bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2021–12–26
twenty-one papers selected by
Ralitsa Radostinova Madsen, University College London
  1. Aurora A and AKT Kinase Signaling Associated with Primary Cilia.
  2. Targeting AKT in ER-Positive HER2-Negative Metastatic Breast Cancer: From Molecular Promises to Real Life Pitfalls?
  3. Lateralized and Segmental Overgrowth in Children.
  4. Multifaceted Regulation of Akt by Diverse C-Terminal Post-translational Modifications.
  5. The Novel Phosphatase Domain Mutations Q171R and Y65S Switch PTEN from Tumor Suppressor to Oncogene.
  6. Multi-Omic Metabolic Enrichment Network Analysis reveals metabolite-protein physical interaction subnetworks altered in cancer.
  7. Resolving the polygenic aetiology of a late onset combined immune deficiency caused by NFKB1 haploinsufficiency and modified by PIK3R1 and TNFRSF13B variants.
  8. Can Systems Biology Advance Clinical Precision Oncology?
  9. Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis.
  10. Dinner is served, sir: Fighting cancer with the right diet.
  11. What doesn't kill you makes you differentiate.
  12. Clone competition as a mechanism to reduce tumor formation.
  13. Differential Dose- and Tissue-Dependent Effects of foxo on Aging, Metabolic and Proteostatic Pathways.
  14. Insulin-Responsive Transcription Factors.
  15. Disruption of the TCA cycle reveals an ATF4-dependent integration of redox and amino acid metabolism.
  16. Unexpected gene activation following CRISPR-Cas9-mediated genome editing.
  17. Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects.
  18. Complexity against current cancer research - are we on the wrong track?
  19. Caveat fluorophore: an insiders' guide to small-molecule fluorescent labels.
  20. Suppression of caspase 8 activity by a coronin 1-PI3Kδ pathway promotes T cell survival independently of TCR and IL-7 signaling.
  21. Crosstalk with keratinocytes causes GNAQ oncogene specificity in melanoma.
  1. Cells. 2021 Dec 20. pii: 3602. [Epub ahead of print]10(12):
    Aurora A and AKT Kinase Signaling Associated with Primary Cilia.
    Yuhei Nishimura, Daishi Yamakawa, Takashi Shiromizu, Masaki Inagaki.
      Dysregulation of kinase signaling is associated with various pathological conditions, including cancer, inflammation, and autoimmunity; consequently, the kinases involved have become major therapeutic targets. While kinase signaling pathways play crucial roles in multiple cellular processes, the precise manner in which their dysregulation contributes to disease is dependent on the context; for example, the cell/tissue type or subcellular localization of the kinase or substrate. Thus, context-selective targeting of dysregulated kinases may serve to increase the therapeutic specificity while reducing off-target adverse effects. Primary cilia are antenna-like structures that extend from the plasma membrane and function by detecting extracellular cues and transducing signals into the cell. Cilia formation and signaling are dynamically regulated through context-dependent mechanisms; as such, dysregulation of primary cilia contributes to disease in a variety of ways. Here, we review the involvement of primary cilia-associated signaling through aurora A and AKT kinases with respect to cancer, obesity, and other ciliopathies.
    Keywords:  AKT kinase; aurora kinase A; cancer; ciliopathy; differentiation; lipid raft; obesity; primary cilium; proliferation; trichoplein
    DOI:  https://doi.org/10.3390/cells10123602
  2. Int J Mol Sci. 2021 Dec 16. pii: 13512. [Epub ahead of print]22(24):
    Targeting AKT in ER-Positive HER2-Negative Metastatic Breast Cancer: From Molecular Promises to Real Life Pitfalls?
    Benoîte Mery, Coralie Poulard, Muriel Le Romancer, Olivier Trédan.
      The AKT protein kinase plays a central role in several interconnected molecular pathways involved in growth, apoptosis, angiogenesis, and cell metabolism. It thereby represents a therapeutic target, especially in hormone receptor-positive (HR) breast cancers, where the PI3K/AKT signaling pathway is largely hyperactivated. Moreover, resistance to therapeutic classes, including endocrine therapy, is associated with the constitutive activation of the PI3K/AKT pathway. Improved knowledge on the molecular mechanisms underlying resistance to endocrine therapy has led to the diversification of the therapeutic arsenal, notably with the development of PI3K and mTOR inhibitors, which are currently approved for the treatment of advanced HR-positive breast cancer patients. AKT itself constitutes a novel pharmacological target for which AKT inhibitors have been developed and tested in clinical trials. However, despite its pivotal role in cell survival and anti-apoptotic mechanisms, as well as in endocrine therapy resistance, few drugs have been developed and are available for clinical practice. The scope of the present review is to focus on the pivotal role of AKT in metastatic breast cancer through the analysis of its molecular features and to discuss clinical implications and remaining challenges in the treatment of HR-positive metastatic breast cancer.
    Keywords:  endocrine resistance; estrogen-receptor-positive metastatic breast cancer; serine/threonine kinase (AKT) signaling pathway
    DOI:  https://doi.org/10.3390/ijms222413512
  3. Cancers (Basel). 2021 Dec 07. pii: 6166. [Epub ahead of print]13(24):
    Lateralized and Segmental Overgrowth in Children.
    Alessandro Mussa, Diana Carli, Simona Cardaropoli, Giovanni Battista Ferrero, Nicoletta Resta.
      Congenital disorders of lateralized or segmental overgrowth (LO) are heterogeneous conditions with increased tissue growth in a body region. LO can affect every region, be localized or extensive, involve one or several embryonic tissues, showing variable severity, from mild forms with minor body asymmetry to severe ones with progressive tissue growth and related relevant complications. Recently, next-generation sequencing approaches have increased the knowledge on the molecular defects in LO, allowing classifying them based on the deranged cellular signaling pathway. LO is caused by either genetic or epigenetic somatic anomalies affecting cell proliferation. Most LOs are classifiable in the Beckwith-Wiedemann spectrum (BWSp), PI3KCA/AKT-related overgrowth spectrum (PROS/AROS), mosaic RASopathies, PTEN Hamartoma Tumor Syndrome, mosaic activating variants in angiogenesis pathways, and isolated LO (ILO). These disorders overlap over common phenotypes, making their appraisal and distinction challenging. The latter is crucial, as specific management strategies are key: some LO is associated with increased cancer risk making imperative tumor screening since childhood. Interestingly, some LO shares molecular mechanisms with cancer: recent advances in tumor biological pathway druggability and growth downregulation offer new avenues for the treatment of the most severe and complicated LO.
    Keywords:  Beckwith–Wiedemann; PIK3CA; PROS; cancer predisposition; cancer screening; lateralized; mosaic; overgrowth; segmental; somatic
    DOI:  https://doi.org/10.3390/cancers13246166
  4. ACS Chem Biol. 2021 Dec 23.
    Multifaceted Regulation of Akt by Diverse C-Terminal Post-translational Modifications.
    Antonieta L Salguero, Maggie Chen, Aaron T Balana, Nam Chu, Hanjie Jiang, Brad A Palanski, Hwan Bae, Katharine M Wright, Sara Nathan, Heng Zhu, Sandra B Gabelli, Matthew R Pratt, Philip A Cole.
      Akt is a Ser/Thr protein kinase that regulates cell growth and metabolism and is considered a therapeutic target for cancer. Regulation of Akt by membrane recruitment and post-translational modifications (PTMs) has been extensively studied. The most well-established mechanism for cellular Akt activation involves phosphorylation on its activation loop on Thr308 by PDK1 and on its C-terminal tail on Ser473 by mTORC2. In addition, dual phosphorylation on Ser477 and Thr479 has been shown to activate Akt. Other C-terminal tail PTMs have been identified, but their functional impacts have not been well-characterized. Here, we investigate the regulatory effects of phosphorylation of Tyr474 and O-GlcNAcylation of Ser473 on Akt. We use expressed protein ligation as a tool to produce semisynthetic Akt proteins containing phosphoTyr474 and O-GlcNAcSer473 to dissect the enzymatic functions of these PTMs. We find that O-GlcNAcylation at Ser473 and phosphorylation at Tyr474 can also partially increase Akt's kinase activity toward both peptide and protein substrates. Additionally, we performed kinase assays employing human protein microarrays to investigate global substrate specificity of Akt, comparing phosphorylated versus O-GlcNAcylated Ser473 forms. We observed a high similarity in the protein substrates phosphorylated by phosphoSer473 Akt and O-GlcNAcSer473 Akt. Two Akt substrates identified using microarrays, PPM1H, a protein phosphatase, and NEDD4L, an E3 ubiquitin ligase, were validated in solution-phase assays and cell transfection experiments.
    DOI:  https://doi.org/10.1021/acschembio.1c00632
  5. Cells. 2021 Dec 05. pii: 3423. [Epub ahead of print]10(12):
    The Novel Phosphatase Domain Mutations Q171R and Y65S Switch PTEN from Tumor Suppressor to Oncogene.
    Jose Antonio Ma G Garrido, Krizelle Mae M Alcantara, Joshua Miguel C Danac, Fidel Emmanuel C Serrano, Eva Maria Cutiongco-de la Paz, Reynaldo L Garcia.
      Phosphatase and tensin homolog deleted on chromosome 10, or PTEN, is a well-characterized tumor suppressor with both lipid and protein phosphatase activities. PTEN is often downregulated by epigenetic mechanisms such as hypermethylation, which leads to constitutive activation of the PI3K-Akt pathway. Large datasets from next-generation sequencing, however, revealed that mutations in PTEN may not only hamper protein function but may also affect interactions with downstream effectors, leading to variable oncogenic readouts. Here, two novel PTEN mutations, Q171R and Y65S, identified in Filipino colorectal cancer patients, were phenotypically characterized in NIH3T3 and HCT116 cells, alongside the C124S canonical mutant and wild-type controls. The novel mutants increased cellular proliferation, resistance to apoptosis and migratory capacity. They induced gross morphological changes including cytoplasmic shrinkage, increased cellular protrusions and extensive cytoskeletal reorganization. The mutants also induced a modest increase in Akt phosphorylation. Further mechanistic studies will help determine the differential oncogenic potencies of these mutants, and resolve whether the structural constraints imposed by the mutations may have altered associations with downstream effectors.
    Keywords:  EGFR pathway; PTEN; colorectal cancer; tumor suppressor
    DOI:  https://doi.org/10.3390/cells10123423
  6. Mol Cell Proteomics. 2021 Dec 18. pii: S1535-9476(21)00161-4. [Epub ahead of print] 100189
    Multi-Omic Metabolic Enrichment Network Analysis reveals metabolite-protein physical interaction subnetworks altered in cancer.
    Benjamin C Blum, Weiwei Lin, Matthew L Lawton, Qian Liu, Julian Kwan, Isabella Turcinovic, Ryan Hekman, Pingzhao Hu, Andrew Emili.
      Metabolism is recognized as an important driver of cancer progression and other complex diseases, but global metabolite profiling remains a challenge. Protein expression profiling is often a poor proxy since existing pathway enrichment models provide an incomplete mapping between the proteome and metabolism. To overcome these gaps, we introduce MOMENTA, an integrative multi-omic data analysis framework for more accurately deducing metabolic pathway changes from proteomics data alone in a gene set analysis context by leveraging protein interaction networks to extend annotated metabolic models. We apply MOMENTA to proteomic data from diverse cancer cell lines and human tumors to demonstrate its utility at revealing variation in metabolic pathway activity across cancer types, which we verify using independent metabolomics measurements. The novel metabolic networks we uncover in breast cancer and other tumors are linked to clinical outcomes, underscoring the pathophysiological relevance of the findings.
    Keywords:  Cancer; Multi-omic; Networks; Proteomics; Systems Biology
    DOI:  https://doi.org/10.1016/j.mcpro.2021.100189
  7. Clin Immunol. 2021 Dec 15. pii: S1521-6616(21)00247-3. [Epub ahead of print]234 108910
    Resolving the polygenic aetiology of a late onset combined immune deficiency caused by NFKB1 haploinsufficiency and modified by PIK3R1 and TNFRSF13B variants.
    Chantal E Hargreaves, Fatima Dhalla, Arzoo M Patel, Andrés Caballero Garcia de Oteyza, Elizabeth Bateman, Joanne Miller, Consuelo Anzilotti, Lisa Ayers, Bodo Grimbacher, Smita Y Patel.
      Genetic variants in PIK3CD, PIK3R1 and NFKB1 cause the primary immune deficiencies, activated PI3Kδ syndrome (APDS) 1, APDS2 and NFκB1 haploinsufficiency, respectively. We have identified a family with known or potentially pathogenic variants NFKB1, TNFRSF13B and PIK3R1. The study's aim was to describe their associated immune and cellular phenotypes and compare with individuals with monogenic disease. NFκB1 pathway function was measured by immunoblotting and PI3Kδ pathway activity by phospho-flow cytometry. p105/p50 expression was absent in two individuals but elevated pS6 only in the index case. Transfection of primary T cells demonstrated increased basal pS6 signalling due to mutant PIK3R1, but not mutant NFKB1 or their wildtype forms. We report on the presence of pathogenic variant NFKB1, with likely modifying variants in TNFRSF13B and PIK3R1 in a family. We describe immune features of both NFκB1 haploinsufficiency and APDS2, and the inhibition of excessive PI3K signalling by rapamycin in vitro.
    Keywords:  Activated phosphoinositol 3-kinase delta syndrome; Combined immune deficiency; NF-kappaB1 haploinsufficiency; NFKB1; PIK3CD; PIK3R1
    DOI:  https://doi.org/10.1016/j.clim.2021.108910
  8. Cancers (Basel). 2021 Dec 16. pii: 6312. [Epub ahead of print]13(24):
    Can Systems Biology Advance Clinical Precision Oncology?
    Andrea Rocca, Boris N Kholodenko.
      Precision oncology is perceived as a way forward to treat individual cancer patients. However, knowing particular cancer mutations is not enough for optimal therapeutic treatment, because cancer genotype-phenotype relationships are nonlinear and dynamic. Systems biology studies the biological processes at the systems' level, using an array of techniques, ranging from statistical methods to network reconstruction and analysis, to mathematical modeling. Its goal is to reconstruct the complex and often counterintuitive dynamic behavior of biological systems and quantitatively predict their responses to environmental perturbations. In this paper, we review the impact of systems biology on precision oncology. We show examples of how the analysis of signal transduction networks allows to dissect resistance to targeted therapies and inform the choice of combinations of targeted drugs based on tumor molecular alterations. Patient-specific biomarkers based on dynamical models of signaling networks can have a greater prognostic value than conventional biomarkers. These examples support systems biology models as valuable tools to advance clinical and translational oncological research.
    Keywords:  cancer systems biology; drug resistance; mathematical models; network analysis; patient-specific network modeling; precision oncology; signaling networks; statistical methods
    DOI:  https://doi.org/10.3390/cancers13246312
  9. PLoS Genet. 2021 Dec 23. 17(12): e1009986
    Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis.
    Jake J Reske, Mike R Wilson, Jeanne Holladay, Rebecca A Siwicki, Hilary Skalski, Shannon Harkins, Marie Adams, John I Risinger, Galen Hostetter, Ken Lin, Ronald L Chandler.
      TP53 and ARID1A are frequently mutated across cancer but rarely in the same primary tumor. Endometrial cancer has the highest TP53-ARID1A mutual exclusivity rate. However, the functional relationship between TP53 and ARID1A mutations in the endometrium has not been elucidated. We used genetically engineered mice and in vivo genomic approaches to discern both unique and overlapping roles of TP53 and ARID1A in the endometrium. TP53 loss with oncogenic PIK3CAH1047R in the endometrial epithelium results in features of endometrial hyperplasia, adenocarcinoma, and intraepithelial carcinoma. Mutant endometrial epithelial cells were transcriptome profiled and compared to control cells and ARID1A/PIK3CA mutant endometrium. In the context of either TP53 or ARID1A loss, PIK3CA mutant endometrium exhibited inflammatory pathway activation, but other gene expression programs differed based on TP53 or ARID1A status, such as epithelial-to-mesenchymal transition. Gene expression patterns observed in the genetic mouse models are reflective of human tumors with each respective genetic alteration. Consistent with TP53-ARID1A mutual exclusivity, the p53 pathway is activated following ARID1A loss in the endometrial epithelium, where ARID1A normally directly represses p53 pathway genes in vivo, including the stress-inducible transcription factor, ATF3. However, co-existing TP53-ARID1A mutations led to invasive adenocarcinoma associated with mutant ARID1A-driven ATF3 induction, reduced apoptosis, TP63+ squamous differentiation and invasion. These data suggest TP53 and ARID1A mutations drive shared and distinct tumorigenic programs in the endometrium and promote invasive endometrial cancer when existing simultaneously. Hence, TP53 and ARID1A mutations may co-occur in a subset of aggressive or metastatic endometrial cancers, with ARID1A loss promoting squamous differentiation and the acquisition of invasive properties.
    DOI:  https://doi.org/10.1371/journal.pgen.1009986
  10. Cell. 2021 Dec 22. pii: S0092-8674(21)01386-6. [Epub ahead of print]184(26): 6226-6228
    Dinner is served, sir: Fighting cancer with the right diet.
    Andrés Méndez-Lucas, Mariia Yuneva.
      Altered metabolism of tumors offers an opportunity to use metabolic interventions as a therapeutic strategy. Lien et al. demonstrate that understanding how specific diets with different carbohydrate and fat composition affect tumor metabolism is essential in order to use this opportunity efficiently.
    DOI:  https://doi.org/10.1016/j.cell.2021.11.036
  11. Dev Cell. 2021 Dec 20. pii: S1534-5807(21)00991-6. [Epub ahead of print]56(24): 3303-3304
    What doesn't kill you makes you differentiate.
    Franziska Peters, Sara A Wickström.
      Tissues need strategies to cope with genomic insults to maintain their integrity. In this issue of Developmental Cell, Kato et al. use in vivo fate tracing to observe selective elimination of epidermal stem cells (EpiSCs) harboring severe genomic lesions through their differentiation and compensatory expansion of surrounding intact cells.
    DOI:  https://doi.org/10.1016/j.devcel.2021.12.002
  12. Dev Cell. 2021 Dec 20. pii: S1534-5807(21)00992-8. [Epub ahead of print]56(24): 3307-3308
    Clone competition as a mechanism to reduce tumor formation.
    Amelia Acha-Sagredo, Ilaria Malanchi, Francesca D Ciccarelli.
      With age, clones carrying somatic mutations in well-known cancer driver genes progressively populate adult tissues, yet cancer transformation is rare. In a recent issue of Nature, Colom et al. showed that competition between mutated clones with different fitness could act as a tumor-protective mechanism.
    DOI:  https://doi.org/10.1016/j.devcel.2021.12.003
  13. Cells. 2021 Dec 18. pii: 3577. [Epub ahead of print]10(12):
    Differential Dose- and Tissue-Dependent Effects of foxo on Aging, Metabolic and Proteostatic Pathways.
    Maria S Manola, Sentiljana Gumeni, Ioannis P Trougakos.
      Aging is the gradual deterioration of physiological functions that culminates in death. Several studies across a wide range of model organisms have revealed the involvement of FOXO (forkhead box, class O) transcription factors in orchestrating metabolic homeostasis, as well as in regulating longevity. To study possible dose- or tissue-dependent effects of sustained foxo overexpression, we utilized two different Drosophila transgenic lines expressing high and relatively low foxo levels and overexpressed foxo, either ubiquitously or in a tissue-specific manner. We found that ubiquitous foxo overexpression (OE) accelerated aging, induced the early onset of age-related phenotypes, increased sensitivity to thermal stress, and deregulated metabolic and proteostatic pathways; these phenotypes were more intense in transgenic flies expressing high levels of foxo. Interestingly, there is a defined dosage of foxo OE in muscles and cardiomyocytes that shifts energy resources into longevity pathways and thus ameliorates not only tissue but also organismal age-related defects. Further, we found that foxo OE stimulates in an Nrf2/cncC dependent-manner, counteracting proteostatic pathways, e.g., the ubiquitin-proteasome pathway, which is central in ameliorating the aberrant foxo OE-mediated toxicity. These findings highlight the differential dose- and tissue-dependent effects of foxo on aging, metabolic and proteostatic pathways, along with the foxo-Nrf2/cncC functional crosstalk.
    Keywords:  Drosophila; FOXO; Nrf2/cncC; proteasome; proteostasis network
    DOI:  https://doi.org/10.3390/cells10123577
  14. Biomolecules. 2021 Dec 15. pii: 1886. [Epub ahead of print]11(12):
    Insulin-Responsive Transcription Factors.
    Gerald Thiel, Lisbeth A Guethlein, Oliver G Rössler.
      The hormone insulin executes its function via binding and activating of the insulin receptor, a receptor tyrosine kinase that is mainly expressed in skeletal muscle, adipocytes, liver, pancreatic β-cells, and in some areas of the central nervous system. Stimulation of the insulin receptor activates intracellular signaling cascades involving the enzymes extracellular signal-regulated protein kinase-1/2 (ERK1/2), phosphatidylinositol 3-kinase, protein kinase B/Akt, and phospholipase Cγ as signal transducers. Insulin receptor stimulation is correlated with multiple physiological and biochemical functions, including glucose transport, glucose homeostasis, food intake, proliferation, glycolysis, and lipogenesis. This review article focuses on the activation of gene transcription as a result of insulin receptor stimulation. Signal transducers such as protein kinases or the GLUT4-induced influx of glucose connect insulin receptor stimulation with transcription. We discuss insulin-responsive transcription factors that respond to insulin receptor activation and generate a transcriptional network executing the metabolic functions of insulin. Importantly, insulin receptor stimulation induces transcription of genes encoding essential enzymes of glycolysis and lipogenesis and inhibits genes encoding essential enzymes of gluconeogenesis. Overall, the activation or inhibition of insulin-responsive transcription factors is an essential aspect of orchestrating a wide range of insulin-induced changes in the biochemistry and physiology of insulin-responsive tissues.
    Keywords:  ChREBP; Egr-1; Elk-1; FoxO1; SREBP-1c; USF; liver X receptor
    DOI:  https://doi.org/10.3390/biom11121886
  15. Elife. 2021 Dec 23. pii: e72593. [Epub ahead of print]10
    Disruption of the TCA cycle reveals an ATF4-dependent integration of redox and amino acid metabolism.
    Dylan Gerard Ryan, Ming Yang, Hiran A Prag, Giovanny Rodriguez Blanco, Efterpi Nikitopoulou, Marc Segarra-Mondejar, Christopher A Powell, Tim Young, Nils Burger, Jan Lj Miljkovic, Michal Minczuk, Michael P Murphy, Alex von Kriegsheim, Christian Frezza.
      The Tricarboxylic Acid Cycle (TCA) cycle is arguably the most critical metabolic cycle in physiology and exists as an essential interface coordinating cellular metabolism, bioenergetics, and redox homeostasis. Despite decades of research, a comprehensive investigation into the consequences of TCA cycle dysfunction remains elusive. Here, we targeted two TCA cycle enzymes, fumarate hydratase (FH) and succinate dehydrogenase (SDH), and combined metabolomics, transcriptomics, and proteomics analyses to fully appraise the consequences of TCA cycle inhibition (TCAi) in murine kidney epithelial cells. Our comparative approach shows that TCAi elicits a convergent rewiring of redox and amino acid metabolism dependent on the activation of ATF4 and the integrated stress response (ISR). Furthermore, we also uncover a divergent metabolic response, whereby acute FHi, but not SDHi, can maintain asparagine levels via reductive carboxylation and maintenance of cytosolic aspartate synthesis. Our work highlights an important interplay between the TCA cycle, redox biology and amino acid homeostasis.
    Keywords:  biochemistry; cell biology; chemical biology; mouse
    DOI:  https://doi.org/10.7554/eLife.72593
  16. EMBO Rep. 2021 Dec 20. e53902
    Unexpected gene activation following CRISPR-Cas9-mediated genome editing.
    Anna G Manjón, Simon Linder, Hans Teunissen, Anoek Friskes, Wilbert Zwart, Elzo de Wit, René H Medema.
      The discovery of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and its development as a genome editing tool has revolutionized the field of molecular biology. In the DNA damage field, CRISPR has brought an alternative to induce endogenous double-strand breaks (DSBs) at desired genomic locations and study the DNA damage response and its consequences. Many systems for sgRNA delivery have been reported in order to efficiently generate this DSB, including lentiviral vectors. However, some of the consequences of these systems are not yet well understood. Here, we report that lentiviral-based sgRNA vectors can integrate into the endogenous genomic target location, leading to undesired activation of the target gene. By generating a DSB in the regulatory region of the ABCB1 gene using a lentiviral sgRNA vector, we can induce the formation of Taxol-resistant colonies. We show that these colonies upregulate ABCB1 via integration of the EEF1A1 and the U6 promoters from the sgRNA vector. We believe that this is an unreported CRISPR/Cas9 on-target effect that researchers need to be aware of when using lentiviral vectors for genome editing.
    Keywords:  CRISPR-Cas9; drug resistance; gene activation; lentiviral integration; on-target effects
    DOI:  https://doi.org/10.15252/embr.202153902
  17. Genome Biol. 2021 Dec 20. 22(1): 343
    Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects.
    Joshua M Dempster, Isabella Boyle, Francisca Vazquez, David E Root, Jesse S Boehm, William C Hahn, Aviad Tsherniak, James M McFarland.
      CRISPR loss of function screens are powerful tools to interrogate biology but exhibit a number of biases and artifacts that can confound the results. Here, we introduce Chronos, an algorithm for inferring gene knockout fitness effects based on an explicit model of cell proliferation dynamics after CRISPR gene knockout. We test Chronos on two pan-cancer CRISPR datasets and one longitudinal CRISPR screen. Chronos generally outperforms competitors in separation of controls and strength of biomarker associations, particularly when longitudinal data is available. Additionally, Chronos exhibits the lowest copy number and screen quality bias of evaluated methods. Chronos is available at https://github.com/broadinstitute/chronos .
    DOI:  https://doi.org/10.1186/s13059-021-02540-7
  18. Int J Cancer. 2021 Dec 18.
    Complexity against current cancer research - are we on the wrong track?
    Yasenya Kasikci, Hinrich Gronemeyer.
      Cancer genetics has led to major discoveries, including proto-oncogene and tumor-suppressor concepts, and cancer genomics generated concepts like driver and passenger genes, revealed tumor heterogeneity and clonal evolution. Reconstructing trajectories of tumorigenesis using spatial and single-cell genomics is possible. Patient stratification and prognostic parameters have been improved. Yet, despite these advances, successful translation into targeted therapies has been scarce and mostly limited to kinase inhibitors. Here, we argue that current cancer research may be on the wrong track, by considering cancer more as a "monogenic" disease, trying to extract common information from thousands of patients, while not properly considering complexity and individual diversity. We suggest to empower a systems cancer approach which reconstructs the information network that has been altered by the tumorigenic events, to analyze hierarchies and predict (druggable) key nodes that could interfere with/block the aberrant information transfer. We also argue that the inter-individual variability between patients of similar cohorts is too high to extract common polygenic network information from large numbers of patients and argue in favor of an individualized approach. The analysis we propose would require a structured multinational and multidisciplinary effort, in which clinicians, and cancer, developmental, cell and computational biologists together with mathematicians and informaticians develop dynamic regulatory networks which integrate the entire information transfer in and between cells and organs in (patho)physiological conditions, revealing hierarchies and available drugs to interfere with key regulators. Based on this blueprint, the altered information transfer in individual cancers could be modeled and possible targeted (combo)therapies proposed. This article is protected by copyright. All rights reserved.
    Keywords:  Conceptual problems in cancer genomics; complexity challenge; information transfer; integrated network analysis
    DOI:  https://doi.org/10.1002/ijc.33912
  19. Nat Methods. 2021 Dec 23.
    Caveat fluorophore: an insiders' guide to small-molecule fluorescent labels.
    Jonathan B Grimm, Luke D Lavis.
      The last three decades have brought a revolution in fluorescence microscopy. The development of new microscopes, fluorescent labels and analysis techniques has pushed the frontiers of biological imaging forward, moving from fixed to live cells, from diffraction-limited to super-resolution imaging and from simple cell culture systems to experiments in vivo. The large and ever-evolving collection of tools can be daunting for biologists, who must invest substantial time and effort in adopting new technologies to answer their specific questions. This is particularly relevant when working with small-molecule fluorescent labels, where users must navigate the jargon, idiosyncrasies and caveats of chemistry. Here, we present an overview of chemical dyes used in biology and provide frank advice from a chemist's perspective.
    DOI:  https://doi.org/10.1038/s41592-021-01338-6
  20. Sci Signal. 2021 Dec 21. 14(714): eabj0057
    Suppression of caspase 8 activity by a coronin 1-PI3Kδ pathway promotes T cell survival independently of TCR and IL-7 signaling.
    Mayumi Mori, Julie Ruer-Laventie, Wandrille Duchemin, Philippe Demougin, Tohnyui Ndinyanka Fabrice, Matthias P Wymann, Jean Pieters.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/scisignal.abj0057
  21. Elife. 2021 Dec 23. pii: e71825. [Epub ahead of print]10
    Crosstalk with keratinocytes causes GNAQ oncogene specificity in melanoma.
    Oscar Urtatiz, Amanda Haage, Guy Tanentzapf, Catherine D Van Raamsdonk.
      Different melanoma subtypes exhibit specific and non-overlapping sets of oncogene and tumor suppressor mutations, despite a common cell of origin in melanocytes. For example, activation of the Gαq/11 signaling pathway is a characteristic initiating event in primary melanomas that arise in the dermis, uveal tract or central nervous system. It is rare in melanomas arising in the epidermis. The mechanism for this specificity is unknown. Here, we present evidence that in the mouse, crosstalk with the epidermal microenvironment actively impairs the survival of melanocytes expressing the GNAQQ209L oncogene. We found that GNAQQ209L, in combination with signaling from the interfollicular epidermis (IFE), stimulates dendrite extension, leads to actin cytoskeleton disorganization, inhibits proliferation and promotes apoptosis in melanocytes. The effect was reversible and paracrine. In contrast, the epidermal environment increased the survival of wildtype and BrafV600E expressing melanocytes. Hence, our studies reveal the flip side of Gaq/11 signaling, which was hitherto unsuspected. In the future, the identification of the epidermal signals that restrain the GNAQQ209L oncogene could suggest novel therapies for GNAQ and GNA11 mutant melanomas.
    Keywords:  cancer biology; genetics; genomics; human; mouse
    DOI:  https://doi.org/10.7554/eLife.71825
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