The significance of research in the HMS LINCS Center derives not only from the ambitions of the overall NIH LINCS program but also from several specific aspects of our approach to choosing perturbations and inferring signatures.

Focus on therapeutic drugs and their targets

Cellular networks can be conceptually classified into four layers: (i) transmembrane receptors; (ii) cytoplasmic signal-processing networks; (iii) interacting transcriptional networks; and (iv) downstream response networks that control integrated cell physiology in response to signaling and transcription. Because of the power of transcript and gene-regulation profiling, most systematic studies have focused on transcriptional networks. Our principle focus will be on signal-processing networks that comprise the “immediate-early” response to signals (largely upstream of transcription) as well as integrated physiology responses. Most un- or under-exploited protein targets that are “druggable” in humans using current technology are in layers (i) and (ii). These include receptor tyrosine kinases, other kinases, and GPCRs. Thus, our data will be of immediate translational significance, and some of our measurements may be useful as clinical biomarkers.

Measurements of known physiological importance

The integrated physiological states we measure include cell cycle progression, cellular senescence, apoptosis, induction/suppression of motile-invasive behavior, and changes in differentiated state such as epithelial-mesenchymal transitions. These phenotypes are directly related to pathogenic and therapeutic processes. Our physiology-centric measurements complement gene-centric measurements currently underway in many research centers.

Use and dissemination of generalizeable technology

The systematic assays of cell and network state we use can be directly applied to any cell type or disease model in cell culture simply by changing the cells, perturbagens, antibodies, and fluorescent probes. Foreseeable extensions will allow their application to mouse disease models by biopsy and live intravital imaging and to human biopsies.

Creation of a unique online resource that disseminates biochemical data on a versatile class of perturbagens (kinase inhibitors)

Small molecules are the most versatile perturbagens: they can be applied to any cell type in culture or in model organisms, they allow exquisite control of the timing and strength of perturbation, QC and reagent sharing are easy, and they have high translational potential. Kinase inhibitors are particularly powerful: most signal-processing networks contain kinases, and a large fraction of all new investigational small-molecule drugs are kinase inhibitors. Systematic data on this perturbagen class, which we disseminate via a dedicated website (the HMS LINCS Database), will benefit a broad research community. The gene family-based small molecule perturbagen approach is extendable to other druggable families, such as GPCRs, nuclear receptors, proteases, HDACs, PARPs, etc. Recently, we have added compounds that target chromatin interactions to our HMS LINCS perturbagen collection.

Tissue- and disease-relevant cell line platform

Learning how disease states perturb network topology and dynamics should be an influential output of the LINCS program. At HMS we primarily investigate broadly how cancer genotypes perturb network responses as well as baseline phenotypes. Although cancer-focused in its current form, this platform provides a model for how to represent human disease state and genetic variation in culture. Building on this platform, we also use human primary cultures, including patient-derived synovial fibroblasts and iPS-derived cardiomyocytes, to model both normal and diseased tissue responses.