A meta-analysis of brain DNA methylation across sex, age and Alzheimer’s disease points for accelerated epigenetic aging in neurodegeneration [preprint]

Alzheimer’s disease (AD) is characterized by specific alterations of brain DNA methylation (DNAm) patterns. Age and sex, two major risk factors for AD, are also known to largely affect the epigenetic profiles in the brain, but their contribution to AD-associated DNAm changes has been poorly investigated. In this study we considered publicly available DNAm datasets of 4 brain regions (temporal, frontal, entorhinal cortex and cerebellum) from healthy adult subjects and AD patients, and performed a meta-analysis to identify sex-, age- and AD-associated epigenetic profiles. We showed that DNAm differences between males and females tend to be shared between the 4 brain regions, while aging differently affects cortical regions compared to cerebellum. We found that the proportion of sex-dependent probes whose methylation changes also during aging is higher than expected, but that differences between males and females tend to be maintained, with only few probes showing sex-by-age interaction. We did not find significant overlaps between AD- and sex-associated probes, nor disease-by-sex interaction effects. On the contrary, we found that AD-related epigenetic modifications are significantly enriched in probes whose DNAm changes with age and that there is a high concordance between the direction of changes (hyper or hypo-methylation) in aging and AD, supporting accelerated epigenetic aging in the disease. In conclusion, we demonstrated that age-associated, but not sex-associated DNAm concurs to the epigenetic deregulation observed in AD, providing new insight on how advanced age enables neurodegeneration

A Meta-Analysis of Brain DNA Methylation Across Sex, Age, and Alzheimer\u27s Disease Points for Accelerated Epigenetic Aging in Neurodegeneration

Alzheimer\u27s disease (AD) is characterized by specific alterations of brain DNA methylation (DNAm) patterns. Age and sex, two major risk factors for AD, are also known to largely affect the epigenetic profiles in brain, but their contribution to AD-associated DNAm changes has been poorly investigated. In this study we considered publicly available DNAm datasets of four brain regions (temporal, frontal, entorhinal cortex, and cerebellum) from healthy adult subjects and AD patients, and performed a meta-analysis to identify sex-, age-, and AD-associated epigenetic profiles. In one of these datasets it was also possible to distinguish 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) profiles. We showed that DNAm differences between males and females tend to be shared between the four brain regions, while aging differently affects cortical regions compared to cerebellum. We found that the proportion of sex-dependent probes whose methylation is modified also during aging is higher than expected, but that differences between males and females tend to be maintained, with only a few probes showing age-by-sex interaction. We did not find significant overlaps between AD- and sex-associated probes, nor disease-by-sex interaction effects. On the contrary, we found that AD-related epigenetic modifications are significantly enriched in probes whose DNAm varies with age and that there is a high concordance between the direction of changes (hyper or hypo-methylation) in aging and AD, supporting accelerated epigenetic aging in the disease. In summary, our results suggest that age-associated DNAm patterns concur to the epigenetic deregulation observed in AD, providing new insights on how advanced age enables neurodegeneration

DTM e dor orofacial: perspectivas curriculares das faculdades de Odontologia do Sudeste brasileiro

Introduction: Orofacial pain (OD) and temporomandibular disorders (TMD) have a high prevalence in the population, causing great suffering for patients. To train general practitioners able to recognize and treat such disorders, it is necessary that Higher Education Institutions (HEIs) offer this content satisfactorily during graduation. Materials and Methods: The research sample consists of all Dentistry Faculties in southeastern Brazil in operation in March 2019, which had active and accredited courses on the e-MEC portal of the Ministry of Education of Brazil, and which provided access to the matrix curriculum through online tools (official website or email). The data were analyzed using the GraphPad Prism 5.0 program. Results: Of the 176 HEIs in the southeastern region, 144 (81.8%) were included in the study because they met the inclusion criteria. Of these, only 36% have disciplines related to TMD and OD in their curricular matrices, being offered more in public (52.6%) than private (33.6%) HEIs, for p = 0.1275. Regarding the nature of the discipline, it is predominantly mandatory in private HEIs, and not mandatory in public HEIs (p = 0.0073). As a positive aspect, it was observed that in relation to the type of content covered, theoretical-practical disciplines are addressed in most institutions (59.37%). The average workload (CH) of the discipline is 58.98h (SD = 20.37), being higher in public HEIs. Conclusion: Our results demonstrate that the majority of Dentistry courses in southeastern Brazil do not offer TMD and DO disciplines, especially private HEIs, which contributes to the training of professionals unprepared to deal with these patients.  Introdução: A dor orofacial (DO) e as disfunções temporomandibulares (DTM) apresentam alta prevalência na população, sendo causa de grande sofrimento para os pacientes. Para formar clínicos gerais aptos em reconhecerem e tratarem tais distúrbios é necessário que as Instituições de Ensino Superior (IES) ofertem este conteúdo de forma satisfatória durante a graduação. Objetivo: Identificar e quantificar a presença da disciplina de DTM e DO nas grades curriculares dos cursos de graduação em Odontologia, bem como características curriculares da disciplina quando presente. Material e Métodos: A amostra da pesquisa constitui-se de todas as faculdades de Odontologia do Sudeste brasileiro em funcionamento  no mês de março de 2019, que estavam com cursos ativos e credenciados no portal e-MEC do Ministério da Educação do Brasil, e que disponibilizaram acesso a matriz curricular por meio de ferramentas online (website oficial ou e-mail). Os dados foram analisados no programa GraphPad Prism 5.0. Resultados: Das 176 IES da região Sudeste, 144 (81,8%) foram incluídas no estudo por preencherem os critérios de inclusão. Destas, apenas 36% apresentam disciplinas relacionadas à DTM e DO em suas matrizes curriculares, sendo mais ofertada em IES públicas (52,6%) do que privadas (33,6%), para p=0,1275. A respeito da natureza da disciplina, é predominantemente obrigatória nas IES privadas, e não obrigatória nas IES públicas (p=0,0073). Como aspecto positivo, foi observado que em relação ao tipo de conteúdo abordado, disciplinas teórico-práticas são abordadas na maioria das instituições (59,37%). A carga horária (CH) média da disciplina é de 58,98h (DP=20,37), sendo maior nas IES públicas. Conclusão: Nossos resultados demostram que a maioria dos cursos de Odontologia do Sudeste brasileiro (63,8%) não oferecem disciplinas de DTM e DO, especialmente IES privadas. &nbsp

Aberrant methylation patterns in colorectal cancer: A meta-analysis

Colorectal cancer is among the leading causes of cancer death worldwide. Despite numerous molecular characterizations of the phenomenon, the exact dynamics of its onset and progression remain elusive. Colorectal cancer onset has been characterized by changes in DNA methylation profiles, that, owing to the stability of their patterns, are promising candidates to shed light on the molecular events laying at the base of this phenomenon. To exploit this stability and reinforce it, we conducted a meta-analysis on publicly available DNA methylation datasets generated on: normal colorectal, adenoma (ADE) and adenocarcinoma (CRC) samples using the Illumina 450k array, in the systems medicine frame, searching for tumor gene episignatures, to produce a carefully selected list of potential drivers, markers and targets of the disease. The analysis proceeds from a differential meta-analysis of the methylation profiles using an analytical pipeline recently developed by our group [1], through network reconstruction, topological and functional analyses, to finally highlight relevant epigenomic features. Our results show that genes already highlighted for their genetic or transcriptional alteration in colorectal cancer are also differentially methylated, reinforcing -regardless of the level of cellular control- their role in the complex of alterations involved in tumorigenesis. These findings were finally validated in an independent cohort from The Cancer Genome Atlas (TCGA)

Integrative analysis of microRNA and mRNA expression profiles of monocyte- derived dendritic cells differentiation during experimental cerebral malaria

Heterogeneity and high plasticity are common features of cells from the mononuclear phagocyte system: monocytes (MOs), macrophages, and dendritic cells (DCs). Upon activation by microbial agents, MO can differentiate into MO- derived DCs (MODCs). In previous work, we have shown that during acute infection with Plasmodium berghei ANKA (PbA), MODCs become, transiently, the main CD11b+ myeloid population in the spleen (SP) and once recruited to the brain play an important role in the development of experimental cerebral malaria (ECM). Here, we isolated 4 cell populations: bone marrow (BM) MOs (BM- MOs) and SP- MOs from uninfected mice; BM inflammatory MOs (BM- iMOs) and SP- MODCs from PbA- infected mice and used a system biology approach to a holistic transcriptomic comparison and provide an interactome analysis by integrating differentially expressed miRNAs (DEMs) and their differentially expressed gene targets (DEGs) data. The Jaccard index (JI) was used for gauging the similarity and diversity among these cell populations. Whereas BM- MOs, BM- iMOs, and SP- MOs presented high similarity of DEGs, SP- MODCs distinguished by showing a greater number of DEGs. Moreover, functional analysis identified an enrichment in canonical pathways, such as DC maturation, neuroinflammation, and IFN signaling. Upstream regulator analysis identified IFNγ as the potential upstream molecule that can explain the observed DEMs- Target DEGs intersections in SP- MODCs. Finally, directed target analysis and in vivo/ex vivo assays indicate that SP- MODCs differentiate in the SP and IFNγ is a main driver of this process.Graphical AbstractInteractome analysis between miRNAs and their target genes in IFNγ- mediated differentiation of splenic MODCs during Plasmodium infection.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/162711/1/jlb10625-sup-0002-TableS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162711/6/jlb10625-sup-0001-FigureS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162711/5/jlb10625.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162711/4/jlb10625_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162711/3/jlb10625-sup-0004-TableS3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162711/2/jlb10625-sup-0003-TableS2.pd

Caspase-8 mediates inflammation and disease in rodent malaria

Earlier studies indicate that either the canonical or non-canonical pathways of inflammasome activation have a limited role on malaria pathogenesis. Here, we report that caspase-8 is a central mediator of systemic inflammation, septic shock in the Plasmodium chabaudi-infected mice and the P. berghei-induced experimental cerebral malaria (ECM). Importantly, our results indicate that the combined deficiencies of caspases-8/1/11 or caspase-8/gasdermin-D (GSDM-D) renders mice impaired to produce both TNFalpha and IL-1beta and highly resistant to lethality in these models, disclosing a complementary, but independent role of caspase-8 and caspases-1/11/GSDM-D in the pathogenesis of malaria. Further, we find that monocytes from malaria patients express active caspases-1, -4 and -8 suggesting that these inflammatory caspases may also play a role in the pathogenesis of human disease

Evaluation of pre-processing on the meta-analysis of DNA methylation data from the Illumina HumanMethylation450 BeadChip platform

INTRODUCTION: Meta-analysis is a powerful means for leveraging the hundreds of experiments being run worldwide into more statistically powerful analyses. This is also true for the analysis of omic data, including genome-wide DNA methylation. In particular, thousands of DNA methylation profiles generated using the Illumina 450k are stored in the publicly accessible Gene Expression Omnibus (GEO) repository. Often, however, the intensity values produced by the BeadChip (raw data) are not deposited, therefore only pre-processed values -obtained after computational manipulation- are available. Pre-processing is possibly different among studies and may then affect meta-analysis by introducing non-biological sources of variability. MATERIAL AND METHODS: To systematically investigate the effect of pre-processing on meta-analysis, we analysed four different collections of DNA methylation samples (datasets), each composed of two subsets, for which raw data from controls (i.e. healthy subjects) and cases (i.e. patients) are available. We pre-processed the data from each dataset with nine among the most common pipelines found in literature. Moreover, we evaluated the performance of regRCPqn, a modification of the RCP algorithm that aims to improve data consistency. For each combination of pre-processing (9 x 9), we first evaluated the between-sample variability among control subjects and, then, we identified genomic positions that are differentially methylated between cases and controls (differential analysis). RESULTS AND CONCLUSION: The pre-processing of DNA methylation data affects both the between-sample variability and the loci identified as differentially methylated, and the effects of pre-processing are strongly dataset-dependent. By contrast, application of our renormalization algorithm regRCPqn: (i) reduces variability and (ii) increases agreement between meta-analysed datasets, both critical components of data harmonization

regRCPqn

Meta-analysis is a powerful means for leveraging the hundreds of experiments being run worldwide into more statistically powerful analyses. This is also true for the analysis of omic data, including genome-wide DNA methylation. In particular, thousands of DNA methylation profiles generated using the Illumina 450k are stored in the publicly accessible Gene Expression Omnibus (GEO) repository. Often, however, the intensity values produced by the BeadChip (raw data) are not deposited, therefore only pre-processed values -obtained after computational manipulation- are available. Pre-processing is possibly different among studies and may then affect meta-analysis by introducing non-biological sources of variability. To systematically investigate the effect of pre-processing on meta-analysis, we analysed four different collections of DNA methylation samples (datasets), each composed of two subsets, for which raw data from controls (i.e. healthy subjects) and cases (i.e. patients) are available. We pre-processed the data from each dataset with nine among the most common pipelines found in literature. Moreover, we evaluated the performance of regRCPqn, a modification of the RCP algorithm that aims to improve data consistency. For each combination of pre-processing (9 7 9), we first evaluated the between-sample variability among control subjects and, then, we identified genomic positions that are differentially methylated between cases and controls (differential analysis). The pre-processing of DNA methylation data affects both the between-sample variability and the loci identified as differentially methylated, and the effects of pre-processing are strongly dataset-dependent. By contrast, application of our renormalization algorithm regRCPqn: (i) reduces variability and (ii) increases agreement between meta-analysed datasets, both critical components of data harmonization

Association of Genetic Variants with Self-Assessed Color Categories in Brazilians

<div><p>The Brazilian population was formed by extensive admixture of three different ancestral roots: Amerindians, Europeans and Africans. Our previous work has shown that at an individual level, ancestry, as estimated using molecular markers, was a poor predictor of color in Brazilians. We now investigate if SNPs known to be associated with human skin pigmentation can be used to predict color in Brazilians. For that, we studied the association of fifteen SNPs, previously known to be linked with skin color, in 243 unrelated Brazilian individuals self-identified as White, Browns or Blacks from Rio de Janeiro and 212 unrelated Brazilian individuals self-identified as White or Blacks from São Paulo. The significance of association of SNP genotypes with self-assessed color was evaluated using partial regression analysis. After controlling for ancestry estimates as covariates, only four SNPs remained significantly associated with skin pigmentation: rs1426654 and rs2555364 within <i>SLC24A5</i>, rs16891982 at <i>SLC45A2</i> and rs1042602 at <i>TYR</i>. These loci are known to be involved in melanin synthesis or transport of melanosomes. We found that neither genotypes of these SNPs, nor their combination with biogeographical ancestry in principal component analysis, could predict self-assessed color in Brazilians at an individual level. However, significant correlations did emerge at group level, demonstrating that even though elements other than skin, eye and hair pigmentation do influence self-assessed color in Brazilians, the sociological act of self-classification is still substantially dependent of genotype at these four SNPs.</p></div

Where are we in the implementation of tissue-specific epigenetic clocks?

Introduction: DNA methylation clocks presents advantageous characteristics with respect to the ambitious goal of identifying very early markers of disease, based on the concept that accelerated ageing is a reliable predictor in this sense.Methods: Such tools, being epigenomic based, are expected to be conditioned by sex and tissue specificities, and this work is about quantifying this dependency as well as that from the regression model and the size of the training set.Results: Our quantitative results indicate that elastic-net penalization is the best performing strategy, and better so when—unsurprisingly—the data set is bigger; sex does not appear to condition clocks performances and tissue specific clocks appear to perform better than generic blood clocks. Finally, when considering all trained clocks, we identified a subset of genes that, to the best of our knowledge, have not been presented yet and might deserve further investigation: CPT1A, MMP15, SHROOM3, SLIT3, and SYNGR.Conclusion: These factual starting points can be useful for the future medical translation of clocks and in particular in the debate between multi-tissue clocks, generally trained on a large majority of blood samples, and tissue-specific clocks