Single-cell sequencing reveals landscape of immune cell subtypes in lung cancer tumours

Despite significant advances, only a minority of individuals benefit from immunotherapy to treat cancer, and the reasons why remain unclear.

Immunotherapy research has largely centred on T cells, a type of immune cell that learns to recognise specific proteins and launch an attack. Tumours, however, are a complex mixture of many different cell types, including other immune cells known collectively as tumour-infiltrating myeloid cells. These cells represent alternative targets for immunotherapy, but their role in tumours is still poorly understood.

To shed light on this under-examined family of immune cells, Harvard Medical School researchers based at the Blavatnik Institute, Massachusetts General Hospital, Beth Israel Deaconess Medical Center and Brigham and Women’s Hospital used single-cell sequencing to map the landscape of myeloid cells in tumours from patients with lung cancer.

Their study, published in the journal Immunity, reveals 25 myeloid cell subpopulations, many previously undescribed, with distinct gene expression signatures that are consistent across patients. Most of these subpopulations were also identified in a mouse model of lung cancer, indicating a high degree of similarity in myeloid cells across species.

The findings serve as a foundation for future research to explain the precise roles of myeloid cells in cancer and to assess their potential as targets for new or improved immunotherapies, the authors said.

“Immunotherapy is clearly a transformational approach to cancer treatment, but there are many patients who don’t respond, and the question is why,” said co-corresponding author Allon Klein, assistant professor of systems biology at HMS.

“Part of the answer could certainly lie at the level of myeloid cells, which interact heavily with both tumour cells and T cells,” Klein continued. “By identifying the rich complexity of myeloid cell states in tumours, we now have a powerful starting point to better understand their functions and clinical applications.”

Of particular importance, the authors said, was the finding that myeloid subpopulations can be reliably identified in different human patients and in mice – an observation that underscores the fundamental use of mouse models in immunotherapy research.

“Tumour cells were different in each patient analysed, but the identity of tumour-infiltrating myeloid cells greatly overlapped between the same patients. Also, many myeloid populations were incredibly well conserved across patients and mice,” said co-corresponding author Mikael Pittet, HMS associate professor of radiology at Mass General.

“This is exciting because a growing body of evidence based on mouse studies suggests that myeloid cells can control cancer progression and affect virtually all types of cancer therapy, including immunotherapy” Pittet added.

Myeloid cells – comprised of immune cells including monocytes, macrophages, dendritic cells and granulocytes – are part of the innate immune system, the body’s first and broad line of defence against foreign pathogens. They play an important role in activating the adaptive immune system, including T cells, which can precisely target and destroy pathogens.

Their analyses revealed myeloid cell gene expression signatures that fell into 25 distinct clusters, greatly expanding the number of known myeloid cell states.

They found that dendritic cells, for example – which Pittet and colleagues previously found are critical to successful anti-PD-1 immunotherapy in mice – contained four different subtypes that are largely mirrored between humans and mice. Monocyte subtypes also matched well between humans and mice, while macrophages were both conserved and varied by species.

Neutrophils, which are the most abundant white blood cells in mammals, formed a spectrum of five similar subtypes in humans and mice, with one subset unique to mice. Pittet, in a previous collaboration with Klein, found that neutrophils expressing high levels of the gene Siglecf have tumour-promoting properties. The new analyses corroborated this finding, showing that these neutrophils are highly enriched in tumours.

“Myeloid cell populations are complex, but we see the same complexity across patients and species, which gives us confidence that insights in mouse models can be translated to humans,” said Pittet.

With the landscape of myeloid cell gene-expression patterns mapped, scientists can mine existing datasets of patients with known clinical outcomes to look for the presence of a given population of myeloid cells and assess their relationship with patient survival.

The team also looked at whether the behaviour of myeloid cells in tumours could be gleaned by sampling myeloid cells circulating in blood and found a poor relationship between the two.

In addition to immediate basic and translational research opportunities, the study findings inform the work of initiatives such as the Human Tumor Atlas, an effort to map the landscape of all cell types in the human body, and the Human Tumor Atlas Network, an effort to create atlases of a wide variety of cancer types in cellular and molecular detail.