bims-pideca 2021-09-19 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2021–09–19
twelve papers selected by
Ralitsa Radostinova Madsen, University College London

Dynamic modelling of the PI3K/MTOR signalling network uncovers biphasic dependence of mTORC1 activity on the mTORC2 subunit SIN1.
Synthetic essentiality between PTEN and core dependency factor PAX7 dictates rhabdomyosarcoma identity.
Regulation of human mTOR complexes by DEPTOR.
Strategies to Overcome Failures in T-Cell Immunotherapies by Targeting PI3K-δ and -γ.
A PtdIns(3,4,5)P3 dispersal switch engages cell ratcheting at specific cell surfaces.
Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace.
Increased fidelity of protein synthesis extends lifespan.
Biogenesis of P-TEFb in CD4+ T cells to reverse HIV latency is mediated by protein kinase C (PKC)-independent signaling pathways.
Monitoring the Cellular Metabolism of a Membrane-Permeant Photo-Caged Phosphatidylinositol 3,4,5-Trisphosphate Derivative.
Developmental chromatin programs determine oncogenic competence in melanoma.
Cell states can give tumorigenesis a head start.
Fasting blood glucose as a predictor of mortality: Lost in translation.

PLoS Comput Biol. 2021 Sep 16. 17(9): e1008513

Dynamic modelling of the PI3K/MTOR signalling network uncovers biphasic dependence of mTORC1 activity on the mTORC2 subunit SIN1.

Milad Ghomlaghi, Guang Yang, Sungyoung Shin, David E James, Lan K Nguyen.

The PI3K/MTOR signalling network regulates a broad array of critical cellular processes, including cell growth, metabolism and autophagy. The mechanistic target of rapamycin (MTOR) kinase functions as a core catalytic subunit in two physically and functionally distinct complexes mTORC1 and mTORC2, which also share other common components including MLST8 (also known as GβL) and DEPTOR. Despite intensive research, how mTORC1 and 2 assembly and activity are coordinated, and how they are functionally linked remain to be fully characterized. This is due in part to the complex network wiring, featuring multiple feedback loops and intricate post-translational modifications. Here, we integrate predictive network modelling, in vitro experiments and -omics data analysis to elucidate the emergent dynamic behaviour of the PI3K/MTOR network. We construct new mechanistic models that encapsulate critical mechanistic details, including mTORC1/2 coordination by MLST8 (de)ubiquitination and the Akt-to-mTORC2 positive feedback loop. Model simulations validated by experimental studies revealed a previously unknown biphasic, threshold-gated dependence of mTORC1 activity on the key mTORC2 subunit SIN1, which is robust against cell-to-cell variation in protein expression. In addition, our integrative analysis demonstrates that ubiquitination of MLST8, which is reversed by OTUD7B, is regulated by IRS1/2. Our results further support the essential role of MLST8 in enabling both mTORC1 and 2's activity and suggest MLST8 as a viable therapeutic target in breast cancer. Overall, our study reports a new mechanistic model of PI3K/MTOR signalling incorporating MLST8-mediated mTORC1/2 formation and unveils a novel regulatory linkage between mTORC1 and mTORC2.

DOI: https://doi.org/10.1371/journal.pcbi.1008513
Nat Commun. 2021 Sep 17. 12(1): 5520

Synthetic essentiality between PTEN and core dependency factor PAX7 dictates rhabdomyosarcoma identity.

Casey G Langdon, Katherine E Gadek, Matthew R Garcia, Myron K Evans, Kristin B Reed, Madeline Bush, Jason A Hanna, Catherine J Drummond, Matthew C Maguire, Patrick J Leavey, David Finkelstein, Hongjian Jin, Patrick A Schreiner, Jerold E Rehg, Mark E Hatley.

PTEN promoter hypermethylation is nearly universal and PTEN copy number loss occurs in ~25% of fusion-negative rhabdomyosarcoma (FN-RMS). Here we show Pten deletion in a mouse model of FN-RMS results in less differentiated tumors more closely resembling human embryonal RMS. PTEN loss activated the PI3K pathway but did not increase mTOR activity. In wild-type tumors, PTEN was expressed in the nucleus suggesting loss of nuclear PTEN functions could account for these phenotypes. Pten deleted tumors had increased expression of transcription factors important in neural and skeletal muscle development including Dbx1 and Pax7. Pax7 deletion completely rescued the effects of Pten loss. Strikingly, these Pten;Pax7 deleted tumors were no longer FN-RMS but displayed smooth muscle differentiation similar to leiomyosarcoma. These data highlight how Pten loss in FN-RMS is connected to a PAX7 lineage-specific transcriptional output that creates a dependency or synthetic essentiality on the transcription factor PAX7 to maintain tumor identity.

DOI: https://doi.org/10.1038/s41467-021-25829-4
Elife. 2021 09 14. pii: e70871. [Epub ahead of print]10

Regulation of human mTOR complexes by DEPTOR.

Matthias Wälchli, Karolin Berneiser, Francesca Mangia, Stefan Imseng, Louise-Marie Craigie, Edward Stuttfeld, Michael N Hall, Timm Maier.

  The vertebrate-specific DEP domain-containing mTOR interacting protein (DEPTOR), an oncoprotein or tumor suppressor, has important roles in metabolism, immunity, and cancer. It is the only protein that binds and regulates both complexes of mammalian target of rapamycin (mTOR), a central regulator of cell growth. Biochemical analysis and cryo-EM reconstructions of DEPTOR bound to human mTOR complex 1 (mTORC1) and mTORC2 reveal that both structured regions of DEPTOR, the PDZ domain and the DEP domain tandem (DEPt), are involved in mTOR interaction. The PDZ domain binds tightly with mildly activating effect, but then acts as an anchor for DEPt association that allosterically suppresses mTOR activation. The binding interfaces of the PDZ domain and DEPt also support further regulation by other signaling pathways. A separate, substrate-like mode of interaction for DEPTOR phosphorylation by mTOR complexes rationalizes inhibition of non-stimulated mTOR activity at higher DEPTOR concentrations. The multifaceted interplay between DEPTOR and mTOR provides a basis for understanding the divergent roles of DEPTOR in physiology and opens new routes for targeting the mTOR-DEPTOR interaction in disease.

Keywords:  DEPTOR; cancer; cryo-EM; human; mTOR; metabolism; molecular biophysics; signaling; structural biology

DOI:  https://doi.org/10.7554/eLife.70871
Front Immunol. 2021 ;12 718621

Strategies to Overcome Failures in T-Cell Immunotherapies by Targeting PI3K-δ and -γ.

Sanjay Chandrasekaran, Christopher Ronald Funk, Troy Kleber, Chrystal M Paulos, Mala Shanmugam, Edmund K Waller.

  PI3K-δ and PI3K-γ are critical regulators of T-cell differentiation, senescence, and metabolism. PI3K-δ and PI3K-γ signaling can contribute to T-cell inhibition via intrinsic mechanisms and regulation of suppressor cell populations, including regulatory T-cells and myeloid derived suppressor cells in the tumor. We examine an exciting new role for using selective inhibitors of the PI3K δ- and γ-isoforms as modulators of T-cell phenotype and function in immunotherapy. Herein we review the current literature on the implications of PI3K-δ and -γ inhibition in T-cell biology, discuss existing challenges in adoptive T-cell therapies and checkpoint blockade inhibitors, and highlight ongoing efforts and future directions to incorporate PI3K-δ and PI3K-γ as synergistic T-cell modulators in immunotherapy.

Keywords:  CAR T cancer therapy; PI3K delta; PI3K gamma; T cell differentiation; TIL (tumor infiltrating lymphocytes); adoptive cell immunotherapy; immune checkpoint inhibition (ICI)

DOI:  https://doi.org/10.3389/fimmu.2021.718621
Dev Cell. 2021 Sep 11. pii: S1534-5807(21)00675-4. [Epub ahead of print]

A PtdIns(3,4,5)P3 dispersal switch engages cell ratcheting at specific cell surfaces.

Hui Miao, Timothy E Vanderleest, Rashmi Budhathoki, Dinah Loerke, J Todd Blankenship.

  Force generation in epithelial tissues is often pulsatile, with actomyosin networks generating contractile forces before cyclically disassembling. This pulsed nature of cytoskeletal forces implies that there must be ratcheting mechanisms that drive processive transformations in cell shape. Previous work has shown that force generation is coordinated with endocytic remodeling; however, how ratcheting becomes engaged at specific cell surfaces remains unclear. Here, we report that PtdIns(3,4,5)P3 is a critical lipid-based cue for ratcheting engagement. The Sbf RabGEF binds to PIP3, and disruption of PIP3 reveals a dramatic switching behavior in which medial ratcheting is activated and epithelial cells begin globally constricting apical surfaces. PIP3 enrichments are developmentally regulated, with mesodermal cells having high apical PIP3 while germband cells have higher interfacial PIP3. Finally, we show that JAK/STAT signaling constitutes a second pathway that combinatorially regulates Sbf/Rab35 recruitment. Our results elucidate a complex lipid-dependent regulatory machinery that directs ratcheting engagement in epithelial tissues.

Keywords:  Drosophila; apical constriction; cell intercalation; cell ratcheting; gastrulation; membrane trafficking; morphogenesis

DOI:  https://doi.org/10.1016/j.devcel.2021.08.016
Elife. 2021 09 14. pii: e68799. [Epub ahead of print]10

Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace.

Maren Heimhalt, Alex Berndt, Jane Wagstaff, Madhanagopal Anandapadamanaban, Olga Perisic, Sarah Maslen, Stephen McLaughlin, Conny Wing-Heng Yu, Glenn R Masson, Andreas Boland, Xiaodan Ni, Keitaro Yamashita, Garib N Murshudov, Mark Skehel, Stefan M Freund, Roger L Williams.

  The mTORC1 kinase complex regulates cell growth, proliferation, and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted mTORC1 with DEPTOR to understand its function. We find that DEPTOR is a unique partial mTORC1 inhibitor that may have evolved to preserve feedback inhibition of PI3K. Counterintuitively, mTORC1 activated by RHEB or oncogenic mutation is much more potently inhibited by DEPTOR. Although DEPTOR partially inhibits mTORC1, mTORC1 prevents this inhibition by phosphorylating DEPTOR, a mutual antagonism that requires no exogenous factors. Structural analyses of the mTORC1/DEPTOR complex showed DEPTOR's PDZ domain interacting with the mTOR FAT region, and the unstructured linker preceding the PDZ binding to the mTOR FRB domain. The linker and PDZ form the minimal inhibitory unit, but the N-terminal tandem DEP domains also significantly contribute to inhibition.

Keywords:  DEPTOR; biochemistry; cancer; chemical biology; cryo-EM; human; mTOR; molecular biophysics; partial inhibition; signal transduction; structural biology

DOI:  https://doi.org/10.7554/eLife.68799
Cell Metab. 2021 Sep 08. pii: S1550-4131(21)00417-4. [Epub ahead of print]

Increased fidelity of protein synthesis extends lifespan.

Victoria Eugenia Martinez-Miguel, Celia Lujan, Tristan Espie-Caullet, Daniel Martinez-Martinez, Saul Moore, Cassandra Backes, Suam Gonzalez, Evgeniy R Galimov, André E X Brown, Mario Halic, Kazunori Tomita, Charalampos Rallis, Tobias von der Haar, Filipe Cabreiro, Ivana Bjedov.

  Loss of proteostasis is a fundamental process driving aging. Proteostasis is affected by the accuracy of translation, yet the physiological consequence of having fewer protein synthesis errors during multi-cellular organismal aging is poorly understood. Our phylogenetic analysis of RPS23, a key protein in the ribosomal decoding center, uncovered a lysine residue almost universally conserved across all domains of life, which is replaced by an arginine in a small number of hyperthermophilic archaea. When introduced into eukaryotic RPS23 homologs, this mutation leads to accurate translation, as well as heat shock resistance and longer life, in yeast, worms, and flies. Furthermore, we show that anti-aging drugs such as rapamycin, Torin1, and trametinib reduce translation errors, and that rapamycin extends further organismal longevity in RPS23 hyperaccuracy mutants. This implies a unified mode of action for diverse pharmacological anti-aging therapies. These findings pave the way for identifying novel translation accuracy interventions to improve aging.

Keywords:  RPS23; aging; archaea; mTOR; protein synthesis; proteostasis; ribosome; translation; translation accuracy; translation fidelity

DOI:  https://doi.org/10.1016/j.cmet.2021.08.017
PLoS Pathog. 2021 Sep 16. 17(9): e1009581

Biogenesis of P-TEFb in CD4+ T cells to reverse HIV latency is mediated by protein kinase C (PKC)-independent signaling pathways.

Uri Mbonye, Konstantin Leskov, Meenakshi Shukla, Saba Valadkhan, Jonathan Karn.

The switch between HIV latency and productive transcription is regulated by an auto-feedback mechanism initiated by the viral trans-activator Tat, which functions to recruit the host transcription elongation factor P-TEFb to proviral HIV. A heterodimeric complex of CDK9 and one of three cyclin T subunits, P-TEFb is expressed at vanishingly low levels in resting memory CD4+ T cells and cellular mechanisms controlling its availability are central to regulation of the emergence of HIV from latency. Using a well-characterized primary T-cell model of HIV latency alongside healthy donor memory CD4+ T cells, we characterized specific T-cell receptor (TCR) signaling pathways that regulate the generation of transcriptionally active P-TEFb, defined as the coordinate expression of cyclin T1 and phospho-Ser175 CDK9. Protein kinase C (PKC) agonists, such as ingenol and prostratin, stimulated active P-TEFb expression and reactivated latent HIV with minimal cytotoxicity, even in the absence of intracellular calcium mobilization with an ionophore. Unexpectedly, inhibition-based experiments demonstrated that PKC agonists and TCR-mobilized diacylglycerol signal through MAP kinases ERK1/2 rather than through PKC to effect the reactivation of both P-TEFb and latent HIV. Single-cell and bulk RNA-seq analyses revealed that of the four known isoforms of the Ras guanine nucleotide exchange factor RasGRP, RasGRP1 is by far the predominantly expressed diacylglycerol-dependent isoform in CD4+ T cells. RasGRP1 should therefore mediate the activation of ERK1/2 via Ras-Raf signaling upon TCR co-stimulation or PKC agonist challenge. Combined inhibition of the PI3K-mTORC2-AKT-mTORC1 pathway and the ERK1/2 activator MEK prior to TCR co-stimulation abrogated active P-TEFb expression and substantially suppressed latent HIV reactivation. Therefore, contrary to prevailing models, the coordinate reactivation of P-TEFb and latent HIV in primary T cells following either TCR co-stimulation or PKC agonist challenge is independent of PKC but rather involves two complementary signaling arms of the TCR cascade, namely, RasGRP1-Ras-Raf-MEK-ERK1/2 and PI3K-mTORC2-AKT-mTORC1.

DOI: https://doi.org/10.1371/journal.ppat.1009581
Chem Phys Lipids. 2021 Sep 09. pii: S0009-3084(21)00077-3. [Epub ahead of print] 105124

Monitoring the Cellular Metabolism of a Membrane-Permeant Photo-Caged Phosphatidylinositol 3,4,5-Trisphosphate Derivative.

Mevlut Citir, Rainer Müller, Sebastian Hauke, Alexis Traynor-Kaplan, Carsten Schultz.

  To deliver charged lipid derivatives to the cell interior, bioactivatable and photo-activatable protecting groups are frequently used. The intracellular metabolism of the protecting groups, as well as the lipid itself, are key factors that determine biological activity. Here, we followed the cellular metabolism of cell-permeant photo-activatable ("caged") and non-caged membrane-permeant analogs of dioctanoyl phosphatidylinositol 3,4,5-trisphosphate (diC8PIP3), carrying biodegradable protecting groups, by mass spectrometry. After successful cell entry, the photo-activatable group can be removed on demand by a light pulse. Hence, UV irradiation acts as a switch to expose the cellular metabolism to a bolus of active compound. To investigate lipid metabolites and to capture a more complete metabolome, we adapted standard extraction methods and employed multi-reaction monitoring mass spectrometry (MRM-MS). This required a previously developed permethylation method that stabilized metabolites and enhanced volatility of the phosphoinositide metabolites. The mass spectrometric analysis allowed for the monitoring of the intracellular removal of photo-activatable caging as well as biodegradable protecting groups from the membrane-permeant phosphoinositides along with cellular turnover, namely by dephosphorylation. We found that phosphate masking groups, namely acetoxymethyl esters, were rapidly removed by endogenous enzymes while butyrates masking hydroxy groups showed a longer lifetime, giving rise to trapped intermediates. We further identified key intermediate metabolites and demonstrated the beneficial effect of caging groups and their removal on the formation of favorable metabolites. Surprisingly, caging and protecting groups were found to influence each other's stability.

Keywords:  Phosphoinositides; mass spectrometry; multi-reaction monitoring; photoactivatable groups; protecting groups

DOI:  https://doi.org/10.1016/j.chemphyslip.2021.105124
Science. 2021 09 03. 373(6559): eabc1048

Developmental chromatin programs determine oncogenic competence in melanoma.

Arianna Baggiolini, Scott J Callahan, Emily Montal, Joshua M Weiss, Tuan Trieu, Mohita M Tagore, Sam E Tischfield, Ryan M Walsh, Shruthy Suresh, Yujie Fan, Nathaniel R Campbell, Sarah C Perlee, Nathalie Saurat, Miranda V Hunter, Theresa Simon-Vermot, Ting-Hsiang Huang, Yilun Ma, Travis Hollmann, Satish K Tickoo, Barry S Taylor, Ekta Khurana, Richard P Koche, Lorenz Studer, Richard M White.

[Figure: see text].

DOI: https://doi.org/10.1126/science.abc1048
Nat Rev Cancer. 2021 Sep 14.

Cell states can give tumorigenesis a head start.

Sarah Seton-Rogers.

DOI: https://doi.org/10.1038/s41568-021-00410-9
Cell Metab. 2021 Sep 08. pii: S1550-4131(21)00376-4. [Epub ahead of print]

Fasting blood glucose as a predictor of mortality: Lost in translation.

Dushani L Palliyaguru, Eric J Shiroma, John K Nam, Eleonora Duregon, Camila Vieira Ligo Teixeira, Nathan L Price, Michel Bernier, Simonetta Camandola, Kelli L Vaughan, Ricki J Colman, Andrew Deighan, Ron Korstanje, Luanne L Peters, Stephanie L Dickinson, Keisuke Ejima, Eleanor M Simonsick, Lenore J Launer, Chee W Chia, Josephine Egan, David B Allison, Gary A Churchill, Rozalyn M Anderson, Luigi Ferrucci, Julie A Mattison, Rafael de Cabo.

  Aging leads to profound changes in glucose homeostasis, weight, and adiposity, which are considered good predictors of health and survival in humans. Direct evidence that these age-associated metabolic alterations are recapitulated in animal models is lacking, impeding progress to develop and test interventions that delay the onset of metabolic dysfunction and promote healthy aging and longevity. We compared longitudinal trajectories, rates of change, and mortality risks of fasting blood glucose, body weight, and fat mass in mice, nonhuman primates, and humans throughout their lifespans and found similar trajectories of body weight and fat in the three species. In contrast, fasting blood glucose decreased late in life in mice but increased over the lifespan of nonhuman primates and humans. Higher glucose was associated with lower mortality in mice but higher mortality in nonhuman primates and humans, providing a cautionary tale for translating age-associated metabolic changes from mice to humans.

Keywords:  fasting blood glucose; humans; metabolism; mice; mortality; nonhuman primates; predictors

DOI:  https://doi.org/10.1016/j.cmet.2021.08.013