A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines

Niepel, Mario; Hafner, Marc; Mills, Caitlin E.; Subramanian, Kartik; Williams, Elizabeth H; Chung, Mirra; Gaudio, Benjamin; Barrette, Anne Marie; Stern, Ari; Hu, Bin; Korkola, James E.; Gray, Joe W.; Birtwistle, Marc R.; Heiser, Laura M.; Sorger, Peter K.; Shamu, Caroline E.; Jayaraman, Gomathi; Azeloglu, Evren U.; Iyengar, Ravi; Sobie, Eric A.; Mills, Gordon B.; Liby, Tiera; Jaffe, Jacob D.; Alimova, Maria; Davison, Desiree; Lü, Xiaodong; Golub, Todd R.; Subramanian, Aravind; Shelley, Brandon; Svendsen, Clive N.; Ma’ayan, Avi; Medvedovic, Mario; Feiler, Heidi S.; Smith, Rebecca; Devlin, Kaylyn L.

doi:10.1016/j.cels.2019.06.005

Cited by 115 publications

(124 citation statements)

References 59 publications

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“…Results from immortalized cell lines exhibit limited reproducibility to in vivo settings due to altered cell physiology and lack of tissue environment. 83,90,91 We therefore assessed if our observations also apply in vivo during IEC infection in the mouse model. We infected mice orally with S. Tm carrying a transcriptional reporter (prgH-GFP) for TTSS-1 expression (S. Tm SPI-1-GFP ) and analyzed the pathogen populations in the cecum tissue (12 hpi) and at systemic sites (spleen, 3 dpi to obtain sufficient bacterial loads).…”

Section: Introductionmentioning

confidence: 99%

Intestinal epithelial NAIP/NLRC4 restricts systemic dissemination of the adapted pathogen Salmonella Typhimurium due to site-specific bacterial PAMP expression

et al. 2020

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Inflammasomes can prevent systemic dissemination of enteropathogenic bacteria. As adapted pathogens including Salmonella Typhimurium (S. Tm) have evolved evasion strategies, it has remained unclear when and where inflammasomes restrict their dissemination. Bacterial population dynamics establish that the NAIP/NLRC4 inflammasome specifically restricts S. Tm migration from the gut to draining lymph nodes. This is solely attributable to NAIP/NLRC4 within intestinal epithelial cells (IECs), while S. Tm evades restriction by phagocyte NAIP/NLRC4. NLRP3 and Caspase-11 also fail to restrict S. Tm mucosa traversal, migration to lymph nodes, and systemic pathogen growth. The ability of IECs (not phagocytes) to mount a NAIP/NLRC4 defense in vivo is explained by particularly high NAIP/NLRC4 expression in IECs and the necessity for epithelium-invading S. Tm to express the NAIP1-6 ligandsflagella and type-III-secretion-system-1. Imaging reveals both ligands to be promptly downregulated following IEC-traversal. These results highlight the importance of intestinal epithelial NAIP/NLRC4 in blocking bacterial dissemination in vivo, and explain why this constitutes a uniquely evasion-proof defense against the adapted enteropathogen S. Tm.Mucosal Immunology (2020) 13:530-544; https://doi.

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Section: Introductionmentioning

confidence: 99%

Intestinal epithelial NAIP/NLRC4 restricts systemic dissemination of the adapted pathogen Salmonella Typhimurium due to site-specific bacterial PAMP expression

et al. 2020

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“…Cell lines are easy to grow, can be maintained in culture indefinitely and allow flexible genetic and pharmacological manipulation. However, the transferability of results to the in vivo scenario is often limited (Antoni, Burckel, Josset, & Noel, ; Ben‐David et al, ; Niepel et al, ). This can be explained by poor mimicking of the complexity and interconnectedness inherent to epithelia in vivo (Antoni et al, ), the disruptive effects of cellular transformation and the gradual accumulation of genetic anomalies during prolonged culture (Ben‐David et al, ; Foulke‐Abel et al, ; Liu et al, ).…”

Section: Introductionmentioning

confidence: 99%

Germ‐free and microbiota‐associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes

Hausmann

Russo

Grossmann

et al. 2020

Cellular Microbiology

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Intestinal epithelial organoids established from gut tissue have become a widely used research tool. However, it remains unclear how environmental cues, divergent microbiota composition and other sources of variation before, during and after establishment confound organoid properties, and how these properties relate to the original tissue. While environmental influences cannot be easily addressed in human organoids, mice offer a controlled assay-system. Here, we probed the effect of donor microbiota differences, previously identified as a confounding factor in murine in vivo studies, on organoids. We analysed the proteomes and transcriptomes of primary organoid cultures established from two colonised and one germ-free mouse colony of C57BL/6J genetic background, and compared them to their tissue of origin and commonly used cell lines. While an imprint of microbiota-exposure was observed on the proteome of epithelial samples, the long-term global impact of donor microbiota on organoid expression patterns was negligible. Instead, stochastic culture-to-culture differences accounted for a moderate variability between independently established organoids. Integration of transcriptome and proteome datasets revealed an organoid-typic expression signature comprising 14 transcripts and 10 proteins that distinguished organoids across all donors from murine epithelial cell lines and fibroblasts and closely mimicked expression patterns in the gut epithelium. This included the inflammasome components ASC, Naip1-6, Nlrc4 and Caspase-1, which were highly expressed in all organoids compared to the reference cell line m-IC c12 or mouse embryonic fibroblasts. Taken together, these results reveal that the donor microbiota has little effect on the organoid phenotype and suggest that organoids represent a more suitable culture model than immortalised cell lines, in particular for studies of intestinal epithelial inflammasomes.

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“…As a case in point, if chemistry is arguably not reducible to physics (yet unifiable at the same time) [72], in the same spirit could we ask if the properties of a biological system (e.g., a cell) can ever be reduced to the properties of its component parts (e.g., proteins)? As another example, if one excludes some obvious explanations, why are certain findings either in molecular biology or clinical medicine not reproducible [193,194]? Approaches to tackle these and other questions of this kind are well-established in the philosophy of science literature, and therefore philosophical biology and philosophy of science are not exclusive of each other.…”

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confidence: 99%

Analytic Philosophy for Biomedical Research: The Imperative of Applying Yesterday’s Timeless Messages to Today’s Impasses

Ehsani¹

2020

Future of Business and Finance

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The mantra that “the best way to predict the future is to invent it” (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word “theory”) as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined.

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A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines

Cited by 115 publications

References 59 publications

Intestinal epithelial NAIP/NLRC4 restricts systemic dissemination of the adapted pathogen Salmonella Typhimurium due to site-specific bacterial PAMP expression

Intestinal epithelial NAIP/NLRC4 restricts systemic dissemination of the adapted pathogen Salmonella Typhimurium due to site-specific bacterial PAMP expression

Germ‐free and microbiota‐associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes

Analytic Philosophy for Biomedical Research: The Imperative of Applying Yesterday’s Timeless Messages to Today’s Impasses

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