The first neutrophil atlas

A complete, high resolution mapping of neutrophils has been generated – for the first time in humans - thanks to the close collaboration between basic and clinical researchers at IRCCS Ospedale San Raffaele.

Neutrophils are cells of the immune system with a crucial role in protecting the organism from infections. This atlas describes how neutrophils modify their gene expression profile under stress conditions like the ones triggered by diseases, such as pancreatic cancer and SARS-CoV2 infection, or during hematopoietic stem cell transplantation.

The results, published on the prestigious Nature Immunology journal, will enable the precise identification of the molecular mechanisms at the base of the development of human neutrophils and the ones responsible of their activation in physiological and pathological conditions, with important clinical implications.

The study was coordinated by Renato Ostuni, who leads the laboratory of Genomics of the innate immune system at the San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) and is associate professor at Vita-Salute San Raffaele University.


Neutrophils: what they are and what is their role in immunity

p3lab_coverostuni's Lab

Ostuni's Lab

Neutrophil granulocytes are the first fundamental line of body defense against infections. Their name derives from the fact that they carry granules loaded with toxic substances that are able to kill microbial pathogens when released. This and other processes – phagocytosis, production of free radicals and release of DNA webs – make neutrophils effective ‘killing machines’. However, the uncontrolled activation of these cells can cause tissue damage, inflammatory and autoimmune diseases.

Despite being highly abundant (up to the 70% of white blood cells), neutrophils live only for a few days in the blood before being substituted by cells produced in the bone marrow – one estimate indicates that adults generate a hundred billion new neutrophils each day. This recycling allows having at any time fresh, perfectly functioning neutrophils able to get rid of pathogens thus limiting potential tissue damages.


Why drawing a neutrophil atlas

As neutrophils have a short half-life, it has always been thought that they had a limited ability of adapting to the external environmental cues.

“In an article published on Nature Reviews Immunology in 2019, we hypothesized that these cells were not only able to sense cues from the microenvironment, but also that this local adaptation could allow neutrophils to support proper tissue homeostasis” Renato Ostuni specifies. “This hypothesis was confirmed by a study published on Cell in 2020 where we contributed to demonstrate that mouse neutrophils gain a gene expression and functional profile that are specific for the tissue where they reside”. The study just published extends these findings to humans.


Practical applications

“Having deciphered the gene network that guides neutrophil differentiation could allow us to develop gene and cell therapy approaches to enhance the production of such cells that are essential for immune responses. This is particularly relevant for immunodeficiencies like congenital neutropenias or chronic granulomatosis disease (CGD), where a defective neutrophil development makes patients vulnerable to bacterial infections”, says Ostuni.

Boosting the ability to produce neutrophils could also increase the safety of bone marrow transplantation, a procedure frequently used to treat blood disorders such as leukemias and that is also at the base of gene therapy protocols with hematopoietic stem cells. Indeed, following chemotherapy – a procedure which is needed to get rid of diseased cells and allow the engraftment of donor cells – patients undergoing transplantation are devoid of neutrophils and hence are particularly vulnerable to pathogen infections.

Another possible applications of the study is using neutrophils as diagnostic/prognostic biomarkers. Indeed, researchers have identified ‘molecular signatures’ that neutrophils acquire in patients with severe infections or during cancer progression, which could be used to follow in a timely manner disease development or help choosing the most effective therapy.


A multidisciplinary effort with cutting-edge technologies

This work employed cutting-edge technologies – including single cell RNA sequencing, in which the Ostuni’s team is among the maximum experts – that allowed defining the gene expression profile in more than one hundred thousand human neutrophils.

“This was an enormous effort because these cells die easily when put in culture, releasing enzymes that degrade RNA molecules. The technical complexity of analyzing neutrophils outside their natural environment is indeed one of the reasons why up to now the mechanisms regulating their transcriptional program was unknown” tells Elisa Montaldo, one of the main researchers of the study.

“The informatics and statistical analysis of sequencing data was a crucial part of the project as it enabled gaining an overall view of the biological system and proposing experimental hypotheses”, explains Eleonora Lusito, a bioinformatician and another main researcher of the study.

Integrating the different skills of SR-Tiget researchers is what made the study successful: from the isolation and ex vivo manipulation of human cells to the application of complex genomic technologies, the computational analysis of sequencing data and the biological and clinical interpretation of the results.


One of the winning moves was the close collaboration between basic research scientists and clinicians of the Ospedale San Raffaele. This allowed us having access to precious biological samples and collaborating daily in the selection of patients and in the clinical interpretation of data generated by the study. Such significant study could have been possible in very few other places in Italy and Europe”, ends Ostuni.