bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2024‒11‒10
24 papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. mTORC1 activity licenses its own release from the lysosomal surface.
  2. mTORC1 restricts TFE3 activity by auto-regulating its presence on lysosomes.
  3. Oncogenic EML4-ALK assemblies suppress growth factor perception and modulate drug tolerance.
  4. Concurrent SOS1 and MEK suppression inhibits signaling and growth of NF1-null melanoma.
  5. The dual role of the TSC complex in cancer.
  6. Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions.
  7. HiDDEN: a machine learning method for detection of disease-relevant populations in case-control single-cell transcriptomics data.
  8. Plausible, robust biological oscillations through allelic buffering.
  9. HSP70 promotes amino acid-dependent mTORC1 signaling by mediating CHIP-induced NPRL2 ubiquitination and degradation.
  10. Extracellular proximal interaction profiling by cell surface-targeted TurboID reveals LDLR as a partner of liganded EGFR.
  11. Two cooperative lipid binding sites within the pleckstrin homology domain are necessary for AKT binding and stabilization to the plasma membrane.
  12. Spatial organization of PI3K-PI(3,4,5)P3-AKT signaling by focal adhesions.
  13. Mutant-selective AKT inhibition through lysine targeting and neo-zinc chelation.
  14. Microvascular insulin resistance with enhanced muscle glucose disposal in CD36 deficiency.
  15. PhosCancer: A comprehensive database for investigating protein phosphorylation in human cancer.
  16. Cancer Metabolism: Historical Landmarks, New Concepts, and Opportunities.
  17. Vertical targeting of the PI3K/AKT pathway at multiple points is synergistic and effective for non-Hodgkin lymphoma.
  18. Development of compact transcriptional effectors using high-throughput measurements in diverse contexts.
  19. Empowering biomedical discovery with AI agents.
  20. A beginner's guide to supervised analysis for mass cytometry data in cancer biology.
  21. Flexibility and sensitivity in gene regulation out of equilibrium.
  22. The PRIDE database at 20 years: 2025 update.
  23. The antibodies don't work! The race to rid labs of molecules that ruin experiments.
  24. Exploring optimal protocols for generating and preserving glucose-responsive insulin-secreting progenitor cells derived from human pluripotent stem cells.
  1. Mol Cell. 2024 Oct 25. pii: S1097-2765(24)00831-1. [Epub ahead of print]
    mTORC1 activity licenses its own release from the lysosomal surface.
    Aishwarya Acharya, Constantinos Demetriades.
      Nutrient signaling converges on mTORC1, which, in turn, orchestrates a physiological cellular response. A key determinant of mTORC1 activity is its shuttling between the lysosomal surface and the cytoplasm, with nutrients promoting its recruitment to lysosomes by the Rag GTPases. Active mTORC1 regulates various cellular functions by phosphorylating distinct substrates at different subcellular locations. Importantly, how mTORC1 that is activated on lysosomes is released to meet its non-lysosomal targets and whether mTORC1 activity itself impacts its localization remain unclear. Here, we show that, in human cells, mTORC1 inhibition prevents its release from lysosomes, even under starvation conditions, which is accompanied by elevated and sustained phosphorylation of its lysosomal substrate TFEB. Mechanistically, "inactive" mTORC1 causes persistent Rag activation, underlining its release as another process actively mediated via the Rags. In sum, we describe a mechanism by which mTORC1 controls its own localization, likely to prevent futile cycling on and off lysosomes.
    Keywords:  GATOR1; Rag GTPases; Rheb; TFE3; TFEB; Torin1; lysosomes; mTORC1; rapamycin
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.008
  2. Mol Cell. 2024 Oct 25. pii: S1097-2765(24)00832-3. [Epub ahead of print]
    mTORC1 restricts TFE3 activity by auto-regulating its presence on lysosomes.
    Susan Zwakenberg, Denise Westland, Robert M van Es, Holger Rehmann, Jasper Anink, Jolita Ciapaite, Marjolein Bosma, Ellen Stelloo, Nalan Liv, Paula Sobrevals Alcaraz, Nanda M Verhoeven-Duif, Judith J M Jans, Harmjan R Vos, Eleonora Aronica, Fried J T Zwartkruis.
      To stimulate cell growth, the protein kinase complex mTORC1 requires intracellular amino acids for activation. Amino-acid sufficiency is relayed to mTORC1 by Rag GTPases on lysosomes, where growth factor signaling enhances mTORC1 activity via the GTPase Rheb. In the absence of amino acids, GATOR1 inactivates the Rags, resulting in lysosomal detachment and inactivation of mTORC1. We demonstrate that in human cells, the release of mTORC1 from lysosomes depends on its kinase activity. In accordance with a negative feedback mechanism, activated mTOR mutants display low lysosome occupancy, causing hypo-phosphorylation and nuclear localization of the lysosomal substrate TFE3. Surprisingly, mTORC1 activated by Rheb does not increase the cytoplasmic/lysosomal ratio of mTORC1, indicating the existence of mTORC1 pools with distinct substrate specificity. Dysregulation of either pool results in aberrant TFE3 activity and may explain nuclear accumulation of TFE3 in epileptogenic malformations in focal cortical dysplasia type II (FCD II) and tuberous sclerosis (TSC).
    Keywords:  FCD IIb; NPRL2; Rag GTPases; Rheb; TFE3; TSC; amino acids; lysosomes; mTORC1
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.009
  3. Nat Commun. 2024 Nov 02. 15(1): 9473
    Oncogenic EML4-ALK assemblies suppress growth factor perception and modulate drug tolerance.
    David Gonzalez-Martinez, Lee Roth, Thomas R Mumford, Juan Guan, Anh Le, Robert C Doebele, Bo Huang, Asmin Tulpule, Magdalena Niewiadomska-Bugaj, Trever G Bivona, Lukasz J Bugaj.
      Drug resistance remains a challenge for targeted therapy of cancers driven by EML4-ALK and related fusion oncogenes. EML4-ALK forms cytoplasmic protein condensates, which result from networks of interactions between oncogene and adapter protein multimers. While these assemblies are associated with oncogenic signaling, their role in drug response is unclear. Here, we use optogenetics and live-cell imaging to find that EML4-ALK assemblies suppress transmembrane receptor tyrosine kinase (RTK) signaling by sequestering RTK adapter proteins including GRB2 and SOS1. Furthermore, ALK inhibition, while suppressing oncogenic signaling, simultaneously releases the sequestered adapters and thereby resensitizes RTK signaling. Resensitized RTKs promote rapid and pulsatile ERK reactivation that originates from paracrine ligands shed by dying cells. Reactivated ERK signaling promotes cell survival, which can be counteracted by combination therapies that block paracrine signaling. Our results identify a regulatory role for RTK fusion assemblies and uncover a mechanism of tolerance to targeted therapies.
    DOI:  https://doi.org/10.1038/s41467-024-53451-7
  4. Cell Rep Med. 2024 Oct 29. pii: S2666-3791(24)00589-5. [Epub ahead of print] 101818
    Concurrent SOS1 and MEK suppression inhibits signaling and growth of NF1-null melanoma.
    Michelangelo Marasco, Dinesh Kumar, Tessa Seale, Santiago Garcia Borrego, Esther Kaplun, Ilinca Aricescu, Soren Cole, Besnik Qeriqi, Juan Qiu, Xiaoping Chen, Amber Bahr, Deborah Fidele, Marco H Hofmann, Daniel Gerlach, Fabio Savarese, Taha Merghoub, Jedd D Wolchok, Zhan Yao, Elisa de Stanchina, David Solit, Sandra Misale, Neal Rosen.
      Neurofibromin (NF1) is a negative regulator of RAS signaling, frequently mutated in cancer. NF1-mutant melanoma is a highly malignant tumor for which targeted therapies are lacking. Here, we use biochemical and pharmacological assays on patient-derived models and isogenic cell lines to identify potential pharmacologic targets, revealing that NF1-null melanomas are dependent on RAS activation and that MEK inhibition relieves ERK-dependent negative feedback, increasing RAS signaling. MEK inhibition with avutometinib abrogates the adaptive rebound in ERK signaling, but the antitumor effects are limited. However, concurrent inhibition of MEK and SOS1 abrogates ERK activation, induces cell death, and suppresses tumor growth. In contrast to the NF1-deficient setting, concurrent SOS1 and SOS2 depletion is required to completely inhibit RAS signaling in NF1 wild-type cells. In sum, our data provide a mechanistic rationale for enhancing the therapeutic efficacy of MEK inhibitors by exploiting the lower residual SOS activity in NF1-null tumor cells.
    Keywords:  MEK inhibition; NF1; SOS1 inhibition; combination therapy; melanoma
    DOI:  https://doi.org/10.1016/j.xcrm.2024.101818
  5. Trends Mol Med. 2024 Nov 01. pii: S1471-4914(24)00276-4. [Epub ahead of print]
    The dual role of the TSC complex in cancer.
    Josephine Hartung, Christine Müller, Cornelis F Calkhoven.
      The tuberous sclerosis complex (TSC1/TSC2/TBC1D7) primarily functions to inhibit the mechanistic target of rapamycin complex 1 (mTORC1), a crucial regulator of cell growth. Mutations in TSC1 or TSC2 cause tuberous sclerosis complex (TSC), a rare autosomal dominant genetic disorder marked by benign tumors in multiple organs that rarely progress to malignancy. Traditionally, TSC proteins are considered tumor suppressive due to their inhibition of mTORC1 and other mechanisms. However, more recent studies have shown that TSC proteins can also promote tumorigenesis in certain cancer types. In this review, we explore the composition and function of the TSC protein complex, the roles of its individual components in cancer biology, and potential future therapeutic targeting strategies.
    Keywords:  MYC; TSC; cancer; mTORC1; molecular glue degraders
    DOI:  https://doi.org/10.1016/j.molmed.2024.10.009
  6. Nat Neurosci. 2024 Nov 05.
    Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions.
    Celia Lerma-Martin, Pau Badia-I-Mompel, Ricardo O Ramirez Flores, Patricia Sekol, Philipp S L Schäfer, Christian J Riedl, Annika Hofmann, Thomas Thäwel, Florian Wünnemann, Miguel A Ibarra-Arellano, Tim Trobisch, Philipp Eisele, Denis Schapiro, Maximilian Haeussler, Simon Hametner, Julio Saez-Rodriguez, Lucas Schirmer.
      Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system. Inflammation is gradually compartmentalized and restricted to specific tissue niches such as the lesion rim. However, the precise cell type composition of such niches, their interactions and changes between chronic active and inactive stages are incompletely understood. We used single-nucleus and spatial transcriptomics from subcortical MS and corresponding control tissues to map cell types and associated pathways to lesion and nonlesion areas. We identified niches such as perivascular spaces, the inflamed lesion rim or the lesion core that are associated with the glial scar and a cilia-forming astrocyte subtype. Focusing on the inflamed rim of chronic active lesions, we uncovered cell-cell communication events between myeloid, endothelial and glial cell types. Our results provide insight into the cellular composition, multicellular programs and intercellular communication in tissue niches along the conversion from a homeostatic to a dysfunctional state underlying lesion progression in MS.
    DOI:  https://doi.org/10.1038/s41593-024-01796-z
  7. Nat Commun. 2024 Nov 02. 15(1): 9468
    HiDDEN: a machine learning method for detection of disease-relevant populations in case-control single-cell transcriptomics data.
    Aleksandrina Goeva, Michael-John Dolan, Judy Luu, Eric Garcia, Rebecca Boiarsky, Rajat M Gupta, Evan Macosko.
      In case-control single-cell RNA-seq studies, sample-level labels are transferred onto individual cells, labeling all case cells as affected, when in reality only a small fraction of them may actually be perturbed. Here, using simulations, we demonstrate that the standard approach to single cell analysis fails to isolate the subset of affected case cells and their markers when either the affected subset is small, or when the strength of the perturbation is mild. To address this fundamental limitation, we introduce HiDDEN, a computational method that refines the case-control labels to accurately reflect the perturbation status of each cell. We show HiDDEN's superior ability to recover biological signals missed by the standard analysis workflow in simulated ground truth datasets of cell type mixtures. When applied to a dataset of human multiple myeloma precursor conditions, HiDDEN recapitulates the expert manual annotation and discovers malignancy in early stage samples missed in the original analysis. When applied to a mouse model of demyelination, HiDDEN identifies an endothelial subpopulation playing a role in early stage blood-brain barrier dysfunction. We anticipate that HiDDEN should find wide usage in contexts that require the detection of subtle transcriptional changes in cell types across conditions.
    DOI:  https://doi.org/10.1038/s41467-024-53666-8
  8. Cell Syst. 2024 Nov 04. pii: S2405-4712(24)00299-0. [Epub ahead of print]
    Plausible, robust biological oscillations through allelic buffering.
    Feng-Shu Hsieh, Duy P M Nguyen, Mathias S Heltberg, Chia-Chou Wu, Yi-Chen Lee, Mogens H Jensen, Sheng-Hong Chen.
      Biological oscillators can specify time- and dose-dependent functions via dedicated control of their oscillatory dynamics. However, how biological oscillators, which recurrently activate noisy biochemical processes, achieve robust oscillations remains unclear. Here, we characterize the long-term oscillations of p53 and its negative feedback regulator Mdm2 in single cells after DNA damage. Whereas p53 oscillates regularly, Mdm2 from a single MDM2 allele exhibits random unresponsiveness to ∼9% of p53 pulses. Using allelic-specific imaging of MDM2 activity, we show that MDM2 alleles buffer each other to maintain p53 pulse amplitude. Removal of MDM2 allelic buffering cripples the robustness of p53 amplitude, thereby elevating p21 levels and cell-cycle arrest. In silico simulations support that allelic buffering enhances the robustness of biological oscillators and broadens their plausible biochemical space. Our findings show how allelic buffering ensures robust p53 oscillations, highlighting the potential importance of allelic buffering for the emergence of robust biological oscillators during evolution. A record of this paper's transparent peer review process is included in the supplemental information.
    Keywords:  DNA damage; Mdm2; allelic buffering; biochemical noise; cell cycle; oscillations; p21; p53; signaling dynamics; stochasticity
    DOI:  https://doi.org/10.1016/j.cels.2024.10.002
  9. FASEB J. 2024 Nov 15. 38(21): e70147
    HSP70 promotes amino acid-dependent mTORC1 signaling by mediating CHIP-induced NPRL2 ubiquitination and degradation.
    Jianfang Gao, Mingjun Lin, Jina Qing, Hongxia Li, Xiao Zeng, Wuzhou Yuan, Tingting Li, Shanping He.
      Mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth and its dysregulation leads to a variety of human diseases. Although NPRL2, an essential component of the GATOR1 complex, is reported to effectively suppress amino acid-induced mTORC1 activation, the regulation of NPRL2 protein stability is unclear. In this study, we show that chaperon-associated ubiquitin ligase CHIP interacts with NPRL2 and promotes its polyubiquitination and proteasomal degradation. Moreover, HSP70 mediates CHIP-induced ubiquitination and degradation of NPRL2. Consistently, overexpression of HSP70 enhances whereas HSP70 depletion inhibits amino acid-induced mTORC1 activation. Accordingly, knockdown of HSP70 promotes basal autophagic flux, and inhibits cell growth and proliferation. Taken together, these results demonstrated that HSP70 is a novel activator of mTORC1 through mediating CHIP-induced ubiquitination and degradation of NPRL2.
    Keywords:  CHIP; HSP70; NPRL2; amino acid; mTORC1; ubiquitination
    DOI:  https://doi.org/10.1096/fj.202401352R
  10. Sci Signal. 2024 Nov 05. 17(861): eadl6164
    Extracellular proximal interaction profiling by cell surface-targeted TurboID reveals LDLR as a partner of liganded EGFR.
    Rasha Al Mismar, Payman Samavarchi-Tehrani, Brendon Seale, Vesal Kasmaeifar, Claire E Martin, Anne-Claude Gingras.
      Plasma membrane proteins play pivotal roles in receiving and transducing signals from other cells and from the environment and are vital for cellular functionality. Enzyme-based, proximity-dependent approaches, such as biotin identification (BioID), combined with mass spectrometry have begun to illuminate the landscape of proximal protein interactions within intracellular compartments. To extend the potential of these approaches to study the extracellular environment, we developed extracellular TurboID (ecTurboID), a method designed to profile the interactions between proteins on the surfaces of living cells over short timescales using the fast-acting biotin ligase TurboID. After optimizing our experimental and data analysis strategies to capture extracellular proximity interactions, we used ecTurboID to reveal the proximal interactomes of several plasma membrane proteins, including the epidermal growth factor receptor (EGFR). We found that EGF stimulation induced an association between EGFR and the low-density lipoprotein receptor (LDLR) and changed the interactome of LDLR by increasing its proximity with proteins that regulate EGFR signaling. The identification of this interaction between two well-studied and clinically relevant receptors illustrates the utility of our modified proximity labeling methodology for identifying dynamic extracellular associations between plasma membrane proteins.
    DOI:  https://doi.org/10.1126/scisignal.adl6164
  11. Structure. 2024 Oct 29. pii: S0969-2126(24)00455-6. [Epub ahead of print]
    Two cooperative lipid binding sites within the pleckstrin homology domain are necessary for AKT binding and stabilization to the plasma membrane.
    Chrysa Soteriou, Mengfan Xu, Simon D Connell, Arwen I I Tyler, Antreas C Kalli, James L Thorne.
      Almost four decades after the identification of the AKT protein and understanding of its role in cancer, barriers remain in the translation of AKT inhibitors for clinical applications. Here, we provide new molecular insight into the first step of AKT activation where AKT binds to the plasma membrane and its orientation is stabilized in a bilayer with lateral heterogeneity (Lo-Ld phase coexistence). We have applied molecular dynamic simulations and molecular and cell biology approaches, and demonstrate that AKT recruitment to the membrane requires a second binding site in the AKT pleckstrin homology (PH) domain that acts cooperatively with the known canonical binding site. Given the precision with which we have identified the protein-lipid interactions, the study offers new directions for AKT-targeted therapy and for testing small molecules to target these specific amino acid-PIP molecular bonds.
    Keywords:  AKT; PIP lipids; cancer; confocal microscopy; molecular dynamic simulations; oncogene; pleckstrin homology domain; protein-lipid interactions; triple-negative breast cancer
    DOI:  https://doi.org/10.1016/j.str.2024.10.020
  12. Mol Cell. 2024 Oct 29. pii: S1097-2765(24)00833-5. [Epub ahead of print]
    Spatial organization of PI3K-PI(3,4,5)P3-AKT signaling by focal adhesions.
    Jing Wang, Zhengyang An, Zhongsheng Wu, Wei Zhou, Pengyu Sun, Piyu Wu, Song Dang, Rui Xue, Xue Bai, Yongtao Du, Rongmei Chen, Wenxu Wang, Pei Huang, Sin Man Lam, Youwei Ai, Suling Liu, Guanghou Shui, Zhe Zhang, Zheng Liu, Jianyong Huang, Xiaohong Fang, Kangmin He.
      The class I phosphatidylinositol 3-kinase (PI3K)-AKT signaling pathway is a key regulator of cell survival, growth, and proliferation and is among the most frequently mutated pathways in cancer. However, where and how PI3K-AKT signaling is spatially activated and organized in mammalian cells remains poorly understood. Here, we identify focal adhesions (FAs) as subcellular signaling hubs organizing the activation of PI3K-PI(3,4,5)P3-AKT signaling in human cancer cells containing p110α mutations under basal conditions. We find that class IA PI3Ks are preferentially recruited to FAs for activation, resulting in localized production of PI(3,4,5)P3 around FAs. As the effector protein of PI(3,4,5)P3, AKT1 molecules are dynamically recruited around FAs for activation. The spatial recruitment/activation of the PI3K-PI(3,4,5)P3-AKT cascade is regulated by activated FA kinase (FAK). Furthermore, combined inhibition of p110α and FAK results in a more potent inhibitory effect on cancer cells. Thus, our results unveil a growth-factor independent, compartmentalized organization mechanism for PI3K-PI(3,4,5)P3-AKT signaling.
    Keywords:  AKT; FAK; PI(3,4,5)P(3); class I PI3K; focal adhesion; lipid signaling; single-molecule imaging
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.010
  13. Nature. 2024 Nov 06.
    Mutant-selective AKT inhibition through lysine targeting and neo-zinc chelation.
    Gregory B Craven, Hang Chu, Jessica D Sun, Jordan D Carelli, Brittany Coyne, Hao Chen, Ying Chen, Xiaolei Ma, Subhamoy Das, Wayne Kong, Adam D Zajdlik, Kin S Yang, Solomon H Reisberg, Peter A Thompson, J Russell Lipford, Jack Taunton.
      Somatic alterations in the oncogenic kinase AKT1 have been identified in a broad spectrum of solid tumours. The most common AKT1 alteration replaces Glu17 with Lys (E17K) in the regulatory pleckstrin homology domain1, resulting in constitutive membrane localization and activation of oncogenic signalling. In clinical studies, pan-AKT inhibitors have been found to cause dose-limiting hyperglycaemia2-6, which has motivated the search for mutant-selective inhibitors. We exploited the E17K mutation to design allosteric, lysine-targeted salicylaldehyde inhibitors with selectivity for AKT1 (E17K) over wild-type AKT paralogues, a major challenge given the presence of three conserved lysines near the allosteric site. Crystallographic analysis of the covalent inhibitor complex unexpectedly revealed an adventitious tetrahedral zinc ion that coordinates two proximal cysteines in the kinase activation loop while simultaneously engaging the E17K-imine conjugate. The salicylaldimine complex with AKT1 (E17K), but not that with wild-type AKT1, recruits endogenous Zn2+ in cells, resulting in sustained inhibition. A salicylaldehyde-based inhibitor was efficacious in AKT1 (E17K) tumour xenograft models at doses that did not induce hyperglycaemia. Our study demonstrates the potential to achieve exquisite residence-time-based selectivity for AKT1 (E17K) by targeting the mutant lysine together with Zn2+ chelation by the resulting salicylaldimine adduct.
    DOI:  https://doi.org/10.1038/s41586-024-08176-4
  14. Diabetologia. 2024 Nov 06.
    Microvascular insulin resistance with enhanced muscle glucose disposal in CD36 deficiency.
    Cyndya A Shibao, Vivek S Peche, Terri A Pietka, Dmitri Samovski, Ian M Williams, Naji N Abumrad, Eric R Gamazon, Ira J Goldberg, David H Wasserman, Nada A Abumrad.
      AIMS/HYPOTHESIS: Microvascular dysfunction contributes to insulin resistance. CD36, a fatty acid transporter and modulator of insulin signalling, is abundant in microvascular endothelial cells. Humans carrying the minor allele (G) of CD36 coding variant rs3211938 have 50% reduced CD36 expression and show endothelial dysfunction. We aimed to determine whether G allele carriers have microvascular resistance to insulin and, if so, how this affects glucose disposal.METHODS: Our multi-disciplinary approach included hyperinsulinaemic-euglycaemic clamps in Cd36-/- and wild-type mice, and in individuals with 50% CD36 deficiency, together with control counterparts, in addition to primary human-derived microvascular endothelial cells with/without CD36 depletion.
    RESULTS: Insulin clamps showed that Cd36-/- mice have enhanced insulin-stimulated glucose disposal but reduced vascular compliance and capillary perfusion. Intravital microscopy of the gastrocnemius showed unaltered transcapillary insulin flux. CD36-deficient humans had better insulin-stimulated glucose disposal but insulin-unresponsive microvascular blood volume (MBV). Human microvascular cells depleted of CD36 showed impaired insulin activation of Akt, endothelial NO synthase and NO generation. Thus, in CD36 deficiency, microvascular insulin resistance paradoxically associated with enhanced insulin sensitivity of glucose disposal.
    CONCLUSIONS/INTERPRETATION: CD36 deficiency was previously shown to reduce muscle/heart fatty acid uptake, whereas here we showed that it reduced vascular compliance and the ability of insulin to increase MBV for optimising glucose and oxygen delivery. The muscle and heart respond to these energy challenges by transcriptional remodelling priming the tissue for insulin-stimulated glycolytic flux. Reduced oxygen delivery activating hypoxia-induced factors, endothelial release of growth factors or small intracellular vesicles might mediate this adaptation. Targeting NO bioavailability in CD36 deficiency could benefit the microvasculature and muscle/heart metabolism.
    TRIAL REGISTRATION: Clinicaltrials.gov NCT03012386 DATA AVAILABILITY: The RNAseq data generated in this study have been deposited in the NCBI Gene Expression Omnibus ( www.ncbi.nlm.nih.gov/geo/ ) under accession code GSE235988 ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235988 ).
    Keywords:  African Americans; Caveolin; Endothelial function; Nitric oxide; rs3211938
    DOI:  https://doi.org/10.1007/s00125-024-06292-4
  15. iScience. 2024 Nov 15. 27(11): 111060
    PhosCancer: A comprehensive database for investigating protein phosphorylation in human cancer.
    Qun Dong, Danqing Shen, Jiachen Ye, Jiaxin Chen, Jing Li.
      Protein phosphorylation is a crucial post-translational modification implicated in cancer pathogenesis, offering potential diagnostic and therapeutic targets. Here, we developed PhosCancer, a user-friendly database for extracting biologically and clinically relevant insights from phosphoproteomics data. Leveraging data from the CNHPP and CPTAC, PhosCancer encompasses 174,587 phosphosites from 14 datasets spanning 12 cancer types. Through extensive statistical analyses and integration of annotations from external resources, PhosCancer serves as a convenient one-stop platform facilitating the exploration of phosphorylation profiles across different cancer types. Not only does PhosCancer encompass basic information, 3D structure, functional domains, and upstream kinases, but also provides quantitative associations with nine clinical features, and the relevance with hallmarks in both cancer-specific and pan-cancer views. PhosCancer is a valuable resource for cancer researchers and clinicians, promoting the identification of clinically actionable biomarkers and further facilitating the clinical applications of phosphoproteomic data.
    Keywords:  biological database; cancer; software tool
    DOI:  https://doi.org/10.1016/j.isci.2024.111060
  16. Cold Spring Harb Perspect Med. 2024 Nov 05. pii: a041814. [Epub ahead of print]
    Cancer Metabolism: Historical Landmarks, New Concepts, and Opportunities.
    Navdeep S Chandel, Karen H Vousden, Ralph J DeBerardinis.
      Cancer cells undergo changes in metabolism that distinguish them from non-malignant tissue. These may provide a growth advantage by promoting oncogenic signaling and redirecting intermediates to anabolic pathways that provide building blocks for new cellular components. Cancer metabolism is far from uniform, however, and recent work has shed light on its heterogenity within and between tumors. This work is also revealing how cancer metabolism adapts to the tumor microenvironment, as well as ways in which we may capitalize on metabolic changes in cancer cells to create new therapies.
    DOI:  https://doi.org/10.1101/cshperspect.a041814
  17. Exp Hematol Oncol. 2024 Nov 01. 13(1): 108
    Vertical targeting of the PI3K/AKT pathway at multiple points is synergistic and effective for non-Hodgkin lymphoma.
    Kristyna Kupcova, Jana Senavova, Filip Jura, Vaclav Herman, Anezka Rajmonova, Mariana Pacheco-Blanco, Tereza Chrbolkova, Iva Hamova, R Eric Davis, Ondrej Havranek.
      The phosphatidylinositol 3‑kinase/protein kinase B (PI3K/AKT) signaling pathway is critically active in many cell types, both normal and neoplastic. Many small-molecule inhibitors targeting different levels of the PI3K/AKT pathway have been developed for cancer therapy, but their efficacy is reduced by compensatory pathway re-activation mechanisms, and their tolerability by toxic side effects. We studied this problem using cell lines representing diffuse large B-cell lymphoma (SUDHL-4 and OCI-Ly7), a genetically-encoded live-cell reporter of AKT activity, and 3 small-molecule inhibitors targeting different levels of the pathway: idelalisib (PI3Kδ), GSK2334470 (PDPK1), and ipatasertib (AKT). Half-maximal (IC50) concentrations of these inhibitors for AKT activity inhibition at 1 h, when used individually, were much lower than their IC50 values for reduction of viable cell number after 4 days. Time-course studies explained this discrepancy: AKT activity in the continuous presence of the inhibitors returned to normal after 24 h, and was supranormal after inhibitor removal. Combining all 3 inhibitors produced sustained inhibition of AKT activity, was broadly synergistic at reducing viable cell number, enabled substantially lower doses of each inhibitor to be used, and was enhanced further by the mTOR inhibitor rapamycin. Moreover, combined PDPK1 and AKT inhibition showed synergy with multiple different PI3K inhibitors. In a syngeneic mouse cell line model of lymphoma (A20), the triple combination showed antitumor activity and no evidence of toxicity. Our findings provide proof of concept suggesting further study of the safety and efficacy of low-dose multilevel PI3K/AKT pathway inhibition, for lymphoma and perhaps other cancers.
    Keywords:  DLBCL; Diffuse large B-cell lymphoma; Idelalisib; Inhibitors; Ipatasertib; NHL; Non-Hodgkin lymphoma; PDPK1; PI3K/AKT pathway; Rapamycin
    DOI:  https://doi.org/10.1186/s40164-024-00568-6
  18. Nat Biotechnol. 2024 Nov 01.
    Development of compact transcriptional effectors using high-throughput measurements in diverse contexts.
    Josh Tycko, Mike V Van, Aradhana, Nicole DelRosso, Hanrong Ye, David Yao, Raeline Valbuena, Alun Vaughan-Jackson, Xiaoshu Xu, Connor Ludwig, Kaitlyn Spees, Katherine Liu, Mingxin Gu, Venya Khare, Adi Xiyal Mukund, Peter H Suzuki, Sophia Arana, Catherine Zhang, Peter P Du, Thea S Ornstein, Gaelen T Hess, Roarke A Kamber, Lei S Qi, Ahmad S Khalil, Lacramioara Bintu, Michael C Bassik.
      Transcriptional effectors are protein domains known to activate or repress gene expression; however, a systematic understanding of which effector domains regulate transcription across genomic, cell type and DNA-binding domain (DBD) contexts is lacking. Here we develop dCas9-mediated high-throughput recruitment (HT-recruit), a pooled screening method for quantifying effector function at endogenous target genes and test effector function for a library containing 5,092 nuclear protein Pfam domains across varied contexts. We also map context dependencies of effectors drawn from unannotated protein regions using a larger library tiling chromatin regulators and transcription factors. We find that many effectors depend on target and DBD contexts, such as HLH domains that can act as either activators or repressors. To enable efficient perturbations, we select context-robust domains, including ZNF705 KRAB, that improve CRISPRi tools to silence promoters and enhancers. We engineer a compact human activator called NFZ, by combining NCOA3, FOXO3 and ZNF473 domains, which enables efficient CRISPRa with better viral delivery and inducible control of chimeric antigen receptor T cells.
    DOI:  https://doi.org/10.1038/s41587-024-02442-6
  19. Cell. 2024 Oct 31. pii: S0092-8674(24)01070-5. [Epub ahead of print]187(22): 6125-6151
    Empowering biomedical discovery with AI agents.
    Shanghua Gao, Ada Fang, Yepeng Huang, Valentina Giunchiglia, Ayush Noori, Jonathan Richard Schwarz, Yasha Ektefaie, Jovana Kondic, Marinka Zitnik.
      We envision "AI scientists" as systems capable of skeptical learning and reasoning that empower biomedical research through collaborative agents that integrate AI models and biomedical tools with experimental platforms. Rather than taking humans out of the discovery process, biomedical AI agents combine human creativity and expertise with AI's ability to analyze large datasets, navigate hypothesis spaces, and execute repetitive tasks. AI agents are poised to be proficient in various tasks, planning discovery workflows and performing self-assessment to identify and mitigate gaps in their knowledge. These agents use large language models and generative models to feature structured memory for continual learning and use machine learning tools to incorporate scientific knowledge, biological principles, and theories. AI agents can impact areas ranging from virtual cell simulation, programmable control of phenotypes, and the design of cellular circuits to developing new therapies.
    Keywords:  AI agent; agent systems; artificial intelligence; biomedical discovery; foundation models; large language models
    DOI:  https://doi.org/10.1016/j.cell.2024.09.022
  20. Cytometry A. 2024 Nov 01.
    A beginner's guide to supervised analysis for mass cytometry data in cancer biology.
    Julia Wlosik, Samuel Granjeaud, Laurent Gorvel, Daniel Olive, Anne-Sophie Chretien.
      Mass cytometry enables deep profiling of biological samples at single-cell resolution. This technology is more than relevant in cancer research due to high cellular heterogeneity and complexity. Downstream analysis of high-dimensional datasets increasingly relies on machine learning (ML) to extract clinically relevant information, including supervised algorithms for classification and regression purposes. In cancer research, they are used to develop predictive models that will guide clinical decision making. However, the development of supervised algorithms faces major challenges, such as sufficient validation, before being translated into the clinics. In this work, we provide a framework for the analysis of mass cytometry data with a specific focus on supervised algorithms and practical examples of their applications. We also raise awareness on key issues regarding good practices for researchers curious to implement supervised ML on their mass cytometry data. Finally, we discuss the challenges of supervised ML application to cancer research.
    Keywords:  cancer; machine learning; mass cytometry; predictive models; supervised analysis
    DOI:  https://doi.org/10.1002/cyto.a.24901
  21. Proc Natl Acad Sci U S A. 2024 Nov 12. 121(46): e2411395121
    Flexibility and sensitivity in gene regulation out of equilibrium.
    Sara D Mahdavi, Gabriel L Salmon, Patill Daghlian, Hernan G Garcia, Rob Phillips.
      Cells adapt to environments and tune gene expression by controlling the concentrations of proteins and their kinetics in regulatory networks. In both eukaryotes and prokaryotes, experiments and theory increasingly attest that these networks can and do consume biochemical energy. How does this dissipation enable cellular behaviors forbidden in equilibrium? This open question demands quantitative models that transcend thermodynamic equilibrium. Here, we study the control of simple, ubiquitous gene regulatory networks to explore the consequences of departing equilibrium in transcription. Employing graph theory to model a set of especially common regulatory motifs, we find that dissipation unlocks nonmonotonicity and enhanced sensitivity of gene expression with respect to a transcription factor's concentration. These features allow a single transcription factor to act as both a repressor and activator at different concentrations or achieve outputs with multiple concentration regimes of locally enhanced sensitivity. We systematically dissect how energetically driving individual transitions within regulatory networks, or pairs of transitions, generates a wide range of more adjustable and sensitive phenotypic responses than in equilibrium. These results generalize to more complex regulatory scenarios, including combinatorial control by multiple transcription factors, which we relate and often find collapse to simple mathematical behaviors. Our findings quantify necessary conditions and detectable consequences of energy expenditure. These richer mathematical behaviors-feasibly accessed using biological energy budgets and rates-may empower cells to accomplish sophisticated regulation with simpler architectures than those required at equilibrium.
    Keywords:  biophysics; gene regulation; nonequilibrium; transcription
    DOI:  https://doi.org/10.1073/pnas.2411395121
  22. Nucleic Acids Res. 2024 Nov 04. pii: gkae1011. [Epub ahead of print]
    The PRIDE database at 20 years: 2025 update.
    Yasset Perez-Riverol, Chakradhar Bandla, Deepti J Kundu, Selvakumar Kamatchinathan, Jingwen Bai, Suresh Hewapathirana, Nithu Sara John, Ananth Prakash, Mathias Walzer, Shengbo Wang, Juan Antonio Vizcaíno.
      The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's leading mass spectrometry (MS)-based proteomics data repository and one of the founding members of the ProteomeXchange consortium. This manuscript summarizes the developments in PRIDE resources and related tools for the last three years. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 534 datasets per month. This has been possible thanks to continuous improvements in infrastructure such as a new file transfer protocol for very large datasets (Globus), a new data resubmission pipeline and an automatic dataset validation process. Additionally, we will highlight novel activities such as the availability of the PRIDE chatbot (based on the use of open-source Large Language Models), and our work to improve support for MS crosslinking datasets. Furthermore, we will describe how we have increased our efforts to reuse, reanalyze and disseminate high-quality proteomics data into added-value resources such as UniProt, Ensembl and Expression Atlas.
    DOI:  https://doi.org/10.1093/nar/gkae1011
  23. Nature. 2024 Nov;635(8037): 26-28
    The antibodies don't work! The race to rid labs of molecules that ruin experiments.
    Diana Kwon.
      
    Keywords:  Biological techniques; Lab life; Microscopy; Research data
    DOI:  https://doi.org/10.1038/d41586-024-03590-0
  24. Eur J Cell Biol. 2024 Oct 24. pii: S0171-9335(24)00081-5. [Epub ahead of print]103(4): 151464
    Exploring optimal protocols for generating and preserving glucose-responsive insulin-secreting progenitor cells derived from human pluripotent stem cells.
    Patrizia Tornabene, James M Wells.
      Human pluripotent stem cells (hPSCs) represent an unlimited source of β-like cells for both disease modeling and cellular therapy for diabetes. Numerous protocols have been published describing the differentiation of hPSCs into β-like cells that secret insulin in response to a glucose challenge. However, among the most widely used protocols it is not clear which yield the most functional cells with reproducible glucose-stimulated insulin-secretion (GSIS). Moreover, the technical challenges in culturing and differentiating hPSCs is a barrier for many researchers. In this study, we performed a side-by-side functional comparison based on three widely used methods to generate insulin expressing cells and identified optimal stages and conditions for cryopreserving and reconstituting stem cell (SC)-derived islets with a robust GSIS. Despite the fact that each protocol yields SC-islets consisting of insulin and glucagon-expressing cells, the SC-islets obtained from the two more recent revised protocols were more functional as measured by robust and reproducible GSIS. Moreover, we demonstrate that pancreatic progenitors and differentiated endocrine cells that have been cryopreserved for up to 10 months, can be reconstituted into glucose responsive SC-islets. These findings should enable the use of human PSC-derived β-like cells technologies even by groups with minimal PSC culture experience.
    Keywords:  Glucose-stimulated insulin secretion, Cryopreservation; Pancreatic differentiation; Pluripotent stem cells
    DOI:  https://doi.org/10.1016/j.ejcb.2024.151464
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