bims-pideca 2024-05-19 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2024–05–19
27 papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

Shear stress and pathophysiological PI3K involvement in vascular malformations.
The CTLH Ubiquitin Ligase Substrates ZMYND19 and MKLN1 Negatively Regulate mTORC1 at the Lysosomal Membrane.
Unexpected roles for AMPK in the suppression of autophagy and the reactivation of MTORC1 signaling during prolonged amino acid deprivation.
Down-regulation of AKT proteins slows the growth of mutant-KRAS pancreatic tumors.
Functional selection in SH3-mediated activation of the PI3 kinase.
Angpt1 binding to Tie1 regulates the signaling required for lymphatic vessel development in zebrafish.
Targeted treatment in complex lymphatic anomaly: a case of synergistic efficacy of trametinib and sirolimus.
The mitogen-activated protein kinase network, wired to dynamically function at multiple scales.
Phantasus, a web-application for visual and interactive gene expression analysis.
A spectrum of AKT3 activating mutations cause focal malformations of cortical development (FMCDs) in cortical organoids.
Delivery of AKT1 phospho-forms to human cells reveals differential substrate selectivity.
Protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique.
PI3K/HSCB axis facilitates FOG1 nuclear translocation to promote erythropoiesis and megakaryopoiesis.
Cerebral cavernous malformations - An overview on genetics, clinical aspects and therapeutic strategies.
Chemoresistance to additive PARP/PI3K dual inhibition in triple-negative breast cancer cell lines is associated with adaptive stem cell-like prevalence.
Betaglycan sustains HGF/Met signaling in lung cancer and endothelial cells promoting cell migration and tumor growth.
Multi-omics delineate growth factor network underlying exercise effects in an Alzheimer's mouse model.
The mechanosensory channel PIEZO1 functions upstream of angiopoietin/TIE/FOXO1 signaling in lymphatic development.
Replication of null results: Absence of evidence or evidence of absence?
State of the Interactomes: an evaluation of molecular networks for generating biological insights.
A guide to artificial intelligence for cancer researchers.
GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks.
AMPK as a mediator of tissue preservation: time for a shift in dogma?
Enhancing genome editing in hPSCs through dual inhibition of DNA damage response and repair pathways.
Why more biologists must embrace quantitative modeling.
OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization.
mTORC1 regulates cell survival under glucose starvation through 4EBP1/2-mediated translational reprogramming of fatty acid metabolism.

J Clin Invest. 2024 May 15. pii: e172843. [Epub ahead of print]134(10):

Shear stress and pathophysiological PI3K involvement in vascular malformations.

Salim Abdelilah-Seyfried, Roxana Ola.

Molecular characterization of vascular anomalies has revealed that affected endothelial cells (ECs) harbor gain-of-function (GOF) mutations in the gene encoding the catalytic α subunit of PI3Kα (PIK3CA). These PIK3CA mutations are known to cause solid cancers when occurring in other tissues. PIK3CA-related vascular anomalies, or "PIKopathies," range from simple, i.e., restricted to a particular form of malformation, to complex, i.e., presenting with a range of hyperplasia phenotypes, including the PIK3CA-related overgrowth spectrum. Interestingly, development of PIKopathies is affected by fluid shear stress (FSS), a physiological stimulus caused by blood or lymph flow. These findings implicate PI3K in mediating physiological EC responses to FSS conditions characteristic of lymphatic and capillary vessel beds. Consistent with this hypothesis, increased PI3K signaling also contributes to cerebral cavernous malformations, a vascular disorder that affects low-perfused brain venous capillaries. Because the GOF activity of PI3K and its signaling partners are excellent drug targets, understanding PIK3CA's role in the development of vascular anomalies may inform therapeutic strategies to normalize EC responses in the diseased state. This Review focuses on PIK3CA's role in mediating EC responses to FSS and discusses current understanding of PIK3CA dysregulation in a range of vascular anomalies that particularly affect low-perfused regions of the vasculature. We also discuss recent surprising findings linking increased PI3K signaling to fast-flow arteriovenous malformations in hereditary hemorrhagic telangiectasias.

DOI: https://doi.org/10.1172/JCI172843
Res Sq. 2024 Apr 24. pii: rs.3.rs-4259395. [Epub ahead of print]

The CTLH Ubiquitin Ligase Substrates ZMYND19 and MKLN1 Negatively Regulate mTORC1 at the Lysosomal Membrane.

Yin Wang, Rui Guo, Brenda Iturbide Piedras, Hsin-Yao Tang, John M Asara, Italo Tempera, Paul M Lieberman, Benjamin E Gewurz.

Most Epstein-Barr virus-associated gastric carcinoma (EBVaGC) harbor non-silent mutations that activate phosphoinositide 3 kinase (PI3K) to drive downstream metabolic signaling. To gain insights into PI3K/mTOR pathway dysregulation in this context, we performed a human genome-wide CRISPR/Cas9 screen for hits that synergistically blocked EBVaGC proliferation together with the PI3K antagonist alpelisib. Multiple subunits of carboxy terminal to LisH (CTLH) E3 ligase, including the catalytic MAEA subunit, were among top screen hits. CTLH negatively regulates gluconeogenesis in yeast, but not in higher organisms. Instead, we identified that the CTLH substrates MKLN1 and ZMYND19, which highly accumulated upon MAEA knockout, associated with one another and with lysosomes to inhibit mTORC1. ZMYND19/MKLN1 bound Raptor and RagA/C, but rather than perturbing mTORC1 lysosomal recruitment, instead blocked a late stage of its activation, independently of the tuberous sclerosis complex. Thus, CTLH enables cells to rapidly tune mTORC1 activity at the lysosomal membrane via the ubiquitin/proteasome pathway.

DOI: https://doi.org/10.21203/rs.3.rs-4259395/v1
Autophagy. 2024 May 14.

Unexpected roles for AMPK in the suppression of autophagy and the reactivation of MTORC1 signaling during prolonged amino acid deprivation.

Dubek Kazyken, Sydney G Dame, Claudia Wang, Maxwell Wadley, Diane C Fingar.

  AMPK promotes catabolic and suppresses anabolic cell metabolism to promote cell survival during energetic stress, in part by inhibiting MTORC1, an anabolic kinase requiring sufficient levels of amino acids. We found that cells lacking AMPK displayed increased apoptotic cell death during nutrient stress caused by prolonged amino acid deprivation. We presumed that impaired macroautophagy/autophagy explained this phenotype, as a prevailing view posits that AMPK initiates autophagy (often a pro-survival response) through phosphorylation of ULK1. Unexpectedly, however, autophagy remained unimpaired in cells lacking AMPK, as monitored by several autophagic readouts in several cell lines. More surprisingly, the absence of AMPK increased ULK1 signaling and MAP1LC3B/LC3B lipidation during amino acid deprivation while AMPK-mediated phosphorylation of ULK1 S555 (a site proposed to initiate autophagy) decreased upon amino acid withdrawal or pharmacological MTORC1 inhibition. In addition, activation of AMPK with compound 991, glucose deprivation, or AICAR blunted autophagy induced by amino acid withdrawal. These results demonstrate that AMPK activation and glucose deprivation suppress autophagy. As AMPK controlled autophagy in an unexpected direction, we examined how AMPK controls MTORC1 signaling. Paradoxically, we observed impaired reactivation of MTORC1 in cells lacking AMPK upon prolonged amino acid deprivation. Together these results oppose established views that AMPK promotes autophagy and inhibits MTORC1 universally. Moreover, they reveal unexpected roles for AMPK in the suppression of autophagy and the support of MTORC1 signaling in the context of prolonged amino acid deprivation. These findings prompt a reevaluation of how AMPK and its control of autophagy and MTORC1 affect health and disease.

Keywords:  ATG16L1; EIF4EBP1/4EBP1; LC3B; MTOR; RPS6KB1/S6K1; ULK1

DOI:  https://doi.org/10.1080/15548627.2024.2355074
bioRxiv. 2024 May 05. pii: 2024.05.03.592345. [Epub ahead of print]

Down-regulation of AKT proteins slows the growth of mutant-KRAS pancreatic tumors.

Chuankai Chen, Ya-Ping Jiang, Inchul You, Nathanael S Gray, Richard Z Lin.

Serine/threonine kinase AKT isoforms play a well-established role in cell metabolism and growth. Most pancreatic adenocarcinoma (PDAC) harbors activation mutations of KRAS, which activates the PI3K/AKT signaling pathway. However, AKT inhibitors are not effective in the treatment of pancreatic cancer. To better understand the role of AKT signaling in mutant-KRAS pancreatic tumors, this study utilizes proteolysis-targeting chimeras (PROTACs) and CRISPR-Cas9-genome editing to investigate AKT proteins. PROTAC down-regulation of AKT proteins markedly slowed the growth of three pancreatic tumor cell lines harboring mutant KRAS. In contrast, inhibition of AKT kinase activity alone had very little effect on the growth of these cell lines. Concurrent genetic deletion of all AKT isoforms (AKT1, AKT2, and AKT3) in the KPC ( Kras G12D ; Trp53 R172H ; Pdx1-Cre ) pancreatic cancer cell line also dramatically slowed its growth in vitro and when orthotopically implanted in syngeneic mice. Surprisingly, insulin-like growth factor-1 (IGF-1), but not epidermal growth factor (EGF), restored KPC cell growth in serum-deprived conditions and the IGF-1 growth stimulation effect was AKT dependent. RNA-seq analysis of AKT1/2/3-deficient KPC cells suggested that reduced cholesterol synthesis may be responsible for the decreased response to IGF-1 stimulation. These results indicate that the presence of all three AKT isoforms supports pancreatic tumor cell growth and pharmacological degradation of AKT proteins may be more effective than AKT catalytic inhibitors for treating pancreatic cancer.

DOI: https://doi.org/10.1101/2024.05.03.592345
bioRxiv. 2024 Apr 30. pii: 2024.04.30.591319. [Epub ahead of print]

Functional selection in SH3-mediated activation of the PI3 kinase.

Safia S Aljedani, Abdullah Aldehaiman, Anandsukeerthi Sandholu, Siba Alharbi, Victor C Y Mak, Haiyan Wu, Adrien Lugari, Mariusz Jaremko, Xavier Morelli, Jonathan W Backer, John E Ladbury, Michał Nowakowski, Lydia W T Cheung, Stefan T Arold.

The phosphoinositide-3 kinase (PI3K), a heterodimeric enzyme, plays a pivotal role in cellular metabolism and survival. Its deregulation is associated with major human diseases, particularly cancer. The p85 regulatory subunit of PI3K binds to the catalytic p110 subunit via its C-terminal domains, stabilising it in an inhibited state. Certain Src homology 3 (SH3) domains can activate p110 by binding to the proline-rich (PR) 1 motif located at the N-terminus of p85. However, the mechanism by which this N-terminal interaction activates the C-terminally bound p110 remains elusive. Moreover, the intrinsically poor ligand selectivity of SH3 domains raises the question of how they can control PI3K. Combining structural, biophysical, and functional methods, we demonstrate that the answers to both these unknown issues are linked: PI3K-activating SH3 domains engage in additional "tertiary" interactions with the C-terminal domains of p85, thereby relieving their inhibition of p110. SH3 domains lacking these tertiary interactions may still bind to p85 but cannot activate PI3K. Thus, p85 uses a functional selection mechanism that precludes nonspecific activation rather than nonspecific binding. This separation of binding and activation may provide a general mechanism for how biological activities can be controlled by promiscuous protein-protein interaction domains.

DOI: https://doi.org/10.1101/2024.04.30.591319
Development. 2024 May 14. pii: dev.202269. [Epub ahead of print]

Angpt1 binding to Tie1 regulates the signaling required for lymphatic vessel development in zebrafish.

Nanami Morooka, Ning Gui, Koji Ando, Keisuke Sako, Moe Fukumoto, Urara Hasegawa, Melina Hußmann, Stefan Schulte-Merker, Naoki Mochizuki, Hiroyuki Nakajima.

  Development of the vascular system is regulated by multiple signaling pathways mediated by receptor tyrosine kinases (RTKs). Among them, angiopoietin (Ang)/Tie signaling regulates lymphatic and blood vessel development in mammals. Of the two Tie receptors, Tie2 is well known as a key mediator of Ang/Tie signaling, but unexpectedly, recent studies reveal that the Tie2 locus has been lost in many vertebrate species, while the Tie1 gene is more commonly present. However, Tie1-driven signaling pathways, including ligands and cellular functions, are not well understood. Here, we performed comprehensive mutant analyses of angiopoietins and Tie receptors in zebrafish and found that only angpt1 and tie1 mutants show defects in trunk lymphatic vessel development. Among zebrafish angiopoietins, only Angpt1 binds to Tie1 as a ligand. We indirectly monitored Ang1/Tie1 signaling and detected Tie1 activation in sprouting endothelial cells (ECs), where Tie1 inhibits nuclear import of EGFP-Foxo1a. Angpt1/Tie1 signaling functions in EC migration, proliferation, and lymphatic specification during early lymphangiogenesis, at least in part by modulating Vegfc/Vegfr3 signaling. Thus, we show Angpt1/Tie1 signaling to constitute an essential signaling pathway for lymphatic development in zebrafish.

Keywords:  Live imaging; Lymphangiogenesis; Tie1; Zebrafish

DOI:  https://doi.org/10.1242/dev.202269
Orphanet J Rare Dis. 2024 May 16. 19(1): 199

Targeted treatment in complex lymphatic anomaly: a case of synergistic efficacy of trametinib and sirolimus.

Emmanuel Seront, Antoine Froidure, Nicole Revencu, Valerie Dekeuleneer, Philippe Clapuyt, Dana Dumitriu, Miikka Vikkula, Laurence M Boon.

  Repurposing anticancer drugs to vascular malformations has significantly improved patient outcomes. Complex Lymphatic Anomalies (CLA) are part of the spectrum of lymphatic malformations (LMs) that share similar oncogenic mutations to cancer. We report the case of a young patient with highly symptomatic CLA who was initially treated with sirolimus, due to the frequent involvement of the PI3K-AKT-mTOR pathway in CLA pathogenesis. Despite an initial reduction in symptoms, sirolimus progressively lost its effectiveness. After an unsuccessful attempt with trametinib alone, sirolimus was added to trametinib and resulted in a significant, rapid and sustained improvement in symptoms. This suggests that, contrary to current dogmas, combination therapy using sub-therapeutic doses targeting both the PI3K and RAS pathways retains efficacy without generating the toxicity known for combination therapies, and is beneficial in the management of CLAs and potentially other vascular anomalies.

Keywords:  Complex lymphatic anomaly; Infection; Lymphedema; Sirolimus; Trametinib; VASE

DOI:  https://doi.org/10.1186/s13023-024-03211-z
Curr Opin Cell Biol. 2024 May 15. pii: S0955-0674(24)00047-4. [Epub ahead of print]88 102368

The mitogen-activated protein kinase network, wired to dynamically function at multiple scales.

Paolo Armando Gagliardi, Olivier Pertz.

The mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) signaling network is a key transducer of signals from various receptors, including receptor tyrosine kinases (RTKs). It controls cell-cycle entry, survival, motility, differentiation, as well as other fates. After four decades of studying this pathway with biochemical methods, the use of fluorescent biosensors has revealed dynamic behaviors such as ERK pulsing, oscillations, and amplitude-modulated activity. Different RTKs equip the MAPK network with specific feedback mechanisms to encode these different ERK dynamics, which are then subsequently decoded into cytoskeletal events and transcriptional programs, actuating cellular fates. Recently, collective ERK wave behaviors have been observed in multiple systems to coordinate cytoskeletal dynamics with fate decisions within cell collectives. This emphasizes that a correct understanding of this pathway requires studying it at multiple scales.

DOI: https://doi.org/10.1016/j.ceb.2024.102368
Elife. 2024 May 14. pii: e85722. [Epub ahead of print]13

Phantasus, a web-application for visual and interactive gene expression analysis.

Maksim Kleverov, Daria Zenkova, Vladislav Kamenev, Margarita Sablina, Maxim N Artyomov, Alexey A Sergushichev.

  Transcriptomic profiling became a standard approach to quantify a cell state, which led to accumulation of huge amount of public gene expression datasets. However, both reuse of these datasets or analysis of newly generated ones requires significant technical expertise. Here we present Phantasus - a user-friendly web-application for interactive gene expression analysis which provides a streamlined access to more than 96000 public gene expression datasets, as well as allows analysis of user-uploaded datasets. Phantasus integrates an intuitive and highly interactive JavaScript-based heatmap interface with an ability to run sophisticated R-based analysis methods. Overall Phantasus allows users to go all the way from loading, normalizing and filtering data to doing differential gene expression and downstream analysis. Phantasus can be accessed on-line at https://alserglab.wustl.edu/phantasus or can be installed locally from Bioconductor (https://bioconductor.org/packages/phantasus). Phantasus source code is available at https://github.com/ctlab/phantasus under MIT license.

Keywords:  computational biology; none; systems biology

DOI:  https://doi.org/10.7554/eLife.85722
Biochim Biophys Acta Mol Basis Dis. 2024 May 15. pii: S0925-4439(24)00221-7. [Epub ahead of print] 167232

A spectrum of AKT3 activating mutations cause focal malformations of cortical development (FMCDs) in cortical organoids.

Ying Xu, Rongrong Lu, Hao Li, Weijun Feng, Rui Zhao.

  Focal malformations of cortical development (FMCDs) are brain disorders mainly caused by hyperactive mTOR signaling due to both inactivating and activating mutations of genes in the PI3K-AKT-mTOR pathway. Among them, mosaic and somatic activating mutations of the mTOR pathway activators are more frequently linked to severe form of FMCDs. A human stem cell-based FMCDs model to study these activating mutations is still lacking. Herein, we genetically engineer human embryonic stem cell lines carrying these activating mutations to generate cortical organoids. Mosaic and somatic expression of AKT3 activating mutations in cortical organoids mimicking the disease presentation with overproliferation and the formation of dysmorphic neurons. In parallel comparison of various AKT3 activating mutations reveals that stronger mutation is associated with more severe neuronal migratory and overgrowth defects. Together, we have established a feasible human stem cell-based model for FMCDs that could help to better understand pathogenic mechanism and develop novel therapeutic strategy.

Keywords:  AKT3 mutations; Cortical organoids; Focal malformations of cortical development (FMCDs); Mosaic and somatic mutations, dysmorphic neurons

DOI:  https://doi.org/10.1016/j.bbadis.2024.167232
IUBMB Life. 2024 May 13.

Delivery of AKT1 phospho-forms to human cells reveals differential substrate selectivity.

Tarana Siddika, Richard Shao, Ilka U Heinemann, Patrick O'Donoghue.

  Protein kinase B (AKT1) is a serine/threonine kinase that regulates fundamental cellular processes, including cell survival, proliferation, and metabolism. AKT1 activity is controlled by two regulatory phosphorylation sites (Thr308, Ser473) that stimulate a downstream signaling cascade through phosphorylation of many target proteins. At either or both regulatory sites, hyperphosphorylation is associated with poor survival outcomes in many human cancers. Our previous biochemical and chemoproteomic studies showed that the phosphorylated forms of AKT1 have differential selectivity toward peptide substrates. Here, we investigated AKT1-dependent activity in human cells, using a cell-penetrating peptide (transactivator of transcription, TAT) to deliver inactive AKT1 or active phospho-variants to cells. We used enzyme engineering and genetic code expansion relying on a phosphoseryl-transfer RNA (tRNA) synthetase (SepRS) and tRNASep pair to produce TAT-tagged AKT1 with programmed phosphorylation at one or both key regulatory sites. We found that all TAT-tagged AKT1 variants were efficiently delivered into human embryonic kidney (HEK 293T) cells and that only the phosphorylated AKT1 (pAKT1) variants stimulated downstream signaling. All TAT-pAKT1 variants induced glycogen synthase kinase (GSK)-3α phosphorylation, as well as phosphorylation of ribosomal protein S6 at Ser240/244, demonstrating stimulation of downstream AKT1 signaling. Fascinatingly, only the AKT1 variants phosphorylated at S473 (TAT-pAKT1S473 or TAT-pAKT1T308,S473) were able to increase phospho-GSK-3β levels. Although each TAT-pAKT1 variant significantly stimulated cell proliferation, cells transduced with TAT-pAKT1T308 grew significantly faster than with the other pAKT1 variants. The data demonstrate differential activity of the AKT1 phospho-forms in modulating downstream signaling and proliferation in human cells.

Keywords:  aminoacyl‐tRNA synthetase; cell proliferation; cellular signaling; cell‐penetrating peptide; genetic code expansion; glycogen synthase kinase 3‐alpha; glycogen synthase kinase 3‐beta; phosphorylation; protein kinase B (AKT1); ribosomal protein S6; tRNASep

DOI:  https://doi.org/10.1002/iub.2826
STAR Protoc. 2024 May 14. pii: S2666-1667(24)00231-4. [Epub ahead of print]5(2): 103066

Protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique.

Manqi Zhou, Hao Zhang, Zilong Bai, Dylan Mann-Krzisnik, Fei Wang, Yue Li.

  The advent of single-cell multi-omics sequencing technology makes it possible for researchers to leverage multiple modalities for individual cells. Here, we present a protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique called moETM. We describe steps for data preprocessing, multi-omics integration, inclusion of prior pathway knowledge, and cross-omics imputation. As a demonstration, we used the single-cell multi-omics data collected from bone marrow mononuclear cells (GSE194122) as in our original study. For complete details on the use and execution of this protocol, please refer to Zhou et al.1.

Keywords:  bioinformatics; computer sciences; genomics; single cell

DOI:  https://doi.org/10.1016/j.xpro.2024.103066
Elife. 2024 May 17. pii: RP95815. [Epub ahead of print]13

PI3K/HSCB axis facilitates FOG1 nuclear translocation to promote erythropoiesis and megakaryopoiesis.

Gang Liu, Yunxuan Hou, Xin Jin, Yixue Zhang, Chaoyue Sun, Chengquan Huang, Yujie Ren, Jianmin Gao, Xiuli Wang, Xiumei Jiang.

  Erythropoiesis and megakaryopoiesis are stringently regulated by signaling pathways. However, the precise molecular mechanisms through which signaling pathways regulate key transcription factors controlling erythropoiesis and megakaryopoiesis remain partially understood. Herein, we identified heat shock cognate B (HSCB), which is well known for its iron-sulfur cluster delivery function, as an indispensable protein for friend of GATA 1 (FOG1) nuclear translocation during erythropoiesis of K562 human erythroleukemia cells and cord-blood-derived human CD34+CD90+hematopoietic stem cells (HSCs), as well as during megakaryopoiesis of the CD34+CD90+HSCs. Mechanistically, HSCB could be phosphorylated by phosphoinositol-3-kinase (PI3K) to bind with and mediate the proteasomal degradation of transforming acidic coiled-coil containing protein 3 (TACC3), which otherwise detained FOG1 in the cytoplasm, thereby facilitating FOG1 nuclear translocation. Given that PI3K is activated during both erythropoiesis and megakaryopoiesis, and that FOG1 is a key transcription factor for these processes, our findings elucidate an important, previously unrecognized iron-sulfur cluster delivery independent function of HSCB in erythropoiesis and megakaryopoiesis.

Keywords:  FOG1 nuclear translocation; HSCB; PI3K; cell biology; erythropoiesis; human; megakaryopoiesis

DOI:  https://doi.org/10.7554/eLife.95815
J Neurol Sci. 2024 May 12. pii: S0022-510X(24)00179-5. [Epub ahead of print]461 123044

Cerebral cavernous malformations - An overview on genetics, clinical aspects and therapeutic strategies.

Adriana Octaviana Dulamea, Ioan Cristian Lupescu.

  Cerebral cavernous malformations (CCMs) are abnormally packed blood vessels lined with endothelial cells, that do not exhibit intervening tight junctions, lack muscular and elastic layers and are usually surrounded by hemosiderin and gliosis. CCMs may be sporadic or familial autosomal dominant (FCCMs) caused by loss of function mutations in CCM1 (KRIT1), CCM2 (MGC4607), and CCM3 (PDCD10) genes. In the FCCMs, patients have multiple CCMs, different family members are affected, and developmental venous anomalies are absent. CCMs may be asymptomatic or may manifest with focal neurological deficits with or without associated hemorrhage andseizures. Recent studies identify a digenic "triple-hit" mechanism involving the aquisition of three distinct genetic mutations that culminate in phosphatidylinositol-3-kinase (PIK3CA) gain of function, as the basis for rapidly growing and clinically symptomatic CCMs. The pathophysiology of CCMs involves signaling aberrations in the neurovascular unit, including proliferative dysangiogenesis, blood-brain barrier hyperpermeability, inflammation and immune mediated processes, anticoagulant vascular domain, and gut microbiome-driven mechanisms. Clinical trials are investigating potential therapies, magnetic resonance imaging and plasma biomarkers for hemorrhage and CCMs-related epilepsy, as well as different techniques of neuronavigation and neurosonology to guide surgery in order to minimize post-operatory morbidity and mortality. This review addresses the recent data about the natural history, genetics, neuroimaging and therapeutic approaches for CCMs.

Keywords:  Cerebral cavernous malformations; Phosphatidylinositol-3-kinase; Stereotactic radiosurgery; Surgery

DOI:  https://doi.org/10.1016/j.jns.2024.123044
bioRxiv. 2024 Apr 30. pii: 2024.04.28.591568. [Epub ahead of print]

Chemoresistance to additive PARP/PI3K dual inhibition in triple-negative breast cancer cell lines is associated with adaptive stem cell-like prevalence.

Paula E Petrella, Jason W Chen, Gabrielle O Ravelo, Benjamin D Cosgrove.

Cancer stem-like cells (CSCs) are posited to exhibit specialized oncogenic capacity to drive malignancies. CSCs are distinguished by enhanced hallmarks of cancer, including apoptosis avoidance, phenotypic plasticity and aberrant growth pathway signaling. Standard-of-care chemotherapies targeted to rapidly cycling cells routinely fail to eliminate this resistant subpopulation, leading to disease recurrence and metastasis. Triple-negative breast cancer (TNBC), a highly aggressive subtype of breast cancer, is enriched for tumor-propagating CD44 + /CD24 -/low CSCs, which are poorly ablated by chemotherapeutics and are associated with poor prognosis. CD44 governs sustained PI3K signaling in breast cancer, which is essential for CSC maintenance. PI3K inhibition can elicit DNA damage and down-regulate BRCA1 expression, which in turn enhance the synthetic lethality of PARP inhibitors. Here, we examined a dual chemotherapeutic approach targeting these pathways by combining a pan-PI3K inhibitor (Buparlisib) and a PARP1 inhibitor (Olaparib) on a panel of TNBC cell lines with distinct mutational profiles and proportions of CSCs. We observed differential sensitivity to this dual inhibition strategy and varying cellular stress and resistance responses across eight TNBC lines. The dual chemotherapeutic effect is associated with a reduction in S-phase cells, an increased in apoptotic cells and elevated expression of cleaved PARP, indicating a provoked replicative stress response. We observed that PARP/PI3K inhibition efficacy was potentiated by repeated administration in some TNBC lines and identified critical treatment schedules, which further potentiated the dual chemotherapeutic effect. Dual inhibition induced small but significant increases in CSC relative abundance as marked by CD44 + /CD24 -/low or ALDH1 + cells and increased stress and survival signaling in multiple TNBC cell lines, suggesting this sub-population contributes to TNBC chemoresistance. These results suggest the additive effects of PARP and PI3K inhibition against CSC phenotypes may be enhanced by temporally-staged administration in TNBC cells.

DOI: https://doi.org/10.1101/2024.04.28.591568
Heliyon. 2024 May 15. 10(9): e30520

Betaglycan sustains HGF/Met signaling in lung cancer and endothelial cells promoting cell migration and tumor growth.

Rodolfo Daniel Cervantes-Villagrana, Valentín Mendoza, Cynthia S Hinck, Rosa Luz de la Fuente-León, Andrew P Hinck, Guadalupe Reyes-Cruz, José Vázquez-Prado, Fernando López-Casillas.

  Persistent HGF/Met signaling drives tumor growth and dissemination. Proteoglycans within the tumor microenvironment might control HGF availability and signaling by affecting its accessibility to Met (HGF receptor), likely defining whether acute or sustained HGF/Met signaling cues take place. Given that betaglycan (BG, also known as type III TGFβ receptor or TGFBR3), a multi-faceted proteoglycan TGFβ co-receptor, can be found within the tumor microenvironment, we addressed its hypothetical role in oncogenic HGF signaling. We found that HGF/Met promotes lung cancer and endothelial cells migration via PI3K and mTOR. This effect was enhanced by recombinant soluble betaglycan (solBG) via a mechanism attributable to its glycosaminoglycan chains, as a mutant without them did not modulate HGF effects. Moreover, soluble betaglycan extended the effect of HGF-induced phosphorylation of Met, Akt, and Erk, and membrane recruitment of the RhoGEF P-Rex1. Data-mining analysis of lung cancer patient datasets revealed a significant correlation between high MET receptor, HGF, and PREX1 expression and reduced patient survival. Soluble betaglycan showed biochemical interaction with HGF and, together, they increased tumor growth in immunocompetent mice. In conclusion, the oncogenic properties of the HGF/Met pathway are enhanced and sustained by GAG-containing soluble betaglycan.

Keywords:  Betaglycan; Cancer cell migration; Glycosaminoglycans; HGF; P-Rex1; RhoGEF; TGFBR3

DOI:  https://doi.org/10.1016/j.heliyon.2024.e30520
bioRxiv. 2024 May 05. pii: 2024.05.02.592289. [Epub ahead of print]

Multi-omics delineate growth factor network underlying exercise effects in an Alzheimer's mouse model.

Xin Li, Chaozhong Liu, Wenbo Li, Yanwan Dai, Chaohao Gu, Wenjun Zhou, Veronica C Ciliberto, Jing Liang, Udhaya Kumar S, Dongyin Guan, Zhaoyong Hu, Hui Zheng, Hu Chen, Zhandong Liu, Ying-Wooi Wan, Zheng Sun.

Physical exercise represents a primary defense against age-related cognitive decline and neurodegenerative disorders like Alzheimer's disease (AD). To impartially investigate the underlying mechanisms, we conducted single-nucleus transcriptomic and chromatin accessibility analyses (snRNA-seq and ATAC-seq) on the hippocampus of mice carrying AD-linked NL-G-F mutations in the amyloid precursor protein gene (APP NL-G-F ) following prolonged voluntary wheel-running exercise. Our study reveals that exercise mitigates amyloid-induced changes in both transcriptomic expression and chromatin accessibility through cell type-specific transcriptional regulatory networks. These networks converge on the activation of growth factor signaling pathways, particularly the epidermal growth factor receptor (EGFR) and insulin signaling, correlating with an increased proportion of immature dentate granule cells and oligodendrocytes. Notably, the beneficial effects of exercise on neurocognitive functions can be blocked by pharmacological inhibition of EGFR and the downstream phosphoinositide 3-kinases (PI3K). Furthermore, exercise leads to elevated levels of heparin-binding EGF (HB-EGF) in the blood, and intranasal administration of HB-EGF enhances memory function in sedentary APP NL-G-F mice. These findings offer a panoramic delineation of cell type-specific hippocampal transcriptional networks activated by exercise and suggest EGF-related growth factor signaling as a druggable contributor to exercise-induced memory enhancement, thereby suggesting therapeutic avenues for combatting AD-related cognitive decline.

DOI: https://doi.org/10.1101/2024.05.02.592289
J Clin Invest. 2024 May 15. pii: e176577. [Epub ahead of print]134(10):

The mechanosensory channel PIEZO1 functions upstream of angiopoietin/TIE/FOXO1 signaling in lymphatic development.

Jing Du, Pan Liu, Yalu Zhou, Sol Misener, Isha Sharma, Phoebe Leeaw, Benjamin R Thomson, Jing Jin, Susan E Quaggin.

  Lymphedema is a debilitating disease with no effective cure and affects an estimated 250 million individuals worldwide. Prior studies have identified mutations in piezo-type mechanosensitive ion channel component 1 (PIEZO1), angiopoietin 2 (ANGPT2), and tyrosine kinase with Ig-like and EGF-like domains 1 (TIE1) in patients with primary lymphedema. Here, we identified crosstalk between these molecules and showed that activation of the mechanosensory channel PIEZO1 in lymphatic endothelial cells (LECs) caused rapid exocytosis of the TIE ligand ANGPT2, ectodomain shedding of TIE1 by disintegrin and metalloproteinase domain-containing protein 17 (ADAM17), and increased TIE/PI3K/AKT signaling, followed by nuclear export of the transcription factor FOXO1. These data establish a functional network between lymphedema-associated genes and provide what we believe to be the first molecular mechanism bridging channel function with vascular signaling and intracellular events culminating in transcriptional regulation of genes expressed in LECs. Our study provides insights into the regulation of lymphatic function and molecular pathways involved in human disease.

Keywords:  Development; Embryonic development; Endothelial cells; Ion channels; Vascular biology

DOI:  https://doi.org/10.1172/JCI176577
Elife. 2024 May 13. pii: RP92311. [Epub ahead of print]12

Replication of null results: Absence of evidence or evidence of absence?

Samuel Pawel, Rachel Heyard, Charlotte Micheloud, Leonhard Held.

  In several large-scale replication projects, statistically non-significant results in both the original and the replication study have been interpreted as a 'replication success.' Here, we discuss the logical problems with this approach: Non-significance in both studies does not ensure that the studies provide evidence for the absence of an effect and 'replication success' can virtually always be achieved if the sample sizes are small enough. In addition, the relevant error rates are not controlled. We show how methods, such as equivalence testing and Bayes factors, can be used to adequately quantify the evidence for the absence of an effect and how they can be applied in the replication setting. Using data from the Reproducibility Project: Cancer Biology, the Experimental Philosophy Replicability Project, and the Reproducibility Project: Psychology we illustrate that many original and replication studies with 'null results' are in fact inconclusive. We conclude that it is important to also replicate studies with statistically non-significant results, but that they should be designed, analyzed, and interpreted appropriately.

Keywords:  Bayesian hypothesis testing; cancer biology; equivalence testing; meta-research; none; null hypothesis; replication success

DOI:  https://doi.org/10.7554/eLife.92311
bioRxiv. 2024 Apr 29. pii: 2024.04.26.587073. [Epub ahead of print]

State of the Interactomes: an evaluation of molecular networks for generating biological insights.

Sarah N Wright, Scott Colton, Leah V Schaffer, Rudolf T Pillich, Christopher Churas, Dexter Pratt, Trey Ideker.

Advancements in genomic and proteomic technologies have powered the use of gene and protein networks ("interactomes") for understanding genotype-phenotype translation. However, the proliferation of interactomes complicates the selection of networks for specific applications. Here, we present a comprehensive evaluation of 46 current human interactomes, encompassing protein-protein interactions as well as gene regulatory, signaling, colocalization, and genetic interaction networks. Our analysis shows that large composite networks such as HumanNet, STRING, and FunCoup are most effective for identifying disease genes, while smaller networks such as DIP and SIGNOR demonstrate strong interaction prediction performance. These findings provide a benchmark for interactomes across diverse network biology applications and clarify factors that influence network performance. Furthermore, our evaluation pipeline paves the way for continued assessment of emerging and updated interaction networks in the future.

DOI: https://doi.org/10.1101/2024.04.26.587073
Nat Rev Cancer. 2024 May 16.

A guide to artificial intelligence for cancer researchers.

Raquel Perez-Lopez, Narmin Ghaffari Laleh, Faisal Mahmood, Jakob Nikolas Kather.

Artificial intelligence (AI) has been commoditized. It has evolved from a specialty resource to a readily accessible tool for cancer researchers. AI-based tools can boost research productivity in daily workflows, but can also extract hidden information from existing data, thereby enabling new scientific discoveries. Building a basic literacy in these tools is useful for every cancer researcher. Researchers with a traditional biological science focus can use AI-based tools through off-the-shelf software, whereas those who are more computationally inclined can develop their own AI-based software pipelines. In this article, we provide a practical guide for non-computational cancer researchers to understand how AI-based tools can benefit them. We convey general principles of AI for applications in image analysis, natural language processing and drug discovery. In addition, we give examples of how non-computational researchers can get started on the journey to productively use AI in their own work.

DOI: https://doi.org/10.1038/s41568-024-00694-7
Nat Commun. 2024 May 14. 15(1): 4055

GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks.

Yazdan Zinati, Abdulrahman Takiddeen, Amin Emad.

We introduce GRouNdGAN, a gene regulatory network (GRN)-guided reference-based causal implicit generative model for simulating single-cell RNA-seq data, in silico perturbation experiments, and benchmarking GRN inference methods. Through the imposition of a user-defined GRN in its architecture, GRouNdGAN simulates steady-state and transient-state single-cell datasets where genes are causally expressed under the control of their regulating transcription factors (TFs). Training on six experimental reference datasets, we show that our model captures non-linear TF-gene dependencies and preserves gene identities, cell trajectories, pseudo-time ordering, and technical and biological noise, with no user manipulation and only implicit parameterization. GRouNdGAN can synthesize cells under new conditions to perform in silico TF knockout experiments. Benchmarking various GRN inference algorithms reveals that GRouNdGAN effectively bridges the existing gap between simulated and biological data benchmarks of GRN inference algorithms, providing gold standard ground truth GRNs and realistic cells corresponding to the biological system of interest.

DOI: https://doi.org/10.1038/s41467-024-48516-6
Nat Rev Endocrinol. 2024 May 17.

AMPK as a mediator of tissue preservation: time for a shift in dogma?

Henning Tim Langer, Maria Rohm, Marcus DaSilva Goncalves, Lykke Sylow.

Ground-breaking discoveries have established 5'-AMP-activated protein kinase (AMPK) as a central sensor of metabolic stress in cells and tissues. AMPK is activated through cellular starvation, exercise and drugs by either directly or indirectly affecting the intracellular AMP (or ADP) to ATP ratio. In turn, AMPK regulates multiple processes of cell metabolism, such as the maintenance of cellular ATP levels, via the regulation of fatty acid oxidation, glucose uptake, glycolysis, autophagy, mitochondrial biogenesis and degradation, and insulin sensitivity. Moreover, AMPK inhibits anabolic processes, such as lipogenesis and protein synthesis. These findings support the notion that AMPK is a crucial regulator of cell catabolism. However, studies have revealed that AMPK's role in cell homeostasis might not be as unidirectional as originally thought. This Review explores emerging evidence for AMPK as a promoter of cell survival and an enhancer of anabolic capacity in skeletal muscle and adipose tissue during catabolic crises. We discuss AMPK-activating interventions for tissue preservation during tissue wasting in cancer-associated cachexia and explore the clinical potential of AMPK activation in wasting conditions. Overall, we provide arguments that call for a shift in the current dogma of AMPK as a mere regulator of cell catabolism, concluding that AMPK has an unexpected role in tissue preservation.

DOI: https://doi.org/10.1038/s41574-024-00992-y
Nat Commun. 2024 May 11. 15(1): 4002

Enhancing genome editing in hPSCs through dual inhibition of DNA damage response and repair pathways.

Ju-Chan Park, Yun-Jeong Kim, Gue-Ho Hwang, Chan Young Kang, Sangsu Bae, Hyuk-Jin Cha.

Precise genome editing is crucial for establishing isogenic human disease models and ex vivo stem cell therapy from the patient-derived hPSCs. Unlike Cas9-mediated knock-in, cytosine base editor and prime editor achieve the desirable gene correction without inducing DNA double strand breaks. However, hPSCs possess highly active DNA repair pathways and are particularly susceptible to p53-dependent cell death. These unique characteristics impede the efficiency of gene editing in hPSCs. Here, we demonstrate that dual inhibition of p53-mediated cell death and distinct activation of the DNA damage repair system upon DNA damage by cytosine base editor or prime editor additively enhanced editing efficiency in hPSCs. The BE4stem system comprised of p53DD, a dominant negative p53, and three UNG inhibitor, engineered to specifically diminish base excision repair, improves cytosine base editor efficiency in hPSCs. Addition of dominant negative MLH1 to inhibit mismatch repair activity and p53DD in the conventional prime editor system also significantly enhances prime editor efficiency in hPSCs. Thus, combined inhibition of the distinct cellular cascades engaged in hPSCs upon gene editing could significantly enhance precise genome editing in these cells.

DOI: https://doi.org/10.1038/s41467-024-48111-9
Integr Comp Biol. 2024 May 13. pii: icae038. [Epub ahead of print]

Why more biologists must embrace quantitative modeling.

Brook G Milligan, Ashley T Rohde.

Biology as a field has transformed since the time of its foundation from an organized enterprise cataloging the diversity of the natural world to a quantitatively rigorous science seeking to answer complex questions about the functions of organisms and their interactions with each other and their environments. As the mathematical rigor of biological analyses has improved, quantitative models have been developed to describe multi-mechanistic systems and to test complex hypotheses. However, applications of quantitative models have been uneven across fields, and many biologists lack the foundational training necessary to apply them in their research or to interpret their results to inform biological problem-solving efforts. This gap in scientific training has created a false dichotomy of "biologists'' and "modelers" that only exacerbates the barriers to working biologists seeking additional training in quantitative modeling. Here, we make the argument that all biologists are modelers, and are capable of using sophisticated quantitative modeling in their work. We highlight four benefits of conducting biological research within the framework of quantitative models, identify the potential producers and consumers of information produced by such models, and make recommendations for strategies to overcome barriers to their widespread implementation. Improved understanding of quantitative modeling could guide the producers of biological information to better apply biological measurements through analyses that evaluate mechanisms, and allow consumers of biological information to better judge the quality and applications of the information they receive. As our explanations of biological phenomena increase in complexity, so too must we embrace modeling as a foundational skill.

DOI: https://doi.org/10.1093/icb/icae038
Nat Methods. 2024 May 14.

OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization.

Gustaf Ahdritz, Nazim Bouatta, Christina Floristean, Sachin Kadyan, Qinghui Xia, William Gerecke, Timothy J O'Donnell, Daniel Berenberg, Ian Fisk, Niccolò Zanichelli, Bo Zhang, Arkadiusz Nowaczynski, Bei Wang, Marta M Stepniewska-Dziubinska, Shang Zhang, Adegoke Ojewole, Murat Efe Guney, Stella Biderman, Andrew M Watkins, Stephen Ra, Pablo Ribalta Lorenzo, Lucas Nivon, Brian Weitzner, Yih-En Andrew Ban, Shiyang Chen, Minjia Zhang, Conglong Li, Shuaiwen Leon Song, Yuxiong He, Peter K Sorger, Emad Mostaque, Zhao Zhang, Richard Bonneau, Mohammed AlQuraishi.

AlphaFold2 revolutionized structural biology with the ability to predict protein structures with exceptionally high accuracy. Its implementation, however, lacks the code and data required to train new models. These are necessary to (1) tackle new tasks, like protein-ligand complex structure prediction, (2) investigate the process by which the model learns and (3) assess the model's capacity to generalize to unseen regions of fold space. Here we report OpenFold, a fast, memory efficient and trainable implementation of AlphaFold2. We train OpenFold from scratch, matching the accuracy of AlphaFold2. Having established parity, we find that OpenFold is remarkably robust at generalizing even when the size and diversity of its training set is deliberately limited, including near-complete elisions of classes of secondary structure elements. By analyzing intermediate structures produced during training, we also gain insights into the hierarchical manner in which OpenFold learns to fold. In sum, our studies demonstrate the power and utility of OpenFold, which we believe will prove to be a crucial resource for the protein modeling community.

DOI: https://doi.org/10.1038/s41592-024-02272-z
Nat Commun. 2024 May 14. 15(1): 4083

mTORC1 regulates cell survival under glucose starvation through 4EBP1/2-mediated translational reprogramming of fatty acid metabolism.

Tal Levy, Kai Voeltzke, Laura Hruby, Khawla Alasad, Zuelal Bas, Marteinn Snaebjörnsson, Ran Marciano, Katerina Scharov, Mélanie Planque, Kim Vriens, Stefan Christen, Cornelius M Funk, Christina Hassiepen, Alisa Kahler, Beate Heider, Daniel Picard, Jonathan K M Lim, Anja Stefanski, Katja Bendrin, Andres Vargas-Toscano, Ulf D Kahlert, Kai Stühler, Marc Remke, Moshe Elkabets, Thomas G P Grünewald, Andreas S Reichert, Sarah-Maria Fendt, Almut Schulze, Guido Reifenberger, Barak Rotblat, Gabriel Leprivier.

Energetic stress compels cells to evolve adaptive mechanisms to adjust their metabolism. Inhibition of mTOR kinase complex 1 (mTORC1) is essential for cell survival during glucose starvation. How mTORC1 controls cell viability during glucose starvation is not well understood. Here we show that the mTORC1 effectors eukaryotic initiation factor 4E binding proteins 1/2 (4EBP1/2) confer protection to mammalian cells and budding yeast under glucose starvation. Mechanistically, 4EBP1/2 promote NADPH homeostasis by preventing NADPH-consuming fatty acid synthesis via translational repression of Acetyl-CoA Carboxylase 1 (ACC1), thereby mitigating oxidative stress. This has important relevance for cancer, as oncogene-transformed cells and glioma cells exploit the 4EBP1/2 regulation of ACC1 expression and redox balance to combat energetic stress, thereby supporting transformation and tumorigenicity in vitro and in vivo. Clinically, high EIF4EBP1 expression is associated with poor outcomes in several cancer types. Our data reveal that the mTORC1-4EBP1/2 axis provokes a metabolic switch essential for survival during glucose starvation which is exploited by transformed and tumor cells.

DOI: https://doi.org/10.1038/s41467-024-48386-y