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The Sobreira lab is committed to researching human gene regulation in complex diseases.Through a wide range of cutting-edge technologies and systems and a Variants-to-Function (V2F) aproach, our primary focus is transforming GWAS-identified genetic susceptibility regions linked to metabolic diseases and traits into their functional roles.

Identification and functional characterization to interpret regulatory variations

Genome-wide association studies (GWAS) have made significant strides in uncovering genetic signals linked to various human traits and conditions. However, they often face challenges in pinpointing the specific genes responsible for these traits, particularly in noncoding regions.

To tackle this challenge, the Sobreira lab has developed a dedicated infrastructure for variant-to-gene (V2F) mapping. This innovative approach harnesses the power of 3D genomics, single-cell epigenomic mapping, and gene expression data, spanning a variety of human tissues and cell lines.

In our ongoing research, we are committed to refining the annotation and identification of genetic variants. Our aim is to enhance our ability to translate GWAS signals associated with metabolic diseases into actionable biological mechanisms.

Tools for decoding regulatory variation

Our primary focus is on developing and applying high-throughput tools to convert GWAS-identified genetic risk locations linked to metabolic diseases and traits into functional insights, a process known as "Variants-to-Function" (V2F).

Our approach combines both computational and experimental methods, aiming to address several key questions:

  • Identifying the causal variant.

  • Pinpointing which gene regulators are affected by the variant.

  • Determining the downstream target gene(s).

  • Identifying the relevant tissue and cell types.

  • Uncovering the cellular and organismal pathways and functions influenced by the variant.

We have implemented various strategies, such as CRISPR perturbation in mouse models, cell lines, and human iPSC-derived cells like adipocytes and neurons. These approaches allow us to directly examine noncoding variants, and we employ database analysis strategies for this purpose. Additionally, we employ the Massively Parallel Reporter Assay (MPRA) to understand how variants impact the functionality of regulatory regions and gene pathways. Our work is also expanding to explore variations in regions that alter transcription or RNA stability.

Dissecting the impact of allelic heterogeneity and epistasis within a locus

In the Sobreira lab, we emphasize the significance of conducting functional experiments when identifying genomic regions linked to diseases. We're using a specific set of genes to explore how various regulatory regions interact and impact gene expression within a genomic locus over time and space. Our main objective is to thoroughly investigate these regulatory elements, gaining deeper insights into how different signals from various regulatory regions collaborate to govern gene expression.

In cases where multiple variants contribute to causality, we apply a combinatorial CRISPR/Cas9 editing approach. This technique involves sequentially editing the same cells to differentiate between epistatic and additive effects. Additionally, we tailor a suite of molecular genetics, in vivo, and in vitro methods to match the specific phenotype and alleles within a given genomic locus. Our research revolves around addressing three essential questions:

  • Are there any indications of variants outside of GWAS associations, potentially with different frequencies, that could also influence gene regulation?

  • Do variants in different enhancers work together to control gene expression?

  • How do combinations of variants within the same or different haplotypes contribute to increased disease risk?

Ultimately, our project aims to develop assays and strategies that advance our understanding of complex metabolic networks and gene regulation.

Generation of molecular and cellular profiles in human
iPSC-derived neurons and adipocytes

Metabolic disorders involve complex interactions among different cell types, and understanding their roles is crucial for effective treatments. Human hypothalamic neurons and adipose tissue cells play essential roles in metabolic regulation, influencing processes like lipid metabolism, appetite control, and energy intake. However, studying human hypothalamic cells directly poses challenges, and obtaining sufficient functional mesenchymal stem cells (MSCs) from adult tissues is often limited.

To overcome these hurdles, the Sobreira lab leverages induced pluripotent stem cell (iPSC) technology to generate hypothalamic neurons and adipocytes. These iPSC-derived cells provide a valuable resource for research.

The Sobreira lab also focuses on characterizing changes in the gene regulatory landscape during the differentiation of hypothalamic and adipocyte cells. By conducting this analysis in a diverse group of over 100 individuals with well-documented genetic profiles, they can integrate this data with GWAS loci associated with various traits and diseases, particularly those with a strong hereditary component in these cell types. This approach allows them to identify potential effector genes and regulatory regions that may control gene expression, shedding light on the molecular mechanisms underlying metabolic disorders.

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