A benchmark for microRNA quantification algorithms using the OpenArray platform

miRcompData R package source. The source code for the miRcompData R package, also available at: http://bioconductor.org/packages/miRcompData/ . (GZ 8765 kb

EXTRACELLULAR VESICLES AND MICRORNA IN BIOFLUIDS, CELL CULTURE AND PRIMARY CELLS IN HEALTH AND HIV-1 AND SIV INFECTIONS

Extracellular vesicle (EV) research is a rapidly growing field, with renewed interest due in part to the discovery of the association of EVs with small extracellular RNAs (exRNA), in particular microRNAs. Roles of EVs and their RNA cargo in facilitating or fighting infection with viruses such as HIV-1 are likely but remain incompletely understood. To investigate one aspect through which EVs might play a role in infection, we first evaluated the EV and exRNA population of cervical-vaginal fluid in Asian macaques, initially in endometriosis and subsequently in animals with naturally suppressed SIV infections. Evaluating the miRNA cargo of EVs from infected animals relative to uninfected animals, we found that miR-186 was more abundant in the infected animals, suggesting it could be a potential restriction factor of SIV. We then used in vitro culture to establish the importance of EVs in HIV proliferation and maturation. We found that when EVs are removed from culture media, cell lines, either acutely or latently infected with HIV-1, experienced increased viral production. Virus produced by these cells was also more infectious than baseline. Restoration of cell-derived EVs to EV-depleted cell culture rescued virus production to normal levels. Finally, we investigated miRNA expression in different blood T-cell subsets of HIV-1 elite suppressors (ES), for comparison with those of healthy (i.e. uninfected) controls (HC) and HIV-1 chronic progressors (CP). EVs and cell-free exRNAs have also been collected from all donors. We found that several miRNA species were differentially regulated in T-cell types in ES compared with HC or CP, consistent with previous studies examining PBMCs. Interestingly, we also found that the miRNA profile of different classes of cells, i.e., Naïve, Central Memory or Effector Memory, clustered together irrespective of CD4+ or CD8+ phenotype in HC. These data taken together demonstrate the importance of EVs and their cargo in the context of retroviral infection and set the stage for future studies to further elucidate the complex relationship between HIV-1, miRNA and EVs

Examining epigenetic variation in the brain in mental illness

Mental health represents one of the most significant and increasing burdens to global public health. Depression and schizophrenia, among other mental illnesses, constitute strong risk factors for suicidality which results in over 800,000 deaths every year. The majority of suicides worldwide are indeed related to psychiatric diseases. A growing body of genetic, epigenetic and epidemiological evidence suggests that psychiatric disorders are highly complex phenotypes originating from the multilevel interplay between the strong genetic component and a range of environmental and psychosocial factors. Deeper understanding about the biology of the genome has led to increased interest for the role of non-sequence-based variation in the etiology of neuropsychiatric phenotypes, including suicidality. Epigenetic alterations and gene expression dysregulation have been repetitively reported in post-mortem brain of individuals who died by suicide. To date, however, studies characterizing disease-associated methylomic and transcriptomic variation in the brain have been limited by screening performed in bulk tissue and by the assessment of a single marker at a time. The main aim of this thesis was to investigate DNA methylation and miRNA expression differences in post-mortem brain associated with suicidality and unravel the complexity of epigenetic signals in a heterogeneous tissue like the human brain by developing a method to profile genomic variation at the resolution of individual neural cell types. The results here reported, provide further support for a suicide-specific epigenetic signature, independent from comorbidity with other psychiatric phenotypes, as well as confirming the strong bias perpetrated by bulk tissue studies hence the need to examine genomic variations in purified cell types. In summary, this thesis has identified a) a suicide-specific signal in two different epigenetic markers (DNA methylation and miRNA expression) and b) a protocol to simultaneously profile DNA methylation levels across three purified cell types in the healthy brain highlighting the utility of cell sorting for identifying cell type-driven epigenetic differences associated with etiological variation in complex psychiatric phenotypes.1) ARUK-PPG2018A-010 – “Developing approaches to address neural cell heterogeneity in genomic studies of Alzheimer's disease”. 2) SBF001\1011 - “Using functional epigenomics to dissect the molecular architecture of schizophrenia