The phenotypic landscape of essential human genes

Funk, Luke; Su, Kuan-Chung; Ly, Jimmy; Feldman, David; Singh, Avtar; Moodie, Brittania; Blainey, Paul C.; Cheeseman, Iain M.

doi:10.1016/j.cell.2022.10.017

Cited by 79 publications

(75 citation statements)

References 105 publications

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“…In this section, we propose a roadmap for the integration of new perturbation modalities and phenotypic measurements, the extension of approaches to new biological model systems, and improvements in workflows to enable greater scale and dissemination of technologies. While some aspects we discuss apply to the broader set of microscopy-based screening technologies, we focus our discussion on future implementations of pooled profiling technologies, in particular, ISS-based optical pooled profiling screens of mammalian cells (Feldman et al, 2019(Feldman et al, , 2022Funk et al, 2022).…”

Section: Roadmap For Future Methodsmentioning

confidence: 99%

“…In our initial demonstration, we studied 952 gene knockouts, measuring p65 localization in about 6 million cells in a series of screens and taking time course measurements of live cells for over 400,000 cells in targeted downstream screening (Feldman et al, 2019). Recently, we extended this approach to screen about 20,000 gRNAs targeting 5,072 essential genes, profiling DNA content, DNA damage, and microtubule and F-actin subcellular organization across 31 million cells (Funk et al, 2022).…”

Section: Pooled Profiling Screensmentioning

confidence: 99%

“…In two examples, Schmitz et al (2010) and our group leveraged live-cell imaging in screens to study the dynamic events of mitosis (Funk et al, 2022). Schmitz et al (2010) identified regulators of mitotic exit through an arrayed RNAi screen with live-cell imaging, tracking individual cells with nuclear and histone fluorescent reporters.…”

Section: Live-cell Imagingmentioning

confidence: 99%

“…Schmitz et al (2010) identified regulators of mitotic exit through an arrayed RNAi screen with live-cell imaging, tracking individual cells with nuclear and histone fluorescent reporters. A decade later, our group used a nuclear stain to perform a live-cell pooled CRISPR KO screen as part of a study identifying essential genes that altered mitotic frequency and duration (Funk et al, 2022).…”

Section: Live-cell Imagingmentioning

confidence: 99%

“…In particular, approaches like 4i, Immuno-SABER, and CODEX appear attractive for multiplexing tens of protein targets at high cellular throughput (Goltsev et al, 2018;Gut et al, 2018;Saka et al, 2019). We expect integrating these approaches into the existing optical pooled screening genotyping procedure to be relatively straightforward, as we have already implemented one reversible IF protocol developed at our institute with optical pooled screens (Funk et al, 2022), although extensive staining, imaging, and destaining may pose challenges for sample stability and feature fidelity at the highest levels of multiplexing.…”

Section: Multiplexed Molecular Measurementsmentioning

confidence: 99%

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Pooled genetic screens with image‐based profiling

Walton

Singh

Blainey

2022

Molecular Systems Biology

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Spatial structure in biology, spanning molecular, organellular, cellular, tissue, and organismal scales, is encoded through a combination of genetic and epigenetic factors in individual cells. Microscopy remains the most direct approach to exploring the intricate spatial complexity defining biological systems and the structured dynamic responses of these systems to perturbations. Genetic screens with deep single‐cell profiling via image features or gene expression programs have the capacity to show how biological systems work in detail by cataloging many cellular phenotypes with one experimental assay. Microscopy‐based cellular profiling provides information complementary to next‐generation sequencing (NGS) profiling and has only recently become compatible with large‐scale genetic screens. Optical screening now offers the scale needed for systematic characterization and is poised for further scale‐up. We discuss how these methodologies, together with emerging technologies for genetic perturbation and microscopy‐based multiplexed molecular phenotyping, are powering new approaches to reveal genotype–phenotype relationships.

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Section: Roadmap For Future Methodsmentioning

confidence: 99%

Section: Pooled Profiling Screensmentioning

confidence: 99%

Section: Live-cell Imagingmentioning

confidence: 99%

Section: Live-cell Imagingmentioning

confidence: 99%

Section: Multiplexed Molecular Measurementsmentioning

confidence: 99%

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Pooled genetic screens with image‐based profiling

Walton

Singh

Blainey

2022

Molecular Systems Biology

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Phosphoserine aminotransferase deficiency diagnosed by whole‐exome sequencing and LC–MS/MS reanalysis: A case report and review of literature

Li,

Wei,

Sun

et al. 2024

Molec Gen & Gen Med

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BackgroundPhosphoserine aminotransferase deficiency (PSATD) is an autosomal recessive disorder associated with hypertonia, psychomotor retardation, and acquired microcephaly. Patients with PSATD have low concentrations of serine in plasma and cerebrospinal fluid.MethodsWe reported a 2‐year‐old female child with developmental delay, dyskinesia, and microcephaly. LC–MS/MS was used to detect amino acid concentration in the blood and whole‐exome sequencing (WES) was used to identify the variants. PolyPhen‐2 web server and PyMol were used to predict the pathogenicity and changes in the 3D model molecular structure of protein caused by variants.ResultsWES demonstrated compound heterozygous variants in PSAT1, which is associated with PSATD, with a paternal likely pathogenic variant (c.235G>A, Gly79Arg) and a maternal likely pathogenic variant (c.43G>C, Ala15Pro). Reduced serine concentration in LC–MS/MS further confirmed the diagnosis of PSATD in this patient.ConclusionsOur findings demonstrate the importance of WES combined with LC–MS/MS reanalysis in the diagnosis of genetic diseases and expand the PSAT1 variant spectrum in PSATD. Moreover, we summarize all the cases caused by PSAT1 variants in the literature. This case provides a vital reference for the diagnosis of future cases.

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Essential genes: a cross-species perspective

Cacheiro

Smedley

2023

Mamm Genome

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Protein coding genes exhibit different degrees of intolerance to loss-of-function variation. The most intolerant genes, whose function is essential for cell or/and organism survival, inform on fundamental biological processes related to cell proliferation and organism development and provide a window on the molecular mechanisms of human disease. Here we present a brief overview of the resources and knowledge gathered around gene essentiality, from cancer cell lines to model organisms to human development. We outline the implications of using different sources of evidence and definitions to determine which genes are essential and highlight how information on the essentiality status of a gene can inform novel disease gene discovery and therapeutic target identification.

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The phenotypic landscape of essential human genes

Cited by 79 publications

References 105 publications

Pooled genetic screens with image‐based profiling

Pooled genetic screens with image‐based profiling

Phosphoserine aminotransferase deficiency diagnosed by whole‐exome sequencing and LC–MS/MS reanalysis: A case report and review of literature

Essential genes: a cross-species perspective

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