bims-pideca 2025-01-19 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2025–01–19
seventeen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

ECM stiffness regulates lung fibroblast survival through RasGRF1 dependent signaling.
Challenging the Astral mass analyzer to quantify up to 5,300 proteins per single cell at unseen accuracy to uncover cellular heterogeneity.
Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics.
CDK2 activity crosstalk on the ERK kinase translocation reporter can be resolved computationally.
AI-driven automated discovery tools reveal diverse behavioral competencies of biological networks.
mTOR signalling controls protein aggregation during heat stress and cellular aging in a translation- and Hsf1-independent manner.
Towards ensuring reproducibility of outsourced data generation.
Mechanistic Target of Rapamycin Signaling Activity in the Human Placenta Across Gestation and in Maternal Obesity.
Optimized Prime Editing of Human Induced Pluripotent Stem Cells to Efficiently Generate Isogenic Models of Mendelian Diseases.
Decoding the functional impact of the cancer genome through protein-protein interactions.
Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq.
Enhanced kinase translocation reporters for simultaneous real-time measurement of PKA, ERK, and calcium.
A PI3Kδ-Foxo1-FasL signaling amplification loop rewires CD4 + T helper cell signaling, differentiation and epigenetic remodeling.
mTORC1 regulates the pyrimidine salvage pathway by controlling UCK2 turnover via the CTLH-WDR26 E3 ligase.
Cell Membrane Fatty Acids and PIPs Modulate the Etiology of Pancreatic Cancer by Regulating AKT.
Molecular Basis of Oncogenic PI3K Proteins.
Evaluating the transcriptional regulators of arterial gene expression via a catalogue of characterized arterial enhancers.

J Biol Chem. 2025 Jan 08. pii: S0021-9258(25)00008-0. [Epub ahead of print] 108161

ECM stiffness regulates lung fibroblast survival through RasGRF1 dependent signaling.

Elizabeth Monaghan-Benson, Julien Aureille, Christophe Guilluy.

  Extracellular matrix stiffness is one of the multiple mechanical signals that alters cellular behavior. During studies exploring the effect of matrix rigidity on lung fibroblast survival we discovered that enhanced survival on stiff substrates is dependent on elevated Ras activity, owing to the activation of the GEF, RasGRF1. Mechanistically, we found that the increased Ras activity lead to the activation of both the AKT and ERK pathways. Pharmacological inhibition of AKT or ERK signaling attenuates the elevated survival observed on stiff substrates. AKT signaling regulates the phosphorylation and inactivation of the transcription factor FOXO3a. RNA interference experiments demonstrate that FOXO3a activity is critical for the cell death observed on soft substrates. Additionally, downregulation of FOXO3a activity on stiff substrate leads to the degradation of the proapoptotic protein Bim. Depletion of Bim increased the survival of cells on soft substrates. Together our data show that enhanced matrix stiffness activates a RasGRF1/Ras signaling cascade that regulates the activity of AKT and ERK-dependent FOXO3a and Bim expression to alter cell survival.

Keywords:  AKT; Bcl-2 family; ERK; FOXO; Ras; apoptosis; extracellular matrix; mechanotransduction; signaling

DOI:  https://doi.org/10.1016/j.jbc.2025.108161
Nat Methods. 2025 Jan 16.

Challenging the Astral mass analyzer to quantify up to 5,300 proteins per single cell at unseen accuracy to uncover cellular heterogeneity.

Julia A Bubis, Tabiwang N Arrey, Eugen Damoc, Bernard Delanghe, Jana Slovakova, Theresa M Sommer, Harunobu Kagawa, Peter Pichler, Nicolas Rivron, Karl Mechtler, Manuel Matzinger.

Despite significant advancements in sample preparation, instrumentation and data analysis, single-cell proteomics is currently limited by proteomic depth and quantitative performance. Here we demonstrate highly improved depth of proteome coverage as well as accuracy and precision for quantification of ultra-low input amounts. Using a tailored library, we identify up to 7,400 protein groups from as little as 250 pg of HeLa cell peptides at a throughput of 50 samples per day. Using a two-proteome mix, we check for optimal parameters of quantification and show that fold change differences of 2 can still be successfully determined at single-cell-level inputs. Eventually, we apply our workflow to A549 cells, yielding a proteome coverage ranging from 1,801 to a maximum of >5,300 protein groups from a single cell depending on cell size and search strategy used, which allows for the study of dependencies between cell size and cell cycle phase. Additionally, our workflow enables us to distinguish between in vitro analogs of two human blastocyst lineages: naive human pluripotent stem cells (epiblast) and trophectoderm-like cells. Our data harmoniously align with transcriptomic data, indicating that single-cell proteomics possesses the capability to identify biologically relevant differences within the blastocyst.

DOI: https://doi.org/10.1038/s41592-024-02559-1
Nat Methods. 2025 Jan 16.

Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics.

Zilu Ye, Pierre Sabatier, Leander van der Hoeven, Maico Y Lechner, Teeradon Phlairaharn, Ulises H Guzman, Zhen Liu, Haoran Huang, Min Huang, Xiangjun Li, David Hartlmayr, Fabiana Izaguirre, Anjali Seth, Hiren J Joshi, Sergey Rodin, Karl-Henrik Grinnemo, Ole B Hørning, Dorte B Bekker-Jensen, Nicolai Bache, Jesper V Olsen.

Single-cell proteomics (SCP) promises to revolutionize biomedicine by providing an unparalleled view of the proteome in individual cells. Here, we present a high-sensitivity SCP workflow named Chip-Tip, identifying >5,000 proteins in individual HeLa cells. It also facilitated direct detection of post-translational modifications in single cells, making the need for specific post-translational modification-enrichment unnecessary. Our study demonstrates the feasibility of processing up to 120 label-free SCP samples per day. An optimized tissue dissociation buffer enabled effective single-cell disaggregation of drug-treated cancer cell spheroids, refining overall SCP analysis. Analyzing nondirected human-induced pluripotent stem cell differentiation, we consistently quantified stem cell markers OCT4 and SOX2 in human-induced pluripotent stem cells and lineage markers such as GATA4 (endoderm), HAND1 (mesoderm) and MAP2 (ectoderm) in different embryoid body cells. Our workflow sets a benchmark in SCP for sensitivity and throughput, with broad applications in basic biology and biomedicine for identification of cell type-specific markers and therapeutic targets.

DOI: https://doi.org/10.1038/s41592-024-02558-2
Cell Syst. 2025 Jan 15. pii: S2405-4712(24)00367-3. [Epub ahead of print]16(1): 101162

CDK2 activity crosstalk on the ERK kinase translocation reporter can be resolved computationally.

Timothy E Hoffman, Chengzhe Tian, Varuna Nangia, Chen Yang, Sergi Regot, Luca Gerosa, Sabrina L Spencer.

  The mitogen-activated protein kinase (MAPK) pathway integrates growth factor signaling through extracellular signal-regulated kinase (ERK) to control cell proliferation. To study ERK dynamics, many researchers use an ERK activity kinase translocation reporter (KTR). Our study reveals that this ERK KTR also partially senses cyclin-dependent kinase 2 (CDK2) activity, making it appear as if ERK activity rises as cells progress through the cell cycle. Through single-cell time-lapse imaging, we identified a residual ERK KTR signal that was eliminated by selective CDK2 inhibitors, indicating crosstalk from CDK2 onto the ERK KTR. By contrast, EKAREN5, a FRET-based ERK sensor, showed no CDK2 crosstalk. A related p38 KTR is also partly affected by CDK2 activity. To address this, we developed linear and non-linear computational correction methods that subtract CDK2 signal from the ERK and p38 KTRs. These findings will allow for more accurate quantification of MAPK activities, especially for studies of actively cycling cells.

Keywords:  CDK2 inhibitor; CDK2 sensor; EKAREN5 FRET reporter; ERK KTR; MAPK inhibitor; kinase translocation reporter; sensor crosstalk; single-cell tracking; time-lapse microscopy

DOI:  https://doi.org/10.1016/j.cels.2024.12.003
Elife. 2025 Jan 13. pii: RP92683. [Epub ahead of print]13

AI-driven automated discovery tools reveal diverse behavioral competencies of biological networks.

Mayalen Etcheverry, Clément Moulin-Frier, Pierre-Yves Oudeyer, Michael Levin.

  Many applications in biomedicine and synthetic bioengineering rely on understanding, mapping, predicting, and controlling the complex behavior of chemical and genetic networks. The emerging field of diverse intelligence investigates the problem-solving capacities of unconventional agents. However, few quantitative tools exist for exploring the competencies of non-conventional systems. Here, we view gene regulatory networks (GRNs) as agents navigating a problem space and develop automated tools to map the robust goal states GRNs can reach despite perturbations. Our contributions include: (1) Adapting curiosity-driven exploration algorithms from AI to discover the range of reachable goal states of GRNs, and (2) Proposing empirical tests inspired by behaviorist approaches to assess their navigation competencies. Our data shows that models inferred from biological data can reach a wide spectrum of steady states, exhibiting various competencies in physiological network dynamics without requiring structural changes in network properties or connectivity. We also explore the applicability of these 'behavioral catalogs' for comparing evolved competencies across biological networks, for designing drug interventions in biomedical contexts and synthetic gene networks for bioengineering. These tools and the emphasis on behavior-shaping open new paths for efficiently exploring the complex behavior of biological networks. For the interactive version of this paper, please visit https://developmentalsystems.org/curious-exploration-of-grn-competencies.

Keywords:  AI for science; basal cognition; computational biology; curiosity-driven exploration; diverse intelligence; gene regulatory network; machine learning; none; systems biology

DOI:  https://doi.org/10.7554/eLife.92683
J Biol Chem. 2025 Jan 09. pii: S0021-9258(25)00019-5. [Epub ahead of print] 108172

mTOR signalling controls protein aggregation during heat stress and cellular aging in a translation- and Hsf1-independent manner.

Arthur Fischbach, Per O Widlund, Xinxin Hao, Thomas Nyström.

  The mTOR (mechanistic target of rapamycin) signaling pathway appears central to the aging process as genetic or pharmacological inhibition of mTOR extends lifespan in most eukaryotes tested. While the regulation of protein synthesis by mTOR has been studied in great detail, its impact on protein misfolding and aggregation during stress and aging is less explored. In this study, we identified the mTOR signaling pathway and the linked SEA complex as central nodes of protein aggregation during heat stress and cellular aging, using Saccharomyces cerevisiae as a model organism. Based on a synthetic genetic array (SGA) screen, we found that reduced mTOR activity, achieved through deletion of TCO89, an mTORC1 subunit, almost completely prevents protein aggregation during heat stress and aging without reducing global translation rates and independently of an Hsf1-dependent stress response. Conversely, increased mTOR activity, achieved through deletion of NPR3, a SEA complex subunit, exacerbates protein aggregation, but not by over-activating translation. In summary, our work demonstrates that mTOR signaling is a central contributor to age-associated and heat shock-induced protein aggregation and that this is unlinked to quantitatively discernable effects on translation and Hsf1.

Keywords:  Aging; mTOR; protein aggregation; proteinopathy; proteostasis; spatial protein quality control

DOI:  https://doi.org/10.1016/j.jbc.2025.108172
PLoS Biol. 2025 Jan;23(1): e3002988

Towards ensuring reproducibility of outsourced data generation.

Daniel B Sloan, Mark D Stenglein.

"Big data" generated from outsourced or centralized facilities often lacks methodological information. Here, we outline how and why researchers, service providers, and other parties should report on methodology and sample metadata to improve scientific reproducibility.

DOI: https://doi.org/10.1371/journal.pbio.3002988
Biol Reprod. 2025 Jan 13. pii: ioaf007. [Epub ahead of print]

Mechanistic Target of Rapamycin Signaling Activity in the Human Placenta Across Gestation and in Maternal Obesity.

Katie L Bidne, Kathryn E Erickson, Theresa L Powell, Thomas Jansson.

  The mechanistic target of rapamycin (mTOR) system is vital to placental development, formation, and function. Alterations in this system in the placenta have been associated with altered fetal growth. However, changes in placental mTOR signaling across gestation are poorly understood. We collected 81 human placental samples from 4-40 weeks' gestation to test the hypothesis that placental mTOR signaling activity increases over gestation and is activated in maternal obesity in early gestation. Proteins involved in upstream mTOR regulation and mTORC1/2 downstream signaling were quantified using immunoblotting in placentas of male or female fetuses. Readouts of mTORC1 activation, phospho-rpS6 and phospho-4EBP1 were highest in first trimester and decreased across gestation. Phosphorylation of AKT (308 and 473) increased over gestation. Interestingly, abundance of cytochrome c oxidase I and mitochondrial ATP synthase, key subunits of mitochondrial complexes III/IV and V, respectively, were elevated in first trimester obese placentas compared to control, but only in placenta from female fetuses. We suggest that the high placental mTOR signaling activity in early pregnancy may be related to the high anabolism and active trophoblast proliferation and invasion in the second half of the first trimester. In addition, we conclude that maternal obesity has only limited impact on this key placental signaling pathway across gestation in women.

Keywords:  first trimester; maternal-fetal exchange; pregnancy; signal transduction; trophoblast

DOI:  https://doi.org/10.1093/biolre/ioaf007
Int J Mol Sci. 2024 Dec 26. pii: 114. [Epub ahead of print]26(1):

Optimized Prime Editing of Human Induced Pluripotent Stem Cells to Efficiently Generate Isogenic Models of Mendelian Diseases.

Rodrigo Cerna-Chavez, Alba Ortega-Gasco, Hafiz Muhammad Azhar Baig, Nathan Ehrenreich, Thibaud Metais, Michael J Scandura, Kinga Bujakowska, Eric A Pierce, Marcela Garita-Hernandez.

  Prime editing (PE) is a CRISPR-based tool for genome engineering that can be applied to generate human induced pluripotent stem cell (hiPSC)-based disease models. PE technology safely introduces point mutations, small insertions, and deletions (indels) into the genome. It uses a Cas9-nickase (nCas9) fused to a reverse transcriptase (RT) as an editor and a PE guide RNA (pegRNA), which introduces the desired edit with great precision without creating double-strand breaks (DSBs). PE leads to minimal off-targets or indels when introducing single-strand breaks (SSB) in the DNA. Low efficiency can be an obstacle to its use in hiPSCs, especially when the genetic context precludes the screening of multiple pegRNAs, and other strategies must be employed to achieve the desired edit. We developed a PE platform to efficiently generate isogenic models of Mendelian disorders. We introduced the c.25G>A (p.V9M) mutation in the NMNAT1 gene with over 25% efficiency by optimizing the PE workflow. Using our optimized system, we generated other isogenic models of inherited retinal diseases (IRDs), including the c.1481C>T (p.T494M) mutation in PRPF3 and the c.6926A>C (p.H2309P) mutation in PRPF8. We modified several determinants of the hiPSC PE procedure, such as plasmid concentrations, PE component ratios, and delivery method settings, showing that our improved workflow increased the hiPSC editing efficiency.

Keywords:  IRDs; editing efficiency; hiPSCs; isogenic models; prime editing

DOI:  https://doi.org/10.3390/ijms26010114
Nat Rev Cancer. 2025 Jan 14.

Decoding the functional impact of the cancer genome through protein-protein interactions.

Haian Fu, Xiulei Mo, Andrey A Ivanov.

Acquisition of genomic mutations enables cancer cells to gain fitness advantages under selective pressure and, ultimately, leads to oncogenic transformation. Interestingly, driver mutations, even within the same gene, can yield distinct phenotypes and clinical outcomes, necessitating a mutation-focused approach. Conversely, cellular functions are governed by molecular machines and signalling networks that are mostly controlled by protein-protein interactions (PPIs). The functional impact of individual genomic alterations could be transmitted through regulated nodes and hubs of PPIs. Oncogenic mutations may lead to modified residues of proteins, enabling interactions with other proteins that the wild-type protein does not typically interact with, or preventing interactions with proteins that the wild-type protein usually interacts with. This can result in the rewiring of molecular signalling cascades and the acquisition of an oncogenic phenotype. Here, we review the altered PPIs driven by oncogenic mutations, discuss technologies for monitoring PPIs and provide a functional analysis of mutation-directed PPIs. These driver mutation-enabled PPIs and mutation-perturbed PPIs present a new paradigm for the development of tumour-specific therapeutics. The intersection of cancer variants and altered PPI interfaces represents a new frontier for understanding oncogenic rewiring and developing tumour-selective therapeutic strategies.

DOI: https://doi.org/10.1038/s41568-024-00784-6
STAR Protoc. 2025 Jan 10. pii: S2666-1667(24)00491-X. [Epub ahead of print]6(1): 103326

Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq.

Shintaro Funasaki, Yuri Miyamura, Shunsuke Kamei, Akhinur Rahman, Masaya Yamazaki, Shingo Usuki, Keiichiro Yasunaga, Yorifumi Satou, Hiroto Ohguchi, Takashi Minami.

  Angiogenesis begins as endothelial cells migrate, forming a sprouting tip and subsequent growth-rich stalk cells. Here, we present a protocol for transcriptomic and epigenomic analyses of tip-like cells in cultured endothelial cells. We describe steps for stimulating human umbilical vein endothelial cells (HUVECs) with vascular endothelial cell growth factor (VEGF) to generate tip-like cells. We then detail procedures for library preparation for single-cell RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq), and data analysis. This scalable protocol is also applicable to diverse omics studies, including proteomics and metabolomics. For complete details on the use and execution of this protocol, please refer to Miyamura et al.1.

Keywords:  Bioinformatics; ChIP; ChIPseq; Chromatin immunoprecipitation; Gene Expression; Genomics; Molecular Biology; RNAseq; Sequence analysis; Signal Transduction; Single Cell

DOI:  https://doi.org/10.1016/j.xpro.2024.103326
J Biol Chem. 2025 Jan 13. pii: S0021-9258(25)00030-4. [Epub ahead of print] 108183

Enhanced kinase translocation reporters for simultaneous real-time measurement of PKA, ERK, and calcium.

Shang-Jui Tsai, Yijing Gong, Austin Dabbs, Fiddia Zahra, Junhao Xu, Aleksander Geske, Michael J Caterina, Stephen J Gould.

Kinase translocation reporters (KTRs) are powerful tools for single-cell measurement of time-integrated kinase activity but suffer from restricted dynamic range and limited sensitivity, particularly in neurons. To address these limitations, we developed enhanced KTRs (eKTRs) for protein kinase A (PKA) and extracellular signal-regulated kinase (ERK) by (i) increasing KTR size, which reduces the confounding effect of KTR diffusion through the nuclear pore, and (ii) modulating the strength of the bipartite nuclear localization signal (bNLS) in their kinase sensor domains, to ensures that the relative distribution of the KTR between the nucleus and cytoplasmic is determined by active nuclear import, active nuclear export, and relative activity of their cognate kinase. The resultant sets of ePKA-KTRs and eERK-KTRs display high sensitivity, broad dynamic range, and cell type-specific tuning. Moreover, co-expression of optically separable ePKA-KTRs and eERK-KTRs allowed us to simultaneously monitor the activation and inhibition of PKA and ERK in live cells, which verified that these eKTRs respond as expected to direct agonists and inhibitors, and that crosstalk between these pathways is highly unbalanced, with activation of PKA suppressing ERK activity, while activation of ERK induces PKA activity. Taken together, our findings highlight the importance of KTR size and bNLS strength to KTR sensitivity and dynamic range, show that different cell types require different eKTRs, and identify ePKA-KTR1.4 and eERK-KTR1.2 as particularly well-suited for monitoring PKA and ERK in primary sensory neurons.

DOI: https://doi.org/10.1016/j.jbc.2025.108183
bioRxiv. 2024 Nov 02. pii: 2024.10.28.620691. [Epub ahead of print]

A PI3Kδ-Foxo1-FasL signaling amplification loop rewires CD4 + T helper cell signaling, differentiation and epigenetic remodeling.

Dominic P Golec, Pedro Gazzinelli-Guimaraes, Daniel Chauss, Hiroyuki Nagashima, Kang Yu, Tom Hill, Luis Nivelo, Jennifer L Cannons, Jillian Perry, Ilin Joshi, Nicolas Pereira, Fabrício Marcus Silva Oliveira, Anthony C Cruz, Kirk M Druey, Justin B Lack, Thomas B Nutman, Alejandro V Villarino, John J O'Shea, Behdad Afzali, Pamela L Schwartzberg.

While inputs regulating CD4 + T helper cell (Th) differentiation are well-defined, the integration of downstream signaling with transcriptional and epigenetic programs that define Th-lineage identity remain unresolved. PI3K signaling is a critical regulator of T cell function; activating mutations affecting PI3Kδ result in an immunodeficiency with multiple T cell defects. Using mice expressing activated-PI3Kδ, we found aberrant expression of proinflammatory Th1-signature genes under Th2-inducing conditions, both in vivo and in vitro . This dysregulation was driven by a robust PI3Kδ-IL-2-Foxo1 signaling loop, fueling Foxo1-inactivation, loss of Th2-lineage restriction, altered chromatin accessibility and global impairment of CTCF-DNA interactions. Surprisingly, ablation of Fasl , a Foxo1-repressed gene, restored normal Th2 differentiation, TCR signaling and CTCF expression. BioID revealed Fas interactions with TCR- signaling components, which were supported by Fas-mediated potentiation of TCR signaling. Our results highlight Fas-FasL signaling as a critical intermediate in phenotypes driven by activated-PI3Kδ, thereby linking two key pathways of immune dysregulation.

DOI: https://doi.org/10.1101/2024.10.28.620691
Cell Rep. 2025 Jan 13. pii: S2211-1247(24)01530-4. [Epub ahead of print]44(1): 115179

mTORC1 regulates the pyrimidine salvage pathway by controlling UCK2 turnover via the CTLH-WDR26 E3 ligase.

Brittany Q Pham, Sang Ah Yi, Alban Ordureau, Heeseon An.

  One critical aspect of cell proliferation is increased nucleotide synthesis, including pyrimidines. Pyrimidines are synthesized through de novo and salvage pathways. Prior studies established that the mammalian target of rapamycin complex 1 (mTORC1) promotes pyrimidine synthesis by activating the de novo pathway for cell proliferation. However, the involvement of mTORC1 in regulating the salvage pathway remains unclear. Here, we report that mTORC1 controls the half-life of uridine cytidine kinase 2 (UCK2), the rate-limiting enzyme in the salvage pathway. Specifically, UCK2 is degraded via the CTLH-WDR26 E3 complex during mTORC1 inhibition, which is prevented when mTORC1 is active. We also find that UCK1, an isoform of UCK2, affects the turnover of UCK2 by influencing its cellular localization. Importantly, altered UCK2 levels through the mTORC1-CTLH E3 pathway affect pyrimidine salvage and the efficacy of pyrimidine analog prodrugs. Therefore, mTORC1-CTLH E3-mediated degradation of UCK2 adds another layer of complexity to mTORC1's role in regulating pyrimidine metabolism.

Keywords:  CP: Metabolism; CP: Molecular biology; CTLH; UCK2; WDR26; YPEL5; degradomics; mTOR; mTORC1; pyrimidine; pyrimidine salvage; ubiquitin

DOI:  https://doi.org/10.1016/j.celrep.2024.115179
Nutrients. 2024 Dec 31. pii: 150. [Epub ahead of print]17(1):

Cell Membrane Fatty Acids and PIPs Modulate the Etiology of Pancreatic Cancer by Regulating AKT.

Carolina Torres, Georgina Mancinelli, Jee-Wei Emily Chen, Jose Cordoba-Chacon, Danielle Pins, Sara Saeed, Ronald McKinney, Karla Castellanos, Giulia Orsi, Megha Singhal, Akshar Patel, Jose Acebedo, Adonis Coleman, Jorge Heneche, Poorna Chandra Rao Yalagala, Papasani V Subbaiah, Cecilia Leal, Sam Grimaldo, Francisco M Ortuno, Faraz Bishehsari, Paul J Grippo.

  Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the worst solid malignancies in regard to outcomes and metabolic dysfunction leading to cachexia. It is alarming that PDAC incidence rates continue to increase and warrant the need for innovative approaches to combat this disease. Due to its relatively slow progression (10-20 years), prevention strategies represent an effective means to improve outcomes. One of the risk factors for many cancers and for pancreatic cancer in particular is diet. Hence, our objective is to understand how a diet rich in ω3 and ω6 polyunsaturated fatty acids affects the progression of this disease. Methods: We investigated polyunsaturated fatty acid (PUFA) effects on disease progression employing both in vitro (PDAC cell lines) and in vivo (EL-Kras and KC mice) approaches. Also, we gathered data from the National Health and Nutrition Examination Survey (NHANES) and the National Cancer Institute (NCI) from 1999 to 2017 for a retrospective observational study. Results: The consumption of PUFAs in a patient population correlates with increased PDAC incidence, particularly when the ω3 intake increases to a lesser extent than ω6. Our data demonstrate dietary PUFAs can be incorporated into plasma membrane lipids affecting PI3K/AKT signaling and support the emergence of membrane-targeted therapies. Moreover, we show that the phospholipid composition of a lipid nanoparticle (LNP) can impact the cell membrane integrity and, ultimately, cell viability after administration of these LNPs. Conclusions: Cancer prevention is impactful particularly for those with very poor prognosis, including pancreatic cancer. Our results point to the importance of dietary intervention in this disease when detected early and the potential to improve the antiproliferative effect of drug efficacy when combined with these regimens in later stages of pancreatic cancer.

Keywords:  PDAC; PI3K/AKT; PIP2 (phosphatidylinositol 4,5-bisphosphate); PIP3 (phosphatidylinositol (3,4,5)-trisphosphate); diet; polyunsaturated fatty acids; prevention

DOI:  https://doi.org/10.3390/nu17010150
Cancers (Basel). 2024 Dec 30. pii: 77. [Epub ahead of print]17(1):

Molecular Basis of Oncogenic PI3K Proteins.

Zhi Sheng, Patrick Beck, Maegan Gabby, Semhar Habte-Mariam, Katherine Mitkos.

  The dysregulation of phosphatidylinositol 3-kinase (PI3K) signaling plays a pivotal role in driving neoplastic transformation by promoting uncontrolled cell survival and proliferation. This oncogenic activity is primarily caused by mutations that are frequently found in PI3K genes and constitutively activate the PI3K signaling pathway. However, tumorigenesis can also arise from nonmutated PI3K proteins adopting unique active conformations, further complicating the understanding of PI3K-driven cancers. Recent structural studies have illuminated the functional divergence among highly homologous PI3K proteins, revealing how subtle structural alterations significantly impact their activity and contribute to tumorigenesis. In this review, we summarize current knowledge of Class I PI3K proteins and aim to unravel the complex mechanism underlying their oncogenic traits. These insights will not only enhance our understanding of PI3K-mediated oncogenesis but also pave the way for the design of novel PI3K-based therapies to combat cancers driven by this signaling pathway.

Keywords:  PI3K; oncogenic mutation; oncogenic transformation; protein structure

DOI:  https://doi.org/10.3390/cancers17010077
Elife. 2025 Jan 17. pii: e102440. [Epub ahead of print]14

Evaluating the transcriptional regulators of arterial gene expression via a catalogue of characterized arterial enhancers.

Svanhild Nornes, Susann Bruche, Niharika Adak, Ian R McCracken, Sarah De Val.

  The establishment and growth of the arterial endothelium requires the coordinated expression of numerous genes. However, regulation of this process is not yet fully understood. Here, we combined in silico analysis with transgenic mice and zebrafish models to characterize arterial-specific enhancers associated with eight key arterial identity genes (Acvrl1/Alk1, Cxcr4, Cxcl12, Efnb2, Gja4/Cx37, Gja5/Cx40, Nrp1 and Unc5b). Next, to elucidate the regulatory pathways upstream of arterial gene transcription, we investigated the transcription factors binding each arterial enhancer compared to a similar assessment of non-arterial endothelial enhancers. These results found that binding of SOXF and ETS factors was a common occurrence at both arterial and pan-endothelial enhancers, suggesting neither are sufficient to direct arterial specificity. Conversely, FOX motifs independent of ETS motifs were over-represented at arterial enhancers. Further, MEF2 and RBPJ binding was enriched but not ubiquitous at arterial enhancers, potentially linked to specific patterns of behaviour within the arterial endothelium. Lastly, there was no shared or arterial-specific signature for WNT-associated TCF/LEF, TGFβ/BMP-associated SMAD1/5 and SMAD2/3, shear stress-associated KLF4 or venous-enriched NR2F2. This cohort of well characterized and in vivo-verified enhancers can now provide a platform for future studies into the interaction of different transcriptional and signalling pathways with arterial gene expression.

Keywords:  developmental biology; genetics; genomics; mouse; zebrafish

DOI:  https://doi.org/10.7554/eLife.102440