bims-pimaco Biomed News
on PI3K and MAPK signalling in colorectal cancer
Issue of 2022–10–30
nineteen papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research
  1. The orchestrated signaling by PI3Kα and PTEN at the membrane interface.
  2. Sensitivities and Dependencies of BRAF Mutant Colorectal Cancer Cell Lines with or without PIK3CA Mutations for Discovery of Vulnerabilities with Therapeutic Potential.
  3. mTORC1 beyond anabolic metabolism: Regulation of cell death.
  4. Drugging KRAS: current perspectives and state-of-art review.
  5. mTOR as a Potential Target for the Treatment of Microbial Infections, Inflammatory Bowel Diseases, and Colorectal Cancer.
  6. The Next Generation of KRAS Targeting: Reasons for Excitement and Concern.
  7. New mechanistic insights into the RAS-SIN1 interaction at the membrane.
  8. A cell-based chemical-genetic screen for amino acid stress response inhibitors reveals torins reverse stress kinase GCN2 signaling.
  9. PTEN Protein Phosphatase Activity Is Not Required for Tumour Suppression in the Mouse Prostate.
  10. Non-canonical β-adrenergic activation of ERK at endosomes.
  11. Bcl-xL is a key mediator of apoptosis following KRASG12C inhibition in KRASG12C mutant colorectal cancer.
  12. Phenotypic plasticity and genetic control in colorectal cancer evolution.
  13. Mechanistic insights into cancer drug resistance through optogenetic PI3K signaling hyperactivation.
  14. FGF1 protects FGFR1-overexpressing cancer cells against drugs targeting tubulin polymerization by activating AKT via two independent mechanisms.
  15. Relating individual cell division events to single-cell ERK and Akt activity time courses.
  16. A doxycycline- and light-inducible Cre recombinase mouse model for optogenetic genome editing.
  17. Algebra, Geometry and Topology of ERK Kinetics.
  18. mTOR gets greasy: lysosomal sensing of cholesterol.
  19. The co-evolution of the genome and epigenome in colorectal cancer.
  1. Comput Struct Biotechnol J. 2022 ;20 5607-5621
    The orchestrated signaling by PI3Kα and PTEN at the membrane interface.
    Danai Maria Kotzampasi, Kyriaki Premeti, Alexandra Papafotika, Vasiliki Syropoulou, Savvas Christoforidis, Zoe Cournia, George Leondaritis.
      The oncogene PI3Kα and the tumor suppressor PTEN represent two antagonistic enzymatic activities that regulate the interconversion of the phosphoinositide lipids PI(4,5)P2 and PI(3,4,5)P3 in membranes. As such, they are defining components of phosphoinositide-based cellular signaling and membrane trafficking pathways that regulate cell survival, growth, and proliferation, and are often deregulated in cancer. In this review, we highlight aspects of PI3Kα and PTEN interplay at the intersection of signaling and membrane trafficking. We also discuss the mechanisms of PI3Kα- and PTEN- membrane interaction and catalytic activation, which are fundamental for our understanding of the structural and allosteric implications on signaling at the membrane interface and may aid current efforts in pharmacological targeting of these proteins.
    Keywords:  Allostery; Membrane trafficking; Membrane-binding; PI3Kα; PTEN; Phosphoinositides
    DOI:  https://doi.org/10.1016/j.csbj.2022.10.007
  2. Medicina (Kaunas). 2022 Oct 21. pii: 1498. [Epub ahead of print]58(10):
    Sensitivities and Dependencies of BRAF Mutant Colorectal Cancer Cell Lines with or without PIK3CA Mutations for Discovery of Vulnerabilities with Therapeutic Potential.
    Ioannis A Voutsadakis.
      Background: Colorectal cancer represents a common malignancy and remains incurable in the metastatic stage. Identification of molecular alterations that are present in colorectal cancer has led to the introduction of targeted therapies that improve outcomes. BRAF and PIK3CA mutations are observed in a subset of colorectal cancers. Colorectal cancers bearing BRAF mutations may be treated with specific BRAF inhibitors. These drugs benefit patients with BRAF mutant colorectal cancers but responses are rather brief, and progression is the rule. In contrast, no PI3K inhibitors have proven successful yet in the disease. Thus, new treatments to supplement the currently available drugs would be welcome to further improve survival. Methods: Profiled colorectal cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) were examined for BRAF and PIK3CA mutations and were interrogated for molecular characteristics and concomitant alterations that mirror clinical sample alterations. The Genomics of Drug Sensitivity in Cancer (GDSC) project was used for determination of drug sensitivities of BRAF mutated colorectal cell lines with or without concomitant PIK3CA mutations. The Cancer Dependency Map project served as the basis for identification of molecular dependencies and vulnerabilities in these cell lines. Results: CCLE includes 84 colorectal cancer cell lines, which recapitulate the molecular landscape of colorectal cancer. Of these, 23 and 24 cell lines possess BRAF and PIK3CA mutations, respectively. Seven BRAF mutant cell lines have V600E mutations and 14 PIK3CA mutant cell lines have hotspot helical or kinase domain mutations. V600E BRAF mutant cell lines with or without hotspot PIK3CA mutations are heterogeneous in their MSI status and mimic colorectal cancer tissues in other prevalent abnormalities including APC and TP53 mutations. Essential genes for survival include CTNNB1, WRN, and pyrimidine metabolism enzyme CAD. Besides BRAF mutations, BRAF inhibitor sensitivity in colorectal cancer cell lines is conferred by SACS mutations and PRKN locus loss. Conclusions: Colorectal cancer cell lines bearing the frequent BRAF and PIK3CA mutations present many alterations of the parental cancer tissue. Described vulnerabilities represent leads for therapeutic exploration in colorectal cancers with the corresponding alterations.
    Keywords:  cell line models; colon cancer; dependencies; signal transduction; targeted therapy
    DOI:  https://doi.org/10.3390/medicina58101498
  3. J Cell Biol. 2022 Dec 05. pii: e202208103. [Epub ahead of print]221(12):
    mTORC1 beyond anabolic metabolism: Regulation of cell death.
    Jiajun Zhu, Hua Wang, Xuejun Jiang.
      The mechanistic target of rapamycin complex 1 (mTORC1), a multi-subunit protein kinase complex, interrogates growth factor signaling with cellular nutrient and energy status to control metabolic homeostasis. Activation of mTORC1 promotes biosynthesis of macromolecules, including proteins, lipids, and nucleic acids, and simultaneously suppresses catabolic processes such as lysosomal degradation of self-constituents and extracellular components. Metabolic regulation has emerged as a critical determinant of various cellular death programs, including apoptosis, pyroptosis, and ferroptosis. In this article, we review the expanding knowledge on how mTORC1 coordinates metabolic pathways to impinge on cell death regulation. We focus on the current understanding on how nutrient status and cellular signaling pathways connect mTORC1 activity with ferroptosis, an iron-dependent cell death program that has been implicated in a plethora of human diseases. In-depth understanding of the principles governing the interaction between mTORC1 and cell death pathways can ultimately guide the development of novel therapies for the treatment of relevant pathological conditions.
    DOI:  https://doi.org/10.1083/jcb.202208103
  4. J Hematol Oncol. 2022 Oct 25. 15(1): 152
    Drugging KRAS: current perspectives and state-of-art review.
    Kaushal Parikh, Giuseppe Banna, Stephen V Liu, Alex Friedlaender, Aakash Desai, Vivek Subbiah, Alfredo Addeo.
      After decades of efforts, we have recently made progress into targeting KRAS mutations in several malignancies. Known as the 'holy grail' of targeted cancer therapies, KRAS is the most frequently mutated oncogene in human malignancies. Under normal conditions, KRAS shuttles between the GDP-bound 'off' state and the GTP-bound 'on' state. Mutant KRAS is constitutively activated and leads to persistent downstream signaling and oncogenesis. In 2013, improved understanding of KRAS biology and newer drug designing technologies led to the crucial discovery of a cysteine drug-binding pocket in GDP-bound mutant KRAS G12C protein. Covalent inhibitors that block mutant KRAS G12C were successfully developed and sotorasib was the first KRAS G12C inhibitor to be approved, with several more in the pipeline. Simultaneously, effects of KRAS mutations on tumour microenvironment were also discovered, partly owing to the universal use of immune checkpoint inhibitors. In this review, we discuss the discovery, biology, and function of KRAS in human malignancies. We also discuss the relationship between KRAS mutations and the tumour microenvironment, and therapeutic strategies to target KRAS. Finally, we review the current clinical evidence and ongoing clinical trials of novel agents targeting KRAS and shine light on resistance pathways known so far.
    DOI:  https://doi.org/10.1186/s13045-022-01375-4
  5. Int J Mol Sci. 2022 Oct 18. pii: 12470. [Epub ahead of print]23(20):
    mTOR as a Potential Target for the Treatment of Microbial Infections, Inflammatory Bowel Diseases, and Colorectal Cancer.
    Obaid Afzal, Abdulmalik S A Altamimi, Bismillah Mubeen, Sami I Alzarea, Waleed Hassan Almalki, Salwa D Al-Qahtani, Eman M Atiya, Fahad A Al-Abbasi, Fatima Ali, Inam Ullah, Muhammad Shahid Nadeem, Imran Kazmi.
      The mammalian target of rapamycin (mTOR) is the major controller of a number of important cellular activities, including protein synthesis, cell expansion, multiplication, autophagy, lysosomal function, and cellular metabolism. When mTOR interacts with specific adaptor proteins, it forms two complexes, mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2). The mTOR signaling system regulates gene transcription and protein manufacturing to control proliferation of cell, differentiation of immune cell, and tumor metabolism. Due to its vital role in case of microbial infections, inflammations and cancer development and progression, mTOR has been considered as a key therapeutic target for the development of targeted medication. As autophagy dysfunction is linked to changes in both innate and adaptive immune responses, bacterial clearance defects, and goblet and Paneth cell malfunction, all of these changes are linked to inflammatory bowel diseases (IBD) and colorectal cancer (CRC) pathogenesis. Preclinical and clinical data have shown that the inhibition and induction of autophagy have significant potential to be translated into the clinical applications. In IBD and several CRC models, mTORC1 inhibitors have been found effective. In the recent years, a number of novel mTOR inhibitors have been investigated in clinical trials, and a number of drugs have shown considerably enhanced efficacy when combined with mTOR inhibitors. The future developments in the mTOR targeting medications can benefit patients in individualized therapy. Advanced and innovative medicines that are more effective and have lower drug resistance are still in high demand. New findings could be relevant in medicine development, pharmacological modification, or future mTOR inhibitor research. Therefore, the goal of this review is to present a comprehensive account of current developments on the mTOR pathway and its inhibitors, with an emphasis on the management of microbial infections, the treatment of inflammatory bowel disease, and the management of colon cancer.
    Keywords:  colorectal cancer (CRC); inflammatory bowel diseases (IBD); mammalian target of rapamycin (mTOR)
    DOI:  https://doi.org/10.3390/ijms232012470
  6. Mol Cancer Ther. 2022 Oct 24. OF1-OF7
    The Next Generation of KRAS Targeting: Reasons for Excitement and Concern.
    Neal S Akhave, Amadeo B Biter, David S Hong.
      The development of selective KRASG12C inhibitors that directly inhibit KRAS, an oncogene historically thought to be "undruggable," represents a watershed moment in oncology and developmental therapeutics. Now, as KRAS-targeted therapy moves into its second phase, there is significant excitement and anticipation for durable disease control in tumor types where options remain limited, with clinical trials testing combination therapies, indirect pan-RAS/MAP kinase pathway inhibitors, and active-state RAS(on) inhibitors. However, there is also reason for caution regarding the safety and tolerability of expanded RAS inhibition. This is evidenced by the intolerability of some combination therapies with selective KRASG12C inhibitors and foreshadowed by prior failures of combination therapies in other oncogene-driven tumors. Herein, we review the landscape of and outlook for KRAS-targeted therapies. We specifically focus upon strategies to combat resistance to KRAS-targeted therapies, and discuss the possibility of off-target or unanticipated on-target effects that may limit clinical use.
    DOI:  https://doi.org/10.1158/1535-7163.MCT-22-0356
  7. Front Cell Dev Biol. 2022 ;10 987754
    New mechanistic insights into the RAS-SIN1 interaction at the membrane.
    Silke Pudewell, Jana Lissy, Hossein Nakhaeizadeh, Niloufar Mosaddeghzadeh, Saeideh Nakhaei-Rad, Radovan Dvorsky, Mohammad R Ahmadian.
      Stress-activated MAP kinase-interacting protein 1 (SIN1) is a central member of the mTORC2 complex that contains an N-terminal domain (NTD), a conserved region in the middle (CRIM), a RAS-binding domain (RBD), and a pleckstrin homology domain. Recent studies provided valuable structural and functional insights into the interactions of SIN1 and the RAS-binding domain of RAS proteins. However, the mechanism for a reciprocal interaction of the RBD-PH tandem with RAS proteins and the membrane as an upstream event to spatiotemporal mTORC2 regulation is not clear. The biochemical assays in this study led to the following results: 1) all classical RAS paralogs, including HRAS, KRAS4A, KRAS4B, and NRAS, can bind to SIN1-RBD in biophysical and SIN1 full length (FL) in cell biology experiments; 2) the SIN1-PH domain modulates interactions with various types of membrane phosphoinositides and constantly maintains a pool of SIN1 at the membrane; and 3) a KRAS4A-dependent decrease in membrane binding of the SIN1-RBD-PH tandem was observed, suggesting for the first time a mechanistic influence of KRAS4A on SIN1 membrane association. Our study strengthens the current mechanistic understanding of SIN1-RAS interaction and suggests membrane interaction as a key event in the control of mTORC2-dependent and mTORC2-independent SIN1 function.
    Keywords:  MAPKAP1; PH domain; RAS; RAS family; SIN1; mTORC2; membrane binding; ras binding domain
    DOI:  https://doi.org/10.3389/fcell.2022.987754
  8. J Biol Chem. 2022 Oct 20. pii: S0021-9258(22)01072-9. [Epub ahead of print] 102629
    A cell-based chemical-genetic screen for amino acid stress response inhibitors reveals torins reverse stress kinase GCN2 signaling.
    Johanna B Brüggenthies, Alessandra Fiore, Marion Russier, Christina Bitsina, Julian Brötzmann, Susanne Kordes, Sascha Menninger, Alexander Wolf, Elena Conti, Jan E Eickhoff, Peter J Murray.
      mTORC1 and GCN2 are serine/threonine kinases that control how cells adapt to amino acid availability. mTORC1 responds to amino acids to promote translation and cell growth while GCN2 senses limiting amino acids to hinder translation via eIF2α phosphorylation. GCN2 is an appealing target for cancer therapies because malignant cells can harness the GCN2 pathway to temper the rate of translation during rapid amino acid consumption. To isolate new GCN2 inhibitors, we created cell-based, amino acid limitation reporters via genetic manipulation of Ddit3 (encoding the transcription factor CHOP). CHOP is strongly induced by limiting amino acids and in this context, GCN2-dependent. Using leucine starvation as a model for essential amino acid sensing, we unexpectedly discovered ATP-competitive PI3 kinase-related kinase inhibitors, including ATR and mTOR inhibitors like torins, completely reversed GCN2 activation in a time-dependent way. Mechanistically, via inhibiting mTORC1-dependent translation, torins increased intracellular leucine, which was sufficient to reverse GCN2 activation and the downstream integrated stress response including stress-induced transcriptional factor ATF4 expression. Strikingly, we found that general translation inhibitors mirrored the effects of torins. Therefore, we propose that mTOR kinase inhibitors concurrently inhibit different branches of amino acid sensing by a dual mechanism involving direct inhibition of mTOR and indirect suppression of GCN2 that are connected by effects on the translation machinery. Collectively, our results highlight distinct ways of regulating GCN2 activity.
    Keywords:  GCN2; amino acid starvation; integrated stress response; mTORC1; torins
    DOI:  https://doi.org/10.1016/j.jbc.2022.102629
  9. Biomolecules. 2022 Oct 19. pii: 1511. [Epub ahead of print]12(10):
    PTEN Protein Phosphatase Activity Is Not Required for Tumour Suppression in the Mouse Prostate.
    Helen M Wise, Adam Harris, Nisha Kriplani, Adam Schofield, Helen Caldwell, Mark J Arends, Ian M Overton, Nick R Leslie.
      Loss PTEN function is one of the most common events driving aggressive prostate cancers and biochemically, PTEN is a lipid phosphatase which opposes the activation of the oncogenic PI3K-AKT signalling network. However, PTEN also has additional potential mechanisms of action, including protein phosphatase activity. Using a mutant enzyme, PTEN Y138L, which selectively lacks protein phosphatase activity, we characterised genetically modified mice lacking either the full function of PTEN in the prostate gland or only lacking protein phosphatase activity. The phenotypes of mice carrying a single allele of either wild-type Pten or PtenY138L in the prostate were similar, with common prostatic intraepithelial neoplasia (PIN) and similar gene expression profiles. However, the latter group, lacking PTEN protein phosphatase activity additionally showed lymphocyte infiltration around PIN and an increased immune cell gene expression signature. Prostate adenocarcinoma, elevated proliferation and AKT activation were only frequently observed when PTEN was fully deleted. We also identify a common gene expression signature of PTEN loss conserved in other studies (including Nkx3.1, Tnf and Cd44). We provide further insight into tumour development in the prostate driven by loss of PTEN function and show that PTEN protein phosphatase activity is not required for tumour suppression.
    Keywords:  PI 3-Kinase; PTEN; phosphatase; prostate cancer; tumour suppressor
    DOI:  https://doi.org/10.3390/biom12101511
  10. Nature. 2022 Oct 26.
    Non-canonical β-adrenergic activation of ERK at endosomes.
    Yonghoon Kwon, Sohum Mehta, Mary Clark, Geneva Walters, Yanghao Zhong, Ha Neul Lee, Roger K Sunahara, Jin Zhang.
      G-protein-coupled receptors (GPCRs), the largest family of signalling receptors, as well as important drug targets, are known to activate extracellular-signal-regulated kinase (ERK)-a master regulator of cell proliferation and survival1. However, the precise mechanisms that underlie GPCR-mediated ERK activation are not clearly understood2-4. Here we investigated how spatially organized β2-adrenergic receptor (β2AR) signalling controls ERK. Using subcellularly targeted ERK activity biosensors5, we show that β2AR signalling induces ERK activity at endosomes, but not at the plasma membrane. This pool of ERK activity depends on active, endosome-localized Gαs and requires ligand-stimulated β2AR endocytosis. We further identify an endosomally localized non-canonical signalling axis comprising Gαs, RAF and mitogen-activated protein kinase kinase, resulting in endosomal ERK activity that propagates into the nucleus. Selective inhibition of endosomal β2AR and Gαs signalling blunted nuclear ERK activity, MYC gene expression and cell proliferation. These results reveal a non-canonical mechanism for the spatial regulation of ERK through GPCR signalling and identify a functionally important endosomal signalling axis.
    DOI:  https://doi.org/10.1038/s41586-022-05343-3
  11. Mol Cancer Ther. 2022 Oct 22. pii: MCT-22-0301. [Epub ahead of print]
    Bcl-xL is a key mediator of apoptosis following KRASG12C inhibition in KRASG12C mutant colorectal cancer.
    Hajrah Khawaja, Rebecca Briggs, Cheryl H Latimer, Mustasin Rassel, Daryl Griffin, Lyndsey Hanson, Alberto Bardelli, Federica Di Nicolantonio, Simon S McDade, Christopher J Scott, Shauna Lambe, Manisha Maurya, Andreas U Lindner, Jochen Hm Prehn, Jose Sousa, Chris Winnington, Melissa J LaBonte, Sarah J Ross, Sandra Van Schaeybroeck.
      Novel covalent inhibitors of KRASG12C have shown limited response rates in KRASG12C mutant (MT) colorectal cancer (CRC) patients. Thus, novel KRASG12C inhibitor combination strategies that can achieve deep and durable responses are needed. Small molecule KRASG12C inhibitors AZ'1569 and AZ'8037 were employed. To identify novel candidate combination strategies for AZ'1569, we performed RNA sequencing, siRNA and high-throughput drug screening. Top hits were validated in a panel of KRASG12CMT CRC cells and in vivo. AZ'1569-resistant CRC cells were generated and characterised. We found that response to AZ'1569 was heterogeneous across the KRASG12CMT models. AZ'1569 was ineffective at inducing apoptosis when used as single-agent or combined with chemotherapy or agents targeting the EGFR/KRAS/AKT axis. Using a systems biology approach, we identified the anti-apoptotic BH3-family member BCL2L1/Bcl-xL as a top hit mediating resistance to AZ'1569. Further analyses identified acute increases in the pro-apoptotic protein BIM following AZ'1569 treatment. ABT-263 (Navitoclax), a pharmacological Bcl-2 family-inhibitor that blocks the ability of Bcl-xL to bind and inhibit BIM, led to dramatic and universal apoptosis when combined with AZ'1569. Furthermore, this combination also resulted in dramatically attenuated tumour growth in KRASG12CMT xenografts. Finally, AZ'1569-resistant cells showed amplification of KRASG12C, EphA2/c-MET activation, increased pro-inflammatory chemokine profile and cross-resistance to several targeted agents. Importantly, KRAS amplification and AZ'1569-resistance were reversible upon drug withdrawal, arguing strongly for the use of drug holidays in the case of KRAS amplification. Taken together, combinatorial targeting of Bcl-xL and KRASG12C is highly effective, suggesting a novel therapeutic strategy for KRAS G12CMT CRC patients.
    DOI:  https://doi.org/10.1158/1535-7163.MCT-22-0301
  12. Nature. 2022 Oct 26.
    Phenotypic plasticity and genetic control in colorectal cancer evolution.
    Jacob Househam, Timon Heide, George D Cresswell, Inmaculada Spiteri, Chris Kimberley, Luis Zapata, Claire Lynn, Chela James, Maximilian Mossner, Javier Fernandez-Mateos, Alessandro Vinceti, Ann-Marie Baker, Calum Gabbutt, Alison Berner, Melissa Schmidt, Bingjie Chen, Eszter Lakatos, Vinaya Gunasri, Daniel Nichol, Helena Costa, Miriam Mitchinson, Daniele Ramazzotti, Benjamin Werner, Francesco Iorio, Marnix Jansen, Giulio Caravagna, Chris P Barnes, Darryl Shibata, John Bridgewater, Manuel Rodriguez-Justo, Luca Magnani, Andrea Sottoriva, Trevor A Graham.
      Genetic and epigenetic variation, together with transcriptional plasticity, contribute to intratumour heterogeneity1. The interplay of these biological processes and their respective contributions to tumour evolution remain unknown. Here we show that intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer (CRC). Using spatially resolved paired whole-genome and transcriptome sequencing, we find that the majority of intratumour variation in gene expression is not strongly heritable but rather 'plastic'. Somatic expression quantitative trait loci analysis identified a number of putative genetic controls of expression by cis-acting coding and non-coding mutations, the majority of which were clonal within a tumour, alongside frequent structural alterations. Consistently, computational inference on the spatial patterning of tumour phylogenies finds that a considerable proportion of CRCs did not show evidence of subclonal selection, with only a subset of putative genetic drivers associated with subclone expansions. Spatial intermixing of clones is common, with some tumours growing exponentially and others only at the periphery. Together, our data suggest that most genetic intratumour variation in CRC has no major phenotypic consequence and that transcriptional plasticity is, instead, widespread within a tumour.
    DOI:  https://doi.org/10.1038/s41586-022-05311-x
  13. Cell Chem Biol. 2022 Oct 21. pii: S2451-9456(22)00356-7. [Epub ahead of print]
    Mechanistic insights into cancer drug resistance through optogenetic PI3K signaling hyperactivation.
    Yoshibumi Ueda, Yuri Miura, Nario Tomishige, Naotoshi Sugimoto, Megumi Murase, Genki Kawamura, Norihiko Sasaki, Toshiyuki Ishiwata, Takeaki Ozawa.
      Hyperactivation of phosphatidylinositol 3-kinase (PI3K) signaling is a prominent feature in cancer cells. However, the mechanism underlying malignant behaviors in the state remains unknown. Here, we describe a mechanism of cancer drug resistance through the protein synthesis pathway, downstream of PI3K signaling. An optogenetic tool (named PPAP2) controlling PI3K signaling was developed. Melanoma cells stably expressing PPAP2 (A375-PPAP2) acquired resistance to a cancer drug in the hyperactivation state. Proteome analyses revealed that expression of the antiapoptotic factor tumor necrosis factor alpha-induced protein 8 (TNFAIP8) was upregulated. TNFAIP8 upregulation was mediated by protein translation from preexisting mRNA. These results suggest that cancer cells escape death via upregulation of TNFAIP8 expression from preexisting mRNA even though alkylating cancer drugs damage DNA.
    Keywords:  PI3K signaling; PIP3; TNFAIP8; cancer drug resistance; optogenetics; phosphatidylinositol 3,4,5-trisphosphate
    DOI:  https://doi.org/10.1016/j.chembiol.2022.10.002
  14. Front Oncol. 2022 ;12 1011762
    FGF1 protects FGFR1-overexpressing cancer cells against drugs targeting tubulin polymerization by activating AKT via two independent mechanisms.
    Jakub Szymczyk, Martyna Sochacka, Patryk Chudy, Lukasz Opalinski, Jacek Otlewski, Malgorzata Zakrzewska.
      Cancer drug resistance is a common, unpredictable phenomenon that develops in many types of tumors, resulting in the poor efficacy of current anticancer therapies. One of the most common, and yet the most complex causes of drug resistance is a mechanism related to dysregulation of tumor cell signaling. Abnormal signal transduction in a cancer cell is often stimulated by growth factors and their receptors, including fibroblast growth factors (FGFs) and FGF receptors (FGFRs). Here, we investigated the effect of FGF1 and FGFR1 activity on the action of drugs that disrupt tubulin polymerization (taltobulin, paclitaxel, vincristine) in FGFR1-positive cell lines, U2OS stably transfected with FGFR1 (U2OSR1) and DMS114 cells. We observed that U2OSR1 cells exhibited reduced sensitivity to the tubulin-targeting drugs, compared to U2OS cells expressing a negligible level of FGFRs. This effect was dependent on receptor activation, as inhibition of FGFR1 by a specific small-molecule inhibitor (PD173074) increased the cells' sensitivity to these drugs. Expression of functional FGFR1 in U2OS cells resulted in increased AKT phosphorylation, with no change in total AKT level. U2OSR1 cells also exhibited an elevated MDR1 and blocking MDR1 activity with cyclosporin A increased the toxicity of paclitaxel and vincristine, but not taltobulin. Analysis of tubulin polymerization pattern using fluorescence microscopy revealed that FGF1 in U2OSR1 cells partially reverses the drug-altered phenotype in paclitaxel- and vincristine-treated cells, but not in taltobulin-treated cells. Furthermore, we showed that FGF1, through activation of FGFR1, reduces caspase 3/7 activity and PARP cleavage, preventing apoptosis induced by tubulin-targeting drugs. Next, using specific kinase inhibitors, we investigated which signaling pathways are responsible for the FGF1-mediated reduction of taltobulin cytotoxicity. We found that AKT kinase is a key factor in FGF1-induced cell protection against taltobulin in U2OSR1 and DMS114 cells. Interestingly, only direct inhibition of AKT or dual-inhibition of PI3K and mTOR abolished this effect for cells treated with taltobulin. This suggests that both canonical (PI3K-dependent) and alternative (PI3K-independent) AKT-activating pathways may regulate FGF1/FGFR1-driven cancer cell survival. Our findings may contribute to the development of more effective therapies and may facilitate the prevention of drug resistance in FGFR1-positive cancer cells.
    Keywords:  AKT; FGF1; FGFR1; anticancer drugs; cancer; drug resistance; taltobulin
    DOI:  https://doi.org/10.3389/fonc.2022.1011762
  15. Sci Rep. 2022 Oct 27. 12(1): 18077
    Relating individual cell division events to single-cell ERK and Akt activity time courses.
    Alan D Stern, Gregory R Smith, Luis C Santos, Deepraj Sarmah, Xiang Zhang, Xiaoming Lu, Federico Iuricich, Gaurav Pandey, Ravi Iyengar, Marc R Birtwistle.
      Biochemical correlates of stochastic single-cell fates have been elusive, even for the well-studied mammalian cell cycle. We monitored single-cell dynamics of the ERK and Akt pathways, critical cell cycle progression hubs and anti-cancer drug targets, and paired them to division events in the same single cells using the non-transformed MCF10A epithelial line. Following growth factor treatment, in cells that divide both ERK and Akt activities are significantly higher within the S-G2 time window (~ 8.5-40 h). Such differences were much smaller in the pre-S-phase, restriction point window which is traditionally associated with ERK and Akt activity dependence, suggesting unappreciated roles for ERK and Akt in S through G2. Simple metrics of central tendency in this time window are associated with subsequent cell division fates. ERK activity was more strongly associated with division fates than Akt activity, suggesting Akt activity dynamics may contribute less to the decision driving cell division in this context. We also find that ERK and Akt activities are less correlated with each other in cells that divide. Network reconstruction experiments demonstrated that this correlation behavior was likely not due to crosstalk, as ERK and Akt do not interact in this context, in contrast to other transformed cell types. Overall, our findings support roles for ERK and Akt activity throughout the cell cycle as opposed to just before the restriction point, and suggest ERK activity dynamics may be more important than Akt activity dynamics for driving cell division in this non-transformed context.
    DOI:  https://doi.org/10.1038/s41598-022-23071-6
  16. Nat Commun. 2022 Oct 28. 13(1): 6442
    A doxycycline- and light-inducible Cre recombinase mouse model for optogenetic genome editing.
    Miguel Vizoso, Colin E J Pritchard, Lorenzo Bombardelli, Bram van den Broek, Paul Krimpenfort, Roderick L Beijersbergen, Kees Jalink, Jacco van Rheenen.
      The experimental need to engineer the genome both in time and space, has led to the development of several photoactivatable Cre recombinase systems. However, the combination of inefficient and non-intentional background recombination has prevented thus far the wide application of these systems in biological and biomedical research. Here, we engineer an optimized photoactivatable Cre recombinase system that we refer to as doxycycline- and light-inducible Cre recombinase (DiLiCre). Following extensive characterization in cancer cell and organoid systems, we generate a DiLiCre mouse line, and illustrated the biological applicability of DiLiCre for light-induced mutagenesis in vivo and positional cell-tracing by intravital microscopy. These experiments illustrate how newly formed HrasV12 mutant cells follow an unnatural movement towards the interfollicular dermis. Together, we develop an efficient photoactivatable Cre recombinase mouse model and illustrate how this model is a powerful genome-editing tool for biological and biomedical research.
    DOI:  https://doi.org/10.1038/s41467-022-33863-z
  17. Bull Math Biol. 2022 Oct 23. 84(12): 137
    Algebra, Geometry and Topology of ERK Kinetics.
    Lewis Marsh, Emilie Dufresne, Helen M Byrne, Heather A Harrington.
      The MEK/ERK signalling pathway is involved in cell division, cell specialisation, survival and cell death (Shaul and Seger in Biochim Biophys Acta (BBA)-Mol Cell Res 1773(8):1213-1226, 2007). Here we study a polynomial dynamical system describing the dynamics of MEK/ERK proposed by Yeung et al. (Curr Biol 2019, https://doi.org/10.1016/j.cub.2019.12.052 ) with their experimental setup, data and known biological information. The experimental dataset is a time-course of ERK measurements in different phosphorylation states following activation of either wild-type MEK or MEK mutations associated with cancer or developmental defects. We demonstrate how methods from computational algebraic geometry, differential algebra, Bayesian statistics and computational algebraic topology can inform the model reduction, identification and parameter inference of MEK variants, respectively. Throughout, we show how this algebraic viewpoint offers a rigorous and systematic analysis of such models.
    Keywords:  Algebraic model reduction and identification; Systems biology; Topological data analysis
    DOI:  https://doi.org/10.1007/s11538-022-01088-2
  18. Cell Res. 2022 Oct 25.
    mTOR gets greasy: lysosomal sensing of cholesterol.
    Liron Bar-Peled, Dudley W Lamming.
      
    DOI:  https://doi.org/10.1038/s41422-022-00740-9
  19. Nature. 2022 Oct 26.
    The co-evolution of the genome and epigenome in colorectal cancer.
    Timon Heide, Jacob Househam, George D Cresswell, Inmaculada Spiteri, Claire Lynn, Maximilian Mossner, Chris Kimberley, Javier Fernandez-Mateos, Bingjie Chen, Luis Zapata, Chela James, Iros Barozzi, Ketevan Chkhaidze, Daniel Nichol, Vinaya Gunasri, Alison Berner, Melissa Schmidt, Eszter Lakatos, Ann-Marie Baker, Helena Costa, Miriam Mitchinson, Rocco Piazza, Marnix Jansen, Giulio Caravagna, Daniele Ramazzotti, Darryl Shibata, John Bridgewater, Manuel Rodriguez-Justo, Luca Magnani, Trevor A Graham, Andrea Sottoriva.
      Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,370 samples from 30 primary cancers and 8 concomitant adenomas and generated 1,207 chromatin accessibility profiles, 527 whole genomes and 297 whole transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent somatic chromatin accessibility alterations, including in regulatory regions of cancer driver genes that were otherwise devoid of genetic mutations. Genome-wide alterations in accessibility for transcription factor binding involved CTCF, downregulation of interferon and increased accessibility for SOX and HOX transcription factor families, suggesting the involvement of developmental genes during tumourigenesis. Somatic chromatin accessibility alterations were heritable and distinguished adenomas from cancers. Mutational signature analysis showed that the epigenome in turn influences the accumulation of DNA mutations. This study provides a map of genetic and epigenetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology.
    DOI:  https://doi.org/10.1038/s41586-022-05202-1
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