Publications by authors named "Sheila N Lopez Acevedo"

Article Synopsis
  • The study focuses on how antibodies are characterized using B cells and highlights the challenges with analyzing plasma cells due to their lack of surface B cell receptors (BCRs).
  • Researchers explored the antibody repertoires from bone marrow and spleen in a mouse model, overcoming technical limitations to include plasma cells in their analysis.
  • Results showed that spleen B cells produced higher affinity antibodies than bone marrow plasma cells, with evidence of shared origins for some antibody clones between the two lymphoid tissues.
View Article and Find Full Text PDF

Adoptive immune therapies based on the transfer of antigen-specific T cells have been used successfully to treat various cancers and viral infections, but improved techniques are needed to identify optimally protective human T cell receptors (TCRs). Here we present a high-throughput approach to the identification of natively paired human TCRα and TCRβ (TCRα:β) genes encoding heterodimeric TCRs that recognize specific peptide antigens bound to major histocompatibility complex molecules (pMHCs). We first captured and cloned TCRα:β genes from individual cells, ensuring fidelity using a suppression PCR.

View Article and Find Full Text PDF
Article Synopsis
  • Continuous emergence of SARS-CoV-2 variants poses challenges for vaccine effectiveness, diagnostics, and treatments, raising concerns about a potential new highly transmissible and fatal betacoronavirus.
  • The study utilized yeast display technology and next-generation sequencing to analyze the specificity of antibodies from two convalescent donors, focusing on their responses to SARS-CoV-2 variants and other betacoronaviruses.
  • Most antibodies from the patients were found to be non-neutralizing, and the degree of somatic hypermutation varied significantly between the individuals, providing insights that could inform strategies against emerging coronavirus threats.
View Article and Find Full Text PDF

New approaches in high-throughput analysis of immune receptor repertoires are enabling major advances in immunology and for the discovery of precision immunotherapeutics. Commensurate with growth of the field, there has been an increased need for the establishment of techniques for quality control of immune receptor data. Our laboratory has standardized the use of multiple quality control techniques in immunoglobulin (IG) and T-cell receptor (TR) sequencing experiments to ensure quality control throughout diverse experimental conditions.

View Article and Find Full Text PDF
Article Synopsis
  • The COVID-19 pandemic has led to the emergence of multiple SARS-CoV-2 variants that show increased resistance to vaccines and treatments, prompting the need for better tools to study these variants.
  • Researchers developed biotin-labeled molecular probes targeting different parts of the SARS-CoV-2 spike protein to help isolate neutralizing antibodies and monitor vaccine effectiveness.
  • The study provides a collection of these probes, which can identify immune responses and aid in the characterization of neutralizing antibodies, with constructs made available for wider research use.
View Article and Find Full Text PDF

Functional analyses of the T cell receptor (TCR) landscape can reveal critical information about protection from disease and molecular responses to vaccines. However, it has proven difficult to combine advanced next-generation sequencing technologies with methods to decode the peptide-major histocompatibility complex (pMHC) specificity of individual TCRs. We developed a new high-throughput approach to enable repertoire-scale functional evaluations of natively paired TCRs.

View Article and Find Full Text PDF
Article Synopsis
  • The COVID-19 pandemic has led to the evolution of SARS-CoV-2, resulting in various variants that can resist vaccines and treatments, particularly due to mutations in the virus's spike protein.
  • The researchers designed biotin-labeled molecular probes for these spike variants, allowing for easier isolation of neutralizing antibodies and assessment of vaccine effectiveness.
  • They validated these probes with yeast displaying virus-binding antibodies and made their findings available through Addgene to help further research on immune responses and antibody characterization against COVID-19 variants.
View Article and Find Full Text PDF
Article Synopsis
  • Antiviral monoclonal antibody (mAb) discovery aims to develop effective treatments for viral infections, but traditional methods are often inefficient due to the high affinity of antibodies not always translating to neutralizing activity.
  • Researchers explored screening for anti-SARS-CoV-2 mAbs at lower pH levels, specifically pH 4.5, and found that neutralizing antibodies were more effectively enriched at this acidity compared to physiological pH (7.4).
  • A new antibody, LP5, was identified that targets a key area of the SARS-CoV-2 virus, demonstrating the potential of low pH screening to enhance the discovery of effective antiviral antibodies.
View Article and Find Full Text PDF

Understanding mechanisms of protective antibody recognition can inform vaccine and therapeutic strategies against SARS-CoV-2. We report a monoclonal antibody, 910-30, targeting the SARS-CoV-2 receptor-binding site for ACE2 as a member of a public antibody response encoded by IGHV3-53/IGHV3-66 genes. Sequence and structural analyses of 910-30 and related antibodies explore how class recognition features correlate with SARS-CoV-2 neutralization.

View Article and Find Full Text PDF
Article Synopsis
  • A new antibody, 910-30, has been identified that targets the SARS-CoV-2 ACE2 receptor binding site, part of a public antibody response encoded by specific IGHV genes.
  • Structural analyses via Cryo-EM show how 910-30 interacts with the SARS-CoV-2 spike trimer, revealing its ability to bind and disassemble the spike protein.
  • The study highlights important sequence and structural signatures for neutralization in the IGHV3-53/3-66 antibody class, with a notable prevalence of antibody precursors found in healthy human B cells.
View Article and Find Full Text PDF

Biotin-labeled molecular probes, comprising specific regions of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike, would be helpful in the isolation and characterization of antibodies targeting this recently emerged pathogen. Here, we design constructs incorporating an N-terminal purification tag, a site-specific protease-cleavage site, the probe region of interest, and a C-terminal sequence targeted by biotin ligase. Probe regions include full-length spike ectodomain as well as various subregions, and we also design mutants that eliminate recognition of the angiotensin-converting enzyme 2 (ACE2) receptor.

View Article and Find Full Text PDF
Article Synopsis
  • - Researchers developed biotin-labeled molecular probes from regions of the SARS-CoV-2 spike protein to help isolate and study antibodies against the virus.
  • - The design involved using a purification tag and a targeted protease-cleavage site, yielding different amounts of biotin-labeled probes, with specific structures confirmed through cryo-electron microscopy.
  • - Funding for the project came from multiple sources, including the National Institute of Allergy and Infectious Diseases and various grants, while no conflicts of interest were reported by the authors.
View Article and Find Full Text PDF
Article Synopsis
  • Researchers created biotin-labeled molecular probes targeting specific regions of the SARS-CoV-2 spike protein to help isolate and study antibodies against the virus.
  • These probes included various designs, such as full-length spike regions and modifications to prevent ACE2 receptor recognition, yielding different amounts during production.
  • The resulting probes were tested for their ability to bind antibodies and were structurally analyzed using advanced imaging techniques, showcasing the effectiveness of combining structural design with purification methods.
View Article and Find Full Text PDF

Emulsion-based techniques have dramatically advanced our understanding of single-cell biology and complex single-cell features over the past two decades. Most approaches for precise single cell isolation rely on microfluidics, which has proven highly effective but requires substantial investment in equipment and expertise that can be difficult to access for researchers that specialize in other areas of bioengineering and molecular biotechnology. Inspired by the robust droplet generation technologies in modern flow cytometry instrumentation, here we established a new platform for high-throughput isolation of single cells within droplets of tunable sizes by combining flow focusing with ultrasonic vibration for rapid and effective droplet formation.

View Article and Find Full Text PDF