bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2022–10–09
23 papers selected by
Ralitsa Radostinova Madsen, University College London
  1. Computational Modeling Implicates Protein Scaffolding in p38 Regulation of Akt.
  2. PI3K-AKT Inhibits PANK4 to Promote De Novo Synthesis of Coenzyme A.
  3. Deletion of skeletal muscle Akt1/2 causes osteosarcopenia and reduces lifespan in mice.
  4. E2F1 transcription factor mediates a link between fat and islets to promote β cell proliferation in response to acute insulin resistance.
  5. Novel Allosteric Inhibitor-Derived AKT Proteolysis Targeting Chimeras (PROTACs) Enable Potent and Selective AKT Degradation in KRAS/BRAF Mutant Cells.
  6. BTK kinase activity is dispensable for the survival of diffuse large B-cell lymphoma.
  7. Spatiotemporal dynamics of membrane surface charge regulates cell polarity and migration.
  8. Linear ubiquitination of PTEN impairs its function to promote prostate cancer progression.
  9. ChemPert: mapping between chemical perturbation and transcriptional response for non-cancer cells.
  10. Common anti-cancer therapies induce somatic mutations in stem cells of healthy tissue.
  11. Tissue-specific impacts of aging and genetics on gene expression patterns in humans.
  12. The initiation of mammalian embryonic transcription: to begin at the beginning.
  13. Marker-free co-selection for successive rounds of prime editing in human cells.
  14. Two independent respiratory chains adapt OXPHOS performance to glycolytic switch.
  15. Non-genomic activation of the AKT-mTOR pathway by the mitochondrial stress response in thyroid cancer.
  16. S6K1 phosphorylates Cdk1 and MSH6 to regulate DNA repair.
  17. Lipid Expansion Microscopy.
  18. Comparative kinase and cancer cell panel profiling of kinase inhibitors approved for clinical use from 2018 to 2020.
  19. EmAtlas: a comprehensive atlas for exploring spatiotemporal activation in mammalian embryogenesis.
  20. A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses.
  21. BIONIC: discovering new biology through deep learning-based network integration.
  22. Functional inference of gene regulation using single-cell multi-omics.
  23. GIGYF1-disturbed IGF-1R recycling: a potential contributor to autism spectrum disorder pathogenesis?
  1. J Theor Biol. 2022 Oct 01. pii: S0022-5193(22)00285-5. [Epub ahead of print] 111294
    Computational Modeling Implicates Protein Scaffolding in p38 Regulation of Akt.
    Patrick C Kinnunen, Gary D Luker, Kathryn E Luker, Jennifer J Linderman.
      Cells process environmental cues by activating intracellular signaling pathways with numerous interconnections and opportunities for cross-regulation. We employed a systems biology approach to investigate intersections of kinase p38, a context-dependent tumor suppressor or promoter, with Akt and ERK, two kinases known to promote cell survival, proliferation, and drug resistance in cancer. Using live, single cell microscopy, multiplexed fluorescent reporters of p38, Akt, and ERK activities, and a custom automated image-processing pipeline, we detected marked heterogeneity of signaling outputs in breast cancer cells stimulated with chemokine CXCL12 or epidermal growth factor (EGF). Basal activity of p38 correlated inversely with amplitude of Akt and ERK activation in response to either ligand. Remarkably, small molecule inhibitors of p38 immediately decreased basal activities of Akt and ERK but increased the proportion of cells with high amplitude ligand-induced activation of Akt signaling. To identify mechanisms underlying cross-talk of p38 with Akt signaling, we developed a computational model with subcellular compartmentalization of signaling molecules by scaffold proteins. Dynamics of this model revealed that subcellular scaffolding of Akt accounted for observed regulation by p38. The model also predicted that differences in the amount of scaffold protein in a subcellular compartment captured the observed single cell heterogeneity in signaling. Finally, our model predicted that reduction in kinase signaling can be accomplished by both scaffolding and direct kinase inhibition. However, scaffolding inhibition can potentiate future kinase activity by redistribution of pathway components, potentially amplifying oncogenic signaling. These studies reveal how computational modeling can decipher mechanisms of cross-talk between the p38 and Akt signaling pathways and point to scaffold proteins as central regulators of signaling dynamics and amplitude.
    Keywords:  Single cell analysis; cell signaling; compartmentalization; live-cell imaging; scaffolding; signaling kinetics
    DOI:  https://doi.org/10.1016/j.jtbi.2022.111294
  2. Cancer Discov. 2022 Oct 05. 12(10): 2229
    PI3K-AKT Inhibits PANK4 to Promote De Novo Synthesis of Coenzyme A.
      AKT inhibits the metabolic enzyme PANK4 to promote the de novo synthesis of coenzyme A (CoA).
    DOI:  https://doi.org/10.1158/2159-8290.CD-RW2022-0140
  3. Nat Commun. 2022 Oct 05. 13(1): 5655
    Deletion of skeletal muscle Akt1/2 causes osteosarcopenia and reduces lifespan in mice.
    Takayoshi Sasako, Toshihiro Umehara, Kotaro Soeda, Kazuma Kaneko, Miho Suzuki, Naoki Kobayashi, Yukiko Okazaki, Miwa Tamura-Nakano, Tomoki Chiba, Domenico Accili, C Ronald Kahn, Tetsuo Noda, Hiroshi Asahara, Toshimasa Yamauchi, Takashi Kadowaki, Kohjiro Ueki.
      Aging is considered to be accelerated by insulin signaling in lower organisms, but it remained unclear whether this could hold true for mammals. Here we show that mice with skeletal muscle-specific double knockout of Akt1/2, key downstream molecules of insulin signaling, serve as a model of premature sarcopenia with insulin resistance. The knockout mice exhibit a progressive reduction in skeletal muscle mass, impairment of motor function and systemic insulin sensitivity. They also show osteopenia, and reduced lifespan largely due to death from debilitation on normal chow and death from tumor on high-fat diet. These phenotypes are almost reversed by additional knocking out of Foxo1/4, but only partially by additional knocking out of Tsc2 to activate the mTOR pathway. Overall, our data suggest that, unlike in lower organisms, suppression of Akt activity in skeletal muscle of mammals associated with insulin resistance and aging could accelerate osteosarcopenia and consequently reduce lifespan.
    DOI:  https://doi.org/10.1038/s41467-022-33008-2
  4. Cell Rep. 2022 Oct 04. pii: S2211-1247(22)01277-3. [Epub ahead of print]41(1): 111436
    E2F1 transcription factor mediates a link between fat and islets to promote β cell proliferation in response to acute insulin resistance.
    Jun Shirakawa, Yu Togashi, Giorgio Basile, Tomoko Okuyama, Ryota Inoue, Megan Fernandez, Mayu Kyohara, Dario F De Jesus, Nozomi Goto, Wei Zhang, Takahiro Tsuno, Tatsuya Kin, Hui Pan, Jonathan M Dreyfuss, A M James Shapiro, Peng Yi, Yasuo Terauchi, Rohit N Kulkarni.
      Prevention or amelioration of declining β cell mass is a potential strategy to cure diabetes. Here, we report the pathways utilized by β cells to robustly replicate in response to acute insulin resistance induced by S961, a pharmacological insulin receptor antagonist. Interestingly, pathways that include CENP-A and the transcription factor E2F1 that are independent of insulin signaling and its substrates appeared to mediate S961-induced β cell multiplication. Consistently, pharmacological inhibition of E2F1 blocks β-cell proliferation in S961-injected mice. Serum from S961-treated mice recapitulates replication of β cells in mouse and human islets in an E2F1-dependent manner. Co-culture of islets with adipocytes isolated from S961-treated mice enables β cells to duplicate, while E2F1 inhibition limits their growth even in the presence of adipocytes. These data suggest insulin resistance-induced proliferative signals from adipocytes activate E2F1, a potential therapeutic target, to promote β cell compensation.
    Keywords:  CP: Metabolism; E2F1; acute insulin resistance; adipocytes; compensation; human beta cells; insulin receptor; inter-organ communication; transcription factor; β cell proliferation
    DOI:  https://doi.org/10.1016/j.celrep.2022.111436
  5. J Med Chem. 2022 Oct 05.
    Novel Allosteric Inhibitor-Derived AKT Proteolysis Targeting Chimeras (PROTACs) Enable Potent and Selective AKT Degradation in KRAS/BRAF Mutant Cells.
    Xufen Yu, Jia Xu, Kaitlyn M Cahuzac, Ling Xie, Yudao Shen, Xian Chen, Jing Liu, Ramon E Parsons, Jian Jin.
      AKT is an important target for cancer therapeutics. Significant advancements have been made in developing ATP-competitive and allosteric AKT inhibitors. Recently, several AKT proteolysis targeting chimeras (PROTACs) derived from ATP-competitive AKT inhibitors have been reported, including MS21. While MS21 potently degraded AKT and inhibited the growth in tumor cells harboring PI3K/PTEN pathway mutation, it was largely ineffective in degrading AKT in KRAS/BRAF mutated cells as a single agent. To overcome the AKT degradation resistance in KRAS/BRAF mutated cells, we developed novel AKT PROTACs derived from an AKT allosteric inhibitor, including degrader 62 (MS15). 62 displayed potent and selective AKT degradation activity and potent antiproliferative activity in KRAS/BRAF mutated cancer cells, in addition to PI3K/PTEN mutated cancer cells. Furthermore, 62 was bioavailable in mice through intraperitoneal administration. Overall, 62 is a valuable chemical tool to degrade AKT in cells harboring KRAS/BRAF mutation and expands the tool box for pharmacologically modulating AKT.
    DOI:  https://doi.org/10.1021/acs.jmedchem.2c01454
  6. J Biol Chem. 2022 Sep 29. pii: S0021-9258(22)00999-1. [Epub ahead of print] 102555
    BTK kinase activity is dispensable for the survival of diffuse large B-cell lymphoma.
    Hongwei Yuan, Yutong Zhu, Yalong Cheng, Junjie Hou, Fengjiao Jin, Menglin Li, Wei Jia, Zhenzhen Cheng, Haimei Xing, Mike Liu, Ting Han.
      Inhibitors targeting Bruton's tyrosine kinase (BTK) have revolutionized the treatment for various B cell malignancies but are limited by acquired resistance after prolonged treatment as a result of mutations in BTK. Here, by a combination of structural modeling, in vitro assays, and deep phospho-tyrosine proteomics, we demonstrated that four clinically observed BTK mutations-C481F, C481Y, C481R, and L528W-inactivated BTK kinase activity both in vitro and in diffuse large B-cell lymphoma (DLBCL) cells. Paradoxically, we found that DLBCL cells harboring kinase-inactive BTK exhibited intact B cell receptor (BCR) signaling, unperturbed transcription, and optimal cellular growth. Moreover, we determined that DLBCL cells with kinase-inactive BTK remained addicted to BCR signaling and were thus sensitive to targeted BTK degradation by the proteolysis targeting chimera (PROTAC). By performing parallel genome-wide CRISPR-Cas9 screening in DLBCL cells with wild-type or kinase-inactive BTK, we discovered that DLBCL cells with kinase-inactive BTK displayed increased dependence on Toll-like receptor 9 (TLR9) for their growth and/or survival. Our study demonstrates that the kinase activity of BTK is not essential for oncogenic BCR signaling and suggests that BTK's non-catalytic function is sufficient to sustain the survival of diffuse large B-cell lymphoma.
    Keywords:  DLBCL; Kinase-inactive BTK; PROTAC; Phospho-tyrosine proteomics; TLR9
    DOI:  https://doi.org/10.1016/j.jbc.2022.102555
  7. Nat Cell Biol. 2022 Oct 06.
    Spatiotemporal dynamics of membrane surface charge regulates cell polarity and migration.
    Tatsat Banerjee, Debojyoti Biswas, Dhiman Sankar Pal, Yuchuan Miao, Pablo A Iglesias, Peter N Devreotes.
      During cell migration and polarization, numerous signal transduction and cytoskeletal components self-organize to generate localized protrusions. Although biochemical and genetic analyses have delineated many specific interactions, how the activation and localization of so many different molecules are spatiotemporally orchestrated at the subcellular level has remained unclear. Here we show that the regulation of negative surface charge on the inner leaflet of the plasma membrane plays an integrative role in the molecular interactions. Surface charge, or zeta potential, is transiently lowered at new protrusions and within cortical waves of Ras/PI3K/TORC2/F-actin network activation. Rapid alterations of inner leaflet anionic phospholipids-such as PI(4,5)P2, PI(3,4)P2, phosphatidylserine and phosphatidic acid-collectively contribute to the surface charge changes. Abruptly reducing the surface charge by recruiting positively charged optogenetic actuators was sufficient to trigger the entire biochemical network, initiate de novo protrusions and abrogate pre-existing polarity. These effects were blocked by genetic or pharmacological inhibition of key signalling components such as AKT and PI3K/TORC2. Conversely, increasing the negative surface charge deactivated the network and locally suppressed chemoattractant-induced protrusions or subverted EGF-induced ERK activation. Computational simulations involving excitable biochemical networks demonstrated that slight changes in feedback loops, induced by recruitment of the charged actuators, could lead to outsized effects on system activation. We propose that key signalling network components act on, and are in turn acted upon, by surface charge, closing feedback loops, which bring about the global-scale molecular self-organization required for spontaneous protrusion formation, cell migration and polarity establishment.
    DOI:  https://doi.org/10.1038/s41556-022-00997-7
  8. Oncogene. 2022 Oct 03.
    Linear ubiquitination of PTEN impairs its function to promote prostate cancer progression.
    Yanmin Guo, Jianfeng He, Hailong Zhang, Ran Chen, Lian Li, Xiaojia Liu, Caihu Huang, Zhe Qiang, Zihan Zhou, Yanli Wang, Jian Huang, Xian Zhao, Junke Zheng, Guo-Qiang Chen, Jianxiu Yu.
      PTEN is frequently mutated in human cancers, which leads to the excessive activation of PI3K/AKT signaling and thus promotes tumorigenesis and drug resistance. Met1-linked ubiquitination (M1-Ubi) is also involved in cancer progression, but the mechanism is poorly defined. Here we find that HOIP, one important component of linear ubiquitin chain assembly complex (LUBAC), promotes prostate cancer (PCa) progression by enhancing AKT signaling in a PTEN-dependent manner. Mechanistically, PTEN is modified by M1-Ubi at two sites K144 and K197, which significantly inhibits PTEN phosphatase activity and thus accelerates PCa progression. More importantly, we identify that the high-frequency mutants PTENR173H and PTENR173C in PCa patients showed the enhanced level of M1-Ubi, which impairs PTEN function in inhibition of AKT phosphorylation and cell growth. We also find that HOIP depletion sensitizes PCa cells to therapeutic agents BKM120 and Enzalutamide. Furthermore, the clinical data analyses confirm that HOIP is upregulated and positively correlated with AKT activation in PCa patient specimen, which may promote PCa progression and increase the risk of PCa biochemical relapse. Together, our study reveals a key role of PTEN M1-Ubi in regulation of AKT activation and PCa progression, which may propose a new strategy for PCa therapy.
    DOI:  https://doi.org/10.1038/s41388-022-02485-6
  9. Nucleic Acids Res. 2022 Oct 06. pii: gkac862. [Epub ahead of print]
    ChemPert: mapping between chemical perturbation and transcriptional response for non-cancer cells.
    Menglin Zheng, Satoshi Okawa, Miren Bravo, Fei Chen, María-Luz Martínez-Chantar, Antonio Del Sol.
      Prior knowledge of perturbation data can significantly assist in inferring the relationship between chemical perturbations and their specific transcriptional response. However, current databases mostly contain cancer cell lines, which are unsuitable for the aforementioned inference in non-cancer cells, such as cells related to non-cancer disease, immunology and aging. Here, we present ChemPert (https://chempert.uni.lu/), a database consisting of 82 270 transcriptional signatures in response to 2566 unique perturbagens (drugs, small molecules and protein ligands) across 167 non-cancer cell types, as well as the protein targets of 57 818 perturbagens. In addition, we develop a computational tool that leverages the non-cancer cell datasets, which enables more accurate predictions of perturbation responses and drugs in non-cancer cells compared to those based onto cancer databases. In particular, ChemPert correctly predicted drug effects for treating hepatitis and novel drugs for osteoarthritis. The ChemPert web interface is user-friendly and allows easy access of the entire datasets and the computational tool, providing valuable resources for both experimental researchers who wish to find datasets relevant to their research and computational researchers who need comprehensive non-cancer perturbation transcriptomics datasets for developing novel algorithms. Overall, ChemPert will facilitate future in silico compound screening for non-cancer cells.
    DOI:  https://doi.org/10.1093/nar/gkac862
  10. Nat Commun. 2022 Oct 07. 13(1): 5915
    Common anti-cancer therapies induce somatic mutations in stem cells of healthy tissue.
    Ewart Kuijk, Onno Kranenburg, Edwin Cuppen, Arne Van Hoeck.
      Genome-wide mutation analyses have revealed that specific anti-cancer drugs are highly mutagenic to cancer cells, but the mutational impact of anti-cancer therapies on normal cells is not known. Here, we examine genome-wide somatic mutation patterns in 42 healthy adult stem cells (ASCs) of the colon or the liver from 14 cancer patients (mean of 3.2 ASC per donor) that received systemic chemotherapy and/or local radiotherapy. The platinum-based chemo-drug Oxaliplatin induces on average 535 ± 260 mutations in colon ASC, while 5-FU shows a complete mutagenic absence in most, but not all colon ASCs. In contrast with the colon, normal liver ASCs escape mutagenesis from systemic treatment with Oxaliplatin and 5-FU. Thus, while chemotherapies are highly effective at killing cancer cells, their systemic use also increases the mutational burden of long-lived normal stem cells responsible for tissue renewal thereby increasing the risk for developing second cancers.
    DOI:  https://doi.org/10.1038/s41467-022-33663-5
  11. Nat Commun. 2022 Oct 03. 13(1): 5803
    Tissue-specific impacts of aging and genetics on gene expression patterns in humans.
    Ryo Yamamoto, Ryan Chung, Juan Manuel Vazquez, Huanjie Sheng, Philippa L Steinberg, Nilah M Ioannidis, Peter H Sudmant.
      Age is the primary risk factor for many common human diseases. Here, we quantify the relative contributions of genetics and aging to gene expression patterns across 27 tissues from 948 humans. We show that the predictive power of expression quantitative trait loci is impacted by age in many tissues. Jointly modelling the contributions of age and genetics to transcript level variation we find expression heritability (h2) is consistent among tissues while the contribution of aging varies by >20-fold with [Formula: see text] in 5 tissues. We find that while the force of purifying selection is stronger on genes expressed early versus late in life (Medawar's hypothesis), several highly proliferative tissues exhibit the opposite pattern. These non-Medawarian tissues exhibit high rates of cancer and age-of-expression-associated somatic mutations. In contrast, genes under genetic control are under relaxed constraint. Together, we demonstrate the distinct roles of aging and genetics on expression phenotypes.
    DOI:  https://doi.org/10.1038/s41467-022-33509-0
  12. Trends Cell Biol. 2022 Sep 28. pii: S0962-8924(22)00211-2. [Epub ahead of print]
    The initiation of mammalian embryonic transcription: to begin at the beginning.
    Anthony C F Perry, Maki Asami, Brian Y H Lam, Giles S H Yeo.
      Gamete (sperm and oocyte) genomes are transcriptionally silent until embryonic genome activation (EGA) following fertilization. EGA in humans had been thought to occur around the eight-cell stage, but recent findings suggest that it is triggered in one-cell embryos, by fertilization. Phosphorylation and other post-translational modifications during fertilization may instate transcriptionally favorable chromatin and activate oocyte-derived transcription factors (TFs) to initiate EGA. Expressed genes lay on cancer-associated pathways and their identities predict upregulation by MYC and other cancer-associated TFs. One interpretation of this is that the onset of EGA, and the somatic cell trajectory to cancer, are mechanistically related: cancer initiates epigenetically. We describe how fertilization might be linked to the initiation of EGA and involve distinctive processes recapitulated in cancer.
    Keywords:  embryonic genome activation (EGA); fertilization; initiation of cancer; totipotency; transcription factor (TF); zygote
    DOI:  https://doi.org/10.1016/j.tcb.2022.08.008
  13. Nat Commun. 2022 Oct 07. 13(1): 5909
    Marker-free co-selection for successive rounds of prime editing in human cells.
    Sébastien Levesque, Diana Mayorga, Jean-Philippe Fiset, Claudia Goupil, Alexis Duringer, Andréanne Loiselle, Eva Bouchard, Daniel Agudelo, Yannick Doyon.
      Prime editing enables the introduction of precise point mutations, small insertions, or short deletions without requiring donor DNA templates. However, efficiency remains a key challenge in a broad range of human cell types. In this work, we design a robust co-selection strategy through coediting of the ubiquitous and essential sodium/potassium pump (Na+/K+ ATPase). We readily engineer highly modified pools of cells and clones with homozygous modifications for functional studies with minimal pegRNA optimization. This process reveals that nicking the non-edited strand stimulates multiallelic editing but often generates tandem duplications and large deletions at the target site, an outcome dictated by the relative orientation of the protospacer adjacent motifs. Our approach streamlines the production of cell lines with multiple genetic modifications to create cellular models for biological research and lays the foundation for the development of cell-type specific co-selection strategies.
    DOI:  https://doi.org/10.1038/s41467-022-33669-z
  14. Cell Metab. 2022 Sep 28. pii: S1550-4131(22)00395-3. [Epub ahead of print]
    Two independent respiratory chains adapt OXPHOS performance to glycolytic switch.
    Erika Fernández-Vizarra, Sandra López-Calcerrada, Ana Sierra-Magro, Rafael Pérez-Pérez, Luke E Formosa, Daniella H Hock, María Illescas, Ana Peñas, Michele Brischigliaro, Shujing Ding, Ian M Fearnley, Charalampos Tzoulis, Robert D S Pitceathly, Joaquín Arenas, Miguel A Martín, David A Stroud, Massimo Zeviani, Michael T Ryan, Cristina Ugalde.
      The structural and functional organization of the mitochondrial respiratory chain (MRC) remains intensely debated. Here, we show the co-existence of two separate MRC organizations in human cells and postmitotic tissues, C-MRC and S-MRC, defined by the preferential expression of three COX7A subunit isoforms, COX7A1/2 and SCAFI (COX7A2L). COX7A isoforms promote the functional reorganization of distinct co-existing MRC structures to prevent metabolic exhaustion and MRC deficiency. Notably, prevalence of each MRC organization is reversibly regulated by the activation state of the pyruvate dehydrogenase complex (PDC). Under oxidative conditions, the C-MRC is bioenergetically more efficient, whereas the S-MRC preferentially maintains oxidative phosphorylation (OXPHOS) upon metabolic rewiring toward glycolysis. We show a link between the metabolic signatures converging at the PDC and the structural and functional organization of the MRC, challenging the widespread notion of the MRC as a single functional unit and concluding that its structural heterogeneity warrants optimal adaptation to metabolic function.
    Keywords:  COX7A1–2; SCAFI/COX7RP/COX7A2L; bioenergetics; glycolysis; metabolic switch; mitochondria; oxidative metabolism; pyruvate dehydrogenase; respiratory chain organizations; respiratory supercomplexes
    DOI:  https://doi.org/10.1016/j.cmet.2022.09.005
  15. Oncogene. 2022 Oct 04.
    Non-genomic activation of the AKT-mTOR pathway by the mitochondrial stress response in thyroid cancer.
    Woo Kyung Lee Doolittle, Sunmi Park, Seul Gi Lee, Seonhyang Jeong, Gibbeum Lee, Dongryeol Ryu, Kristina Schoonjans, Johan Auwerx, Jandee Lee, Young Suk Jo.
      Cancer progression is associated with metabolic reprogramming and causes significant intracellular stress; however, the mechanisms that link cellular stress and growth signalling are not fully understood. Here, we identified a mechanism that couples the mitochondrial stress response (MSR) with tumour progression. We demonstrated that the MSR is activated in a significant proportion of human thyroid cancers via the upregulation of heat shock protein D family members and the mitokine, growth differentiation factor 15. Our study also revealed that MSR triggered AKT/S6K signalling by activating mTORC2 via activating transcription factor 4/sestrin 2 activation whilst promoting leucine transporter and nutrient-induced mTORC1 activation. Importantly, we found that an increase in mtDNA played an essential role in MSR-induced mTOR activation and that crosstalk between MYC and MSR potentiated mTOR activation. Together, these findings suggest that the MSR could be a predictive marker for aggressive human thyroid cancer as well as a useful therapeutic target.
    DOI:  https://doi.org/10.1038/s41388-022-02484-7
  16. Elife. 2022 Oct 03. pii: e79128. [Epub ahead of print]11
    S6K1 phosphorylates Cdk1 and MSH6 to regulate DNA repair.
    Adi Amar-Schwartz, Vered Ben Hur, Amina Jbara, Yuval Cohen, Georgina D Barnabas, Eliran Arbib, Zahava Siegfried, Bayan Mashahreh, Fouad Hassouna, Asaf Shilo, Mohammad Abu-Odeh, Michael Berger, Reuven Wiener, Rami Aqeilan, Tamar Geiger, Rotem Karni.
      The mTORC1 substrate, S6 Kinase 1 (S6K1), is involved in the regulation of cell growth, ribosome biogenesis, glucose homeostasis, and adipogenesis. Accumulating evidence has suggested a role for mTORC1 signaling in the DNA damage response. This is mostly based on the findings that mTORC1 inhibitors sensitized cells to DNA damage. However, a direct role of the mTORC1-S6K1 signaling pathway in DNA repair and the mechanism by which this signaling pathway regulates DNA repair is unknown. In this study, we discovered a novel role for S6K1 in regulating DNA repair through the coordinated regulation of the cell cycle, homologous recombination (HR) DNA repair (HRR) and mismatch DNA repair (MMR) mechanisms. Here, we show that S6K1 orchestrates DNA repair by phosphorylation of Cdk1 at serine 39, causing G2/M cell cycle arrest enabling homologous recombination and by phosphorylation of MSH6 at serine 309, enhancing MMR. Moreover, breast cancer cells harboring RPS6KB1 gene amplification show increased resistance to several DNA damaging agents and S6K1 expression is associated with poor survival of breast cancer patients treated with chemotherapy. Our findings reveal an unexpected function of S6K1 in the DNA repair pathway, serving as a tumorigenic barrier by safeguarding genomic stability.
    Keywords:  CDK1; DNA repair; MSH2; MSH6; S6K1; biochemistry; cancer biology; cdk1(cdc2); chemical biology; dna repair; mTORC1; msh2; msh6; s6k1
    DOI:  https://doi.org/10.7554/eLife.79128
  17. J Am Chem Soc. 2022 Oct 03.
    Lipid Expansion Microscopy.
    Brittany M White, Pratik Kumar, Amanda N Conwell, Kane Wu, Jeremy M Baskin.
      Strategies to visualize cellular membranes with light microscopy are restricted by the diffraction limit of light, which far exceeds the dimensions of lipid bilayers. Here, we describe a method for super-resolution imaging of metabolically labeled phospholipids within cellular membranes. Guided by the principles of expansion microscopy, we develop an all-small molecule approach that enables direct chemical anchoring of bioorthogonally labeled phospholipids into a hydrogel network and is capable of super-resolution imaging of cellular membranes. We apply this method, termed lipid expansion microscopy (LExM), to visualize organelle membranes with precision, including a unique class of membrane-bound structures known as nuclear invaginations. Compatible with standard confocal microscopes, LExM will be widely applicable for super-resolution imaging of phospholipids and cellular membranes in numerous physiological contexts.
    DOI:  https://doi.org/10.1021/jacs.2c03743
  18. Front Oncol. 2022 ;12 953013
    Comparative kinase and cancer cell panel profiling of kinase inhibitors approved for clinical use from 2018 to 2020.
    Jeffrey J Kooijman, Wilhelmina E van Riel, Jelle Dylus, Martine B W Prinsen, Yvonne Grobben, Tessa J J de Bitter, Antoon M van Doornmalen, Janneke J T M Melis, Joost C M Uitdehaag, Yugo Narumi, Yusuke Kawase, Jeroen A D M de Roos, Nicole Willemsen-Seegers, Guido J R Zaman.
      During the last two decades, kinase inhibitors have become the major drug class for targeted cancer therapy. Although the number of approved kinase inhibitors increases rapidly, comprehensive in vitro profiling and comparison of inhibitor activities is often lacking in the public domain. Here we report the extensive profiling and comparison of 21 kinase inhibitors approved by the FDA for oncology indications since June 2018 and 13 previously approved comparators on panels of 255 biochemical kinase assays and 134 cancer cell line viability assays. Comparison of the cellular inhibition profiles of the EGFR inhibitors gefitinib, dacomitinib, and osimertinib identified the uncommon EGFR p.G719S mutation as a common response marker for EGFR inhibitors. Additionally, the FGFR inhibitors erdafitinib, infigratinib, and pemigatinib potently inhibited the viability of cell lines which harbored oncogenic alterations in FGFR1-3, irrespective of the specific clinical indications of the FGFR inhibitors. These results underscore the utility of in vitro kinase inhibitor profiling in cells for identifying new potential stratification markers for patient selection. Furthermore, comparison of the in vitro inhibition profiles of the RET inhibitors pralsetinib and selpercatinib revealed they had very similar biochemical and cellular selectivity. As an exception, an NTRK3 fusion-positive cell line was potently inhibited by pralsetinib but not by selpercatinib, which could be explained by the targeting of TRK kinases in biochemical assays by pralsetinib but not selpercatinib. This illustrates that unexpected differences in cellular activities between inhibitors that act through the same primary target can be explained by subtle differences in biochemical targeting. Lastly, FLT3-mutant cell lines were responsive to both FLT3 inhibitors gilteritinib and midostaurin, and the PI3K inhibitor duvelisib. Biochemical profiling revealed that the FLT3 and PI3K inhibitors targeted distinct kinases, indicating that unique dependencies can be identified by combined biochemical and cellular profiling of kinase inhibitors. This study provides the first large scale kinase assay or cell panel profiling study for newly approved kinase inhibitors, and shows that comprehensive in vitro profiling of kinase inhibitors can provide rationales for therapy selection and indication expansion of approved kinase inhibitors.
    Keywords:  biochemical assay; cancer cell line; cell viability assay; drug profiling; indication expansion; kinase inhibitor
    DOI:  https://doi.org/10.3389/fonc.2022.953013
  19. Nucleic Acids Res. 2022 Oct 03. pii: gkac848. [Epub ahead of print]
    EmAtlas: a comprehensive atlas for exploring spatiotemporal activation in mammalian embryogenesis.
    Lei Zheng, Pengfei Liang, Chunshen Long, Haicheng Li, Hanshuang Li, Yuchao Liang, Xiang He, Qilemuge Xi, Yongqiang Xing, Yongchun Zuo.
      The emerging importance of embryonic development research rapidly increases the volume for a professional resource related to multi-omics data. However, the lack of global embryogenesis repository and systematic analysis tools limits the preceding in stem cell research, human congenital diseases and assisted reproduction. Here, we developed the EmAtlas, which collects the most comprehensive multi-omics data and provides multi-scale tools to explore spatiotemporal activation during mammalian embryogenesis. EmAtlas contains data on multiple types of gene expression, chromatin accessibility, DNA methylation, nucleosome occupancy, histone modifications, and transcription factors, which displays the complete spatiotemporal landscape in mouse and human across several time points, involving gametogenesis, preimplantation, even fetus and neonate, and each tissue involves various cell types. To characterize signatures involved in the tissue, cell, genome, gene and protein levels during mammalian embryogenesis, analysis tools on these five scales were developed. Additionally, we proposed EmRanger to deliver extensive development-related biological background annotations. Users can utilize these tools to analyze, browse, visualize, and download data owing to the user-friendly interface. EmAtlas is freely accessible at http://bioinfor.imu.edu.cn/ematlas.
    DOI:  https://doi.org/10.1093/nar/gkac848
  20. Commun Biol. 2022 Oct 07. 5(1): 1066
    A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses.
    Sean M Gross, Mark A Dane, Rebecca L Smith, Kaylyn L Devlin, Ian C McLean, Daniel S Derrick, Caitlin E Mills, Kartik Subramanian, Alexandra B London, Denis Torre, John Erol Evangelista, Daniel J B Clarke, Zhuorui Xie, Cemal Erdem, Nicholas Lyons, Ted Natoli, Sarah Pessa, Xiaodong Lu, James Mullahoo, Jonathan Li, Miriam Adam, Brook Wassie, Moqing Liu, David F Kilburn, Tiera A Liby, Elmar Bucher, Crystal Sanchez-Aguila, Kenneth Daily, Larsson Omberg, Yunguan Wang, Connor Jacobson, Clarence Yapp, Mirra Chung, Dusica Vidovic, Yiling Lu, Stephan Schurer, Albert Lee, Ajay Pillai, Aravind Subramanian, Malvina Papanastasiou, Ernest Fraenkel, Heidi S Feiler, Gordon B Mills, Jake D Jaffe, Avi Ma'ayan, Marc R Birtwistle, Peter K Sorger, James E Korkola, Joe W Gray, Laura M Heiser.
      The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods ( synapse.org/LINCS_MCF10A ). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes. Beyond these analyses, this dataset will serve as a resource for the broader scientific community to mine for biological insights, to compare signals carried across distinct molecular modalities, and to develop new computational methods for integrative data analysis.
    DOI:  https://doi.org/10.1038/s42003-022-03975-9
  21. Nat Methods. 2022 Oct 03.
    BIONIC: discovering new biology through deep learning-based network integration.
      
    DOI:  https://doi.org/10.1038/s41592-022-01617-w
  22. Cell Genom. 2022 Sep 14. pii: 100166. [Epub ahead of print]2(9):
    Functional inference of gene regulation using single-cell multi-omics.
    Vinay K Kartha, Fabiana M Duarte, Yan Hu, Sai Ma, Jennifer G Chew, Caleb A Lareau, Andrew Earl, Zach D Burkett, Andrew S Kohlway, Ronald Lebofsky, Jason D Buenrostro.
      Cells require coordinated control over gene expression when responding to environmental stimuli. Here we apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting and stimulated human blood cells. Collectively, we generate ~91,000 single-cell profiles, allowing us to probe the cis-regulatory landscape of the immunological response across cell types, stimuli, and time. Advancing tools to integrate multi-omics data, we develop functional inference of gene regulation (FigR), a framework to computationally pair scA-TAC-seq with scRNA-seq cells, connect distal cis-regulatory elements to genes, and infer gene-regulatory networks (GRNs) to identify candidate transcription factor (TF) regulators. Utilizing these paired multi-omics data, we define domains of regulatory chromatin (DORCs) of immune stimulation and find that cells alter chromatin accessibility and gene expression at timescales of minutes. Construction of the stimulation GRN elucidates TF activity at disease-associated DORCs. Overall, FigR enables elucidation of regulatory interactions across single-cell data, providing new opportunities to understand the function of cells within tissues.
    DOI:  https://doi.org/10.1016/j.xgen.2022.100166
  23. J Clin Invest. 2022 10 03. pii: e163553. [Epub ahead of print]132(19):
    GIGYF1-disturbed IGF-1R recycling: a potential contributor to autism spectrum disorder pathogenesis?
    Mengen Xing, Qing Zhang, Weihong Song.
      Autism spectrum disorder (ASD) is a highly variable and heritable neurodevelopmental disease (NDD) with strong genetic underpinnings. In this issue of the JCI, Chen et al. analyzed 2 previously reported, large-scale sequenced ASD cohorts and reported that GIGYF1 is the second most mutated among ASD risk genes. In this issue of the JCI, Chen et al. used a conditional mouse model combined with molecular technologies based on human genetic analyses to determine the critical role of GIGYF1 in ASD. GIGYF1-deficiency affected the recycling of IGF-1R, thereby suppressing the IGF-1R/ERK signaling pathway. Disruption of GIGYF1 in the developing mouse brain led to social deficits and cognitive impairments. These findings extend our understanding of ASD pathogenesis and provide an avenue for developing potentially effective preventions and treatments for patients with ASD.
    DOI:  https://doi.org/10.1172/JCI163553
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