Schizophrenia is a disabling psychiatric and neurodevelopmental disorder that represents a tremendous public health burden. Despite the inroads made in the treatment of its symptoms, understanding its etiology and pathophysiology remains challenging due to the genetic heterogeneity of the disease and the corresponding complexity of the neural systems which it affects. In recent years, the development of next generation sequencing and substantial progress in the field of psychiatric genetics have revealed the important role of individually rare but collectively common heritable and de novo mutations (DNMs) in the complex genetic architecture of schizophrenia. Previously, we had identified SETD1A encoding a histone methyltransferase, as a high-risk gene for schizophrenia, which has been confirmed extensively through follow-up meta-analyses. This discovery emphasized the important role that neural gene regulation plays in the coordination of complex cognitive processes. However, it is unclear how to translate a ubiquitous molecular process such as chromatin modification into a mechanistic and disease-specific insight. Our previous comprehensive analysis of mutant mice carrying a loss of function (LoF) allele in the Setd1a orthologue uncovered the role of SETD1A in gene regulation, neuronal architecture, synaptic plasticity, neuronal ensemble activity and cognitive function and showed that neurocognitive deficits that derive from Setd1a deficiency can be reversed by pharmacological interventions during adulthood. Our previous ChIP-Seq analysis showed a striking overlap between SETD1A, MEF2, and LSD1 targets at enhancers in the prefrontal cortex (PFC). Since MEF2 is an activity dependent transcription factor, we hypothesized that SETD1A may also modulate activity-dependent gene expression in the brain. To elucidate the effects of Setd1a deficiency on activity-dependent transcription, we established an in vitro neuronal activity dependent gene (ADG) expression assay and identified genes modulated by neuronal activity using ChIP-Seq and RNA-Seq assays. We found a remarkable overlap of a dynamic pattern of activity-dependent recruitment of SETD1A, LSD1 and MEF2 to enhancers of ADGs. Our results showed Setd1a deficiency affects transcription in an activity-dependent manner and transcriptional alteration induced by Setd1a deficiency under neuronal activation can be attenuated by inhibition of LSD1 activity. In addition, we investigated how SETD1A modulates MEF2 transactivation activity by performing luciferase assays. Our results suggest that SETD1A represses MEF2 activity but the repression is unlikely to be mediated by lysine methylation. We also performed behavioral analyses of Setd1a+/- mice and found that the social behavior and social memory were impaired in female Setd1a+/- mice but remained intact in male Setd1a+/- mice. Ultimately, future work is underway to analyze the targets of SETD1A, which in turn could lead to the development of therapeutic strategies to reverse the progression of schizophrenia.

Acute leukemias are the main type of malignancy affecting children. They are defined by their precursor cell lineage: myeloid lineage for acute myeloid leukemia (AML) and lymphoid lineage for acute lymphoblastic leukemia (ALL). In this thesis, we use systems biology approaches to characterize transcription factor (TF) programs that define novel AML subtypes. We combine this approach with machine learning methods to group patients sharing similar TF programs and risk-stratify them. We identify a 9-cluster solution with statistically significant survival differences ranging from 84% for the best group to 41% for the worst. Each of the clusters is composed of patients with various cytogenetic aberrations that would not necessarily have been classified together. We identify top aberrantly activated TFs and potential master regulators or drug targets in each cluster. We also propose a novel stratification for FLT3-ITD patients with no other cytogenetic abnormalities. These patients are currently all classified as high-risk; however, we find a low-risk subtype and identify a TF signature that is predictive of risk in this subtype. Finally, we develop a binary classifier that is able to stratify the patients into two risk groups. We find that the activity of a large cluster of HOXA TFs is highly correlated with poor prognosis. In the second part, we characterize some mechanisms of relapse in B-ALL at a single-cell resolution focusing again on the patterns of activation and deactivation of TF activity in the course of the disease in matched trios of samples (diagnosis, remission and relapse). After a discussion on some of the technical aspects of differentiating normal cells and leukemic cells at a single-cell RNA sequencing resolution, we perform computational pseudo-lineage reconstruction based on groups of TFs whose activities rise and fall together through pseudotime. We find that each patient has unique mechanisms at the earliest pseudotimes but they seem to converge at the later pseudotimes into signatures in which the B-cell identity (in the case of B-ALL) gradually fades away. We also identify small populations of cells isolated at diagnosis in the later pseudotimes which is consistent with the view that many of the persistent cells in ALL pre-exist the malignancy and are selected by the treatment. This novel systems biology approach for characterizing clinical outcome in patients and defining lineage reconstruction identifies biochemical mechanisms and signaling pathways that are responsible for the development and maintenance of the malignancy and identifies potential therapeutic targets. The results exposed in this thesis will lead to a better understanding of some of the inner workings of pediatric acute leukemias and may lead to the development of improved targeted therapies.

The audiological characteristics of the Monge family of Costa Rica were investigated in a sample of fifty-two affected members and twelve unaffected members. Through laboratory analysis by staff personnel from the University of Costa Rica and audiological test results obtained in the present investigation, it was concluded that affected Monge members demonstrate a slowly progressive low frequency sensorineural hearing loss of autosomal dominant transmission. The initial site of lesion appears to be the apical portion of the cochlea, with significant onset occurring during early childhood following normal speech and language acquisition. The rate at which the hearing loss progresses and the frequency regions affected are contingent upon chronological age, culminating in a flat profound hearing impairment by age thirty for all affected members.

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