# Novel microfluidic platform to profile host-pathogen interaction under controlled infection and single cell resolution

> **NIH NIH R21** · UNIVERSITY OF CHICAGO · 2020 · $197,738

## Abstract

Abstract
Much of human history has been dictated by the invisible force of pathogens and infections remain a leading
cause of ailment, mortality, and loss of food source or livelihood. In part, this is because our understanding of
infection is stymied by the significant variability that exists in patient/host response to infection due to the
patient’s unique genetic makeup, as well as the variability in pathogen genomes. This variability determines
susceptibility, duration of infection, treatment options, and often, future response to pathogens. Controlled tests
to understand the sources of these variabilities cannot be performed on humans due to ethical and practical
reasons. An in vitro model is therefore needed that will allow precise control/ tuning of different factors
influencing infection outcome. In this proposal, we aim to build a set of droplet microfluidic and molecular
biology tools that will allow us to address the issue of variability in infection outcome. Knowing the sources of
variability and their genetic underpinnings will help fight infection better, improve patient outcome, reduce cost
of care and formulate better treatment strategies in future.
We will use custom droplet microfluidics, time-lapse imaging and droplet sorting to: Aim 1: Encapsulate single
pathogen cell with single host cell in order to isolate, infect, and image their interaction over time in a
representative micro-environment recreated in drops. We will use human macrophage cells as host and
Candida albicans for pathogen, as model systems. Host and pathogen cells will be labelled with fluorescent
reporters. Fluorescence and cell morphology will be used to determine infection outcome; Aim 2: Use
microfluidics to sort infection droplets into two groups based on interaction outcome: Group A, where host cell
has successfully overcome pathogen, with pathogen cell undergoing lysis, and Group B, where the pathogen
persists resulting in the host cell’s death. We will perform bulk RNA-seq on each group to identify host genes
responsible for successful infection suppression in Group A and pathogen genes that likely cause increased
virulence in Group B; Aim 3: Build microfluidic and molecular biology tools to profile host-pathogen
transcriptomics at single-cell resolution to characterize infection outcome at systems level. The workflow is
customizable, modular, and collectively our proposed platform may be used to profile infection in other host
or pathogen species at superior control, statistical resolution (~105 host-pathogen pairs), and at low cost
(~$0.1/pair).

## Key facts

- **NIH application ID:** 9847943
- **Project number:** 5R21AI144417-02
- **Recipient organization:** UNIVERSITY OF CHICAGO
- **Principal Investigator:** Anindita Basu
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $197,738
- **Award type:** 5
- **Project period:** 2019-01-10 → 2020-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9847943

## Citation

> US National Institutes of Health, RePORTER application 9847943, Novel microfluidic platform to profile host-pathogen interaction under controlled infection and single cell resolution (5R21AI144417-02). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9847943. Licensed CC0.

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