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| Status |
Public on Aug 12, 2021 |
| Title |
Atlas of Clinically Distinct Cell States and Cellular Ecosystems Across Human Solid Tumors |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Determining how cells vary with their local signaling environment and organize into distinct cellular communities is critical for understanding processes as diverse as development, aging, and cancer. Here we introduce EcoTyper, a new machine learning framework for large-scale identification and validation of cell states and multicellular communities from bulk, single-cell, and spatially-resolved gene expression data. When applied to 12 major cell lineages across 16 types of human carcinoma, EcoTyper identified 69 transcriptionally-defined cell states. Most states were specific to neoplastic tissue, ubiquitous across tumor types, and significantly prognostic. By analyzing cell state co-occurrence patterns, we discovered 10 clinically-distinct multicellular communities with unexpectedly strong conservation, including four with unique myeloid and stromal elements, one enriched in normal tissue, and two associated with early cancer development. This study elucidates fundamental units of cellular organization in human carcinoma and provides a framework for large-scale profiling of cellular ecosystems in any tissue (https://ecotyper.stanford.edu).
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| Overall design |
6 samples from 3 patients, 2 replicates from patient nr 380, 1 replicate from patient nr 406, 3 replicates from patient nr 393
Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns.'
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| Contributor(s) |
Matusiak M, Zhu C, van de Rijn M |
| Citation(s) |
34597583 |
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| Submission date |
Aug 10, 2021 |
| Last update date |
Oct 14, 2021 |
| Contact name |
Magdalena Matusiak |
| E-mail(s) |
mmatusia@stanford.edu
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| Phone |
6502783762
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| Organization name |
Stanford University
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| Department |
Pathology
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| Lab |
van de Rijn West lab
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| Street address |
300 Pasteur Dr
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94025 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA753520 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE181817_TPM_spindly_foamy_MACs.txt.gz |
275.6 Kb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
| Raw data not provided for this record |
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