A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.

We previously piloted the concept of a Connectivity Map (CMap), whereby genes, drugs, and disease states are connected by virtue of common gene-expression signatures. Here, we report more than a 1,000-fold scale-up of the CMap as part of the NIH LINCS Consortium, made possible by a new, low-cost, high-throughput reduced representation expression profiling method that we term L1000. We show that L1000 is highly reproducible, comparable to RNA sequencing, and suitable for computational inference of the expression levels of 81% of non-measured transcripts. We further show that the expanded CMap can be used to discover mechanism of action of small molecules, functionally annotate genetic variants of disease genes, and inform clinical trials. The 1.3 million L1000 profiles described here, as well as tools for their analysis, are available at https://clue.io.

Genetic and transcriptional evolution alters cancer cell line drug response.

Human cancer cell lines are the workhorse of cancer research. Although cell lines are known to evolve in culture, the extent of the resultant genetic and transcriptional heterogeneity and its functional consequences remain understudied. Here we use genomic analyses of 106 human cell lines grown in two laboratories to show extensive clonal diversity. Further comprehensive genomic characterization of 27 strains of the common breast cancer cell line MCF7 uncovered rapid genetic diversification. Similar results were obtained with multiple strains of 13 additional cell lines. Notably, genetic changes were associated with differential activation of gene expression programs and marked differences in cell morphology and proliferation. Barcoding experiments showed that cell line evolution occurs as a result of positive clonal selection that is highly sensitive to culture conditions. Analyses of single-cell-derived clones demonstrated that continuous instability quickly translates into heterogeneity of the cell line. When the 27 MCF7 strains were tested against 321 anti-cancer compounds, we uncovered considerably different drug responses: at least 75% of compounds that strongly inhibited some strains were completely inactive in others. This study documents the extent, origins and consequences of genetic variation within cell lines, and provides a framework for researchers to measure such variation in efforts to support maximally reproducible cancer research.

A model and experimental approach to the middle ear transfer function related to hearing in the humpback whale (Megaptera novaeangliae).

At present, there are no direct measures of hearing for any baleen whale (Mysticeti). The most viable alternative to in vivo approaches to simulate the audiogram is through modeling outer, middle, and inner ear functions based on the anatomy and material properties of each component. This paper describes a finite element model of the middle ear for the humpback whale (Megaptera novaeangliae) to calculate the middle ear transfer function (METF) to determine acoustic energy transmission to the cochlea. The model was developed based on high resolution computed tomography imaging and direct anatomical measurements of the middle ear components for this mysticete species. Mechanical properties for the middle ear tissues were determined from experimental measurements and published values. The METF for the humpback whale predicted a better frequency range between approximately 15 Hz and 3 kHz or between 200 Hz and 9 kHz based on two potential stimulation locations. Experimental measures of the ossicular chain, tympanic membrane, and tympanic bone velocities showed frequency response characteristics consistent with the model. The predicted best sensitivity hearing ranges match well with known vocalizations of this species.

A prediction of the minke whale (Balaenoptera acutorostrata) middle-ear transfer function.

The lack of baleen whale (Cetacea Mysticeti) audiograms impedes the assessment of the impacts of anthropogenic noise on these animals. Estimates of audiograms, which are difficult to obtain behaviorally or electrophysiologically for baleen whales, can be made by simulating the audiogram as a series of components representing the outer, middle, and inner ear (Rosowski, 1991; Ruggero and Temchin, 2002). The middle-ear portion of the system can be represented by the middle-ear transfer function (METF), a measure of the transmission of acoustic energy from the external ear to the cochlea. An anatomically accurate finite element model of the minke whale (Balaenoptera acutorostrata) middle ear was developed to predict the METF for a mysticete species. The elastic moduli of the auditory ossicles were measured by using nanoindentation. Other mechanical properties were estimated from experimental stiffness measurements or from published values. The METF predicted a best frequency range between approximately 30 Hz and 7.5 kHz or between 100 Hz and 25 kHz depending on stimulation location. Parametric analysis found that the most sensitive parameters are the elastic moduli of the glove finger and joints and the Rayleigh damping stiffness coefficient ß. The predicted hearing range matches well with the vocalization range.

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations.

Although the value of proteomics has been demonstrated, cost and scale are typically prohibitive, and gene expression profiling remains dominant for characterizing cellular responses to perturbations. However, high-throughput sentinel assays provide an opportunity for proteomics to contribute at a meaningful scale. We present a systematic library resource (90 drugs × 6 cell lines) of proteomic signatures that measure changes in the reduced-representation phosphoproteome (P100) and changes in epigenetic marks on histones (GCP). A majority of these drugs elicited reproducible signatures, but notable cell line- and assay-specific differences were observed. Using the "connectivity" framework, we compared signatures across cell types and integrated data across assays, including a transcriptional assay (L1000). Consistent connectivity among cell types revealed cellular responses that transcended lineage, and consistent connectivity among assays revealed unexpected associations between drugs. We further leveraged the resource against public data to formulate hypotheses for treatment of multiple myeloma and acute lymphocytic leukemia. This resource is publicly available at https://clue.io/proteomics.

Elastic modulus of cetacean auditory ossicles.

In order to model the hearing capabilities of marine mammals (cetaceans), it is necessary to understand the mechanical properties, such as elastic modulus, of the middle ear bones in these species. Biologically realistic models can be used to investigate the biomechanics of hearing in cetaceans, much of which is currently unknown. In the present study, the elastic moduli of the auditory ossicles (malleus, incus, and stapes) of eight species of cetacean, two baleen whales (mysticete) and six toothed whales (odontocete), were measured using nanoindentation. The two groups of mysticete ossicles overall had lower average elastic moduli (35.2 ± 13.3 GPa and 31.6 ± 6.5 GPa) than the groups of odontocete ossicles (53.3 ± 7.2 GPa to 62.3 ± 4.7 GPa). Interior bone generally had a higher modulus than cortical bone by up to 36%. The effects of freezing and formalin-fixation on elastic modulus were also investigated, although samples were few and no clear trend could be discerned. The high elastic modulus of the ossicles and the differences in the elastic moduli between mysticetes and odontocetes are likely specializations in the bone for underwater hearing.