bims-pideca 2021-05-23 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2021–05–23
ten papers selected by
Ralitsa Radostinova Madsen, University College London

Pharmacological inhibition of PI5P4Kα/β disrupts cell energy metabolism and selectively kills p53-null tumor cells.
First Experiences with Alpelisib in Clinical Routine: Case Reports from a German Breast Center.
Conservation of metabolic regulation by phosphorylation and non-covalent small-molecule interactions.
Fructose-1,6-bisphosphate promotes PI3K and glycolysis in T cells?
Copy number aberrations drive kinase rewiring, leading to genetic vulnerabilities in cancer.
Therapeutically actionable signaling node to rescue AURKA driven loss of primary cilia in VHL-deficient cells.
Employing core regulatory circuits to define cell identity.
Analysis of genomic and non-genomic signaling of estrogen receptor in PDX models of breast cancer treated with a combination of the PI3K inhibitor alpelisib (BYL719) and fulvestrant.
The insulin receptor family and protein kinase B (Akt) are activated in the heart by alkaline pH and α1-adrenergic receptors.
Signaling levels mold the RAS mutation tropism of urethane.

Proc Natl Acad Sci U S A. 2021 May 25. pii: e2002486118. [Epub ahead of print]118(21):

Pharmacological inhibition of PI5P4Kα/β disrupts cell energy metabolism and selectively kills p53-null tumor cells.

Song Chen, Caroline Chandra Tjin, Xiang Gao, Yi Xue, Haoyan Jiao, Ruilin Zhang, Mengnan Wu, Zunyu He, Jonathan Ellman, Ya Ha.

  Most human cancer cells harbor loss-of-function mutations in the p53 tumor suppressor gene. Genetic experiments have shown that phosphatidylinositol 5-phosphate 4-kinase α and β (PI5P4Kα and PI5P4Kβ) are essential for the development of late-onset tumors in mice with germline p53 deletion, but the mechanism underlying this acquired dependence remains unclear. PI5P4K has been previously implicated in metabolic regulation. Here, we show that inhibition of PI5P4Kα/β kinase activity by a potent and selective small-molecule probe disrupts cell energy homeostasis, causing AMPK activation and mTORC1 inhibition in a variety of cell types. Feedback through the S6K/insulin receptor substrate (IRS) loop contributes to insulin hypersensitivity and enhanced PI3K signaling in terminally differentiated myotubes. Most significantly, the energy stress induced by PI5P4Kαβ inhibition is selectively toxic toward p53-null tumor cells. The chemical probe, and the structural basis for its exquisite specificity, provide a promising platform for further development, which may lead to a novel class of diabetes and cancer drugs.

Keywords:  chemical biology; lipid kinase; p53; pip4k; synthetic lethality

DOI:  https://doi.org/10.1073/pnas.2002486118
Breast Care (Basel). 2021 Apr;16(2): 129-134

First Experiences with Alpelisib in Clinical Routine: Case Reports from a German Breast Center.

Anna Hester, Franziska Henze, Christiane Travi, Nadia Harbeck, Rachel Wuerstlein.

   Introduction: The phosphatidylinositol-3-kinase (PI3K) inhibitor alpelisib is the only approved agent for treating -PIK3CA-mutated, hormone receptor-positive (HR+) human epidermal growth factor receptor 2-negative (HER2-) advanced breast cancer (ABC). Trials have reported hyperglycemia, diarrhea, and rash as the main grade 3 side effects.
Methods: In a managed access program (ClinicalTrials.gov ID: NCT03706573; start: 06/2019), 8 HR+ HER2- ABC patients with a median 4.5 prior therapy lines were treated with alpelisib at the Breast Center of the Ludwig-Maximilian University (LMU) Hospital, Munich, based on the results of a new-generation sequencing (NGS) panel and PIK3CA mutation analysis by the Molecular Tumor Board of the Comprehensive Cancer Center, Munich.
Results: Median therapy duration was 3.42 months for patients who discontinued and 3.95 months for those still on alpelisib (4 pts). Five had hyperglycemia (1 with grade 3) with fasting glucose levels of up to 450 mg/dL that required hospitalization and insulin therapy. Two experienced rash (grades 1 and 3) and 2 reported grade 3 diarrhea. Supportive therapy as well as interruption and/or dose reduction were necessary to control treatment-associated side effects.
Conclusion: Patient education and a well-trained, interdisciplinary team including diabetologists, from the initiation of alpelisib treatment onwards, are essential to safely treat ABC patients with this new drug and to maintain their quality of life and ensure their survival.

Keywords:  Alpelisib; Breast cancer; PI3K; PIK3CA; Real-world experience

DOI:  https://doi.org/10.1159/000514794
Cell Syst. 2021 May 10. pii: S2405-4712(21)00152-6. [Epub ahead of print]

Conservation of metabolic regulation by phosphorylation and non-covalent small-molecule interactions.

Christoph H Gruber, Maren Diether, Uwe Sauer.

  Here, we review extant observations of protein phosphorylation and small-molecule interactions in metabolism and ask which of their specific regulatory functions are conserved in Escherichia coli and Homo sapiens. While the number of phosphosites is dramatically higher in humans, the number of metabolite-protein interactions remains largely constant. Moreover, we found the regulatory logic of metabolite-protein interactions, and in many cases also the effector molecules, to be conserved. Post-translational regulation through phosphorylation does not appear to replace this regulation in human but rather seems to add additional opportunities for fine-tuning and more complex responses. The abundance of metabolite-protein interactions in metabolism, their conserved cross-species abundance, and the apparent conservation of regulatory logic across enormous phylogenetic distance demonstrate their relevance for maintaining cellular homeostasis in these ancient biological processes.

Keywords:  alanine cycle; cancer; cancer metabolism; isotope tracing; melanoma; metabolite exchange; metabolomics; zebrafish

DOI:  https://doi.org/10.1016/j.cels.2021.04.009
Trends Endocrinol Metab. 2021 May 18. pii: S1043-2760(21)00113-2. [Epub ahead of print]

Fructose-1,6-bisphosphate promotes PI3K and glycolysis in T cells?

Philippe Icard, Marco Alifano, Emmanuel Donnadieu, Luca Simula.

  We propose that fructose-1,6-bisphosphate (F-1,6-BP) promotes a feedback loop between phosphofructokinase-1 (PFK1), phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt), and PFK2/PFKFB3, which enhances aerobic glycolysis and sustains effector T (Teff) cell activation, while oxidative metabolism is concomitantly downregulated. This regulation, promoted by low citrate and mitochondrial ATP synthesis, also sustains the Warburg effect in cancer cells.

Keywords:  T cell; Warburg effect; cancer cell; citrate; fructose-1,6-bisphosphate; metabolism

DOI:  https://doi.org/10.1016/j.tem.2021.04.013
Cell Rep. 2021 May 18. pii: S2211-1247(21)00497-6. [Epub ahead of print]35(7): 109155

Copy number aberrations drive kinase rewiring, leading to genetic vulnerabilities in cancer.

Danish Memon, Michael B Gill, Evangelia K Papachristou, David Ochoa, Clive S D'Santos, Martin L Miller, Pedro Beltrao.

  Somatic DNA copy number variations (CNVs) are prevalent in cancer and can drive cancer progression, albeit with often uncharacterized roles in altering cell signaling states. Here, we integrate genomic and proteomic data for 5,598 tumor samples to identify CNVs leading to aberrant signal transduction. The resulting associations recapitulate known kinase-substrate relationships, and further network analysis prioritizes likely causal genes. Of the 303 significant associations we identify from the pan-tumor analysis, 43% are replicated in cancer cell lines, including 44 robust gene-phosphosite associations identified across multiple tumor types. Several predicted regulators of hippo signaling are experimentally validated. Using RNAi, CRISPR, and drug screening data, we find evidence of kinase addiction in cancer cell lines, identifying inhibitors for targeting of kinase-dependent cell lines. We propose copy number status of genes as a useful predictor of differential impact of kinase inhibition, a strategy that may be of use in the future for anticancer therapies.

Keywords:  cancer; copy number aberrations; genetic associations; kinase addiction; phospho-regulation; precision medicine

DOI:  https://doi.org/10.1016/j.celrep.2021.109155
Sci Rep. 2021 May 17. 11(1): 10461

Therapeutically actionable signaling node to rescue AURKA driven loss of primary cilia in VHL-deficient cells.

Pratim Chowdhury, Dimuthu Perera, Reid T Powell, Tia Talley, Durga Nand Tripathi, Yong Sung Park, Michael A Mancini, Peter Davies, Clifford Stephan, Cristian Corfa, Ruhee Dere.

Loss of primary cilia in cells deficient for the tumor suppressor von Hippel Lindau (VHL) arise from elevated Aurora Kinase A (AURKA) levels. VHL in its role as an E3 ubiquitin ligase targets AURKA for degradation and in the absence of VHL, high levels of AURKA result in destabilization of the primary cilium. We identified NVP-BEZ235, a dual PI3K/AKT and mTOR inhibitor, in an image-based high throughput screen, as a small molecule that restored primary cilia in VHL-deficient cells. We identified the ability of AKT to modulate AURKA expression at the transcript and protein level. Independent modulation of AKT and mTOR signaling decreased AURKA expression in cells confirming AURKA as a new signaling node downstream of the PI3K cascade. Corroborating these data, a genetic knockdown of AKT in cells deficient for VHL rescued the ability of these cells to ciliate. Finally, inhibition of AKT/mTOR using NVP-BEZ235 was efficacious in reducing tumor burden in a 786-0 xenograft model of renal cell carcinoma. These data highlight a previously unappreciated signaling node downstream of the AKT/mTOR pathway via AURKA that can be targeted in VHL-null cells to restore ciliogenesis.

DOI: https://doi.org/10.1038/s41598-021-89933-7
EMBO J. 2021 May 17. 40(10): e106785

Employing core regulatory circuits to define cell identity.

Nathalia Almeida, Matthew W H Chung, Elena M Drudi, Elise N Engquist, Eva Hamrud, Abigail Isaacson, Victoria S K Tsang, Fiona M Watt, Francesca M Spagnoli.

  The interplay between extrinsic signaling and downstream gene networks controls the establishment of cell identity during development and its maintenance in adult life. Advances in next-generation sequencing and single-cell technologies have revealed additional layers of complexity in cell identity. Here, we review our current understanding of transcription factor (TF) networks as key determinants of cell identity. We discuss the concept of the core regulatory circuit as a set of TFs and interacting factors that together define the gene expression profile of the cell. We propose the core regulatory circuit as a comprehensive conceptual framework for defining cellular identity and discuss its connections to cell function in different contexts.

Keywords:  GRN; cell identity; core regulatory circuit; regenerative medicine; transcription factor

DOI:  https://doi.org/10.15252/embj.2020106785
Breast Cancer Res. 2021 May 21. 23(1): 57

Analysis of genomic and non-genomic signaling of estrogen receptor in PDX models of breast cancer treated with a combination of the PI3K inhibitor alpelisib (BYL719) and fulvestrant.

Julien Jacquemetton, Loay Kassem, Coralie Poulard, Ahmed Dahmani, Ludmilla De Plater, Elodie Montaudon, Laura Sourd, Ludivine Morisset, Rania El Botty, Sophie Chateau-Joubert, Sophie Vacher, Ivan Bièche, Isabelle Treilleux, Olivier Trédan, Elisabetta Marangoni, Muriel Le Romancer.

   BACKGROUND: Endocrine therapies targeting estrogen signaling have significantly improved breast cancer (BC) patient survival, although 40% of ERα-positive BCs do not respond to those therapies. Aside from genomic signaling, estrogen triggers non-genomic pathways by forming a complex containing methylERα/Src/PI3K, a hallmark of aggressiveness and resistance to tamoxifen. We aimed to confirm the prognostic value of this complex and investigated whether its targeting could improve tumor response in vivo.
METHODS: The interaction of ERα/Src and ERα/PI3K was studied by proximity ligation assay (PLA) in a cohort of 440 BC patients. We then treated patient-derived BC xenografts (PDXs) with fulvestrant or the PI3K inhibitor alpelisib (BYL719) alone or in combination. We analyzed their anti-proliferative effects on 6 ERα+ and 3 ERα- PDX models. Genomic and non-genomic estrogen signaling were assessed by measuring ERα/PI3K interaction by PLA and the expression of estrogen target genes by RT-QPCR, respectively.
RESULTS: We confirmed that ERα/Src and ERα/PI3K interactions were associated with a trend to poorer survival, the latter displaying the most significant effects. In ERα+ tumors, the combination of BYL719 and fulvestrant was more effective than fulvestrant alone in 3 models, irrespective of PI3K, PTEN status, or ERα/PI3K targeting. Remarkably, resistance to fulvestrant was associated with non-genomic ERα signaling, since genomic degradation of ERα was unaltered in these tumors, whereas the treatment did not diminish the level of ERα/PI3K interaction. Interestingly, in 2 ERα- models, fulvestrant alone impacted tumor growth, and this was associated with a decrease in ERα/PI3K interaction.
CONCLUSIONS: Our results demonstrate that ERα/PI3K may constitute a new prognostic marker, as well as a new target in BC. Indeed, resistance to fulvestrant in ERα+ tumors was associated with a lack of impairment of ERα/PI3K interaction in the cytoplasm. In addition, an efficient targeting of ERα/PI3K in ERα- tumors could constitute a promising therapeutic option.

Keywords:  Biomarker; Breast cancer; Estrogen signaling; PDX; PI3K; Resistance

DOI:  https://doi.org/10.1186/s13058-021-01433-8
Biochem J. 2021 May 18. pii: BCJ20210144. [Epub ahead of print]

The insulin receptor family and protein kinase B (Akt) are activated in the heart by alkaline pH and α1-adrenergic receptors.

Daniel Meijles, Stephen J Fuller, Joshua J Cull, Hajed O Alharbi, Susanna Te Cooper, Peter H Sugden, Angela Clerk.

  Insulin and insulin-like growth factor stimulate protein synthesis and cardioprotection in the heart, acting through their receptors (INSRs, IGF1Rs) and signalling via protein kinase B (PKB, also known as Akt). Protein synthesis is increased in hearts perfused at alkaline pHo to the same extent as with insulin. Moreover, α1-adrenergic receptor (α1-AR) agonists (e.g. phenylephrine) increase protein synthesis in cardiomyocytes, activating PKB/Akt. In both cases, the mechanisms are not understood. Our aim was to determine if insulin receptor-related receptors (INSRRs, activated in kidney by alkaline pH) may account for the effects of alkaline pHo on cardiac protein synthesis, and establish if α1-ARs signal through the insulin receptor family. Alkaline pHo activated PKB/Akt signalling to the same degree as insulin in perfused adult male rat hearts. INSRRs were expressed in rat hearts and, by immunoblotting for phosphorylation (activation) of INSRRs/INSRs/IGF1Rs, we established that INSRRs, together with INSRs/IGF1Rs, are activated by alkaline pHo. The INSRR/INSR/IGF1R kinase inhibitor, linsitinib prevented PKB/Akt activation by alkaline pHo, indicating that INSRRs/INSRs/IGF1Rs are required. Activation of PKB/Akt in cardiomyocytes by α1-AR agonists was also inhibited by linsitinib. Furthermore, linsitinib inhibited cardiomyocyte hypertrophy induced by α1-ARs in cultured cells, reduced the initial cardiac adaptation (24 h) to phenylephrine in vivo (assessed by echocardiography) and increased cardiac fibrosis over 4 d. We conclude that INSRRs are expressed in the heart and, together with INSRs/IGF1Rs, the insulin receptor family provide a potent system for promoting protein synthesis and cardioprotection. Moreover, this system is required for adaptive hypertrophy induced by α1-ARs.

Keywords:  Gq protein coupled receptors; Receptor cross-talk; protein synthesis

DOI:  https://doi.org/10.1042/BCJ20210144
Elife. 2021 May 17. pii: e67172. [Epub ahead of print]10

Signaling levels mold the RAS mutation tropism of urethane.

Siqi Li, Christopher M Counter.

  RAS genes are commonly mutated in human cancer. Despite many possible mutations, individual cancer types often have a 'tropism' towards a specific subset of RAS mutations. As driver mutations, these patterns ostensibly originate from normal cells. High oncogenic RAS activity causes oncogenic stress and different oncogenic mutations can impart different levels of activity, suggesting a relationship between oncoprotein activity and RAS mutation tropism. Here, we show that changing rare codons to common in the murine Kras gene to increase protein expression shifts tumors induced by the carcinogen urethane from arising from canonical Q61 to biochemically less active G12 Kras driver mutations, despite the carcinogen still being biased towards generating Q61 mutations. Conversely, inactivating the tumor suppressor p53 to blunt oncogenic stress partially reversed this effect, restoring Q61 mutations. One interpretation of these findings is that the RAS mutation tropism of urethane arises from selection in normal cells for specific mutations that impart a narrow window of signaling that promotes proliferation without causing oncogenic stress.

Keywords:  RAS; cancer biology; carcinogenesis; codon bias; mouse; oncogenesis; protooncogenes; tumor initiation

DOI:  https://doi.org/10.7554/eLife.67172