bims-pideca 2022-12-04 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2022–12–04
24 papers selected by
Ralitsa Radostinova Madsen, University College London

Cardiac PI3K p110α attenuation delays aging and extends lifespan.
Clinical and functional characterization of germline PIK3CA variants in patients with PIK3CA-related overgrowth Spectrum disorders.
Discovery of GDC-0077 (Inavolisib), a Highly Selective Inhibitor and Degrader of Mutant PI3Kα.
Ras drives malignancy through stem cell crosstalk with the microenvironment.
Systematic identification of biochemical networks in cancer cells by Functional Pathway Inference Analysis.
mTORC1 links pathology in experimental models of Still's disease and macrophage activation syndrome.
GOLPH3 protein controls organ growth by interacting with TOR signaling proteins in Drosophila.
Proximity sequencing for single-cell measurement of protein complexes.
Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation.
GLUT4 translocation and dispersal operate in multiple cell types and are negatively correlated with cell size in adipocytes.
A high throughput proliferation and cytotoxicity assay for co-cultured isogenic cell lines.
Genetically encoded dual fluorophore reporters for graded oxygen-sensing in light microscopy.
Quantification of extracellular proteins, protein complexes and mRNAs in single cells by proximity sequencing.
Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks.
Expanding registered reports.
Deduction of signaling mechanisms from cellular responses to multiple cues.
Monitoring of cell-cell communication and contact history in mammals.
Meta-analysis of human cancer single cell RNA-seq datasets using the IMMUcan database.
Metabolic determinants of tumour initiation.
A reference human induced pluripotent stem cell line for large-scale collaborative studies.
Greater genetic diversity is needed in human pluripotent stem cell models.
Comparison of PIK3CA Mutation Prevalence in Breast Cancer Across Predicted Ancestry Populations.
PPM1D suppresses p53-dependent transactivation and cell death by inhibiting the Integrated Stress Response.
Towards an accurate and robust analysis pipeline for somatic mutation calling.

Cell Stress. 2022 Aug;6(8): 72-75

Cardiac PI3K p110α attenuation delays aging and extends lifespan.

Mahmoud Abdellatif, Tobias Eisenberg, Alexander Martin Heberle, Kathrin Thedieck, Guido Kroemer, Simon Sedej.

  Phosphoinositide 3-kinase (PI3K) is a key component of the insulin signaling pathway that controls cellular me-tabolism and growth. Loss-of-function mutations in PI3K signaling and other downstream effectors of the insulin signaling pathway extend the lifespan of various model organisms. However, the pro-longevity effect appears to be sex-specific and young mice with reduced PI3K signaling have increased risk of cardiac disease. Hence, it remains elusive as to whether PI3K inhibition is a valid strategy to delay aging and extend healthspan in humans. We recently demonstrated that reduced PI3K activity in cardiomyocytes delays cardiac growth, causing subnormal contractility and cardiopulmonary functional capacity, as well as increased risk of mortality at young age. In stark contrast, in aged mice, experi-mental attenuation of PI3K signaling reduced the age-dependent decline in cardiac function and extended maximal lifespan, suggesting a biphasic effect of PI3K on cardiac health and survival. The cardiac anti-aging effects of reduced PI3K activity coincided with enhanced oxida-tive phosphorylation and required increased autophagic flux. In humans, explanted failing hearts showed in-creased PI3K signaling, as indicated by increased phos-phorylation of the serine/threonine-protein kinase AKT. Hence, late-life cardiac-specific targeting of PI3K might have a therapeutic potential in cardiac aging and related diseases.

Keywords:  IGF1; PI3K; aging; autophagy; cardiomyopathy; heart failure; insulin signaling; mitochondrial dysfunction

DOI:  https://doi.org/10.15698/cst2022.08.270
Hum Mol Genet. 2022 Dec 02. pii: ddac296. [Epub ahead of print]

Clinical and functional characterization of germline PIK3CA variants in patients with PIK3CA-related overgrowth Spectrum disorders.

Jessica A Cooley Coleman, Jennifer M Gass, Sujata Srikanth, Rini Pauly, Catherine A Ziats, David B Everman, Steven A Skinner, Shannon Bell, Raymond J Louie, Lauren Cascio, Wesley G Patterson, Julie R Jones, Nataliya Di Donato, Roger E Stevenson, Luigi Boccuto.

Mosaic variants in the PIK3CA gene, encoding the catalytic subunit of phosphatidylinositol 3-kinase (PI3K), produce constitutive PI3K activation which causes PIK3CA-related overgrowth spectrum (PROS) disorders. To date, fewer than 20 patients have been described with germline alterations in PIK3CA. In this study, we describe three unrelated individuals with overgrowth and germline PIK3CA variants. These variants were discovered through whole-exome sequencing and confirmed as germline by testing multiple tissue types, when available. Functional analysis using Patient 1's fibroblast cell line and two previously reported patients' cell lines showed increased phosphorylation of AKT during cellular starvation revealing constitutive activation of the PI3K/AKT/mTOR pathway. Alternatively, stimulation of the cells by fetal bovine serum produced a reduced response, indicating an activated status of the PI3K complex reducing the pathway response to further external stimulation. Additional studies utilizing Biolog Phenotype Microarray technology indicated reduced energy production when cells were exposed to growth factors stimulating the PI3K/AKT/mTOR pathway, confirming the trend observed in the AKT phosphorylation test after stimulation. Furthermore, treatment with inhibitors of the PI3K/AKT/mTOR pathway rescued the normal energy response in the patients' cells. Collectively, these data demonstrate that disease-causing germline PIK3CA variants have a functional consequence, similar to mosaic variants in the PI3K/AKT/mTOR pathway.

DOI: https://doi.org/10.1093/hmg/ddac296
J Med Chem. 2022 Dec 01.

Discovery of GDC-0077 (Inavolisib), a Highly Selective Inhibitor and Degrader of Mutant PI3Kα.

Emily J Hanan, Marie-Gabrielle Braun, Robert A Heald, Calum MacLeod, Connie Chan, Saundra Clausen, Kyle A Edgar, Charles Eigenbrot, Richard Elliott, Nicholas Endres, Lori S Friedman, Emily Gogol, Xiao-Hui Gu, Rebecca Hong Thibodeau, Philip S Jackson, James R Kiefer, Jamie D Knight, Michelle Nannini, Raman Narukulla, Amanda Pace, Jodie Pang, Hans E Purkey, Laurent Salphati, Deepak Sampath, Stephen Schmidt, Steve Sideris, Kyung Song, Swathi Sujatha-Bhaskar, Mark Ultsch, Heidi Wallweber, Jianfeng Xin, SiewKuen Yeap, Amy Young, Yu Zhong, Steven T Staben.

Small molecule inhibitors that target the phosphatidylinositol 3-kinase (PI3K) signaling pathway have received significant interest for the treatment of cancers. The class I isoform PI3Kα is most commonly associated with solid tumors via gene amplification or activating mutations. However, inhibitors demonstrating both PI3K isoform and mutant specificity have remained elusive. Herein, we describe the optimization and characterization of a series of benzoxazepin-oxazolidinone ATP-competitive inhibitors of PI3Kα which also induce the selective degradation of the mutant p110α protein, the catalytic subunit of PI3Kα. Structure-based design informed isoform-specific interactions within the binding site, leading to potent inhibitors with greater than 300-fold selectivity over the other Class I PI3K isoforms. Further optimization of pharmacokinetic properties led to excellent in vivo exposure and efficacy and the identification of clinical candidate GDC-0077 (inavolisib, 32), which is now under evaluation in a Phase III clinical trial as a treatment for patients with PIK3CA-mutant breast cancer.

DOI: https://doi.org/10.1021/acs.jmedchem.2c01422
Nature. 2022 Nov 30.

Ras drives malignancy through stem cell crosstalk with the microenvironment.

Shaopeng Yuan, Katherine S Stewart, Yihao Yang, Merve Deniz Abdusselamoglu, S Martina Parigi, Tamar Y Feinberg, Karen Tumaneng, Hanseul Yang, John M Levorse, Lisa Polak, David Ng, Elaine Fuchs.

Squamous cell carcinomas are triggered by marked elevation of RAS-MAPK signalling and progression from benign papilloma to invasive malignancy1-4. At tumour-stromal interfaces, a subset of tumour-initiating progenitors, the cancer stem cells, obtain increased resistance to chemotherapy and immunotherapy along this pathway5,6. The distribution and changes in cancer stem cells during progression from a benign state to invasive squamous cell carcinoma remain unclear. Here we show in mice that, after oncogenic RAS activation, cancer stem cells rewire their gene expression program and trigger self-propelling, aberrant signalling crosstalk with their tissue microenvironment that drives their malignant progression. The non-genetic, dynamic cascade of intercellular exchanges involves downstream pathways that are often mutated in advanced metastatic squamous cell carcinomas with high mutational burden7. Coupling our clonal skin HRASG12V mouse model with single-cell transcriptomics, chromatin landscaping, lentiviral reporters and lineage tracing, we show that aberrant crosstalk between cancer stem cells and their microenvironment triggers angiogenesis and TGFβ signalling, creating conditions that are conducive for hijacking leptin and leptin receptor signalling, which in turn launches downstream phosphoinositide 3-kinase (PI3K)-AKT-mTOR signalling during the benign-to-malignant transition. By functionally examining each step in this pathway, we reveal how dynamic temporal crosstalk with the microenvironment orchestrated by the stem cells profoundly fuels this path to malignancy. These insights suggest broad implications for cancer therapeutics.

DOI: https://doi.org/10.1038/s41586-022-05475-6
Bioinformatics. 2022 Nov 30. pii: btac769. [Epub ahead of print]

Systematic identification of biochemical networks in cancer cells by Functional Pathway Inference Analysis.

Irbaz I Badshah, Pedro R Cutillas.

MOTIVATION: Pathway inference methods are key for annotating the genome, for providing insights into the mechanisms of biochemical processes and allow the discovery of signalling members and potential new drug targets. Here, we tested the hypothesis that genes with similar impact on cell viability across multiple cell lines belong to a common pathway, thus providing a conceptual basis for a pathway inference method based on correlated anti-proliferative gene properties.
METHODS: To test this concept, we used recently available large scale RNAi screens to develop a method, termed Functional Pathway Inference Analysis (FPIA), to systemically identify correlated gene dependencies.
RESULTS: To assess FPIA, we initially focused on PI3K/AKT/MTOR signalling, a prototypic oncogenic pathway for which we have good sense of ground truth. Dependencies for AKT1, MTOR and PDPK1 were among the most correlated with those for PIK3CA (encoding PI3Kα), as returned by FPIA, whereas negative regulators of PI3K/AKT/MTOR signalling, such as PTEN were anti-correlated. Following FPIA, MTOR, PIK3CA and PIK3CB produced significantly greater correlations for genes in the PI3K-Akt pathway versus other pathways. Application of FPIA to two additional pathways (p53 and MAPK) returned expected associations (e.g., MDM2 and TP53BP1 for p53 and MAPK1 and BRAF for MEK1). Over-representation analysis of FPIA-returned genes enriched the respective pathway, and FPIA restricted to specific tumour lineages uncovered cell type-specific networks. Overall, our study demonstrates the ability of FPIA to identify members of pro-survival biochemical pathways in cancer cells.
AVAILABILITY: FPIA is implemented in a new R package named 'cordial' freely available from https://github.com/CutillasLab/cordial.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btac769
Nat Commun. 2022 Nov 28. 13(1): 6915

mTORC1 links pathology in experimental models of Still's disease and macrophage activation syndrome.

Zhengping Huang, Xiaomeng You, Liang Chen, Yan Du, Kailey Brodeur, Hyuk Jee, Qiang Wang, Grace Linder, Roxane Darbousset, Pierre Cunin, Margaret H Chang, Alexandra Wactor, Brian M Wauford, Marc J C Todd, Kevin Wei, Ying Li, Anais Levescot, Yoichiro Iwakura, Virginia Pascual, Nicole E Baldwin, Pierre Quartier, Tianwang Li, Maria T Gianatasio, Robert P Hasserjian, Lauren A Henderson, David B Sykes, Elizabeth D Mellins, Scott W Canna, Julia F Charles, Peter A Nigrovic, Pui Y Lee.

Still's disease is a severe inflammatory syndrome characterized by fever, skin rash and arthritis affecting children and adults. Patients with Still's disease may also develop macrophage activation syndrome, a potentially fatal complication of immune dysregulation resulting in cytokine storm. Here we show that mTORC1 (mechanistic target of rapamycin complex 1) underpins the pathology of Still's disease and macrophage activation syndrome. Single-cell RNA sequencing in a murine model of Still's disease shows preferential activation of mTORC1 in monocytes; both mTOR inhibition and monocyte depletion attenuate disease severity. Transcriptomic data from patients with Still's disease suggest decreased expression of the mTORC1 inhibitors TSC1/TSC2 and an mTORC1 gene signature that strongly correlates with disease activity and treatment response. Unrestricted activation of mTORC1 by Tsc2 deletion in mice is sufficient to trigger a Still's disease-like syndrome, including both inflammatory arthritis and macrophage activation syndrome with hemophagocytosis, a cellular manifestation that is reproduced in human monocytes by CRISPR/Cas-mediated deletion of TSC2. Consistent with this observation, hemophagocytic histiocytes from patients with macrophage activation syndrome display prominent mTORC1 activity. Our study suggests a mechanistic link of mTORC1 to inflammation that connects the pathogenesis of Still's disease and macrophage activation syndrome.

DOI: https://doi.org/10.1038/s41467-022-34480-6
Cell Death Dis. 2022 Nov 27. 13(11): 1003

GOLPH3 protein controls organ growth by interacting with TOR signaling proteins in Drosophila.

Anna Frappaolo, Angela Karimpour-Ghahnavieh, Giuliana Cesare, Stefano Sechi, Roberta Fraschini, Thomas Vaccari, Maria Grazia Giansanti.

The oncoprotein GOLPH3 (Golgi phosphoprotein 3) is an evolutionarily conserved phosphatidylinositol 4-phosphate effector, mainly localized to the Golgi apparatus, where it supports organelle architecture and vesicular trafficking. Overexpression of human GOLPH3 correlates with poor prognosis in several cancer types and is associated with enhanced signaling downstream of mTOR (mechanistic target of rapamycin). However, the molecular link between GOLPH3 and mTOR remains elusive. Studies in Drosophila melanogaster have shown that Translationally controlled tumor protein (Tctp) and 14-3-3 proteins are required for organ growth by supporting the function of the small GTPase Ras homolog enriched in the brain (Rheb) during mTORC1 (mTOR complex 1) signaling. Here we demonstrate that Drosophila GOLPH3 (dGOLPH3) physically interacts with Tctp and 14-3-3ζ. RNAi-mediated knockdown of dGOLPH3 reduces wing and eye size and enhances the phenotypes of Tctp RNAi. This phenotype is partially rescued by overexpression of Tctp, 14-3-3ζ, or Rheb. We also show that the Golgi localization of Rheb in Drosophila cells depends on dGOLPH3. Consistent with dGOLPH3 involvement in Rheb-mediated mTORC1 activation, depletion of dGOLPH3 also reduces levels of phosphorylated ribosomal S6 kinase, a downstream target of mTORC1. Finally, the autophagy flux and the expression of autophagic transcription factors of the TFEB family, which anti correlates with mTOR signaling, are compromised upon reduction of dGOLPH3. Overall, our data provide the first in vivo demonstration that GOLPH3 regulates organ growth by directly associating with mTOR signaling proteins.

DOI: https://doi.org/10.1038/s41419-022-05438-9
Nat Methods. 2022 Dec;19(12): 1528-1529

Proximity sequencing for single-cell measurement of protein complexes.

DOI: https://doi.org/10.1038/s41592-022-01686-x
Nat Commun. 2022 Dec 02. 13(1): 7431

Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation.

Henrik M Hammarén, Eva-Maria Geissen, Clement M Potel, Martin Beck, Mikhail M Savitski.

Post-translational modifications (PTMs) regulate various aspects of protein function, including degradation. Mass spectrometric methods relying on pulsed metabolic labeling are popular to quantify turnover rates on a proteome-wide scale. Such data have traditionally been interpreted in the context of protein proteolytic stability. Here, we combine theoretical kinetic modeling with experimental pulsed stable isotope labeling of amino acids in cell culture (pSILAC) for the study of protein phosphorylation. We demonstrate that metabolic labeling combined with PTM-specific enrichment does not measure effects of PTMs on protein stability. Rather, it reveals the relative order of PTM addition and removal along a protein's lifetime-a fundamentally different metric. This is due to interconversion of the measured proteoform species. Using this framework, we identify temporal phosphorylation sites on cell cycle-specific factors and protein complex assembly intermediates. Our results thus allow tying PTMs to the age of the modified proteins.

DOI: https://doi.org/10.1038/s41467-022-35054-2
Sci Rep. 2022 Nov 29. 12(1): 20535

GLUT4 translocation and dispersal operate in multiple cell types and are negatively correlated with cell size in adipocytes.

Anna M Koester, Angéline Geiser, Peter R T Bowman, Sebastian van de Linde, Nikolaj Gadegaard, Nia J Bryant, Gwyn W Gould.

The regulated translocation of the glucose transporter, GLUT4, to the surface of adipocytes and muscle is a key action of insulin. This is underpinned by the delivery and fusion of GLUT4-containing vesicles with the plasma membrane. Recent studies have revealed that a further action of insulin is to mediate the dispersal of GLUT4 molecules away from the site of GLUT4 vesicle fusion with the plasma membrane. Although shown in adipocytes, whether insulin-stimulated dispersal occurs in other cells and/or is exhibited by other proteins remains a matter of debate. Here we show that insulin stimulates GLUT4 dispersal in the plasma membrane of adipocytes, induced pluripotent stem cell-derived cardiomyocytes and HeLa cells, suggesting that this phenomenon is specific to GLUT4 expressed in all cell types. By contrast, insulin-stimulated dispersal of TfR was not observed in HeLa cells, suggesting that the mechanism may be unique to GLUT4. Consistent with dispersal being an important physiological mechanism, we observed that insulin-stimulated GLUT4 dispersal is reduced under conditions of insulin resistance. Adipocytes of different sizes have been shown to exhibit distinct metabolic properties: larger adipocytes exhibit reduced insulin-stimulated glucose transport compared to smaller cells. Here we show that both GLUT4 delivery to the plasma membrane and GLUT4 dispersal are reduced in larger adipocytes, supporting the hypothesis that larger adipocytes are refractory to insulin challenge compared to their smaller counterparts, even within a supposedly homogeneous population of cells.

DOI: https://doi.org/10.1038/s41598-022-24736-y
MethodsX. 2022 ;9 101927

A high throughput proliferation and cytotoxicity assay for co-cultured isogenic cell lines.

Syed Ahmad, Kris C Wood, John E Scott.

  PTEN is a well-known tumor suppressor that is inactivated or suppressed at a high frequency in cancer. We sought an assay to screen compounds for ones that differentially inhibited proliferation or induced cytotoxicity in PTEN mutated cancer cells. We employed the isogenic pair of cell lines MCF10-A breast cell line (wild type, WT) and the same cell line with PTEN knocked out (KO) by CRISPR. We sought an assay where these PTEN WT and KO isogenic cell lines were co-cultured in the same well for compound testing. The KO cell line, but not the WT, was tagged with the red fluorescent protein mKate2. We employed a real time microscopic imaging instrument to identify cell populations in co-culture based on red fluorescence to obtain a cell count for each cell line. To acquire cytotoxicity data for each population, the dye CellTox Green was added to the media. To assess the assay, we determined the concentration response of paclitaxel. In order to assess the potential for screening, we performed mock screening in 384-well plate format. Thus, we developed a high throughput co-culture cell cytotoxicity and proliferation assay method that could be employed for any pair of cell lines to identify selective compounds.

Keywords:  Cancer; Isogenic; PTEN

DOI:  https://doi.org/10.1016/j.mex.2022.101927
Biosens Bioelectron. 2022 Nov 17. pii: S0956-5663(22)00957-5. [Epub ahead of print]221 114917

Genetically encoded dual fluorophore reporters for graded oxygen-sensing in light microscopy.

Nadine Bauer, Ivan Maisuls, Abel Pereira da Graça, Dirk Reinhardt, Raghu Erapaneedi, Nils Kirschnick, Michael Schäfers, Carsten Grashoff, Katharina Landfester, Dietmar Vestweber, Cristian A Strassert, Friedemann Kiefer.

  Hypoxia is an essential regulator of cell metabolism, affects cell migration and angiogenesis during development and contributes to a wide range of pathological conditions. Multiple techniques to assess hypoxia through oxygen-imaging have been developed. However, significant limitations include low spatiotemporal resolution, limited tissue penetration of exogenous probes and non-dynamic signals due to irreversible probe-chemistry. First genetically-encoded reporters only partly overcame these limitations as the green and red fluorescent proteins (GFP/RFP) families require molecular oxygen for fluorescence. For the herein presented ratiometric and FRET-FLIM reporters dUnORS and dUnOFLS, we exploited oxygen-dependent maturation in combination with the hypoxia-tolerant fluorescent-protein UnaG. For ratiometric measurements, UnaG was fused to the orange large Stokes Shift protein CyOFP1, allowing excitation with a single light-source, while fusion of UnaG with mOrange2 allowed FRET-FLIM analysis. Imaging live or fixed cultured cells for calibration, we applied both reporters in spheroid and tumor transplantation-models and obtained graded information on oxygen-availability at cellular resolution, establishing these sensors as promising tools for visualizing oxygen-gradients in-vivo.

Keywords:  FRET-FLIM; Fluorescent reporter; Live-cell imaging; Oxygen-sensing; Ratiometric sensor; Tumor-hypoxia

DOI:  https://doi.org/10.1016/j.bios.2022.114917
Nat Methods. 2022 Dec;19(12): 1578-1589

Quantification of extracellular proteins, protein complexes and mRNAs in single cells by proximity sequencing.

Luke Vistain, Hoang Van Phan, Bijentimala Keisham, Christian Jordi, Mengjie Chen, Sai T Reddy, Savaş Tay.

We present proximity sequencing (Prox-seq) for simultaneous measurement of proteins, protein complexes and mRNAs in thousands of single cells. Prox-seq combines proximity ligation assay with single-cell sequencing to measure proteins and their complexes from all pairwise combinations of targeted proteins, providing quadratically scaled multiplexing. We validate Prox-seq and analyze a mixture of T cells and B cells to show that it accurately identifies these cell types and detects well-known protein complexes. Next, by studying human peripheral blood mononuclear cells, we discover that naïve CD8+ T cells display the protein complex CD8-CD9. Finally, we study protein interactions during Toll-like receptor (TLR) signaling in human macrophages. We observe the formation of signal-specific protein complexes, find CD36 co-receptor activity and additive signal integration under lipopolysaccharide (TLR4) and Pam2CSK4 (TLR2) stimulation, and show that quantification of protein complexes identifies signaling inputs received by macrophages. Prox-seq provides access to an untapped measurement modality for single-cell phenotyping and can discover uncharacterized protein interactions in different cell types.

DOI: https://doi.org/10.1038/s41592-022-01684-z
Cell Syst. 2022 Nov 11. pii: S2405-4712(22)00435-5. [Epub ahead of print]

Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks.

Ryan H Boe, Vinay Ayyappan, Lea Schuh, Arjun Raj.

  Genetic networks should respond to signals but prevent the transmission of spontaneous fluctuations. Limited data from mammalian cells suggest that noise transmission is uncommon, but systematic claims about noise transmission have been limited by the inability to directly measure it. Here, we build a mathematical framework modeling allelic correlation and noise transmission, showing that allelic correlation and noise transmission correspond across model parameters and network architectures. Limiting noise transmission comes with the trade-off of being unresponsive to signals, and within responsive regimes, there is a further trade-off between response time and basal noise transmission. Analysis of allele-specific single-cell RNA-sequencing data revealed that genes encoding upstream factors in signaling pathways and cell-type-specific factors have higher allelic correlation than downstream factors, suggesting they are more subject to regulation. Overall, our findings suggest that some noise transmission must result from signal responsiveness, but it can be minimized by trading off for a slower response. A record of this paper's transparent peer review process is included in the supplemental information.

Keywords:  allelic correlation; network modeling; noise transmission; signal processing; transcriptional noise

DOI:  https://doi.org/10.1016/j.cels.2022.10.008
Nat Commun. 2022 Nov 28. 13(1): 7267

Expanding registered reports.

DOI: https://doi.org/10.1038/s41467-022-34107-w
NPJ Syst Biol Appl. 2022 Nov 30. 8(1): 48

Deduction of signaling mechanisms from cellular responses to multiple cues.

Soutick Saha, Hye-Ran Moon, Bumsoo Han, Andrew Mugler.

Cell signaling networks are complex and often incompletely characterized, making it difficult to obtain a comprehensive picture of the mechanisms they encode. Mathematical modeling of these networks provides important clues, but the models themselves are often complex, and it is not always clear how to extract falsifiable predictions. Here we take an inverse approach, using experimental data at the cell level to deduce the minimal signaling network. We focus on cells' response to multiple cues, specifically on the surprising case in which the response is antagonistic: the response to multiple cues is weaker than the response to the individual cues. We systematically build candidate signaling networks one node at a time, using the ubiquitous ingredients of (i) up- or down-regulation, (ii) molecular conversion, or (iii) reversible binding. In each case, our method reveals a minimal, interpretable signaling mechanism that explains the antagonistic response. Our work provides a systematic way to deduce molecular mechanisms from cell-level data.

DOI: https://doi.org/10.1038/s41540-022-00262-5
Science. 2022 Dec 02. 378(6623): eabo5503

Monitoring of cell-cell communication and contact history in mammals.

Shaohua Zhang, Huan Zhao, Zixin Liu, Kuo Liu, Huan Zhu, Wenjuan Pu, Lingjuan He, Rong A Wang, Bin Zhou.

Monitoring of cell-cell communication in multicellular organisms is fundamental to understanding diverse biological processes such as embryogenesis and tumorigenesis. To track cell-cell contacts in vivo, we developed an intercellular genetic technology to monitor cell-cell contact and to trace cell contact histories by permanently marking contacts between cells. In mice, we engineered an artificial Notch ligand into one cell (the sender cell) and an artificial receptor into another cell (the receiver cell). Contact between the sender and receiver cells triggered a synthetic Notch signaling that activated downstream transcriptional programs in the receiver cell, thereby transiently or permanently labeling it. In vivo cell-cell contact was observed during development, tissue homeostasis, and tumor growth. This technology may be useful for studying dynamic in vivo cell-cell contacts and cell fate plasticity.

DOI: https://doi.org/10.1126/science.abo5503
Cancer Res. 2022 Dec 02. pii: CAN-22-0074. [Epub ahead of print]

Meta-analysis of human cancer single cell RNA-seq datasets using the IMMUcan database.

Jordi Camps, Floriane Noël, Robin Liechti, Lucile Massenet-Regad, Sidwell Rigade, Lou Götz, Caroline Hoffmann, Elise Amblard, Melissa Saichi, Mahmoud M Ibrahim, Jack Pollard, Jasna Medvedovic, Helge G Roider, Vassili Soumelis.

The development of single cell RNA-sequencing (scRNA-seq) technologies has greatly contributed to deciphering the tumor microenvironment (TME). An enormous amount of independent scRNA-seq studies have been published representing a valuable resource that provides opportunities for meta-analysis studies. However, the massive amount of biological information, the marked heterogeneity and variability between studies, and the technical challenges in processing heterogeneous datasets create major bottlenecks for the full exploitation of scRNA-seq data. We have developed IMMUcan scDB (https://immucanscdb.vital-it.ch), a fully integrated scRNA-seq database exclusively dedicated to human cancer and accessible to non-specialists. IMMUcan scDB encompasses 144 datasets on 56 different cancer types, annotated in 50 fields containing precise clinical, technological and biological information. A data processing pipeline was developed and organized in 4 steps: 1) data collection; 2) data processing (quality control and sample integration); 3) supervised cell annotation with a cell ontology classifier of the TME; and 4) interface to analyze TME in a cancer type-specific or global manner. This framework was used to explore datasets across tumor locations in a gene centric (CXCL13) and cell-centric (B cells) manner as well as to conduct meta-analysis studies such as ranking immune cell types and genes correlated to malignant transformation. This integrated, freely accessible and user-friendly resource represents and unprecedented level of detailed annotation, offering vast possibilities for downstream exploitation of human cancer scRNAseq data for discovery and validation studies.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-0074
Nat Rev Endocrinol. 2022 Nov 29.

Metabolic determinants of tumour initiation.

Julia S Brunner, Lydia W S Finley.

Tumours exhibit notable metabolic alterations compared with their corresponding normal tissue counterparts. These metabolic alterations can support anabolic growth, enable survival in hostile environments and regulate gene expression programmes that promote malignant progression. Whether these metabolic changes are selected for during malignant transformation or can themselves be drivers of tumour initiation is unclear. However, intriguingly, many of the major bottlenecks for tumour initiation - control of cell fate, survival and proliferation - are all amenable to metabolic regulation. In this article, we review evidence demonstrating a critical role for metabolic pathways in processes that support the earliest stages of tumour development. We discuss how cell-intrinsic factors, such as the cell of origin or transforming oncogene, and cell-extrinsic factors, such as local nutrient availability, promote or restrain tumour initiation. Deeper insight into how metabolic pathways control tumour initiation will improve our ability to design metabolic interventions to limit tumour incidence.

DOI: https://doi.org/10.1038/s41574-022-00773-5
Cell Stem Cell. 2022 Dec 01. pii: S1934-5909(22)00451-9. [Epub ahead of print]29(12): 1685-1702.e22

A reference human induced pluripotent stem cell line for large-scale collaborative studies.

Caroline B Pantazis, Andrian Yang, Erika Lara, Justin A McDonough, Cornelis Blauwendraat, Lirong Peng, Hideyuki Oguro, Jitendra Kanaujiya, Jizhong Zou, David Sebesta, Gretchen Pratt, Erin Cross, Jeffrey Blockwick, Philip Buxton, Lauren Kinner-Bibeau, Constance Medura, Christopher Tompkins, Stephen Hughes, Marianita Santiana, Faraz Faghri, Mike A Nalls, Daniel Vitale, Shannon Ballard, Yue A Qi, Daniel M Ramos, Kailyn M Anderson, Julia Stadler, Priyanka Narayan, Jason Papademetriou, Luke Reilly, Matthew P Nelson, Sanya Aggarwal, Leah U Rosen, Peter Kirwan, Venkat Pisupati, Steven L Coon, Sonja W Scholz, Theresa Priebe, Miriam Öttl, Jian Dong, Marieke Meijer, Lara J M Janssen, Vanessa S Lourenco, Rik van der Kant, Dennis Crusius, Dominik Paquet, Ana-Caroline Raulin, Guojun Bu, Aaron Held, Brian J Wainger, Rebecca M C Gabriele, Jackie M Casey, Selina Wray, Dad Abu-Bonsrah, Clare L Parish, Melinda S Beccari, Don W Cleveland, Emmy Li, Indigo V L Rose, Martin Kampmann, Carles Calatayud Aristoy, Patrik Verstreken, Laurin Heinrich, Max Y Chen, Birgitt Schüle, Dan Dou, Erika L F Holzbaur, Maria Clara Zanellati, Richa Basundra, Mohanish Deshmukh, Sarah Cohen, Richa Khanna, Malavika Raman, Zachary S Nevin, Madeline Matia, Jonas Van Lent, Vincent Timmerman, Bruce R Conklin, Katherine Johnson Chase, Ke Zhang, Salome Funes, Daryl A Bosco, Lena Erlebach, Marc Welzer, Deborah Kronenberg-Versteeg, Guochang Lyu, Ernest Arenas, Elena Coccia, Lily Sarrafha, Tim Ahfeldt, John C Marioni, William C Skarnes, Mark R Cookson, Michael E Ward, Florian T Merkle.

  Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate human iPSC lines and deeply characterized their genetic properties using whole genome sequencing, their genomic stability upon CRISPR-Cas9-based gene editing, and their phenotypic properties including differentiation to commonly used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field.

Keywords:  CRISPR; differentiation; iPSC; karyotype; p53; pluripotent; reference; single-cell; stem cell; whole-genome

DOI:  https://doi.org/10.1016/j.stem.2022.11.004
Nat Commun. 2022 Nov 26. 13(1): 7301

Greater genetic diversity is needed in human pluripotent stem cell models.

Sulagna Ghosh, Ralda Nehme, Lindy E Barrett.

DOI: https://doi.org/10.1038/s41467-022-34940-z
JCO Precis Oncol. 2022 Nov;6 e2200341

Comparison of PIK3CA Mutation Prevalence in Breast Cancer Across Predicted Ancestry Populations.

Jessica W Chen, Karthikeyan Murugesan, Justin Y Newberg, Ethan S Sokol, Heidi M Savage, Thomas J Stout, Sophia L Maund, Katherine E Hutchinson.

PURPOSE: Understanding the differences in biomarker prevalence that may exist among diverse populations is invaluable to accurately forecast biomarker-driven clinical trial enrollment metrics and to advance inclusive research and health equity. This study evaluated the frequency and types of PIK3CA mutations (PIK3CAmut) detected in predicted genetic ancestry subgroups across breast cancer (BC) subtypes.
METHODS: Analyses were conducted using real-world genomic data from adult patients with BC treated in an academic or community setting in the United States and whose tumor tissue was submitted for comprehensive genomic profiling.
RESULTS: Of 36,151 patients with BC (median age, 58 years; 99% female), the breakdown by predicted genetic ancestry was 75% European, 14% African, 6% Central/South American, 3% East Asian, and 1% South Asian. We demonstrated that patients of African ancestry are less likely to have tumors that harbor PIK3CAmut compared with patients of European ancestry with estrogen receptor-positive/human epidermal growth factor receptor 2-negative (ER+/HER2-) BC (37% [949/2,593] v 44% [7,706/17,637]; q = 4.39E-11) and triple-negative breast cancer (8% [179/2,199] v 14% [991/7,072]; q = 6.07E-13). Moreover, we found that PIK3CAmut were predominantly composed of hotspot mutations, of which mutations at H1047 were the most prevalent across BC subtypes (35%-41% ER+/HER2- BC; 43%-61% HER2+ BC; 40%-59% triple-negative breast cancer).
CONCLUSION: This analysis established that tumor PIK3CAmut prevalence can differ among predicted genetic ancestries across BC subtypes on the basis of the largest comprehensive genomic profiling data set of patients with cancer treated in the United States. This study highlights the need for equitable representation in research studies, which is imperative to ensuring better health outcomes for all.

DOI: https://doi.org/10.1200/PO.22.00341
Nat Commun. 2022 Dec 01. 13(1): 7400

PPM1D suppresses p53-dependent transactivation and cell death by inhibiting the Integrated Stress Response.

Zdenek Andrysik, Kelly D Sullivan, Jeffrey S Kieft, Joaquin M Espinosa.

The p53 transcription factor is a master regulator of cellular stress responses inhibited by repressors such as MDM2 and the phosphatase PPM1D. Activation of p53 with pharmacological inhibitors of its repressors is being tested in clinical trials for cancer therapy, but efficacy has been limited by poor induction of tumor cell death. We demonstrate that dual inhibition of MDM2 and PPM1D induces apoptosis in multiple cancer cell types via amplification of the p53 transcriptional program through the eIF2α-ATF4 pathway. PPM1D inhibition induces phosphorylation of eIF2α, ATF4 accumulation, and ATF4-dependent enhancement of p53-dependent transactivation upon MDM2 inhibition. Dual inhibition of p53 repressors depletes heme and induces HRI-dependent eIF2α phosphorylation. Pharmacological induction of eIF2α phosphorylation synergizes with MDM2 inhibition to induce cell death and halt tumor growth in mice. These results demonstrate that PPM1D inhibits both the p53 network and the integrated stress response controlled by eIF2α-ATF4, with clear therapeutic implications.

DOI: https://doi.org/10.1038/s41467-022-35089-5
Front Genet. 2022 ;13 979928

Towards an accurate and robust analysis pipeline for somatic mutation calling.

Jingjie Jin, Zixi Chen, Jinchao Liu, Hongli Du, Gong Zhang.

  Accurate and robust somatic mutation detection is essential for cancer treatment, diagnostics and research. Various analysis pipelines give different results and thus should be systematically evaluated. In this study, we benchmarked 5 commonly-used somatic mutation calling pipelines (VarScan, VarDictJava, Mutect2, Strelka2 and FANSe) for their precision, recall and speed, using standard benchmarking datasets based on a series of real-world whole-exome sequencing datasets. All the 5 pipelines showed very high precision in all cases, and high recall rate in mutation rates higher than 10%. However, for the low frequency mutations, these pipelines showed large difference. FANSe showed the highest accuracy (especially the sensitivity) in all cases, and VarScan and VarDictJava outperformed Mutect2 and Strelka2 in low frequency mutations at all sequencing depths. The flaws in filter was the major cause of the low sensitivity of the four pipelines other than FANSe. Concerning the speed, FANSe pipeline was 8.8∼19x faster than the other pipelines. Our benchmarking results demonstrated performance of the somatic calling pipelines and provided a reference for a proper choice of such pipelines in cancer applications.

Keywords:  accuracy; algorithm; next-generation sequencing—NGS; performance; somatic mutation analysis

DOI:  https://doi.org/10.3389/fgene.2022.979928