bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2024‒09‒01
nineteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas.
  2. STRAIGHT-IN: a platform for rapidly generating panels of genetically modified human pluripotent stem cell lines.
  3. Alterations of the AKT Pathway in Sporadic Human Tumors, Inherited Susceptibility to Cancer, and Overgrowth Syndromes.
  4. Unveiling the Role of PIK3R1 in Cancer: A Comprehensive Review of Regulatory Signaling and Therapeutic Implications.
  5. mTORC1 hampers Hedgehog signaling in Tsc2 deficient cells.
  6. A KLF2-BMPER-Smad1/5 checkpoint regulates high fluid shear stress-mediated artery remodeling.
  7. SignalingProfiler 2.0 a network-based approach to bridge multi-omics data to phenotypic hallmarks.
  8. Delivery of US28 by incoming HCMV particles rapidly attenuates Akt activity to suppress HCMV lytic replication in monocytes.
  9. Potentiation by Protein Synthesis Inducers of Translational Readthrough of Pathogenic Premature Termination Codons in PTEN Isoforms.
  10. Secreted PTEN binds PLXDC2 on macrophages to drive antitumor immunity and tumor suppression.
  11. De Novo Cancer Mutations Frequently Associate with Recurrent Chromosomal Abnormalities during Long-Term Human Pluripotent Stem Cell Culture.
  12. Recovering biomolecular network dynamics from single-cell omics data requires three time points.
  13. Community assessment of methods to deconvolve cellular composition from bulk gene expression.
  14. The evolution of computational research in a data-centric world.
  15. Lactate Oxidase Disrupts Lactate-Activated RAS and PI3K Oncogenic Signaling.
  16. Robust Differentiation of Human Pluripotent Stem Cells into Lymphatic Endothelial Cells Using Transcription Factors.
  17. mTORC1 mediates the expansion of hematopoietic stem and progenitor cells through ribosome biogenesis protein Urb2 in zebrafish.
  18. A case report of sirolimus use in early fetal management of lymphatic malformation.
  19. EditABLE: A Simple Web Application for Designing Genome Editing Experiments.
  1. Cell. 2024 Aug 22. pii: S0092-8674(24)00829-8. [Epub ahead of print]187(17): 4520-4545
    Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas.
    Jennifer E Rood, Anna Hupalowska, Aviv Regev.
      Comprehensively charting the biologically causal circuits that govern the phenotypic space of human cells has often been viewed as an insurmountable challenge. However, in the last decade, a suite of interleaved experimental and computational technologies has arisen that is making this fundamental goal increasingly tractable. Pooled CRISPR-based perturbation screens with high-content molecular and/or image-based readouts are now enabling researchers to probe, map, and decipher genetically causal circuits at increasing scale. This scale is now eminently suitable for the deployment of artificial intelligence and machine learning (AI/ML) to both direct further experiments and to predict or generate information that was not-and sometimes cannot-be gathered experimentally. By combining and iterating those through experiments that are designed for inference, we now envision a Perturbation Cell Atlas as a generative causal foundation model to unify human cell biology.
    DOI:  https://doi.org/10.1016/j.cell.2024.07.035
  2. Nat Protoc. 2024 Aug 23.
    STRAIGHT-IN: a platform for rapidly generating panels of genetically modified human pluripotent stem cell lines.
    Albert Blanch-Asensio, Catarina Grandela, Christine L Mummery, Richard P Davis.
      Targeted integration of large DNA cargoes (>10 kb) or genomic replacements in mammalian cells, such as human pluripotent stem cells (hPS cells), remains challenging. Here we describe a platform termed serine and tyrosine recombinase-assisted integration of genes for high-throughput investigation (STRAIGHT-IN) to circumvent this. First, a landing pad cassette is precisely inserted or used to replace specific genomic regions. The site-specific integrase Bxb1 then enables DNA constructs, including those >50 kb, to be integrated into the genome, while Cre recombinase excises auxiliary DNA sequences to prevent postintegrative silencing. Using a strategy whereby the positive selection marker is only expressed if the donor plasmid carrying the payload is correctly targeted, we can obtain 100% enrichment for cells containing the DNA payload. Procedures for expressing Cre efficiently also mean that a clonal isolation step is no longer essential to derive the required genetically modified hPS cells containing the integrated DNA, potentially reducing clonal variability. Furthermore, STRAIGHT-IN facilitates rapid and multiplexed generation of genetically matched hPS cells when multiple donor plasmids are delivered simultaneously. STRAIGHT-IN has various applications, which include integrating complex genetic circuits for synthetic biology, as well as creating panels of hPS cells lines containing, as necessary, hundreds of disease-linked variants for disease modeling and drug discovery. After establishing the hPS cell line containing the landing pad, the entire procedure, including donor plasmid synthesis, takes 1.5-3 months, depending on whether single or multiple DNA payloads are integrated. This protocol only requires the researcher to be skilled in molecular biology and standard cell culture techniques.
    DOI:  https://doi.org/10.1038/s41596-024-01039-2
  3. Curr Top Microbiol Immunol. 2024 Aug 28.
    Alterations of the AKT Pathway in Sporadic Human Tumors, Inherited Susceptibility to Cancer, and Overgrowth Syndromes.
    Craig W Menges, Dalal Hassan, Mitchell Cheung, Alfonso Bellacosa, Joseph R Testa.
      The AKT kinases are critical signaling molecules that regulate cellular physiology upon the activation of tyrosine kinase receptors and phosphatidylinositol 3-kinases (PI3K). AKT kinases govern many cellular processes considered hallmarks of cancer, including cell proliferation and survival, cell size, tumor invasion, metastasis, and angiogenesis. AKT signaling is regulated by multiple tumor suppressors and oncogenic proteins whose loss or activation, respectively, leads to dysregulation of this pathway, thereby contributing to oncogenesis. Herein, we review the enormous body of literature documenting how the AKT pathway becomes hyperactivated in sporadic human tumors and various hereditary cancer syndromes. We also discuss the role of activating mutations of AKT pathway genes in various chimeric overgrowth disorders, including Proteus syndrome, hypoglycemia with hypertrophy, CLOVES and SOLAMEN syndromes, and hemimegalencephaly.
    DOI:  https://doi.org/10.1007/82_2024_278
  4. Semin Cancer Biol. 2024 Aug 26. pii: S1044-579X(24)00062-2. [Epub ahead of print]
    Unveiling the Role of PIK3R1 in Cancer: A Comprehensive Review of Regulatory Signaling and Therapeutic Implications.
    Ishita Gupta, Daria A Gaykalova.
      Phosphoinositide 3-kinase (PI3K) is responsible for phosphorylating phosphoinositides to generate secondary signaling molecules crucial for regulating various cellular processes, including cell growth, survival, and metabolism. The PI3K is a heterodimeric enzyme complex comprising of a catalytic subunit (p110α, p110β, or p110δ) and a regulatory subunit (p85). The binding of the regulatory subunit, p85, with the catalytic subunit, p110, forms an integral component of the PI3K enzyme. PIK3R1 (phosphoinositide-3-kinase regulatory subunit 1) belongs to class IA of the PI3K family. PIK3R1 exhibits structural complexity due to alternative splicing, giving rise to distinct isoforms, prominently p85α and p55α. While the primary p85α isoform comprises multiple domains, including Src homology 3 (SH3) domains, a Breakpoint Cluster Region Homology (BH) domain, and Src homology 2 (SH2) domains (iSH2 and nSH2), the shorter isoform, p55α, lacks certain domains present in p85α. In this review, we will highlight the intricate regulatory mechanisms governing PI3K signaling along with the impact of PIK3R1 alterations on cellular processes. We will further delve into the clinical significance of PIK3R1 mutations in various cancer types and their implications for prognosis and treatment outcomes. Additionally, we will discuss the evolving landscape of targeted therapies aimed at modulating PI3K-associated pathways. Overall, this review will provide insights into the dynamic interplay of PIK3R1 in cancer, fostering advancements in precision medicine and the development of targeted interventions.
    Keywords:  PI3K; PIK3R1; cancer; p85α; therapeutic targets; tumor suppressor
    DOI:  https://doi.org/10.1016/j.semcancer.2024.08.004
  5. Life Sci Alliance. 2024 Nov;pii: e202302419. [Epub ahead of print]7(11):
    mTORC1 hampers Hedgehog signaling in Tsc2 deficient cells.
    Lasse Jonsgaard Larsen, Elsebet Østergaard, Lisbeth Birk Møller.
      The mTORC1-complex is negatively regulated by TSC1 and TSC2. Activation of Hedgehog signaling is strictly dependent on communication between Smoothened and the Hedgehog-signaling effector and transcription factor, GLI2, in the primary cilium. Details about this communication are not known, and we wanted to explore this further. Here we report that in Tsc2 -/- MEFs constitutively activated mTORC1 led to mis-localization of Smoothened to the plasma membrane, combined with increased concentration of GLI2 in the cilia and reduced Hedgehog signaling, measured by reduced expression of the Hedgehog target gene, Gli1 Inhibition of mTORC1 rescued the cellular localization of Smoothened to the cilia, reduced the cilia concentration of GLI2, and restored Hedgehog signaling. Our results reveal evidence for a two-step activation process of GLI2. The first step includes GLI2 stabilization and cilium localization, whereas the second step includes communication with cilia-localized Smoothened. We found that mTORC1 inhibits the second step. This is the first demonstration that mTORC1 is involved in the regulation of Hedgehog signaling.
    DOI:  https://doi.org/10.26508/lsa.202302419
  6. Nat Cardiovasc Res. 2024 Jul;3(7): 785-798
    A KLF2-BMPER-Smad1/5 checkpoint regulates high fluid shear stress-mediated artery remodeling.
    Hanqiang Deng, Jiasheng Zhang, Yewei Wang, Divyesh Joshi, Xinchun Pi, Sarah De Val, Martin A Schwartz.
      Vascular remodeling to match arterial diameter to tissue requirements commonly fails in ischemic disease. Endothelial cells sense fluid shear stress (FSS) from blood flow to maintain FSS within a narrow range in healthy vessels. Thus, high FSS induces vessel outward remodeling, but mechanisms are poorly understood. We previously reported that Smad1/5 is maximally activated at physiological FSS. Smad1/5 limits Akt activation, suggesting that inhibiting Smad1/5 may facilitate outward remodeling. Here we report that high FSS suppresses Smad1/5 by elevating KLF2, which induces the bone morphogenetic protein (BMP) pathway inhibitor, BMP-binding endothelial regulator (BMPER), thereby de-inhibiting Akt. In mice, surgically induced high FSS elevated BMPER expression, inactivated Smad1/5 and induced vessel outward remodeling. Endothelial BMPER deletion impaired blood flow recovery and vascular remodeling. Blocking endothelial cell Smad1/5 activation with BMP9/10 blocking antibodies improved vascular remodeling in mouse models of type 1 and type 2 diabetes. Suppression of Smad1/5 is thus a potential therapeutic approach for ischemic disease.
    DOI:  https://doi.org/10.1038/s44161-024-00496-y
  7. NPJ Syst Biol Appl. 2024 Aug 23. 10(1): 95
    SignalingProfiler 2.0 a network-based approach to bridge multi-omics data to phenotypic hallmarks.
    Veronica Venafra, Francesca Sacco, Livia Perfetto.
      Unraveling how cellular signaling is remodeled upon perturbation is crucial for understanding disease mechanisms and identifying potential drug targets. In this pursuit, computational tools generating mechanistic hypotheses from multi-omics data have invaluable potential. Here, we present a newly implemented version (2.0) of SignalingProfiler, a multi-step pipeline to draw mechanistic hypotheses on the signaling events impacting cellular phenotypes. SignalingProfiler 2.0 derives context-specific signaling networks by integrating proteogenomic data with the prior knowledge-causal network. This is a freely accessible and flexible tool that incorporates statistical, footprint-based, and graph algorithms to accelerate the integration and interpretation of multi-omics data. Through a benchmarking process on three proof-of-concept studies, we demonstrate the tool's ability to generate hierarchical mechanistic networks recapitulating novel and known perturbed signaling and phenotypic outcomes, in both human and mice contexts. In summary, SignalingProfiler 2.0 addresses the emergent need to derive biologically relevant information from complex multi-omics data by extracting interpretable networks.
    DOI:  https://doi.org/10.1038/s41540-024-00417-6
  8. Sci Signal. 2024 Aug 27. 17(851): eadn8727
    Delivery of US28 by incoming HCMV particles rapidly attenuates Akt activity to suppress HCMV lytic replication in monocytes.
    Jamil Mahmud, Brittany W Geiler, Juthi Biswas, Michael J Miller, Julia E Myers, Stephen M Matthews, Amanda B Wass, Christine M O'Connor, Gary C Chan.
      Establishing a nonproductive, quiescent infection within monocytes is essential for the spread of human cytomegalovirus (HCMV). We investigated the mechanisms through which HCMV establishes a quiescent infection in monocytes. US28 is a virally encoded G protein-coupled receptor (GPCR) that is essential for silent infections within cells of the myeloid lineage. We found that preformed US28 was rapidly delivered to monocytes by HCMV viral particles, whereas the de novo synthesis of US28 was delayed for several days. A recombinant mutant virus lacking US28 (US28Δ) was unable to establish a quiescent infection, resulting in a fully productive lytic infection able to produce progeny virus. Infection with US28Δ HCMV resulted in the phosphorylation of the serine and threonine kinase Akt at Ser473 and Thr308, in contrast with the phosphorylation of Akt only at Ser473 after WT viral infection. Inhibiting the dual phosphorylation of Akt prevented the lytic replication of US28Δ, and ectopic expression of a constitutively phosphorylated Akt variant triggered lytic replication of wild-type HCMV. Mechanistically, we found that US28 was necessary and sufficient to attenuate epidermal growth factor receptor (EGFR) signaling induced during the entry of WT virus, which led to the site-specific phosphorylation of Akt at Ser473. Thus, particle-delivered US28 fine-tunes Akt activity by limiting HCMV-induced EGFR activation during viral entry, enabling quiescent infection in monocytes.
    DOI:  https://doi.org/10.1126/scisignal.adn8727
  9. Cancers (Basel). 2024 Aug 13. pii: 2836. [Epub ahead of print]16(16):
    Potentiation by Protein Synthesis Inducers of Translational Readthrough of Pathogenic Premature Termination Codons in PTEN Isoforms.
    Leire Torices, Caroline E Nunes-Xavier, Rafael Pulido.
      The PTEN tumor suppressor is frequently targeted in tumors and patients with PTEN hamartoma tumor syndrome (PHTS) through nonsense mutations generating premature termination codons (PTC) that may cause the translation of truncated non-functional PTEN proteins. We have previously described a global analysis of the readthrough reconstitution of the protein translation and function of the human canonical PTEN isoform by aminoglycosides. Here, we report the efficient functional readthrough reconstitution of the PTEN translational isoform PTEN-L, which displays a minimal number of PTC in its specific N-terminal extension in association with disease. We illustrate the importance of the specific PTC and its nucleotide proximal sequence for optimal readthrough and show that the more frequent human PTEN PTC variants and their mouse PTEN PTC equivalents display similar patterns of readthrough efficiency. The heterogeneous readthrough response of the different PTEN PTC variants was independent of the length of the PTEN protein being reconstituted, and we found a correlation between the amount of PTEN protein being synthesized and the PTEN readthrough efficiency. Furthermore, combination of aminoglycosides and protein synthesis inducers increased the readthrough response of specific PTEN PTC. Our results provide insights with which to improve the functional reconstitution of human-disease-related PTC pathogenic variants from PTEN isoforms by increasing protein synthesis coupled to translational readthrough.
    Keywords:  PHTS; genetic disease; precision therapy; premature termination codon; translational readthrough
    DOI:  https://doi.org/10.3390/cancers16162836
  10. Dev Cell. 2024 Aug 26. pii: S1534-5807(24)00486-6. [Epub ahead of print]
    Secreted PTEN binds PLXDC2 on macrophages to drive antitumor immunity and tumor suppression.
    Cheng Zhang, Hong-Ming Ma, Shuai Wu, Jia-Ming Shen, Na Zhang, Yi-Lu Xu, Cheng-Xiao Li, Ping He, Meng-Kai Ge, Xi-Li Chu, Yu-Xue Zhang, Jun-Ke Zheng, Guo-Qiang Chen, Shao-Ming Shen.
      Loss of phosphatase and tensin homolog (PTEN) has been linked to an immunosuppressive tumor microenvironment, but its underlying mechanisms remain largely enigmatic. Here, we report that PTEN can be secreted by the transmembrane emp24 domain-containing protein 10 (TMED10)-channeled protein secretion pathway. Inhibiting PTEN secretion from tumor cells contributes to immunosuppression and impairs the tumor-suppressive role of PTEN, while intratumoral injection of PTEN protein promotes antitumor immunity and suppresses tumor growth in mice. Mechanistically, extracellular PTEN binds to the plexin domain-containing protein 2 (PLXDC2) on macrophages, triggering subsequent activation of JAK2-STAT1 signaling, which switches tumor-associated macrophages (TAMs) from the immunosuppressive to inflammatory phenotype, leading to enhanced activation of CD8+ T and natural killer cells. Importantly, PTEN treatment also enhances the therapeutic efficacy of anti-PD-1 treatment in mice and reverses the immune-suppressive phenotype of patient-derived primary TAMs. These data identify a cytokine-like role of PTEN in immune activation and tumor suppression and demonstrate the therapeutic potential for extracellular administration of PTEN in cancer immunotherapy.
    Keywords:  JAK2; PLXDC2; PTEN; TMED10; antitumor immunity; macrophages; unconventional protein secretion
    DOI:  https://doi.org/10.1016/j.devcel.2024.08.003
  11. Cells. 2024 Aug 21. pii: 1395. [Epub ahead of print]13(16):
    De Novo Cancer Mutations Frequently Associate with Recurrent Chromosomal Abnormalities during Long-Term Human Pluripotent Stem Cell Culture.
    Diana Al Delbany, Manjusha S Ghosh, Nuša Krivec, Anfien Huyghebaert, Marius Regin, Mai Chi Duong, Yingnan Lei, Karen Sermon, Catharina Olsen, Claudia Spits.
      Human pluripotent stem cells (hPSCs) are pivotal in regenerative medicine, yet their in vitro expansion often leads to genetic abnormalities, raising concerns about their safety in clinical applications. This study analyzed ten human embryonic stem cell lines across multiple passages to elucidate the dynamics of chromosomal abnormalities and single-nucleotide variants (SNVs) in 380 cancer-related genes. Prolonged in vitro culture resulted in 80% of the lines acquiring gains of chromosome 20q or 1q, both known for conferring an in vitro growth advantage. 70% of lines also acquired other copy number variants (CNVs) outside the recurrent set. Additionally, we detected 122 SNVs in 88 genes, with all lines acquiring at least one de novo SNV during culture. Our findings showed higher loads of both CNVs and SNVs at later passages, which were due to the cumulative acquisition of mutations over a longer time in culture, and not to an increased rate of mutagenesis over time. Importantly, we observed that SNVs and rare CNVs followed the acquisition of chromosomal gains in 1q and 20q, while most of the low-passage and genetically balanced samples were devoid of cancer-associated mutations. This suggests that recurrent chromosomal abnormalities are potential drivers for the acquisition of other mutations.
    Keywords:  cancer-related genes; copy number variation; genetic instability; human pluripotent stem cells; single-nucleotide variants
    DOI:  https://doi.org/10.3390/cells13161395
  12. NPJ Syst Biol Appl. 2024 Aug 27. 10(1): 97
    Recovering biomolecular network dynamics from single-cell omics data requires three time points.
    Shu Wang, Muhammad Ali Al-Radhawi, Douglas A Lauffenburger, Eduardo D Sontag.
      Single-cell omics technologies can measure millions of cells for up to thousands of biomolecular features, enabling data-driven studies of complex biological networks. However, these high-throughput experimental techniques often cannot track individual cells over time, thus complicating the understanding of dynamics such as time trajectories of cell states. These "dynamical phenotypes" are key to understanding biological phenomena such as differentiation fates. We show by mathematical analysis that, in spite of high dimensionality and lack of individual cell traces, three time-points of single-cell omics data are theoretically necessary and sufficient to uniquely determine the network interaction matrix and associated dynamics. Moreover, we show through numerical simulations that an interaction matrix can be accurately determined with three or more time-points even in the presence of sampling and measurement noise typical of single-cell omics. Our results can guide the design of single-cell omics time-course experiments, and provide a tool for data-driven phase-space analysis.
    DOI:  https://doi.org/10.1038/s41540-024-00424-7
  13. Nat Commun. 2024 Aug 27. 15(1): 7362
    Community assessment of methods to deconvolve cellular composition from bulk gene expression.
    Tumor Deconvolution DREAM Challenge consortium
      We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression of tumor samples, through a community-wide DREAM Challenge. We assess six published and 22 community-contributed methods using in vitro and in silico transcriptional profiles of admixed cancer and healthy immune cells. Several published methods predict most cell types well, though they either were not trained to evaluate all functional CD8+ T cell states or do so with low accuracy. Several community-contributed methods address this gap, including a deep learning-based approach, whose strong performance establishes the applicability of this paradigm to deconvolution. Despite being developed largely using immune cells from healthy tissues, deconvolution methods predict levels of tumor-derived immune cells well. Our admixed and purified transcriptional profiles will be a valuable resource for developing deconvolution methods, including in response to common challenges we observe across methods, such as sensitive identification of functional CD4+ T cell states.
    DOI:  https://doi.org/10.1038/s41467-024-50618-0
  14. Cell. 2024 Aug 22. pii: S0092-8674(24)00839-0. [Epub ahead of print]187(17): 4449-4457
    The evolution of computational research in a data-centric world.
    Dhrithi Deshpande, Karishma Chhugani, Tejasvene Ramesh, Matteo Pellegrini, Sagiv Shiffman, Malak S Abedalthagafi, Saleh Alqahtani, Jimmie Ye, Xiaole Shirley Liu, Jeffrey T Leek, Alvis Brazma, Roel A Ophoff, Gauri Rao, Atul J Butte, Jason H Moore, Vsevolod Katritch, Serghei Mangul.
      Computational data-centric research techniques play a prevalent and multi-disciplinary role in life science research. In the past, scientists in wet labs generated the data, and computational researchers focused on creating tools for the analysis of those data. Computational researchers are now becoming more independent and taking leadership roles within biomedical projects, leveraging the increased availability of public data. We are now able to generate vast amounts of data, and the challenge has shifted from data generation to data analysis. Here we discuss the pitfalls, challenges, and opportunities facing the field of data-centric research in biology. We discuss the evolving perception of computational data-driven research and its rise as an independent domain in biomedical research while also addressing the significant collaborative opportunities that arise from integrating computational research with experimental and translational biology. Additionally, we discuss the future of data-centric research and its applications across various areas of the biomedical field.
    DOI:  https://doi.org/10.1016/j.cell.2024.07.045
  15. Cancers (Basel). 2024 Aug 10. pii: 2817. [Epub ahead of print]16(16):
    Lactate Oxidase Disrupts Lactate-Activated RAS and PI3K Oncogenic Signaling.
    Chandler R Keller, Steve R Martinez, Alexys Keltz, Michelle Chen, Weimin Li.
      LOX was recently shown to inhibit cancer cell proliferation and tumor growth. The mechanism of this inhibition, however, has been exclusively attributed to LOX depletion of TME lactate, a cancer cell energy source, and production of H2O2, an oxidative stressor. We report that TME lactate triggers the assembly of the lactate receptor hydroxycarboxylic acid receptor 1 (HCAR1)-associated protein complex, which includes GRB2, SOS1, KRAS, GAB1, and PI3K, for the activation of both the RAS and the PI3K oncogenic signaling pathways in breast cancer (BCa) cells. LOX treatment decreased the levels of the proteins in the protein complex via induction of their proteasomal degradation. In addition, LOX inhibited lactate-stimulated expression of the lactate transporters MCT1 and MCT4. Our data suggest that HCAR1 activation by lactate is crucial for the assembly and function of the RAS and PI3K signaling nexus. Shutting down lactate signaling by disrupting this nexus could be detrimental to cancer cells. HCAR1 is therefore a promising target for the control of the RAS and the PI3K signaling required for BCa progression. Thus, our study provides insights into lactate signaling regulation of cancer progression and extends our understanding of LOX's functional mechanisms that are fundamental for exploring its therapeutic potential.
    Keywords:  RAS/PI3K signaling; breast cancer (BCa); lactate oxidase (LOX); lactate receptor HCAR1; tumor microenvironment (TME)
    DOI:  https://doi.org/10.3390/cancers16162817
  16. Cells Tissues Organs. 2024 Aug 28.
    Robust Differentiation of Human Pluripotent Stem Cells into Lymphatic Endothelial Cells Using Transcription Factors.
    Sanjoy Saha, Francine Graham, James Knopp, Christopher Patzke, Donny Hanjaya-Putra.
      INTRODUCTION: Generating new lymphatic vessels has been postulated as an innovative therapeutic strategy for various disease phenotypes, including neurodegenerative diseases, metabolic syndrome, cardiovascular disease, and lymphedema. Yet, compared to the blood vascular system, protocols to differentiate human induced pluripotent stem cells (hiPSCs) into lymphatic endothelial cells (LECs) are still lacking.METHODS: Transcription factors, ETS2 and ETV2 are key regulators of embryonic vascular development, including lymphatic specification. While ETV2 has been shown to efficiently generate blood endothelial cells, little is known about ETS2 and its role in lymphatic differentiation. Here, we describe a method for rapid and efficient generation of LECs using transcription factors, ETS2 and ETV2.
    RESULTS: This approach reproducibly differentiates four diverse hiPSCs into LECs with exceedingly high efficiency. Timely activation of ETS2 was critical, to enable its interaction with Prox1, a master lymphatic regulator. Differentiated LECs express key lymphatic markers, VEGFR-3, LYVE-1, and Podoplanin, in comparable levels to mature LECs. The differentiated LECs are able to assemble into stable lymphatic vascular networks in vitro, and secrete key lymphangiocrine, reelin.
    CONCLUSION: Overall, our protocol has broad applications for basic study of lymphatic biology, as well as toward various approaches in lymphatic regeneration and personalized medicine.
    DOI:  https://doi.org/10.1159/000539699
  17. Stem Cell Reports. 2024 Aug 19. pii: S2213-6711(24)00220-0. [Epub ahead of print]
    mTORC1 mediates the expansion of hematopoietic stem and progenitor cells through ribosome biogenesis protein Urb2 in zebrafish.
    Wenming Huang, Yu Yue, Weifeng Hao, Zhenan Zhang, Pengcheng Cai, Deqin Yang.
      Mammalian target of rapamycin (mTOR) serves as the key sensor to control protein synthesis, cell growth, and survival. Despite mTOR is reported to regulate hematopoietic stem and progenitor cell (HSPC) engraftment and multiple-lineage hematopoiesis in mice, the roles of unique mTOR complexes (mTORCs) in early HSPC development and HSPC pool formation have not been adequately elucidated. Here, we uncover that mTORC1 is essential for early HSPC expansion in zebrafish. mTORC1 signaling was highly activated in definitive HSPCs during the emerging and expanding stages. Pharmacological or genetic inactivation of mTORC1 would cause defective HSPC expansion and migration due to disrupted cell proliferation. Interestingly, mTORC2 is dispensable for early HSPC development. Ribosome biogenesis protein Urb2 was downregulated upon mTORC1 inhibition, and urb2 overexpression partially rescued the hematopoietic defects in mTORC1-deficient embryos. These data demonstrate that mTORC1 signaling regulates early HSPC expansion through Urb2, and this work will deepen our understanding of mTOR in different physiological processes.
    Keywords:  Urb2; hematopoietic; mTOR; proliferation; zebrafish
    DOI:  https://doi.org/10.1016/j.stemcr.2024.07.011
  18. Nat Cardiovasc Res. 2023 Jun;2(6): 595-599
    A case report of sirolimus use in early fetal management of lymphatic malformation.
    Emmanuel Seront, Jean Marc Biard, An Van Damme, Nicole Revencu, Benoit Lengelé, Sandra Schmitz, Caroline de Toeuf, Philippe Clapuyt, Francis Veyckemans, Caroline Prégardien, Miikka Vikkula, Pierre Bernard, Laurence M Boon.
      Sirolimus, by targeting the mammalian target of rapamycin (mTOR) pathway, has demonstrated efficacy on lymphatic malformations (LMs) in adults and neonates. The current hypothesis is that the earlier the lesion is treated, the better it responds. This has prompted the idea that sirolimus administration might be efficacious to treat fetal LMs as well. Here we report a successful management of a cervicofacial fetal LM with sirolimus taken orally by the mother from the 22nd week of pregnancy until 2 weeks before planned delivery. Repeated cordocentesis recorded a 30% transplacental crossing of sirolimus. Continuation of sirolimus after birth allowed resection of the residual mass. We have followed the physical and neurological evolution of the child for 6 years since the fetal administration of sirolimus. We conclude that early administration of sirolimus during pregnancy with maternal serum monitoring may be proposed to high-risk fetal LMs in selected cases.
    DOI:  https://doi.org/10.1038/s44161-023-00280-4
  19. Res Sq. 2024 Aug 16. pii: rs.3.rs-4775705. [Epub ahead of print]
    EditABLE: A Simple Web Application for Designing Genome Editing Experiments.
    Demetrios S Maxim, David Wei Wu, Najani Shanee Johnson, Vivek Charu, Jennefer N Carter, Shuchi Anand, George M Church, Vivek Bhalla.
      CRISPR-Cas genome editing is transformative; however, there is no simple tool available for determining the optimal genome editing technology to create specific mutations for experimentation or to correct mutations as a curative therapy for specific diseases. We developed editABLE, an online resource (editable-app.stanford.edu) to provide computationally validated CRISPR editors and guide RNAs based on user provided sequence data. We demonstrate the utility of editABLE by applying it to one of the most common monogenic disorders, autosomal dominant polycystic kidney disease (ADPKD), identifying specific editing tools across the landscape of ADPKD mutations.
    DOI:  https://doi.org/10.21203/rs.3.rs-4775705/v1
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