Gene regulation of the immune response to cancer

BAVA Alessio

Alessio Bava Team Leader Tel:

We are a research laboratory in the fields of Molecular Biology and Cancer Immunology. We develop and apply advanced technologies to address 4 main questions.

1. Why is the immune system unable to eradicate cancer cells?

Recent progress in immunotherapy shows that our immune system has the potential to fight many types of cancer successfully. We would like to understand why, without our intervention, it is unable to do so.

2. How does cancer evade the immune system?

Cancer cells have the extraordinary ability to adapt to new environments quickly, which includes surviving to any kind of attack from the immune system. We are interested in studying the underlying mechanisms, and to which extent this is an active vs a passive process

3. How is gene expression affected by cancer-immune cells interaction?

When immune and cancer cells interact, their gene expression programs are rewired. We aim at elucidating the mechanisms of gene regulation that lead to functional changes both in cancer and immune cells.

4. How can we modulate gene expression to restore/achieve effective immune response to cancer cells?

Our final goal is to find ways to restore the correct gene regulation programs in immune cells, to enhance their function and eradicate cancer cells.

To address these questions we develop, implement and apply the following technologies:

Multiplexed Imaging
Here the goal is to add spatial resolution to cytometry-data in order to understand, in a tissue, WHERE immune and cancer cells interact
We design, develop and apply methods for multiplexed visualization of protein and RNA molecules in tissue sections.
To characterize the tissue architecture associated to dysfunctional states of the immune system in cancer settings, we make use of both confocal fluorescent microscopy and multiplexed secondary ion beam imaging.
We make use of barcoding systems that enable multi-parametric fluorescent imaging of proteins and RNAs.
We make use of NanoSIMs machine for multiplexed high-resolution imaging of intracellular structures.

Multiplexed 3D visualization od the indicated RNAs in mouse visual cortex
Multiplexed 3D visualization od the indicated RNAs in mouse visual cortex

Multiplexed Cytometry
Here the goal is to understand HOW immune and cancer cells interact.
We make use of both flow-cytometry and mass-cytometry.
To define the phenotype and function of specific cellular populations involved in the cross-talk between cancer and immune cells we make use of both flow-cytometry and mass-cytometry.
We make use of fluorescently-labeled antibodies and FACS machines to sort specific cellular populations.
We make use of mass-cytometry to perform multi-dimensional analysis of up to 40-45 parameters in millions of single cells. For details on mass-cytometry please read here  https://www.ncbi.nlm.nih.gov/pubmed/27153492
For analysis, we benefit from the multiple pipelines that Prof. Nolan’s laboratory at Stanford University has developed over the years.

Single-cell resolution map of cytokine induction in human PBMCs. (a) viSNE maps based on cell-surface marker expression. (b) selected protein markers and (c) eight cytokine transcripts, overlaid and color-coded by expression level. From Frei et al., 2016
Single-cell resolution map of cytokine induction in human PBMCs. (a) viSNE maps based on cell-surface marker expression. (b) selected protein markers and (c) eight cytokine transcripts, overlaid and color-coded by expression level. From Frei et al., 2016

Sequencing
Here the goal is to understand WHICH molecules are responsible for the immune-system inability to eradicate cancer cells
We perform RNA-sequencing experiments in sorted populations or single cells.
To understand how gene expression is regulated in immune and cancer cells during their interaction, we perform sequencing experiments in multiple experimental conditions.
We develop protocols for new sequencing approaches, in order to derive mechanisms of gene-regulation at multiple levels such as: DNA structure, chromatin states and RNA expression.
We develop novel barcoding methods to increase the resolution of conventional sequencing settings.

Proximity Ligation AssaY for RNA (PLAYR). The main steps of the PLAYR protocol for simultaneous detection of proteins and RNAs in single cells. From Frei et al., 2016
Proximity Ligation AssaY for RNA (PLAYR). The main steps of the PLAYR protocol for simultaneous detection of proteins and RNAs in single cells. From Frei et al., 2016

Key publications

Year of publication 2018

Wang X, Allen WE, Wright MA, Sylwestrak EL, Samusik N, Vesuna S, Evans K, Liu C, Ramakrishnan C, Liu J, Nolan GP*, Bava FA*, Deisseroth K*. *co-last, co-corresponding author (2018 Jul 27)

Three-dimensional intact-tissue sequencing of single-cell transcriptional states.

Science (New York, N.Y.) : DOI : eaat5691
All publications