Implementation of a qPCR-based assay for the quantification of SARS-CoV-2-specific T cells in immunocompromised patients

NIH Pandemic-Era Grants

Pandemic Era Grants

2024

Document text

Principal Investigator: Ernesto  Guccione
Organization: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
Fiscal Year: 2024
Award: $350,358
Funding agency: National Cancer Institute

SUMMARY
 Long-term protection from viral infections is mediated by both the humoral and cellular immune pathways.
Multiple Myeloma (MM) is the second most common hematological malignancy in the US and is characterized
by clonal plasma cell production, resulting in immune suppression and recurrent bacterial and viral infections.
 SARS-CoV-2-specific antibody quantification are currently being used as clinical endpoints to determine
immune protection against COVID-19, and this information is even more relevant in immunocompromised
individuals who lack a humoral response, but are protected by the cellular immunity (i.e. MM patients).
 Despite the urgent need to quantify cellular immunity, the complexity and lack of scalability of traditional
methods (e.g. ELISpot, flow cytometry) to detect antigen-specific T cells has so far prevented large scale studies.
 To address this problem, we developed a direct qPCR-based rapid T cell activation (dqTACT) assay based
on ex vivo stimulation of whole blood samples with a pool of viral peptides (i.e.immunodominant peptides
covering SARS-CoV-2 Spike protein),
SARS-CoV-2 antigen-specific T cells, and CXCL10,
followed by direct amplification of IFNG 𝛾 or IL2 which are produced by
 which is produced by monocytes and neutrophils in
,
response
to
T cell activation.
The overarching aim of this proposal is to develop and implement a qPCR method that can be used as a proxy
to measure the presence and functionality of antigen specific T cells in MM patients. Specifically, we hypothesize
that SARS-CoV-2 specific T cells might be a biomarker of previous infection and of efficacy of vaccination
strategies, complementary to quantification of the humoral response.
 In the UH2 phase, we will define analytical sensitivity and specificity and establish cut-off/thresholds and
appropriate positive and quality controls, accuracy and false result rate by comparing the dqTACT assay with
the gold standard assays such as flow cytometry and ELISpot for measuring cellular immune responses.
 In the UH3 phase, we will test the presence and persistence of cellular immunity to SARS-CoV-2 in
convalescent and vaccinated myeloma patients. Well annotated patient populations will be used to define
sensitivity, specificity, and thresholds with response to clinical end-points, such as presence and persistence of
humoral and cellular immunity to SARS-CoV-2. We will estimate the prevalence of the markers within vaccinated
myeloma patients. We will then extend our studies and use banked as well as fresh samples from our large
myeloma/immunocompromised population and healthy controls enrolled in IRB approved studies.
 The overarching goal is to use the dqTACT assay to test the presence of T cells due to natural infection or
vaccination in myeloma patients, possibly aiding in nationwide booster strategies or passive antibody infusion
support to protect these vulnerable population.
 Key deliverables an assay to rapidly quantify the functionality of T cellular immunity at scale.

Terms: <2019 novel corona virus><2019 novel coronavirus><2019-nCoV><2019-nCoV S protein><2019-nCoV spike glycoprotein><2019-nCoV spike protein><7S Gamma Globulin><Address><Aldesleukin Gene><Antibodies><Antibody Response><Assay><Bacterial Infections><Bioassay><Biological Assay><Biological Markers><Biotech><Biotechnology><Blood><Blood Neutrophil><Blood Plasma Cell><Blood Polymorphonuclear Neutrophil><Blood Reticuloendothelial System><Blood Sample><Blood monocyte><Blood specimen><Bypass><COVID assay><COVID complications><COVID related complications><COVID-19><COVID-19 S protein><COVID-19 antigen><COVID-19 assay><COVID-19 complications><COVID-19 immunity><COVID-19 infection><COVID-19 related complications><COVID-19 spike><COVID-19 spike glycoprotein><COVID-19 spike protein><COVID-19 vaccination><COVID-19 virus><COVID-19 virus infection><COVID19 assay><COVID19 infection><COVID19 virus><CRG-2><CV-19><CXCL10><CXCL10 gene><Cancer Patient><Cell Body><Cell Mediated Immunology><Cell-Mediated Immunity><Cells><Cellular Immunity><Clinical><CoV-2><CoV2><Cohort Studies><Concurrent Studies><Coronavirus Infectious Disease 2019><Data><Enrollment><Flow Cytofluorometries><Flow Cytofluorometry><Flow Cytometry><Flow Microfluorimetry><Flow Microfluorometry><Goals><Hematologic Cancer><Hematologic Malignancies><Hematologic Neoplasms><Hematological Malignancies><Hematological Neoplasms><Hematological Tumor><Hematology><Hematopoietic Cancer><Humoral Immunities><IFI10><IFN-Gamma><IFN-g><IFN-γ><IFNG><IFNγ><IL-2 Gene><IL2><IL2 gene><INP10><IP-10><IRB><IRBs><IgG><Immune><Immune Interferon><Immune response><Immunes><Immunity><Immunocompromised><Immunocompromised Host><Immunocompromised Patient><Immunoglobulin G><Immunological response><Immunosuppressed Host><Immunosuppression><Immunosuppression Effect><Immunosuppressive Effect><Individual><Infection><Infusion><Infusion procedures><Institutional Review Boards><Interferon Gamma><Interferon Type II><Interleukin 2 Precursor Gene><Interleukin-2 Gene><MOB-1><Malignant Cell><Malignant Hematologic Neoplasm><Marrow Neutrophil><Marrow monocyte><Measures><Mediating><Methods><Modeling><Monitor><Multiple Myeloma><Nature><Neutrophilic Granulocyte><Neutrophilic Leukocyte><Oncology><Oncology Cancer><Outcome><PBMC><Pathway interactions><Patients><Peptides><Peripheral Blood Mononuclear Cell><Phase><Physical distancing><Plasma Cells><Plasma-Cell Myeloma><Plasmacytes><Polymorphonuclear Cell><Polymorphonuclear Leukocytes><Polymorphonuclear Neutrophils><Population><Prevalence><Production><Proxy><Publishing><Quality Control><RNA purification><Recommendation><Recurrence><Recurrent><Reporting><SARS corona virus 2><SARS-CO-V2><SARS-COVID-2><SARS-CoV-2><SARS-CoV-2 S><SARS-CoV-2 S protein><SARS-CoV-2 antigen><SARS-CoV-2 assay><SARS-CoV-2 immunity><SARS-CoV-2 infection><SARS-CoV-2 spike><SARS-CoV-2 spike glycoprotein><SARS-CoV-2 spike protein><SARS-CoV-2 vaccination><SARS-CoV2><SARS-CoV2 infection><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><SCYB10><Sampling><Sensitivity and Specificity><Severe Acute Respiratory Coronavirus 2><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome coronavirus 2 S protein><Severe acute respiratory syndrome coronavirus 2 immunity><Severe acute respiratory syndrome coronavirus 2 infection><Severe acute respiratory syndrome coronavirus 2 spike glycoprotein><Severe acute respiratory syndrome coronavirus 2 spike protein><Severe acute respiratory syndrome coronavirus 2 vaccination><Severe acute respiratory syndrome related corona virus 2><Social Distance><Specificity><Steroid Compound><Steroids><T-Cell Activation><T-Cell Growth Factor Gene><T-Cells><T-Lymphocyte><TCGF Gene><Testing><Time><Vaccinated><Vaccination><Vaccinee><Vaccines><Validation><Viral><Viral Antibodies><Viral Diseases><Virus Diseases><Vulnerable Populations><Whole Blood><Work><Wuhan coronavirus><activate T cells><anti-viral antibody><antibody-based immunity><antigen based detection><antigen detection><antigen-specific T cells><bacteria infection><bacterial disease><bio-markers><biologic marker><biomarker><booster dose><booster shot><booster vaccine><cancer cell><chemotherapy><co-morbid><co-morbidity><cohort><comorbidity><complications due to COVID-19><coronavirus disease 2019><coronavirus disease 2019 S protein><coronavirus disease 2019 antigen><coronavirus disease 2019 assay><coronavirus disease 2019 immunity><coronavirus disease 2019 infection><coronavirus disease 2019 spike glycoprotein><coronavirus disease 2019 spike protein><coronavirus disease 2019 vaccination><coronavirus disease 2019 virus><coronavirus disease assay><coronavirus disease-19><coronavirus disease-19 virus><coronavirus infectious disease-19><detect antigen><elderly patient><enroll><flow cytophotometry><gIP-10><hCoV19><host response><hypogammaglobulinemia><immune suppression><immune suppressive activity><immune suppressive function><immune system response><immunity against COVID-19><immunity against SARS-CoV-2><immunity against Severe acute respiratory syndrome coronavirus 2><immunity against coronavirus disease 2019><immunity to COVID-19><immunity to SARS-CoV-2><immunity to Severe acute respiratory syndrome coronavirus 2><immunity to coronavirus disease 2019><immunization strategy><immunoresponse><immunosuppressed patient><immunosuppressive activity><immunosuppressive function><immunosuppressive response><infected with COVID-19><infected with COVID19><infected with SARS-CoV-2><infected with SARS-CoV2><infected with coronavirus disease 2019><infected with severe acute respiratory syndrome coronavirus 2><infusions><lFN-Gamma><monocyte><myeloma><myelomatosis><nCoV2><neutralizing antibody><neutrophil><older patient><passive antibodies><pathway><patient population><plasmocyte><prevent><preventing><prophylactic><response><severe acute respiratory syndrome coronavirus 2 antigen><severe acute respiratory syndrome coronavirus 2 assay><spike proteins on SARS-CoV-2><targeted drug therapy><targeted drug treatments><targeted therapeutic><targeted therapeutic agents><targeted therapy><targeted treatment><thymus derived lymphocyte><vaccinate against COVID-19><vaccinate against SARS-CoV-2><vaccinate against coronavirus disease 2019><vaccinate against severe acute respiratory syndrome coronavirus 2><vaccinated individual><vaccinated participant><vaccinated patient><vaccinated person><vaccinated subject><vaccination against COVID-19><vaccination against SARS-CoV-2><vaccination against Severe acute respiratory syndrome coronavirus 2><vaccination against coronavirus disease 2019><vaccination strategy><vaccine boost><validations><viral infection><virus infection><virus-induced disease><vulnerable group><vulnerable individual><vulnerable people>