bims-pideca 2023-02-12 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2023–02–12
34 papers selected by
Ralitsa Radostinova Madsen, University College London

PI(3,5)P 2 Controls the Signaling Activity of Class I PI3K.
Phosphoinositol 3-kinase-driven NET formation involves different isoforms and signaling partners depending on the stimulus.
Targeting Class I-II-III PI3Ks in Cancer Therapy: Recent Advances in Tumor Biology and Preclinical Research.
Phosphoproteomics Profiling Defines a Target Landscape of the Basophilic Protein Kinases AKT, S6K, and RSK in Skeletal Myotubes.
ATP-competitive and allosteric inhibitors induce differential conformational changes at the autoinhibitory interface of Akt1.
Failed down-regulation of PI3K signaling makes autoreactive B cells receptive to bystander T cell help.
Insulin receptor-inspired soluble insulin binder.
Loss of Pten in Renal Tubular Cells Leads to Water Retention by Upregulating AQP2.
scMINER: a mutual information-based framework for identifying hidden drivers from single-cell omics data.
PKD autoinhibition in trans regulates activation loop autophosphorylation in cis.
CRaTER enrichment for on-target gene-editing enables generation of variant libraries in hiPSCs.
An optimised protocol for the investigation of insulin signalling in a human cell culture model of adipogenesis.
Neurovascular development in Pten and Tsc2 mouse mutants.
Engineering 3D micro-compartments for highly efficient and scale-independent expansion of human pluripotent stem cells in bioreactors.
satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications.
Phase separation enhances probability of receptor signalling and drug targeting.
The PROTECTOR strategy employs dCas orthologs to sterically shield off-target sites from CRISPR/Cas activity.
Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation.
Metabolic stress-induced human beta-cell death is mediated by increased intracellular levels of adenosine.
AlphaFold and beyond.
ZBTB12 is a molecular barrier to dedifferentiation in human pluripotent stem cells.
Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT.
AKT Phosphorylates FAM13A and Promotes Its Degradation via CUL4A/DDB1/DCAF1 E3 Complex.
Epigenetics as a mediator of plasticity in cancer.
Allosteric regulation of CAD modulates de novo pyrimidine synthesis during the cell cycle.
Compressed phenotypic screens for complex multicellular models and high-content assays.
Recycling of modified H2A-H2B provides short-term memory of chromatin states.
When cancer strikes (twice).
Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes.
Rethinking academia in a time of climate crisis.
Systems Biology in ELIXIR: modelling in the spotlight.
Multilingual translation for zero-shot biomedical classification using BioTranslator.
Day-night and seasonal variation of human gene expression across tissues.
Mitotic DNA synthesis in response to replication stress requires the sequential action of DNA polymerases zeta and delta in human cells.

bioRxiv. 2023 Jan 25. pii: 2023.01.25.525550. [Epub ahead of print]

PI(3,5)P 2 Controls the Signaling Activity of Class I PI3K.

Jiachen Sun, Seohyeon Song, Indira Singaram, Ashutosh Sharma, Wei Wang, Yusi Hu, Wen-Ting Lo, Philipp Alexander Koch, Jean J Zhao, Volker Haucke, Ruixuan Gao, Wonhwa Cho.

3'-Phosphoinositides are ubiquitous cellular lipids that play pivotal regulatory roles in health and disease. Generation of 3'-phosphoinositides are driven by three families of phosphoinositide 3-kinases (PI3K) but the mechanisms underlying their regulation and cross-talk are not fully understood. Among 3'-phosphoinositides, phosphatidylinositol-3,5-bisphosphate (PI(3,5)P 2 ) remains the least understood species in terms of its spatiotemporal dynamics and physiological function due to the lack of specific probes. By means of spatiotemporally resolved in situ quantitative imaging of PI(3,5)P 2 using a newly developed ratiometric PI(3,5)P 2 sensor we demonstrate that a special pool of PI(3,5)P 2 is generated on lysosomes and late endosomes in response to growth factor stimulation. This PI(3,5)P 2 pool, the formation of which is mediated by Class II PI3KC2β and PIKFyve, plays a crucial role in terminating the activity of growth factor-stimulated Class I PI3K, one of the most frequently mutated proteins in cancer, via specific interaction with its regulatory p85 subunit. Cancer-causing mutations of Class I PI3K inhibit the p85-PI(3,5)P 2 interaction and thereby induce sustained activation of Class I PI3K. Our results unravel a hitherto unknown tight regulatory interplay between Class I and II PI3Ks mediated by PI(3,5)P 2 , which may be important for controlling the strength of PI3K-mediated growth factor signaling. These results also suggest a new therapeutic possibility of treating cancer patients with p85 mutations.

DOI: https://doi.org/10.1101/2023.01.25.525550
Front Immunol. 2023 ;14 1042686

Phosphoinositol 3-kinase-driven NET formation involves different isoforms and signaling partners depending on the stimulus.

Vanessa de Carvalho Oliveira, Olga Tatsiy, Patrick P McDonald.

  Neutrophil extracellular traps (NETs) serve to immobilize and kill pathogens, but also can contribute to the progression of several inflammatory and auto-immune diseases, as well as cancer. Whence the importance of elucidating the mechanisms underlying NET formation. In this regard, the PI3K signaling pathway has been shown to be crucial; yet little is known about which of its components are involved. Here, we identified the PI3K isoforms and associated signaling partners that are mobilized in response to different classes of physiological NET inducers (inflammatory cytokines, growth factors, chemoattractants). NET generation was assessed by microscopy and signalling molecule activation by immunoblot using phospho-antibodies. Across the various stimuli, PI3Kα and PI3Kγ isoforms clearly contributed to NET induction, while the participation of other isoforms was stimulus-dependent. Some PI3K isoforms were also found to signal through Akt, the canonical downstream effector of PI3K, while others did not. Downstream of PI3K, mTOR and PLCγ2 were used by all stimuli to control NET generation. Conversely, the involvement of other kinases depended on the stimulus - both TNFα and GM-CSF relied on PDK1 and Akt; and both TNFα and fMLP additionally used S6K. We further established that all PI3K isoforms and downstream effectors act belatedly in NET generation, as reported previously for PI3K. Finally, we revisited the PI3K-PDK1-Akt signaling hierarchy in human neutrophils and again found stimulus-dependent differences. Our data uncover unsuspected complexity and redundancy in the signaling machinery controlling NET formation through the all-important PI3K pathway. Conserved signaling molecules represent therapeutic targets for pathologies involving NETs and in this regard, the existence of drugs currently used in the clinic or undergoing clinical trials (which target PI3K isoforms, mTOR or Akt), underscores the translational potential of our findings.

Keywords:  Akt; PDK1; PI 3-kinase; PLCγ2; mTOR; neutrophil extracellular traps

DOI:  https://doi.org/10.3389/fimmu.2023.1042686
Cancers (Basel). 2023 Jan 27. pii: 784. [Epub ahead of print]15(3):

Targeting Class I-II-III PI3Ks in Cancer Therapy: Recent Advances in Tumor Biology and Preclinical Research.

Benoît Thibault, Fernanda Ramos-Delgado, Julie Guillermet-Guibert.

  Phosphatidylinositol-3-kinase (PI3K) enzymes, producing signaling phosphoinositides at plasma and intracellular membranes, are key in intracellular signaling and vesicular trafficking pathways. PI3K is a family of eight enzymes divided into three classes with various functions in physiology and largely deregulated in cancer. Here, we will review the recent evidence obtained during the last 5 years on the roles of PI3K class I, II and III isoforms in tumor biology and on the anti-tumoral action of PI3K inhibitors in preclinical cancer models. The dependency of tumors to PI3K isoforms is dictated by both genetics and context (e.g., the microenvironment). The understanding of class II/III isoforms in cancer development and progression remains scarce. Nonetheless, the limited available data are consistent and reveal that there is an interdependency between the pathways controlled by all PI3K class members in their role to promote cancer cell proliferation, survival, growth, migration and metabolism. It is unknown whether this feature contributes to partial treatment failure with isoform-selective PI3K inhibitors. Hence, a better understanding of class II/III functions to efficiently inhibit their positive and negative interactions with class I PI3Ks is needed. This research will provide the proof-of-concept to develop combination treatment strategies targeting several PI3K isoforms simultaneously.

Keywords:  PI3K; cancer; cell signaling; combi/hybrid molecules; combination therapeutics

DOI:  https://doi.org/10.3390/cancers15030784
J Proteome Res. 2023 Feb 10.

Phosphoproteomics Profiling Defines a Target Landscape of the Basophilic Protein Kinases AKT, S6K, and RSK in Skeletal Myotubes.

Anna L Fricke, Wignand W D Mühlhäuser, Lena Reimann, Johannes P Zimmermann, Christa Reichenbach, Bettina Knapp, Christian D Peikert, Alexander M Heberle, Erik Faessler, Sascha Schäuble, Udo Hahn, Kathrin Thedieck, Gerald Radziwill, Bettina Warscheid.

  Phosphorylation-dependent signal transduction plays an important role in regulating the functions and fate of skeletal muscle cells. Central players in the phospho-signaling network are the protein kinases AKT, S6K, and RSK as part of the PI3K-AKT-mTOR-S6K and RAF-MEK-ERK-RSK pathways. However, despite their functional importance, knowledge about their specific targets is incomplete because these kinases share the same basophilic substrate motif RxRxxp[ST]. To address this, we performed a multifaceted quantitative phosphoproteomics study of skeletal myotubes following kinase inhibition. Our data corroborate a cross talk between AKT and RAF, a negative feedback loop of RSK on ERK, and a putative connection between RSK and PI3K signaling. Altogether, we report a kinase target landscape containing 49 so far unknown target sites. AKT, S6K, and RSK phosphorylate numerous proteins involved in muscle development, integrity, and functions, and signaling converges on factors that are central for the skeletal muscle cytoskeleton. Whereas AKT controls insulin signaling and impinges on GTPase signaling, nuclear signaling is characteristic for RSK. Our data further support a role of RSK in glucose metabolism. Shared targets have functions in RNA maturation, stability, and translation, which suggests that these basophilic kinases establish an intricate signaling network to orchestrate and regulate processes involved in translation.

Keywords:  RXRXXS/T motif; cross talk; kinase inhibitors; kinase−substrate enrichment analysis (KSEA); kinase−substrate relationship; label-free; mass spectrometry; parallel reaction monitoring (PRM); protein phosphorylation; quantification; signal transduction; skeletal muscle cells; stable isotope labeling by amino acids in cell culture; text mining

DOI:  https://doi.org/10.1021/acs.jproteome.2c00505
Structure. 2023 Jan 30. pii: S0969-2126(23)00009-6. [Epub ahead of print]

ATP-competitive and allosteric inhibitors induce differential conformational changes at the autoinhibitory interface of Akt1.

Alexandria L Shaw, Matthew A H Parson, Linda Truebestein, Meredith L Jenkins, Thomas A Leonard, John E Burke.

  Akt is a master regulator of pro-growth signaling in the cell. Akt is activated by phosphoinositides that disrupt the autoinhibitory interface between the kinase and pleckstrin homology (PH) domains and then is phosphorylated at T308 and S473. Akt hyperactivation is oncogenic, which has spurred development of potent and selective inhibitors as therapeutics. Using hydrogen deuterium exchange mass spectrometry (HDX-MS), we interrogated the conformational changes upon binding Akt ATP-competitive and allosteric inhibitors. We compared inhibitors against three different states of Akt1. The allosteric inhibitor caused substantive conformational changes and restricts membrane binding. ATP-competitive inhibitors caused extensive allosteric conformational changes, altering the autoinhibitory interface and leading to increased membrane binding, suggesting that the PH domain is more accessible for membrane binding. This work provides unique insight into the autoinhibitory conformation of the PH and kinase domain and conformational changes induced by Akt inhibitors and has important implications for the design of Akt targeted therapeutics.

Keywords:  ATP-competitive inhibitors; Akt; Akt1; HDX-MS; PKB; allosteric inhibitor; allostery; hydrogen exchange; protein kinase

DOI:  https://doi.org/10.1016/j.str.2023.01.007
bioRxiv. 2023 Jan 23. pii: 2023.01.23.525206. [Epub ahead of print]

Failed down-regulation of PI3K signaling makes autoreactive B cells receptive to bystander T cell help.

Brigita E Fiske, Andrew Getahun.

The role of T cell help in autoantibody responses is not well understood. Since tolerance mechanisms govern both T and B cell responses, one might predict that both T cell tolerance and B cell tolerance must be defeated in autoantibody responses requiring T cell help. To define whether autoreactive B cells depend on T cells to generate autoantibody responses, we studied the role of T cells in autoantibody responses resulting from acute cell-specific deletion of regulatory phosphatases. Ars/A1 B cells are DNA-reactive and require continuous inhibitory signaling by the tyrosine phosphatase SHP-1 and the inositol phosphatases SHIP-1 and PTEN to maintain unresponsiveness. Acute B cell-restricted deletion of any of these phosphatases results in an autoantibody response. Here we show that CD40-CD40L interactions are required to support autoantibody responses of B cells whose anergy has been compromised. If the B cell-intrinsic driver of loss of tolerance is failed negative regulation of PI3K signaling, bystander T cells provide sufficient CD40-mediated signal 2 to support an autoantibody response. However, while autoantibody responses driven by acute B cell-targeted deletion of SHP-1 also require T cells, bystander T cell help does not suffice. These results demonstrate that upregulation of PI3K signaling in autoreactive B cells, recapitulating the effect of multiple autoimmunity risk alleles, promotes autoantibody responses both by increasing B cellsâ€™ cooperation with non-cognate T cell help, as well as by altering BCR signaling. Receptiveness to bystander T cell help enables autoreactive B cells to circumvent the fail-safe of T cell tolerance.
Significance: Phosphatase suppression of PI3K signaling is an important mechanism by which peripheral autoreactive B cells are kept in an unresponsive/anergic state. Loss of this suppression, due to genetic alleles that confer risk of autoimmunity, often occurs in autoreactive B cells of individuals who develop autoimmune disease. Here we demonstrate that de-repression of PI3K signaling promotes autoantibody responses of a DNA-reactive B cell clone by relaxing dependence of autoantibody responses on T cell-derived helper signals. These results suggest that impaired regulation of PI3K signaling can promote autoantibody responses in two ways: by restoring antigen receptor signaling and by enabling autoreactive B cells to circumvent restrictions imposed by T cell tolerance mechanisms.

DOI: https://doi.org/10.1101/2023.01.23.525206
Eur J Cell Biol. 2023 Feb 03. pii: S0171-9335(23)00008-0. [Epub ahead of print]102(2): 151293

Insulin receptor-inspired soluble insulin binder.

Christopher Mendoza, Cameron Hanegan, Alek Sperry, Logan Vargas, Trevor Case, Benjamin Bikman, Dario Mizrachi.

  The insulin receptor (IR) is a 320 kDa membrane receptor tyrosine kinase mediating the pleiotropic actions of insulin, leading to phosphorylation of several intracellular substrates including serine/threonine-protein kinase (AKT1), and IR autophosphorylation. Structural details of the IR have been recently revealed. A high-binding insulin site, L1 (Kd =2 nM), consists of two distant domains in the primary sequence of the IR. Our design simplified the L1 binding site and transformed it into a soluble insulin binder (sIB). The sIB, a 17 kDa protein, binds insulin with 38 nM affinity. The sIB competes with IR for insulin and reduces by more than 50% phosphorylation of AKT1 in HEK 293 T cells, with similar effects on IR autophosphorylation. The sIB represents a new tool for research of insulin binding and signaling properties.

Keywords:  AKT; Insulin; Insulin receptor

DOI:  https://doi.org/10.1016/j.ejcb.2023.151293
Kidney Dis (Basel). 2023 Jan;9(1): 58-71

Loss of Pten in Renal Tubular Cells Leads to Water Retention by Upregulating AQP2.

Zhuo Sun, Xiaotong Shao, Haotian Wu, Yaxian Zhao, Yidan Cao, Danhua Li, Ying Sun, Qingling Wang.

   Introduction: Phosphatase and tensin (PTEN) is a multifunctional gene associated with the normal development and physiological function of various tissues including the kidney. However, its role in renal tubular reabsorption function has not been well elucidated.
Methods: We generated a renal tubule-specific Pten knockout mouse model by crossing Ptenfl/fl mice with Ksp-Cre transgenic mice, evaluated the effect of Pten loss on renal tubular function, and investigated the underlying mechanisms.
Results: Pten loss resulted in abnormal renal structure and function and water retention in multiple organs. Our results also demonstrated that aquaporin-2 (AQP2), an important water channel protein, was upregulated and concentrated on the apical plasma membrane of collecting duct cells, which could be responsible for the impaired water balance in Pten loss mice. The regulation of Pten loss on AQP2 was mediated by protein kinase B (AKT) activation.
Conclusions: Our results reveal a connection between PTEN gene inactivation and water retention, suggesting the importance of PTEN in normal kidney development and function.

Keywords:  AQP2; Kidney; PTEN; Water retention

DOI:  https://doi.org/10.1159/000528010
bioRxiv. 2023 Jan 27. pii: 2023.01.26.523391. [Epub ahead of print]

scMINER: a mutual information-based framework for identifying hidden drivers from single-cell omics data.

Liang Ding, Hao Shi, Chenxi Qian, Chad Burdyshaw, Joao Pedro Veloso, Alireza Khatamian, Qingfei Pan, Yogesh Dhungana, Zhen Xie, Isabel Risch, Xu Yang, Xin Huang, Lei Yan, Michael Rusch, Michael Brewer, Koon-Kiu Yan, Hongbo Chi, Jiyang Yu.

The sparse nature of single-cell omics data makes it challenging to dissect the wiring and rewiring of the transcriptional and signaling drivers that regulate cellular states. Many of the drivers, referred to as "hidden drivers", are difficult to identify via conventional expression analysis due to low expression and inconsistency between RNA and protein activity caused by post-translational and other modifications. To address this issue, we developed scMINER, a mutual information (MI)-based computational framework for unsupervised clustering analysis and cell-type specific inference of intracellular networks, hidden drivers and network rewiring from single-cell RNA-seq data. We designed scMINER to capture nonlinear cell-cell and gene-gene relationships and infer driver activities. Systematic benchmarking showed that scMINER outperforms popular single-cell clustering algorithms, especially in distinguishing similar cell types. With respect to network inference, scMINER does not rely on the binding motifs which are available for a limited set of transcription factors, therefore scMINER can provide quantitative activity assessment for more than 6,000 transcription and signaling drivers from a scRNA-seq experiment. As demonstrations, we used scMINER to expose hidden transcription and signaling drivers and dissect their regulon rewiring in immune cell heterogeneity, lineage differentiation, and tissue specification. Overall, activity-based scMINER is a widely applicable, highly accurate, reproducible and scalable method for inferring cellular transcriptional and signaling networks in each cell state from scRNA-seq data. The scMINER software is publicly accessible via: https://github.com/jyyulab/scMINER .

DOI: https://doi.org/10.1101/2023.01.26.523391
Proc Natl Acad Sci U S A. 2023 Feb 14. 120(7): e2212909120

PKD autoinhibition in trans regulates activation loop autophosphorylation in cis.

Ronja Reinhardt, Kai Hirzel, Gisela Link, Stephan A Eisler, Tanja Hägele, Matthew A H Parson, John E Burke, Angelika Hausser, Thomas A Leonard.

  Phosphorylation is a ubiquitous mechanism by which signals are transduced in cells. Protein kinases, enzymes that catalyze the phosphotransfer reaction are, themselves, often regulated by phosphorylation. Paradoxically, however, a substantial fraction of more than 500 human protein kinases are capable of catalyzing their own activation loop phosphorylation. Commonly, these kinases perform this autophosphorylation reaction in trans, whereby transient dimerization leads to the mutual phosphorylation of the activation loop of the opposing protomer. In this study, we demonstrate that protein kinase D (PKD) is regulated by the inverse mechanism of dimerization-mediated trans-autoinhibition, followed by activation loop autophosphorylation in cis. We show that PKD forms a stable face-to-face homodimer that is incapable of either autophosphorylation or substrate phosphorylation. Dissociation of this trans-autoinhibited dimer results in activation loop autophosphorylation, which occurs exclusively in cis. Phosphorylation serves to increase PKD activity and prevent trans-autoinhibition, thereby switching PKD on. Our findings not only reveal the mechanism of PKD regulation but also have profound implications for the regulation of many other eukaryotic kinases.

Keywords:  autoinhibition; autophosphorylation; cis; kinase; trans

DOI:  https://doi.org/10.1073/pnas.2212909120
bioRxiv. 2023 Jan 26. pii: 2023.01.25.525582. [Epub ahead of print]

CRaTER enrichment for on-target gene-editing enables generation of variant libraries in hiPSCs.

Clayton E Friedman, Shawn Fayer, Sriram Pendyala, Wei-Ming Chien, Linda Tran, Leslie Chao, Ashley Mckinstry, Elaheh Karbassi, Aidan M Fenix, Alexander Loiben, Charles E Murry, Lea M Starita, Douglas M Fowler, Kai-Chun Yang.

Standard transgenic cell line generation requires screening 100-1000s of colonies to isolate correctly edited cells. We describe CR ISPR a On- T arget E diting R etrieval (CRaTER) which enriches for cells with on-target knock-in of a cDNA-fluorescent reporter transgene by transient activation of the targeted locus followed by flow sorting to recover edited cells. We show CRaTER recovers rare cells with heterozygous, biallelic-editing of the transcriptionally-inactive MYH7 locus in human induced pluripotent stem cells (hiPSCs), enriching on average 25-fold compared to standard antibiotic selection. We leveraged CRaTER to enrich for heterozygous knock-in of a library of single nucleotide variants (SNVs) in MYH7 , a gene in which missense mutations cause cardiomyopathies, and recovered hiPSCs with 113 different MYH7 SNVs. We differentiated these hiPSCs to cardiomyocytes and show MYH7 fusion proteins can localize as expected. Thus, CRaTER substantially reduces screening required for isolation of gene-edited cells, enabling generation of transgenic cell lines at unprecedented scale.

DOI: https://doi.org/10.1101/2023.01.25.525582
Adipocyte. 2023 Feb 10. 2179339

An optimised protocol for the investigation of insulin signalling in a human cell culture model of adipogenesis.

Jonathan M Gamwell, Keanu Paphiti, Leanne Hodson, Fredrik Karpe, Katherine E Pinnick, Marijana Todorčević.

  While there is no standardised protocol for the differentiation of human adipocytes in culture, common themes exist in the use of supra-physiological glucose and hormone concentrations, and an absence of exogenous fatty acids. These factors can have detrimental effects on some aspects of adipogenesis and adipocyte function. Here, we present methods for modifying the adipogenic differentiation protocol to overcome impaired glucose uptake and insulin signalling in human adipose-derived stem cell lines derived from the stromovascular fraction of abdominal and gluteal subcutaneous adipose tissue. By reducing the length of exposure to adipogenic hormones, in combination with a physiological glucose concentration (5 mM), and the provision of exogenous fatty acids (reflecting typical dietary fatty acids), we were able to restore early insulin signalling events and glucose uptake, which were impaired by extended use of hormones and a high glucose concentration, respectively. Furthermore, the addition of exogenous fatty acids greatly increased the storage of triglycerides and removed the artificial demand to synthesise all fatty acids by de novo lipogenesis. Thus, modifying the adipogenic cocktail can enhance functional aspects of human adipocytes in vitro and is an important variable to consider prior to in vitro investigations into adipocyte biology.

Keywords:  Adipogenic cocktail; adipocyte; adipose stem cell; cell model; glucose uptake; insulin signalling

DOI:  https://doi.org/10.1080/21623945.2023.2179339
eNeuro. 2023 Feb 09. pii: ENEURO.0340-22.2023. [Epub ahead of print]

Neurovascular development in Pten and Tsc2 mouse mutants.

Mary Dusing, Candi L LaSarge, Angela White, Lilian G Jerow, Christina Gross, Steve C Danzer.

  Hyperactivation of the mTOR signaling pathway is linked to more than a dozen neurological diseases, causing a range of pathologies, including excess neuronal growth, disrupted neuronal migration, cortical dysplasia, epilepsy and autism. The mTOR pathway also regulates angiogenesis. For the present study, therefore, we queried whether loss of Pten or Tsc2, both mTOR negative regulators, alters brain vasculature in three mouse models: one with Pten loss restricted to hippocampal dentate granule cells (DGC-Pten KOs), a second with widespread Pten loss from excitatory forebrain neurons (FB-Pten KOs) and a third with focal loss of Tsc2 from cortical excitatory neurons (f-Tsc2 KOs). Total hippocampal vessel length and volume per dentate gyrus were dramatically increased in DGC-Pten knockouts. DGC-Pten knockouts had larger dentate gyri overall, however, and when normalized to these larger structures, vessel density was preserved. In addition, tests of blood-brain barrier integrity did not reveal increased permeability. FB-Pten KOs recapitulated the findings in the more restricted DGC-Pten KOs, with increased vessel area, but preserved vessel density. FB-Pten KOs did, however, exhibit elevated levels of the angiogenic factor VegfA. In contrast to findings with Pten, focal loss of Tsc2 from cortical excitatory neurons produced a localized increase in vessel density. Together, these studies demonstrate that hypervascularization is not a consistent feature of mTOR hyperactivation models and suggest that loss of different mTOR pathway regulatory genes exert distinct effects on angiogenesis.Significance StatementHere, we examined three mouse models to determine whether mTOR hyperactivation consistently drives brain hypervascularization. Both focal loss of Pten from dentate granule cells, and widespread loss from forebrain produced larger brain structures and corresponding increases in vascular growth, but normal vessel density. By contrast, focal cortical Tsc2 lesions exhibited significantly increased vessel density. Findings indicate that hypervascularization is not characteristic of all mTOR hyperactivation models and suggest vascular changes may be driven by gene-specific effects.

Keywords:  Angiogenesis; Focal Cortical Dysplasia; Vegf; mTOR; mtoropathy; tuberous sclerosis

DOI:  https://doi.org/10.1523/ENEURO.0340-22.2023
Biomaterials. 2023 Feb 02. pii: S0142-9612(23)00041-8. [Epub ahead of print]295 122033

Engineering 3D micro-compartments for highly efficient and scale-independent expansion of human pluripotent stem cells in bioreactors.

Philippe J R Cohen, Elisa Luquet, Justine Pletenka, Andrea Leonard, Elise Warter, Basile Gurchenkov, Jessica Carrere, Clément Rieu, Jerome Hardouin, Fabien Moncaubeig, Michael Lanero, Eddy Quelennec, Helene Wurtz, Emilie Jamet, Maelle Demarco, Celine Banal, Paul Van Liedekerke, Pierre Nassoy, Maxime Feyeux, Nathalie Lefort, Kevin Alessandri.

  Human pluripotent stem cells (hPSCs) have emerged as the most promising cellular source for cell therapies. To overcome the scale-up limitations of classical 2D culture systems, suspension cultures have been developed to meet the need for large-scale culture in regenerative medicine. Despite constant improvements, current protocols that use microcarriers or generate cell aggregates only achieve moderate amplification performance. Here, guided by reports showing that hPSCs can self-organize in vitro into cysts reminiscent of the epiblast stage in embryo development, we developed a physio-mimetic approach for hPSC culture. We engineered stem cell niche microenvironments inside microfluidics-assisted core-shell microcapsules. We demonstrate that lumenized three-dimensional colonies significantly improve viability and expansion rates while maintaining pluripotency compared to standard hPSC culture platforms such as 2D cultures, microcarriers, and aggregates. By further tuning capsule size and culture conditions, we scale up this method to industrial-scale stirred tank bioreactors and achieve an unprecedented hPSC amplification rate of 277-fold in 6.5 days. In brief, our findings indicate that our 3D culture system offers a suitable strategy both for basic stem cell biology experiments and for clinical applications.

Keywords:  3D culture; Biomicrofluidics; Cell expansion; Human induced pluripotent stem cells; Stem cell niche

DOI:  https://doi.org/10.1016/j.biomaterials.2023.122033
F1000Res. 2021 ;10 374

satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications.

Jeroen Gilis, Kristoffer Vitting-Seerup, Koen Van den Berge, Lieven Clement.

  Alternative splicing produces multiple functional transcripts from a single gene. Dysregulation of splicing is known to be associated with disease and as a hallmark of cancer. Existing tools for differential transcript usage (DTU) analysis either lack in performance, cannot account for complex experimental designs or do not scale to massive scRNA-seq data. We introduce satuRn, a fast and flexible quasi-binomial generalized linear modelling framework that is on par with the best performing DTU methods from the bulk RNA-seq realm, while providing good false discovery rate control, addressing complex experimental designs and scaling to scRNA-seq applications.

Keywords:  RNA-seq; differential transcript usage; satuRn; single-cell transcriptomics; splicing; statistical framework

DOI:  https://doi.org/10.12688/f1000research.51749.1
Trends Biochem Sci. 2023 Feb 07. pii: S0968-0004(23)00018-X. [Epub ahead of print]

Phase separation enhances probability of receptor signalling and drug targeting.

John E Ladbury, Chi-Chuan Lin, Kin Man Suen.

  The probability of a given receptor tyrosine kinase (RTK) triggering a defined cellular outcome is low because of the promiscuous nature of signalling, the randomness of molecular diffusion through the cell, and the ongoing nonfunctional submembrane signalling activity or noise. Signal transduction is therefore a 'numbers game', where enough cell surface receptors and effector proteins must initially be engaged to guarantee formation of a functional signalling complex against a background of redundant events. The presence of intracellular liquid-liquid phase separation (LLPS) at the plasma membrane provides a mechanism through which the probabilistic nature of signalling can be weighted in favour of the required, discrete cellular outcome and mutual exclusivity in signal initiation.

Keywords:  phase separation kinase signalling; protein condensate; protein droplet

DOI:  https://doi.org/10.1016/j.tibs.2023.01.005
Sci Rep. 2023 Feb 09. 13(1): 2280

The PROTECTOR strategy employs dCas orthologs to sterically shield off-target sites from CRISPR/Cas activity.

Daniel M Sapozhnikov, Moshe Szyf.

Off-target mutagenesis of CRISPR/Cas systems must be solved to facilitate safe gene therapy. Here, we report a novel approach, termed "PROTECTOR", to shield known off-target sites by directing the binding of an orthologous nuclease-dead Cas protein to the off-target site to sterically interfere with Cas activity. We show that this method reduces off-target mutation rates of two well-studied guide RNAs without compromising on-target activity and that it can be used in combination with high-fidelity Cas enzymes to further reduce off-target editing. This expands the suite of off-target mitigation strategies and offers an ability to protect off-target sites even when their sequences are fully identical to target sites.

DOI: https://doi.org/10.1038/s41598-023-29332-2
Elife. 2023 Feb 07. pii: e84319. [Epub ahead of print]12

Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation.

Marco Caligaris, Raffaele Nicastro, Zehan Hu, Farida Tripodi, Johannes Erwin Hummel, Benjamin Pillet, Marie-Anne Deprez, Joris Winderickx, Sabine Rospert, Paola Coccetti, Jörn Dengjel, Claudio De Virgilio.

  The AMP-activated protein kinase (AMPK) and the target of rapamycin complex 1 (TORC1) are central kinase modules of two opposing signaling pathways that control eukaryotic cell growth and metabolism in response to the availability of energy and nutrients. Accordingly, energy depletion activates AMPK to inhibit growth, while nutrients and high energy levels activate TORC1 to promote growth. Both in mammals and lower eukaryotes such as yeast, the AMPK and TORC1 pathways are wired to each other at different levels, which ensures homeostatic control of growth and metabolism. In this context, a previous study (Hughes Hallet et. al, 2015) reported that AMPK in yeast, i.e. Snf1, prevents the transient TORC1 reactivation during the early phase following acute glucose starvation, but the underlying mechanism has remained elusive. Using a combination of unbiased mass spectrometry (MS)-based phosphoproteomics, genetic, biochemical, and physiological experiments, we show here that Snf1 temporally maintains TORC1 inactive in glucose-starved cells primarily through the TORC1-regulatory protein Pib2. Our data, therefore, extend the function of Pib2 to a hub that integrates both glucose and, as reported earlier, glutamine signals to control TORC1. We further demonstrate that Snf1 phosphorylates the TORC1 effector kinase Sch9 within its N-terminal region and thereby antagonizes the phosphorylation of a C-terminal TORC1-target residue within Sch9 itself that is critical for its activity. The consequences of Snf1-mediated phosphorylation of Pib2 and Sch9 are physiologically additive and sufficient to explain the role of Snf1 in short-term inhibition of TORC1 in acutely glucose-starved cells.

Keywords:  S. cerevisiae; biochemistry; cell biology; chemical biology

DOI:  https://doi.org/10.7554/eLife.84319
Front Endocrinol (Lausanne). 2023 ;14 1060675

Metabolic stress-induced human beta-cell death is mediated by increased intracellular levels of adenosine.

Anongnad Ngamjariyawat, Jing Cen, Romain Said, Ceren Incedal, Olof Idevall-Hagren, Nils Welsh.

   Introduction: High intracellular concentrations of adenosine and 2'-deoxyadenosine have been suggested to be an important mediator of cell death. The aim of the present study was to characterize adenosine-induced death in insulin-producing beta-cells, at control and high glucose + palmitate-induced stress conditions.
Methods: Human insulin-producing EndoC-betaH1 cells were treated with adenosine, 2'-deoxyadenosine, inosine and high glucose + sodium palmitate, and death rates using flow cytometry were studied.
Results: We observed that adenosine and the non-receptor-activating analogue 2-deoxyadenosine, but not the adenosine deamination product inosine, promoted beta-cell apoptosis at concentrations exceeding maximal adenosine-receptor stimulating concentrations. Both adenosine and inosine were efficiently taken up by EndoC-betaH1 cells, and inosine counteracted the cell death promoting effect of adenosine by competing with adenosine for uptake. Both adenosine and 2'-deoxyadenosine promptly reduced insulin-stimulated production of plasma membrane PI(3,4,5)P3, an effect that was reversed upon wash out of adenosine. In line with this, adenosine, but not inosine, rapidly diminished Akt phosphorylation. Both pharmacological Bax inhibition and Akt activation blocked adenosine-induced beta-cell apoptosis, indicating that adenosine/2'-deoxyadenosine inhibits the PI3K/Akt/BAD anti-apoptotic pathway. High glucose + palmitate-induced cell death was paralleled by increased intracellular adenosine and inosine levels. Overexpression of adenosine deaminase-1 (ADA1) in EndoC-betaH1 cells, which increased Akt phosphorylation, prevented both adenosine-induced apoptosis and high glucose + palmitate-induced necrosis. ADA2 overexpression not only failed to protect against adenosine and high glucose + palmitate-activated cell death, but instead potentiated the apoptosis-stimulating effect of adenosine. In line with this, ADA1 overexpression increased inosine production from adenosine-exposed cells, whereas ADA2 did not. Knockdown of ADA1 resulted in increased cell death rates in response to both adenosine and high glucose + palmitate. Inhibition of miR-30e-3p binding to the ADA1 mRNA 3'-UTR promoted the opposite effects on cell death rates and reduced intracellular adenosine contents.
Discussion: It is concluded that intracellular adenosine/2'-deoxyadenosine regulates negatively the PI3K pathway and is therefore an important mediator of beta-cell apoptosis. Adenosine levels are controlled, at least in part, by ADA1, and strategies to upregulate ADA1 activity, during conditions of metabolic stress, could be useful in attempts to preserve beta-cell mass in diabetes.

Keywords:  PIP3K-signaling; adenosine; apoptosis; beta-cells; metabolic stress; sodium palmitate

DOI:  https://doi.org/10.3389/fendo.2023.1060675
Nat Methods. 2023 Feb;20(2): 163

AlphaFold and beyond.

DOI: https://doi.org/10.1038/s41592-023-01790-6
Nat Commun. 2023 Feb 09. 14(1): 632

ZBTB12 is a molecular barrier to dedifferentiation in human pluripotent stem cells.

Dasol Han, Guojing Liu, Yujeong Oh, Seyoun Oh, Seungbok Yang, Lori Mandjikian, Neha Rani, Maria C Almeida, Kenneth S Kosik, Jiwon Jang.

Development is generally viewed as one-way traffic of cell state transition from primitive to developmentally advanced states. However, molecular mechanisms that ensure the unidirectional transition of cell fates remain largely unknown. Through exact transcription start site mapping, we report an evolutionarily conserved BTB domain-containing zinc finger protein, ZBTB12, as a molecular barrier for dedifferentiation of human pluripotent stem cells (hPSCs). Single-cell RNA sequencing reveals that ZBTB12 is essential for three germ layer differentiation by blocking hPSC dedifferentiation. Mechanistically, ZBTB12 fine-tunes the expression of human endogenous retrovirus H (HERVH), a primate-specific retrotransposon, and targets specific transcripts that utilize HERVH as a regulatory element. In particular, the downregulation of HERVH-overlapping long non-coding RNAs (lncRNAs) by ZBTB12 is necessary for a successful exit from a pluripotent state and lineage derivation. Overall, we identify ZBTB12 as a molecular barrier that safeguards the unidirectional transition of metastable stem cell fates toward developmentally advanced states.

DOI: https://doi.org/10.1038/s41467-023-36178-9
Nat Commun. 2023 Feb 08. 14(1): 688

Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT.

Indranil Paul, Dante Bolzan, Ahmed Youssef, Keith A Gagnon, Heather Hook, Gopal Karemore, Michael U J Oliphant, Weiwei Lin, Qian Liu, Sadhna Phanse, Carl White, Dzmitry Padhorny, Sergei Kotelnikov, Christopher S Chen, Pingzhao Hu, Gerald V Denis, Dima Kozakov, Brian Raught, Trevor Siggers, Stefan Wuchty, Senthil K Muthuswamy, Andrew Emili.

A proper understanding of disease etiology will require longitudinal systems-scale reconstruction of the multitiered architecture of eukaryotic signaling. Here we combine state-of-the-art data acquisition platforms and bioinformatics tools to devise PAMAF, a workflow that simultaneously examines twelve omics modalities, i.e., protein abundance from whole-cells, nucleus, exosomes, secretome and membrane; N-glycosylation, phosphorylation; metabolites; mRNA, miRNA; and, in parallel, single-cell transcriptomes. We apply PAMAF in an established in vitro model of TGFβ-induced epithelial to mesenchymal transition (EMT) to quantify >61,000 molecules from 12 omics and 10 timepoints over 12 days. Bioinformatics analysis of this EMT-ExMap resource allowed us to identify; -topological coupling between omics, -four distinct cell states during EMT, -omics-specific kinetic paths, -stage-specific multi-omics characteristics, -distinct regulatory classes of genes, -ligand-receptor mediated intercellular crosstalk by integrating scRNAseq and subcellular proteomics, and -combinatorial drug targets (e.g., Hedgehog signaling and CAMK-II) to inhibit EMT, which we validate using a 3D mammary duct-on-a-chip platform. Overall, this study provides a resource on TGFβ signaling and EMT.

DOI: https://doi.org/10.1038/s41467-023-36122-x
Am J Respir Cell Mol Biol. 2023 Feb 07.

AKT Phosphorylates FAM13A and Promotes Its Degradation via CUL4A/DDB1/DCAF1 E3 Complex.

Lu Gong, Samuel Bates, Yujun Li, Xin Lin, Wenyi Wei, Xiaobo Zhou.

  Single-nucleotide polymorphisms (SNPs) within FAM13A gene are significantly associated with chronic obstructive pulmonary disease (COPD) and lung function in genome-wide association studies (GWAS). However, how FAM13A protein is regulated under physiological and pathological condition remains largely elusive. Herein, we report that FAM13A is phosphorylated at the Serine 312 residue by AKT kinase after cigarette smoke extract treatment and thereby recognized by the CULLIN4A/DCAF1 E3 ligase complex, rendering the ubiquitination-mediated degradation of FAM13A. More broadly, downregulation of FAM13A protein upon AKT activation, as a general cellular response to acute stress, was also detected in influenza- or naphthalene-injured lungs in mice. Functionally, reduced protein levels of FAM13A leads to accelerated epithelial cell proliferation in murine lungs during recovery phase after injury. In summary, we characterized a novel molecular mechanism that regulates the stability of FAM13A protein, which enables the fine-tuning of lung epithelial repair post injuries. These significant findings will expand our molecular understanding on the regulation of protein stability that may modulate lung epithelial repair implicated in the development of COPD and other lung diseases.

Keywords:  AKT; E3 ligase; FAM13A; cellular response; protein degradation

DOI:  https://doi.org/10.1165/rcmb.2022-0362OC
Science. 2023 Feb 10. 379(6632): eaaw3835

Epigenetics as a mediator of plasticity in cancer.

Andrew P Feinberg, Andre Levchenko.

The concept of an epigenetic landscape describing potential cellular fates arising from pluripotent cells, first advanced by Conrad Waddington, has evolved in light of experiments showing nondeterministic outcomes of regulatory processes and mathematical methods for quantifying stochasticity. In this Review, we discuss modern approaches to epigenetic and gene regulation landscapes and the associated ideas of entropy and attractor states, illustrating how their definitions are both more precise and relevant to understanding cancer etiology and the plasticity of cancerous states. We address the interplay between different types of regulatory landscapes and how their changes underlie cancer progression. We also consider the roles of cellular aging and intrinsic and extrinsic stimuli in modulating cellular states and how landscape alterations can be quantitatively mapped onto phenotypic outcomes and thereby used in therapy development.

DOI: https://doi.org/10.1126/science.aaw3835
Nat Metab. 2023 Feb 06.

Allosteric regulation of CAD modulates de novo pyrimidine synthesis during the cell cycle.

Jong Shin, Hannan Mir, Maaz A Khurram, Kenji M Fujihara, Brian D Dynlacht, Timothy J Cardozo, Richard Possemato.

Metabolism is a fundamental cellular process that is coordinated with cell cycle progression. Despite this association, a mechanistic understanding of cell cycle phase-dependent metabolic pathway regulation remains elusive. Here we report the mechanism by which human de novo pyrimidine biosynthesis is allosterically regulated during the cell cycle. Combining traditional synchronization methods and metabolomics, we characterize metabolites by their accumulation pattern during cell cycle phases and identify cell cycle phase-dependent regulation of carbamoyl-phosphate synthetase 2, aspartate transcarbamylase and dihydroorotase (CAD), the first, rate-limiting enzyme in de novo pyrimidine biosynthesis. Through systematic mutational scanning and structural modelling, we find allostery as a major regulatory mechanism that controls the activity change of CAD during the cell cycle. Specifically, we report evidence of two Animalia-specific loops in the CAD allosteric domain that involve sensing and binding of uridine 5'-triphosphate, a CAD allosteric inhibitor. Based on homology with a mitochondrial carbamoyl-phosphate synthetase homologue, we identify a critical role for a signal transmission loop in regulating the formation of a substrate channel, thereby controlling CAD activity.

DOI: https://doi.org/10.1038/s42255-023-00735-9
bioRxiv. 2023 Jan 23. pii: 2023.01.23.525189. [Epub ahead of print]

Compressed phenotypic screens for complex multicellular models and high-content assays.

Benjamin E Mead, Conner Kummerlowe, Nuo Liu, Walaa E Kattan, Thomas Cheng, Jaime H Cheah, Christian K Soule, Josh Peters, Kristen E Lowder, Paul C Blainey, William C Hahn, Brian Cleary, Bryan Bryson, Peter S Winter, Srivatsan Raghavan, Alex K Shalek.

High-throughput phenotypic screens leveraging biochemical perturbations, high-content readouts, and complex multicellular models could advance therapeutic discovery yet remain constrained by limitations of scale. To address this, we establish a method for compressing screens by pooling perturbations followed by computational deconvolution. Conducting controlled benchmarks with a highly bioactive small molecule library and a high-content imaging readout, we demonstrate increased efficiency for compressed experimental designs compared to conventional approaches. To prove generalizability, we apply compressed screening to examine transcriptional responses of patient-derived pancreatic cancer organoids to a library of tumor-microenvironment (TME)-nominated recombinant protein ligands. Using single-cell RNA-seq as a readout, we uncover reproducible phenotypic shifts induced by ligands that correlate with clinical features in larger datasets and are distinct from reference signatures available in public databases. In sum, our approach enables phenotypic screens that interrogate complex multicellular models with rich phenotypic readouts to advance translatable drug discovery as well as basic biology.

DOI: https://doi.org/10.1101/2023.01.23.525189
Cell. 2023 Feb 02. pii: S0092-8674(23)00007-7. [Epub ahead of print]

Recycling of modified H2A-H2B provides short-term memory of chromatin states.

Valentin Flury, Nazaret Reverón-Gómez, Nicolas Alcaraz, Kathleen R Stewart-Morgan, Alice Wenger, Robert J Klose, Anja Groth.

  Chromatin landscapes are disrupted during DNA replication and must be restored faithfully to maintain genome regulation and cell identity. The histone H3-H4 modification landscape is restored by parental histone recycling and modification of new histones. How DNA replication impacts on histone H2A-H2B is currently unknown. Here, we measure H2A-H2B modifications and H2A.Z during DNA replication and across the cell cycle using quantitative genomics. We show that H2AK119ub1, H2BK120ub1, and H2A.Z are recycled accurately during DNA replication. Modified H2A-H2B are segregated symmetrically to daughter strands via POLA1 on the lagging strand, but independent of H3-H4 recycling. Post-replication, H2A-H2B modification and variant landscapes are quickly restored, and H2AK119ub1 guides accurate restoration of H3K27me3. This work reveals epigenetic transmission of parental H2A-H2B during DNA replication and identifies cross talk between H3-H4 and H2A-H2B modifications in epigenome propagation. We propose that rapid short-term memory of recycled H2A-H2B modifications facilitates restoration of stable H3-H4 chromatin states.

Keywords:  DNA replication; H2A; H2A.Z; H2B; chromatin; histone PTM cross talk; histone recycling; polycomb; post-translational modifications; ubiquitination

DOI:  https://doi.org/10.1016/j.cell.2023.01.007
Elife. 2023 Feb 10. pii: e86758. [Epub ahead of print]12

When cancer strikes (twice).

Nicole Swann.

  A young group leader reflects on academic culture and working while going through cancer treatments.

Keywords:  being a scientist; cancer; equity diversity inclusion; motherhood; research culture; sparks of change

DOI:  https://doi.org/10.7554/eLife.86758
Nat Commun. 2023 Feb 06. 14(1): 634

Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes.

Mayank N K Choudhary, Kara Quaid, Xiaoyun Xing, Heather Schmidt, Ting Wang.

Transposable elements (TEs) are major contributors of genetic material in mammalian genomes. These often include binding sites for architectural proteins, including the multifarious master protein, CTCF, which shapes the 3D genome by creating loops, domains, compartment borders, and RNA-DNA interactions. These play a role in the compact packaging of DNA and have the potential to facilitate regulatory function. In this study, we explore the widespread contribution of TEs to mammalian 3D genomes by quantifying the extent to which they give rise to loops and domain border differences across various cell types and species using several 3D genome mapping technologies. We show that specific families and subfamilies of TEs have contributed to lineage-specific 3D chromatin structures across mammalian species. In many cases, these loops may facilitate sustained interaction between distant cis-regulatory elements and target genes, and domains may segregate chromatin state to impact gene expression in a lineage-specific manner. An experimental validation of our analytical findings using CRISPR-Cas9 to delete a candidate TE resulted in disruption of species-specific 3D chromatin structure. Taken together, we comprehensively quantify and selectively validate our finding that TEs contribute to shaping 3D genome organization and may, in some cases, impact gene regulation during the course of mammalian evolution.

DOI: https://doi.org/10.1038/s41467-023-36364-9
Elife. 2023 Feb 07. pii: e84991. [Epub ahead of print]12

Rethinking academia in a time of climate crisis.

Anne E Urai, Clare Kelly.

  Addressing the climate crisis requires radical and urgent action at all levels of society. Universities are ideally positioned to lead such action but are largely failing to do so. At the same time, many academic scientists find their work impeded by bureaucracy, excessive competitiveness, and a loss of academic freedom. Here, drawing on the framework of "Doughnut Economics," developed by Kate Raworth, we suggest seven new principles for rethinking the norms of scientific practice. Based on these, we propose a call to action, and encourage academics to take concrete steps towards the creation of a flourishing scientific enterprise that is fit for the challenges of the 21st century.

Keywords:  activism; climate change; none; point of view; research culture; universities

DOI:  https://doi.org/10.7554/eLife.84991
F1000Res. 2022 ;pii: ELIXIR-1265. [Epub ahead of print]11

Systems Biology in ELIXIR: modelling in the spotlight.

Vitor Martins Dos Santos, Mihail Anton, Barbara Szomolay, Marek Ostaszewski, Ilja Arts, Rui Benfeitas, Victoria Dominguez Del Angel, Polonca Ferk, Dirk Fey, Carole Goble, Martin Golebiewski, Kristina Gruden, Katharina F Heil, Henning Hermjakob, Pascal Kahlem, Maria I Klapa, Jasper Koehorst, Alexey Kolodkin, Martina Kutmon, Brane Leskošek, Sébastien Moretti, Wolfgang Müller, Marco Pagni, Tadeja Rezen, Miguel Rocha, Damjana Rozman, David Šafránek, Rahuman S Malik Sheriff, Maria Suarez Diez, Kristel Van Steen, Hans V Westerhoff, Ulrike Wittig, Katherine Wolstencroft, Anze Zupanic, Chris T Evelo, John M Hancock.

  In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR's future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.

Keywords:  Biological data; Biomolecular Models; Biotechnology; ELIXIR Communities; FAIR; Network Biology; Systems Biology; Systems Medicine

DOI:  https://doi.org/10.12688/f1000research.126734.1
Nat Commun. 2023 Feb 10. 14(1): 738

Multilingual translation for zero-shot biomedical classification using BioTranslator.

Hanwen Xu, Addie Woicik, Hoifung Poon, Russ B Altman, Sheng Wang.

Existing annotation paradigms rely on controlled vocabularies, where each data instance is classified into one term from a predefined set of controlled vocabularies. This paradigm restricts the analysis to concepts that are known and well-characterized. Here, we present the novel multilingual translation method BioTranslator to address this problem. BioTranslator takes a user-written textual description of a new concept and then translates this description to a non-text biological data instance. The key idea of BioTranslator is to develop a multilingual translation framework, where multiple modalities of biological data are all translated to text. We demonstrate how BioTranslator enables the identification of novel cell types using only a textual description and how BioTranslator can be further generalized to protein function prediction and drug target identification. Our tool frees scientists from limiting their analyses within predefined controlled vocabularies, enabling them to interact with biological data using free text.

DOI: https://doi.org/10.1038/s41467-023-36476-2
PLoS Biol. 2023 Feb 06. 21(2): e3001986

Day-night and seasonal variation of human gene expression across tissues.

Valentin Wucher, Reza Sodaei, Raziel Amador, Manuel Irimia, Roderic Guigó.

Circadian and circannual cycles trigger physiological changes whose reflection on human transcriptomes remains largely uncharted. We used the time and season of death of 932 individuals from GTEx to jointly investigate transcriptomic changes associated with those cycles across multiple tissues. Overall, most variation across tissues during day-night and among seasons was unique to each cycle. Although all tissues remodeled their transcriptomes, brain and gonadal tissues exhibited the highest seasonality, whereas those in the thoracic cavity showed stronger day-night regulation. Core clock genes displayed marked day-night differences across multiple tissues, which were largely conserved in baboon and mouse, but adapted to their nocturnal or diurnal habits. Seasonal variation of expression affected multiple pathways, and it was enriched among genes associated with the immune response, consistent with the seasonality of viral infections. Furthermore, they unveiled cytoarchitectural changes in brain regions. Altogether, our results provide the first combined atlas of how transcriptomes from human tissues adapt to major cycling environmental conditions. This atlas may have multiple applications; for example, drug targets with day-night or seasonal variation in gene expression may benefit from temporally adjusted doses.

DOI: https://doi.org/10.1371/journal.pbio.3001986
Nat Commun. 2023 Feb 09. 14(1): 706

Mitotic DNA synthesis in response to replication stress requires the sequential action of DNA polymerases zeta and delta in human cells.

Wei Wu, Szymon A Barwacz, Rahul Bhowmick, Katrine Lundgaard, Marisa M Gonçalves Dinis, Malgorzata Clausen, Masato T Kanemaki, Ying Liu.

Oncogene activation creates DNA replication stress (RS) in cancer cells, which can generate under-replicated DNA regions (UDRs) that persist until cells enter mitosis. UDRs also have the potential to generate DNA bridges in anaphase cells or micronuclei in the daughter cells, which could promote genomic instability. To suppress such damaging changes to the genome, human cells have developed a strategy to conduct 'unscheduled' DNA synthesis in mitosis (termed MiDAS) that serves to rescue under-replicated loci. Previous studies have shown that MiDAS proceeds via a POLD3-dependent pathway that shows some features of break-induced replication. Here, we define how human cells utilize both DNA gap filling (REV1 and Pol ζ) and replicative (Pol δ) DNA polymerases to complete genome duplication following a perturbed S-phase. We present evidence for the existence of a polymerase-switch during MiDAS that is required for new DNA synthesis at UDRs. Moreover, we reveal that, upon oncogene activation, cancer cell survival is significantly compromised when REV1 is depleted, suggesting that REV1 inhibition might be a feasible approach for the treatment of some human cancers.

DOI: https://doi.org/10.1038/s41467-023-35992-5