Zaida Ramirez-Ortiz

Early Career Tenure-track Researcher, University of Massachusetts Medical School

4 active projects

ZGR_Introductory example of GWAS with type 2 diabetes phenotype

Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.

Scientific Questions Being Studied

Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.

Project Purpose(s)

  • Educational

Scientific Approaches

Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.

Anticipated Findings

Not applicable - this workspace is intended to be an introductory example of how to do a genome-wide association study on the All of Us genomic data that individuals can easily click through and understand.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Zaida Ramirez-Ortiz - Early Career Tenure-track Researcher, University of Massachusetts Medical School

Exploring Hypertension data types

not applicable- this workspace is intended for educational purpose at the 2022 UBR Summit to learn how to use Researcher Workbench by analyzing a data type for hypertension

Scientific Questions Being Studied

not applicable- this workspace is intended for educational purpose at the 2022 UBR Summit to learn how to use Researcher Workbench by analyzing a data type for hypertension

Project Purpose(s)

  • Educational

Scientific Approaches

not applicable- this workspace is intended for educational purpose at the 2022 UBR Summit to learn how to use Researcher Workbench by analyzing a data type for hypertension

Anticipated Findings

not applicable- this workspace is intended for educational purpose at the 2022 UBR Summit to learn how to use Researcher Workbench by analyzing a data type for hypertension

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Registered Tier

Research Team

Owner:

  • Zaida Ramirez-Ortiz - Early Career Tenure-track Researcher, University of Massachusetts Medical School

ZGR-Duplicate of Quick Demo of Plots and Analyses

Not applicable - this workspace is intended to be an introductory example of how to easily click-through analyses for new users to the All of Us Researcher Workbench with whom this Notebook will be shared. This workspace is adapted from…

Scientific Questions Being Studied

Not applicable - this workspace is intended to be an introductory example of how to easily click-through analyses for new users to the All of Us Researcher Workbench with whom this Notebook will be shared. This workspace is adapted from the demo workspace "How to Get Started with the Registered Tier Data"

Project Purpose(s)

  • Educational
  • Methods Development

Scientific Approaches

Not applicable - this workspace is intended to be an introductory example of how to easily click-through analyses for new users to the All of Us Researcher Workbench with whom this Notebook will be shared. This workspace is adapted from the demo workspace "How to Get Started with the Registered Tier Data"

Anticipated Findings

Not applicable - this workspace is intended to be an introductory example of how to easily click-through analyses for new users to the All of Us Researcher Workbench with whom this Notebook will be shared. This workspace is adapted from the demo workspace "How to Get Started with the Registered Tier Data"

Demographic Categories of Interest

  • Race / Ethnicity
  • Access to Care
  • Education Level
  • Income Level

Data Set Used

Registered Tier

Research Team

Owner:

  • Zaida Ramirez-Ortiz - Early Career Tenure-track Researcher, University of Massachusetts Medical School

Role of SCARF1 in efferocytosis

Deficiency in the clearance of cellular debris is a major pathogenic factor in the emergence of autoimmune diseases. Our lab showed that mice deficient for scavenger receptor class F member 1 (SCARF1) develop a lupus-like autoimmune disease with symptoms like…

Scientific Questions Being Studied

Deficiency in the clearance of cellular debris is a major pathogenic factor in the emergence of autoimmune diseases. Our lab showed that mice deficient for scavenger receptor class F member 1 (SCARF1) develop a lupus-like autoimmune disease with symptoms like human lupus, including production of autoantibodies, skin inflammation & kidney disease, and pronounced accumulation of apoptotic cells with higher prevalence in the female population (Ramirez-Ortiz, 2014). Recently, we discovered the presence of SCARF1 autoantibodies in lupus patients, which was associated with dsDNA antibody positivity and defects in the removal of cellular debris (Jorge, 2022). The goal is to characterize the role of SCARF1 in efferocytosis & inflammation pathways. We hypothesize that SCARF1 is necessary for efferocytosis & modulates immune homeostasis via anti-inflammatory pathway. Elucidating this process will present new targets not only for lupus but for many autoimmune, metabolic, and infectious diseases.

Project Purpose(s)

  • Disease Focused Research (systemic lupus erythematosus)

Scientific Approaches

# 1: Define the SCARF1-mediated signaling mechanism in the inflammatory response.
To define the SCARF1 signaling pathway in healthy and SLE models (human), we will (1) analyze early response gene regulation mediated by SCARF1 using dataset available via All of Us; (2) identify the SCARF1 regulatory molecules that lead to a pro- vs. anti-inflammatory response using integrated gene expression analysis and protein interaction; & (3) determine the cell-specific role of SCARF1 in inflammation using cell biology & biochemistry assays.

# 2: Evaluate the role of autoantibodies & glycosylation patterns in SCARF1-mediated efferocytosis. We will investigate glycosylation of both SCARF1 auto-antibodies & SCARF1. We will use previously collected human patients or healthy controls to: (1) to determine the glycosylation patterns of anti-SCARF1autoantibodies using mass spec, (2) we will analyze data from All of Us to identify mutations in SCARF1 antibodies.

Anticipated Findings

# 1: We anticipate that activation of SCARF1 on dendritic cells induces the secretion of anti-inflammatory cytokines. Dysregulation of SCARF1 will lead to the production of proinflammatory cytokines. Understanding the cell-specific role of SCARF1 could lead to future therapeutics. Moreover, delineating an atlas of transcriptional networks that distinguish cellular populations in the context of SLE will provide an unprecedented window into the biology underlying this important inflammatory disease.

Aim 2: We expect that aberrant glycosylation is responsible for blocking efferocytosis. The data acquired from Aim 2 will provide insights into pathogenic autoantibodies. In addition, a more comprehensive understanding of SCARF1 autoantibodies may identify novel biomarkers. We propose, as an alternative, that anti-SCARF1 autoantibodies are binding to bridging proteins, such as the complement receptor C1q, and, therefore, inhibiting the identification of ACs for removal.

Demographic Categories of Interest

  • Race / Ethnicity
  • Sex at Birth
  • Gender Identity
  • Sexual Orientation
  • Geography
  • Disability Status
  • Access to Care
  • Education Level
  • Income Level

Data Set Used

Registered Tier

Research Team

Owner:

  • Zaida Ramirez-Ortiz - Early Career Tenure-track Researcher, University of Massachusetts Medical School
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