Scientists from the Memorial Sloan Kettering Cancer Center have published a molecular atlas of small cell lung cancer that reveals an unusual cell type that could explain why it’s so aggressive.

“The most exciting thing we found is a rare population of stem-like cells within these tumors that is closely correlated with patient outcomes,” explained Charles Rubin, MD, PhD, a physician-scientist at MSK who co-led the lung cancer project. “The more enriched they are in the tumor, the worse the prognosis.”

Not only that, but these stem-like cells have metastatic properties and researchers found them across many SCLC tumors that otherwise were different.

“That was a massive surprise,” said Dana Pe’er, PhD, an MSK computational biologist who is a principal investigator of the Human Tumor Atlas Network (HTAN), and co-led the lung cancer atlas project. “It raises the possibility that this tiny fraction of cells could be driving metastatic behavior across tumors.”

Small cell lung cancer is one of the deadliest cancers. It tends to spread early and aggressively; two-thirds of cases are already metastatic at diagnosis. Chemotherapy is not very effective.

The team hopes its news atlas (“Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer”), published in Cancer Cell, will lead to improvements in care for people with the disease.

“Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined by differential expression of ASCL1NEUROD1, and POU2F3 (SCLC-A, -N, and -P, respectively). To define the heterogeneity of tumors and their associated microenvironments across subtypes, we sequenced 155,098 transcriptomes from 21 human biospecimens, including 54,523 SCLC transcriptomes. We observe greater tumor diversity in SCLC than lung adenocarcinoma, driven by canonical, intermediate, and admixed subtypes,” write the investigators.

“We discover a PLCG2-high SCLC phenotype with stem-like, pro-metastatic features that recurs across subtypes and predicts worse overall survival. SCLC exhibits greater immune sequestration and less immune infiltration than lung adenocarcinoma, and SCLC-N shows less immune infiltrate and greater T cell dysfunction than SCLC-A.

“We identify a profibrotic, immunosuppressive monocyte/macrophage population in SCLC tumors that is particularly associated with the recurrent, PLCG2-high subpopulation.”

A collaborative effort

Building the atlas required years of collaborative work from two groups with different areas of expertise according to Rudin, a clinician with disease-specific expertise in small cell lung cancer and computational biologists like Pe’er and her team.

Rudin points to the fact that there are four co-first authors on the paperas evidence of the diversity of skillsets needed to complete a study like this. The co-first authors are Joseph Chan, Alvaro Quintanal-Villalonga, Vianne Ran Gao, and Yubin Xie.

Pe’er, chair of the computational and systems biology program at the Sloan Kettering Institute, took the lead on the computational side of things. She is an expert in single-cell RNA seq (scRNAseq), that allows scientists to get a detailed picture of which genes are turned on in many hundreds of cells at the same time.

By applying scRNAseq to SCLC tumor specimens obtained from patients at MSK, Pe’er and her team were able to find this rare population of stem cell-like cells lurking amid the cells of the surrounding tumor, like locating a needle in a haystack.

“We would never have been able spot these cells with bulk sequencing,” she said. “We really needed single cell analysis to find them.”

Bulk sequencing is what researchers would do before scRNAseq was available, essentially putting the tumor in a blender and sequencing all the RNA that fell out.

Homing in on molecular changes

The single cell technique also allowed the team to go further. Within the cells making up this tiny population, one gene stood out: PLCG2. This gene makes a protein that acts as a “second messenger,” relaying signals from one protein to another.

PLCG2 did not initially strike me as the sort of gene that would be involved in regulating stem cell populations,” said Rudin. “It seems like more of a worker bee.”

PLCG2 does seem to be playing an important role. The gene is most highly expressed in this stem cell-like population, the scientists found. And when they experimentally increased or lowered its activity in cancer cell lines, it altered the ability of the cancer cells to metastasize.

They researchers think that these PLCG2-high cells could be part of the explanation for SCLC’s aggressiveness. If so, it could open up new possibilities for treatment.

“The thought is that if we can develop strategies to selectively target this cell population, we might be able to suppress metastasis and ultimately improve outcomes for patients with small cell lung cancer,” noted Rudin.

“What we really want to do is try to stop metastasis in its tracks,” Pe’er added “But to do that, we need to better understand these rare cell populations that seem to be driving it. That’s the goal of this atlas.”

The HTAN was created to develop high-resolution maps of many kinds of cancer so that doctors could have a more-complete view of the textured terrain of tumors, including how they change over time to become more deadly. HTAN is funded by the National Cancer Institute and involves a consortium of cancer centers across the U.S.