Browsing by Author "Blanco Luquin, Idoia"
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Publication Open Access Association of blood-based DNA methylation markers with late-onset alzheimer disease: a potential diagnostic approach(Lippincott Williams & Wilkins, 2023) Acha Santamaría, Blanca; Corroza, Jon; Sánchez Ruiz de Gordoa, Javier; Cabello, Carolina; Robles Solano, Maitane; Méndez López, Iván; Macías, Mónica; Zueco, Sara; Roldán, Miren; Urdánoz Casado, Amaya; Jericó Pascual, Ivonne; Erro Aguirre, María Elena; Alcolea, Daniel; Lleo, Alberto; Blanco Luquin, Idoia; Mendióroz Iriarte, Maite; Ciencias de la Salud; Osasun ZientziakBackground and Objectives: There is an urgent need to identify novel noninvasive biomarkers for Alzheimer disease (AD) diagnosis. Recent advances in blood-based measurements of phosphorylated tau (pTau) species are promising but still insufficient to address clinical needs. Epigenetics has been shown to be helpful to better understand AD pathogenesis. Epigenetic biomarkers have been successfully implemented in other medical disciplines, such as oncology. The objective of this study was to explore the diagnostic accuracy of a blood-based DNA methylation marker panel as a noninvasive tool to identify patients with late-onset Alzheimer compared with age-matched controls. Methods: A case-control study was performed. Blood DNA methylation levels at 46 cytosine-guanine sites (21 genes selected after a comprehensive literature search) were measured by bisulfite pyrosequencing in patients with “probable AD dementia” following National Institute on Aging and the Alzheimer's Association guidelines (2011) and age-matched and sex-matched controls recruited at Neurology Department-University Hospital of Navarre, Spain, selected by convenience sampling. Plasma pTau181 levels were determined by Simoa technology. Multivariable logistic regression analysis was performed to explore the optimal model to discriminate patients with AD from controls. Furthermore, we performed a stratified analysis by sex. Results: The final study cohort consisted of 80 patients with AD (age: median [interquartile range] 79 [11] years; 58.8% female) and 100 cognitively healthy controls (age 77 [10] years; 58% female). A panel including DNA methylation levels at NXN, ABCA7, and HOXA3 genes and plasma pTau181 significantly improved (area under the receiver operating characteristic curve 0.93, 95% CI 0.89–0.97) the diagnostic performance of a single pTau181-based model, adjusted for age, sex, and APOE ɛ4 genotype. The sensitivity and specificity of this panel were 83.30% and 90.00%, respectively. After sex-stratified analysis, HOXA3 DNA methylation levels showed consistent association with AD. Discussion: These results highlight the potential translational value of blood-based DNA methylation biomarkers for noninvasive diagnosis of AD. Registration Information: Research Ethics Committee of the University Hospital of Navarre (PI17/02218).Publication Open Access CDH22 hypermethylation is an independent prognostic biomarker in breast cancer(BioMed Central, 2017) Martín Sánchez, Esperanza; Mendaza Lainez, Saioa; Ulazia Garmendia, Ane; Monreal Santesteban, Iñaki; Córdoba Iturriagagoitia, Alicia; Vicente García, Francisco; Blanco Luquin, Idoia; Cruz, Susana de la; Aramendia, Ana; Guerrero Setas, David; Ciencias de la Salud; Osasun ZientziakBackground: Cadherin-like protein 22 (CDH22) is a transmembrane glycoprotein involved in cell-cell adhesion and metastasis. Its role in cancer is controversial because it has been described as being upregulated in colorectal cancer, whereas it is downregulated in metastatic melanoma. However, its status in breast cancer (BC) is unknown. The purpose of our study was to determine the molecular status and clinical value of CDH22 in BC. Results: We observed by immunohistochemistry that the level of CDH22 expression was lower in BC tissues than in their matched adjacent-to-tumour and non-neoplastic tissues from reduction mammoplasties. Since epigenetic alteration is one of the main causes of gene silencing, we analysed the hypermethylation of 3 CpG sites in the CDH22 promoter by pyrosequencing in a series of 142 infiltrating duct BC cases. CDH22 was found to be hypermethylated in tumoral tissues relative to non-neoplastic mammary tissues. Importantly, this epigenetic alteration was already present in adjacent-to-tumour tissues, although to a lesser extent than in tumoral samples. Furthermore, CDH22 gene regulation was dynamically modulated in vitro by epigenetic drugs. Interestingly, CDH22 hypermethylation in all 3 CpG sites simultaneously, but not expression, was significantly associated with shorter progression-free survival (p = 0.015) and overall survival (p = 0.021) in our patient series. Importantly, CDH22 hypermethylation was an independent factor that predicts poor progression-free survival regardless of age and stage (p = 0.006). Conclusions: Our results are the first evidence that CDH22 is hypermethylated in BC and that this alteration is an independent prognostic factor in BC. Thus, CDH22 hypermethylation could be a potential biomarker of poor prognosis in BC.Publication Open Access Changes in gene expression profiling of apoptotic genes in neuroblastoma cell lines upon retinoic acid treatment(Public Library of Science, 2013) Celay Leoz, Ion; Blanco Luquin, Idoia; Lázcoz Ripoll, Paula; Rotinen Díaz, Mirja Sofia; Castresana, Javier S.; Encío Martínez, Ignacio; Ciencias de la Salud; Osasun Zientziak; Gobierno de Navarra / Nafarroako GobernuaTo determine the effect of retinoic acid (RA) in neuroblastoma we treated RA sensitive neuroblastoma cell lines with 9-cis RA or ATRA for 9 days, or for 5 days followed by absence of RA for another 4 days. Both isomers induced apoptosis and reduced cell density as a result of cell differentiation and/or apoptosis. Flow cytometry revealed that 9-cis RA induced apoptosis more effectively than ATRA. The expression profile of apoptosis and survival pathways was cell line specific and depended on the isomer used.Publication Open Access CHL1 hypermethylation as a potential biomarker of poor prognosis in breast cancer(Impact Journals, 2017) Martín Sánchez, Esperanza; Mendaza Lainez, Saioa; Ulazia Garmendia, Ane; Monreal Santesteban, Iñaki; Blanco Luquin, Idoia; Córdoba Iturriagagoitia, Alicia; Vicente García, Francisco; Pérez Janices, Noemi; Escors Murugarren, David; Megías, Diego; Ciencias de la Salud; Osasun Zientziak; Gobierno de Navarra / Nafarroako GobernuaThe CHL1 gene encodes a cell-adhesion molecule proposed as being a putative tumour-suppressor gene in breast cancer (BC). However, neither the underlying molecular mechanisms nor the clinical value of CHL1 downregulation in BC has been explored. The methylation status of three CpG sites in the CHL1 promoter was analysed by pyrosequencing in neoplastic biopsies from 142 patients with invasive BC and compared with that of non-neoplastic tissues. We found higher CHL1 methylation levels in breast tumours than in non-neoplastic tissues, either from mammoplasties or adjacent-to-tumour, which correlated with lower levels of protein expression in tumours measured by immunohistochemistry. A panel of five BC cell lines was treated with two epigenetic drugs, and restoration of CHL1 expression was observed, indicating in vitro dynamic epigenetic regulation. CHL1 was silenced by shRNA in immortalized but non-neoplastic mammary cells, and enhanced cell proliferation and migration, but not invasion, were found by real-time cell analysis. The prognostic value of CHL1 hypermethylation was assessed by the log-rank test and fitted in a Cox regression model. Importantly, CHL1 hypermethylation was very significantly associated with shorter progression-free survival in our BC patient series, independent of age and stage (p = 0.001). In conclusion, our results indicate that CHL1 is downregulated by hypermethylation and that this epigenetic alteration is an independent prognostic factor in BC.Publication Open Access Circular RNA expression profile in blood according to ischemic stroke etiology(BioMed Central, 2020) Ostolaza, Aiora; Blanco Luquin, Idoia; Urdánoz Casado, Amaya; Rubio, Idoya; Labarga Gutiérrez, Alberto; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Gobierno de Navarra / Nafarroako GobernuaBackground: The discovery of novel biomarkers of stroke etiology would be most helpful in management of acute ischemic stroke patients. Recently, circular RNAs (circRNAs) have been proposed as candidate biomarkers of neurological conditions due to its high stability. circRNAs function as sponges, sequestering miRNAs and are involved in most relevant biological functions. Our aim was to identify differentially expressed circRNAs in acute ischemic stroke patients according to stroke etiology. Methods: A comprehensive expression profile of blood circRNAs was conducted by Arraystar Human circRNA arrays (13,617 probes) on a discovery cohort of 30 stroke patients with different stroke etiologies by TOAST classification. Real-time quantitative PCR (RT-qPCR) was used to validate array results in a cohort of 50 stroke patients. Functional in silico analysis was performed to identify potential interactions with microRNAs (miRNAs) and pathways underlying deregulated circRNAs. Results: A set of 60 circRNAs were found to be upregulated in atherotrombotic versus cardioembolic strokes (fold-change > = 1.5 and p-value ≤ 0.05). Differential expression of hsa_circRNA_102488, originated from UBA52 gene, was replicated in the validation cohort. RNA-binding proteins (RBPs) sites of hsa_circRNA_102488 clustered around AGO2 and FUS proteins. Further functional analysis revealed interactions between deregulated circRNAs and a set of miRNAs involved in stroke-related pathways, such as fatty acid biogenesis or lysine degradation. Conclusion: Different stroke subtypes show specific profiles of circRNAs expression. circRNAs may serve as a new source of biomarkers of stroke etiology in acute ischemic stroke patients.Publication Open Access Early epigenetic changes of Alzheimer's disease in the human hippocampus(2020) Blanco Luquin, Idoia; Acha Santamaría, Blanca; Urdánoz Casado, Amaya; Sánchez Ruiz de Gordoa, Javier; Vicuña-Urriza, Janire; Roldán, Miren; Labarga Gutiérrez, Alberto; Zelaya Huerta, María Victoria; Cabello, Carolina; Méndez López, Iván; Mendióroz Iriarte, Maite; Ciencias de la Salud; Osasun Zientziak; Sociología y Trabajo Social; Soziologia eta Gizarte Lana; Gobierno de Navarra / Nafarroako GobernuaThe discovery of new biomarkers would be very valuable to improve the detection of early Alzheimer's disease (AD). DNA methylation marks may serve as epigenetic biomarkers of early AD. Here we identified epigenetic marks that are present in the human hippocampus from the earliest stages of AD. A previous methylome dataset of the human AD hippocampus was used to select a set of eight differentially methylated positions (DMPs) since early AD stages. Next, bisulphite pyrosequencing was performed in an expanded homogeneous cohort of 18 pure controls and 35 hippocampal samples with neuropathological changes of pure AD. Correlation between DNA methylation levels in DMPs and phospho-tau protein burden assessed by immunohistochemistry in the hippocampus was also determined. We found four DMPs showing higher levels of DNA methylation at early AD stages compared to controls, involving ELOVL2, GIT1/TP53I13 and the histone gene locus at chromosome 6. DNA methylation levels assessed by bisulphite pyrosequencing correlated with phospho-tau protein burden for ELOVL2 and HIST1H3E/HIST1H3 F genes. In this discovery study, a set of four epigenetic marks of early AD stages have been identified in the human hippocampus. It would be worth studying in-depth the specific pathways related to these epigenetic marks. These early alterations in DNA methylation in the AD hippocampus could be regarded as candidate biomarkers to be explored in future translational studies.Publication Embargo Estudio de los cambios dinámicos de la metilación en genes relacionados con la enfermedad del Alzheimer durante la práctica de mindfulness(2025) Marro Ojer, Ibai; Blanco Luquin, Idoia; Mendióroz Iriarte, Maite; Escuela Técnica Superior de Ingeniería Agronómica y Biociencias; Nekazaritzako Ingeniaritzako eta Biozientzietako Goi Mailako Eskola TeknikoaContexto y objetivos. La meditación, y en particular el mindfulness, se ha asociado a efectos beneficiosos a nivel fisiológico, incluyendo la modulación de procesos epigenéticos como la metilación del DNA, un mecanismo clave en la regulación de la expresión génica. Estudios recientes sugieren que la meditación puede influir en la metilación de genes relacionados con la respuesta al estrés, la inflamación y el envejecimiento celular. El objetivo de este trabajo fue estudiar los efectos de la meditación en la regulación epigenética de genes relacionados con la enfermedad de Alzheimer mediante el análisis de sus niveles de metilación antes y después de un retiro de meditación. Métodos. Se realizó un estudio de intervención cuasi-experimental en un grupo de 17 practicantes de mindfulness de larga duración que participaron en un retiro de meditación Vipassana de 1 mes de duración. Para el estudio de metilación, las muestras extraídas de DNA de la capa leucocitaria/buffy coat fueron convertidas con bisulfito sódico y analizadas mediante pirosecuenciación con bisulfito. El análisis estadístico se realizó con el software IBM SPSS Statistics 25.0. Resultados. Se identificaron diferencias estadísticamente significativas entre las muestras antes y después del retiro para 4 de las 19 CpGs evaluadas. Tras el retiro, en las posiciones ABCA7 _CpG2 y HOXA3_CpG2 se observó una disminución de los niveles de metilación del DNA, mientras que las posiciones ADAM10_CpG2 y APOE_CpG2 mostraron un aumento en los niveles de metilación del DNA. Por otro lado, no se encontraron diferencias significativas en los niveles de metilación de los genes NXN, TREM2 y TREML2. Conclusiones. Nuestros hallazgos sugieren que la práctica de mindfulness tiene un efecto epigenético en genes clave para la EA y merecería estudiarse con mayor profundidad como estrategia preventiva o intervención no farmacológica en pacientes con EA, al influir en mecanismos epigenéticos relacionados con la respuesta al estrés y la neuroinflamación.Publication Open Access Gender-dependent deregulation of linear and circular RNA variants of homer1 in the entorhinal cortex of Alzheimer’s disease(MDPI, 2021) Urdánoz Casado, Amaya; Sánchez Ruiz de Gordoa, Javier; Robles Solano, Maitane; Acha Santamaría, Blanca; Roldán, Miren; Zelaya Huerta, María Victoria; Blanco Luquin, Idoia; Mendióroz Iriarte, Maite; Ciencias de la Salud; Osasun Zientziak; Gobierno de Navarra / Nafarroako GobernuaThe HOMER1 gene is involved in synaptic plasticity, learning and memory. Recent studies show that circular RNA derived from HOMER1 (circHOMER1) expression is altered in some Alzheimer’s disease (AD) brain regions. In addition, HOMER1 messenger (mRNA) levels have been associated with β-Amyloid (Aβ) deposits in brain cortical regions. Our aim was to measure the expression levels of HOMER1 circRNAs and their linear forms in the human AD entorhinal cortex. First, we showed downregulation of HOMER1B/C and HOMER1A mRNA and hsa_circ_0006916 and hsa_circ_0073127 levels in AD female cases compared to controls by RT-qPCR. A positive correlation was observed between HOMER1B/C, HOMER1A mRNA, and hsa_circ_0073128 with HOMER1B/C protein only in females. Global average area of Aβ deposits in entorhinal cortex samples was negatively correlated with HOMER1B/C, HOMER1A mRNA, and hsa_circ_0073127 in both genders. Furthermore, no differences in DNA methylation were found in two regions of HOMER1 promoter between AD cases and controls. To sum up, we demonstrate that linear and circular RNA variants of HOMER1 are downregulated in the entorhinal cortex of female patients with AD. These results add to the notion that HOMER1 and its circular forms could be playing a female-specific role in the pathogenesis of AD.Publication Embargo Identificación de biomarcadores epigenéticos de metilación del DNA en la sangre periférica de pacientes con enfermedad de Alzheimer(2024) Acha Santamaría, Blanca; Mendióroz Iriarte, Maite; Blanco Luquin, Idoia; Ciencias de la Salud; Osasun ZientziakEn esta tesis doctoral, se investiga el papel de la metilación del DNA como un potencial biomarcador diagnóstico de la EA, dada la novedad que los mecanismos epigenéticos han supuesto en la búsqueda de biomarcadores en la última década. Para su desarrollo, se plantea una aproximación de gen candidato. Tras una extensa revisión bibliográfica, se seleccionaron 21 genes candidatos, cuyos niveles de metilación del DNA se midieron mediante la técnica de pirosecuencación por bisulfito en un grupo de 80 pacientes con EA y 100 controles. El análisis estadístico identificó 11 posiciones (CpGs) de metilación diferencial entre pacientes y controles. Con estos resultados se construyó un modelo de regresión logística multivariable que incluyó las posiciones diferencialmente metiladas (Differentially Methylated Positions, DMPs) identificadas en los genes NXN, TREML2, ABCA7 y HOXA3, cuya capacidad de discriminación de pacientes con EA fue del 87%. La construcción de un modelo de regresión logística donde se combinaron las marcas de metilación del DNA y pTau181 plasmático, con una capacidad de discriminación del 93%, mejoró la capacidad diagnóstica de pTau181 plasmático (85%), considerada la herramienta diagnóstica plasmática más promotedora hasta la fecha. El sexo y el genotipo APOE son, junto con la edad, los principales factores de riesgo (FR) de la EA, por lo que se estudió su asociación con las marcas de metilación del DNA identificadas en este estudio. Se encontraron marcas de metilación del DNA diferenciales entre pacientes con EA y controles en función del sexo y del genotipo APOE. Curiosamente, los niveles de metilación de la CpG localizada en el gen HOXA3 Chr7:27153577 mostraron diferencias estadísticamente significativas entre pacientes con EA y controles en la cohorte global y en todos los grupos tras la estratificación por sexo y genotipo APOE. Además, también mostraron correlación con la variable que refleja el estado cognitivo, el MMSE, y con los niveles de pTau181 plasmático, postulándose como una herramienta prometedora en la mejora de la precisión diagnóstica de la EA como parte de un panel de biomarcadores en sangre periférica. A su vez, las DMPs localizadas en los genes IRS2, HAND2 y RHBDF2 correlacionaron con los niveles de los biomarcadores core de líquido cefalorraquídeo (LCR) en los pacientes con EA de nuestra cohorte iBEAS, sin ser validados en una cohorte externa cedida por el Hospital Sant Pau (Barcelona). Como conclusión, este trabajo muestra la existencia de marcas de metilación del DNA en la sangre como potenciales herramientas en la mejora de la capacidad diagnóstica en la EA, ntegrados en paneles de biomarcadores periféricos. Además, estos resultados apoyan la posible implicación de la metilación del DNA en la patología de la EA.Publication Open Access Identificación de circRNAs como biomarcadores epigenéticos candidatos en la enfermedad de Alzheimer(2022) Urdánoz Casado, Amaya; Blanco Luquin, Idoia; Mendióroz Iriarte, Maite; Ciencias de la Salud; Osasun Zientziak; Gobierno de Navarra / Nafarroako GobernuaLa enfermedad de Alzheimer (EA) es una enfermedad neurodegenerativa, crónica y, por el momento, irreversible que representa la primera causa de demencia relacionada con la edad. Su diagnóstico sigue siendo un reto. En los últimos años, se han identificado diferentes biomarcadores diagnósticos pero, debido a su coste o dificultad de acceso, se ha limitado su implantación de rutina en muchos centros sanitarios. Por ello se están investigando nuevos biomarcadores no invasivos en sangre, como los biomarcadores epigenéticos, entre los que se encuentran los RNAs circulares (circRNAs), una clase de RNAs no codificantes. El objetivo de esta tesis es identificar circRNAs con una expresión diferencial en la corteza entorrinal (CE) humana, una región cerebral especialmente vulnerable a la EA, en pacientes con EA respecto a controles.Publication Open Access In vitro assessment of the role of p53 on chemotherapy treatments in neuroblastoma cell lines(MDPI, 2021) Blanco Luquin, Idoia; Lázcoz Ripoll, Paula; Celay Leoz, Ion; Castresana, Javier S.; Encío Martínez, Ignacio; Ciencias de la Salud; Osasun Zientziak; Gobierno de Navarra / Nafarroako GobernuaNeuroblastoma is the most frequent malignant extracranial solid tumor of infancy. The overall objective of this work consists of determining the presence of alterations in the p53/MDM2 /p14ARF signaling pathway in neuroblastoma cell lines and deciphering their possible relationship with resistance to known antineoplastic drugs and to differentiation agents. Firstly, we characterized 10 neuroblastoma cell lines for alterations at the p53/MDM2/p14ARF signaling pathway by analysis of TP53 point mutations, MYCN and MDM2 amplification, and p14ARF methylation, homozygous deletions, and expression. Secondly, we chose SK-N-FI (mutated at TP53) and SK-N-Be(2) (wild-type TP53) cell lines, treated them with chemotherapeutic agents (doxorubicin, etoposide, cisplatin, and melphalan) and with two isomers of retinoic acid (RA): (9-cis and all-trans). Finally, we analyzed the distribution of the cell cycle, the induction of apoptosis, and the expression levels of p53, p21, and Bcl-2 in those two cell lines. P14ARF did not present promoter methylation, homozygous deletions, and protein expression in any of the 10 neuroblastoma cell lines. One TP53 point mutation was detected in the SK-N-FI cell line. MYCN amplification was frequent, while most cell lines did not present MDM2 amplification. Treatment of SK-N-FI and SK-N-Be(2) cells with doxorubicin, etopo-side, cisplatin, and melphalan increased apoptosis and blocked the cycle in G2/M, while retinoic acid isomers induced apoptosis and decreased the percentage of cells in S phase in TP53 mutated SK-N-FI cells, but not in TP53 wild-type SK-N-Be(2) cells. Treatment with cisplatin, melphalan, or 9-cis RA decreased p53 expression levels in SK-N-FI cells but not in SK-N-Be (2). The expression of p21 was not modified in either of the two cell lines. Bcl-2 levels were reduced only in SK-N-FI cells after treatment with cisplatin. However, treatments with doxorubicin, etoposide, or 9-cis-RA did not modify the levels of this protein in either of the two cell lines. In conclusion, TP53 mutated SK-N-FI cells respond better to the retinoic isomers than TP53 wild-type SK-N-Be(2) cells. Although these are in vitro results, it seems that deciphering the molecular alterations of the p53/MDM2/p14ARF signaling pathway prior to treating patients of neuroblastoma might be useful for standardizing therapies with the aim of improving survival.Publication Open Access Liquid biopsy in alzheimer's disease patients reveals epigenetic changes in the PRLHR gene(MDPI, 2023) Macías, Mónica; Acha Santamaría, Blanca; Corroza, Jon; Urdánoz Casado, Amaya; Roldán, Miren; Robles Solano, Maitane; Sánchez Ruiz de Gordoa, Javier; Erro Aguirre, María Elena; Jericó Pascual, Ivonne; Blanco Luquin, Idoia; Mendióroz Iriarte, Maite; Ciencias de la Salud; Osasun ZientziakIn recent years, new DNA methylation variants have been reported in genes biologically relevant to Alzheimer’s disease (AD) in human brain tissue. However, this AD-specific epigenetic information remains brain-locked and unreachable during patients’ lifetimes. In a previous methylome performed in the hippocampus of 26 AD patients and 12 controls, we found higher methylation levels in AD patients in the promoter region of PRLHR, a gene involved in energy balance regulation. Our aim was to further characterize PRLHR’s role in AD and to evaluate if the liquid biopsy technique would provide life access to this brain information in a non-invasive way. First, we extended the methylation mapping of PRLHR and validated previous methylome results via bisulfite cloning sequencing. Next, we observed a positive correlation between PRLHR methylation levels and AD-related neuropathological changes and a decreased expression of PRLHR in AD hippocampus. Then, we managed to replicate the hippocampal methylation differences in plasma cfDNA from an additional cohort of 35 AD patients and 35 controls. The isolation of cfDNA from the plasma of AD patients may constitute a source of potential epigenetic biomarkers to aid AD clinical management.Publication Open Access NXN gene epigenetic changes in an adult neurogenesis model of Alzheimer's disease(MDPI, 2022) Blanco Luquin, Idoia; Acha Santamaría, Blanca; Urdánoz Casado, Amaya; Gómez Orte, Eva; Roldán, Miren; Pérez Rodríguez, Diego R.; Cabello, Juan; Mendióroz Iriarte, Maite; Ciencias de la Salud; Osasun Zientziak; Gobierno de Navarra / Nafarroako GobernuaIn view of the proven link between adult hippocampal neurogenesis (AHN) and learning and memory impairment, we generated a straightforward adult neurogenesis in vitro model to recapitulate DNA methylation marks in the context of Alzheimer’s disease (AD). Neural progenitor cells (NPCs) were differentiated for 29 days and Aβ peptide 1–42 was added. mRNA expression of Neuronal Differentiation 1 (NEUROD1), Neural Cell Adhesion Molecule 1 (NCAM1), Tubulin Beta 3 Class III (TUBB3), RNA Binding Fox-1 Homolog 3 (RBFOX3), Calbindin 1 (CALB1), and Glial Fibrillary Acidic Protein (GFAP) was determined by RT-qPCR to characterize the culture and framed within the multistep process of AHN. Hippocampal DNA methylation marks previously identified in Contactin-Associated Protein 1 (CNTNAP1), SEPT5-GP1BB Readthrough (SEPT5-GP1BB), T-Box Transcription Factor 5 (TBX5), and Nucleoredoxin (NXN) genes were profiled by bisulfite pyrosequencing or bisulfite cloning sequencing; mRNA expression was also measured. NXN outlined a peak of DNA methylation overlapping type 3 neuroblasts. Aβ-treated NPCs showed transient decreases of mRNA expression for SEPT5-GP1BB and NXN on day 9 or 19 and an increase in DNA methylation on day 29 for NXN. NXN and SEPT5-GP1BB may reflect alterations detected in the brain of AD human patients, broadening our understanding of this disease.Publication Open Access Profile of TREM2-derived circRNA and mRNA variants in the entorhinal cortex of Alzheimer's disease patients(MDPI, 2022) Urdánoz Casado, Amaya; Sánchez Ruiz de Gordoa, Javier; Robles Solano, Maitane; Roldán, Miren; Zelaya Huerta, María Victoria; Blanco Luquin, Idoia; Mendióroz Iriarte, Maite; Ciencias de la Salud; Osasun Zientziak; Gobierno de Navarra / Nafarroako GobernuaGenetic variants in TREM2, a microglia-related gene, are well-known risk factors for Alzheimer’s disease (AD). Here, we report that TREM2 originates from circular RNAs (circRNAs), a novel class of non-coding RNAs characterized by a covalent and stable closed-loop structure. First, divergent primers were designed to amplify circRNAs by RT-PCR, which were further assessed by Sanger sequencing. Then, additional primer sets were used to confirm back-splicing junctions. In addition, HMC3 cells were used to assess the microglial expression of circTREM2s. Three candidate circTREM2s were identified in control and AD human entorhinal samples. One of the circRNAs, circTREM2_1, was consistently amplified by all divergent primer sets in control and AD entorhinal cortex samples as well as in HMC3 cells. In AD cases, a moderate negative correlation (r = −0.434) was found between the global average area of Aβ deposits in the entorhinal cortex and circTREM2_1 expression level. In addition, by bioinformatics tools, a total of 16 miRNAs were predicted to join with circTREM2s. Finally, TREM2 mRNA corresponding to four isoforms was profiled by RTqPCR. TREM2 mRNA levels were found elevated in entorhinal samples of AD patients with low or intermediate ABC scores compared to controls. To sum up, a novel circRNA derived from the TREM2 gene, circTREM2_1, has been identified in the human entorhinal cortex and TREM2 mRNA expression has been detected to increase in AD compared to controls. Unraveling the molecular genetics of the TREM2 gene may help to better know the innate immune response in AD.