. Finally, we analyzed the expression of genes involved in metabolic pathways in clinical samples of brain gliomas of different CNS WHO grades. RT-qPCR analysis showed that in CNS WHO grade 3 and 4 gliomas, the expression levels of
,
,
,
,
,
,
,
, and
were higher than those of CNS WHO grade 1 and 2 glioma biopsies. Hence, our results suggest that reference genes from metabolic pathways have different expression profiles depending on the stratification of gliomas and constitute a potential model for studying the development of this type of tumor and the search for molecular targets to treat gliomas.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>34573317</pmid><doi>10.3390/genes12091335</doi><orcidid>https://orcid.org/0000-0002-6262-8106</orcidid><orcidid>https://orcid.org/0000-0001-6137-6499</orcidid><orcidid>https://orcid.org/0000-0003-2095-9182</orcidid><orcidid>https://orcid.org/0000-0002-6580-3440</orcidid><orcidid>https://orcid.org/0000-0003-4117-6689</orcidid><orcidid>https://orcid.org/0000-0003-3939-6930</orcidid><orcidid>https://orcid.org/0000-0002-1451-8754</orcidid><orcidid>https://orcid.org/0000-0003-1556-9956</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
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| ispartof | Genes, 2021-08, Vol.12 (9), p.1335 |
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| source | MDPI - Multidisciplinary Digital Publishing Institute; MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access |
| subjects | Adolescent Algorithms Biopsy Brain cancer Brain Neoplasms - genetics Brain Neoplasms - pathology Brain tumors Cell cycle Cell Line, Tumor Child Child, Preschool Dehydrogenases Fatty acids Female Gene expression Gene Expression Profiling - methods Gene Expression Profiling - standards Gene Expression Regulation, Neoplastic Glial cells Glioma Glioma - genetics Glioma - pathology Glucosephosphate dehydrogenase Glyceraldehyde-3-phosphate dehydrogenase Humans Kinases Male Medical prognosis Metabolic pathways Metabolism Microglia Neoplasm Grading Parenchyma Pediatrics Proteins Real-Time Polymerase Chain Reaction - standards Reference Standards Tumors |
| title | Validation and Selection of New Reference Genes for RT-qPCR Analysis in Pediatric Glioma of Different Grades |
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