Identification of potential epigenetic biomarkers in supratentorial ZFTA ependymomas

O ependimoma (EPN) é o terceiro tumor do sistema nervoso central mais comum em crianças. Atualmente é subdivido em dez subgrupos moleculares, sendo os EPNs supratentoriais (ST) (YAP1 e ZFTA) e fossa posterior Grupo A (FPA) os mais prevalentes na infância. O subgrupo ST-ZFTA corresponde a cerca de 70% dos EPNs-ST e tem o pior prognóstico clínico. Modificações epigenéticas contribuem para o desenvolvimento e progressão dos tumores e são promissores alvos terapêuticos. No entanto, há poucas evidências da importância da metilação diferencial e do papel de enzimas reguladoras epigenéticas na tumorigênese de ST-ZFTA. O objetivo deste estudo foi identificar genes diferencialmente metilados com potencial valor prognóstico e entender as vias e processos biológicos envolvidos na progressão tumoral de EPNs ST-ZFTA. Foi explorada a distribuição de CpGs entre ST-ZFTA e ST-YAP1, com ST-ZFTA apresentando perfil hipermetilado em comparação ao ST-YAP1. A expressão gênica de DNA metiltransferases (DNMTs) foi analisada, com DNMT1 e DNMT3A apresentando maior expressão gênica no subgrupo ST-ZFTA em comparação aos subgrupos ST-YAP1 e FPA. Análises in silico identificaram biomarcadores candidatos hipermetilados/hipoexpressos e hipometilados/hiperexpressos entre ST-ZFTA vs. STYAP1. A inibição farmacológica de DNMT usando 5-Aza e Zeb resultou em efeitos antiproliferativos, pró-apoptóticos e parada do ciclo celular (G2/M) na linhagem celular BXD-1425 (ST-ZFTA). Além disso, o RNA-Seq após o tratamento com 5-Aza evidenciou genes candidatos que apresentaram reversão transcricional após a desmetilação. A expressão de dezoito HDACs também foi analisada, sendo que EPNs ST-ZFTA apresentaram maior expressão gênica de HDAC4 em comparação a ST-YAP1 e FPA e baixa expressão de HDAC7 e SIRT2. Nossos resultados identificaram genes candidatos controlados por metilação de DNA com valores prognósticos, além de novos insights sobre HDAC4 em ST-ZFTA. No entanto, mais estudos são necessários para validar os genes candidatos regulados pela metilação do DNA e o envolvimento de HDAC4 isolado ou em combinação com metilação de DNA na carcinogênese de ST-ZFTA.Ependymoma (EPN) is the third most common central nervous system tumor in children. It is currently subdivided in ten molecular subgroups, with supratentorial (ST) EPNs (YAP1 and ZFTA) and posterior fossa Group A (PFA) EPNs being the most prevalent in childhood. The ST-ZFTA subgroup accounts for about 70% of ST-EPNs and has the worst clinical prognosis. Epigenetic changes contribute to the development and progression of tumors and are promising therapeutic targets. However, there is little evidence for the importance of differential methylation and the role of epigenetic regulatory enzymes in ST-ZFTA tumorigenesis. The aim of this study was to identify differentially methylated genes with potential prognostic value and to understand the pathways and biological processes involved in the tumoral progression of ST-ZFTA EPNs. The distribution of CpGs between ST-ZFTA and ST-YAP1 was explored, with ST-ZFTA showing a hypermethylated profile compared to ST-YAP1. The gene expression of DNA methyltransferases (DNMTs) was analyzed, with DNMT1 and DNMT3A showing higher gene expression in the ST-ZFTA subgroup compared to the ST-YAP1 and PFA subgroups. In silico analyses identified candidate biomarkers that were hypermethylated/hypoexpressed and hypomethylated/hyperexpressed between ST-ZFTA vs. ST-YAP1. Pharmacological inhibition of DNMT using 5-Aza and Zeb resulted in anti-proliferative, pro-apoptotic effects, and cell cycle arrest (G2/M) in the BXD-1425 cell line (ST-ZFTA). Additionally, RNA-Seq after treatment with 5-Aza showed candidate genes that exhibited transcriptional reversal after demethylation. The expression of eighteen HDACs was also analyzed, with ST-ZFTA EPNs showing higher gene expression of HDAC4 compared to ST-YAP1 and FPA, and low expression of HDAC7 and SIRT2. Our results identified candidate genes controlled by DNA methylation with prognostic values, as well as new insights into HDAC4 in ST-ZFTA. However, further studies are needed to validate the candidate genes regulated by DNA methylation and the involvement of HDAC4 alone or in combination with DNA methylation in the carcinogenesis of ST-ZFTA

Molecular classification of the pediatric ependymomas

Introdução: Os ependimomas são tumores gliais raros e compreendem o terceiro tumor do sistema nervoso central mais frequente na infância. Apesar dos avanços terapêuticos, cerca de 50% dos pacientes desenvolvem recidiva local e 40% dos pacientes vão ao óbito. Uma das causas do insucesso das terapias é a alta heterogeneidade do tumor e a inconsistência do diagnóstico histológico. Em 2015, foi publicada pela primeira vez a caracterização molecular de ependimomas, sendo descrito nove subgrupos tumorais com perfis clínicos, demográficos e moleculares distintos. Objetivo: Estabelecer e padronizar a classificação molecular em amostras de ependimomas pediátricos e correlacionar a classificação com dados clínicos dos pacientes. Casuística e Métodos: Foram estudados 65 casos de ependimomas, diagnosticados no período entre 2001 a 2016 e provenientes do Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto e de São Paulo e do Centro Infantil Boldrini-Campinas. Vinte e seis casos eram ependimomas supratentoriais, classificados com base na presença de fusões gênicas C11orf95-RELA, YAP1-MAMLD1 e YAP1-FAM118B utilizando RT-PCR seguida por sequenciamento de Sanger. Trinta e nove casos de fossa posterior foram classificados em Grupos A, B ou não A e B através do perfil de expressão proteica e gênica dos marcadores: LAMA2, NELL2 e TNC utilizando imuno-histoquímica e PCR quantitativo em tempo real, respectivamente. Resultados: Dentre os ependimomas supratentoriais foram identificadas três amostras primárias e cinco amostras recidivadas com presença de fusão RELA, média de idade de 7 anos (variação de 2,6-13,7 anos), predominância do sexo masculino e grau de ressecção cirúrgica completa. Já a fusão YAP1- MAMLD1 foi identificada em quatro casos, diagnosticados em crianças mais novas, média de idade de 0,9 anos (variação de 0,75-2 anos). Adicionalmente, foi encontrado um caso variante em ependimoma supratentorial, denominado fusão C11orf95-LOC-RELA. Dentre os casos de ependimoma de fossa posterior, foram identificadas 26 amostras primárias e sete recidivas sugestivas de pertencerem ao Grupo A (LAMA2+/ NELL2 -) e seis amostras do Grupo não-A e não-B (LAMA2 +/ NELL2 + e LAMA2 -/NELL2-). Entre os pacientes considerados Grupo A, 90% (24/28) apresentaram marcação positiva para TNC, indicando serem tumores de pior prognóstico. A expressão gênica de LAMA2 e NELL2 apresentou correlação negativa e os genes TNC e LAMA2 uma correlação positiva, p<0,01 e p<0,05, respectivamente. Em ependimoma de fossa posterior Grupo A, os pacientes submetidos às ressecções completa e incompleta apresentaram diferença significativa na sobrevida global (5 anos) de 71,2% ± 14,5% versus 21,4% ± 17,8%, p< 0,01 e na SLE (2 anos) 63,5% ± 14,8% versus 25% ± 15.3%, p <0.001. Conclusões: De acordo com os resultados obtidos foi possível estabelecer a classificação molecular em uma casuística brasileira, seguindo os padrões descritos na literatura. Dados gerados a partir dessa padronização serão de fundamental importância para melhoria da estratificação tumoral, contribuindo tanto para determinação de estratégicas terapêuticas subgrupo-específicas, quanto na busca de novos alvos terapêuticos.Introduction: Ependymomas are rare glial cell-derived tumors and comprise the third most frequent central nervous system tumor in childhood. Despite the therapeutic advances, about 50% of patients develop local recurrence and 40% of patients go to death. One of the causes of the failure of the therapies is the high tumor heterogeneity and the inconsistency of the histological diagnosis. In 2015, the molecular characterization of ependymomas was published for the first time, and nine tumor subgroups with distinct clinical, demographic and molecular profiles were described. Aim: To establish and standardize molecular classification in pediatric ependymoma samples and to correlate the classification with clinical data of the patients. Methods: We studied 65 cases of ependymomas, diagnosed between 2001 and 2016, from the Clinics Hospital of the Medical School of Ribeirão Preto and São Paulo and the Boldrini Children\'s Center-Campinas. Twenty-six cases were supratentorial ependymomas, classified based on the presence of gene fusions C11orf95- RELA, YAP1-MAMLD1 and YAP1-FAM118B using RT-PCR followed by Sanger sequencing. Thirty-nine posterior fossa cases were classified into Groups A, B or non A and B through the protein and gene expression profile of the markers: LAMA2, NELL2 and TNC using immunohistochemistry and quantitative real-time PCR, respectively. Results: Among the supratentorial ependymomas, three primary samples and five relapsed samples with RELA fusion, mean age of 7 years (range of 2.6-13.7 years), male predominance, and degree of complete surgical resection were identified. The YAP1-MAMLD1 fusion was identified in four cases, diagnosed in younger children, mean age 0.9 years (range of 0.75-2 years). In addition, a variant case was found in supratentorial ependymoma, called fusion C11orf95- LOC-RELA. Twenty-six primary samples and seven recurrences suggestive of Group A (LAMA2 + / NELL2-) and six non-A and non-B Group samples (LAMA2 + / NELL2 + and LAMA2 - / NELL2-). Among the patients considered Group A, 90% (24/28) presented positive staining for TNC, indicating that tumors had a worse prognosis. The gene expression of LAMA2 and NELL2 presented negative correlation and the TNC and LAMA2 genes had a positive correlation, p <0.01 and p <0.05, respectively. In the group A posterior fossa ependymoma, patients submitted to complete and incomplete surgical presented a significant difference in overall survival (5 years) of 71.2% ± 14.5% versus 21.4% ± 17.8%, p <0 , 01 and in SLE (2 years) 63.5% ± 14.8% versus 25% ± 15.3%, p <0.001. Conclusions: According to the results obtained, it was possible to establish the molecular classification in a Brazilian cohort, following the standards described in the literature. Data generated from this standardization will be of fundamental importance for the improvement of tumor stratification, contributing both to the determination of subgroup-specific therapeutic strategies and to the search for new therapeutic targets

Molecular classification of the pediatric ependymomas

Introdução: Os ependimomas são tumores gliais raros e compreendem o terceiro tumor do sistema nervoso central mais frequente na infância. Apesar dos avanços terapêuticos, cerca de 50% dos pacientes desenvolvem recidiva local e 40% dos pacientes vão ao óbito. Uma das causas do insucesso das terapias é a alta heterogeneidade do tumor e a inconsistência do diagnóstico histológico. Em 2015, foi publicada pela primeira vez a caracterização molecular de ependimomas, sendo descrito nove subgrupos tumorais com perfis clínicos, demográficos e moleculares distintos. Objetivo: Estabelecer e padronizar a classificação molecular em amostras de ependimomas pediátricos e correlacionar a classificação com dados clínicos dos pacientes. Casuística e Métodos: Foram estudados 65 casos de ependimomas, diagnosticados no período entre 2001 a 2016 e provenientes do Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto e de São Paulo e do Centro Infantil Boldrini-Campinas. Vinte e seis casos eram ependimomas supratentoriais, classificados com base na presença de fusões gênicas C11orf95-RELA, YAP1-MAMLD1 e YAP1-FAM118B utilizando RT-PCR seguida por sequenciamento de Sanger. Trinta e nove casos de fossa posterior foram classificados em Grupos A, B ou não A e B através do perfil de expressão proteica e gênica dos marcadores: LAMA2, NELL2 e TNC utilizando imuno-histoquímica e PCR quantitativo em tempo real, respectivamente. Resultados: Dentre os ependimomas supratentoriais foram identificadas três amostras primárias e cinco amostras recidivadas com presença de fusão RELA, média de idade de 7 anos (variação de 2,6-13,7 anos), predominância do sexo masculino e grau de ressecção cirúrgica completa. Já a fusão YAP1- MAMLD1 foi identificada em quatro casos, diagnosticados em crianças mais novas, média de idade de 0,9 anos (variação de 0,75-2 anos). Adicionalmente, foi encontrado um caso variante em ependimoma supratentorial, denominado fusão C11orf95-LOC-RELA. Dentre os casos de ependimoma de fossa posterior, foram identificadas 26 amostras primárias e sete recidivas sugestivas de pertencerem ao Grupo A (LAMA2+/ NELL2 -) e seis amostras do Grupo não-A e não-B (LAMA2 +/ NELL2 + e LAMA2 -/NELL2-). Entre os pacientes considerados Grupo A, 90% (24/28) apresentaram marcação positiva para TNC, indicando serem tumores de pior prognóstico. A expressão gênica de LAMA2 e NELL2 apresentou correlação negativa e os genes TNC e LAMA2 uma correlação positiva, p<0,01 e p<0,05, respectivamente. Em ependimoma de fossa posterior Grupo A, os pacientes submetidos às ressecções completa e incompleta apresentaram diferença significativa na sobrevida global (5 anos) de 71,2% ± 14,5% versus 21,4% ± 17,8%, p< 0,01 e na SLE (2 anos) 63,5% ± 14,8% versus 25% ± 15.3%, p <0.001. Conclusões: De acordo com os resultados obtidos foi possível estabelecer a classificação molecular em uma casuística brasileira, seguindo os padrões descritos na literatura. Dados gerados a partir dessa padronização serão de fundamental importância para melhoria da estratificação tumoral, contribuindo tanto para determinação de estratégicas terapêuticas subgrupo-específicas, quanto na busca de novos alvos terapêuticos.Introduction: Ependymomas are rare glial cell-derived tumors and comprise the third most frequent central nervous system tumor in childhood. Despite the therapeutic advances, about 50% of patients develop local recurrence and 40% of patients go to death. One of the causes of the failure of the therapies is the high tumor heterogeneity and the inconsistency of the histological diagnosis. In 2015, the molecular characterization of ependymomas was published for the first time, and nine tumor subgroups with distinct clinical, demographic and molecular profiles were described. Aim: To establish and standardize molecular classification in pediatric ependymoma samples and to correlate the classification with clinical data of the patients. Methods: We studied 65 cases of ependymomas, diagnosed between 2001 and 2016, from the Clinics Hospital of the Medical School of Ribeirão Preto and São Paulo and the Boldrini Children\'s Center-Campinas. Twenty-six cases were supratentorial ependymomas, classified based on the presence of gene fusions C11orf95- RELA, YAP1-MAMLD1 and YAP1-FAM118B using RT-PCR followed by Sanger sequencing. Thirty-nine posterior fossa cases were classified into Groups A, B or non A and B through the protein and gene expression profile of the markers: LAMA2, NELL2 and TNC using immunohistochemistry and quantitative real-time PCR, respectively. Results: Among the supratentorial ependymomas, three primary samples and five relapsed samples with RELA fusion, mean age of 7 years (range of 2.6-13.7 years), male predominance, and degree of complete surgical resection were identified. The YAP1-MAMLD1 fusion was identified in four cases, diagnosed in younger children, mean age 0.9 years (range of 0.75-2 years). In addition, a variant case was found in supratentorial ependymoma, called fusion C11orf95- LOC-RELA. Twenty-six primary samples and seven recurrences suggestive of Group A (LAMA2 + / NELL2-) and six non-A and non-B Group samples (LAMA2 + / NELL2 + and LAMA2 - / NELL2-). Among the patients considered Group A, 90% (24/28) presented positive staining for TNC, indicating that tumors had a worse prognosis. The gene expression of LAMA2 and NELL2 presented negative correlation and the TNC and LAMA2 genes had a positive correlation, p <0.01 and p <0.05, respectively. In the group A posterior fossa ependymoma, patients submitted to complete and incomplete surgical presented a significant difference in overall survival (5 years) of 71.2% ± 14.5% versus 21.4% ± 17.8%, p <0 , 01 and in SLE (2 years) 63.5% ± 14.8% versus 25% ± 15.3%, p <0.001. Conclusions: According to the results obtained, it was possible to establish the molecular classification in a Brazilian cohort, following the standards described in the literature. Data generated from this standardization will be of fundamental importance for the improvement of tumor stratification, contributing both to the determination of subgroup-specific therapeutic strategies and to the search for new therapeutic targets

Full-house nephropathy associated with high expression of SPATA5L1 due to a genetic pathogenic variant

DEAR EDITOR, Non-lupus full-house nephropathy is a diagnostic challenge of yet unknown aetiology that does not satisfy criteria for SLE classification . Spermatogenesis-associated protein 5-like protein 1 (SPATA5L1) is ubiquitously expressed in kidney and other tissues and has been previously associated with renal failure and chronic kidney disease (CKD) . We describe a non-lupus full-house nephropathy case showing high SPATA5L1 protein expression in the kidney and other tissues due to a pathogenic missense genetic variant. The study was approved by the Clinical Hospital of the Ribeirão Preto Medical School Research Ethics Committee (process number 3.454.601/2019), and written informed consent was obtained from the parents

Integration of single-nuclei RNA-sequencing, spatial transcriptomics and histochemistry defines the complex microenvironment of NF1-associated plexiform neurofibromas

Abstract Plexiform neurofibroma (PN) is a leading cause of morbidity in children with the genetic condition Neurofibromatosis Type 1 (NF1), often disfiguring or threatening vital structures. During formation of PN, a complex tumor microenvironment (TME) develops, with recruitment of neoplastic and non-neoplastic cell types being critical for growth and progression. Due to the cohesive cellularity of PN, single-cell RNA-sequencing is difficult and may result in a loss of detection of critical cellular subpopulations. To bypass this barrier, we performed single-nuclei RNA-sequencing (snRNA-seq) on 8 frozen PN samples, and integrated this with spatial transcriptomics (ST) in 4 PN samples and immunohistochemistry to provide morphological context to transcriptomic data. SnRNA-seq analysis definitively charted the heterogeneous cellular subpopulations in the PN TME, with the predominant fraction being fibroblast subtypes. PN showed a remarkable amount of inter-sample homogeneity regarding cellular subpopulation proportions despite being resected from a variety of anatomical locations. ST analysis identified distinct cellular subpopulations which were annotated using snRNA-seq data and correlated with histological features. Schwann cell/fibroblast interactions were identified by receptor/ligand interaction analysis demonstrating a high probability of Neurexin 1/Neuroligin 1 (NRXN1/NLGN1) receptor-ligand cross-talk predicted between fibroblasts and non-myelinated Schwann cells (NM-SC) and subtypes, respectively. We observed aberrant expression of NRXN1 and NLGN1 in our PN snRNA-seq data compared to a normal mouse sciatic nerve single-cell RNA-seq dataset. This pathway has never been described in PN and may indicate a clear and direct communication pathway between putative NM-SC cells of origin and surrounding fibroblasts, potentially driving disease progression. SnRNA-seq integrated with spatial transcriptomics advances our understanding of the complex cellular heterogeneity of PN TME and identify potential novel communication pathways that may drive disease progression, a finding that could provide translational therapy options for patients with these devastating tumors of childhood and early adulthood

YAP1 Is a Potential Predictive Molecular Biomarker for Response to SMO Inhibitor in Medulloblastoma Cells

Advances in genomics have led to the identification of twelve relevant molecular subtypes within medulloblastoma (MB). The alpha subtype of Sonic hedgehog-driven MB is resistant to therapy (including smoothened inhibitors) due to activation of genes from the non-canonical SHH pathway, such as MYCN, YAP1, or TP53. Using retrospective cohort microarray data, we found that YAP1 is overexpressed in SHH alpha MB and patients profiled as resistant to SMO inhibitors compared to good responders. Here, we performed YAP1 depletion via CRISPR/Cas9 in two in vitro models of SHH-like MB cells and found that this protein is involved in responsiveness to the SMO inhibitor regarding proliferation, apoptosis, and colony formation. Further, considering the synergic combination of YAP1 depletion with SMO inhibition, we assessed single-cell RNA-seq data from five patients and found that SMO and YAP1 are enriched within cells of SHH MB. Importantly, our data suggest that YAP1 is not only a reliable biomarker for cellular response to SMOi but may indicate prospective testing of combination therapy using YAP1 and SMO inhibitors in preclinical models of SHH MB

A novel N95 respirator with chitosan nanoparticles: mechanical, antiviral, microbiological and cytotoxicity evaluations

Abstract Background It is known that some sectors of hospitals have high bacteria and virus loads that can remain as aerosols in the air and represent a significant health threat for patients and mainly professionals that work in the place daily. Therefore, the need for a respirator able to improve the filtration barrier of N95 masks and even inactivating airborne virus and bacteria becomes apparent. Such a fact motivated the creation of a new N95 respirator which employs chitosan nanoparticles on its intermediate layer (SN95 + CNP). Results The average chitosan nanoparticle size obtained was 165.20 ± 35.00 nm, with a polydispersity index of 0.36 ± 0.03 and a zeta potential of 47.50 ± 1.70 mV. Mechanical tests demonstrate that the SN95 + CNP respirator is more resistant and meets the safety requisites of aerosol penetration, resistance to breath and flammability, presenting higher potential to filtrate microbial and viral particles when compared to conventional SN95 respirators. Furthermore, biological in vitro tests on bacteria, fungi and mammalian cell lines (HaCat, Vero E6 and CCL-81) corroborate the hypothesis that our SN95 + CNP respirator presents strong antimicrobial activity and is safe for human use. There was a reduction of 96.83% of the alphacoronavirus virus and 99% of H1N1 virus and MHV-3 betacoronavirus after 120 min of contact compared to the conventional respirator (SN95), demonstrating that SN95 + CNP have a relevant potential as personal protection equipment. Conclusions Due to chitosan nanotechnology, our novel N95 respirator presents improved mechanical, antimicrobial and antiviral characteristics

Núcleos de Ensino da Unesp: artigos 2007

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Núcleos de Ensino da Unesp: artigos 2008

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq