Comprehensive and unbiased multiparameter high-throughput screening by compaRe finds effective and subtle drug responses in AML models
- University of Copenhagen, Denmark
- University of Helsinki, Finland
- Rigshospitalet, Denmark
- University of Dundee, United Kingdom
- Memorial Sloan Kettering Cancer Center, United States
Abstract
Large-scale multiparameter screening has become increasingly feasible and straightforward to perform thanks to developments in technologies such as high-content microscopy and high-throughput flow cytometry. The automated toolkits for analyzing similarities and differences between large numbers of tested conditions have not kept pace with these technological developments. Thus, effective analysis of multiparameter screening datasets becomes a bottleneck and a limiting factor in unbiased interpretation of results. Here we introduce compaRe, a toolkit for large-scale multiparameter data analysis, which integrates quality control, data bias correction, and data visualization methods with a mass-aware gridding algorithm-based similarity analysis providing a much faster and more robust analyses than existing methods. Using mass and flow cytometry data from acute myeloid leukemia and myelodysplastic syndrome patients, we show that compaRe can reveal interpatient heterogeneity and recognizable phenotypic profiles. By applying compaRe to high-throughput flow cytometry drug response data in AML models, we robustly identified multiple types of both deep and subtle phenotypic response patterns, highlighting how this analysis could be used for therapeutic discoveries. In conclusion, compaRe is a toolkit that uniquely allows for automated, rapid, and precise comparisons of large-scale multiparameter datasets, including high-throughput screens.
Data availability
Mass cytometry datasets were downloaded from Cytobank Community with the experiment ID 44185. AML mouse and human high-throughput flow cytometry data have been deposited in FLOWRepository with the repository IDs FR-FCM-Z357 and FR-FCM-Z3DP respectively. Flow cytometry data of AML and MDS patients have been deposited in FLOWRepository with the repository ID FR-FCM-Z3ET. Acquisition, installation and more technical details are available in compaRe's online tutorial on (https://github.com/morchalabi/COMPARE-suite). Similarity measurement and clustering modules as stand-alone tools have been merged into a separate R package and are available for download at (https://github.com/morchalabi/compaRe).
Article and author information
Author details
Morteza Chalabi Hajkarim
Krister Wennerberg
Funding
Novo Nordisk Foundation center for Stem Cell Biology (NNF17CC0027852)
- Kirsten Grønbæk
- Kristian Helin
- Krister Wennerberg
- Kyoung-Jae Won
Kræftens Bekæmpelse (R223‐A13071)
- Kirsten Grønbæk
- Kristian Helin
- Krister Wennerberg
- Kyoung-Jae Won
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Human subjects: The informed consent, and consent to publish of patient samples in this study has been approved by the Danish National Science Ethics Committee/National Videnskabsetisk Komite: Målrettet behandling af patienter med blodsygdomme, license no. 1705391.
Copyright
© 2022, Chalabi Hajkarim et al.
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.
Metrics
-
- 1,381
- views
-
- 219
- downloads
-
- 3
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Comprehensive and unbiased multiparameter high-throughput screening by compaRe finds effective and subtle drug responses in AML models
eLife 11:e73760.
https://doi.org/10.7554/eLife.73760
Further reading
-
- Computational and Systems Biology
- Genetics and Genomics
Root causal gene expression levels – or root causal genes for short – correspond to the initial changes to gene expression that generate patient symptoms as a downstream effect. Identifying root causal genes is critical towards developing treatments that modify disease near its onset, but no existing algorithms attempt to identify root causal genes from data. RNA-sequencing (RNA-seq) data introduces challenges such as measurement error, high dimensionality and non-linearity that compromise accurate estimation of root causal effects even with state-of-the-art approaches. We therefore instead leverage Perturb-seq, or high-throughput perturbations with single-cell RNA-seq readout, to learn the causal order between the genes. We then transfer the causal order to bulk RNA-seq and identify root causal genes specific to a given patient for the first time using a novel statistic. Experiments demonstrate large improvements in performance. Applications to macular degeneration and multiple sclerosis also reveal root causal genes that lie on known pathogenic pathways, delineate patient subgroups and implicate a newly defined omnigenic root causal model.
-
- Computational and Systems Biology
Artificial intelligence (AI) models have been used to study the compositional regularities of proteins in nature, enabling it to assist in protein design to improve the efficiency of protein engineering and reduce manufacturing cost. However, in industrial settings, proteins are often required to work in extreme environments where they are relatively scarce or even non-existent in nature. Since such proteins are almost absent in the training datasets, it is uncertain whether AI model possesses the capability of evolving the protein to adapt extreme conditions. Antibodies are crucial components of affinity chromatography, and they are hoped to remain active at the extreme environments where most proteins cannot tolerate. In this study, we applied an advanced large language model (LLM), the Pro-PRIME model, to improve the alkali resistance of a representative antibody, a VHH antibody capable of binding to growth hormone. Through two rounds of design, we ensured that the selected mutant has enhanced functionality, including higher thermal stability, extreme pH resistance, and stronger affinity, thereby validating the generalized capability of the LLM in meeting specific demands. To the best of our knowledge, this is the first LLM-designed protein product, which is successfully applied in mass production.
