bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2022–02–20
twenty-one papers selected by
Ralitsa Radostinova Madsen, University College London
  1. PIK3CA co-occurring mutations and copy-number gain in hormone receptor positive and HER2 negative breast cancer.
  2. Recognition of observer effect is required for rigor and reproducibility of preclinical animal studies.
  3. Ghost mitochondria drive metastasis through adaptive GCN2/Akt therapeutic vulnerability.
  4. ATF-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mTORC1.
  5. PTEN loss confers sensitivity to rapalogs in clear cell renal cell carcinoma.
  6. Alpelisib-Induced Diabetes Mellitus: Case Report, Pharmacodynamics and Management Considerations.
  7. Revealing new biology from multiplexed, metal-isotope-tagged, single-cell readouts.
  8. Case Report: Primary Pleural Angiosarcoma in a Patient With Klippel-Trenaunay Syndrome.
  9. Computational Methods to Identify Cell-Fate Determinants, Identity Transcription Factors, and Niche-Induced Signaling Pathways for Stem Cell Research.
  10. Dual clathrin and integrin signaling systems regulate growth factor receptor activation.
  11. Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants.
  12. Idelalisib reduces regulatory T cells and activates T helper 17 cell differentiation in relapsed refractory patients with chronic lymphocytic leukaemia.
  13. Uncovering the mesendoderm gene regulatory network through multi-omic data integration.
  14. CRISPR-Based Screening for Stress Response Factors in Mammalian Cells.
  15. Single Organoids Droplet-Based Staining Method for High-End 3D Imaging of Mammary Organoids.
  16. Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation.
  17. Insulin Receptor Signaling in Osteoblasts Regulates Postnatal Bone Acquisition and Body Composition.
  18. IL-6-induced FOXO1 activity determines the dynamics of metabolism in CD8 T cells cross-primed by liver sinusoidal endothelial cells.
  19. Patient-specific Boolean models of signalling networks guide personalised treatments.
  20. Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium.
  21. Redefining precision cancer prevention to promote health equity.
  1. NPJ Breast Cancer. 2022 Feb 18. 8(1): 24
    PIK3CA co-occurring mutations and copy-number gain in hormone receptor positive and HER2 negative breast cancer.
    Ilenia Migliaccio, Marta Paoli, Emanuela Risi, Chiara Biagioni, Laura Biganzoli, Matteo Benelli, Luca Malorni.
      We aim to elucidate the prognostic value of PIK3CA mutations and copy number (CN) gain (PIK3CA-mut/gain) in hormone receptor-positive and HER2-negative (HR + /HER2-) breast cancer (BC). We analyzed primary HR + /HER2- BC from three publicly available datasets comprising over 2000 samples and assessed the associations with tumoral and clinical characteristics and outcome. Clinical benefit (CB) in alpelisib-treated patients from two studies including 46 patients was analyzed. About 8-10% of HR + /HER2- primary BC had PIK3CA-mut/gain. In two of the datasets analyzed, among patients with PIK3CA mutant tumors, those with mut/gain had significantly worse outcome compared to those with CN neutral (PIK3CA-mut/neut) and PIK3CA-mut/gain remained an independent prognostic factor. CB of alpelisib-treated patients with PIK3CA-mut/gain and PIK3CA-mut/neut tumors was comparable. PIK3CA CN might help clarifying the prognostic and predictive role of PIK3CA mutations. Further studies are warranted.
    DOI:  https://doi.org/10.1038/s41523-022-00382-5
  2. Cancer Cell. 2022 Feb 08. pii: S1535-6108(22)00017-4. [Epub ahead of print]
    Recognition of observer effect is required for rigor and reproducibility of preclinical animal studies.
    Chi-Ping Day, Eva Pérez-Guijarro, Amélie Lopès, Romina S Goldszmid, Meera Murgai, Lalage Wakefield, Glenn Merlino.
      
    DOI:  https://doi.org/10.1016/j.ccell.2022.01.015
  3. Proc Natl Acad Sci U S A. 2022 Feb 22. pii: e2115624119. [Epub ahead of print]119(8):
    Ghost mitochondria drive metastasis through adaptive GCN2/Akt therapeutic vulnerability.
    Jagadish C Ghosh, Michela Perego, Ekta Agarwal, Irene Bertolini, Yuan Wang, Aaron R Goldman, Hsin-Yao Tang, Andrew V Kossenkov, Catherine J Libby, Lucia R Languino, Edward F Plow, Annamaria Morotti, Luisa Ottobrini, Marco Locatelli, David W Speicher, M Cecilia Caino, Joel Cassel, Joseph M Salvino, Marie E Robert, Valentina Vaira, Dario C Altieri.
      Cancer metabolism, including in mitochondria, is a disease hallmark and therapeutic target, but its regulation is poorly understood. Here, we show that many human tumors have heterogeneous and often reduced levels of Mic60, or Mitofilin, an essential scaffold of mitochondrial structure. Despite a catastrophic collapse of mitochondrial integrity, loss of bioenergetics, and oxidative damage, tumors with Mic60 depletion slow down cell proliferation, evade cell death, and activate a nuclear gene expression program of innate immunity and cytokine/chemokine signaling. In turn, this induces epithelial-mesenchymal transition (EMT), activates tumor cell movements through exaggerated mitochondrial dynamics, and promotes metastatic dissemination in vivo. In a small-molecule drug screen, compensatory activation of stress response (GCN2) and survival (Akt) signaling maintains the viability of Mic60-low tumors and provides a selective therapeutic vulnerability. These data demonstrate that acutely damaged, "ghost" mitochondria drive tumor progression and expose an actionable therapeutic target in metastasis-prone cancers.
    Keywords:  cell motility; metastasis; mitochondria
    DOI:  https://doi.org/10.1073/pnas.2115624119
  4. Nat Commun. 2022 Feb 18. 13(1): 967
    ATF-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mTORC1.
    Cyril Statzer, Jin Meng, Richard Venz, Monet Bland, Stacey Robida-Stubbs, Krina Patel, Dunja Petrovic, Raffaella Emsley, Pengpeng Liu, Ianessa Morantte, Cole Haynes, William B Mair, Alban Longchamp, Milos R Filipovic, T Keith Blackwell, Collin Y Ewald.
      Inhibition of the master growth regulator mTORC1 (mechanistic target of rapamycin complex 1) slows ageing across phyla, in part by reducing protein synthesis. Various stresses globally suppress protein synthesis through the integrated stress response (ISR), resulting in preferential translation of the transcription factor ATF-4. Here we show in C. elegans that inhibition of translation or mTORC1 increases ATF-4 expression, and that ATF-4 mediates longevity under these conditions independently of ISR signalling. ATF-4 promotes longevity by activating canonical anti-ageing mechanisms, but also by elevating expression of the transsulfuration enzyme CTH-2 to increase hydrogen sulfide (H2S) production. This H2S boost increases protein persulfidation, a protective modification of redox-reactive cysteines. The ATF-4/CTH-2/H2S pathway also mediates longevity and increased stress resistance from mTORC1 suppression. Increasing H2S levels, or enhancing mechanisms that H2S influences through persulfidation, may represent promising strategies for mobilising therapeutic benefits of the ISR, translation suppression, or mTORC1 inhibition.
    DOI:  https://doi.org/10.1038/s41467-022-28599-9
  5. Acta Pharmacol Sin. 2022 Feb 14.
    PTEN loss confers sensitivity to rapalogs in clear cell renal cell carcinoma.
    Xiao-Lian Liu, Gui-Ming Zhang, Si-Si Huang, Wen-Hui Shi, Lin-Xuan Ye, Zhong-Lu Ren, Jia-Jie Zhang, Shu-Wen Liu, Le Yu, Yi-Lei Li.
      Rapalogs (everolimus and temsirolimus) are allosteric mTORC1 inhibitors and approved agents for advanced clear cell renal cell carcinoma (ccRCC), although only a subset of patients derive clinical benefit. Progress in genomic characterization has made it possible to generate comprehensive profiles of genetic alterations in ccRCC; however, the correlations between recurrent somatic mutations and rapalog efficacy remain unclear. Here, we demonstrate by using multiple patient-derived ccRCC cell lines that compared to PTEN-proficient cells, PTEN-deficient cells exhibit hypersensitivity to rapalogs. Rapalogs inhibit cell proliferation by inducing G0/G1 arrest without inducing apoptosis in PTEN-deficient ccRCC cell lines. Using isogenic cell lines generated by CRISPR/Cas9, we validate the correlation between PTEN loss and rapalog hypersensitivity. In contrast, deletion of VHL or chromatin-modifying genes (PBRM1, SETD2, BAP1, or KDM5C) fails to influence the cellular response to rapalogs. Our mechanistic study shows that ectopic expression of an activating mTOR mutant (C1483F) antagonizes PTEN-induced cell growth inhibition, while introduction of a resistant mTOR mutant (A2034V) enables PTEN-deficient ccRCC cells to escape the growth inhibitory effect of rapalogs, suggesting that PTEN loss generates vulnerability to mTOR inhibition. PTEN-deficient ccRCC cells are more sensitive to the inhibitory effects of temsirolimus on cell migration and tumor growth in zebrafish and xenograft mice, respectively. Of note, PTEN protein loss as detected by immunohistochemistry is much more frequent than mutations in the PTEN gene in ccRCC patients. Our study suggests that PTEN loss correlates with rapalog sensitivity and could be used as a marker for ccRCC patient selection for rapalog therapy.
    Keywords:  PTEN; clear cell renal cell carcinoma; mTOR; rapalogs; recurrent mutations; sensitivity
    DOI:  https://doi.org/10.1038/s41401-022-00862-1
  6. Front Endocrinol (Lausanne). 2022 ;13 802612
    Alpelisib-Induced Diabetes Mellitus: Case Report, Pharmacodynamics and Management Considerations.
    Begoña Pla Peris, Alfonso Arranz Martin, Anabel Ballesteros García, Fernando Sebastián-Valles, Monica Marazuela Azpiroz.
       Introduction: Alpelisib is an orally selective PI3K alpha inhibitor recently available for the treatment of advanced breast cancer. PI3K pathway is an intracellular signaling pathway that plays an important role in regulating glucose metabolism. Hyperglycemia is the most common adverse event associated.
    Methods: We describe the case of a severe hyperglycemia associated with alpelisib treatment in a patient with metastatic breast cancer and previously near-normal glycemia. We analyze the clinical presentation, PI3K inhibitor pharmacodynamic aspects, its influence in glycemic control and the required treatment approach.
    Results: An important impairment of glycemic control was observed after initiation of alpelisib. In addition to insulin sensitizers drugs, intensive insulin regimen was necessary. Flash glucose monitoring (FGM) information has been helpful in understanding the pharmacodynamic aspects of alpelisib and insulin titration. Development of hyperglycemia is fast, already observed 24 hours after initiation of therapy. FGM shows severe and persistent hyperglycemia during most of the day, with a significant downward effect in the 4 hours after each daily intake, which evidences the strong but transitory effect of the drug enzyme blockade. C-peptide level is remarkable in accordance with drug pharmacodynamics, consistent with a significant insulin resistance.
    Conclusions: Glucose monitoring should always be performed in patients treated with alpelisib, especially in patients with diabetes and prediabetes. It is crucial to anticipate in these patients. Any delay can lead to a worsening in metabolic control resulting in the discontinuation or reduction of alpelisib, which would lead to a decrease in its effectiveness, and consequently would deny patients an effective treatment with an impact on survival.
    Keywords:  PI3K inhibitor; alpelisib; diabetes mellitus; flash glucose monitoring (FGM); hyperglycemia
    DOI:  https://doi.org/10.3389/fendo.2022.802612
  7. Trends Cell Biol. 2022 Feb 16. pii: S0962-8924(22)00027-7. [Epub ahead of print]
    Revealing new biology from multiplexed, metal-isotope-tagged, single-cell readouts.
    Reema Baskar, Sam C Kimmey, Sean C Bendall.
      Mass cytometry (MC) is a recent technology that pairs plasma-based ionization of cells in suspension with time-of-flight (TOF) mass spectrometry to sensitively quantify the single-cell abundance of metal-isotope-tagged affinity reagents to key proteins, RNA, and peptides. Given the ability to multiplex readouts (~50 per cell) and capture millions of cells per experiment, MC offers a robust way to assay rare, transitional cell states that are pertinent to human development and disease. Here, we review MC approaches that let us probe the dynamics of cellular regulation across multiple conditions and sample types in a single experiment. Additionally, we discuss current limitations and future extensions of MC as well as computational tools commonly used to extract biological insight from single-cell proteomic datasets.
    Keywords:  cell cycle; high-dimensional data; mass cytometry; metabolism; single-cell analysis; single-cell proteomics
    DOI:  https://doi.org/10.1016/j.tcb.2022.01.012
  8. Front Genet. 2022 ;13 792466
    Case Report: Primary Pleural Angiosarcoma in a Patient With Klippel-Trenaunay Syndrome.
    Jing Xu, Mengyao Liu, Hongtu Yuan, Zengjun Liu, Dongyuan Zhu.
      Klippel-Trenaunay syndrome (KTS) was demonstrated as a mosaic activating PIK3CA mutations related overgrowth syndrome. We present the first case of primary pleural angiosarcoma in a 17-year-old woman with a history of KTS. The combined targeted DNA and RNA sequencing revealed an activating mutation in PIK3CA in the tumor tissue. Our case suggested an association and perhaps a causal link between the two different PIK3CA-related genetic diseases.
    Keywords:  PIK3CA; angiosarcoma; klippel-trenaunay syndrome; pleura; somatic mutations
    DOI:  https://doi.org/10.3389/fgene.2022.792466
  9. Methods Mol Biol. 2022 ;2471 83-109
    Computational Methods to Identify Cell-Fate Determinants, Identity Transcription Factors, and Niche-Induced Signaling Pathways for Stem Cell Research.
    Muhammad Ali, Mariana Messias Ribeiro, Antonio Del Sol.
      The large-scale development of high-throughput sequencing technologies has not only allowed the generation of reliable omics data related to various regulatory layers but also the development of novel computational models in the field of stem cell research. These computational approaches have enabled the disentangling of a complex interplay between these interrelated layers of regulation by interpreting large quantities of biomedical data in a systematic way. In the context of stem cell research, network modeling of complex gene-gene interactions has been successfully used for understanding the mechanisms underlying stem cell differentiation and cellular conversion. Notably, it has proven helpful for predicting cell-fate determinants and signaling molecules controlling such processes. This chapter will provide an overview of various computational approaches that rely on single-cell and/or bulk RNA sequencing data for elucidating the molecular underpinnings of cell subpopulation identities, lineage specification, and the process of cell-fate decisions. Furthermore, we discuss how these computational methods provide the right framework for computational modeling of biological systems in order to address long-standing challenges in the stem cell field by guiding experimental efforts in stem cell research and regenerative medicine.
    Keywords:  Cell-fate determinants; Cellular reprogramming; Core identity TFs; Gene regulatory networks; Lineage specifier; Stem cell research; Systems biology
    DOI:  https://doi.org/10.1007/978-1-0716-2193-6_4
  10. Nat Commun. 2022 Feb 16. 13(1): 905
    Dual clathrin and integrin signaling systems regulate growth factor receptor activation.
    Marco A Alfonzo-Méndez, Kem A Sochacki, Marie-Paule Strub, Justin W Taraska.
      The crosstalk between growth factor and adhesion receptors is key for cell growth and migration. In pathological settings, these receptors are drivers of cancer. Yet, how growth and adhesion signals are spatially organized and integrated is poorly understood. Here we use quantitative fluorescence and electron microscopy to reveal a mechanism where flat clathrin lattices partition and activate growth factor signals via a coordinated response that involves crosstalk between epidermal growth factor receptor (EGFR) and the adhesion receptor β5-integrin. We show that ligand-activated EGFR, Grb2, Src, and β5-integrin are captured by clathrin coated-structures at the plasma membrane. Clathrin structures dramatically grow in response to EGF into large flat plaques and provide a signaling platform that link EGFR and β5-integrin through Src-mediated phosphorylation. Disrupting this EGFR/Src/β5-integrin axis prevents both clathrin plaque growth and dampens receptor signaling. Our study reveals a reciprocal regulation between clathrin lattices and two different receptor systems to coordinate and enhance signaling. These findings have broad implications for the regulation of growth factor signaling, adhesion, and endocytosis.
    DOI:  https://doi.org/10.1038/s41467-022-28373-x
  11. Nat Biotechnol. 2022 Feb 14.
    Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants.
    Francisco J Sánchez-Rivera, Bianca J Diaz, Edward R Kastenhuber, Henri Schmidt, Alyna Katti, Margaret Kennedy, Vincent Tem, Yu-Jui Ho, Josef Leibold, Stella V Paffenholz, Francisco M Barriga, Kevan Chu, Sukanya Goswami, Alexandra N Wuest, Janelle M Simon, Kaloyan M Tsanov, Debyani Chakravarty, Hongxin Zhang, Christina S Leslie, Scott W Lowe, Lukas E Dow.
      Base editing can be applied to characterize single nucleotide variants of unknown function, yet defining effective combinations of single guide RNAs (sgRNAs) and base editors remains challenging. Here, we describe modular base-editing-activity 'sensors' that link sgRNAs and cognate target sites in cis and use them to systematically measure the editing efficiency and precision of thousands of sgRNAs paired with functionally distinct base editors. By quantifying sensor editing across >200,000 editor-sgRNA combinations, we provide a comprehensive resource of sgRNAs for introducing and interrogating cancer-associated single nucleotide variants in multiple model systems. We demonstrate that sensor-validated tools streamline production of in vivo cancer models and that integrating sensor modules in pooled sgRNA libraries can aid interpretation of high-throughput base editing screens. Using this approach, we identify several previously uncharacterized mutant TP53 alleles as drivers of cancer cell proliferation and in vivo tumor development. We anticipate that the framework described here will facilitate the functional interrogation of cancer variants in cell and animal models.
    DOI:  https://doi.org/10.1038/s41587-021-01172-3
  12. Br J Haematol. 2022 Feb 15.
    Idelalisib reduces regulatory T cells and activates T helper 17 cell differentiation in relapsed refractory patients with chronic lymphocytic leukaemia.
    Deepti Gadi, Alec Griffith, Zixu Wang, Svitlana Tyekucheva, Vanessa Rai, Stacey M Fernandes, John-Hanson Machado, Veerendra Munugalavadla, James Lederer, Jennifer R Brown.
      Phosphatidylinositol 3 kinase (PI3K) inhibitors such as idelalisib have been associated with potentially severe autoimmune toxicity. In the present study, we demonstrate that relapsed refractory patients with chronic lymphocytic leukaemia treated with idelalisib rituximab on the phase III registration trial show uniform decrease in regulatory T cells (Tregs) and increase in CD8 T cells with treatment. Patients who do not develop toxicity show enrichment for T cells expressing multiple chemokine receptors, while those who do develop toxicity have an activated CD8 T cell population with T helper 17 cell differentiation at baseline, which then increases, leading to an increased CD8:Treg ratio that likely triggers autoimmune toxicity.
    DOI:  https://doi.org/10.1111/bjh.18053
  13. Cell Rep. 2022 02 15. pii: S2211-1247(22)00085-7. [Epub ahead of print]38(7): 110364
    Uncovering the mesendoderm gene regulatory network through multi-omic data integration.
    Camden Jansen, Kitt D Paraiso, Jeff J Zhou, Ira L Blitz, Margaret B Fish, Rebekah M Charney, Jin Sun Cho, Yuuri Yasuoka, Norihiro Sudou, Ann Rose Bright, Marcin Wlizla, Gert Jan C Veenstra, Masanori Taira, Aaron M Zorn, Ali Mortazavi, Ken W Y Cho.
      Mesendodermal specification is one of the earliest events in embryogenesis, where cells first acquire distinct identities. Cell differentiation is a highly regulated process that involves the function of numerous transcription factors (TFs) and signaling molecules, which can be described with gene regulatory networks (GRNs). Cell differentiation GRNs are difficult to build because existing mechanistic methods are low throughput, and high-throughput methods tend to be non-mechanistic. Additionally, integrating highly dimensional data composed of more than two data types is challenging. Here, we use linked self-organizing maps to combine chromatin immunoprecipitation sequencing (ChIP-seq)/ATAC-seq with temporal, spatial, and perturbation RNA sequencing (RNA-seq) data from Xenopus tropicalis mesendoderm development to build a high-resolution genome scale mechanistic GRN. We recover both known and previously unsuspected TF-DNA/TF-TF interactions validated through reporter assays. Our analysis provides insights into transcriptional regulation of early cell fate decisions and provides a general approach to building GRNs using highly dimensional multi-omic datasets.
    Keywords:  ATAC-seq; ChIP-seq; RNA-seq; Xenopus; cis-regulatory modules; endoderm; gene regulatory networks; linked self-organizing maps; mesoderm; multi-omic
    DOI:  https://doi.org/10.1016/j.celrep.2022.110364
  14. Methods Mol Biol. 2022 ;2428 19-40
    CRISPR-Based Screening for Stress Response Factors in Mammalian Cells.
    Xiaoyan Guo, Martin Kampmann.
      In the presence of different physiological and environmental stresses, cells rapidly initiate stress responses to re-establish cellular homeostasis. Stress responses usually orchestrate both transcriptional and translational programs via distinct mechanisms. With the advance of transcriptomics and proteomics technologies, transcriptional and translational outputs to a particular stress condition have become easier to measure; however, these technologies lack the ability to reveal the upstream regulatory pathways. Unbiased genetic screens based on a transcriptional or translational reporter are powerful approaches to identify regulatory factors of a specific stress response. CRISPR/Cas-based technologies, together with next-generation sequencing, enable genome-scale pooled screens to systematically elucidate gene function in mammalian cells, with a significant reduction in the rate of off-target effects compared to the previously used RNAi technology. Here, we describe our fluorescence-activated cell sorting (FACS)-based CRISPR interference (CRISPRi) screening platform using a translational reporter to identify novel genetic factors of the mitochondrial stress response in mammalian cells. This protocol provides a general framework for scientists who wish to establish a reporter-based CRISPRi screening platform to address questions in their area of research.
    Keywords:  CRISPRi; FACS; Genetic screens; Mammalian cells; Mitochondrial stress response; Transcriptional reporter; Translational reporter
    DOI:  https://doi.org/10.1007/978-1-0716-1975-9_2
  15. Methods Mol Biol. 2022 ;2471 259-269
    Single Organoids Droplet-Based Staining Method for High-End 3D Imaging of Mammary Organoids.
    Jakub Sumbal, Zuzana Koledova.
      In the last decade, organoids became a tremendously popular technique in developmental and cancer biology for their high pathophysiological relevance to in vivo models with the advantage of easier manipulation, real-time observation, potential for high-throughput studies, and reduced ethical issues. Among other fundamental biological questions, mammary organoids have helped to reveal mechanisms of mammary epithelial morphogenesis, mammary stem cell potential, regulation of lineage specification, mechanisms of breast cancer invasion or resistance to therapy, and their regulation by stromal microenvironment. To exploit the potential of organoid technology to the fullest, together with optimal organoid culture protocols, visualization of organoid architecture and composition in high resolution in three dimensions (3D) is required. Whole-mount imaging of immunolabeled organoids enables preservation of the 3D cellular context, but conventional confocal microscopy of organoid cultures struggles with the large organoid sample size and relatively long distance from the objective to the organoid due to the 3D extracellular matrix (ECM) that surrounds the organoid. We have overcome these issues by physical separation of single organoids with their immediate stroma from the bulk ECM. Here we provide a detail protocol for the procedure, which entails single organoid collection and droplet-based staining and clearing to allow visualization of organoids in the greatest detail.
    Keywords:  3D culture; Clearing; Confocal imaging; Microenvironment; Organoid; Staining
    DOI:  https://doi.org/10.1007/978-1-0716-2193-6_14
  16. Cell Stem Cell. 2022 Feb 15. pii: S1934-5909(22)00034-0. [Epub ahead of print]
    Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation.
    Florian T Merkle, Sulagna Ghosh, Giulio Genovese, Robert E Handsaker, Seva Kashin, Daniel Meyer, Konrad J Karczewski, Colm O'Dushlaine, Carlos Pato, Michele Pato, Daniel G MacArthur, Steven A McCarroll, Kevin Eggan.
      Despite their widespread use in research, there has not yet been a systematic genomic analysis of human embryonic stem cell (hESC) lines at a single-nucleotide resolution. We therefore performed whole-genome sequencing (WGS) of 143 hESC lines and annotated their single-nucleotide and structural genetic variants. We found that while a substantial fraction of hESC lines contained large deleterious structural variants, finer-scale structural and single-nucleotide variants (SNVs) that are ascertainable only through WGS analyses were present in hESC genomes and human blood-derived genomes at similar frequencies. Moreover, WGS allowed us to identify SNVs associated with cancer and other diseases that could alter cellular phenotypes and compromise the safety of hESC-derived cellular products transplanted into humans. As a resource to enable reproducible hESC research and safer translation, we provide a user-friendly WGS data portal and a data-driven scheme for cell line maintenance and selection.
    Keywords:  embryonic stem cell; genetic variant; genomics; pluripotent; rational selection; resource; whole-genome sequencing
    DOI:  https://doi.org/10.1016/j.stem.2022.01.011
  17. Cell. 2022 Feb 17. pii: S0092-8674(22)00074-5. [Epub ahead of print]185(4): 746
    Insulin Receptor Signaling in Osteoblasts Regulates Postnatal Bone Acquisition and Body Composition.
    Keertik Fulzele, Ryan C Riddle, Douglas J DiGirolamo, Xuemei Cao, Chao Wan, Dongquan Chen, Marie-Claude Faugere, Susan Aja, Mehboob A Hussain, Jens C Brüning, Thomas L Clemens.
      
    DOI:  https://doi.org/10.1016/j.cell.2022.01.016
  18. Cell Rep. 2022 02 15. pii: S2211-1247(22)00110-3. [Epub ahead of print]38(7): 110389
    IL-6-induced FOXO1 activity determines the dynamics of metabolism in CD8 T cells cross-primed by liver sinusoidal endothelial cells.
    Michael Dudek, Kerstin Lohr, Sainitin Donakonda, Tobias Baumann, Max Lüdemann, Silke Hegenbarth, Lena Dübbel, Carola Eberhagen, Savvoula Michailidou, Abdallah Yassin, Marco Prinz, Bastian Popper, Stefan Rose-John, Hans Zischka, Percy A Knolle.
      Liver sinusoidal endothelial cells (LSECs) are liver-resident antigen (cross)-presenting cells that generate memory CD8 T cells, but metabolic properties of LSECs and LSEC-primed CD8 T cells remain understudied. Here, we report that high-level mitochondrial respiration and constitutive low-level glycolysis support LSEC scavenger and sentinel functions. LSECs fail to increase glycolysis and co-stimulation after TLR4 activation, indicating absence of metabolic and functional maturation compared with immunogenic dendritic cells. LSEC-primed CD8 T cells show a transient burst of oxidative phosphorylation and glycolysis. Mechanistically, co-stimulatory IL-6 signaling ensures high FOXO1 expression in LSEC-primed CD8 T cells, curtails metabolic activity associated with T cell activation, and is indispensable for T cell functionality after re-activation. Thus, distinct immunometabolic features characterize non-immunogenic LSECs compared with immunogenic dendritic cells and LSEC-primed CD8 T cells with memory features compared with effector CD8 T cells. This reveals local features of metabolism and function of T cells in the liver.
    Keywords:  glycolysis; immune cell metabolism; liver immune tolerance; memory T cells; mitochondrial respiration; non-professional antigen-presenting cells
    DOI:  https://doi.org/10.1016/j.celrep.2022.110389
  19. Elife. 2022 Feb 15. pii: e72626. [Epub ahead of print]11
    Patient-specific Boolean models of signalling networks guide personalised treatments.
    Arnau Montagud, Jonas Béal, Luis Tobalina, Pauline Traynard, Vigneshwari Subramanian, Bence Szalai, Róbert Alföldi, László Puskás, Alfonso Valencia, Emmanuel Barillot, Julio Saez-Rodriguez, Laurence Calzone.
      Prostate cancer is the second most occurring cancer in men worldwide. To better understand the mechanisms of tumorigenesis and possible treatment responses, we developed a mathematical model of prostate cancer which considers the major signalling pathways known to be deregulated. We personalised this Boolean model to molecular data to reflect the heterogeneity and specific response to perturbations of cancer patients. 488 prostate samples were used to build patient-specific models and compared to available clinical data. Additionally, eight prostate cell-line-specific models were built to validate our approach with dose-response data of several drugs. The effects of single and combined drugs were tested in these models under different growth conditions. We identified 15 actionable points of interventions in one cell-line-specific model whose inactivation hinders tumorigenesis. To validate these results, we tested nine small molecule inhibitors of five of those putative targets and found a dose-dependent effect on four of them, notably those targeting HSP90 and PI3K. These results highlight the predictive power of our personalised Boolean models and illustrate how they can be used for precision oncology.
    Keywords:  computational biology; human; systems biology
    DOI:  https://doi.org/10.7554/eLife.72626
  20. Nat Commun. 2022 Feb 17. 13(1): 943
    Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium.
    Manako Yamaguchi, Hirofumi Nakaoka, Kazuaki Suda, Kosuke Yoshihara, Tatsuya Ishiguro, Nozomi Yachida, Kyota Saito, Haruka Ueda, Kentaro Sugino, Yutaro Mori, Kaoru Yamawaki, Ryo Tamura, Sundaramoorthy Revathidevi, Teiichi Motoyama, Kazuki Tainaka, Roel G W Verhaak, Ituro Inoue, Takayuki Enomoto.
      It has become evident that somatic mutations in cancer-associated genes accumulate in the normal endometrium, but spatiotemporal understanding of the evolution and expansion of mutant clones is limited. To elucidate the timing and mechanism of the clonal expansion of somatic mutations in cancer-associated genes in the normal endometrium, we sequence 1311 endometrial glands from 37 women. By collecting endometrial glands from different parts of the endometrium, we show that multiple glands with the same somatic mutations occupy substantial areas of the endometrium. We demonstrate that "rhizome structures", in which the basal glands run horizontally along the muscular layer and multiple vertical glands rise from the basal gland, originate from the same ancestral clone. Moreover, mutant clones detected in the vertical glands diversify by acquiring additional mutations. These results suggest that clonal expansions through the rhizome structures are involved in the mechanism by which mutant clones extend their territories. Furthermore, we show clonal expansions and copy neutral loss-of-heterozygosity events occur early in life, suggesting such events can be tolerated many years in the normal endometrium. Our results of the evolutionary dynamics of mutant clones in the human endometrium will lead to a better understanding of the mechanisms of endometrial regeneration during the menstrual cycle and the development of therapies for the prevention and treatment of endometrium-related diseases.
    DOI:  https://doi.org/10.1038/s41467-022-28568-2
  21. Trends Cancer. 2022 Feb 15. pii: S2405-8033(22)00016-4. [Epub ahead of print]
    Redefining precision cancer prevention to promote health equity.
    Eboneé N Butler, Asad Umar, Brandy M Heckman-Stoddard, Kathryn A Kundrod, Lisa B Signorello, Philip E Castle.
      Precision cancer prevention as it is currently envisioned is a targeted, molecular-based approach to intercept carcinogenesis before cancer develops or before it becomes untreatable. Unfortunately, due to systemic biases, current precision cancer prevention interventions might not be effective in all populations, especially in minoritized communities. In addition, not all cancer risk is attributable to genetic or even biological factors, but includes social determinants of health (SDH). Here, we propose a broader framework for precision cancer prevention, anchored in optimizing the benefits to harms for all people. We propose that precision cancer prevention considers not only what is being delivered, but also for whom, where, and how, with a goal of achieving cancer prevention health equity.
    Keywords:  health disparities; health inequities; precision cancer prevention
    DOI:  https://doi.org/10.1016/j.trecan.2022.01.009
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