# A novel approach for deep phenotyping the CD4 T cell response to Mycobacterium Tuberculosis

> **NIH NIH R21** · TRANSLATIONAL GENOMICS RESEARCH INST · 2020 · $255,206

## Abstract

PROJECT SUMMARY
Mycobacterium tuberculosis (Mtb) caused 1.3 million global deaths in 2017, yet an effective vaccine remains
elusive. A major challenge in the field has been selecting which Mtb antigens (from among >4000 proteins) to
include in a vaccine, and what T cell functions it should aim to elicit. Previous attempts to define protective
immunity against Mtb have shown mixed success and have focused on diversity in one dimension at a time –
eg using proteins / lyates to identify diverse CD4 T cell states (eg cytokine polyfunctionality), or defining
cytokine production in response to diverse peptides predicted to bind human leukocyte antigens (HLAs). We
hypothesize that deep, simultaneous analysis of both T cell specificity and phenotype will: (i) reveal an
interdependence between these 2 dimensions of the anti-Mtb response that is not currently well-understood,
and (ii) enable, in future studies, improved correlates of protection against disease that can empower vaccine
studies and inform treatment strategies. To achieve this new `deep-2D' view of the response, we propose to
integrate 2 novel technologies: (i) a platform we recently developed for experimentally screening the Mtb
proteome for peptides that bind diverse HLA class II proteins (`PepSeq'), and (ii) single cell sequencing,
enabling linked analysis of transcriptome and peptide:HLA binding within thousands of T cells. If successful,
this project would establish a rationale and toolkit for `deep-2D' analysis of the T cell response to Mtb that we
could subsequently apply to larger cohorts designed to reveal correlates of disease protection in both natural
history and vaccine settings. The approach would also be directly applicable to other complex pathogens.

## Key facts

- **NIH application ID:** 9875632
- **Project number:** 1R21AI149311-01
- **Recipient organization:** TRANSLATIONAL GENOMICS RESEARCH INST
- **Principal Investigator:** John Altin
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $255,206
- **Award type:** 1
- **Project period:** 2020-02-18 → 2022-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9875632

## Citation

> US National Institutes of Health, RePORTER application 9875632, A novel approach for deep phenotyping the CD4 T cell response to Mycobacterium Tuberculosis (1R21AI149311-01). Retrieved via AI Analytics 2026-05-21 from https://api.ai-analytics.org/grant/nih/9875632. Licensed CC0.

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