Fluopack screening platform for unbiased cellular phenotype profiling

Zhao, Kang; Moutsatsos, Ioannis K.; Moretti, Francesca; Bergman, Philip S.; Zhang, Xian; Nyfeler, Beat; Antczak, Christophe

doi:10.1038/s41598-020-58861-3

Cited by 14 publications

(14 citation statements)

References 14 publications

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“…We then quantified this observation by measuring the area of individual droplets from a single imaging plane in at least 23 cells per clone and found that the average size of individual lipid droplets was up to 10 times larger among TMEM41B KO clones relative to wildtype cells ( Figure 4E ). Moretti et al reported a similar observation in TMEM41B KO H4 neuroglioma cells and it was later shown that these droplets contain neutral and sterol lipids ( Kang et al, 2020 ; Moretti et al, 2018 ).…”

Section: Resultsmentioning

confidence: 53%

“…To confirm these were indeed lipid droplets, we stained wildtype and six independent TMEM41B KO Huh-7.5 clones with Nile red and found that in all clones lipid droplets are considerably larger as compared to wildtype cells ( Figure 4D). We KO H4 neuroglioma cells and it was later shown that these droplets contain neutral and sterol lipids (Kang et al, 2020;Moretti et al, 2018).…”

Section: Tmem41b Snp Constructs Are Able To Maintain Normal Lipid Dismentioning

confidence: 99%

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TMEM41B is a pan-flavivirus host factor

Hoffmann

Schneider

Rozen-Gagnon

et al. 2020

Preprint

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SUMMARYFlaviviruses pose a constant threat to human health. These RNA viruses are transmitted by the bite of infected mosquitoes and ticks and regularly cause outbreaks. To identify host factors required for flavivirus infection we performed full-genome loss of function CRISPR-Cas9 screens. Based on these results we focused our efforts on characterizing the roles that TMEM41B and VMP1 play in the virus replication cycle. Our mechanistic studies on TMEM41B revealed that all members of the Flaviviridae family that we tested require TMEM41B. We tested 12 additional virus families and found that SARS-CoV-2 of the Coronaviridae also required TMEM41B for infection. Remarkably, single nucleotide polymorphisms (SNPs) present at nearly twenty percent in East Asian populations reduce flavivirus infection. Based on our mechanistic studies we hypothesize that TMEM41B is recruited to flavivirus RNA replication complexes to facilitate membrane curvature, which creates a protected environment for viral genome replication.HIGHLIGHTSTMEM41B and VMP1 are required for both autophagy and flavivirus infection, however, autophagy is not required for flavivirus infection.TMEM41B associates with viral proteins and likely facilitates membrane remodeling to establish viral RNA replication complexes.TMEM41B single nucleotide polymorphisms (SNPs) present at nearly twenty percent in East Asian populations reduce flavivirus infection.TMEM41B-deficient cells display an exaggerated innate immune response upon high multiplicity flavivirus infection.

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Section: Resultsmentioning

confidence: 53%

Section: Tmem41b Snp Constructs Are Able To Maintain Normal Lipid Dismentioning

confidence: 99%

TMEM41B is a pan-flavivirus host factor

Hoffmann

Schneider

Rozen-Gagnon

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“… Moretti et al. (2018) reported a similar observation in TMEM41B KO H4 neuroglioma cells, and it was later shown that these droplets contain neutral and sterol lipids ( Kang et al., 2020 ).…”

Section: Resultsmentioning

confidence: 60%

TMEM41B Is a Pan-flavivirus Host Factor

Hoffmann

Schneider

Rozen-Gagnon

et al. 2021

Cell

145

162

View full text Add to dashboard Cite

Flaviviruses pose a constant threat to human health. These RNA viruses are transmitted by the bite of infected mosquitoes and ticks and regularly cause outbreaks. To identify host factors required for flavivirus infection, we performed full-genome loss of function CRISPR-Cas9 screens. Based on these results, we focused our efforts on characterizing the roles that TMEM41B and VMP1 play in the virus replication cycle. Our mechanistic studies on TMEM41B revealed that all members of the Flaviviridae family that we tested require TMEM41B. We tested 12 additional virus families and found that SARS-CoV-2 of the Coronaviridae also required TMEM41B for infection. Remarkably, single nucleotide polymorphisms present at nearly 20% in East Asian populations reduce flavivirus infection. Based on our mechanistic studies, we propose that TMEM41B is recruited to flavivirus RNA replication complexes to facilitate membrane curvature, which creates a protected environment for viral genome replication.

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“…Imaging mass cytometry also offers substantial multiplexing capacity, but requires expensive, slow instrumentation 175 , 176 . Multiplexed image profiles can also be created by combining readouts from multiple separate assays, each treated with a different fluorescent probe 177 , although preparing multiple wells per sample limits this approach to relatively small numbers of samples.…”

mentioning

confidence: 99%

Image-based profiling for drug discovery: due for a machine-learning upgrade?

Chandrasekaran

Ceulemans

Boyd

et al. 2020

Nat Rev Drug Discov

295

242

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Image-based profiling is a maturing strategy by which the rich information present in biological images is reduced to a multidimensional profile, a collection of extracted image-based features. These profiles can be mined for relevant patterns, revealing unexpected biological activity that is useful for many steps in the drug discovery process. Such applications include identifying disease-associated screenable phenotypes, understanding disease mechanisms and predicting a drug’s activity, toxicity or mechanism of action. Several of these applications have been recently validated and have moved into production mode within academia and the pharmaceutical industry. Some of these have yielded disappointing results in practice but are now of renewed interest due to improved machine-learning strategies that better leverage image-based information. Although challenges remain, novel computational technologies such as deep learning and single-cell methods that better capture the biological information in images hold promise for accelerating drug discovery.

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Fluopack screening platform for unbiased cellular phenotype profiling

Cited by 14 publications

References 14 publications

TMEM41B is a pan-flavivirus host factor

TMEM41B is a pan-flavivirus host factor

TMEM41B Is a Pan-flavivirus Host Factor

Image-based profiling for drug discovery: due for a machine-learning upgrade?

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