Lightnews — Scholar-powered news

JT Neal

@jtneal.bsky.social

1.1K followers 610 following 35 posts

PI @ http://neallab.org. Scientist building tools to understand genetic variation in health and disease. Trail runner & World’s Okayest Dad.

neallab.org.

Posts Media Videos Starter Packs

Pinned

JT Neal @jtneal.bsky.social · Jan 27

Our paper “A genome-wide atlas of human cell morphology” is finally out today in @naturemethods.bsky.social ! www.nature.com/articles/s41...

(I tweeted about our preprint in 2023 over at the bad place, but deactivated my account, so here we go again!)

A genome-wide atlas of human cell morphology - Nature Methods

An optical pooled cell profiling platform (PERISCOPE) based on Cell Painting and optical sequencing of molecular barcodes was used to develop the first unbiased genome-wide morphology-based perturbati...

www.nature.com

2 40 140

JT Neal @jtneal.bsky.social · Mar 6

I will be there!

(note: the speaking portion of the event has been moved to Boston Common)

#standupforscience2025

www.eventbrite.com/e/stand-up-f...

Flyer says:
Stand up for Science 2025. March 7, 2025 Washington, DC and nationwide. Science is for Everyone. Find your local rally site and other ways to get involved at standupforscience2025.org

Reposted by JT Neal

Dr. Becca @docbecca.bsky.social · Feb 19

If the block on the Federal Register isn’t removed in the next few months, I fear a majority of labs will close within a year. This small procedural wrench has the power to kill US science indefinitely, losing an entire generation of discovery and innovation.

Brian Stevenson Ph.D. spirochete lab @bstevensonlab.bsky.social · Feb 19

I had two grant proposals up for review in the NIH Bacterial Virulence (BV) study section. It was canceled without notice this morning.
Without those grants, my lab must close within a year.
And so the purge of scientific research in the US continues
🤬
#MicroSky 🦠🧫🧪🧬🔬

24 520 1K

Reposted by JT Neal

Maitreyi Das @daslabpombe.com · Feb 7

I don't know who needs to hear this, but none of the preemptive obedience is going to save us.

1 71 800

JT Neal @jtneal.bsky.social · Jan 29

screenshot of famous dril tweet: "im not owned! im not owned!!", i continue to insist as i slowly shrink and transform into a corn cob.”

1 1 4

JT Neal @jtneal.bsky.social · Jan 29

Thanks Gary - I thought I saw you there!

JT Neal @jtneal.bsky.social · Jan 27

Side note: if you happen to be attending #SLAS2025, I’ll be talking about this work at 10AM Tuesday in the Functional Genomics session, stop by and say hi!

1 5

JT Neal @jtneal.bsky.social · Jan 27

All of our data and analysis tools are open source and freely available (see Code and Data availability), and there is much more in the paper than I was able to cover here, so check it out and let us know what you think!

JT Neal @jtneal.bsky.social · Jan 27

We think this atlas will be a useful resource for both biological interrogation and for the development and testing of new image analysis methods.

JT Neal @jtneal.bsky.social · Jan 27

In addition, we present a draft genome scale atlas of human cell morphology containing more than 30 million perturbation-assigned cell images and high-dimensional single cell profiles.

JT Neal @jtneal.bsky.social · Jan 27

We believe this combination of accessibility and cost effectiveness make PERISCOPE-style screens a democratizing platform technology for linking genotypes to cellular programs.

JT Neal @jtneal.bsky.social · Jan 27

In sum, pooled optical screens are a powerful approach for generating high-dimensional genotype-phenotype maps, and we demonstrate that these maps can now be generated routinely (and at a low cost per cell profile) at genome scale using standard imaging equipment and open source analysis pipelines.

JT Neal @jtneal.bsky.social · Jan 27

As an aside, though this finding was scooped by two concurrent papers in @science.org while we were preparing the preprint, it’s encouraging to see a hit from our unbiased imaging screen robustly validated by numerous groups!(www.science.org/doi/10.1126/..., www.science.org/doi/10.1126/...)

The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection

Genome-scale CRISPR screens identify a key protein in lysosome biogenesis relevant for inherited disease and viral infection.

www.science.org

1 1

JT Neal @jtneal.bsky.social · Jan 27

We were also able to use this clustering-by-morphological similarity information (plus mechanistic follow-up) to identify a role for the poorly characterized gene TMEM251 in lysosomal protein trafficking through the M6P-system.

figure showing genes that had high cosine similarity to TMEM251 in our screen

JT Neal @jtneal.bsky.social · Jan 27

as well as identifying shared and media-specific responses to gene perturbation in cells cultured in DMEM vs human plasma-like media (HPLM).

network diagram showing HeLa DMEM and HPLM screen hit cellular processes

JT Neal @jtneal.bsky.social · Jan 27

These screens generated rich phenotypic data, enabling us to use morphological profile similarity to explore relationships between perturbed genes such as clustering protein complex members by morphological similarity, and capturing membership/directionality of signaling pathways.

UMAP showing clustering of genes by physiological function from the HeLa DMEM screen

1 1

JT Neal @jtneal.bsky.social · Jan 27

We then applied these methods to execute 3 whole genome (80,862 sgRNAs targeting 20,393 genes) CRISPR KO screens in A549, and HeLa (paired screens with different growth media).

1 2

JT Neal @jtneal.bsky.social · Jan 27

We ( @erinweisbart.bsky.social , @bethcimini.bsky.social , Greg Way) also built scalable, distributed open source analysis pipelines for alignment/cropping/background correction/barcode calling/etc. allowing us to turn millions of fluorescence images into sgRNA-assigned single cell profiles

schematic showing the overall analysis pipeline

1 1

JT Neal @jtneal.bsky.social · Jan 27

To do this, we first built a variant of the Cell Painting panel that allowed destaining of fluorophores from a subset of markers (via cleavable disulfide or azidomethyl linker) so that we could perform four color in situ sequencing-by-synthesis without fluorescence overlap.

PERISCOPE destaining schematic showing 5 color imaging followed by 4 color in situ sequencing-by-synthesis

1 2

JT Neal @jtneal.bsky.social · Jan 27

So, we teamed up with Anne and Paul’s lab, along with Calvin Jan at Calico, with the aim of building an accessible & unbiased high-content cell profiling platform that could be applied to genome-scale CRISPR screens (Project PERISCOPE).

1 1 2

JT Neal @jtneal.bsky.social · Jan 27

Fortunately, the Blainey Lab and others solved this problem by developing methods to sequence individual perturbation barcodes using in situ sequencing, so we can now assign quantitative cell phenotypes AND barcodes to individual cells, enabling optical pooled screens. www.cell.com/cell/fulltex...

Optical Pooled Screens in Human Cells

A screening approach that combines high-content imaging with in situ sequencing can identify genes that affect spatially and temporally defined phenotypes like morphology and subcellular localization,...

www.cell.com

1 2

JT Neal @jtneal.bsky.social · Jan 27

Such data can be generated easily & cheaply, but historically hasn’t been ideal for large-scale functional genomics because imaging experiments could not use pooled genetic perturbation libraries (no way to optically determine which cell received which perturbation).

1 2

JT Neal @jtneal.bsky.social · Jan 27

Cell images, especially multicolor fluorescence images, are an immense source of phenotypic information, and thanks to approaches like Cell Painting from @drannecarpenter.bsky.social , we can extract this information as quantitative features (size, shape, texture, etc.) in automated fashion.

1 2

JT Neal @jtneal.bsky.social · Jan 27

Even so, and despite amazing recent advances in this space, such as www.cell.com/cell/fulltex... from @weissmanlab.bsky.social, these studies can still be quite difficult to execute at genome-scale. So we turned to another approach: optical fluorescence imaging.

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

Unbiased, genome-scaling profiling of genetic perturbations via single-cell RNA sequencing enables systematic assignment of function to genes and in-depth study of complex cellular phenotypes such as ...

www.cell.com

1 2

JT Neal @jtneal.bsky.social · Jan 27

We’re big fans of using expression-based profiling (specifically Perturb-seq) to generate high-dimensional phenotypic profiles of perturbed cells, and w/ @oana-ursu.bsky.social & @boehmjesse.bsky.social have used it successfully for generating variant effect maps (www.nature.com/articles/s41...)

Massively parallel phenotyping of coding variants in cancer with Perturb-seq - Nature Biotechnology

The functional impact of somatic mutations in cancer genes is determined by pooled Perturb-seq.

www.nature.com

1 1 1

JT Neal @jtneal.bsky.social · Jan 27

For the last several years, a major focus of our lab has been building scalable tools to allow us to link genotypes to cellular programs at genome scale to understand gene and variant function in cancer and metabolic diseases.

1 1