How Ana Cvejic built an immune atlas of lung cancer

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Lung cancer is the deadliest form of cancer worldwide. Non-small cell lung cancer (NSCLC) is the most common form, making up 85% of cases. In a paper published today in Nature Communications, Open Targets researchers and collaborators used single-cell RNA sequencing to create a high resolution molecular map of immune cells in NSCLC tumours, to better understand the role of these cells in disease progression.

This is a companion discussion topic for the original entry at https://blog.opentargets.org/ana-cvejic-immune-atlas-of-lung-cancer
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Hi Ana and team, congratulations on this awesome work, this will accelerate science and research at a considerable pace! Would love to take a look at the dataset, how do I access it?
Thanks,
Arindam

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Hi @arindamatgene, and welcome to the Open Targets Community! :tada:

The scRNA-seq and Visium datasets generated in this study are publicly available at BioStudies with accession numbers E-MTAB-13526 and E-MTAB-13530, respectively. The remaining data are available within the Article, Supplementary Information or Source Data file provided with the paper. The paper is Open Access.

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Hi Helena and team,

Thanks for the wonderful work! Is patient-level smoker status information available? Does this dataset contain data from never-smokers?

Thanks,

Sanna

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Hi @Sanna_Madan and welcome to the Open Targets Community! :tada:

Information about smoking is included in Suppl. Data Table 1 published alongside with the paper (Single-cell and spatial transcriptomics analysis of non-small cell lung cancer | Nature Communications).

The patients’ available smoking history in that table is as follows:

Patient 1: ex; Patient 2: ex; Patient 3: ex; Patient 4: ex; Patient 5: no; Patient 6: current; Patient 7: no; Patient 8: ex; Patient 9: ex; Patient 10: no; Patient 11: ex; Patient 12: ex; Patient 13: ex; Patient 14: ex, exposed to asbestos; Patient 15: current; Patient 16: current; Patient 17: ex; Patient 18: current; Patient 19: ex; Patient 20: current; Patient 21: ex; Patient 22: ex; Patient 23: ex; Patient 24: ex; Patient 25: ex; Donor 1: NA; Donor 2: NA.

It appears that patients 7 and 10 were the only ones who had never smoked.

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Hi Helena,

Thank you so much for the prompt and helpful response! Much appreciated!!

Best,

Sanna

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