bims-pideca 2023-07-09 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2023–07–09
24 papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

Allosteric activation or inhibition of PI3Kγ mediated through conformational changes in the p110γ helical domain.
Structural and mechanistic insights provided by single particle cryo-EM analysis of phosphoinositide 3-kinase (PI3Kα).
PTEN is both an activator and a substrate of chaperone-mediated autophagy.
Rictor induces AKT signaling to regulate lymphatic valve formation.
Targeting Ras signaling excitability in cancer cells through combined inhibition of FAK and PI3K.
Insulin feedback is a targetable resistance mechanism of PI3K inhibition in glioblastoma.
Nuclear class 3 PI3K coactivates circadian clock.
Global and tissue-specific aging effects on murine proteomes.
Class 3 PI3K coactivates the circadian clock to promote rhythmic de novo purine synthesis.
Ten quick tips for avoiding pitfalls in multi-omics data integration analyses.
Detecting somatic mutations in single-cell data sets.
B cell receptor-induced protein dynamics and the emerging role of SUMOylation revealed by proximity proteomics.
Building human artery and vein endothelial cells from pluripotent stem cells, and enduring mysteries surrounding arteriovenous development.
MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms.
Vitamin B2 enables regulation of fasting glucose availability.
Transcription factors interact with RNA to regulate genes.
nf-encyclopedia: A Cloud-Ready Pipeline for Chromatogram Library Data-Independent Acquisition Proteomics Workflows.
Optogenetic control of Wnt signaling models cell-intrinsic embryogenic patterning using 2D human pluripotent stem cell culture.
De novo detection of somatic mutations in high-throughput single-cell profiling data sets.
Oncogene-like addiction to aneuploidy in human cancers.
PEPseq quantifies transcriptome-wide changes in protein occupancy and reveals selective translational repression after translational stress.
Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy.
Senescence-induced cellular reprogramming drives cnidarian whole-body regeneration.
Loss of CDK4/6 activity in S/G2 phase leads to cell cycle reversal.

Elife. 2023 Jul 07. pii: RP88058. [Epub ahead of print]12

Allosteric activation or inhibition of PI3Kγ mediated through conformational changes in the p110γ helical domain.

Noah J Harris, Meredith L Jenkins, Sung-Eun Nam, Manoj K Rathinaswamy, Matthew A H Parson, Harish Ranga-Prasad, Udit Dalwadi, Brandon E Moeller, Eleanor Sheeky, Scott D Hansen, Calvin K Yip, John E Burke.

  PI3Kγ is a critical immune signaling enzyme activated downstream of diverse cell surface molecules, including Ras, PKCβ activated by the IgE receptor, and Gβγ subunits released from activated GPCRs. PI3Kγ can form two distinct complexes, with the p110γ catalytic subunit binding to either a p101 or p84 regulatory subunit, with these complexes being differentially activated by upstream stimuli. Here, using a combination of cryo electron microscopy, HDX-MS, and biochemical assays, we have identified novel roles of the helical domain of p110γ in regulating lipid kinase activity of distinct PI3Kγ complexes. We defined the molecular basis for how an allosteric inhibitory nanobody potently inhibits kinase activity through rigidifying the helical domain and regulatory motif of the kinase domain. The nanobody did not block either p110γ membrane recruitment or Ras/Gβγ binding, but instead decreased ATP turnover. We also identified that p110γ can be activated by dual PKCβ helical domain phosphorylation leading to partial unfolding of an N-terminal region of the helical domain. PKCβ phosphorylation is selective for p110γ-p84 compared to p110γ-p101, driven by differential dynamics of the helical domain of these different complexes. Nanobody binding prevented PKCβ-mediated phosphorylation. Overall, this work shows an unexpected allosteric regulatory role of the helical domain of p110γ that is distinct between p110γ-p84 and p110γ-p101 and reveals how this can be modulated by either phosphorylation or allosteric inhibitory binding partners. This opens possibilities of future allosteric inhibitor development for therapeutic intervention.

Keywords:  HDX-MS; PI3K; PI3Kγ; PIK3CG; PIK3R5; biochemistry; chemical biology; human; molecular biophysics; nanobody; p101; structural biology

DOI:  https://doi.org/10.7554/eLife.88058
Biochim Biophys Acta Rev Cancer. 2023 Jun 30. pii: S0304-419X(23)00096-3. [Epub ahead of print]1878(5): 188947

Structural and mechanistic insights provided by single particle cryo-EM analysis of phosphoinositide 3-kinase (PI3Kα).

Peter K Vogt, Jonathan R Hart, Su Yang, Qingtong Zhou, Dehua Yang, Ming-Wei Wang.

  Recent cryo-electron microscopic (cryo-EM) investigations have succeeded in the analysis of various structural conformations and functional states of PI3Kα, a dimer consisting of the catalytic subunit p110α and the regulatory subunit p85α of class IA of phosphoinositide 3-kinase. High resolution structures have been obtained of the unliganded and of BYL-719-bound PI3Kα. The latter provides information on excessively flexible domains of p85α that are then further analyzed with nanobodies and CXMS (chemical cross-linking, digestion and mass spectrometry). Analysis of p110α helical and kinase domain mutations reveals mutant-specific features that can be linked to the gain of function in enzymatic and signaling activities.

Keywords:  BYL-719; CXMS; Mutants; Nanobody; Phosphoinositide 3-kinase

DOI:  https://doi.org/10.1016/j.bbcan.2023.188947
J Cell Biol. 2023 Sep 04. pii: e202208150. [Epub ahead of print]222(9):

PTEN is both an activator and a substrate of chaperone-mediated autophagy.

Katherine K Zhang, Calvin M Burns, Mary E Skinner, David B Lombard, Richard A Miller, S Joseph Endicott.

PTEN is a crucial negative regulator of the INS/PI3K/AKT pathway and is one of the most commonly mutated tumor suppressors in cancer. Global overexpression (OE) of PTEN in mice shifts metabolism to favor oxidative phosphorylation over glycolysis, reduces fat mass, and extends the lifespan of both sexes. We demonstrate that PTEN regulates chaperone-mediated autophagy (CMA). Using cultured cells and mouse models, we show that PTEN OE enhances CMA, dependent upon PTEN's lipid phosphatase activity and AKT inactivation. Reciprocally, PTEN knockdown reduces CMA, which can be rescued by inhibiting class I PI3K or AKT. Both PTEN and CMA are negative regulators of glycolysis and lipid droplet formation. We show that suppression of glycolysis and lipid droplet formation downstream of PTEN OE depends on CMA activity. Finally, we show that PTEN protein levels are sensitive to CMA and that PTEN accumulates in lysosomes with elevated CMA. Collectively, these data suggest that CMA is both an effector and a regulator of PTEN.

DOI: https://doi.org/10.1083/jcb.202208150
bioRxiv. 2023 Jun 13. pii: 2023.06.12.544698. [Epub ahead of print]

Rictor induces AKT signaling to regulate lymphatic valve formation.

Richa Banerjee, Luz A Knauer, Drishya Iyer, Sara E Barlow, Joshua P Scallan, Ying Yang.

Lymphatic valves are specialized structures of the collecting lymphatic vessels and are crucial for preventing retrograde lymph flow. Mutations in valve-forming genes have been clinically implicated in the pathology of congenital lymphedema. Lymphatic valves form when oscillatory shear stress (OSS) from lymph flow signals through the PI3K/AKT pathway to promote the transcription of valve-forming genes that trigger the growth and maintenance of lymphatic valves throughout life. Conventionally, in other tissue types, AKT activation requires dual kinase activity and the mammalian target of rapamycin complex 2 (mTORC2) commands this process by phosphorylating AKT at Ser473. Here we showed that embryonic and postnatal lymphatic deletion of Rictor , a critical component of mTORC2, led to a significant decrease in lymphatic valves and prevented the maturation of collecting lymphatic vessels. RICTOR knockdown in human lymphatic endothelial cells (hdLECs) not only significantly reduced the level of activated AKT and the expression of valve-forming genes under no-flow conditions, but also abolished the upregulation of AKT activity and valve-forming genes in response to flow. We further showed that the AKT target, FOXO1, a repressor of lymphatic valve formation, had increased nuclear activity in Rictor knockout mesenteric LECs, in vivo . Deletion of Foxo1 in Rictor knockout mice restored the number of valves to control levels in both mesenteric and ear lymphatics. Our work revealed a novel role of RICTOR signaling in the mechanotransduction signaling pathway, wherein it activates AKT and prevents the nuclear accumulation of the valve repressor, FOXO1, which ultimately allows the formation and maintenance of a normal lymphatic valve.

DOI: https://doi.org/10.1101/2023.06.12.544698
bioRxiv. 2023 Jun 13. pii: 2023.06.12.544386. [Epub ahead of print]

Targeting Ras signaling excitability in cancer cells through combined inhibition of FAK and PI3K.

Chao-Cheng Chen, Suyang Wang, Jr-Ming Yang, Chuan-Hsiang Huang.

The Ras/PI3K/ERK signaling network is frequently mutated in various human cancers including cervical cancer and pancreatic cancer. Previous studies showed that the Ras/PI3K/ERK signaling network displays features of excitable systems including propagation of activity waves, all-or-none responses, and refractoriness. Oncogenic mutations lead to enhanced excitability of the network. A positive feedback loop between Ras, PI3K, the cytoskeleton, and FAK was identified as a driver of excitability. In this study, we investigated the effectiveness of targeting signaling excitability by inhibiting both FAK and PI3K in cervical and pancreatic cancer cells. We found that the combination of FAK and PI3K inhibitors synergistically suppressed the growth of select cervical and pancreatic cancer cell lines through increased apoptosis and decreased mitosis. In particular, FAK inhibition caused downregulation of PI3K and ERK signaling in cervical cancer but not pancreatic cancer cells. Interestingly, PI3K inhibitors activated multiple receptor tyrosine kinases (RTKs), including insulin receptor and IGF-1R in cervical cancer cells, as well as EGFR, Her2, Her3, Axl, and EphA2 in pancreatic cancer cells. Our results highlight the potential of combining FAK and PI3K inhibition for treating cervical and pancreatic cancer, although appropriate biomarkers for drug sensitivity are needed, and concurrent targeting of RTKs may be required for resistant cells.

DOI: https://doi.org/10.1101/2023.06.12.544386
Neuro Oncol. 2023 Jul 03. pii: noad117. [Epub ahead of print]

Insulin feedback is a targetable resistance mechanism of PI3K inhibition in glioblastoma.

Evan K Noch, Laura N Palma, Isaiah Yim, Nayah Bullen, Yuqing Qiu, Hiranmayi Ravichandran, Junbum Kim, Andre Rendeiro, Melissa B Davis, Olivier Elemento, David J Pisapia, Kevin Zhai, H Carl LeKaye, Jason A Koutcher, Patrick Y Wen, Keith L Ligon, Lewis C Cantley.

   BACKGROUND: Insulin feedback is a critical mechanism responsible for poor clinical efficacy of PI3K inhibition in cancer, and hyperglycemia is an independent factor associated with poor prognosis in glioblastoma. We investigated combination anti-hyperglycemic therapy in a mouse model of glioblastoma and evaluated the association of glycemic control in clinical trial data from patients with glioblastoma.
METHODS: The effect of the anti-hyperglycemic regimens metformin and the ketogenic diet were evaluated in combination with PI3K inhibition in patient-derived glioblastoma cells and an orthotopic glioblastoma mouse model. Insulin feedback and the immune microenvironment were retrospectively evaluated in blood and tumor tissue from a Phase 2 clinical trial of buparlisib in patients with recurrent glioblastoma.
RESULTS: We found that PI3K inhibition induces hyperglycemia and hyperinsulinemia in mice and that combining metformin with PI3K inhibition improves treatment efficacy in an orthotopic glioblastoma xenograft model. Through examination of clinical trial data, we found that hyperglycemia was an independent factor associated with poor progression-free survival in patients with glioblastoma. We also found that PI3K inhibition increased insulin receptor activation and T cell and microglia abundance in tumor tissue from these patients.
CONCLUSION: Reducing insulin feedback improves the efficacy of PI3K inhibition in glioblastoma in mice, and hyperglycemia worsens progression-free survival in patients with glioblastoma treated with PI3K inhibition. These findings indicate that hyperglycemia is a critical resistance mechanism associated with PI3K inhibition in glioblastoma and that anti-hyperglycemic therapy may enhance PI3K inhibitor efficacy in glioblastoma patients.

Keywords:  Glioblastoma; hyperglycemia; insulin; metformin; phosphatidylinositol 3-kinase

DOI:  https://doi.org/10.1093/neuonc/noad117
Nat Cell Biol. 2023 Jul 06.

Nuclear class 3 PI3K coactivates circadian clock.

DOI: https://doi.org/10.1038/s41556-023-01186-w
Cell Rep. 2023 Jul 04. pii: S2211-1247(23)00726-X. [Epub ahead of print]42(7): 112715

Global and tissue-specific aging effects on murine proteomes.

Gregory R Keele, Ji-Gang Zhang, John Szpyt, Ron Korstanje, Steven P Gygi, Gary A Churchill, Devin K Schweppe.

  Maintenance of protein homeostasis degrades with age, contributing to aging-related decline and disease. Previous studies have primarily surveyed transcriptional aging changes. To define the effects of age directly at the protein level, we perform discovery-based proteomics in 10 tissues from 20 C57BL/6J mice, representing both sexes at adult and late midlife ages (8 and 18 months). Consistent with previous studies, age-related changes in protein abundance often have no corresponding transcriptional change. Aging results in increases in immune proteins across all tissues, consistent with a global pattern of immune infiltration with age. Our protein-centric data reveal tissue-specific aging changes with functional consequences, including altered endoplasmic reticulum and protein trafficking in the spleen. We further observe changes in the stoichiometry of protein complexes with important roles in protein homeostasis, including the CCT/TriC complex and large ribosomal subunit. These data provide a foundation for understanding how proteins contribute to systemic aging across tissues.

Keywords:  B6; C57BL/6J; CP: Genomics; CP: Metabolism; TMT; multitissue; organismal aging; protein complex; protein homeostasis; proteomics; proteostasis; tandem mass tag

DOI:  https://doi.org/10.1016/j.celrep.2023.112715
Nat Cell Biol. 2023 Jul 06.

Class 3 PI3K coactivates the circadian clock to promote rhythmic de novo purine synthesis.

Chantal Alkhoury, Nathaniel F Henneman, Volodymyr Petrenko, Yui Shibayama, Arianna Segaloni, Alexis Gadault, Ivan Nemazanyy, Edouard Le Guillou, Amare Desalegn Wolide, Konstantina Antoniadou, Xin Tong, Teruya Tamaru, Takeaki Ozawa, Muriel Girard, Karim Hnia, Dominik Lutter, Charna Dibner, Ganna Panasyuk.

Metabolic demands fluctuate rhythmically and rely on coordination between the circadian clock and nutrient-sensing signalling pathways, yet mechanisms of their interaction remain not fully understood. Surprisingly, we find that class 3 phosphatidylinositol-3-kinase (PI3K), known best for its essential role as a lipid kinase in endocytosis and lysosomal degradation by autophagy, has an overlooked nuclear function in gene transcription as a coactivator of the heterodimeric transcription factor and circadian driver Bmal1-Clock. Canonical pro-catabolic functions of class 3 PI3K in trafficking rely on the indispensable complex between the lipid kinase Vps34 and regulatory subunit Vps15. We demonstrate that although both subunits of class 3 PI3K interact with RNA polymerase II and co-localize with active transcription sites, exclusive loss of Vps15 in cells blunts the transcriptional activity of Bmal1-Clock. Thus, we establish non-redundancy between nuclear Vps34 and Vps15, reflected by the persistent nuclear pool of Vps15 in Vps34-depleted cells and the ability of Vps15 to coactivate Bmal1-Clock independently of its complex with Vps34. In physiology we find that Vps15 is required for metabolic rhythmicity in liver and, unexpectedly, it promotes pro-anabolic de novo purine nucleotide synthesis. We show that Vps15 activates the transcription of Ppat, a key enzyme for the production of inosine monophosphate, a central metabolic intermediate for purine synthesis. Finally, we demonstrate that in fasting, which represses clock transcriptional activity, Vps15 levels are decreased on the promoters of Bmal1 targets, Nr1d1 and Ppat. Our findings open avenues for establishing the complexity for nuclear class 3 PI3K signalling for temporal regulation of energy homeostasis.

DOI: https://doi.org/10.1038/s41556-023-01171-3
PLoS Comput Biol. 2023 Jul;19(7): e1011224

Ten quick tips for avoiding pitfalls in multi-omics data integration analyses.

Davide Chicco, Fabio Cumbo, Claudio Angione.

Data are the most important elements of bioinformatics: Computational analysis of bioinformatics data, in fact, can help researchers infer new knowledge about biology, chemistry, biophysics, and sometimes even medicine, influencing treatments and therapies for patients. Bioinformatics and high-throughput biological data coming from different sources can even be more helpful, because each of these different data chunks can provide alternative, complementary information about a specific biological phenomenon, similar to multiple photos of the same subject taken from different angles. In this context, the integration of bioinformatics and high-throughput biological data gets a pivotal role in running a successful bioinformatics study. In the last decades, data originating from proteomics, metabolomics, metagenomics, phenomics, transcriptomics, and epigenomics have been labelled -omics data, as a unique name to refer to them, and the integration of these omics data has gained importance in all biological areas. Even if this omics data integration is useful and relevant, due to its heterogeneity, it is not uncommon to make mistakes during the integration phases. We therefore decided to present these ten quick tips to perform an omics data integration correctly, avoiding common mistakes we experienced or noticed in published studies in the past. Even if we designed our ten guidelines for beginners, by using a simple language that (we hope) can be understood by anyone, we believe our ten recommendations should be taken into account by all the bioinformaticians performing omics data integration, including experts.

DOI: https://doi.org/10.1371/journal.pcbi.1011224
Nat Biotechnol. 2023 Jul 06.

Detecting somatic mutations in single-cell data sets.

DOI: https://doi.org/10.1038/s41587-023-01883-9
J Cell Sci. 2023 Jul 07. pii: jcs.261119. [Epub ahead of print]

B cell receptor-induced protein dynamics and the emerging role of SUMOylation revealed by proximity proteomics.

Luqman O Awoniyi, Diogo M Cunha, Alexey V Sarapulov, Sara Hernández-Pérez, Marika Runsala, Blanca Tejeda-González, Vid Šuštar, M Özge Balci, Petar Petrov, Pieta K Mattila.

  Successful B cell activation, critical for high-affinity antibody production, is controlled by the B cell antigen receptor (BCR). However, we still lack a comprehensive protein-level view of the very dynamic multi-branched cellular events triggered by antigen binding. Here, we employed APEX2 proximity biotinylation to study antigen-induced changes, 5-15 min after receptor activation, at the vicinity of the plasma membrane lipid rafts, wherein BCR enriches upon activation. The data reveals dynamics of signaling proteins, as well as various players linked to the subsequent processes, such as actin cytoskeleton remodelling and endocytosis. Interestingly, our differential expression analysis identified dynamic responses in various proteins previously not linked to early B cell activation. We demonstrate active SUMOylation at the sites of BCR activation in various conditions and report its functional role in BCR signaling through Akt and MAPK axes.

Keywords:  APEX2; B cells; BCR; Lipid rafts; Proximity proteomics; Receptor signalling

DOI:  https://doi.org/10.1242/jcs.261119
Semin Cell Dev Biol. 2023 Jun 29. pii: S1084-9521(23)00132-5. [Epub ahead of print]

Building human artery and vein endothelial cells from pluripotent stem cells, and enduring mysteries surrounding arteriovenous development.

Kyle M Loh, Lay Teng Ang.

  Owing to their manifold roles in health and disease, there have been intense efforts to synthetically generate blood vessels in vitro from human pluripotent stem cells (hPSCs). However, there are multiple types of blood vessel, including arteries and veins, which are molecularly and functionally different. How can we specifically generate either arterial or venous endothelial cells (ECs) from hPSCs in vitro? Here, we summarize how arterial or venous ECs arise during embryonic development. VEGF and NOTCH arbitrate the bifurcation of arterial vs. venous ECs in vivo. While manipulating these two signaling pathways biases hPSC differentiation towards arterial and venous identities, efficiently generating these two subtypes of ECs has remained challenging until recently. Numerous questions remain to be fully addressed. What is the complete identity, timing and combination of extracellular signals that specify arterial vs. venous identities? How do these extracellular signals intersect with fluid flow to modulate arteriovenous fate? What is a unified definition for endothelial progenitors or angioblasts, and when do arterial vs. venous potentials segregate? How can we regulate hPSC-derived arterial and venous ECs in vitro, and generate organ-specific ECs? In turn, answers to these questions could avail the production of arterial and venous ECs from hPSCs, accelerating vascular research, tissue engineering, and regenerative medicine.

Keywords:  Artery endothelial cell; Developmental biology; Human pluripotent stem cell; Vein endothelial cell

DOI:  https://doi.org/10.1016/j.semcdb.2023.06.004
Nat Commun. 2023 Jul 06. 14(1): 3991

MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms.

Cemal Erdem, Sean M Gross, Laura M Heiser, Marc R Birtwistle.

Robust identification of context-specific network features that control cellular phenotypes remains a challenge. We here introduce MOBILE (Multi-Omics Binary Integration via Lasso Ensembles) to nominate molecular features associated with cellular phenotypes and pathways. First, we use MOBILE to nominate mechanisms of interferon-γ (IFNγ) regulated PD-L1 expression. Our analyses suggest that IFNγ-controlled PD-L1 expression involves BST2, CLIC2, FAM83D, ACSL5, and HIST2H2AA3 genes, which were supported by prior literature. We also compare networks activated by related family members transforming growth factor-beta 1 (TGFβ1) and bone morphogenetic protein 2 (BMP2) and find that differences in ligand-induced changes in cell size and clustering properties are related to differences in laminin/collagen pathway activity. Finally, we demonstrate the broad applicability and adaptability of MOBILE by analyzing publicly available molecular datasets to investigate breast cancer subtype specific networks. Given the ever-growing availability of multi-omics datasets, we envision that MOBILE will be broadly useful for identification of context-specific molecular features and pathways.

DOI: https://doi.org/10.1038/s41467-023-39729-2
Elife. 2023 Jul 07. pii: e84077. [Epub ahead of print]12

Vitamin B2 enables regulation of fasting glucose availability.

Peter M Masschelin, Pradip Saha, Scott A Ochsner, Aaron R Cox, Kang Ho Kim, Jessica B Felix, Robert Sharp, Xin Li, Lin Tan, Jun Hyoung Park, Liping Wang, Vasanta Putluri, Philip L Lorenzi, Alli M Nuotio-Antar, Zheng Sun, Benny Abraham Kaipparettu, Nagireddy Putluri, David D Moore, Scott A Summers, Neil J McKenna, Sean M Hartig.

  Flavin adenine dinucleotide (FAD) interacts with flavoproteins to mediate oxidation-reduction reactions required for cellular energy demands. Not surprisingly, mutations that alter FAD binding to flavoproteins cause rare inborn errors of metabolism (IEMs) that disrupt liver function and render fasting intolerance, hepatic steatosis, and lipodystrophy. In our study, depleting FAD pools in mice with a vitamin B2-deficient diet (B2D) caused phenotypes associated with organic acidemias and other IEMs, including reduced body weight, hypoglycemia, and fatty liver disease. Integrated discovery approaches revealed B2D tempered fasting activation of target genes for the nuclear receptor PPARα, including those required for gluconeogenesis. We also found PPARα knockdown in the liver recapitulated B2D effects on glucose excursion and fatty liver disease in mice. Finally, treatment with the PPARα agonist fenofibrate activated the integrated stress response and refilled amino acid substrates to rescue fasting glucose availability and overcome B2D phenotypes. These findings identify metabolic responses to FAD availability and nominate strategies for the management of organic acidemias and other rare IEMs.

Keywords:  FAD; cell biology; gluconeogenesis; inborn errors of metabolism; metabolism; mouse; nuclear receptor

DOI:  https://doi.org/10.7554/eLife.84077
Mol Cell. 2023 Jun 27. pii: S1097-2765(23)00434-3. [Epub ahead of print]

Transcription factors interact with RNA to regulate genes.

Ozgur Oksuz, Jonathan E Henninger, Robert Warneford-Thomson, Ming M Zheng, Hailey Erb, Adrienne Vancura, Kalon J Overholt, Susana Wilson Hawken, Salman F Banani, Richard Lauman, Lauren N Reich, Anne L Robertson, Nancy M Hannett, Tong I Lee, Leonard I Zon, Roberto Bonasio, Richard A Young.

  Transcription factors (TFs) orchestrate the gene expression programs that define each cell's identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or corepressors. We find that at least half of TFs also bind RNA, doing so through a previously unrecognized domain with sequence and functional features analogous to the arginine-rich motif of the HIV transcriptional activator Tat. RNA binding contributes to TF function by promoting the dynamic association between DNA, RNA, and TF on chromatin. TF-RNA interactions are a conserved feature important for vertebrate development and disrupted in disease. We propose that the ability to bind DNA, RNA, and protein is a general property of many TFs and is fundamental to their gene regulatory function.

Keywords:  RNA; RNA-binding proteins; arginine-rich motif; chromatin; development; gene regulation; single-molecule imaging; transcription factor; zebrafish

DOI:  https://doi.org/10.1016/j.molcel.2023.06.012
J Proteome Res. 2023 Jul 07.

nf-encyclopedia: A Cloud-Ready Pipeline for Chromatogram Library Data-Independent Acquisition Proteomics Workflows.

Carolyn Allen, Rico Meinl, J Sebastian Paez, Brian C Searle, Seth Just, Lindsay K Pino, William E Fondrie.

  Data-independent acquisition (DIA) mass spectrometry methods provide systematic and comprehensive quantification of the proteome; yet, relatively few open-source tools are available to analyze DIA proteomics experiments. Fewer still are tools that can leverage gas phase fractionated (GPF) chromatogram libraries to enhance the detection and quantification of peptides in these experiments. Here, we present nf-encyclopedia, an open-source NextFlow pipeline that connects three open-source tools, MSConvert, EncyclopeDIA, and MSstats, to analyze DIA proteomics experiments with or without chromatogram libraries. We demonstrate that nf-encyclopedia is reproducible when run on either a cloud platform or a local workstation and provides robust peptide and protein quantification. Additionally, we found that MSstats enhances protein-level quantitative performance over EncyclopeDIA alone. Finally, we benchmarked the ability of nf-encyclopedia to scale to large experiments in the cloud by leveraging the parallelization of compute resources. The nf-encyclopedia pipeline is available under a permissive Apache 2.0 license; run it on your desktop, cluster, or in the cloud: https://github.com/TalusBio/nf-encyclopedia.

Keywords:  bioinformatics; cloud; data-independent acquisition; mass spectrometry; pipeline; proteomics; reproducibility; workflow

DOI:  https://doi.org/10.1021/acs.jproteome.2c00613
Development. 2023 Jul 04. pii: dev.201386. [Epub ahead of print]

Optogenetic control of Wnt signaling models cell-intrinsic embryogenic patterning using 2D human pluripotent stem cell culture.

Nicole A Repina, Hunter J Johnson, Xiaoping Bao, Joshua A Zimmermann, David A Joy, Shirley Z Bi, Ravi S Kane, David V Schaffer.

  In embryonic stem cell (ESC) models for early development, spatially and temporally varying patterns of signaling and cell types emerge spontaneously. However, mechanistic insight into this dynamic self-organization is limited by a lack of methods for spatiotemporal control of signaling, and the relevance of signal dynamics and cell-to-cell variability to pattern emergence remains unknown. Here, we combine optogenetic stimulation, imaging, and transcriptomic approaches to study self-organization of human ESCs (hESC) in two-dimensional (2D) culture. Morphogen dynamics were controlled via optogenetic activation of canonical Wnt/β-catenin signaling (optoWnt), which drove broad transcriptional changes and mesendoderm differentiation at high efficiency (>99% cells). When activated within cell subpopulations, optoWnt induced cell self-organization into distinct epithelial and mesenchymal domains, mediated by changes in cell migration, an epithelial to mesenchymal-like transition, and TGF-β signaling. Furthermore, we demonstrate that such optogenetic control of cell subpopulations can be used to uncover signaling feedback mechanisms between neighboring cell types. These findings reveal that cell-to-cell variability in Wnt signaling is sufficient to generate tissue-scale patterning and establish an hESC model system for investigating feedback mechanisms relevant to early human embryogenesis.

Keywords:  Differentiation; Heterogeneity; Morphogenesis; Optogenetics; Patterning; Wnt signaling

DOI:  https://doi.org/10.1242/dev.201386
Nat Biotechnol. 2023 Jul 06.

De novo detection of somatic mutations in high-throughput single-cell profiling data sets.

Francesc Muyas, Carolin M Sauer, Jose Espejo Valle-Inclán, Ruoyan Li, Raheleh Rahbari, Thomas J Mitchell, Sahand Hormoz, Isidro Cortés-Ciriano.

Characterization of somatic mutations at single-cell resolution is essential to study cancer evolution, clonal mosaicism and cell plasticity. Here, we describe SComatic, an algorithm designed for the detection of somatic mutations in single-cell transcriptomic and ATAC-seq (assay for transposase-accessible chromatin sequence) data sets directly without requiring matched bulk or single-cell DNA sequencing data. SComatic distinguishes somatic mutations from polymorphisms, RNA-editing events and artefacts using filters and statistical tests parameterized on non-neoplastic samples. Using >2.6 million single cells from 688 single-cell RNA-seq (scRNA-seq) and single-cell ATAC-seq (scATAC-seq) data sets spanning cancer and non-neoplastic samples, we show that SComatic detects mutations in single cells accurately, even in differentiated cells from polyclonal tissues that are not amenable to mutation detection using existing methods. Validated against matched genome sequencing and scRNA-seq data, SComatic achieves F1 scores between 0.6 and 0.7 across diverse data sets, in comparison to 0.2-0.4 for the second-best performing method. In summary, SComatic permits de novo mutational signature analysis, and the study of clonal heterogeneity and mutational burdens at single-cell resolution.

DOI: https://doi.org/10.1038/s41587-023-01863-z
Science. 2023 Jul 06. eadg4521

Oncogene-like addiction to aneuploidy in human cancers.

Vishruth Girish, Asad A Lakhani, Sarah L Thompson, Christine M Scaduto, Leanne M Brown, Ryan A Hagenson, Erin L Sausville, Brianna E Mendelson, Pranav K Kandikuppa, Devon A Lukow, Monet Lou Yuan, Eric C Stevens, Sophia N Lee, Klaske M Schukken, Saron M Akalu, Anand Vasudevan, Charles Zou, Barbora Salovska, Wenxue Li, Joan C Smith, Alison M Taylor, Robert A Martienssen, Yansheng Liu, Ruping Sun, Jason M Sheltzer.

Most cancers exhibit aneuploidy, but its functional significance in tumor development is controversial. Here, we describe ReDACT (Restoring Disomy in Aneuploid cells using CRISPR Targeting), a set of chromosome engineering tools that allow us to eliminate specific aneuploidies from cancer genomes. Using ReDACT, we created a panel of isogenic cells that have or lack common aneuploidies, and we demonstrate that trisomy of chromosome 1q is required for malignant growth in cancers harboring this alteration. Mechanistically, gaining chromosome 1q increases the expression of MDM4 and suppresses p53 signaling, and we show that TP53 mutations are mutually-exclusive with 1q aneuploidy in human cancers. Thus, tumor cells can be dependent on specific aneuploidies, raising the possibility that these "aneuploidy addictions" could be targeted as a therapeutic strategy.

DOI: https://doi.org/10.1126/science.adg4521
Nucleic Acids Res. 2023 Jul 03. pii: gkad557. [Epub ahead of print]

PEPseq quantifies transcriptome-wide changes in protein occupancy and reveals selective translational repression after translational stress.

Jakob Trendel, Etienne Boileau, Marco Jochem, Christoph Dieterich, Jeroen Krijgsveld.

Post-transcriptional gene regulation is accomplished by the interplay of the transcriptome with RNA-binding proteins, which occurs in a dynamic manner in response to altered cellular conditions. Recording the combined occupancy of all proteins binding to the transcriptome offers the opportunity to interrogate if a particular treatment leads to any interaction changes, pointing to sites in RNA that undergo post-transcriptional regulation. Here, we establish a method to monitor protein occupancy in a transcriptome-wide fashion by RNA sequencing. To this end, peptide-enhanced pull-down for RNA sequencing (or PEPseq) uses metabolic RNA labelling with 4-thiouridine (4SU) for light-induced protein-RNA crosslinking, and N-hydroxysuccinimide (NHS) chemistry to isolate protein-crosslinked RNA fragments across all long RNA biotypes. We use PEPseq to investigate changes in protein occupancy during the onset of arsenite-induced translational stress in human cells and reveal an increase of protein interactions in the coding region of a distinct set of mRNAs, including mRNAs coding for the majority of cytosolic ribosomal proteins. We use quantitative proteomics to demonstrate that translation of these mRNAs remains repressed during the initial hours of recovery after arsenite stress. Thus, we present PEPseq as a discovery platform for the unbiased investigation of post-transcriptional regulation.

DOI: https://doi.org/10.1093/nar/gkad557
bioRxiv. 2023 Jun 14. pii: 2023.03.10.531983. [Epub ahead of print]

Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy.

José L McFaline-Figueroa, Sanjay Srivatsan, Andrew J Hill, Molly Gasperini, Dana L Jackson, Lauren Saunders, Silvia Domcke, Samuel G Regalado, Paul Lazarchuck, Sarai Alvarez, Raymond J Monnat, Jay Shendure, Cole Trapnell.

Chemical genetic screens are a powerful tool for exploring how cancer cells' response to drugs is shaped by their mutations, yet they lack a molecular view of the contribution of individual genes to the response to exposure. Here, we present sci-Plex- G ene-by- E nvironment (sci-Plex- G x E ), a platform for combined single-cell genetic and chemical screening at scale. We highlight the advantages of large-scale, unbiased screening by defining the contribution of each of 522 human kinases to the response of glioblastoma to different drugs designed to abrogate signaling from the receptor tyrosine kinase pathway. In total, we probed 14,121 gene-by-environment combinations across 1,052,205 single-cell transcriptomes. We identify an expression signature characteristic of compensatory adaptive signaling regulated in a MEK/MAPK-dependent manner. Further analyses aimed at preventing adaptation revealed promising combination therapies, including dual MEK and CDC7/CDK9 or NF-kB inhibitors, as potent means of preventing transcriptional adaptation of glioblastoma to targeted therapy.

DOI: https://doi.org/10.1101/2023.03.10.531983
Cell Rep. 2023 Jun 27. pii: S2211-1247(23)00698-8. [Epub ahead of print] 112687

Senescence-induced cellular reprogramming drives cnidarian whole-body regeneration.

Miguel Salinas-Saavedra, Febrimarsa, Gabriel Krasovec, Helen R Horkan, Andreas D Baxevanis, Uri Frank.

  Cell fate stability is essential to maintaining "law and order" in complex animals. However, high stability comes at the cost of reduced plasticity and, by extension, poor regenerative ability. This evolutionary trade-off has resulted in most modern animals being rather simple and regenerative or complex and non-regenerative. The mechanisms mediating cellular plasticity and allowing for regeneration remain unknown. We show that signals emitted by senescent cells can destabilize the differentiated state of neighboring somatic cells, reprogramming them into stem cells that are capable of driving whole-body regeneration in the cnidarian Hydractinia symbiolongicarpus. Pharmacological or genetic inhibition of senescence prevents reprogramming and regeneration. Conversely, induction of transient ectopic senescence in a regenerative context results in supernumerary stem cells and faster regeneration. We propose that senescence signaling is an ancient mechanism mediating cellular plasticity. Understanding the senescence environment that promotes cellular reprogramming could provide an avenue to enhance regeneration.

Keywords:  CP: Stem cell research; Hydractinia; cnidaria; optogenetics; reprogramming; senescence; stem cells; whole-body regeneration

DOI:  https://doi.org/10.1016/j.celrep.2023.112687
Nature. 2023 Jul 05.

Loss of CDK4/6 activity in S/G2 phase leads to cell cycle reversal.

James A Cornwell, Adrijana Crncec, Marwa M Afifi, Kristina Tang, Ruhul Amin, Steven D Cappell.

In mammalian cells, the decision to proliferate is thought to be irreversibly made at the restriction point of the cell cycle1,2, when mitogen signalling engages a positive feedback loop between cyclin A2/cyclin-dependent kinase 2 (CDK2) and the retinoblastoma protein3-5. Contrary to this textbook model, here we show that the decision to proliferate is actually fully reversible. Instead, we find that all cycling cells will exit the cell cycle in the absence of mitogens unless they make it to mitosis and divide first. This temporal competition between two fates, mitosis and cell cycle exit, arises because cyclin A2/CDK2 activity depends upon CDK4/6 activity throughout the cell cycle, not just in G1 phase. Without mitogens, mitosis is only observed when the half-life of cyclin A2 protein is long enough to sustain CDK2 activity throughout G2/M. Thus, cells are dependent on mitogens and CDK4/6 activity to maintain CDK2 activity and retinoblastoma protein phosphorylation throughout interphase. Consequently, even a 2-h delay in a cell's progression towards mitosis can induce cell cycle exit if mitogen signalling is lost. Our results uncover the molecular mechanism underlying the restriction point phenomenon, reveal an unexpected role for CDK4/6 activity in S and G2 phases and explain the behaviour of all cells following loss of mitogen signalling.

DOI: https://doi.org/10.1038/s41586-023-06274-3