Unsupervised machine learning reveals risk stratifying glioblastoma tumor cells

Abstract
Data availability
Article and author information
Metrics

Abstract

A goal of cancer research is to reveal cell subsets linked to continuous clinical outcomes to generate new therapeutic and biomarker hypotheses. We introduce a machine learning algorithm, Risk Assessment Population IDentification (RAPID), that is unsupervised and automated, identifies phenotypically distinct cell populations, and determines whether these populations stratify patient survival. With a pilot mass cytometry dataset of 2 million cells from 28 glioblastomas, RAPID identified tumor cells whose abundance independently and continuously stratified patient survival. Statistical validation within the workflow included repeated runs of stochastic steps and cell subsampling. Biological validation used an orthogonal platform, immunohistochemistry, and a larger cohort of 73 glioblastoma patients to confirm the findings from the pilot cohort. RAPID was also validated to find known risk-stratifying cells and features using published data from blood cancer. Thus, RAPID provides an automated, unsupervised approach for finding statistically and biologically significant cells using cytometry data from patient samples.

Data availability

Annotated flow data files are available at the following link: https://flowrepository.org/id/FR-FCM-Z24K. Patient specific views of population abundance and channel mass signals for all analyzed patients in this study are currently available in Supplementary File 6. RAPID code is currently available on Github, together with example analysis data: https://github.com/cytolab/RAPID

The following data sets were generated

1. Leelatian N
2. Sinnaeve J
3. Mistry A
4. Barone S
5. Brockman A
6. Diggins K
7. Greenplate A
8. Weaver K
9. Thompson R
10. Chambless L
11. Moble B
12. Ihrie R
13. Irish
14. J
(2019) Unsupervised machine learning reveals risk stratifying gliobalstoma tumor cells
FlowRepository, FR-FCM-Z24K.

https://flowrepository.org/id/RvFrKN2ctDJmmVNE4ZnMJrAZeVraXbwvrhjx3YaBZIV6nWIanMrbhrVBx7yvODtX

The following previously published data sets were used

1. Good Z
2. Sarno J
3. Jager A
4. Samusik N
5. Aghaeepour
6. Simonds EF
7. White L
8. Lacayo NJ
9. Fantl WJ
10. Fazio G
11. Gaipa G
12. Biondi A
13. Tibshirani R
14. Bendall SC
15. Nolan GP
16. Davis KL
(2018) Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse
Github Mass cytometry data for DDPR project.

https://github.com/kara-davis-lab/DDPR/releases

Article and author information

Author details

Nalin Leelatian

Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States

Competing interests
No competing interests declared.
Justine Sinnaeve

Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0001-9303-7969
Akshitkumar M Mistry

Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-7918-5153
Sierra M Barone

Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0001-5944-750X
Asa A Brockman

Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States

Competing interests
No competing interests declared.
Kirsten E Diggins

Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States

Competing interests
No competing interests declared.
Allison R Greenplate

Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, United States

Competing interests
No competing interests declared.
Kyle D Weaver

Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States

Competing interests
No competing interests declared.
Reid C Thompson

Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States

Competing interests
No competing interests declared.
Lola B Chambless

Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States

Competing interests
No competing interests declared.
Bret C Mobley

Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, United States

Competing interests
No competing interests declared.
Rebecca A Ihrie

Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States

For correspondence
rebecca.ihrie@vanderbilt.edu

Competing interests
No competing interests declared.
Jonathan M Irish

Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States

For correspondence
jonathan.irish@vanderbilt.edu

Competing interests
Jonathan M Irish, was a co-founder and a board member of Cytobank Inc. and received research support from Incyte Corp, Janssen, and Pharmacyclics.

"This ORCID iD identifies the author of this article:" 0000-0001-9428-8866

Funding

National Institutes of Health (R00 CA143231)

Jonathan M Irish

National Institutes of Health (F31 CA199993)

Allison R Greenplate

National Institutes of Health (R25 CA136440-04)

Kirsten E Diggins

Vanderbilt Ingram Cancer Center (Provocative Question)

Jonathan M Irish

National Institutes of Health (R01 CA226833)

Jonathan M Irish

National Institutes of Health (U54 CA217450)

Jonathan M Irish

National Institutes of Health (U01 AI125056)

Sierra M Barone
Jonathan M Irish

National Institutes of Health (R01 NS096238)

Rebecca A Ihrie

U.S. Department of Defense (W81XWH-16-1-0171)

Rebecca A Ihrie

Michael David Greene Brain Cancer Fund

Rebecca A Ihrie
Jonathan M Irish

Vanderbilt Institute for Clinical and Translational Research (VR51342)

Bret C Mobley
Rebecca A Ihrie

Vanderbilt Ingram Cancer Center (P30 CA68485)

Jonathan M Irish

Vanderbilt Ingram Cancer Center (Ambassadors Award)

Rebecca A Ihrie
Jonathan M Irish

Southeastern Brain Tumor Foundation

Rebecca A Ihrie
Jonathan M Irish

Vanderbilt University (International Scholars Program)

Nalin Leelatian

Vanderbilt University (Discovery Grant)

Nalin Leelatian
Jonathan M Irish

Alpha Omega Alpha Honor Medical Society (Postgraduate Award)

Akshitkumar M Mistry

Society of Neurological Surgeons (RUNN Award)

Akshitkumar M Mistry

National Institutes of Health (F32 CA224962-01)

Akshitkumar M Mistry

Burroughs Wellcome Fund (1018894)

Akshitkumar M Mistry

National Institutes of Health (T32 HD007502)

Justine Sinnaeve

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.