bims-pideca 2023-08-20 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2023‒08‒20
thirty papers selected by
Ralitsa Radostinova Madsen
MRC-PPU

Molding a PI(3,5)P2 biosensor.
Control of gastruloid patterning and morphogenesis by the Erk and Akt signaling pathways.
Protein interaction network analysis of mTOR signaling reveals modular organization.
Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation.
Structural insights into the interaction of three Y-shaped ligands with PI3Kα.
FAM120A couples SREBP-dependent transcription and splicing of lipogenesis enzymes downstream of mTORC1.
A Phosphoproteomics Data Resource for Systems-level Modeling of Kinase Signaling Networks.
A sweet way to regulate cellular growth: OGT and mTOR join forces.
Quantitative proteomics and phosphoproteomics of PP2A-PPP2R5D variants reveal deregulation of RPS6 phosphorylation via converging signaling cascades.
Endothelial ERα promotes glucose tolerance by enhancing endothelial insulin transport to skeletal muscle.
Pan-cancer proteogenomics connects oncogenic drivers to functional states.
Balancing lysosome abundance in health and disease.
Molecular mechanism for activation of the 26S proteasome by ZFAND5.
Phospho-Analyst: An Interactive, Easy-to-Use Web Platform To Analyze Quantitative Phosphoproteomics Data.
PI3K/AKT/mTOR signaling transduction pathway and targeted therapies in cancer.
BRD7 improves glucose homeostasis independent of IRS proteins.
Proteogenomic data and resources for pan-cancer analysis.
PINE-TREE enables highly efficient genetic modification of human cell lines.
Low risk of embryonic and other cancers in PIK3CA-related overgrowth spectrum: Impact on screening recommendations.
Simultaneous inhibition of DNA-PK and Polϴ improves integration efficiency and precision of genome editing.
One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids.
CellBender removes technical artifacts from single-cell RNA sequencing data.
Stretching the limits of extracellular signal-related kinase (ERK) signaling - Cell mechanosensing to ERK activation.
Context-dependent TGFβ family signalling in cell fate regulation.
PTEN deficiency exposes a requirement for an ARF GTPase module for integrin-dependent invasion in ovarian cancer.
The specious art of single-cell genomics.
Continuous lifelong learning for modeling of gene regulation from single cell multiome data by leveraging atlas-scale external data.
Lactate activates the mitochondrial electron transport chain independent of its metabolism.
Control of mRNA fate by its encoded nascent polypeptide.
DNAJB3 attenuates ER stress through direct interaction with AKT.

J Cell Biol. 2023 09 04. pii: e202308004. [Epub ahead of print]222(9):

Molding a PI(3,5)P2 biosensor.

Claire C Weckerly, Gerald R V Hammond.

The lipid phosphatidylinositol 3,5-bisphosphate-PI(3,5)P2-is known to be a key regulator of cellular traffic in health and disease, but its cellular localization was somewhat enigmatic until now, with the discovery of a new PI(3,5)P2 biosensor reported in this issue of JCB by Vines et al. (2023. J. Cell Biol.https://doi.org/10.1083/jcb.202209077).

DOI: https://doi.org/10.1083/jcb.202308004
Development. 2023 Aug 15. pii: dev201663. [Epub ahead of print]150(16):

Control of gastruloid patterning and morphogenesis by the Erk and Akt signaling pathways.

Evan J Underhill, Jared E Toettcher.

  Many developmental processes rely on the localized activation of receptor tyrosine kinases and their canonical downstream effectors Erk and Akt, yet the specific roles played by each of these signals is still poorly understood. Gastruloids, 3D cell culture models of mammalian gastrulation and axial elongation, enable quantitative dissection of signaling patterns and cell responses in a simplified, experimentally accessible context. We find that mouse gastruloids contain posterior-to-anterior gradients of Erk and Akt phosphorylation induced by distinct receptor tyrosine kinases, with features of the Erk pattern and expression of its downstream target Snail exhibiting hallmarks of size-invariant scaling. Both Erk and Akt signaling contribute to cell proliferation, whereas Erk activation is also sufficient to induce Snail expression and precipitate profound tissue shape changes. We further uncover that Erk signaling is sufficient to convert the entire gastruloid to one of two mesodermal fates depending on position along the anteroposterior axis. In all, these data demonstrate functional roles for two core signaling gradients in mammalian development and suggest how these modules might be harnessed to engineer user-defined tissues with predictable shapes and cell fates.

Keywords:  Cell signaling; Gastruloid; Morphogenesis

DOI:  https://doi.org/10.1242/dev.201663
bioRxiv. 2023 Aug 04. pii: 2023.08.04.552011. [Epub ahead of print]

Protein interaction network analysis of mTOR signaling reveals modular organization.

Devin T Wehle, Carter S Bass, Josef Sulc, Ghayda Mirzaa, Stephen E P Smith.

The mammalian target of rapamycin (mTOR) is a serine-threonine kinase that acts as a central mediator of translation, and plays important roles in cell growth, synaptic plasticity, cancer, and a wide range of developmental disorders. The signaling cascade linking lipid kinases (PI3Ks), protein kinases (AKT) and translation initiation complexes (EIFs) to mTOR has been extensively modeled, but does not fully describe mTOR system behavior. Here, we use quantitative multiplex co-immunoprecipitation to monitor a protein interaction network (PIN) composed of 300+ binary interactions among mTOR-related proteins. Using a simple model system of serum deprived or fresh-media-fed mouse 3T3 fibroblasts, we observed extensive PIN remodeling involving 27+ individual protein interactions after one hour, despite phosphorylation changes observed after only five minutes. Using small molecule inhibitors of PI3K, AKT, mTOR, MEK and ERK, we define subsets of the PIN, termed 'modules', that respond differently to each inhibitor. Using primary fibroblasts from individuals with overgrowth disorders caused by pathogenic PIK3CA or MTOR variants, we find that hyperactivation of mTOR pathway components is reflected in a hyperactive PIN. Our data define a "modular" organization of the mTOR PIN in which coordinated groups of interactions respond to activation or inhibition of distinct nodes, and demonstrate that kinase inhibitors affect the modular network architecture in a complex manner, inconsistent with simple linear models of signal transduction.

DOI: https://doi.org/10.1101/2023.08.04.552011
Cell. 2023 Aug 09. pii: S0092-8674(23)00781-X. [Epub ahead of print]

Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation.

Clinical Proteomic Tumor Analysis Consortium

  Post-translational modifications (PTMs) play key roles in regulating cell signaling and physiology in both normal and cancer cells. Advances in mass spectrometry enable high-throughput, accurate, and sensitive measurement of PTM levels to better understand their role, prevalence, and crosstalk. Here, we analyze the largest collection of proteogenomics data from 1,110 patients with PTM profiles across 11 cancer types (10 from the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium [CPTAC]). Our study reveals pan-cancer patterns of changes in protein acetylation and phosphorylation involved in hallmark cancer processes. These patterns revealed subsets of tumors, from different cancer types, including those with dysregulated DNA repair driven by phosphorylation, altered metabolic regulation associated with immune response driven by acetylation, affected kinase specificity by crosstalk between acetylation and phosphorylation, and modified histone regulation. Overall, this resource highlights the rich biology governed by PTMs and exposes potential new therapeutic avenues.

Keywords:  CPTAC; DNA damage response; genomics; mass spectrometry; metabolism; pan-cancer; post-translational modifications; proteomics; transcriptomics

DOI:  https://doi.org/10.1016/j.cell.2023.07.013
Proc Natl Acad Sci U S A. 2023 Aug 22. 120(34): e2304071120

Structural insights into the interaction of three Y-shaped ligands with PI3Kα.

Qingtong Zhou, Xiao Liu, Dario Neri, Wenxin Li, Nicholas Favalli, Gabriele Bassi, Su Yang, Dehua Yang, Peter K Vogt, Ming-Wei Wang.

  Class IA phosphoinositide 3-kinase alpha (PI3Kα) is an important drug target because it is one of the most frequently mutated proteins in human cancers. However, small molecule inhibitors currently on the market or under development have safety concerns due to a lack of selectivity. Therefore, other chemical scaffolds or unique mechanisms of catalytic kinase inhibition are needed. Here, we report the cryo-electron microscopy structures of wild-type PI3Kα, the dimer of p110α and p85α, in complex with three Y-shaped ligands [cpd16 (compound 16), cpd17 (compound 17), and cpd18 (compound 18)] of different affinities and no inhibitory effect on the kinase activity. Unlike ATP-competitive inhibitors, cpd17 adopts a Y-shaped conformation with one arm inserted into a binding pocket formed by R770 and W780 and the other arm lodged in the ATP-binding pocket at an angle that is different from that of the ATP phosphate tail. Such a special interaction induces a conformation of PI3Kα resembling that of the unliganded protein. These observations were confirmed with two isomers (cpd16 and cpd18). Further analysis of these Y-shaped ligands revealed the structural basis of differential binding affinities caused by stereo- or regiochemical modifications. Our results may offer a different direction toward the design of therapeutic agents against PI3Kα.

Keywords:  binding pocket; chemical scaffold; drug target; ligand; phosphoinositide 3-kinase

DOI:  https://doi.org/10.1073/pnas.2304071120
Mol Cell. 2023 Aug 17. pii: S1097-2765(23)00560-9. [Epub ahead of print]83(16): 3010-3026.e8

FAM120A couples SREBP-dependent transcription and splicing of lipogenesis enzymes downstream of mTORC1.

Sungyun Cho, Yujin Chun, Long He, Cuauhtemoc B Ramirez, Kripa S Ganesh, Kyungjo Jeong, Junho Song, Jin Gyu Cheong, Zhongchi Li, Jungmin Choi, Joohwan Kim, Nikos Koundouros, Fangyuan Ding, Noah Dephoure, Cholsoon Jang, John Blenis, Gina Lee.

  The mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth that stimulates macromolecule synthesis through transcription, RNA processing, and post-translational modification of metabolic enzymes. However, the mechanisms of how mTORC1 orchestrates multiple steps of gene expression programs remain unclear. Here, we identify family with sequence similarity 120A (FAM120A) as a transcription co-activator that couples transcription and splicing of de novo lipid synthesis enzymes downstream of mTORC1-serine/arginine-rich protein kinase 2 (SRPK2) signaling. The mTORC1-activated SRPK2 phosphorylates splicing factor serine/arginine-rich splicing factor 1 (SRSF1), enhancing its binding to FAM120A. FAM120A directly interacts with a lipogenic transcription factor SREBP1 at active promoters, thereby bridging the newly transcribed lipogenic genes from RNA polymerase II to the SRSF1 and U1-70K-containing RNA-splicing machinery. This mTORC1-regulated, multi-protein complex promotes efficient splicing and stability of lipogenic transcripts, resulting in fatty acid synthesis and cancer cell proliferation. These results elucidate FAM120A as a critical transcription co-factor that connects mTORC1-dependent gene regulation programs for anabolic cell growth.

Keywords:  FAM120A; RNA splicing; RNA stability; SREBP; SRPK2; SRSF1; lipid metabolism; mTOR signaling

DOI:  https://doi.org/10.1016/j.molcel.2023.07.017
bioRxiv. 2023 Aug 03. pii: 2023.08.03.551714. [Epub ahead of print]

A Phosphoproteomics Data Resource for Systems-level Modeling of Kinase Signaling Networks.

Song Feng, James A Sanford, Thomas Weber, Chelsea M Hutchinson-Bunch, Panshak P Dakup, Vanessa L Paurus, Kwame Attah, Herbert M Sauro, Wei-Jun Qian, H Steven Wiley.

Building mechanistic models of kinase-driven signaling pathways requires quantitative measurements of protein phosphorylation across physiologically relevant conditions, but this is rarely done because of the insensitivity of traditional technologies. By using a multiplexed deep phosphoproteome profiling workflow, we were able to generate a deep phosphoproteomics dataset of the EGFR-MAPK pathway in non-transformed MCF10A cells across physiological ligand concentrations with a time resolution of <12 min and in the presence and absence of multiple kinase inhibitors. An improved phosphosite mapping technique allowed us to reliably identify >46,000 phosphorylation sites on >6600 proteins, of which >4500 sites from 2110 proteins displayed a >2-fold increase in phosphorylation in response to EGF. This data was then placed into a cellular context by linking it to 15 previously published protein databases. We found that our results were consistent with much, but not all previously reported data regarding the activation and negative feedback phosphorylation of core EGFR-ERK pathway proteins. We also found that EGFR signaling is biphasic with substrates downstream of RAS/MAPK activation showing a maximum response at <3ng/ml EGF while direct substrates, such as HGS and STAT5B, showing no saturation. We found that RAS activation is mediated by at least 3 parallel pathways, two of which depend on PTPN11. There appears to be an approximately 4-minute delay in pathway activation at the step between RAS and RAF, but subsequent pathway phosphorylation was extremely rapid. Approximately 80 proteins showed a >2-fold increase in phosphorylation across all experiments and these proteins had a significantly higher median number of phosphorylation sites (~18) relative to total cellular phosphoproteins (~4). Over 60% of EGF-stimulated phosphoproteins were downstream of MAPK and included mediators of cellular processes such as gene transcription, transport, signal transduction and cytoskeletal arrangement. Their phosphorylation was either linear with respect to MAPK activation or biphasic, corresponding to the biphasic signaling seen at the level of the EGFR. This deep, integrated phosphoproteomics data resource should be useful in building mechanistic models of EGFR and MAPK signaling and for understanding how downstream responses are regulated.

DOI: https://doi.org/10.1101/2023.08.03.551714
Mol Cell. 2023 Aug 17. pii: S1097-2765(23)00559-2. [Epub ahead of print]83(16): 2832-2833

A sweet way to regulate cellular growth: OGT and mTOR join forces.

Pedro Latorre-Muro, Pere Puigserver.

In this issue, Xu and Pan et al1 report a glucose-sensing and activation mechanism of mTORC1 through the glycosyltransferase OGT, which activates Raptor, allowing lysosomal targeting of mTORC1 to promote cell proliferation.

DOI: https://doi.org/10.1016/j.molcel.2023.07.016
J Biol Chem. 2023 Aug 10. pii: S0021-9258(23)02182-8. [Epub ahead of print] 105154

Quantitative proteomics and phosphoproteomics of PP2A-PPP2R5D variants reveal deregulation of RPS6 phosphorylation via converging signaling cascades.

K A Smolen, C M Papke, M R Swingle, A Musiyenko, C Li, E A Salter, A D Camp, R E Honkanen, A N Kettenbach.

  Genetic germline variants of PPP2R5D (encoding: phosphoprotein phosphatase-2 regulatory protein-5D) result in PPP2R5D-related disorder (Jordan's Syndrome), which is characterized by intellectual disability, hypotonia, seizures, macrocephaly, autism spectrum disorder, and delayed motor skill development. The disorder originates from de novo single nucleotide mutations, generating missense variants that act in a dominant manner. Pathogenic mutations altering 13 different amino acids have been identified, with the E198K variant accounting for ∼40% of reported cases. However, the generation of a heterozygous E198K variant cell line to study the molecular effects of the pathogenic mutation has been challenging. Here, we use CRISPR-PRIME genomic editing to introduce a transition (c.592G>A) in a single PPP2R5D allele in HEK293 cells, generating E198K-heterozygous lines to complement existing E420K variant lines. We generate global protein and phosphorylation profiles of WT, E198K, and E420K cell lines and find unique and shared changes between variants and WT cells in kinase- and phosphatase-controlled signaling cascades. We observed ribosomal protein S6 (RPS6) hyperphosphorylation as a shared signaling alteration, indicative of increased ribosomal protein S6-kinase activity. Treatment with rapamycin or an RPS6-kinase inhibitor (LY2584702) suppressed RPS6 phosphorylation in both, suggesting upstream activation of mTORC1/p70S6K. Intriguingly, our data suggests ERK-dependent activation of mTORC1 in both E198K and E420K variant cells, with additional AKT-mediated mTORC1 activation in the E420K variant. Thus, although upstream activation of mTORC1 differs between PPP2R5D-related disorder genotypes, inhibition of mTORC1 or RPS6-kinases warrants further investigation as potential therapeutic strategies for patients.

Keywords:  Jordan’s Syndrome; LY2584702; PP2A; PPP2R5D; PPP2R5D-related neurodevelopmental disorder; Phosphatase; Phosphoproteomics; Proteomics; mTOR; rapamycin

DOI:  https://doi.org/10.1016/j.jbc.2023.105154
Nat Commun. 2023 Aug 17. 14(1): 4989

Endothelial ERα promotes glucose tolerance by enhancing endothelial insulin transport to skeletal muscle.

Anastasia Sacharidou, Ken Chambliss, Jun Peng, Jose Barrera, Keiji Tanigaki, Katherine Luby-Phelps, İpek Özdemir, Sohaib Khan, Shashank R Sirsi, Sung Hoon Kim, Benita S Katzenellenbogen, John A Katzenellenbogen, Mohammed Kanchwala, Adwait A Sathe, Andrew Lemoff, Chao Xing, Kenneth Hoyt, Chieko Mineo, Philip W Shaul.

The estrogen receptor (ER) designated ERα has actions in many cell and tissue types that impact glucose homeostasis. It is unknown if these include mechanisms in endothelial cells, which have the potential to influence relative obesity, and processes in adipose tissue and skeletal muscle that impact glucose control. Here we show that independent of impact on events in adipose tissue, endothelial ERα promotes glucose tolerance by enhancing endothelial insulin transport to skeletal muscle. Endothelial ERα-deficient male mice are glucose intolerant and insulin resistant, and in females the antidiabetogenic actions of estradiol (E2) are absent. The glucose dysregulation is due to impaired skeletal muscle glucose disposal that results from attenuated muscle insulin delivery. Endothelial ERα activation stimulates insulin transcytosis by skeletal muscle microvascular endothelial cells. Mechanistically this involves nuclear ERα-dependent upregulation of vesicular trafficking regulator sorting nexin 5 (SNX5) expression, and PI3 kinase activation that drives plasma membrane recruitment of SNX5. Thus, coupled nuclear and non-nuclear actions of ERα promote endothelial insulin transport to skeletal muscle to foster normal glucose homeostasis.

DOI: https://doi.org/10.1038/s41467-023-40562-w
Cell. 2023 Aug 14. pii: S0092-8674(23)00780-8. [Epub ahead of print]

Pan-cancer proteogenomics connects oncogenic drivers to functional states.

Clinical Proteomic Tumor Analysis Consortium

  Cancer driver events refer to key genetic aberrations that drive oncogenesis; however, their exact molecular mechanisms remain insufficiently understood. Here, our multi-omics pan-cancer analysis uncovers insights into the impacts of cancer drivers by identifying their significant cis-effects and distal trans-effects quantified at the RNA, protein, and phosphoprotein levels. Salient observations include the association of point mutations and copy-number alterations with the rewiring of protein interaction networks, and notably, most cancer genes converge toward similar molecular states denoted by sequence-based kinase activity profiles. A correlation between predicted neoantigen burden and measured T cell infiltration suggests potential vulnerabilities for immunotherapies. Patterns of cancer hallmarks vary by polygenic protein abundance ranging from uniform to heterogeneous. Overall, our work demonstrates the value of comprehensive proteogenomics in understanding the functional states of oncogenic drivers and their links to cancer development, surpassing the limitations of studying individual cancer types.

Keywords:  CPTAC; cancer hallmark; oncogenic driver; pan-cancer; phosphoproteomics; protein complex; proteogenomics; proteomics; therapeutic target

DOI:  https://doi.org/10.1016/j.cell.2023.07.014
Nat Cell Biol. 2023 Aug 14.

Balancing lysosome abundance in health and disease.

Anders P Mutvei, Michal J Nagiec, John Blenis.

Lysosomes are catabolic organelles that govern numerous cellular processes, including macromolecule degradation, nutrient signalling and ion homeostasis. Aberrant changes in lysosome abundance are implicated in human diseases. Here we outline the mechanisms of lysosome biogenesis and turnover, and discuss how changes in the lysosome pool impact physiological and pathophysiological processes.

DOI: https://doi.org/10.1038/s41556-023-01197-7
Mol Cell. 2023 Aug 17. pii: S1097-2765(23)00566-X. [Epub ahead of print]83(16): 2959-2975.e7

Molecular mechanism for activation of the 26S proteasome by ZFAND5.

Donghoon Lee, Yanan Zhu, Louis Colson, Xiaorong Wang, Siyi Chen, Emre Tkacik, Lan Huang, Qi Ouyang, Alfred L Goldberg, Ying Lu.

  Various hormones, kinases, and stressors (fasting, heat shock) stimulate 26S proteasome activity. To understand how its capacity to degrade ubiquitylated proteins can increase, we studied mouse ZFAND5, which promotes protein degradation during muscle atrophy. Cryo-electron microscopy showed that ZFAND5 induces large conformational changes in the 19S regulatory particle. ZFAND5's AN1 Zn-finger domain interacts with the Rpt5 ATPase and its C terminus with Rpt1 ATPase and Rpn1, a ubiquitin-binding subunit. Upon proteasome binding, ZFAND5 widens the entrance of the substrate translocation channel, yet it associates only transiently with the proteasome. Dissociation of ZFAND5 then stimulates opening of the 20S proteasome gate. Using single-molecule microscopy, we showed that ZFAND5 binds ubiquitylated substrates, prolongs their association with proteasomes, and increases the likelihood that bound substrates undergo degradation, even though ZFAND5 dissociates before substrate deubiquitylation. These changes in proteasome conformation and reaction cycle can explain the accelerated degradation and suggest how other proteasome activators may stimulate proteolysis.

Keywords:  ZFAND5; muscle atrophy; proteasome activation; proteasomes; protein degradation; ubiquitin

DOI:  https://doi.org/10.1016/j.molcel.2023.07.023
J Proteome Res. 2023 Aug 16.

Phospho-Analyst: An Interactive, Easy-to-Use Web Platform To Analyze Quantitative Phosphoproteomics Data.

Haijian Zhang, Joel R Steele, Hossein Valipour Kahrood, Deanna Deveson Lucas, Anup D Shah, Ralf B Schittenhelm.

  Phosphoproteomics is nowadays the method of choice to comprehensively identify and quantify thousands of phosphorylated peptides and their associated proteins with the goal of interrogating changes in signal transduction pathways and other cellular processes. One of the most popular software suites to analyze phosphoproteomic data sets is MaxQuant, which converts mass spectrometric raw data into quantitative information on phosphopeptides and proteins. However, despite the increased utilization of phosphoproteomics in biomedical research, simple and user-friendly tools supporting downstream statistical analysis and interpretation of these highly complex outputs are still lacking. We have therefore developed Phospho-Analyst, which─similar to its sibling LFQ-Analyst─is an easy-to-use, interactive web application specifically designed to reproducibly perform differential expression analyses with "one click" and to visualize phosphoproteomic results in a meaningful and practical manner. Furthermore, if quantitative total proteomic information is available for the same samples, Phospho-Analyst automatically normalizes all phosphoproteomic results to underlying protein abundance levels, thereby ensuring that only genuine changes in phosphorylation events are considered. As such, Phospho-Analyst can not only be used by experienced proteomic veterans but also by researchers without any prior knowledge in (phospho)proteomics, statistics, or bioinformatics. Phospho-Analyst, including a detailed manual, is freely available at https://analyst-suites.org/apps/phospho-analyst/.

Keywords:  R; ShinyApp; bioinformatics; data analysis; mass spectrometry; phosphoproteomics; statistical analysis; web-based software tool

DOI:  https://doi.org/10.1021/acs.jproteome.3c00186
Mol Cancer. 2023 Aug 18. 22(1): 138

PI3K/AKT/mTOR signaling transduction pathway and targeted therapies in cancer.

Antonino Glaviano, Aaron S C Foo, Hiu Y Lam, Kenneth C H Yap, William Jacot, Robert H Jones, Huiyan Eng, Madhumathy G Nair, Pooyan Makvandi, Birgit Geoerger, Matthew H Kulke, Richard D Baird, Jyothi S Prabhu, Daniela Carbone, Camilla Pecoraro, Daniel B L Teh, Gautam Sethi, Vincenzo Cavalieri, Kevin H Lin, Nathalie R Javidi-Sharifi, Eneda Toska, Matthew S Davids, Jennifer R Brown, Patrizia Diana, Justin Stebbing, David A Fruman, Alan P Kumar.

  The PI3K/AKT/mTOR (PAM) signaling pathway is a highly conserved signal transduction network in eukaryotic cells that promotes cell survival, cell growth, and cell cycle progression. Growth factor signalling to transcription factors in the PAM axis is highly regulated by multiple cross-interactions with several other signaling pathways, and dysregulation of signal transduction can predispose to cancer development. The PAM axis is the most frequently activated signaling pathway in human cancer and is often implicated in resistance to anticancer therapies. Dysfunction of components of this pathway such as hyperactivity of PI3K, loss of function of PTEN, and gain-of-function of AKT, are notorious drivers of treatment resistance and disease progression in cancer. In this review we highlight the major dysregulations in the PAM signaling pathway in cancer, and discuss the results of PI3K, AKT and mTOR inhibitors as monotherapy and in co-administation with other antineoplastic agents in clinical trials as a strategy for overcoming treatment resistance. Finally, the major mechanisms of resistance to PAM signaling targeted therapies, including PAM signaling in immunology and immunotherapies are also discussed.

Keywords:  AKT inhibitors; ATP-competitive mTOR inhibitors; Allosteric mTOR inhibitors; Bi-steric mTOR inhibitors; Cancer; Dual PI3K/mTOR inhibitors; Isoform-specific PI3K inhibitors; PDK1 inhibitors; PI3K/AKT/mTORC pathway; Pan PI3K inhibitors

DOI:  https://doi.org/10.1186/s12943-023-01827-6
J Endocrinol. 2023 09 01. pii: e230119. [Epub ahead of print]258(3):

BRD7 improves glucose homeostasis independent of IRS proteins.

Yoo Kim, Junsik M Lee, Youngah Han, Rongya Tao, Morris F White, Renyan Liu, Sang Won Park.

  Bromodomain-containing protein 7 (BRD7) has emerged as a player in the regulation of glucose homeostasis. Hepatic BRD7 levels are decreased in obese mice, and the reinstatement of hepatic BRD7 in obese mice has been shown to establish euglycemia and improve glucose homeostasis. Of note, the upregulation of hepatic BRD7 levels activates the AKT cascade in response to insulin without enhancing the sensitivity of the insulin receptor (InsR)-insulin receptor substrate (IRS) axis. In this report, we provide evidence for the existence of an alternative insulin signaling pathway that operates independently of IRS proteins and demonstrate the involvement of BRD7 in this pathway. To investigate the involvement of BRD7 as a downstream component of InsR, we utilized liver-specific InsR knockout mice. Additionally, we employed liver-specific IRS1/2 knockout mice to examine the requirement of IRS1/2 for the action of BRD7. Our investigation of glucose metabolism parameters and insulin signaling unveiled the significance of InsR activation in mediating BRD7's effect on glucose homeostasis in the liver. Moreover, we identified an interaction between BRD7 and InsR. Notably, our findings indicate that IRS1/2 is not necessary for BRD7's regulation of glucose metabolism, particularly in the context of obesity. The upregulation of hepatic BRD7 significantly reduces blood glucose levels and restores glucose homeostasis in high-fat diet-challenged liver-specific IRS1/2 knockout mice. These findings highlight the presence of an alternative insulin signaling pathway that operates independently of IRS1/2 and offer novel insights into the mechanisms of a previously unknown insulin signaling in obesity.

Keywords:  BRD7; glucose metabolism; insulin receptor signaling; insulin receptor substrates

DOI:  https://doi.org/10.1530/JOE-23-0119
Cancer Cell. 2023 Aug 14. pii: S1535-6108(23)00219-2. [Epub ahead of print]41(8): 1397-1406

Proteogenomic data and resources for pan-cancer analysis.

Clinical Proteomic Tumor Analysis Consortium

  The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and computational resources for aiding biological discoveries. We also discuss challenges for multi-omics data integration and analysis, specifically the unique challenges of working with both nucleotide sequencing and mass spectrometry proteomics data.

Keywords:  CPTAC; data harmonization; multi-omics; open data; pan-cancer; proteogenomics

DOI:  https://doi.org/10.1016/j.ccell.2023.06.009
Mol Ther Nucleic Acids. 2023 Sep 12. 33 483-492

PINE-TREE enables highly efficient genetic modification of human cell lines.

Carlye Frisch, William W Kostes, Brooke Galyon, Brycelyn Whitman, Stefan J Tekel, Kylie Standage-Beier, Gayathri Srinivasan, Xiao Wang, David A Brafman.

  Prime editing technologies enable precise genome editing without the caveats of CRISPR nuclease-based methods. Nonetheless, current approaches to identify and isolate prime-edited cell populations are inefficient. Here, we established a fluorescence-based system, prime-induced nucleotide engineering using a transient reporter for editing enrichment (PINE-TREE), for real-time enrichment of prime-edited cell populations. We demonstrated the broad utility of PINE-TREE for highly efficient introduction of substitutions, insertions, and deletions at various genomic loci. Finally, we employ PINE-TREE to rapidly and efficiently generate clonal isogenic human pluripotent stem cell lines, a cell type recalcitrant to genome editing.

Keywords:  CRISPR; MT: RNA/DNA; genome modification; human pluripotent stem cells; prime editing

DOI:  https://doi.org/10.1016/j.omtn.2023.07.007
Clin Genet. 2023 Aug 14.

Low risk of embryonic and other cancers in PIK3CA-related overgrowth spectrum: Impact on screening recommendations.

Laurence Faivre, Jean-Charles Crépin, Manon Réda, Sophie Nambot, Virginie Carmignac, Caroline Abadie, Tristan Mirault, Cécile Faure-Conter, Juliette Mazereeuw-Hautier, Aude Maza, Eve Puzenat, Marie-Agnès Collonge-Rame, Anne-Claire Bursztejn, Christophe Philippe, Christel Thauvin-Robinet, Martin Chevarin, Claire Abasq-Thomas, Jeanne Amiel, Stéphanie Arpin, Sébastien Barbarot, Geneviève Baujat, Didier Bessis, Emmanuelle Bourrat, Odile Boute, Nicolas Chassaing, Christine Coubes, Bénédicte Demeer, Patrick Edery, Salima El Chehadeh, Alice Goldenberg, Smail Hadj-Rabia, Damien Haye, Bertrand Isidor, Marie-Line Jacquemont, Philippe Khau Van Kien, Didier Lacombe, Daphné Lehalle, Laetitia Lambert, Ludovic Martin, Annabel Maruani, Fanny Morice-Picard, Florence Petit, Alice Phan, Lucile Pinson, Massimiliano Rossi, Renaud Touraine, Clémence Vanlerberghe, Marie Vincent, Catherine Vincent-Delorme, Sandra Whalen, Marjolaine Willems, Nathalie Marle, Virginie Verkarre, Christine Devalland, Mojgan Devouassoux-Shisheboran, Marine Abad, Nathalie Rioux-Leclercq, Bertille Bonniaud, Yannis Duffourd, Jehanne Martel, Christine Binquet, Paul Kuentz, Pierre Vabres.

  The PIK3CA-related overgrowth spectrum (PROS) encompasses various conditions caused by mosaic activating PIK3CA variants. PIK3CA somatic variants are also involved in various cancer types. Some generalized overgrowth syndromes are associated with an increased risk of Wilms tumor (WT). In PROS, abdominal ultrasound surveillance has been advocated to detect WT. We aimed to determine the risk of embryonic and other types of tumors in patients with PROS in order to evaluate surveillance relevance. We searched the clinical charts from 267 PROS patients for the diagnosis of cancer, and reviewed the medical literature for the risk of cancer. In our cohort, six patients developed a cancer (2.2%), and Kaplan Meier analyses estimated cumulative probabilities of cancer occurrence at 45 years of age was 5.6% (95% CI = 1.35%-21.8%). The presence of the PIK3CA variant was only confirmed in two out of four tumor samples. In the literature and our cohort, six cases of Wilms tumor/nephrogenic rests (0.12%) and four cases of other cancers have been reported out of 483 proven PIK3CA patients, in particular the p.(His1047Leu/Arg) variant. The risk of WT in PROS being lower than 5%, this is insufficient evidence to recommend routine abdominal imaging. Long-term follow-up studies are needed to evaluate the risk of other cancer types, as well as the relationship with the extent of tissue mosaicism and the presence or not of the variant in the tumor samples.

Keywords:  PIK3CA; PIK3CA-related overgrowth spectrum (PROS); Wilms tumor; cancer

DOI:  https://doi.org/10.1111/cge.14410
Nat Commun. 2023 Aug 14. 14(1): 4761

Simultaneous inhibition of DNA-PK and Polϴ improves integration efficiency and precision of genome editing.

Sandra Wimberger, Nina Akrap, Mike Firth, Johan Brengdahl, Susanna Engberg, Marie K Schwinn, Michael R Slater, Anders Lundin, Pei-Pei Hsieh, Songyuan Li, Silvia Cerboni, Jonathan Sumner, Burcu Bestas, Bastian Schiffthaler, Björn Magnusson, Silvio Di Castro, Preeti Iyer, Mohammad Bohlooly-Y, Thomas Machleidt, Steve Rees, Ola Engkvist, Tyrell Norris, Elaine B Cadogan, Josep V Forment, Saša Šviković, Pinar Akcakaya, Amir Taheri-Ghahfarokhi, Marcello Maresca.

Genome editing, specifically CRISPR/Cas9 technology, has revolutionized biomedical research and offers potential cures for genetic diseases. Despite rapid progress, low efficiency of targeted DNA integration and generation of unintended mutations represent major limitations for genome editing applications caused by the interplay with DNA double-strand break repair pathways. To address this, we conduct a large-scale compound library screen to identify targets for enhancing targeted genome insertions. Our study reveals DNA-dependent protein kinase (DNA-PK) as the most effective target to improve CRISPR/Cas9-mediated insertions, confirming previous findings. We extensively characterize AZD7648, a selective DNA-PK inhibitor, and find it to significantly enhance precise gene editing. We further improve integration efficiency and precision by inhibiting DNA polymerase theta (Polϴ). The combined treatment, named 2iHDR, boosts templated insertions to 80% efficiency with minimal unintended insertions and deletions. Notably, 2iHDR also reduces off-target effects of Cas9, greatly enhancing the fidelity and performance of CRISPR/Cas9 gene editing.

DOI: https://doi.org/10.1038/s41467-023-40344-4
Nat Commun. 2023 Aug 17. 14(1): 4998

One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids.

Maarten H Geurts, Shashank Gandhi, Matteo G Boretto, Ninouk Akkerman, Lucca L M Derks, Gijs van Son, Martina Celotti, Sarina Harshuk-Shabso, Flavia Peci, Harry Begthel, Delilah Hendriks, Paul Schürmann, Amanda Andersson-Rolf, Susana M Chuva de Sousa Lopes, Johan H van Es, Ruben van Boxtel, Hans Clevers.

Optimization of CRISPR/Cas9-mediated genome engineering has resulted in base editors that hold promise for mutation repair and disease modeling. Here, we demonstrate the application of base editors for the generation of complex tumor models in human ASC-derived organoids. First we show efficacy of cytosine and adenine base editors in modeling CTNNB1 hot-spot mutations in hepatocyte organoids. Next, we use C > T base editors to insert nonsense mutations in PTEN in endometrial organoids and demonstrate tumorigenicity even in the heterozygous state. Moreover, drug sensitivity assays on organoids harboring either PTEN or PTEN and PIK3CA mutations reveal the mechanism underlying the initial stages of endometrial tumorigenesis. To further increase the scope of base editing we combine SpCas9 and SaCas9 for simultaneous C > T and A > G editing at individual target sites. Finally, we show that base editor multiplexing allow modeling of colorectal tumorigenesis in a single step by simultaneously transfecting sgRNAs targeting five cancer genes.

DOI: https://doi.org/10.1038/s41467-023-40701-3
Nat Methods. 2023 Aug 17.

CellBender removes technical artifacts from single-cell RNA sequencing data.

DOI: https://doi.org/10.1038/s41592-023-01946-4
Curr Opin Cell Biol. 2023 Aug 11. pii: S0955-0674(23)00066-2. [Epub ahead of print]84 102217

Stretching the limits of extracellular signal-related kinase (ERK) signaling - Cell mechanosensing to ERK activation.

Tsuyoshi Hirashima, Naoya Hino, Kazuhiro Aoki, Michiyuki Matsuda.

  Extracellular signal-regulated kinase (ERK) has been recognized as a critical regulator in various physiological and pathological processes. Extensive research has elucidated the signaling mechanisms governing ERK activation via biochemical regulations with upstream molecules, particularly receptor tyrosine kinases (RTKs). However, recent advances have highlighted the role of mechanical forces in activating the RTK-ERK signaling pathways, thereby opening new avenues of research into mechanochemical interplay in multicellular tissues. Here, we review the force-induced ERK activation in cells and propose possible mechanosensing mechanisms underlying the mechanoresponsive ERK activation. We conclude that mechanical forces are not merely passive factors shaping cells and tissues but also active regulators of cellular signaling pathways controlling collective cell behaviors.

Keywords:  ERK/MAP kinase signaling; Intercellular signal transmission; Mechanochemical feedback; Mechanosensing; Receptor tyrosine kinases

DOI:  https://doi.org/10.1016/j.ceb.2023.102217
Nat Rev Mol Cell Biol. 2023 Aug 18.

Context-dependent TGFβ family signalling in cell fate regulation.

Louise Richardson, Scott G Wilcockson, Luca Guglielmi, Caroline S Hill.

The transforming growth factor-β (TGFβ) family are a large group of evolutionarily conserved cytokines whose signalling modulates cell fate decision-making across varying cellular contexts at different stages of life. Here we discuss new findings in early embryos that reveal how, in contrast to our original understanding of morphogen interpretation, robust cell fate specification can originate from a noisy combination of signalling inputs and a broad range of signalling levels. We compare this evidence with novel findings on the roles of TGFβ family signalling in tissue maintenance and homeostasis during juvenile and adult life, spanning the skeletal, haemopoietic and immune systems. From these comparisons, it emerges that in contrast to robust developing systems, relatively small perturbations in TGFβ family signalling have detrimental effects at later stages in life, leading to aberrant cell fate specification and disease, for example in cancer or congenital disorders. Finally, we highlight novel strategies to target and amend dysfunction in signalling and discuss how gleaning knowledge from different fields of biology can help in the development of therapeutics for aberrant TGFβ family signalling in disease.

DOI: https://doi.org/10.1038/s41580-023-00638-3
EMBO J. 2023 Aug 14. e113987

PTEN deficiency exposes a requirement for an ARF GTPase module for integrin-dependent invasion in ovarian cancer.

Konstantina Nikolatou, Emma Sandilands, Alvaro Román-Fernández, Erin M Cumming, Eva Freckmann, Sergio Lilla, Lori Buetow, Lynn McGarry, Matthew Neilson, Robin Shaw, David Strachan, Crispin Miller, Danny T Huang, Iain A McNeish, James C Norman, Sara Zanivan, David M Bryant.

  Dysregulation of the PI3K/AKT pathway is a common occurrence in high-grade serous ovarian carcinoma (HGSOC), with the loss of the tumour suppressor PTEN in HGSOC being associated with poor prognosis. The cellular mechanisms of how PTEN loss contributes to HGSOC are largely unknown. We here utilise time-lapse imaging of HGSOC spheroids coupled to a machine learning approach to classify the phenotype of PTEN loss. PTEN deficiency induces PI(3,4,5)P3 -rich and -dependent membrane protrusions into the extracellular matrix (ECM), resulting in a collective invasion phenotype. We identify the small GTPase ARF6 as a crucial vulnerability of HGSOC cells upon PTEN loss. Through a functional proteomic CRISPR screen of ARF6 interactors, we identify the ARF GTPase-activating protein (GAP) AGAP1 and the ECM receptor β1-integrin (ITGB1) as key ARF6 interactors in HGSOC regulating PTEN loss-associated invasion. ARF6 functions to promote invasion by controlling the recycling of internalised, active β1-integrin to maintain invasive activity into the ECM. The expression of the CYTH2-ARF6-AGAP1 complex in HGSOC patients is inversely associated with outcome, allowing the identification of patient groups with improved versus poor outcome. ARF6 may represent a therapeutic vulnerability in PTEN-depleted HGSOC.

Keywords:  3D spheroids; ARF6; Ovarian Cancer; PTEN; integrins

DOI:  https://doi.org/10.15252/embj.2023113987
PLoS Comput Biol. 2023 Aug;19(8): e1011288

The specious art of single-cell genomics.

Tara Chari, Lior Pachter.

Dimensionality reduction is standard practice for filtering noise and identifying relevant features in large-scale data analyses. In biology, single-cell genomics studies typically begin with reduction to 2 or 3 dimensions to produce "all-in-one" visuals of the data that are amenable to the human eye, and these are subsequently used for qualitative and quantitative exploratory analysis. However, there is little theoretical support for this practice, and we show that extreme dimension reduction, from hundreds or thousands of dimensions to 2, inevitably induces significant distortion of high-dimensional datasets. We therefore examine the practical implications of low-dimensional embedding of single-cell data and find that extensive distortions and inconsistent practices make such embeddings counter-productive for exploratory, biological analyses. In lieu of this, we discuss alternative approaches for conducting targeted embedding and feature exploration to enable hypothesis-driven biological discovery.

DOI: https://doi.org/10.1371/journal.pcbi.1011288
bioRxiv. 2023 Aug 03. pii: 2023.08.01.551575. [Epub ahead of print]

Continuous lifelong learning for modeling of gene regulation from single cell multiome data by leveraging atlas-scale external data.

Qiuyue Yuan, Zhana Duren.

Accurate context-specific Gene Regulatory Networks (GRNs) inference from genomics data is a crucial task in computational biology. However, existing methods face limitations, such as reliance on gene expression data alone, lower resolution from bulk data, and data scarcity for specific cellular systems. Despite recent technological advancements, including single-cell sequencing and the integration of ATAC-seq and RNA-seq data, learning such complex mechanisms from limited independent data points still presents a daunting challenge, impeding GRN inference accuracy. To overcome this challenge, we present LINGER (LIfelong neural Network for GEne Regulation), a novel deep learning-based method to infer GRNs from single-cell multiome data with paired gene expression and chromatin accessibility data from the same cell. LINGER incorporates both 1) atlas-scale external bulk data across diverse cellular contexts and 2) the knowledge of transcription factor (TF) motif matching to cis -regulatory elements as a manifold regularization to address the challenge of limited data and extensive parameter space in GRN inference. Our results demonstrate that LINGER achieves 2-3 fold higher accuracy over existing methods. LINGER reveals a complex regulatory landscape of genome-wide association studies, enabling enhanced interpretation of disease-associated variants and genes. Additionally, following the GRN inference from a reference sc-multiome data, LINGER allows for the estimation of TF activity solely from bulk or single-cell gene expression data, leveraging the abundance of available gene expression data to identify driver regulators from case-control studies. Overall, LINGER provides a comprehensive tool for robust gene regulation inference from genomics data, empowering deeper insights into cellular mechanisms.

DOI: https://doi.org/10.1101/2023.08.01.551575
bioRxiv. 2023 Aug 04. pii: 2023.08.02.551712. [Epub ahead of print]

Lactate activates the mitochondrial electron transport chain independent of its metabolism.

Xin Cai, Charles C Ng, Olivia Jones, Tak Shun Fung, Keunwoo Ryu, Dayi Li, Craig B Thompson.

Lactate has long been considered a cellular waste product. However, we found that as extracellular lactate accumulates, it also enters the mitochondrial matrix and stimulates mitochondrial electron transport chain (ETC) activity. The resulting increase in mitochondrial ATP synthesis suppresses glycolysis and increases the utilization of pyruvate and/or alternative respiratory substrates. The ability of lactate to increase oxidative phosphorylation does not depend on its metabolism. Both L- and D-lactate are effective at enhancing ETC activity and suppressing glycolysis. Furthermore, the selective induction of mitochondrial oxidative phosphorylation by unmetabolized D-lactate reversibly suppressed aerobic glycolysis in both cancer cell lines and proliferating primary cells in an ATP-dependent manner and enabled cell growth on respiratory-dependent bioenergetic substrates. In primary T cells, D-lactate enhanced cell proliferation and effector function. Together, these findings demonstrate that lactate is a critical regulator of the ability of mitochondrial oxidative phosphorylation to suppress glucose fermentation.

DOI: https://doi.org/10.1101/2023.08.02.551712
Mol Cell. 2023 Aug 17. pii: S1097-2765(23)00550-6. [Epub ahead of print]83(16): 2840-2855

Control of mRNA fate by its encoded nascent polypeptide.

Markus Höpfler, Ramanujan S Hegde.

  Cells tightly regulate mRNA processing, localization, and stability to ensure accurate gene expression in diverse cellular states and conditions. Most of these regulatory steps have traditionally been thought to occur before translation by the action of RNA-binding proteins. Several recent discoveries highlight multiple co-translational mechanisms that modulate mRNA translation, localization, processing, and stability. These mechanisms operate by recognition of the nascent protein, which is necessarily coupled to its encoding mRNA during translation. Hence, the distinctive sequence or structure of a particular nascent chain can recruit recognition factors with privileged access to the corresponding mRNA in an otherwise crowded cellular environment. Here, we draw on both well-established and recent examples to provide a conceptual framework for how cells exploit nascent protein recognition to direct mRNA fate. These mechanisms allow cells to dynamically and specifically regulate their transcriptomes in response to changes in cellular states to maintain protein homeostasis.

Keywords:  mRNA decay; mRNA localization; nascent chain; protein biogenesis; ribosome; translational regulation

DOI:  https://doi.org/10.1016/j.molcel.2023.07.014
PLoS One. 2023 ;18(8): e0290340

DNAJB3 attenuates ER stress through direct interaction with AKT.

Zeyaul Islam, Abdoulaye Diane, Namat Khattab, Mohammed Dehbi, Paul Thornalley, Prasanna R Kolatkar.

Metabolic stress involved in several dysregulation disorders such as type 2 diabetes mellitus (T2DM) results in down regulation of several heat shock proteins (HSPs) including DNAJB3. This down regulation of HSPs is associated with insulin resistance (IR) and interventions which induce the heat shock response (HSR) help to increase the insulin sensitivity. Metabolic stress leads to changes in signaling pathways through increased activation of both c-jun N-terminal kinase-1 (JNK1) and the inhibitor of κB inflammatory kinase (IKKβ) which in turn leads to inactivation of insulin receptor substrates 1 and 2 (IRS-1 and IRS-2). DNAJB3 interacts with both JNK1 and IKKβ kinases to mitigate metabolic stress. In addition DNAJB3 also activates the PI3K-PKB/AKT pathway through increased phosphorylation of AKT1 and its substrate AS160, a Rab GTPase-activating protein, which results in mobilization of GLUT4 transporter protein and improved glucose uptake. We show through pull down that AK T1 is an interacting partner of DNAJB3, further confirmed by isothermal titration calorimetry (ITC) which quantified the avidity of AKT1 for DNAJB3. The binding interface was identified by combining protein modelling with docking of the AKT1-DNAJB3 complex. DNAJB3 is localized in the cytoplasm and ER, where it interacts directly with AKT1 and mobilizes AS160 for glucose transport. Inhibition of AKT1 resulted in loss of GLUT4 translocation activity mediated by DNAJB3 and also abolished the protective effect of DNAJB3 on tunicamycin-induced ER stress. Taken together, our findings provide evidence for a direct protein-protein interaction between DNAJB3 and AKT1 upon which DNAJB3 alleviates ER stress and promotes GLUT4 translocation.

DOI: https://doi.org/10.1371/journal.pone.0290340