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Series GSE127465 Query DataSets for GSE127465
Status Public on Apr 09, 2019
Title Single cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Tumor-infiltrating myeloid cells (TIMs) comprise monocytes, macrophages, dendritic cells and neutrophils, and have emerged as key regulators of cancer growth. These cells can diversify into a spectrum of states, which may promote or limit tumor outgrowth, but remain poorly understood. Here, we used single-cell RNA sequencing to map TIMs in non-small cell lung cancer patients. We uncovered 25 TIM states, most of which were reproducibly found across patients. To facilitate translational research of these populations, we also profiled TIMs in mice. In comparing TIMs across species, we identified a near-complete congruence of population structures among dendritic cells and monocytes; conserved neutrophil subsets; and species differences among macrophages. By contrast, myeloid cell population structures in patients’ blood showed limited overlap with those of TIMs. This study determines the lung TIM landscape and sets the stage for future investigations into the potential of TIMs as immunotherapy targets.
Overall design Single cell RNA sequencing (scRNAseq) of RBC-depleted cells from non-small cell lung tumor and from blood of 7 patients. ScRNAseq of CD45-positive cells from lungs of 2 healthy mice and 2 lung tumor-bearing mice.

Human raw data are not available for this Series due to patient privacy concerns.
Web link
Contributor(s) Zilionis R, Engblom C, Pfirschke C, Savova V, Zemmour D, Saatcioglu HD, Krishnan I, Maroni G, Meyerovitz CV, Kerwin CM, Choi S, Richards WG, De Rienzo A, Tenen DG, Bueno R, Levantini E, Pittet MJ, Klein AM
Citation(s) 30979687
NIH grant(s)
Grant ID Grant title Affiliation Name
P50 CA086355 Imaging Immune Cell Modulation in Cancer Therapy MASSACHUSETTS GENERAL HOSPITAL Mikael PITTET
R01 AI084880 In vivo behavior of monocytes in resting and inflammatory conditions MASSACHUSETTS GENERAL HOSPITAL Mikael PITTET
R01 CA206890 Imaging tumor associated macrophage (TAM) function MASSACHUSETTS GENERAL HOSPITAL Mikael PITTET
R01 CA218579 Single Cell Genome-Wide Myeloid Response Profiling in Immunotherapy HARVARD UNIVERSITY (MEDICAL SCHOOL) Mikael PITTET
R01 CA218579 Single Cell Genome-Wide Myeloid Response Profiling in Immunotherapy HARVARD UNIVERSITY (MEDICAL SCHOOL) Allon Moshe Klein
R33 CA212697 Droplet microfluidic technology for single cell cancer genomics HARVARD UNIVERSITY (MEDICAL SCHOOL) Allon Moshe Klein
R35 CA197697 Mechanisms of regulation by RNA in acute myeloid leukemia BETH ISRAEL DEACONESS MEDICAL CENTER DANIEL G TENEN
Submission date Feb 28, 2019
Last update date Sep 11, 2019
Contact name Allon Klein
Organization name Harvard Medical School
Department Systems Biology
Lab Klein
Street address 200 Longwood Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (40)
GSM3635278 patient_1_tumor [human_p1t1]
GSM3635279 patient_1_tumor [human_p1t2]
GSM3635280 patient_1_tumor [human_p1t3]
BioProject PRJNA524857
SRA SRP187083

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE127465_RAW.tar 160.2 Mb (http)(custom) TAR (of TSV)
GSE127465_gene_names_human_41861.tsv.gz 102.2 Kb (ftp)(http) TSV
GSE127465_gene_names_mouse_28205.tsv.gz 72.1 Kb (ftp)(http) TSV
GSE127465_human_cell_metadata_54773x25.tsv.gz 3.9 Mb (ftp)(http) TSV
GSE127465_human_counts_normalized_54773x41861.mtx.gz 503.8 Mb (ftp)(http) MTX
GSE127465_mouse_cell_metadata_15939x12.tsv.gz 442.4 Kb (ftp)(http) TSV
GSE127465_mouse_counts_normalized_15939x28205.mtx.gz 166.2 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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