Q & A
Q: What is the overall goal of the program?
- LINCS is working to establish a new understanding of health and disease through an integrative approach that identifies patterns of common networks and cellular responses (called cellular signatures) across different types of tissues and cells in response to a broad range of perturbations.
- The underlying premise of the LINCS program is that disrupting any one of the many steps of a given biological process will cause related changes in the molecular and cellular characteristics, behavior, and/or function of the cell – also known as the cellular phenotype. A cellular phenotype, in turn, can be reflected by signatures derived from comparable assays of clinical states. Observing how and when a cell phenotype is altered by specific stressors can provide clues about the mechanisms involved in perturbation and, ultimately, disease.
Q: What are cellular signatures?
- A cellular signature of a perturbagen response is the set of reduced dimensionality descriptors of the underlying data that provide insight into mechanism and serve as predictors. Therefore, meaningful signatures are dependent on the assay, and on how diverse assays are integrated together, either into predictive patterns or signaling networks that could lead to mechanistic interpretations.
- To develop meaningful signatures, data from diverse assays must be scaled and normalized. Integration, normalization and scaling of heterogeneous, multi-parameter dose-response data is a non-trivial task involving conceptual and practical hurdles.
Q: What assays are being run?
- The program has six data and signature generation centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center.
- The Drug Toxicity Signature Generation Center’s assays monitor gene and protein expression, as well as phenotype assays that are applied to understand the response of differentiated iPSCs to single and combinations of FDA approved drug perturbations.
- The HMS LINCS Center monitors cell responses using multiple biochemical, imaging and cell biological assays. They range from direct assays of drug-kinase interaction in cell extracts, to multiplex biochemical assays of cell signaling proteins, to imaging assays, to assays of transcriptional response (in collaboration with the LINCS Center for Transcriptomics) and cell viability assays. More details about HMS LINCS Center assays can be found here.
- The LINCS Center for Transcriptomics uses the L1000 assay which is a gene-expression profiling assay based on the direct measurement of a reduced representation of the transcriptome and computational inference of the portion of the transcriptome not explicitly measured. Measurements are (a) of endogenous mRNA (i.e not reporter-based system) (b) from treated whole cell lysates (c) current detection method is by optically-addressed microspheres based Luminex system.
- The LINCS Proteomic Characterization Center for Signaling and Epigenetics performs two assays: P100 reduced representation phosphoprofiling (3 hour time point) and GCP global chromatin profiling (24 hour time point). The P100 assay is a mass spectrometry-based targeted proteomics assay that detects and quantifies a representative set of ~100 phosphopeptide probes that are present in a wide range of cell types and have been demonstrated to be modulated via perturbations. The Global Chromatin Profiling assay is a mass spectrometry-based targeted proteomics assay that detects and quantifies an extensive set of chromatin modifications (specifically, post-translational modifications on histone proteins).
- The MEP LINCS Center’s assays start with a novel assay that image cancer cell lines placed in a micro-environment array. Selected conditions are then followed with transcriptomics (L1000) and proteomics assays (RPPA).
- The NeuroLINCS Center is focused on studying the properties of iPSCs derived from normal, familial and sporadic ALS patients. These cells are differentiated into motor neurons and assayed using targeted proteomics, transcriptomics (RNA-seq) and imaging assays.
Q: What perturbations are being used?
- The program uses small molecules, ligands, micro-environments, CRISPR gene over-expression and knockdown perturbations.
- Each data and signature generation center has its own set of perturbations and they are determined primarily by the assay technology being used to determine response.
- The Drug Toxicity Signature Generation Center’s perturbations are FDA approved drugs applied individually or in combinations.
- HMS LINCS Center currently focuses on two types of perturbagens, small molecule protein kinase inhibitors and naturally occurring growth factors, cytokines and chemokines in various combinations. Complete information about all perturbagens used at HMS LINCS can be found in the HMS LINCS Database.
- The LINCS Center for Transcriptomics and the LINCS Proteomic Characterization Center for Signaling and Epigenetics profile over 20,000 small-molecules and 5,000 human genes. See lincscloud.org for more details.
- The MEP LINCS Center’s perturbations are over 3,000 unique micro-environment conditions where an extracellular matrix protein is combined with an extracellular ligand to define a unique condition.
- The NeuroLINCS Center’s perturbations are simply the disease ALS motor neuron cells compared with cells from subjects that do not have the disease.
Q: Is there a timeline available for release of data?
- New releases of data will become available every quarter and the release schedule is summarized here.
- Metadata annotations of LINCS data will be available along with each data release. We are working diligently to include sufficient metadata with each release of data.
- In addition to the data generated by the LINCS data and signature generation centers, the BD2K-LINCS DCIC is extracting signatures from the public domain and these can be accessed here. APIs, attribute tables and meta-data are expected to be provided soon.
Q: So where are the signatures?
- The signatures are available via multiple methods: (a) APIs to programmatically search and download the signatures; (b) Tools that display the signatures and provide integrative analyses.
Q: What are your future plans?
- In the coming months you will see more user interfaces to query LINCS data and signatures, and publications demonstrating the utility of the LINCS approach.
- We are also focusing on generating data in primary cells and iPS cells and data pertaining to these will be available soon.
Q: What data integration challenges are you taking on?
- Data is being collected via a joint project called the “Dense Cube” between all the data and signature generation centers. This project will focus on five common cell lines to explore the relationship between immediate early cell signaling events, transcription and phenotypes. This will constitute the largest such public dataset, generated in a coherent manner, available for download and querying.
- One of the biggest challenges we have is to build standards for metadata for all of LINCS perturbations, assays and experiments. We want to annotate these consistently, and to make them available consistently so that outside groups can perform their own analysis and build better methods to extract signatures from the LINCS data.
Q: Any opportunities to collaborate?
- There are several funding opportunities to enable collaborations with the BD2K-LINCS DCIC and the LINCS data and signature generation centers.
- There are also LINCS Data Science Research Webinars that can be used to learn about the various LINCS datasets and research projects.
- Details about outreach opportunities related to LINCS can be found in the Community section of this website.