bims-pideca 2023-05-14 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2023–05–14
thirty papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag.
Utilizing flow cytometry sorting signal width to enrich for cells positive to endogenous gene integration of fluorescent proteins.
MTHFD2 reprograms macrophage polarization by inhibiting PTEN.
Predictive data-driven modeling of C-terminal tyrosine function in the EGFR signaling network.
Confinement of unliganded EGFR by tetraspanin nanodomains gates EGFR ligand binding and signaling.
A prime editor mouse to model a broad spectrum of somatic mutations in vivo.
The Ribosomal S6 Kinase 2 (RSK2)-SPRED2 complex regulates phosphorylation of RSK substrates and MAPK signaling.
PIK3CA mutation in endometriotic epithelial cells promotes viperin-dependent inflammatory response to insulin.
Mechanisms of skin vascular maturation and maintenance captured by longitudinal imaging of live mice.
Cancer researchers' perceptions of the importance of the sex of cell lines, animals, and human samples for cancer biology research.
Triggered Golgi membrane enrichment promotes PtdIns(4,5)P2 generation for plasma membrane repair.
Stimulation of the catalytic activity of the tyrosine kinase Btk by the adaptor protein Grb2.
GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery.
Activated EGFR and PDGFR internalize in separate vesicles and downstream AKT and ERK1/2 signaling are differentially impacted by cholesterol depletion.
Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples.
The epithelial-mesenchymal plasticity landscape: principles of design and mechanisms of regulation.
E2 ubiquitin-conjugating enzymes, UBE2D1 and UBE2D2, regulate VEGFR2 dynamics and endothelial function.
Efficient cancer modeling through CRISPR-Cas9/HDR-based somatic precision gene editing in mice.
scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics.
How their environment influences endothelial cells.
Zebrafish imaging reveals hidden oncogenic-normal cell communication during primary tumorigenesis.
Long lifetime and selective accumulation of the A-type lamins accounts for the tissue specificity of Hutchinson-Gilford progeria syndrome.
Daily briefing: New organelle discovered inside animal cell.
A platform for efficient establishment and drug-response profiling of high-grade serous ovarian cancer organoids.
The Edge Effect in High-Throughput Proteomics: A Cautionary Tale.
Hepatic mTORC2 compensates for loss of adipose mTORC2 in mediating energy storage and glucose homeostasis.
Predicting cellular responses to complex perturbations in high-throughput screens.
The PECAn image and statistical analysis pipeline identifies Minute cell competition genes and features.
Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis.
Macromolecular crowding limits growth under pressure.

Nat Methods. 2023 May 08.

Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag.

Shun-Qing Liang, Pengpeng Liu, Karthikeyan Ponnienselvan, Sneha Suresh, Zexiang Chen, Christian Kramme, Pranam Chatterjee, Lihua Julie Zhu, Erik J Sontheimer, Wen Xue, Scot A Wolfe.

Prime editors have a broad range of potential research and clinical applications. However, methods to delineate their genome-wide editing activities have generally relied on indirect genome-wide editing assessments or the computational prediction of near-cognate sequences. Here we describe a genome-wide approach for the identification of potential prime editor off-target sites, which we call PE-tag. This method relies on the attachment or insertion of an amplification tag at sites of prime editor activity to allow their identification. PE-tag enables genome-wide profiling of off-target sites in vitro using extracted genomic DNA, in mammalian cell lines and in the adult mouse liver. PE-tag components can be delivered in a variety of formats for off-target site detection. Our studies are consistent with the high specificity previously described for prime editor systems, but we find that off-target editing rates are influenced by prime editing guide RNA design. PE-tag represents an accessible, rapid and sensitive approach for the genome-wide identification of prime editor activity and the evaluation of prime editor safety.

DOI: https://doi.org/10.1038/s41592-023-01859-2
Cytometry A. 2023 May 09.

Utilizing flow cytometry sorting signal width to enrich for cells positive to endogenous gene integration of fluorescent proteins.

Gabriel P Faber, Hagit Hauschner, Mohammad K Atrash, Liat Bilinsky, Yaron Shav-Tal.

  Endogenous gene knock-in using CRIPSR is becoming the standard for fluorescent tagging of endogenous proteins. Some protocols, particularly those that utilize insert cassettes that carry a fluorescent protein tag, can yield many types of cells with off-target insertions that have diffuse fluorescent signal throughout the whole cell in addition to scarce cells with on-target gene insertions that show the correct sub-cellular localization of the tagged protein. As such, when searching for cells with on-target integration using flow cytometry, the off-target fluorescent cells yield a high percentage of false positives. Here, we show that by changing the gating used to select for fluorescence during flow cytometry sorting, namely utilizing the width of the signal as opposed to the area, we can highly enrich for positively integrated cells. Reproducible gates were created to select even minuscule percentages of correct subcellular signal, and these parameters were validated by fluorescence microscopy. This method is a powerful tool to rapidly enhance the generation of cell lines with correctly integrated gene knock-ins encoding endogenous fluorescent proteins.

Keywords:  CRISPR Cas12a; FACS; cell sorting; gene knock-in

DOI:  https://doi.org/10.1002/cyto.a.24735
Cell Rep. 2023 May 05. pii: S2211-1247(23)00492-8. [Epub ahead of print]42(5): 112481

MTHFD2 reprograms macrophage polarization by inhibiting PTEN.

Man Shang, Lina Ni, Xiao Shan, Yan Cui, Penghui Hu, Zemin Ji, Long Shen, Yanan Zhang, Jinxue Zhou, Bing Chen, Ting Wang, Qiujing Yu.

  The one-carbon metabolism enzyme methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) is involved in the regulation of tumor oncogenesis and immune cell functions, but whether it can contribute to macrophage polarization remains elusive. Here, we show that MTHFD2 suppresses polarization of interferon-γ-activated macrophages (M(IFN-γ)) but enhances that of interleukin-4-activated macrophages (M(IL-4)) both in vitro and in vivo. Mechanistically, MTHFD2 interacts with phosphatase and tensin homolog (PTEN) to suppress PTEN's phosphatidylinositol 3,4,5-trisphosphate (PIP3) phosphatase activity and enhance downstream Akt activation, independent of the N-terminal mitochondria-targeting signal of MTHFD2. MTHFD2-PTEN interaction is promoted by IL-4 but not IFN-γ. Furthermore, amino acid residues (aa 215-225) of MTHFD2 directly target PTEN catalytic center (aa 118-141). Residue D168 of MTHFD2 is also critical for regulating PTEN's PIP3 phosphatase activity by affecting MTHFD2-PTEN interaction. Our study suggests a non-metabolic function of MTHFD2 by which MTHFD2 inhibits PTEN activity, orchestrates macrophage polarization, and alters macrophage-mediated immune responses.

Keywords:  CP: Immunology; MTHFD2; PTEN; macrophage polarization

DOI:  https://doi.org/10.1016/j.celrep.2023.112481
Life Sci Alliance. 2023 Aug;pii: e202201466. [Epub ahead of print]6(8):

Predictive data-driven modeling of C-terminal tyrosine function in the EGFR signaling network.

Jacqueline S Gerritsen, Joseph S Faraguna, Rudy Bonavia, Frank B Furnari, Forest M White.

The epidermal growth factor receptor (EGFR) has been studied extensively because of its critical role in cellular signaling and association with disease. Previous models have elucidated interactions between EGFR and downstream adaptor proteins or showed phenotypes affected by EGFR. However, the link between specific EGFR phosphorylation sites and phenotypic outcomes is still poorly understood. Here, we employed a suite of isogenic cell lines expressing site-specific mutations at each of the EGFR C-terminal phosphorylation sites to interrogate their role in the signaling network and cell biological response to stimulation. Our results demonstrate the resilience of the EGFR network, which was largely similar even in the context of multiple Y-to-F mutations in the EGFR C-terminal tail, while also revealing nodes in the network that have not previously been linked to EGFR signaling. Our data-driven model highlights the signaling network nodes associated with distinct EGF-driven cell responses, including migration, proliferation, and receptor trafficking. Application of this same approach to less-studied RTKs should provide a plethora of novel associations that should lead to an improved understanding of these signaling networks.

DOI: https://doi.org/10.26508/lsa.202201466
Nat Commun. 2023 May 09. 14(1): 2681

Confinement of unliganded EGFR by tetraspanin nanodomains gates EGFR ligand binding and signaling.

Michael G Sugiyama, Aidan I Brown, Jesus Vega-Lugo, Jazlyn P Borges, Andrew M Scott, Khuloud Jaqaman, Gregory D Fairn, Costin N Antonescu.

The epidermal growth factor receptor (EGFR) is a central regulator of cell physiology. EGFR is activated by ligand binding, triggering receptor dimerization, activation of kinase activity, and intracellular signaling. EGFR is transiently confined within various plasma membrane nanodomains, yet how this may contribute to regulation of EGFR ligand binding is poorly understood. To resolve how EGFR nanoscale compartmentalization gates ligand binding, we developed single-particle tracking methods to track the mobility of ligand-bound and total EGFR, in combination with modeling of EGFR ligand binding. In comparison to unliganded EGFR, ligand-bound EGFR is more confined and distinctly regulated by clathrin and tetraspanin nanodomains. Ligand binding to unliganded EGFR occurs preferentially in tetraspanin nanodomains, and disruption of tetraspanin nanodomains impairs EGFR ligand binding and alters the conformation of the receptor's ectodomain. We thus reveal a mechanism by which EGFR confinement within tetraspanin nanodomains regulates receptor signaling at the level of ligand binding.

DOI: https://doi.org/10.1038/s41467-023-38390-z
Nat Biotechnol. 2023 May 11.

A prime editor mouse to model a broad spectrum of somatic mutations in vivo.

Zackery A Ely, Nicolas Mathey-Andrews, Santiago Naranjo, Samuel I Gould, Kim L Mercer, Gregory A Newby, Christina M Cabana, William M Rideout, Grissel Cervantes Jaramillo, Jennifer M Khirallah, Katie Holland, Peyton B Randolph, William A Freed-Pastor, Jessie R Davis, Zachary Kulstad, Peter M K Westcott, Lin Lin, Andrew V Anzalone, Brendan L Horton, Nimisha B Pattada, Sean-Luc Shanahan, Zhongfeng Ye, Stefani Spranger, Qiaobing Xu, Francisco J Sánchez-Rivera, David R Liu, Tyler Jacks.

Genetically engineered mouse models only capture a small fraction of the genetic lesions that drive human cancer. Current CRISPR-Cas9 models can expand this fraction but are limited by their reliance on error-prone DNA repair. Here we develop a system for in vivo prime editing by encoding a Cre-inducible prime editor in the mouse germline. This model allows rapid, precise engineering of a wide range of mutations in cell lines and organoids derived from primary tissues, including a clinically relevant Kras mutation associated with drug resistance and Trp53 hotspot mutations commonly observed in pancreatic cancer. With this system, we demonstrate somatic prime editing in vivo using lipid nanoparticles, and we model lung and pancreatic cancer through viral delivery of prime editing guide RNAs or orthotopic transplantation of prime-edited organoids. We believe that this approach will accelerate functional studies of cancer-associated mutations and complex genetic combinations that are challenging to construct with traditional models.

DOI: https://doi.org/10.1038/s41587-023-01783-y
J Biol Chem. 2023 May 04. pii: S0021-9258(23)01817-3. [Epub ahead of print] 104789

The Ribosomal S6 Kinase 2 (RSK2)-SPRED2 complex regulates phosphorylation of RSK substrates and MAPK signaling.

Jocelyne Lopez, Daniel A Bonsor, Matthew J Sale, Anatoly Urisman, Jennifer L Mehalko, Miranda Cabanski-Dunning, Pau Castel, Dhirendra K Simanshu, Frank McCormick.

  Sprouty-related EVH-1 domain-containing (SPRED) proteins are a family of proteins that negatively regulate the RAS-MAPK pathway, which is involved in the regulation of the mitogenic response and cell proliferation. However, the mechanism by which these proteins affect RAS-MAPK signaling has not been fully elucidated. Patients with mutations in SPRED give rise to unique disease phenotypes, thus we hypothesized that distinct interactions across SPRED proteins may account for alternative nodes of regulation. To characterize the SPRED interactome and evaluate how members of the SPRED family function through unique binding partners, here we performed affinity purification mass spectrometry. We identified 90-kDa ribosomal S6 kinase 2 (RSK2) as a specific interactor of SPRED2, but not SPRED1 or SPRED3. We identified that the N-terminal kinase domain of RSK2 mediates interaction between amino acids 123-201 of SPRED2. Using X-ray crystallography, we determined the structure of the SPRED2-RSK2 complex and identified the SPRED2 motif, F145A, as critical for interaction. Additionally, we found that formation of this interaction is regulated by MAPK signaling events. We also find that that this interaction between SPRED2 and RSK2 has functional consequences, whereby knockdown of SPRED2 resulted in increased phosphorylation of RSK substrates, YB1 and CREB. Furthermore, SPRED2 knockdown hindered phospho-RSK membrane and nuclear subcellular localization. Lastly, we report that disruption of the SPRED2-RSK complex has effects on RAS-MAPK signaling dynamics. Overall, our analysis reveals that members of the SPRED family have unique protein binding partners and describes the molecular and functional determinants of SPRED2-RSK2 complex dynamics.

Keywords:  RASopathy; RSK2; SPRED2; neurofibromin

DOI:  https://doi.org/10.1016/j.jbc.2023.104789
Reprod Biol Endocrinol. 2023 May 11. 21(1): 43

PIK3CA mutation in endometriotic epithelial cells promotes viperin-dependent inflammatory response to insulin.

Mike R Wilson, Shannon Harkins, Jake J Reske, Rebecca A Siwicki, Marie Adams, Victoria L Bae-Jump, Jose M Teixeira, Ronald L Chandler.

  Endometrial epithelia are known to harbor cancer driver mutations in the absence of any pathologies, including mutations in PIK3CA. Insulin plays an important role in regulating uterine metabolism during pregnancy, and hyperinsulinemia is associated with conditions impacting fertility. Hyperinsulinemia also promotes cancer, but the direct action of insulin on mutated endometrial epithelial cells is unknown. Here, we treated 12Z endometriotic epithelial cells carrying the PIK3CAH1047R oncogene with insulin and examined transcriptomes by RNA-seq. While cells naively responded to insulin, the magnitude of differential gene expression (DGE) was nine times greater in PIK3CAH1047R cells, representing a synergistic effect between insulin signaling and PIK3CAH1047R expression. Interferon signaling and the unfolded protein response (UPR) were enriched pathways among affected genes. Insulin treatment in wild-type cells activated normal endoplasmic reticulum stress (ERS) response programs, while PIK3CAH1047R cells activated programs necessary to avoid ERS-induced apoptosis. PIK3CAH1047R expression alone resulted in overexpression (OE) of Viperin (RSAD2), which is involved in viral response and upregulated in the endometrium during early pregnancy. The transcriptional changes induced by insulin in PIK3CAH1047R cells were rescued by knockdown of Viperin, while Viperin OE alone was insufficient to induce a DGE response to insulin, suggesting that Viperin is necessary but not sufficient for the synergistic effect of PIK3CAH1047R and insulin treatment. We identified interferon signaling, viral response, and protein targeting pathways that are induced by insulin but dependent on Viperin in PIK3CAH1047R mutant cells. These results suggest that response to insulin signaling is altered in mutated endometriotic epithelial cells.

Keywords:  Endometrium; Endoplasmic reticulum stress; Insulin; Interferon; Phosphatidylinositide 3-kinase

DOI:  https://doi.org/10.1186/s12958-023-01094-6
Cell. 2023 May 03. pii: S0092-8674(23)00413-0. [Epub ahead of print]

Mechanisms of skin vascular maturation and maintenance captured by longitudinal imaging of live mice.

Chen Yuan Kam, Ishani D Singh, David G Gonzalez, Catherine Matte-Martone, Paloma Solá, Guiomar Solanas, Júlia Bonjoch, Edward Marsh, Karen K Hirschi, Valentina Greco.

  A functional network of blood vessels is essential for organ growth and homeostasis, yet how the vasculature matures and maintains homeostasis remains elusive in live mice. By longitudinally tracking the same neonatal endothelial cells (ECs) over days to weeks, we found that capillary plexus expansion is driven by vessel regression to optimize network perfusion. Neonatal ECs rearrange positions to evenly distribute throughout the developing plexus and become positionally stable in adulthood. Upon local ablation, adult ECs survive through a plasmalemmal self-repair response, while neonatal ECs are predisposed to die. Furthermore, adult ECs reactivate migration to assist vessel repair. Global ablation reveals coordinated maintenance of the adult vascular architecture that allows for eventual network recovery. Lastly, neonatal remodeling and adult maintenance of the skin vascular plexus are orchestrated by temporally restricted, neonatal VEGFR2 signaling. Our work sheds light on fundamental mechanisms that underlie both vascular maturation and adult homeostasis in vivo.

Keywords:  angiogenesis; blood flow; capillary; endothelial cell; live imaging; neonatal development; skin; vascular homeostasis; vascular repair; vessel regression

DOI:  https://doi.org/10.1016/j.cell.2023.04.017
iScience. 2023 Apr 21. 26(4): 106212

Cancer researchers' perceptions of the importance of the sex of cell lines, animals, and human samples for cancer biology research.

Berna C Özdemir, Anke Richters, Cristina Espinosa da Silva, Alison May Berner.

  Sex differences in cancer risk and outcome are currently a topic of major interest in clinical oncology. It is however unknown to what extent cancer researchers consider sex as a biological variable for their research. We conducted an international survey among 1243 academic cancer researchers and collected both quantitative and qualitative data. Although most of the participants indicated that they were familiar with the concept of studying sex differences in cancer biology, they did not think it was important to investigate sex differences in every context of cancer research nor in all tumor types. This is in stark contrast to the current recommendations and guidelines and illustrates the need for increased awareness among cancer researchers regarding the potential impact of the sex of cell lines, animals, and human samples in their studies.

Keywords:  Cancer; Cellular physiology; Oncology

DOI:  https://doi.org/10.1016/j.isci.2023.106212
J Cell Biol. 2023 Aug 07. pii: e202303017. [Epub ahead of print]222(8):

Triggered Golgi membrane enrichment promotes PtdIns(4,5)P2 generation for plasma membrane repair.

Xinan Meng, Chandra Sugiarto Wijaya, Qingfang Shao, Suhong Xu.

The maintenance of plasma membrane integrity and a capacity for efficiently repairing damaged membranes are essential for cell survival. Large-scale wounding depletes various membrane components at the wound sites, including phosphatidylinositols, yet little is known about how phosphatidylinositols are generated after depletion. Here, working with our in vivo C. elegans epidermal cell wounding model, we discovered phosphatidylinositol 4-phosphate (PtdIns4P) accumulation and local phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] generation at the wound site. We found that PtdIns(4,5)P2 generation depends on the delivery of PtdIns4P, PI4K, and PI4P 5-kinase PPK-1. In addition, we show that wounding triggers enrichment of the Golgi membrane to the wound site, and that is required for membrane repair. Moreover, genetic and pharmacological inhibitor experiments support that the Golgi membrane provides the PtdIns4P for PtdIns(4,5)P2 generation at the wounds. Our findings demonstrate how the Golgi apparatus facilitates membrane repair in response to wounding and offers a valuable perspective on cellular survival mechanisms upon mechanical stress in a physiological context.

DOI: https://doi.org/10.1083/jcb.202303017
Elife. 2023 Apr 26. pii: e82676. [Epub ahead of print]12

Stimulation of the catalytic activity of the tyrosine kinase Btk by the adaptor protein Grb2.

Laura M Nocka, Timothy J Eisen, Anthony T Iavarone, Jay T Groves, John Kuriyan.

  The Tec-family kinase Btk contains a lipid-binding Pleckstrin homology and Tec homology (PH-TH) module connected by a proline-rich linker to a 'Src module', an SH3-SH2-kinase unit also found in Src-family kinases and Abl. We showed previously that Btk is activated by PH-TH dimerization, which is triggered on membranes by the phosphatidyl inositol phosphate PIP3, or in solution by inositol hexakisphosphate (IP6) (Wang et al., 2015, https://doi.org/10.7554/eLife.06074). We now report that the ubiquitous adaptor protein growth-factor-receptor-bound protein 2 (Grb2) binds to and substantially increases the activity of PIP3-bound Btk on membranes. Using reconstitution on supported-lipid bilayers, we find that Grb2 can be recruited to membrane-bound Btk through interaction with the proline-rich linker in Btk. This interaction requires intact Grb2, containing both SH3 domains and the SH2 domain, but does not require that the SH2 domain be able to bind phosphorylated tyrosine residues - thus Grb2 bound to Btk is free to interact with scaffold proteins via the SH2 domain. We show that the Grb2-Btk interaction recruits Btk to scaffold-mediated signaling clusters in reconstituted membranes. Our findings indicate that PIP3-mediated dimerization of Btk does not fully activate Btk, and that Btk adopts an autoinhibited state at the membrane that is released by Grb2.

Keywords:  B-cell; Btk; E. coli; Grb2; adaptor; biochemistry; chemical biology; immune signaling; molecular biophysics; protein kinase; structural biology

DOI:  https://doi.org/10.7554/eLife.82676
Nucleic Acids Res. 2023 May 11. pii: gkad399. [Epub ahead of print]

GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery.

Giacomo B Marino, Michael Ngai, Daniel J B Clarke, Reid H Fleishman, Eden Z Deng, Zhuorui Xie, Nasheath Ahmed, Avi Ma'ayan.

Several atlasing efforts aim to profile human gene and protein expression across tissues, cell types and cell lines in normal physiology, development and disease. One utility of these resources is to examine the expression of a single gene across all cell types, tissues and cell lines in each atlas. However, there is currently no centralized place that integrates data from several atlases to provide this type of data in a uniform format for visualization, analysis and download, and via an application programming interface. To address this need, GeneRanger is a web server that provides access to processed data about gene and protein expression across normal human cell types, tissues and cell lines from several atlases. At the same time, TargetRanger is a related web server that takes as input RNA-seq data from profiled human cells and tissues, and then compares the uploaded input data to expression levels across the atlases to identify genes that are highly expressed in the input and lowly expressed across normal human cell types and tissues. Identified targets can be filtered by transmembrane or secreted proteins. The results from GeneRanger and TargetRanger are visualized as box and scatter plots, and as interactive tables. GeneRanger and TargetRanger are available from https://generanger.maayanlab.cloud and https://targetranger.maayanlab.cloud, respectively.

DOI: https://doi.org/10.1093/nar/gkad399
Biochem Biophys Res Commun. 2023 May 03. pii: S0006-291X(23)00530-2. [Epub ahead of print]665 195-201

Activated EGFR and PDGFR internalize in separate vesicles and downstream AKT and ERK1/2 signaling are differentially impacted by cholesterol depletion.

Erik Wåhlén, Frida Olsson, Doroteya Raykova, Ola Söderberg, Johan Heldin, Johan Lennartsson.

  The interplay between membrane subregions and receptor tyrosine kinases (RTK) will influence signaling in both normal and pathological RTK conditions. In this study, epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor β (PDGFR-β) internalizations were investigated by immunofluorescent microscopy following simultaneous treatment with EGF and PDGF-BB. We found that the two receptors utilize separate routes of internalization, which merges in a common perinuclear endosomal compartment after 45 min of stimulation. This is further strengthened when contrasting the recruitment of either EGFR or PDGFR-β to either clathrin or caveolin-1: PDGFR-β dissociates from caveolin-1 upon stimulation, and engages clathrin, whilst an increased recruitment of EGFR, to both clathrin and caveolin-1, was observed upon EGF stimulation. The association between EGFR and caveolin-1 is supported by the observation that EGFR was localized in lipid raft associated fractions, whereas PDGFR-β was not. We also found that disruption of lipid rafts using MβCD led to an increased EGFR dimerization and phosphorylation in response to ligand, as well as a dramatic decrease in AKT- and a smaller but robust decrease in ERK1/2 phosphorylation. This suggest that lipid rafts may be important to effectively connect the EGFR with downstream proteins to facilitate signaling. Our data implies that cholesterol depletion of the plasma membrane affect the signaling of EGFR and PDGFRβ differently.

Keywords:  EGF; EGFR; Internalization; Lipid rafts; Membrane raft; PDGF; PDGFR; Receptor tyrosine kinase

DOI:  https://doi.org/10.1016/j.bbrc.2023.04.099
bioRxiv. 2023 Apr 30. pii: 2023.04.28.538731. [Epub ahead of print]

Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples.

Hratch Baghdassarian, Daniel Dimitrov, Erick Armingol, Julio Saez-Rodriguez, Nathan E Lewis.

In recent years, data-driven inference of cell-cell communication has helped reveal coordinated biological processes across cell types. While multiple cell-cell communication tools exist, results are specific to the tool of choice, due to the diverse assumptions made across computational frameworks. Moreover, tools are often limited to analyzing single samples or to performing pairwise comparisons. As experimental design complexity and sample numbers continue to increase in single-cell datasets, so does the need for generalizable methods to decipher cell-cell communication in such scenarios. Here, we integrate two tools, LIANA and Tensor-cell2cell, which combined can deploy multiple existing methods and resources, to enable the robust and flexible identification of cell-cell communication programs across multiple samples. In this protocol, we show how the integration of our tools facilitates the choice of method to infer cell-cell communication and subsequently perform an unsupervised deconvolution to obtain and summarize biological insights. We explain how to perform the analysis step-by-step in both Python and R, and we provide online tutorials with detailed instructions available at https://ccc-protocols.readthedocs.io/ . This protocol typically takes ∼1.5h to complete from installation to downstream visualizations on a GPU-enabled computer, for a dataset of ∼63k cells, 10 cell types, and 12 samples.

DOI: https://doi.org/10.1101/2023.04.28.538731
Nat Rev Genet. 2023 May 11.

The epithelial-mesenchymal plasticity landscape: principles of design and mechanisms of regulation.

Jef Haerinck, Steven Goossens, Geert Berx.

Epithelial-mesenchymal plasticity (EMP) enables cells to interconvert between several states across the epithelial-mesenchymal landscape, thereby acquiring hybrid epithelial/mesenchymal phenotypic features. This plasticity is crucial for embryonic development and wound healing, but also underlies the acquisition of several malignant traits during cancer progression. Recent research using systems biology and single-cell profiling methods has provided novel insights into the main forces that shape EMP, which include the microenvironment, lineage specification and cell identity, and the genome. Additionally, key roles have emerged for hysteresis (cell memory) and cellular noise, which can drive stochastic transitions between cell states. Here, we review these forces and the distinct but interwoven layers of regulatory control that stabilize EMP states or facilitate epithelial-mesenchymal transitions (EMTs) and discuss the therapeutic potential of manipulating the EMP landscape.

DOI: https://doi.org/10.1038/s41576-023-00601-0
J Cell Sci. 2023 May 09. pii: jcs.260657. [Epub ahead of print]

E2 ubiquitin-conjugating enzymes, UBE2D1 and UBE2D2, regulate VEGFR2 dynamics and endothelial function.

William R Critchley, Gina A Smith, Ian C Zachary, Michael A Harrison, Sreenivasan Ponnambalam.

  Vascular endothelial growth factor receptor 2 (VEGFR2) regulates endothelial function and angiogenesis. VEGFR2 undergoes ubiquitination which programs this receptor for trafficking and proteolysis but the ubiquitin-modifying enzymes involved are ill-defined. Herein, we used a reverse genetics screen of the human E2 family of ubiquitin-conjugating enzymes to identify gene products which regulate VEGFR2 ubiquitination and proteolysis. We find that depletion of either UBE2D1 or UBE2D2 in endothelial cells cause a rise in steady-state VEGFR2 levels. This rise in plasma membrane VEGFR2 levels impact on VEGF-A-stimulated signalling, with increased activation of canonical MAPK, phospholipase C1, and Akt pathways. Analysis of biosynthetic VEGFR2 is consistent with a role for UBE2D enzymes in influencing plasma membrane VEGFR2 levels. Cell surface biotinylation and recycling studies show an increase in VEGFR2 recycling to the plasma membrane upon reduction in UBE2D levels. Depletion of either UBE2D1 or UBE2D2 stimulates endothelial tubulogenesis which is consistent with increased VEGFR2 plasma membrane levels promoting the cellular response to exogenous VEGF-A. Our studies identify a key role for UBE2D1 and UBE2D2 in regulating VEGFR2 function in angiogenesis.

Keywords:  Angiogenesis; Endothelial; Signalling; UBE2D1; UBE2D2; Ubiquitin; VEGFR2

DOI:  https://doi.org/10.1242/jcs.260657
Sci Adv. 2023 May 12. 9(19): eade0059

Efficient cancer modeling through CRISPR-Cas9/HDR-based somatic precision gene editing in mice.

Wen Bu, Chad J Creighton, Kelsey S Heavener, Carolina Gutierrez, Yongchao Dou, Amy T Ku, Yiqun Zhang, Weiyu Jiang, Jazmin Urrutia, Wen Jiang, Fei Yue, Luyu Jia, Ahmed Atef Ibrahim, Bing Zhang, Shixia Huang, Yi Li.

CRISPR-Cas9 has been used successfully to introduce indels in somatic cells of rodents; however, precise editing of single nucleotides has been hampered by limitations of flexibility and efficiency. Here, we report technological modifications to the CRISPR-Cas9 vector system that now allows homology-directed repair-mediated precise editing of any proto-oncogene in murine somatic tissues to generate tumor models with high flexibility and efficiency. Somatic editing of either Kras or Pik3ca in both normal and hyperplastic mammary glands led to swift tumorigenesis. The resulting tumors shared some histological, transcriptome, and proteome features with tumors induced by lentivirus-mediated expression of the respective oncogenes, but they also exhibited some distinct characteristics, particularly showing less intertumor variation, thus potentially offering more consistent models for cancer studies and therapeutic development. Therefore, this technological advance fills a critical gap between the power of CRISPR technology and high-fidelity mouse models for studying human tumor evolution and preclinical drug testing.

DOI: https://doi.org/10.1126/sciadv.ade0059
Nat Biotechnol. 2023 May 11.

scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics.

Dongyuan Song, Qingyang Wang, Guanao Yan, Tianyang Liu, Tianyi Sun, Jingyi Jessica Li.

We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories and spatial locations; and generates in silico negative and positive controls for benchmarking computational tools.

DOI: https://doi.org/10.1038/s41587-023-01772-1
Elife. 2023 May 09. pii: e88248. [Epub ahead of print]12

How their environment influences endothelial cells.

Xuejing Liu, Zhen Bouman Chen.

  Changes in gene expression in cultured endothelial cells can be partially reversed by simulating in vivo conditions.

Keywords:  cell biology; endothelial cell; gene expression; human; molecular biology; transcriptome; vascular biology

DOI:  https://doi.org/10.7554/eLife.88248
Cell Struct Funct. 2023 May 11.

Zebrafish imaging reveals hidden oncogenic-normal cell communication during primary tumorigenesis.

Yukinari Haraoka, Mai Miyake, Tohru Ishitani.

  Oncogenic mutations drive tumorigenesis, and single cells with oncogenic mutations act as the tumor seeds that gradually evolve into fully transformed tumors. However, oncogenic cell behavior and communication with neighboring cells during primary tumorigenesis remain poorly understood. We used the zebrafish, a small vertebrate model suitable for in vivo cell biology, to address these issues. We describe the cooperative and competitive communication between oncogenic cells and neighboring cells, as revealed by our recent zebrafish imaging studies. Newly generated oncogenic cells are actively eliminated by neighboring cells in healthy epithelia, whereas oncogenic cells cooperate with their neighbors to prime tumorigenesis in unhealthy epithelia via additional mutations or inflammation. In addition, we discuss the potential of zebrafish in vivo imaging to determine the initial steps of human tumorigenesis.Key words: zebrafish, imaging, cell-cell communication, cell competition, EDAC, senescence, primary tumorigenesis.

Keywords:  EDAC; cell competition; cell-cell communication; imaging; primary tumorigenesis; senescence; zebrafish

DOI:  https://doi.org/10.1247/csf.23026
bioRxiv. 2023 Apr 28. pii: 2023.02.04.527139. [Epub ahead of print]

Long lifetime and selective accumulation of the A-type lamins accounts for the tissue specificity of Hutchinson-Gilford progeria syndrome.

John Hasper, Kevin Welle, Kyle Swovick, Jennifer Hryhorenko, Sina Ghaemmaghami, Abigail Buchwalter.

Mutations to the LMNA gene cause laminopathies including Hutchinson-Gilford progeria syndrome (HGPS) that severely affect the cardiovascular system. The origins of tissue specificity in these diseases are unclear, as the A-type Lamins are abundant and broadly expressed proteins. We show that A-type Lamin protein and transcript levels are uncorrelated across tissues. As protein-transcript discordance can be caused by variations in protein lifetime, we applied quantitative proteomics to profile protein turnover rates in healthy and progeroid tissues. We discover that tissue context and disease mutation each influence A-type Lamin protein lifetime. Lamin A/C has a weeks-long lifetime in the aorta, heart, and fat, where progeroid pathology is apparent, but a days-long lifetime in the liver and gastrointestinal tract, which are spared from disease. The A-type Lamins are insoluble and densely bundled in cardiovascular tissues, which may present an energetic barrier to degradation and promote long protein lifetime. Progerin is even more long-lived than Lamin A/C in the cardiovascular system and accumulates there over time. Progerin accumulation interferes broadly with protein homeostasis, as hundreds of abundant proteins turn over more slowly in progeroid tissues. These findings indicate that potential gene therapy interventions for HGPS will have significant latency and limited potency in disrupting the long-lived Progerin protein. Finally, we reveal that human disease alleles are significantly over-represented in the long-lived proteome, indicating that long protein lifetime may influence disease pathology and present a significant barrier to gene therapies for numerous human diseases.
Significance statement: Many human diseases are caused by mutations to broadly expressed proteins, yet disease mysteriously manifests only in specific tissues. An example of this is Hutchinson-Gilford progeria syndrome (HGPS), which is caused by a mutation to the Lamin A/C protein. We show that this mutation slows the turnover of Lamin A/C proteins in disease-afflicted tissues, causing the mutant "Progerin" protein to accumulate over time and interfere with the normal turnover of hundreds of other proteins. Because Progerin is a long-lived protein, effective therapies for this disease will need to attack the protein and not just the gene that encodes it.

DOI: https://doi.org/10.1101/2023.02.04.527139
Nature. 2023 May 05.

Daily briefing: New organelle discovered inside animal cell.

Flora Graham.

DOI: https://doi.org/10.1038/d41586-023-01570-4
Dev Cell. 2023 May 02. pii: S1534-5807(23)00182-X. [Epub ahead of print]

A platform for efficient establishment and drug-response profiling of high-grade serous ovarian cancer organoids.

Wojciech Senkowski, Laura Gall-Mas, Matías Marín Falco, Yilin Li, Kari Lavikka, Mette C Kriegbaum, Jaana Oikkonen, Daria Bulanova, Elin J Pietras, Karolin Voßgröne, Yan-Jun Chen, Erdogan Pekcan Erkan, Jun Dai, Anastasia Lundgren, Mia Kristine Grønning Høg, Ida Marie Larsen, Tarja Lamminen, Katja Kaipio, Jutta Huvila, Anni Virtanen, Lars Engelholm, Pernille Christiansen, Eric Santoni-Rugiu, Kaisa Huhtinen, Olli Carpén, Johanna Hynninen, Sampsa Hautaniemi, Anna Vähärautio, Krister Wennerberg.

  The broad research use of organoids from high-grade serous ovarian cancer (HGSC) has been hampered by low culture success rates and limited availability of fresh tumor material. Here, we describe a method for generation and long-term expansion of HGSC organoids with efficacy markedly improved over previous reports (53% vs. 23%-38%). We established organoids from cryopreserved material, demonstrating the feasibility of using viably biobanked tissue for HGSC organoid derivation. Genomic, histologic, and single-cell transcriptomic analyses revealed that organoids recapitulated genetic and phenotypic features of original tumors. Organoid drug responses correlated with clinical treatment outcomes, although in a culture conditions-dependent manner and only in organoids maintained in human plasma-like medium (HPLM). Organoids from consenting patients are available to the research community through a public biobank and organoid genomic data are explorable through an interactive online tool. Taken together, this resource facilitates the application of HGSC organoids in basic and translational ovarian cancer research.

Keywords:  3D cell culture, culture conditions; HPLM; functional precision medicine; high-grade serous ovarian cancer; organoid biobank; organoids; personalized medicine; scRNA-seq; tumor models

DOI:  https://doi.org/10.1016/j.devcel.2023.04.012
J Am Soc Mass Spectrom. 2023 May 08.

The Edge Effect in High-Throughput Proteomics: A Cautionary Tale.

Colleen B Maxwell, Jatinderpal K Sandhu, Thong H Cao, Gerry P McCann, Leong L Ng, Donald J L Jones.

In order for mass spectrometry to continue to grow as a platform for high-throughput clinical and translational research, careful consideration must be given to quality control by ensuring that the assay performs reproducibly and accurately and precisely. In particular, the throughput required for large cohort clinical validation in biomarker discovery and diagnostic screening has driven the growth of multiplexed targeted liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) assays paired with sample preparation and analysis in multiwell plates. However, large scale MS-based proteomics studies are often plagued by batch effects: sources of technical variation in the data, which can arise from a diverse array of sources such as sample preparation batches, different reagent lots, or indeed MS signal drift. These batch effects can confound the detection of true signal differences, resulting in incorrect conclusions being drawn about significant biological effects or lack thereof. Here, we present an intraplate batch effect termed the edge effect arising from temperature gradients in multiwell plates, commonly reported in preclinical cell culture studies but not yet reported in a clinical proteomics setting. We present methods herein to ameliorate the phenomenon including proper assessment of heating techniques for multiwell plates and incorporation of surrogate standards, which can normalize for intraplate variation.

DOI: https://doi.org/10.1021/jasms.3c00035
Am J Physiol Endocrinol Metab. 2023 May 11.

Hepatic mTORC2 compensates for loss of adipose mTORC2 in mediating energy storage and glucose homeostasis.

Irina C Frei, Diana Weissenberger, Christoph Müller, Michael N Hall, Mitsugu Shimobayashi.

  Mammalian target of rapamycin complex 2 (mTORC2) is a protein kinase complex that plays an important role in energy homeostasis. Loss of adipose mTORC2 reduces lipogenic enzyme expression and de novo lipogenesis in adipose tissue. Adipose-specific mTORC2 knockout mice also display triglyceride accumulation in the liver. However, the mechanism and physiological role of hepatic triglyceride accumulation upon loss of adipose mTORC2 are unknown. Here, we show that loss of adipose mTORC2 increases expression of de novo lipogenic enzymes in the liver, thereby causing accumulation of hepatic triglyceride and hypertriglyceridemia. Simultaneous inhibition of lipogenic enzymes in adipose tissue and liver by ablating mTORC2 in both tissues prevented accumulation of hepatic triglycerides and hypertriglyceridemia. However, loss of adipose and hepatic mTORC2 caused severe insulin resistance and glucose intolerance. Thus, our findings suggest that increased hepatic lipogenesis is a compensatory mechanism to cope with loss of lipogenesis in adipose tissue, and further suggest that mTORC2 in adipose tissue and liver plays a crucial role in maintaining whole-body energy homeostasis.

Keywords:  adipose tissue; de novo lipogenesis; glucose homeostasis; liver; mTORC2

DOI:  https://doi.org/10.1152/ajpendo.00338.2022
Mol Syst Biol. 2023 May 08. e11517

Predicting cellular responses to complex perturbations in high-throughput screens.

Mohammad Lotfollahi, Anna Klimovskaia Susmelj, Carlo De Donno, Leon Hetzel, Yuge Ji, Ignacio L Ibarra, Sanjay R Srivatsan, Mohsen Naghipourfar, Riza M Daza, Beth Martin, Jay Shendure, Jose L McFaline-Figueroa, Pierre Boyeau, F Alexander Wolf, Nafissa Yakubova, Stephan Günnemann, Cole Trapnell, David Lopez-Paz, Fabian J Theis.

  Recent advances in multiplexed single-cell transcriptomics experiments facilitate the high-throughput study of drug and genetic perturbations. However, an exhaustive exploration of the combinatorial perturbation space is experimentally unfeasible. Therefore, computational methods are needed to predict, interpret, and prioritize perturbations. Here, we present the compositional perturbation autoencoder (CPA), which combines the interpretability of linear models with the flexibility of deep-learning approaches for single-cell response modeling. CPA learns to in silico predict transcriptional perturbation response at the single-cell level for unseen dosages, cell types, time points, and species. Using newly generated single-cell drug combination data, we validate that CPA can predict unseen drug combinations while outperforming baseline models. Additionally, the architecture's modularity enables incorporating the chemical representation of the drugs, allowing the prediction of cellular response to completely unseen drugs. Furthermore, CPA is also applicable to genetic combinatorial screens. We demonstrate this by imputing in silico 5,329 missing combinations (97.6% of all possibilities) in a single-cell Perturb-seq experiment with diverse genetic interactions. We envision CPA will facilitate efficient experimental design and hypothesis generation by enabling in silico response prediction at the single-cell level and thus accelerate therapeutic applications using single-cell technologies.

Keywords:  generative modeling; high-throughput screening; machine learning; perturbation prediction; single-cell transcriptomics

DOI:  https://doi.org/10.15252/msb.202211517
Nat Commun. 2023 May 10. 14(1): 2686

The PECAn image and statistical analysis pipeline identifies Minute cell competition genes and features.

Michael E Baumgartner, Paul F Langton, Remi Logeay, Alex Mastrogiannopoulos, Anna Nilsson-Takeuchi, Iwo Kucinski, Jules Lavalou, Eugenia Piddini.

Investigating organ biology often requires methodologies to induce genetically distinct clones within a living tissue. However, the 3D nature of clones makes sample image analysis challenging and slow, limiting the amount of information that can be extracted manually. Here we develop PECAn, a pipeline for image processing and statistical data analysis of complex multi-genotype 3D images. PECAn includes data handling, machine-learning-enabled segmentation, multivariant statistical analysis, and graph generation. This enables researchers to perform rigorous analyses rapidly and at scale, without requiring programming skills. We demonstrate the power of this pipeline by applying it to the study of Minute cell competition. We find an unappreciated sexual dimorphism in Minute cell growth in competing wing discs and identify, by statistical regression analysis, tissue parameters that model and correlate with competitive death. Furthermore, using PECAn, we identify several genes with a role in cell competition by conducting an RNAi-based screen.

DOI: https://doi.org/10.1038/s41467-023-38287-x
Science. 2023 May 12. 380(6645): eadd5327

Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis.

Cassandra Burdziak, Direna Alonso-Curbelo, Thomas Walle, José Reyes, Francisco M Barriga, Doron Haviv, Yubin Xie, Zhen Zhao, Chujun Julia Zhao, Hsuan-An Chen, Ojasvi Chaudhary, Ignas Masilionis, Zi-Ning Choo, Vianne Gao, Wei Luan, Alexandra Wuest, Yu-Jui Ho, Yuhong Wei, Daniela F Quail, Richard Koche, Linas Mazutis, Ronan Chaligné, Tal Nawy, Scott W Lowe, Dana Pe'er.

The response to tumor-initiating inflammatory and genetic insults can vary among morphologically indistinguishable cells, suggesting as yet uncharacterized roles for epigenetic plasticity during early neoplasia. To investigate the origins and impact of such plasticity, we performed single-cell analyses on normal, inflamed, premalignant, and malignant tissues in autochthonous models of pancreatic cancer. We reproducibly identified heterogeneous cell states that are primed for diverse, late-emerging neoplastic fates and linked these to chromatin remodeling at cell-cell communication loci. Using an inference approach, we revealed signaling gene modules and tissue-level cross-talk, including a neoplasia-driving feedback loop between discrete epithelial and immune cell populations that was functionally validated in mice. Our results uncover a neoplasia-specific tissue-remodeling program that may be exploited for pancreatic cancer interception.

DOI: https://doi.org/10.1126/science.add5327
Nat Phys. 2022 Apr;18(4): 411-416

Macromolecular crowding limits growth under pressure.

Baptiste Alric, Cécile Formosa-Dague, Etienne Dague, Liam J Holt, Morgan Delarue.

Cells that grow in confined spaces eventually build up mechanical compressive stress. This growth-induced pressure (GIP) decreases cell growth. GIP is important in a multitude of contexts from cancer, to microbial infections, to biofouling, yet our understanding of its origin and molecular consequences remains limited. Here, we combine microfluidic confinement of the yeast Saccharomyces cerevisiae, with rheological measurements using genetically encoded multimeric nanoparticles (GEMs) to reveal that growth-induced pressure is accompanied with an increase in a key cellular physical property: macromolecular crowding. We develop a fully calibrated model that predicts how increased macromolecular crowding hinders protein expression and thus diminishes cell growth. This model is sufficient to explain the coupling of growth rate to pressure without the need for specific molecular sensors or signaling cascades. As molecular crowding is similar across all domains of life, this could be a deeply conserved mechanism of biomechanical feedback that allows environmental sensing originating from the fundamental physical properties of cells.

DOI: https://doi.org/10.1038/s41567-022-01506-1