13b14dd8ab72dc17a25245980f063336 pmc_35158906.pdf 558e40e7f3596fe9f57b7a63c3133cfb9242d998 pmc_35158906.pdf 60174edda90227a7d9ed15f5cc7171bf2c573bc25c7ebef3ebbb304e6eba415c pmc_35158906.pdf Title: Identification of Circulating lncRNAs Associated with Gallbladder Cancer Risk by Tissue-Based Preselection, Cis-eQTL Validation, and Analysis of Association with Genotype-Based Expression Subject: Long noncoding RNAs (lncRNAs) play key roles in cell processes and are good candidates for cancer risk prediction. Few studies have investigated the association between individual genotypes and lncRNA expression. Here we integrate three separate datasets with information on lncRNA expression only, both lncRNA expression and genotype, and genotype information only to identify circulating lncRNAs associated with the risk of gallbladder cancer (GBC) using robust linear and logistic regression techniques. In the first dataset, we preselect lncRNAs based on expression changes along the sequence “gallstones dysplasia GBC”. In the second dataset, we validate associations between genetic variants and serum expression levels of the preselected lncRNAs (cis-lncRNA-eQTLs) and build lncRNA expression prediction models. In the third dataset, we predict serum lncRNA expression based on individual genotypes and assess the association between genotype-based expression and GBC risk. AC084082.3 and LINC00662 showed increasing expression levels (p-value = 0.009), while C22orf34 expression decreased in the sequence from gallstones to GBC (p-value = 0.04). We identified and validated two cis-LINC00662-eQTLs (r2 = 0.26) and three cis-C22orf34-eQTLs (r2 = 0.24). Only LINC00662 showed a genotyped-based serum expression associated with GBC risk (OR = 1.25 per log2 expression unit, 95% CI 1.04–1.52, p-value = 0.02). Our results suggest that preselection of lncRNAs based on tissue samples and exploitation of cis-lncRNA-eQTLs may facilitate the identification of circulating noncoding RNAs linked to cancer risk. Keywords: gallbladder cancer; lncRNAs; eQTLs; genetic association study; molecular phenotypes Author: Alice Blandino, Dominique Scherer, Trine B. Rounge, Sinan U. Umu, Felix Boekstegers, Carol Barahona Ponce, Katherine Marcelain, Valentina Gárate-Calderón, Melanie Waldenberger, Erik Morales, Armando Rojas, César Munoz, Javier Retamales, Gonzalo de Toro, Olga Barajas, María Teresa Rivera, Analía Cortés, Denisse Loader, Javiera Saavedra, Lorena Gutiérrez, Alejandro Ortega, Maria Enriqueta Bertrán, Fernando Gabler, Mónica Campos, Juan Alvarado, Fabrizio Moisán, Loreto Spencer, Bruno Nervi, Daniel E. Carvajal-Hausdorf, Héctor Losada, Mauricio Almau, Plinio Fernández, Ivan Gallegos, Jordi Olloquequi, Macarena Fuentes-Guajardo, Rolando Gonzalez-Jose, Maria Cátira Bortolini, Carla Gallo, Andres Ruiz Linares, Francisco Rothhammer and Justo Lorenzo Bermejo Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Thu Jan 27 10:55:23 2022 CET ModDate: Thu Jan 27 11:06:10 2022 CET Custom Metadata: no Metadata Stream: no Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 15 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 3150584 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- GVIDPI+VnURWPalladioL Type 1 Custom yes yes no 10 0 SUPYGK+URWPalladioL-Bold Type 1 Custom yes yes no 15 0 YHYHMI+URWPalladioL-Roma Type 1 Custom yes yes no 20 0 BIFUVV+URWPalladioL-Ital Type 1 Custom yes yes no 24 0 JYPLJJ+VnURWPalladioL-Bold Type 1 Custom yes yes no 28 0 MCBCCI+SourceSansRoman-Regular Type 1C Custom yes yes no 36 0 MCBCCM+SourceSansRoman.613wght Type 1C Custom yes yes no 40 0 MCBCCO+SourceSansRoman-Bold Type 1C Custom yes yes no 44 0 LCJEVJ+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 57 0 WVJXAL+CMSY10 Type 1 Builtin yes yes no 79 0 CRJHCU+PazoMath-Italic Type 1 Builtin yes yes no 103 0 RFLZJB+CMR10 Type 1 Builtin yes yes no 107 0 QQXUPP+PazoMath Type 1 Builtin yes yes no 111 0 BKKOEG+PalatinoLinotype TrueType WinAnsi yes yes no 121 0 JKEEEO+URWPalladioL-BoldItal Type 1 Custom yes yes no 128 0 BKKOEG+PalatinoLinotype TrueType WinAnsi yes yes no 138 0 BKKOPE+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 141 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2024-05-07 04:29:48 CEST RepresentationInformation: pmc_35158906.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2022-02-27 18:44:52 CET Size: 3150584 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 325 FreeObjects: 5 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: section.1 Item: Title: Materials and Methods Destination: section.2 Children: Item: Title: RNA Extraction and Small RNA Sequencing Destination: subsection.2.1 Item: Title: DNA Extraction and Genotyping Destination: subsection.2.2 Item: Title: Patients and Statistical Analyses for lncRNA Preselection Destination: subsection.2.3 Item: Title: Individuals and Statistical Analyses for lncRNA-eQTL Validation Destination: subsection.2.4 Item: Title: Patients and Population-Based Controls and Statistical Analyses on the Association between Genotype-Based lncRNA Expression and GBC Risk Destination: subsection.2.5 Item: Title: Results Destination: section.3 Children: Item: Title: Preselected lncRNAs Destination: subsection.3.1 Item: Title: Validated lncRNA-eQTLs Destination: subsection.3.2 Item: Title: LncRNAs with Genotype-Based Plasma Expression Associated with GBC Risk Destination: subsection.3.3 Item: Title: Discussion Destination: section.4 Item: Title: Conclusions Destination: section.5 Item: Title: References Destination: section.5 Info: Title: Identification of Circulating lncRNAs Associated with Gallbladder Cancer Risk by Tissue-Based Preselection, Cis-eQTL Validation, and Analysis of Association with Genotype-Based Expression Author: Alice Blandino, Dominique Scherer, Trine B. Rounge, Sinan U. Umu, Felix Boekstegers, Carol Barahona Ponce, Katherine Marcelain, Valentina Gárate-Calderón, Melanie Waldenberger, Erik Morales, Armando Rojas, César Munoz, Javier Retamales, Gonzalo de Toro, Olga Barajas, María Teresa Rivera, Analía Cortés, Denisse Loader, Javiera Saavedra, Lorena Gutiérrez, Alejandro Ortega, Maria Enriqueta Bertrán, Fernando Gabler, Mónica Campos, Juan Alvarado, Fabrizio Moisán, Loreto Spencer, Bruno Nervi, Daniel E. Carvajal-Hausdorf, Héctor Losada, Mauricio Almau, Plinio Fernández, Ivan Gallegos, Jordi Olloquequi, Macarena Fuentes-Guajardo, Rolando Gonzalez-Jose, Maria Cátira Bortolini, Carla Gallo, Andres Ruiz Linares, Francisco Rothhammer and Justo Lorenzo Bermejo Subject: Long noncoding RNAs (lncRNAs) play key roles in cell processes and are good candidates for cancer risk prediction. Few studies have investigated the association between individual genotypes and lncRNA expression. Here we integrate three separate datasets with information on lncRNA expression only, both lncRNA expression and genotype, and genotype information only to identify circulating lncRNAs associated with the risk of gallbladder cancer (GBC) using robust linear and logistic regression techniques. In the first dataset, we preselect lncRNAs based on expression changes along the sequence “gallstones dysplasia GBC”. In the second dataset, we validate associations between genetic variants and serum expression levels of the preselected lncRNAs (cis-lncRNA-eQTLs) and build lncRNA expression prediction models. In the third dataset, we predict serum lncRNA expression based on individual genotypes and assess the association between genotype-based expression and GBC risk. AC084082.3 and LINC00662 showed increasing expression levels (p-value = 0.009), while C22orf34 expression decreased in the sequence from gallstones to GBC (p-value = 0.04). We identified and validated two cis-LINC00662-eQTLs (r2 = 0.26) and three cis-C22orf34-eQTLs (r2 = 0.24). Only LINC00662 showed a genotyped-based serum expression associated with GBC risk (OR = 1.25 per log2 expression unit, 95% CI 1.04 1.52, p-value = 0.02). Our results suggest that preselection of lncRNAs based on tissue samples and exploitation of cis-lncRNA-eQTLs may facilitate the identification of circulating noncoding RNAs linked to cancer risk. 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