Publications

In Preparation
Marian Kalocsay, Matthew J. Berberich, Robert A. Everley, Maulik K. Nariya, Mirra Chung, Ben Gaudio, Chiara Victor, Gary A. Bradshaw, Marc Hafner, Peter K. Sorger, Caitlin E.Mills, and Kartik Subramanian. In Preparation. “Proteomic profiling of breast cancer cell lines and models”. Publisher's VersionAbstract
We performed quantitative proteomics on 61 human-derived breast cancer cell lines to a depth of ~13,000 proteins. The resulting high-throughput datasets were assessed for quality and reproducibility. We used the datasets to identify and characterize the subtypes of breast cancer and showed that they conform to known transcriptional subtypes, revealing that molecular subtypes are preserved even in under-sampled protein feature sets. All datasets are freely available as public resources on the LINCS portal. We anticipate that these datasets, either in isolation or in combination with complimentary measurements such as genomics, transcriptomics and phosphoproteomics, can be mined for the purpose of predicting drug response, informing cell line specific context in models of signalling pathways, and identifying markers of sensitivity or resistance to therapeutics.
2020
Jason Qian, Sarah A. Boswell, Christopher Chidley, Zhi-xiang Lu, Mary E. Pettit, Benjamin L. Gaudio, Jesse M. Fajnzylber, Ryan T. Ingram, Rebecca H. Ward, Jonathan Z. Li, and Michael Springer. 5/29/2020. “An enhanced isothermal amplification assay for viral detection.” Nature Communications. Publisher's VersionAbstract
Rapid, inexpensive, robust diagnostics are essential to control the spread of infectious diseases. Current state of the art diagnostics are highly sensitive and specific, but slow, and require expensive equipment. We developed a molecular diagnostic test for SARS-CoV-2, FIND (Fast Isothermal Nucleic acid Detection), based on an enhanced isothermal recombinase polymerase amplification reaction. FIND has a detection limit on patient samples close to that of RT-qPCR, requires minimal instrumentation, and is highly scalable and cheap. It can be performed in high throughput, does not cross-react with other common coronaviruses, avoids bottlenecks caused by the current worldwide shortage of RNA isolation kits, and takes ~45 minutes from sample collection to results. FIND can be adapted to future novel viruses in days once sequence is available.
2019
Mario Niepel, Marc Hafner, Caitlin E.Mills, Kartik Subramanian, Elizabeth H. Williams, Mirra Chung, Benjamin Gaudio, and Anne Marie Barrett. 7/24/2019. “A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines.” Cell Systems, 9, 1, Pp. 35-48. Publisher's VersionAbstract
Evidence that some high-impact biomedical results cannot be repeated has stimulated interest in practices that generate findable, accessible, interoperable, and reusable (FAIR) data. Multiple papers have identified specific examples of irreproducibility, but practical ways to make data more reproducible have not been widely studied. Here, five research centers in the NIH LINCS Program Consortium investigate the reproducibility of a prototypical perturbational assay: quantifying the responsiveness of cultured cells to anti-cancer drugs. Such assays are important for drug development, studying cellular networks, and patient stratification. While many experimental and computational factors impact intra- and inter-center reproducibility, the factors most difficult to identify and control are those with a strong dependency on biological context. These factors often vary in magnitude with the drug being analyzed and with growth conditions. We provide ways to identify such context-sensitive factors, thereby improving both the theory and practice of reproducible cell-based assays.