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Morphology and gene expression profiling provide complementary information for mapping cell state.

ABSTRACT: Morphological and gene expression profiling can cost-effectively capture thousands of features in thousands of samples across perturbations by disease, mutation, or drug treatments, but it is unclear to what extent the two modalities capture overlapping versus complementary information. Here, using both the L1000 and Cell Painting assays to profile gene expression and cell morphology, respectively, we perturb human A549 lung cancer cells with 1,327 small molecules from the Drug Repurposing Hub across six doses, providing a data resource including dose-response data from both assays. The two assays capture both shared and complementary information for mapping cell state. Cell Painting profiles from compound perturbations are more reproducible and show more diversity but measure fewer distinct groups of features. Applying unsupervised and supervised methods to predict compound mechanisms of action (MOAs) and gene targets, we find that the two assays not only provide a partially shared but also a complementary view of drug mechanisms. Given the numerous applications of profiling in biology, our analyses provide guidance for planning experiments that profile cells for detecting distinct cell types, disease phenotypes, and response to chemical or genetic perturbations.

SUBMITTER: Way GP

PROVIDER: S-EPMC10246468 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Morphology and gene expression profiling provide complementary information for mapping cell state.

Way Gregory P GP Natoli Ted T Adeboye Adeniyi A Litichevskiy Lev L Yang Andrew A Lu Xiaodong X Caicedo Juan C JC Cimini Beth A BA Karhohs Kyle K Logan David J DJ Rohban Mohammad H MH Kost-Alimova Maria M Hartland Kate K Bornholdt Michael M Chandrasekaran Srinivas Niranj SN Haghighi Marzieh M Weisbart Erin E Singh Shantanu S Subramanian Aravind A Carpenter Anne E AE

Cell systems 20221028 11

Morphological and gene expression profiling can cost-effectively capture thousands of features in thousands of samples across perturbations by disease, mutation, or drug treatments, but it is unclear to what extent the two modalities capture overlapping versus complementary information. Here, using both the L1000 and Cell Painting assays to profile gene expression and cell morphology, respectively, we perturb human A549 lung cancer cells with 1,327 small molecules from the Drug Repurposing Hub a ...[more]

PMID: 36395727

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Project description:BackgroundIn recent years, there has been an increase in the utilization of complementary and integrative health (CIH) care, and an increase in information-seeking behavior focused on CIH. Thus, understanding the quality of CIH information that is available on the internet is imperative. Although there have been a limited number of studies evaluating the quality of websites providing information about specific CIH-related topics, a broad evaluation of CIH websites has not been conducted.ObjectiveThis study was designed to fill that gap. We set out to assess website quality in 5 CIH domains: (1) acupuncture, (2) homeopathy, (3) massage, (4) reiki, and (5) yoga. This study aimed to 1) characterize the websites by type and quality; 2) evaluate website characteristics which may affect readers' perceptions, specifically message content, structural features, and presentation style, and 3) investigate the extent to which harms, benefits and purposes of use are stated on websites.MethodsThis study employed a systematic search strategy to identify websites in each of the target domains to be evaluated. The websites were then classified by type, and a set of checklists focusing on quality, message content, structural features, and presentation style was used to evaluate the websites. Lastly, we performed content analysis to identify harms, benefits, and perceived purposes of use.ResultsThere were similarities across domains regarding their overall quality and their message content. Across all domains, a high proportion of websites received strong scores in terms of ownership, currency, interactivity and navigability. Scores were more variable concerning authorship, balanced presentation of information and the use of sources of information. However, there were differences regarding their structural features and presentation style. Acupuncture and reiki sites tended to include more external links, and yoga, fewer. There was variation across domains in the extent to which the websites contained domain-specific terminology. Websites tended to provide an extensive list of potential benefits, while reporting of harms was scarce.ConclusionsThis is the first study to perform a multidimensional assessment of websites in multiple CIH domains. This review showed that while there are similarities among websites of different CIH domains, there are also differences. The diverse distribution of website types suggests that, regardless of CIH domain, the public encounters information through many different types of media, and it would be useful to consider how the presentation of this content may differ depending on the medium. The characteristics for which variability exist are areas that warrant greater attention from researchers, policy makers, clinicians and patients. There is also a need to better understand how individuals may interact with CIH websites, and to develop tools to assist people to interpret the CIH-related information that they encounter.

Dataset Information

Morphology and gene expression profiling provide complementary information for mapping cell state.

Publications

Morphology and gene expression profiling provide complementary information for mapping cell state.

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