bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2021‒10‒17
twenty-four papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute
  1. Integrating thousands of PTEN variant activity and abundance measurements reveals variant subgroups and new dominant negatives in cancers.
  2. Bioenergetic Requirements and Spatiotemporal Profile of Nerve Growth Factor Induced PI3K-Akt Signaling Along Sensory Axons.
  3. Mutant clones in normal epithelium outcompete and eliminate emerging tumours.
  4. PI3K functions as a hub in mechanotransduction.
  5. Generation of scalable cancer models by combining AAV-intron-trap, CRISPR/Cas9, and inducible Cre-recombinase.
  6. PI3Kδ coordinates transcriptional, chromatin, and metabolic changes to promote effector CD8+ T cells at the expense of central memory.
  7. A leucine-derived fatty acid unlocks the mTOR to development.
  8. Case Report: Five-Year Experience of AKT Inhibition with Miransertib (MK-7075) in an Individual with Proteus Syndrome.
  9. SomaMutDB: a database of somatic mutations in normal human tissues.
  10. Convergent somatic mutations in metabolism genes in chronic liver disease.
  11. Tyrosine Phosphorylation of DEPTOR Functions as a Molecular Switch to Activate mTOR Signaling.
  12. Nutrients in the fate of pluripotent stem cells.
  13. Systems-level effects of allosteric perturbations to a model molecular switch.
  14. Noise distorts the epigenetic landscape and shapes cell-fate decisions.
  15. CeDR Atlas: a knowledgebase of cellular drug response.
  16. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes.
  17. Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas.
  18. Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions.
  19. A cell cycle regulator branches out.
  20. mTOR-dependent translation amplifies microglia priming in aging mice.
  21. Gene bookmarking by the heat shock transcription factor programs the insulin-like signaling pathway.
  22. mTOR-dependent immunometabolism as Achilles' heel of anticancer therapy.
  23. The Signaling Pathways Involved in Ovarian Follicle Development.
  24. Cancer gene mutation frequencies for the U.S. population.
  1. Genome Med. 2021 Oct 14. 13(1): 165
    Integrating thousands of PTEN variant activity and abundance measurements reveals variant subgroups and new dominant negatives in cancers.
    Kenneth A Matreyek, Jason J Stephany, Ethan Ahler, Douglas M Fowler.
      BACKGROUND: PTEN is a multi-functional tumor suppressor protein regulating cell growth, immune signaling, neuronal function, and genome stability. Experimental characterization can help guide the clinical interpretation of the thousands of germline or somatic PTEN variants observed in patients. Two large-scale mutational datasets, one for PTEN variant intracellular abundance encompassing 4112 missense variants and one for lipid phosphatase activity encompassing 7244 variants, were recently published. The combined information from these datasets can reveal variant-specific phenotypes that may underlie various clinical presentations, but this has not been comprehensively examined, particularly for somatic PTEN variants observed in cancers.METHODS: Here, we add to these efforts by measuring the intracellular abundance of 764 new PTEN variants and refining abundance measurements for 3351 previously studied variants. We use this expanded and refined PTEN abundance dataset to explore the mutational patterns governing PTEN intracellular abundance, and then incorporate the phosphatase activity data to subdivide PTEN variants into four functionally distinct groups.
    RESULTS: This analysis revealed a set of highly abundant but lipid phosphatase defective variants that could act in a dominant-negative fashion to suppress PTEN activity. Two of these variants were, indeed, capable of dysregulating Akt signaling in cells harboring a WT PTEN allele. Both variants were observed in multiple breast or uterine tumors, demonstrating the disease relevance of these high abundance, inactive variants.
    CONCLUSIONS: We show that multidimensional, large-scale variant functional data, when paired with public cancer genomics datasets and follow-up assays, can improve understanding of uncharacterized cancer-associated variants, and provide better insights into how they contribute to oncogenesis.
    Keywords:  Cancer genomics; Dominant-negative; Multiplex assays of variant effect; PTEN; Protein variants; VAMP-seq
    DOI:  https://doi.org/10.1186/s13073-021-00984-x
  2. Front Mol Neurosci. 2021 ;14 726331
    Bioenergetic Requirements and Spatiotemporal Profile of Nerve Growth Factor Induced PI3K-Akt Signaling Along Sensory Axons.
    Rajiv Sainath, Gianluca Gallo.
      Nerve Growth Factor (NGF) promotes the elaboration of axonal filopodia and branches through PI3K-Akt. NGF activates the TrkA receptor resulting in an initial transient high amplitude burst of PI3K-Akt signaling followed by a maintained lower steady state, hereafter referred to as initiation and steady state phases. Akt initially undergoes phosphorylation at T308 followed by phosphorylation at S473, resulting in maximal kinase activation. We report that during the initiation phase the localization of PI3K signaling, reported by visualizing sites of PIP3 formation, and Akt signaling, reflected by Akt phosphorylation at T308, correlates with the positioning of axonal mitochondria. Mitochondrial oxidative phosphorylation but not glycolysis is required for Akt phosphorylation at T308. In contrast, the phosphorylation of Akt at S473 is not spatially associated with mitochondria and is dependent on both oxidative phosphorylation and glycolysis. Under NGF steady state conditions, maintenance of phosphorylation at T308 shows dual dependence on oxidative phosphorylation and glycolysis. Phosphorylation at S473 is more dependent on glycolysis but also requires oxidative phosphorylation for maintenance over longer time periods. The data indicate that NGF induced PI3K-Akt signaling along axons is preferentially initiated at sites containing mitochondria, in a manner dependent on oxidative phosphorylation. Steady state signaling is discussed in the context of combined contributions by mitochondria and the possibility of glycolysis occurring in association with endocytosed signalosomes.
    Keywords:  Akt; PI3K; axon; glycolysis; mitochondria
    DOI:  https://doi.org/10.3389/fnmol.2021.726331
  3. Nature. 2021 Oct 13.
    Mutant clones in normal epithelium outcompete and eliminate emerging tumours.
    B Colom, A Herms, M W J Hall, S C Dentro, C King, R K Sood, M P Alcolea, G Piedrafita, D Fernandez-Antoran, S H Ong, J C Fowler, K T Mahbubani, K Saeb-Parsy, M Gerstung, B A Hall, P H Jones.
      Human epithelial tissues accumulate cancer-driver mutations with age1-9, yet tumour formation remains rare. The positive selection of these mutations suggests that they alter the behaviour and fitness of proliferating cells10-12. Thus, normal adult tissues become a patchwork of mutant clones competing for space and survival, with the fittest clones expanding by eliminating their less competitive neighbours11-14. However, little is known about how such dynamic competition in normal epithelia influences early tumorigenesis. Here we show that the majority of newly formed oesophageal tumours are eliminated through competition with mutant clones in the adjacent normal epithelium. We followed the fate of nascent, microscopic, pre-malignant tumours in a mouse model of oesophageal carcinogenesis and found that most were rapidly lost with no indication of tumour cell death, decreased proliferation or an anti-tumour immune response. However, deep sequencing of ten-day-old and one-year-old tumours showed evidence of selection on the surviving neoplasms. Induction of highly competitive clones in transgenic mice increased early tumour removal, whereas pharmacological inhibition of clonal competition reduced tumour loss. These results support a model in which survival of early neoplasms depends on their competitive fitness relative to that of mutant clones in the surrounding normal tissue. Mutant clones in normal epithelium have an unexpected anti-tumorigenic role in purging early tumours through cell competition, thereby preserving tissue integrity.
    DOI:  https://doi.org/10.1038/s41586-021-03965-7
  4. Trends Biochem Sci. 2021 Nov;pii: S0968-0004(21)00108-0. [Epub ahead of print]46(11): 878-888
    PI3K functions as a hub in mechanotransduction.
    M Di-Luoffo, Z Ben-Meriem, P Lefebvre, M Delarue, J Guillermet-Guibert.
      Mammalian cells integrate different types of stimuli that govern their fate. These stimuli encompass biochemical as well as biomechanical cues (shear, tensile, and compressive stresses) that are usually studied separately. The phosphatidylinositol 3-kinase (PI3K) enzymes, producing signaling phosphoinositides at plasma and intracellular membranes, are key in intracellular signaling and vesicular trafficking pathways. Recent evidence in cancer research demonstrates that these enzymes are essential in mechanotransduction. Despite this, the importance of the integration of biomechanical cues and PI3K-driven biochemical signals is underestimated. In this opinion article, we make the hypothesis that modeling of biomechanical cues is critical to understand PI3K oncogenicity. We also identify known/missing knowledge in terms of isoform specificity and molecular pathways of activation, knowledge that is needed for clinical applications.
    Keywords:  PI3K; cell signaling; compression; mechanotransduction; shear stress; tension
    DOI:  https://doi.org/10.1016/j.tibs.2021.05.005
  5. Commun Biol. 2021 Oct 13. 4(1): 1184
    Generation of scalable cancer models by combining AAV-intron-trap, CRISPR/Cas9, and inducible Cre-recombinase.
    Prajwal C Boddu, Abhishek K Gupta, Jung-Sik Kim, Karla M Neugebauer, Todd Waldman, Manoj M Pillai.
      Scalable isogenic models of cancer-associated mutations are critical to studying dysregulated gene function. Nonsynonymous mutations of splicing factors, which typically affect one allele, are common in many cancers, but paradoxically confer growth disadvantage to cell lines, making their generation and expansion challenging. Here, we combine AAV-intron trap, CRISPR/Cas9, and inducible Cre-recombinase systems to achieve >90% efficiency to introduce the oncogenic K700E mutation in SF3B1, a splicing factor commonly mutated in multiple cancers. The intron-trap design of AAV vector limits editing to one allele. CRISPR/Cas9-induced double stranded DNA breaks direct homologous recombination to the desired genomic locus. Inducible Cre-recombinase allows for the expansion of cells prior to loxp excision and expression of the mutant allele.  Importantly, AAV or CRISPR/Cas9 alone results in much lower editing efficiency and the edited cells do not expand due to toxicity of SF3B1-K700E. Our approach can be readily adapted to generate scalable isogenic systems where mutant oncogenes confer a growth disadvantage.
    DOI:  https://doi.org/10.1038/s42003-021-02690-1
  6. Cell Rep. 2021 Oct 12. pii: S2211-1247(21)01264-X. [Epub ahead of print]37(2): 109804
    PI3Kδ coordinates transcriptional, chromatin, and metabolic changes to promote effector CD8+ T cells at the expense of central memory.
    Jennifer L Cannons, Alejandro V Villarino, Senta M Kapnick, Silvia Preite, Han-Yu Shih, Julio Gomez-Rodriguez, Zenia Kaul, Hirofumi Shibata, Julie M Reilley, Bonnie Huang, Robin Handon, Ian T McBain, Selamawit Gossa, Tuoqi Wu, Helen C Su, Dorian B McGavern, John J O'Shea, Peter J McGuire, Gulbu Uzel, Pamela L Schwartzberg.
      Patients with activated phosphatidylinositol 3-kinase delta (PI3Kδ) syndrome (APDS) present with sinopulmonary infections, lymphadenopathy, and cytomegalvirus (CMV) and/or Epstein-Barr virus (EBV) viremia, yet why patients fail to clear certain chronic viral infections remains incompletely understood. Using patient samples and a mouse model (Pik3cdE1020K/+ mice), we demonstrate that, upon activation, Pik3cdE1020K/+ CD8+ T cells exhibit exaggerated features of effector populations both in vitro and after viral infection that are associated with increased Fas-mediated apoptosis due to sustained FoxO1 phosphorylation and Fasl derepression, enhanced mTORC1 and c-Myc signatures, metabolic perturbations, and an altered chromatin landscape. Conversely, Pik3cdE1020K/+ CD8+ cells fail to sustain expression of proteins critical for central memory, including TCF1. Strikingly, activated Pik3cdE1020K/+ CD8+ cells exhibit altered transcriptional and epigenetic circuits characterized by pronounced interleukin-2 (IL-2)/STAT5 signatures and heightened IL-2 responses that prevent differentiation to memory-like cells in IL-15. Our data position PI3Kδ as integrating multiple signaling nodes that promote CD8+ T cell effector differentiation, providing insight into phenotypes of patients with APDS.
    Keywords:  CD8 T cell memory; IL-2; Myc; Phosphatidylinositide 3 Kinase delta (PI3Kδ); TCF1; apoptosis; effector T cells; long-lived effector cells (LLEC); mTOR; metabolism
    DOI:  https://doi.org/10.1016/j.celrep.2021.109804
  7. Dev Cell. 2021 Oct 11. pii: S1534-5807(21)00735-8. [Epub ahead of print]56(19): 2681-2682
    A leucine-derived fatty acid unlocks the mTOR to development.
    Chung-Yang Yeh, Dudley W Lamming.
      Understanding how nutrient-sensitive signaling pathways regulate development and aging is an active area of research. In this issue of Developmental Cell,Zhu and colleagues (2021) identify a specific monomethylated branched-chain fatty acid that overrides nutrient deprivation signaling and activates mTORC1 in C. elegans and mammalian cells.
    DOI:  https://doi.org/10.1016/j.devcel.2021.09.017
  8. Cold Spring Harb Mol Case Stud. 2021 Oct 14. pii: mcs.a006134. [Epub ahead of print]
    Case Report: Five-Year Experience of AKT Inhibition with Miransertib (MK-7075) in an Individual with Proteus Syndrome.
    Christopher A Ours, Julie C Sapp, Mia B Hodges, Allison J de Moya, Leslie G Biesecker.
      Proteus syndrome is a rare overgrowth disorder caused by postzygotic activating variants in AKT1. Individuals may develop a range of skin, bone, and soft tissue overgrowth leading to functional impairment and disfigurement. Therapy for this disorder is limited to supportive care and surgical intervention. Inhibitors of AKT, originally designed as cancer therapeutics, are a rational, targeted pharmacologic strategy to mitigate the devastating morbidity of Proteus syndrome. We present the five-year follow up of an 18-year-old male with Proteus syndrome treated with miransertib (MK-7075), an oral pan-AKT inhibitor. At completion of a planned 48-week phase 1 pharmacodynamic study, the individual derived sufficient benefit that the study was amended to permit continued use and assess the long-term safety of miransertib. The treatment has been well tolerated with mild treatment-attributed side effects including headache, transient hyperglycemia, and transient elevations of aspartate aminotransferase, alanine aminotransferase, and bilirubin. He has experienced sustained improvement of pain and slowed growth of bilateral plantar cerebriform connective tissue nevi. This case report supplements the data from our prior study extending those findings out to five years. It shows that at the doses used, miransertib has a favorable safety profile and durable benefit of improving symptoms of pain and slowing progression of overgrowth in Proteus syndrome in a single individual. While an uncontrolled single report cannot prove safety or efficacy, these data lend support to the encouraging preliminary data of our prior phase 1 pharmacodynamic study.
    Keywords:  Bone pain; Connective tissue nevi; Multiple skeletal anomalies; Overgrowth
    DOI:  https://doi.org/10.1101/mcs.a006134
  9. Nucleic Acids Res. 2021 Oct 11. pii: gkab914. [Epub ahead of print]
    SomaMutDB: a database of somatic mutations in normal human tissues.
    Shixiang Sun, Yujue Wang, Alexander Y Maslov, Xiao Dong, Jan Vijg.
      De novo mutations, a consequence of errors in DNA repair or replication, have been reported to accumulate with age in normal tissues of humans and model organisms. This accumulation during development and aging has been implicated as a causal factor in aging and age-related pathology, including but not limited to cancer. Due to their generally very low abundance mutations have been difficult to detect in normal tissues. Only with recent advances in DNA sequencing of single-cells, clonal lineages or ultra-high-depth sequencing of small tissue biopsies, somatic mutation frequencies and spectra have been unveiled in several tissue types. The rapid accumulation of such data prompted us to develop a platform called SomaMutDB (https://vijglab.einsteinmed.org/SomaMutDB) to catalog the 2.42 million single nucleotide variations (SNVs) and 0.12 million small insertions and deletions (INDELs) thus far identified using these advanced methods in nineteen human tissues or cell types as a function of age or environmental stress conditions. SomaMutDB employs a user-friendly interface to display and query somatic mutations with their functional annotations. Moreover, the database provides six powerful tools for analyzing mutational signatures associated with the data. We believe such an integrated resource will prove valuable for understanding somatic mutations and their possible role in human aging and age-related diseases.
    DOI:  https://doi.org/10.1093/nar/gkab914
  10. Nature. 2021 Oct 13.
    Convergent somatic mutations in metabolism genes in chronic liver disease.
    Stanley W K Ng, Foad J Rouhani, Simon F Brunner, Natalia Brzozowska, Sarah J Aitken, Ming Yang, Federico Abascal, Luiza Moore, Efterpi Nikitopoulou, Lia Chappell, Daniel Leongamornlert, Aleksandra Ivovic, Philip Robinson, Timothy Butler, Mathijs A Sanders, Nicholas Williams, Tim H H Coorens, Jon Teague, Keiran Raine, Adam P Butler, Yvette Hooks, Beverley Wilson, Natalie Birtchnell, Huw Naylor, Susan E Davies, Michael R Stratton, Iñigo Martincorena, Raheleh Rahbari, Christian Frezza, Matthew Hoare, Peter J Campbell.
      The progression of chronic liver disease to hepatocellular carcinoma is caused by the acquisition of somatic mutations that affect 20-30 cancer genes1-8. Burdens of somatic mutations are higher and clonal expansions larger in chronic liver disease9-13 than in normal liver13-16, which enables positive selection to shape the genomic landscape9-13. Here we analysed somatic mutations from 1,590 genomes across 34 liver samples, including healthy controls, alcohol-related liver disease and non-alcoholic fatty liver disease. Seven of the 29 patients with liver disease had mutations in FOXO1, the major transcription factor in insulin signalling. These mutations affected a single hotspot within the gene, impairing the insulin-mediated nuclear export of FOXO1. Notably, six of the seven patients with FOXO1S22W hotspot mutations showed convergent evolution, with variants acquired independently by up to nine distinct hepatocyte clones per patient. CIDEB, which regulates lipid droplet metabolism in hepatocytes17-19, and GPAM, which produces storage triacylglycerol from free fatty acids20,21, also had a significant excess of mutations. We again observed frequent convergent evolution: up to fourteen independent clones per patient with CIDEB mutations and up to seven clones per patient with GPAM mutations. Mutations in metabolism genes were distributed across multiple anatomical segments of the liver, increased clone size and were seen in both alcohol-related liver disease and non-alcoholic fatty liver disease, but rarely in hepatocellular carcinoma. Master regulators of metabolic pathways are a frequent target of convergent somatic mutation in alcohol-related and non-alcoholic fatty liver disease.
    DOI:  https://doi.org/10.1038/s41586-021-03974-6
  11. J Biol Chem. 2021 Oct 08. pii: S0021-9258(21)01096-6. [Epub ahead of print] 101291
    Tyrosine Phosphorylation of DEPTOR Functions as a Molecular Switch to Activate mTOR Signaling.
    Laurence M Gagné, Nadine Morin, Noémie Lavoie, Nicolas Bisson, Jean-Philippe Lambert, Frédérick A Mallette, Marc-Étienne Huot.
      Metabolic dysfunction is a major driver of tumorigenesis. The serine/threonine kinase mTOR constitutes a key central regulator of metabolic pathways promoting cancer cell proliferation and survival. mTOR activity is regulated by metabolic sensors as well as by numerous factors comprising the PTEN/PI3K/AKT canonical pathway, which are often mutated in cancer. However, some cancers displaying constitutively active mTOR do not carry alterations within this canonical pathway, suggesting alternative modes of mTOR regulation. Since DEPTOR, an endogenous inhibitor of mTOR, was previously found to modulate both mTOR complexe 1 and 2, we investigated the different post-transltionnal modification that could affect its inhibitory function. We found that tyrosine 289 phosphorylation of DEPTOR impairs its interaction with mTOR, leading to increased mTOR activation. Using proximity biotinylation assays, we identified SYK (Spleen tyrosine kinase) as a kinase involved in DEPTOR tyrosine 289 phosphorylation in an ephrin (EPH) receptor-dependent manner. Altogether, our work reveals that phosphorylation of tyrosine 289 of DEPTOR represents a novel molecular switch involved in the regulation of both mTORC1 and mTORC2.
    Keywords:  DEPTOR; EPHB2; mTOR; tyrosine phosphorylation
    DOI:  https://doi.org/10.1016/j.jbc.2021.101291
  12. Cell Metab. 2021 Oct 06. pii: S1550-4131(21)00432-0. [Epub ahead of print]
    Nutrients in the fate of pluripotent stem cells.
    Vivian Lu, Irena J Roy, Michael A Teitell.
      Pluripotent stem cells model certain features of early mammalian development ex vivo. Medium-supplied nutrients can influence self-renewal, lineage specification, and earliest differentiation of pluripotent stem cells. However, which specific nutrients support these distinct outcomes, and their mechanisms of action, remain under active investigation. Here, we evaluate the available data on nutrients and their metabolic conversion that influence pluripotent stem cell fates. We also discuss key questions open for investigation in this rapidly expanding area of increasing fundamental and practical importance.
    Keywords:  development; differentiation; fate; metabolism; nutrients; pluripotent stem cell
    DOI:  https://doi.org/10.1016/j.cmet.2021.09.013
  13. Nature. 2021 Oct 13.
    Systems-level effects of allosteric perturbations to a model molecular switch.
    Tina Perica, Christopher J P Mathy, Jiewei Xu, Gwendolyn Μ Jang, Yang Zhang, Robyn Kaake, Noah Ollikainen, Hannes Braberg, Danielle L Swaney, David G Lambright, Mark J S Kelly, Nevan J Krogan, Tanja Kortemme.
      Molecular switch proteins whose cycling between states is controlled by opposing regulators1,2 are central to biological signal transduction. As switch proteins function within highly connected interaction networks3, the fundamental question arises of how functional specificity is achieved when different processes share common regulators. Here we show that functional specificity of the small GTPase switch protein Gsp1 in Saccharomyces cerevisiae (the homologue of the human protein RAN)4 is linked to differential sensitivity of biological processes to different kinetics of the Gsp1 (RAN) switch cycle. We make 55 targeted point mutations to individual protein interaction interfaces of Gsp1 (RAN) and show through quantitative genetic5 and physical interaction mapping that Gsp1 (RAN) interface perturbations have widespread cellular consequences. Contrary to expectation, the cellular effects of the interface mutations group by their biophysical effects on kinetic parameters of the GTPase switch cycle and not by the targeted interfaces. Instead, we show that interface mutations allosterically tune the GTPase cycle kinetics. These results suggest a model in which protein partner binding, or post-translational modifications at distal sites, could act as allosteric regulators of GTPase switching. Similar mechanisms may underlie regulation by other GTPases, and other biological switches. Furthermore, our integrative platform to determine the quantitative consequences of molecular perturbations may help to explain the effects of disease mutations that target central molecular switches.
    DOI:  https://doi.org/10.1038/s41586-021-03982-6
  14. Cell Syst. 2021 Oct 05. pii: S2405-4712(21)00339-2. [Epub ahead of print]
    Noise distorts the epigenetic landscape and shapes cell-fate decisions.
    Megan A Coomer, Lucy Ham, Michael P H Stumpf.
      The Waddington epigenetic landscape has become an iconic representation of the cellular differentiation process. Recent single-cell transcriptomic data provide new opportunities for quantifying this originally conceptual tool, offering insight into the gene regulatory networks underlying cellular development. While many methods for constructing the landscape have been proposed, by far the most commonly employed approach is based on computing the landscape as the negative logarithm of the steady-state probability distribution. Here, we use simple models to highlight the complexities and limitations that arise when reconstructing the potential landscape in the presence of stochastic fluctuations. We consider how the landscape changes in accordance with different stochastic systems and show that it is the subtle interplay between the deterministic and stochastic components of the system that ultimately shapes the landscape. We further discuss how the presence of noise has important implications for the identifiability of the regulatory dynamics from experimental data. A record of this paper's transparent peer review process is included in the supplemental information.
    Keywords:  additive noise; bifurcations; developmental dynamics; epigenentic landscape; multiplicative noise; potential; stochastic dynamical systems
    DOI:  https://doi.org/10.1016/j.cels.2021.09.002
  15. Nucleic Acids Res. 2021 Oct 11. pii: gkab897. [Epub ahead of print]
    CeDR Atlas: a knowledgebase of cellular drug response.
    Yin-Ying Wang, Hongen Kang, Tianyi Xu, Lili Hao, Yiming Bao, Peilin Jia.
      Drug response to many diseases varies dramatically due to the complex genomics and functional features and contexts. Cellular diversity of human tissues, especially tumors, is one of the major contributing factors to the different drug response in different samples. With the accumulation of single-cell RNA sequencing (scRNA-seq) data, it is now possible to study the drug response to different treatments at the single cell resolution. Here, we present CeDR Atlas (available at https://ngdc.cncb.ac.cn/cedr), a knowledgebase reporting computational inference of cellular drug response for hundreds of cell types from various tissues. We took advantage of the high-throughput profiling of drug-induced gene expression available through the Connectivity Map resource (CMap) as well as hundreds of scRNA-seq data covering cells from a wide variety of organs/tissues, diseases, and conditions. Currently, CeDR maintains the results for more than 582 single cell data objects for human, mouse and cell lines, including about 140 phenotypes and 1250 tissue-cell combination types. All the results can be explored and searched by keywords for drugs, cell types, tissues, diseases, and signature genes. Overall, CeDR fine maps drug response at cellular resolution and sheds lights on the design of combinatorial treatments, drug resistance and even drug side effects.
    DOI:  https://doi.org/10.1093/nar/gkab897
  16. Cell. 2021 Oct 09. pii: S0092-8674(21)01065-5. [Epub ahead of print]
    Enhanced prime editing systems by manipulating cellular determinants of editing outcomes.
    Peter J Chen, Jeffrey A Hussmann, Jun Yan, Friederike Knipping, Purnima Ravisankar, Pin-Fang Chen, Cidi Chen, James W Nelson, Gregory A Newby, Mustafa Sahin, Mark J Osborn, Jonathan S Weissman, Britt Adamson, David R Liu.
      While prime editing enables precise sequence changes in DNA, cellular determinants of prime editing remain poorly understood. Using pooled CRISPRi screens, we discovered that DNA mismatch repair (MMR) impedes prime editing and promotes undesired indel byproducts. We developed PE4 and PE5 prime editing systems in which transient expression of an engineered MMR-inhibiting protein enhances the efficiency of substitution, small insertion, and small deletion prime edits by an average 7.7-fold and 2.0-fold compared to PE2 and PE3 systems, respectively, while improving edit/indel ratios by 3.4-fold in MMR-proficient cell types. Strategic installation of silent mutations near the intended edit can enhance prime editing outcomes by evading MMR. Prime editor protein optimization resulted in a PEmax architecture that enhances editing efficacy by 2.8-fold on average in HeLa cells. These findings enrich our understanding of prime editing and establish prime editing systems that show substantial improvement across 191 edits in seven mammalian cell types.
    Keywords:  CRISPR-Cas9; Repair-seq; genome editing; mismatch repair; prime editing
    DOI:  https://doi.org/10.1016/j.cell.2021.09.018
  17. iScience. 2021 Oct 22. 24(10): 103149
    Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas.
    Udit Parekh, Daniella McDonald, Amir Dailamy, Yan Wu, Thekla Cordes, Kun Zhang, Ann Tipps, Christian Metallo, Prashant Mali.
      Deconstructing tissue-specific effects of genes and variants on proliferation is critical to understanding cellular transformation and systematically selecting cancer therapeutics. This requires scalable methods for multiplexed genetic screens tracking fitness across time, across lineages, and in a suitable niche, since physiological cues influence functional differences. Towards this, we present an approach, coupling single-cell cancer driver screens in teratomas with hit enrichment by serial teratoma reinjection, to simultaneously screen drivers across multiple lineages in vivo. Using this system, we analyzed population shifts and lineage-specific enrichment for 51 cancer associated genes and variants, profiling over 100,000 cells spanning over 20 lineages, across two rounds of serial reinjection. We confirmed that c-MYC alone or combined with myristoylated AKT1 potently drives proliferation in progenitor neural lineages, demonstrating signatures of malignancy. Additionally, mutant MEK1 S218D/S222D provides a proliferative advantage in mesenchymal lineages like fibroblasts. Our method provides a powerful platform for multi-lineage longitudinal study of oncogenesis.
    Keywords:  Molecular biology; Systems biology; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2021.103149
  18. Nat Commun. 2021 Oct 14. 12(1): 6012
    Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions.
    Alma Andersson, Ludvig Larsson, Linnea Stenbeck, Fredrik Salmén, Anna Ehinger, Sunny Z Wu, Ghamdan Al-Eryani, Daniel Roden, Alex Swarbrick, Åke Borg, Jonas Frisén, Camilla Engblom, Joakim Lundeberg.
      In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra- and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. By integration with single cell data, we spatially map tumor-associated cell types to find tertiary lymphoid-like structures, and a type I interferon response overlapping with regions of T-cell and macrophage subset colocalization. We construct a predictive model to infer presence of tertiary lymphoid-like structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define a high resolution map of cellular interactions in tumors and provide tools generalizing across tissues and diseases.
    DOI:  https://doi.org/10.1038/s41467-021-26271-2
  19. Science. 2021 Oct 15. 374(6565): 263-264
    A cell cycle regulator branches out.
    Robert P Fisher.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/science.abm2010
  20. J Clin Invest. 2021 Oct 15. pii: e155208. [Epub ahead of print]131(20):
    mTOR-dependent translation amplifies microglia priming in aging mice.
    Lily Keane, Ignazio Antignano, Sean-Patrick Riechers, Raphael Zollinger, Anaelle A Dumas, Nina Offermann, Maria E Bernis, Jenny Russ, Frederike Graelmann, Patrick Neil McCormick, Julia Esser, Dario Tejera, Ai Nagano, Jun Wang, Claude Chelala, Yvonne Biederbick, Annett Halle, Paolo Salomoni, Michael T Heneka, Melania Capasso.
      
    DOI:  https://doi.org/10.1172/JCI155208
  21. Mol Cell. 2021 Oct 05. pii: S1097-2765(21)00775-9. [Epub ahead of print]
    Gene bookmarking by the heat shock transcription factor programs the insulin-like signaling pathway.
    Srijit Das, Sehee Min, Veena Prahlad.
      Maternal stress can have long-lasting epigenetic effects on offspring. To examine how epigenetic changes are triggered by stress, we examined the effects of activating the universal stress-responsive heat shock transcription factor HSF-1 in the germline of Caenorhabditis elegans. We show that, when activated in germ cells, HSF-1 recruits MET-2, the putative histone 3 lysine 9 (H3K9) methyltransferase responsible for repressive H3K9me2 (H3K9 dimethyl) marks in chromatin, and negatively bookmarks the insulin receptor daf-2 and other HSF-1 target genes. Increased H3K9me2 at these genes persists in adult progeny and shifts their stress response strategy away from inducible chaperone expression as a mechanism to survive stress and instead rely on decreased insulin/insulin growth factor (IGF-1)-like signaling (IIS). Depending on the duration of maternal heat stress exposure, this epigenetic memory is inherited by the next generation. Thus, paradoxically, HSF-1 recruits the germline machinery normally responsible for erasing transcriptional memory but, instead, establishes a heritable epigenetic memory of prior stress exposure.
    Keywords:  C. elegans; H3K9 methyltransferase; HSF1; MET-2; daf-2; epigenetic; heat shock; stress; transcriptional memory; transgenerational
    DOI:  https://doi.org/10.1016/j.molcel.2021.09.022
  22. Eur J Immunol. 2021 Oct 14.
    mTOR-dependent immunometabolism as Achilles' heel of anticancer therapy.
    Clarissa Braun, Thomas Weichhart.
      Immune cells are important constituents of the tumor microenvironment and essential in eradicating tumor cells during conventional therapies or novel immunotherapies. The mechanistic target of rapamycin (mTOR) signaling pathway senses the intra- and extracellular nutrient status, growth factor supply and cell stress-related changes to coordinate cellular metabolism and activation dictating effector and memory functions in mainly all hematopoietic immune cells. In addition, the mTOR complex 1 (mTORC1) and mTORC2 are frequently deregulated and become activated in cancer cells to drive cell transformation, survival, neovascularization, and invasion. In this review we provide an overview of the influence of mTOR complexes on immune and cancer cell function and metabolism. We discuss how mTOR inhibitors aiming to target cancer cells will influence immunometabolic cell functions participating either in anti-tumor responses or favoring tumor cell progression in individual immune cells. We suggest immunometabolism as the weak spot of anticancer therapy and propose to evaluate patients according to their predominant immune cell subtype in the cancer tissue. Advances in metabolic drug development that hold promise for more effective treatments in different types of cancer will have to consider their effects on the immune system. This article is protected by copyright. All rights reserved.
    Keywords:  Immunometabolism; cancer treatment; immunotherapy; mTORC1; tumor microenvironment
    DOI:  https://doi.org/10.1002/eji.202149270
  23. Front Physiol. 2021 ;12 730196
    The Signaling Pathways Involved in Ovarian Follicle Development.
    Liyuan Li, Xiaojin Shi, Yun Shi, Zhao Wang.
      The follicle is the functional unit of the ovary, which is composed of three types of cells: oocytes, granulosa cells, and theca cells. Ovarian follicle development and the subsequent ovulation process are coordinated by highly complex interplay between endocrine, paracrine, and autocrine signals, which coordinate steroidogenesis and gametogenesis. Follicle development is regulated mainly by three organs, the hypothalamus, anterior pituitary, and gonad, which make up the hypothalamic-pituitary-gonadal axis. Steroid hormones and their receptors play pivotal roles in follicle development and participate in a series of classical signaling pathways. In this review, we summarize and compare the role of classical signaling pathways, such as the WNT, insulin, Notch, and Hedgehog pathways, in ovarian follicle development and the underlying regulatory mechanism. We have also found that these four signaling pathways all interact with FOXO3, a transcription factor that is widely known to be under control of the PI3K/AKT signaling pathway and has been implicated as a major signaling pathway in the regulation of dormancy and initial follicular activation in the ovary. Although some of these interactions with FOXO3 have not been verified in ovarian follicle cells, there is a high possibility that FOXO3 plays a core role in follicular development and is regulated by classical signaling pathways. In this review, we present these signaling pathways from a comprehensive perspective to obtain a better understanding of the follicular development process.
    Keywords:  Hedgehog signaling; Notch signaling; PI3K-AKT signaling; WNT signaling; follicular development; insulin signaling
    DOI:  https://doi.org/10.3389/fphys.2021.730196
  24. Nat Commun. 2021 Oct 13. 12(1): 5961
    Cancer gene mutation frequencies for the U.S. population.
    Gaurav Mendiratta, Eugene Ke, Meraj Aziz, David Liarakos, Melinda Tong, Edward C Stites.
      Mutations play a fundamental role in the development of cancer, and many create targetable vulnerabilities. There are both public health and basic science benefits from the determination of the proportion of all cancer cases within a population that include a mutant form of a gene. Here, we provide the first such estimates by combining genomic and epidemiological data. We estimate KRAS is mutated in only 11% of all cancers, which is less than PIK3CA (13%) and marginally higher than BRAF (8%). TP53 is the most commonly mutated gene (35%), and KMT2C, KMT2D, and ARID1A are among the ten most commonly mutated driver genes, highlighting the role of epigenetic dysregulation in cancer. Analysis of major cancer subclassifications highlighted varying dependencies upon individual cancer drivers. Overall, we find that cancer genetics is less dominated by high-frequency, high-profile cancer driver genes than studies limited to a subset of cancer types have suggested.
    DOI:  https://doi.org/10.1038/s41467-021-26213-y
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