bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2022‒07‒03
eighteen papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute
  1. The mTORC1-SLC4A7 axis stimulates bicarbonate import to enhance de novo nucleotide synthesis.
  2. Lymphangiogenesis requires Ang2/Tie/PI3K signaling for VEGFR3 cell surface expression.
  3. Inhibition of lipid kinase PIKfyve reveals a role for phosphatase Inpp4b in the regulation of PI(3)P-mediated lysosome dynamics through VPS34 activity.
  4. Zonated leucine sensing by Sestrin-mTORC1 in the liver controls the response to dietary leucine.
  5. AKT inhibition associated with improved OS.
  6. Mutational landscape of pan-cancer patients with PIK3CA alterations in Chinese population.
  7. BAFFR activates PI3K/AKT signaling in human naive but not in switched memory B cells through direct interactions with B cell antigen receptors.
  8. Cystathionine-β-synthase is essential for AKT-induced senescence and suppresses the development of gastric cancers with PI3K/AKT activation.
  9. Alpelisib monotherapy for PI3K-altered, pre-treated advanced breast cancer: a phase 2 study.
  10. Acyl chain selection couples the consumption and synthesis of phosphoinositides.
  11. Genome-scale single-cell CRISPR screens.
  12. High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing.
  13. Androgens regulate tau phosphorylation through PI3K-Akt-GSK3β signaling.
  14. Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites.
  15. Systematic pan-cancer analysis of mutation-treatment interactions using large real-world clinicogenomics data.
  16. The integrated stress response remodels the microtubule organizing center to clear unfolded proteins following proteotoxic stress.
  17. Regulation of age-associated insulin resistance by MT1-MMP-mediated cleavage of insulin receptor.
  18. CDK4 is an essential insulin effector in adipocytes.
  1. Mol Cell. 2022 Jun 24. pii: S1097-2765(22)00544-5. [Epub ahead of print]
    The mTORC1-SLC4A7 axis stimulates bicarbonate import to enhance de novo nucleotide synthesis.
    Eunus S Ali, Anna Lipońska, Brendan P O'Hara, David R Amici, Michael D Torno, Peng Gao, John M Asara, Mee-Ngan F Yap, Marc L Mendillo, Issam Ben-Sahra.
      Bicarbonate (HCO3-) ions maintain pH homeostasis in eukaryotic cells and serve as a carbonyl donor to support cellular metabolism. However, whether the abundance of HCO3- is regulated or harnessed to promote cell growth is unknown. The mechanistic target of rapamycin complex 1 (mTORC1) adjusts cellular metabolism to support biomass production and cell growth. We find that mTORC1 stimulates the intracellular transport of HCO3- to promote nucleotide synthesis through the selective translational regulation of the sodium bicarbonate cotransporter SLC4A7. Downstream of mTORC1, SLC4A7 mRNA translation required the S6K-dependent phosphorylation of the translation factor eIF4B. In mTORC1-driven cells, loss of SLC4A7 resulted in reduced cell and tumor growth and decreased flux through de novo purine and pyrimidine synthesis in human cells and tumors without altering the intracellular pH. Thus, mTORC1 signaling, through the control of SLC4A7 expression, harnesses environmental bicarbonate to promote anabolic metabolism, cell biomass, and growth.
    Keywords:  SLC4A7/NBCn1; bicarbonate metabolism; mTOR signaling; purine metabolism; pyrimidine metabolism
    DOI:  https://doi.org/10.1016/j.molcel.2022.06.008
  2. J Clin Invest. 2022 Jun 28. pii: e155478. [Epub ahead of print]
    Lymphangiogenesis requires Ang2/Tie/PI3K signaling for VEGFR3 cell surface expression.
    Emilia A Korhonen, Aino Murtomäki, Sawan Kumar Jha, Andrey Anisimov, Anne Pink, Yan Zhang, Simon Stritt, Inam Liaqat, Lukas Stanczuk, Laura Alderfer, Zhiliang Sun, Emmi Kapiainen, Abhishek Singh, Ibrahim Sultan, Anni Lantta, Veli-Matti Leppänen, Lauri Eklund, Yulong He, Hellmut G Augustin, Kari Vaahtomeri, Pipsa Saharinen, Taija Mäkinen, Kari Alitalo.
      Vascular endothelial growth factor C (VEGF-C) induces lymphangiogenesis via VEGF receptor-3 (VEGFR3), encoded by the most frequently mutated gene in human primary lymphedema. Angiopoietins (Angs) and their Tie receptors regulate lymphatic vessel development and mutations of the ANGPT2 gene were recently found in human primary lymphedema. However, the mechanistic basis of Ang2 activity in lymphangiogenesis is not fully understood. Here we used gene deletion, blocking antibodies, transgene induction and gene transfer to study how Ang2, its Tie2 receptor and Tie1 regulate lymphatic vessels. We discovered that VEGF-C-induced Ang2 secretion from lymphatic endothelial cells (LECs) is involved in full Akt activation downstream of phosphoinositide-3 kinase (PI3K). Neonatal deletion of genes encoding the Tie receptors or Ang2 in LECs, or administration of Ang2 blocking antibody decreased VEGFR3 presentation on LECs and inhibited lymphangiogenesis. A similar effect was observed in LECs upon deletion of PI3K catalytic p110α subunit or with small molecule inhibition of a constitutively active PI3K located downstream of Ang2. Deletion of Tie receptors or blockade of Ang2 decreased VEGF-C-induced lymphangiogenesis also in adult mice. Our results reveal important crosstalk between the VEGF-C and Ang signaling pathways and suggest new avenues for therapeutic manipulation of lymphangiogenesis by targeting Ang2-Tie-PI3K signaling.
    Keywords:  Cardiovascular disease; Endothelial cells; Growth factors; Vascular Biology
    DOI:  https://doi.org/10.1172/JCI155478
  3. J Biol Chem. 2022 Jun 24. pii: S0021-9258(22)00629-9. [Epub ahead of print] 102187
    Inhibition of lipid kinase PIKfyve reveals a role for phosphatase Inpp4b in the regulation of PI(3)P-mediated lysosome dynamics through VPS34 activity.
    Golam T Saffi, Cheng An Wang, Emily M Mangialardi, Jean Vacher, Roberto J Botelho, Leonardo Salmena.
      Lysosome membranes contain diverse phosphoinositide (PtdIns) lipids that coordinate lysosome function and dynamics. The PtdIns repertoire on lysosomes is tightly regulated by the actions of diverse PtdIns kinases and phosphatases; however, specific roles for PtdIns in lysosomal functions and dynamics are currently unclear and require further investigation. It was previously shown that PIKfyve, a lipid kinase that synthesizes PtdIns(3,5)P2 from PtdIns(3)P, controls lysosome "fusion-fission" cycle dynamics, autophagosome turnover, and endocytic cargo delivery. Furthermore, INPP4B, a PtdIns 4-phosphatase that hydrolyzes PtdIns(3,4)P2 to form PtdIns(3)P, is emerging as a cancer-associated protein with roles in lysosomal biogenesis and other lysosomal functions. Here, we investigated the consequences of disrupting PIKfyve function in Inpp4b-deficient mouse embryonic fibroblasts. Through confocal fluorescence imaging, we observed the formation of massively enlarged lysosomes, accompanied by exacerbated reduction of endocytic trafficking, disrupted lysosome fusion-fission dynamics, and inhibition of autophagy. Finally, HPLC scintillation quantification of 3H-myo-inositol labelled phosphoinositides and phosphoinositide immunofluorescence staining, we observed that lysosomal PtdIns(3)P levels were significantly elevated in Inpp4b-deficient cells due to the hyperactivation of phosphatidylinositol 3-kinase catalytic subunit VPS34 enzymatic activity. In conclusion, our study identifies a novel signaling axis that maintains normal lysosomal homeostasis and dynamics, which includes the catalytic functions of Inpp4b, PIKfyve, and VPS34.
    Keywords:  Apilimod; Inpp4b; Lysosomes; PIKfyve; PtdIns(3)P; Vps34
    DOI:  https://doi.org/10.1016/j.jbc.2022.102187
  4. Science. 2022 Jul;377(6601): 47-56
    Zonated leucine sensing by Sestrin-mTORC1 in the liver controls the response to dietary leucine.
    Andrew L Cangelosi, Anna M Puszynska, Justin M Roberts, Andrea Armani, Thao P Nguyen, Jessica B Spinelli, Tenzin Kunchok, Brianna Wang, Sze Ham Chan, Caroline A Lewis, William C Comb, George W Bell, Aharon Helman, David M Sabatini.
      The mechanistic target of rapamycin complex 1 (mTORC1) kinase controls growth in response to nutrients, including the amino acid leucine. In cultured cells, mTORC1 senses leucine through the leucine-binding Sestrin proteins, but the physiological functions and distribution of Sestrin-mediated leucine sensing in mammals are unknown. We find that mice lacking Sestrin1 and Sestrin2 cannot inhibit mTORC1 upon dietary leucine deprivation and suffer a rapid loss of white adipose tissue (WAT) and muscle. The WAT loss is driven by aberrant mTORC1 activity and fibroblast growth factor 21 (FGF21) production in the liver. Sestrin expression in the liver lobule is zonated, accounting for zone-specific regulation of mTORC1 activity and FGF21 induction by leucine. These results establish the mammalian Sestrins as physiological leucine sensors and reveal a spatial organization to nutrient sensing by the mTORC1 pathway.
    DOI:  https://doi.org/10.1126/science.abi9547
  5. Nat Rev Clin Oncol. 2022 Jul 01.
    AKT inhibition associated with improved OS.
    David Killock.
      
    DOI:  https://doi.org/10.1038/s41571-022-00662-w
  6. BMC Med Genomics. 2022 Jul 01. 15(1): 146
    Mutational landscape of pan-cancer patients with PIK3CA alterations in Chinese population.
    Qingfeng Huang, Yang Zhou, Bowen Wang, Yi Zhao, Fengxia Zhang, Bowen Ding.
      PURPOSE: To analyze the mutational landscape of pan-cancer patients with PIK3CA mutations in Chinese population in real-world.METHODS: We analyzed PIK3CA mutation status in sequencing data of cell-free DNA from plasma and genomic DNA from matched peripheral blood lymphocyte in 11,904 Chinese pan-cancer patients, and compared them with genomic data from the Catalogue of Somatic Mutations in Cancer (COSMIC) database. Besides, concomitant genomic aberrations in PIK3CA-mutated samples were detected to investigate cancer driver genes, as well as their enriched pathways. Meanwhile, the mutations of Alpelisib targeting genes were screened and their co-alterations were analyzed according to OncoKB definition to identify the potential actionable ones.
    RESULTS: The proportion of patients with PIK3CA mutations varied among 21 types of cancer, with the top being BRCA, CESC, SCL, and UCEC. The most common PIK3CA mutation hotspots were found to be E545K, E542K and H1047R. The Chinese cohort had significantly lower frequencies of PIK3CA mutations in breast and stomach cancers, but markedly higher PIK3CA mutation frequencies in large intestine, kidney and lung cancers than the COSMIC cohort. Compared with COSMIC cohort, the mutation frequencies of Alpelisib-targeted genes in breast cancer were significantly reduced in the Chinese cohort. All PIK3CA-mutated patients had concomitant genomic aberrations. While the most common concomitant genomic alterations occurred in TP53, EGFR and FAT1, these co-mutated genes were mainly enriched in RTK/RAS pathway, PI3K pathway and P53 pathway. Moreover, 83.6% of patients carrying mutations in Alpelisib-targeted genes had at least one actionable concomitant alteration. Level 1 actionable alteration was identified in LUAD, BRCA, COAD, LUSC, READ, and STAD.
    CONCLUSION: Compared with the Western cohort, the mutation frequency of PIK3CA in breast cancer was reduced in the Chinese cohort. RTK/RAS pathway, PI3K pathway and P53 pathway were identified as the most common co-mutation pathways, suggesting that they may potentially serve as targets for possible Alpelisib-based combination therapy.
    Keywords:  Alpelisib; Chinese population; Concomitant genomic aberrations; PIK3CA mutation
    DOI:  https://doi.org/10.1186/s12920-022-01297-7
  7. Cell Rep. 2022 Jun 28. pii: S2211-1247(22)00808-7. [Epub ahead of print]39(13): 111019
    BAFFR activates PI3K/AKT signaling in human naive but not in switched memory B cells through direct interactions with B cell antigen receptors.
    Eirini Sevdali, Violeta Block, Marie Lataretu, Huiying Li, Cristian R Smulski, Jana-Susann Briem, Yannic Heitz, Beate Fischer, Neftali-Jose Ramirez, Bodo Grimbacher, Hans-Martin Jäck, Reinhard E Voll, Martin Hölzer, Pascal Schneider, Hermann Eibel.
      Binding of BAFF to BAFFR activates in mature B cells PI3K/AKT signaling regulating protein synthesis, metabolic fitness, and survival. In humans, naive and memory B cells express the same levels of BAFFR, but only memory B cells seem to survive without BAFF. Here, we show that BAFF activates PI3K/AKT only in naive B cells and changes the expression of genes regulating migration, proliferation, growth, and survival. BAFF-induced PI3K/AKT activation requires direct interactions between BAFFR and the B cell antigen receptor (BCR) components CD79A and CD79B and is enhanced by the AKT coactivator TCL1A. Compared to memory B cells, naive B cells express more surface BCRs, which interact better with BAFFR than IgG or IgA, thus allowing stronger responses to BAFF. As ablation of BAFFR in naive and memory B cells causes cell death independent of BAFF-induced signaling, BAFFR seems to act also as an intrinsic factor for B cell survival.
    Keywords:  BAFF; BAFFR; BCR; CP: Immunology; PI3K signaling; human memory B cells
    DOI:  https://doi.org/10.1016/j.celrep.2022.111019
  8. Elife. 2022 06 27. pii: e71929. [Epub ahead of print]11
    Cystathionine-β-synthase is essential for AKT-induced senescence and suppresses the development of gastric cancers with PI3K/AKT activation.
    Haoran Zhu, Keefe T Chan, Xinran Huang, Carmelo Cerra, Shaun Blake, Anna S Trigos, Dovile Anderson, Darren J Creek, David P De Souza, Xi Wang, Caiyun Fu, Metta Jana, Elaine Sanij, Richard B Pearson, Jian Kang.
      Hyperactivation of oncogenic pathways downstream of RAS and PI3K/AKT in normal cells induces a senescence-like phenotype that acts as a tumor-suppressive mechanism that must be overcome during transformation. We previously demonstrated that AKT-induced senescence (AIS) is associated with profound transcriptional and metabolic changes. Here, we demonstrate that human fibroblasts undergoing AIS display upregulated cystathionine-β-synthase (CBS) expression and enhanced uptake of exogenous cysteine, which lead to increased hydrogen sulfide (H2S) and glutathione (GSH) production, consequently protecting senescent cells from oxidative stress-induced cell death. CBS depletion allows AIS cells to escape senescence and re-enter the cell cycle, indicating the importance of CBS activity in maintaining AIS. Mechanistically, we show this restoration of proliferation is mediated through suppressing mitochondrial respiration and reactive oxygen species (ROS) production by reducing mitochondrial localized CBS while retaining antioxidant capacity of transsulfuration pathway. These findings implicate a potential tumor-suppressive role for CBS in cells with aberrant PI3K/AKT pathway activation. Consistent with this concept, in human gastric cancer cells with activated PI3K/AKT signaling, we demonstrate that CBS expression is suppressed due to promoter hypermethylation. CBS loss cooperates with activated PI3K/AKT signaling in promoting anchorage-independent growth of gastric epithelial cells, while CBS restoration suppresses the growth of gastric tumors in vivo. Taken together, we find that CBS is a novel regulator of AIS and a potential tumor suppressor in PI3K/AKT-driven gastric cancers, providing a new exploitable metabolic vulnerability in these cancers.
    Keywords:  PI3K/AKT signaling; cancer biology; cell biology; cystathionine-β-synthase; gastric cancer; glutathione; human; mouse; oxidative stress; senescence
    DOI:  https://doi.org/10.7554/eLife.71929
  9. Cancer Discov. 2022 Jun 30. pii: cd.21.1696. [Epub ahead of print]
    Alpelisib monotherapy for PI3K-altered, pre-treated advanced breast cancer: a phase 2 study.
    Peter Savas, Louisa L Lo, Stephen J Luen, Elizabeth F Blackley, Jason Callahan, Kate Moodie, Courtney T van Geelen, Yi-An Ko, Chen-Fang Weng, Lironne Wein, Maria Joao Silva, Andjelija Zivanovic Bujak, Miriam M Yeung, Sarah Ftouni, Rodney J Hicks, Prudence A Francis, Chee Khoon Lee, Sarah-Jane Dawson, Sherene Loi.
      There is limited knowledge on the benefit of the α-subunit specific PI3K inhibitor alpelisib in later lines of therapy for advanced ER+HER2- and triple negative breast cancer (TNBC). We conducted a phase 2 multi-cohort study of alpelisib monotherapy in patients with advanced PI3K pathway mutant ER+HER2- and TNBC. In the intention to treat ER+ cohort, the overall response rate was 30% and the clinical benefit rate was 36%. Decline in PI3K pathway mutant ctDNA levels from baseline to week 8 while on therapy was significantly associated with a partial response, clinical benefit and improved progression free-survival (HR 0.24 95% CI 0.083 - 0.67, P = 0.0065). Detection of ESR1 mutations at baseline in plasma was also associated with clinical benefit and improved progression free survival (HR 0.22 95% CI 0.078 - 0.60, P = 0.003).
    DOI:  https://doi.org/10.1158/2159-8290.CD-21-1696
  10. EMBO J. 2022 Jun 30. e110038
    Acyl chain selection couples the consumption and synthesis of phosphoinositides.
    David Barneda, Vishnu Janardan, Izabella Niewczas, Daniel M Collins, Sabina Cosulich, Jonathan Clark, Len R Stephens, Phillip T Hawkins.
      Phosphoinositides (PIPn) in mammalian tissues are enriched in the stearoyl/arachidonoyl acyl chain species ("C38:4"), but its functional significance is unclear. We have used metabolic tracers (isotopologues of inositol, glucose and water) to study PIPn synthesis in cell lines in which this enrichment is preserved to differing relative extents. We show that PIs synthesised from glucose are initially enriched in shorter/more saturated acyl chains, but then rapidly remodelled towards the C38:4 species. PIs are also synthesised by a distinct 're-cycling pathway', which utilises existing precursors and exhibits substantial selectivity for the synthesis of C38:4-PA and -PI. This re-cycling pathway is rapidly stimulated during receptor activation of phospholipase-C, both allowing the retention of the C38:4 backbone and the close coupling of PIPn consumption to its resynthesis, thus maintaining pool sizes. These results suggest that one property of the specific acyl chain composition of PIPn is that of a molecular code, to facilitate 'metabolic channelling' from PIP2 to PI via pools of intermediates (DG, PA and CDP-DG) common to other lipid metabolic pathways.
    Keywords:  CDP-DG; CDS; DGK; H218O; PI
    DOI:  https://doi.org/10.15252/embj.2021110038
  11. Nat Rev Genet. 2022 Jun 27.
    Genome-scale single-cell CRISPR screens.
    Lucia Brunello.
      
    DOI:  https://doi.org/10.1038/s41576-022-00517-1
  12. NPJ Breast Cancer. 2022 Jun 29. 8(1): 76
    High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing.
    Anna Kostecka, Tomasz Nowikiewicz, Paweł Olszewski, Magdalena Koczkowska, Monika Horbacz, Monika Heinzl, Maria Andreou, Renato Salazar, Theresa Mair, Piotr Madanecki, Magdalena Gucwa, Hanna Davies, Jarosław Skokowski, Patrick G Buckley, Rafał Pęksa, Ewa Śrutek, Łukasz Szylberg, Johan Hartman, Michał Jankowski, Wojciech Zegarski, Irene Tiemann-Boege, Jan P Dumanski, Arkadiusz Piotrowski.
      The mammary gland undergoes hormonally stimulated cycles of proliferation, lactation, and involution. We hypothesized that these factors increase the mutational burden in glandular tissue and may explain high cancer incidence rate in the general population, and recurrent disease. Hence, we investigated the DNA sequence variants in the normal mammary gland, tumor, and peripheral blood from 52 reportedly sporadic breast cancer patients. Targeted resequencing of 542 cancer-associated genes revealed subclonal somatic pathogenic variants of: PIK3CA, TP53, AKT1, MAP3K1, CDH1, RB1, NCOR1, MED12, CBFB, TBX3, and TSHR in the normal mammary gland at considerable allelic frequencies (9 × 10-2- 5.2 × 10-1), indicating clonal expansion. Further evaluation of the frequently damaged PIK3CA and TP53 genes by ultra-sensitive duplex sequencing demonstrated a diversified picture of multiple low-level subclonal (in 10-2-10-4 alleles) hotspot pathogenic variants. Our results raise a question about the oncogenic potential in non-tumorous mammary gland tissue of breast-conserving surgery patients.
    DOI:  https://doi.org/10.1038/s41523-022-00443-9
  13. Neuroscience. 2022 Jun 28. pii: S0306-4522(22)00335-9. [Epub ahead of print]
    Androgens regulate tau phosphorylation through PI3K-Akt-GSK3β signaling.
    Mingzhong Yao, Emily R Rosario, Jenna Carroll Soper, Christian J Pike.
      Age-related testosterone depletion in men is a risk factor for Alzheimer's disease (AD). How testosterone modulates AD risk remains to be fully elucidated, although regulation of tau phosphorylation has been suggested as a contributing protective action. To investigate the relationship between testosterone and tau phosphorylation, we first evaluated the effect of androgen status on tau phosphorylation in 3xTg-AD mice. Depletion of endogenous androgens via gonadectomy resulted in increased tau phosphorylation that was prevented by acute testosterone treatment. Parallel alterations in the phosphorylation of both GSK3β and Akt suggest possible components of the underlying signaling pathway. To further explore mechanism, primary cultured neurons were treated with a physiological concentration of testosterone or its active metabolite dihydrotestosterone (DHT). Results showed that testosterone and DHT induced significant decreases in phosphorylated tau and significant increases in phosphorylation of Akt and GSK3β. Pharmacological inhibition of phosphatidylinositol 3-kinase (PI3K) effectively inhibited androgen-induced increases in Akt and GSK3β phosphorylation, and decreases in tau phosphorylation. In addition, androgen receptor (AR) knock-down by small interfering RNA prevented androgen-induced changes in the phosphorylation of Akt, GSK3β and tau, suggesting an AR-dependent mechanism. Additional experiments demonstrated androgen-induced changes in Akt, GSK3β and tau phosphorylation in AR-expressing PC12 cells but not in AR-negative PC12 cells. Together, these results suggest an AR-dependent pathway involving PI3K-Akt-GSK3β signaling through which androgens can reduce tau phosphorylation. These findings identify an additional protective mechanism of androgens that can improve neural health and inhibit development of AD.
    Keywords:  Alzheimer’s disease; androgen receptor; glycogen synthase kinase-3β; phosphatidylinositol 3-kinase; testosterone
    DOI:  https://doi.org/10.1016/j.neuroscience.2022.06.034
  14. Nat Commun. 2022 Jun 27. 13(1): 3685
    Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites.
    Jianli Tao, Qi Wang, Carlos Mendez-Dorantes, Kathleen H Burns, Roberto Chiarle.
      CRISPR/Cas9-based genome editing has revolutionized experimental molecular biology and entered the clinical world for targeted gene therapy. Identifying DNA modifications occurring at CRISPR/Cas9 target sites is critical to determine efficiency and safety of editing tools. Here we show that insertions of LINE-1 (L1) retrotransposons can occur frequently at CRISPR/Cas9 editing sites. Together with PolyA-seq and an improved amplicon sequencing, we characterize more than 2500 de novo L1 insertions at multiple CRISPR/Cas9 editing sites in HEK293T, HeLa and U2OS cells. These L1 retrotransposition events exploit CRISPR/Cas9-induced DSB formation and require L1 RT activity. Importantly, de novo L1 insertions are rare during genome editing by prime editors (PE), cytidine or adenine base editors (CBE or ABE), consistent with their reduced DSB formation. These data demonstrate that insertions of retrotransposons might be a potential outcome of CRISPR/Cas9 genome editing and provide further evidence on the safety of different CRISPR-based editing tools.
    DOI:  https://doi.org/10.1038/s41467-022-31322-3
  15. Nat Med. 2022 Jun 30.
    Systematic pan-cancer analysis of mutation-treatment interactions using large real-world clinicogenomics data.
    Ruishan Liu, Shemra Rizzo, Sarah Waliany, Marius Rene Garmhausen, Navdeep Pal, Zhi Huang, Nayan Chaudhary, Lisa Wang, Chris Harbron, Joel Neal, Ryan Copping, James Zou.
      Quantifying the effectiveness of different cancer therapies in patients with specific tumor mutations is critical for improving patient outcomes and advancing precision medicine. Here we perform a large-scale computational analysis of 40,903 US patients with cancer who have detailed mutation profiles, treatment sequences and outcomes derived from electronic health records. We systematically identify 458 mutations that predict the survival of patients on specific immunotherapies, chemotherapy agents or targeted therapies across eight common cancer types. We further characterize mutation-mutation interactions that impact the outcomes of targeted therapies. This work demonstrates how computational analysis of large real-world data generates insights, hypotheses and resources to enable precision oncology.
    DOI:  https://doi.org/10.1038/s41591-022-01873-5
  16. Elife. 2022 Jun 27. pii: e77780. [Epub ahead of print]11
    The integrated stress response remodels the microtubule organizing center to clear unfolded proteins following proteotoxic stress.
    Brian Hurwitz, Nicola Guzzi, Anita Gola, Vincent F Fiore, Ataman Sendoel, Maria Nikolova, Douglas Barrows, Thomas S Carroll, H Amalia Pasolli, Elaine Fuchs.
      Cells encountering stressful situations activate the integrated stress response (ISR) pathway to limit protein synthesis and redirect translation to better cope. The ISR has also been implicated in cancers, but redundancies in the stress-sensing kinases that trigger the ISR have posed hurdles to dissecting physiological relevance. To overcome this challenge, we targeted the regulatory node of these kinases, namely the S51 phosphorylation site of eukaryotic translation initiation factor eIF2α and genetically replaced eIF2α with eIF2α-S51A in mouse squamous cell carcinoma (SCC) stem cells of skin. While inconsequential under normal growth conditions, the vulnerability of this ISR-null state was unveiled when SCC stem cells experienced proteotoxic stress. Seeking mechanistic insights into the protective roles of the ISR, we combined ribosome profiling and functional approaches to identify and probe the functional importance of translational differences between ISR-competent and ISR-null SCC stem cells when exposed to proteotoxic stress. In doing so, we learned that the ISR redirects translation to centrosomal proteins that orchestrate the microtubule dynamics needed to efficiently concentrate unfolded proteins at the microtubule organizing center so that they can be cleared by the perinuclear degradation machinery. Thus, rather than merely maintaining survival during proteotoxic stress, the ISR also functions in promoting cellular recovery once the stress has subsided. Remarkably, this molecular program is unique to transformed skin stem cells hence exposing a vulnerability in cancer that could be exploited therapeutically.
    Keywords:  cancer biology; cell biology; mouse
    DOI:  https://doi.org/10.7554/eLife.77780
  17. Nat Commun. 2022 Jun 29. 13(1): 3749
    Regulation of age-associated insulin resistance by MT1-MMP-mediated cleavage of insulin receptor.
    Xuanming Guo, Pallavi Asthana, Susma Gurung, Shuo Zhang, Sheung Kin Ken Wong, Samane Fallah, Chi Fung Willis Chow, Sijia Che, Lixiang Zhai, Zening Wang, Xin Ge, Zhixin Jiang, Jiayan Wu, Yijing Zhang, Xiaoyu Wu, Keyang Xu, Cheng Yuan Lin, Hiu Yee Kwan, Aiping Lyu, Zhongjun Zhou, Zhao-Xiang Bian, Hoi Leong Xavier Wong.
      Insulin sensitivity progressively declines with age. Currently, the mechanism underlying age-associated insulin resistance remains unknown. Here, we identify membrane-bound matrix metalloproteinase 14 (MT1-MMP/MMP14) as a central regulator of insulin sensitivity during ageing. Ageing promotes MMP14 activation in insulin-sensitive tissues, which cleaves Insulin Receptor to suppress insulin signaling. MT1-MMP inhibition restores Insulin Receptor expression, improving insulin sensitivity in aged mice. The cleavage of Insulin Receptor by MT1-MMP also contributes to obesity-induced insulin resistance and inhibition of MT1-MMP activities normalizes metabolic dysfunctions in diabetic mouse models. Conversely, overexpression of MT1-MMP in the liver reduces the level of Insulin Receptor, impairing hepatic insulin sensitivity in young mice. The soluble Insulin Receptor and circulating MT1-MMP are positively correlated in plasma from aged human subjects and non-human primates. Our findings provide mechanistic insights into regulation of insulin sensitivity during physiological ageing and highlight MT1-MMP as a promising target for therapeutic avenue against diabetes.
    DOI:  https://doi.org/10.1038/s41467-022-31563-2
  18. J Clin Invest. 2022 Jul 01. pii: e162359. [Epub ahead of print]132(13):
    CDK4 is an essential insulin effector in adipocytes.
    Sylviane Lagarrigue, Isabel C Lopez-Mejia, Pierre-Damien Denechaud, Xavier Escoté, Judit Castillo-Armengol, Veronica Jimenez, Carine Chavey, Albert Giralt, Qiuwen Lai, Lianjun Zhang, Laia Martinez-Carreres, Brigitte Delacuisine, Jean-Sébastien Annicotte, Emilie Blanchet, Sébastien Huré, Anna Abella, Francisco J Tinahones, Joan Vendrell, Pierre Dubus, Fatima Bosch, C Ronald Kahn, Lluis Fajas.
      
    DOI:  https://doi.org/10.1172/JCI162359
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