bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2023–06–04
nineteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. A bi-steric mTORC1-selective inhibitor overcomes drug resistance in breast cancer.
  2. Reversing pathological cell states: the road less travelled can extend the therapeutic horizon.
  3. Kinetics of RTK activation determine ERK reactivation and resistance to dual BRAF/MEK inhibition in melanoma.
  4. Reducing the inherent auto-inhibitory interaction within the pegRNA enhances prime editing efficiency.
  5. CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing.
  6. EMT/MET plasticity in cancer and Go-or-Grow decisions in quiescence: the two sides of the same coin?
  7. Pancreatic tumors exhibit myeloid-driven amino acid stress and upregulate arginine biosynthesis.
  8. RTK signalling promotes epithelial columnar cell shape and apical junction maintenance in human lung progenitor cells.
  9. SIMBA: single-cell embedding along with features.
  10. Light-switchable transcription factors obtained by direct screening in mammalian cells.
  11. In situ tumour arrays reveal early environmental control of cancer immunity.
  12. ULK1-mediated metabolic reprogramming regulates Vps34 lipid kinase activity by its lactylation.
  13. Maturing differentiated human pluripotent stem cells in vitro: methods and challenges.
  14. Nutrient regulation of development and cell fate decisions.
  15. Visualizing gene expression changes in time, space, and single cells with expressyouRcell.
  16. Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets.
  17. ssDNA is not superior to dsDNA as long HDR donors for CRISPR-mediated endogenous gene tagging in human diploid RPE1 and HCT116 cells.
  18. Protocol for biallelic tagging of an endogenous gene using CRISPR-Cas9 in human cells.
  19. Robust Tissue Fabrication for Long-Term Culture of iPSC-Derived Brain Organoids for Aging Research.
  1. Oncogene. 2023 Jun 01.
    A bi-steric mTORC1-selective inhibitor overcomes drug resistance in breast cancer.
    Delong Meng, Xin Zhao, Yu Chi Yang, Albertas Navickas, Ciara Helland, Hani Goodarzi, Mallika Singh, Sourav Bandyopadhyay.
      Activation of the PI3K-mTOR pathway is central to breast cancer pathogenesis including resistance to many targeted therapies. The mTOR kinase forms two distinct complexes, mTORC1 and mTORC2, and understanding which is required for the survival of malignant cells has been limited by tools to selectively and completely impair either subcomplex. To address this, we used RMC-6272, a bi-steric molecule with a rapamycin-like moiety linked to an mTOR active-site inhibitor that displays >25-fold selectivity for mTORC1 over mTORC2 substrates. Complete suppression of mTORC1 by RMC-6272 causes apoptosis in ER+/HER2- breast cancer cell lines, particularly in those that harbor mutations in PIK3CA or PTEN, due to inhibition of the rapamycin resistant, mTORC1 substrate 4EBP1 and reduction of the pro-survival protein MCL1. RMC-6272 reduced translation of ribosomal mRNAs, MYC target genes, and components of the CDK4/6 pathway, suggesting enhanced impairment of oncogenic pathways compared to the partial mTORC1 inhibitor everolimus. RMC-6272 maintained efficacy in hormone therapy-resistant acquired cell lines and patient-derived xenografts (PDX), showed increased efficacy in CDK4/6 inhibitor treated acquired resistant cell lines versus their parental counterparts, and was efficacious in a PDX from a patient experiencing resistance to CDK4/6 inhibition. Bi-steric mTORC1-selective inhibition may be effective in overcoming multiple forms of therapy-resistance in ER+ breast cancers.
    DOI:  https://doi.org/10.1038/s41388-023-02737-z
  2. Trends Cell Biol. 2023 May 16. pii: S0962-8924(23)00078-8. [Epub ahead of print]
    Reversing pathological cell states: the road less travelled can extend the therapeutic horizon.
    Boris N Kholodenko, Walter Kolch, Oleksii S Rukhlenko.
      Acquisition of omics data advances at a formidable pace. Yet, our ability to utilize these data to control cell phenotypes and design interventions that reverse pathological states lags behind. Here, we posit that cell states are determined by core networks that control cell-wide networks. To steer cell fate decisions, core networks connecting genotype to phenotype must be reconstructed and understood. A recent method, cell state transition assessment and regulation (cSTAR), applies perturbation biology to quantify causal connections and mechanistically models how core networks influence cell phenotypes. cSTAR models are akin to digital cell twins enabling us to purposefully convert pathological states back to physiologically normal states. While this capability has a range of applications, here we discuss reverting oncogenic transformation.
    Keywords:  cell state transition assessment and regulation method; control of cell state transitions and fate decisions; digital cell twins; omics data
    DOI:  https://doi.org/10.1016/j.tcb.2023.04.004
  3. Cell Rep. 2023 May 29. pii: S2211-1247(23)00581-8. [Epub ahead of print]42(6): 112570
    Kinetics of RTK activation determine ERK reactivation and resistance to dual BRAF/MEK inhibition in melanoma.
    Sungsoo Kim, Richard Carvajal, Minah Kim, Hee Won Yang.
      The combination of BRAF and MEK inhibitors (BRAFi/MEKi) has shown promising response rates in treating BRAF-mutant melanoma by inhibiting ERK activation. However, treatment efficacy is limited by the emergence of drug-tolerant persister cells (persisters). Here, we show that the magnitude and duration of receptor tyrosine kinase (RTK) activation determine ERK reactivation and persister development. Our single-cell analysis reveals that only a small subset of melanoma cells exhibits effective RTK and ERK activation and develops persisters, despite uniform external stimuli. The kinetics of RTK activation directly influence ERK signaling dynamics and persister development. These initially rare persisters form major resistant clones through effective RTK-mediated ERK activation. Consequently, limiting RTK signaling suppresses ERK activation and cell proliferation in drug-resistant cells. Our findings provide non-genetic mechanistic insights into the role of heterogeneity in RTK activation kinetics in ERK reactivation and BRAFi/MEKi resistance, suggesting potential strategies for overcoming drug resistance in BRAF-mutant melanoma.
    Keywords:  BRAF; CP: Cancer; ERK; RTK; melanoma; persister cells; signaling dynamics
    DOI:  https://doi.org/10.1016/j.celrep.2023.112570
  4. Nucleic Acids Res. 2023 May 29. pii: gkad456. [Epub ahead of print]
    Reducing the inherent auto-inhibitory interaction within the pegRNA enhances prime editing efficiency.
    Karthikeyan Ponnienselvan, Pengpeng Liu, Thomas Nyalile, Sarah Oikemus, Stacy A Maitland, Nathan D Lawson, Jeremy Luban, Scot A Wolfe.
      Prime editing systems have enabled the incorporation of precise edits within a genome without introducing double strand breaks. Previous studies defined an optimal primer binding site (PBS) length for the pegRNA of ∼13 nucleotides depending on the sequence composition. However, optimal PBS length characterization has been based on prime editing outcomes using plasmid or lentiviral expression systems. In this study, we demonstrate that for prime editor (PE) ribonucleoprotein complexes, the auto-inhibitory interaction between the PBS and the spacer sequence affects pegRNA binding efficiency and target recognition. Destabilizing this auto-inhibitory interaction by reducing the complementarity between the PBS-spacer region enhances prime editing efficiency in multiple prime editing formats. In the case of end-protected pegRNAs, a shorter PBS length with a PBS-target strand melting temperature near 37°C is optimal in mammalian cells. Additionally, a transient cold shock treatment of the cells post PE-pegRNA delivery further increases prime editing outcomes for pegRNAs with optimized PBS lengths. Finally, we show that prime editor ribonucleoprotein complexes programmed with pegRNAs designed using these refined parameters efficiently correct disease-related genetic mutations in patient-derived fibroblasts and efficiently install precise edits in primary human T cells and zebrafish.
    DOI:  https://doi.org/10.1093/nar/gkad456
  5. PLoS Comput Biol. 2023 May 30. 19(5): e1011137
    CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing.
    Marta Sanvicente-García, Albert García-Valiente, Socayna Jouide, Jessica Jaraba-Wallace, Eric Bautista, Marc Escobosa, Avencia Sánchez-Mejías, Marc Güell.
      Gene editing characterization with currently available tools does not always give precise relative proportions among the different types of gene edits present in an edited bulk of cells. We have developed CRISPR-Analytics, CRISPR-A, which is a comprehensive and versatile genome editing web application tool and a nextflow pipeline to give support to gene editing experimental design and analysis. CRISPR-A provides a robust gene editing analysis pipeline composed of data analysis tools and simulation. It achieves higher accuracy than current tools and expands the functionality. The analysis includes mock-based noise correction, spike-in calibrated amplification bias reduction, and advanced interactive graphics. This expanded robustness makes this tool ideal for analyzing highly sensitive cases such as clinical samples or experiments with low editing efficiencies. It also provides an assessment of experimental design through the simulation of gene editing results. Therefore, CRISPR-A is ideal to support multiple kinds of experiments such as double-stranded DNA break-based engineering, base editing (BE), primer editing (PE), and homology-directed repair (HDR), without the need of specifying the used experimental approach.
    DOI:  https://doi.org/10.1371/journal.pcbi.1011137
  6. Mol Cancer. 2023 05 31. 22(1): 90
    EMT/MET plasticity in cancer and Go-or-Grow decisions in quiescence: the two sides of the same coin?
    Azamat Akhmetkaliyev, Noura Alibrahim, Darya Shafiee, Eugene Tulchinsky.
      Epithelial mesenchymal transition (EMT) and mesenchymal epithelial transition (MET) are genetic determinants of cellular plasticity. These programs operate in physiological (embryonic development, wound healing) and pathological (organ fibrosis, cancer) conditions. In cancer, EMT and MET interfere with various signalling pathways at different levels. This results in gross alterations in the gene expression programs, which affect most, if not all hallmarks of cancer, such as response to proliferative and death-inducing signals, tumorigenicity, and cell stemness. EMT in cancer cells involves large scale reorganisation of the cytoskeleton, loss of epithelial integrity, and gain of mesenchymal traits, such as mesenchymal type of cell migration. In this regard, EMT/MET plasticity is highly relevant to the Go-or-Grow concept, which postulates the dichotomous relationship between cell motility and proliferation. The Go-or-Grow decisions are critically important in the processes in which EMT/MET plasticity takes the central stage, mobilisation of stem cells during wound healing, cancer relapse, and metastasis. Here we outline the maintenance of quiescence in stem cell and metastatic niches, focusing on the implication of EMT/MET regulatory networks in Go-or-Grow switches. In particular, we discuss the analogy between cells residing in hybrid quasi-mesenchymal states and GAlert, an intermediate phase allowing quiescent stem cells to enter the cell cycle rapidly.
    Keywords:  Cancer; Cancer stem cells; EMT; MET; Quiescence; Stem cells
    DOI:  https://doi.org/10.1186/s12943-023-01793-z
  7. Elife. 2023 May 31. pii: e81289. [Epub ahead of print]12
    Pancreatic tumors exhibit myeloid-driven amino acid stress and upregulate arginine biosynthesis.
    Juan J Apiz Saab, Lindsey N Dzierozynski, Patrick B Jonker, Roya AminiTabrizi, Hardik Shah, Rosa Elena Menjivar, Andrew J Scott, Zeribe C Nwosu, Zhou Zhu, Riona N Chen, Moses Oh, Colin Sheehan, Daniel R Wahl, Marina Pasca di Magliano, Costas A Lyssiotis, Kay F Macleod, Christopher R Weber, Alexander Muir.
      Nutrient stress in the tumor microenvironment requires cancer cells to adopt adaptive metabolic programs for survival and proliferation. Therefore, knowledge of microenvironmental nutrient levels and how cancer cells cope with such nutrition is critical to understand the metabolism underpinning cancer cell biology. Previously, we performed quantitative metabolomics of the interstitial fluid (the local perfusate) of murine pancreatic ductal adenocarcinoma (PDAC) tumors to comprehensively characterize nutrient availability in the microenvironment of these tumors (M. R. Sullivan, Danai, et al., 2019). Here, we develop Tumor Interstitial Fluid Medium (TIFM), a cell culture medium that contains nutrient levels representative of the PDAC microenvironment, enabling us to study PDAC metabolism ex vivo under physiological nutrient conditions. We show that PDAC cells cultured in TIFM adopt a cellular state closer to that of PDAC cells present in tumors compared to standard culture models. Further, using the TIFM model, we found arginine biosynthesis is active in PDAC and allows PDAC cells to maintain levels of this amino acid despite microenvironmental arginine depletion. We also show that myeloid derived arginase activity is largely responsible for the low levels of arginine in PDAC tumors. Altogether, these data indicate that nutrient availability in tumors is an important determinant of cancer cell metabolism and behavior, and cell culture models that incorporate physiological nutrient availability have improved fidelity to in vivo systems and enable the discovery of novel cancer metabolic phenotypes.
    Keywords:  biochemistry; cancer biology; chemical biology; human; mouse
    DOI:  https://doi.org/10.7554/eLife.81289
  8. Development. 2023 Jun 01. pii: dev201284. [Epub ahead of print]150(11):
    RTK signalling promotes epithelial columnar cell shape and apical junction maintenance in human lung progenitor cells.
    Shuyu Liu, Dawei Sun, Richard Butler, Emma L Rawlins.
      Multipotent epithelial progenitor cells can be expanded from human embryonic lungs as organoids and maintained in a self-renewing state using a defined medium. The organoid cells are columnar, resembling the cell morphology of the developing lung tip epithelium in vivo. Cell shape dynamics and fate are tightly coordinated during development. We therefore used the organoid system to identify signalling pathways that maintain the columnar shape of human lung tip progenitors. We found that EGF, FGF7 and FGF10 have distinct functions in lung tip progenitors. FGF7 activates MAPK/ERK and PI3K/AKT signalling, and is sufficient to promote columnar cell shape in primary tip progenitors. Inhibitor experiments show that MAPK/ERK and PI3K/AKT signalling are key downstream pathways, regulating cell proliferation, columnar cell shape and cell junctions. We identified integrin signalling as a key pathway downstream of MAPK/ERK in the tip progenitors; disrupting integrin alters polarity, cell adhesion and tight junction assembly. By contrast, stimulation with FGF10 or EGF alone is not sufficient to maintain organoid columnar cell shape. This study employs organoids to provide insight into the cellular mechanisms regulating human lung development.
    Keywords:  EGF; FGF; Integrin; KTR reporter; Organoid
    DOI:  https://doi.org/10.1242/dev.201284
  9. Nat Methods. 2023 May 29.
    SIMBA: single-cell embedding along with features.
    Huidong Chen, Jayoung Ryu, Michael E Vinyard, Adam Lerer, Luca Pinello.
      Most current single-cell analysis pipelines are limited to cell embeddings and rely heavily on clustering, while lacking the ability to explicitly model interactions between different feature types. Furthermore, these methods are tailored to specific tasks, as distinct single-cell problems are formulated differently. To address these shortcomings, here we present SIMBA, a graph embedding method that jointly embeds single cells and their defining features, such as genes, chromatin-accessible regions and DNA sequences, into a common latent space. By leveraging the co-embedding of cells and features, SIMBA allows for the study of cellular heterogeneity, clustering-free marker discovery, gene regulation inference, batch effect removal and omics data integration. We show that SIMBA provides a single framework that allows diverse single-cell problems to be formulated in a unified way and thus simplifies the development of new analyses and extension to new single-cell modalities. SIMBA is implemented as a comprehensive Python library ( https://simba-bio.readthedocs.io ).
    DOI:  https://doi.org/10.1038/s41592-023-01899-8
  10. Nat Commun. 2023 Jun 02. 14(1): 3185
    Light-switchable transcription factors obtained by direct screening in mammalian cells.
    Liyuan Zhu, Harold M McNamara, Jared E Toettcher.
      Optogenetic tools can provide fine spatial and temporal control over many biological processes. Yet the development of new light-switchable protein variants remains challenging, and the field still lacks general approaches to engineering or discovering protein variants with light-switchable biological functions. Here, we adapt strategies for protein domain insertion and mammalian-cell expression to generate and screen a library of candidate optogenetic tools directly in mammalian cells. The approach is based on insertion of the AsLOV2 photoswitchable domain at all possible positions in a candidate protein of interest, introduction of the library into mammalian cells, and light/dark selection for variants with photoswitchable activity. We demonstrate the approach's utility using the Gal4-VP64 transcription factor as a model system. Our resulting LightsOut transcription factor exhibits a > 150-fold change in transcriptional activity between dark and blue light conditions. We show that light-switchable function generalizes to analogous insertion sites in two additional Cys6Zn2 and C2H2 zinc finger domains, providing a starting point for optogenetic regulation of a broad class of transcription factors. Our approach can streamline the identification of single-protein optogenetic switches, particularly in cases where structural or biochemical knowledge is limited.
    DOI:  https://doi.org/10.1038/s41467-023-38993-6
  11. Nature. 2023 May 31.
    In situ tumour arrays reveal early environmental control of cancer immunity.
    Guadalupe Ortiz-Muñoz, Markus Brown, Catherine B Carbone, Ximo Pechuan-Jorge, Vincent Rouilly, Henrik Lindberg, Alex T Ritter, Gautham Raghupathi, Qianbo Sun, Tess Nicotra, Shreya R Mantri, Angela Yang, Jonas Doerr, Deepti Nagarkar, Spyros Darmanis, Benjamin Haley, Sanjeev Mariathasan, Yulei Wang, Carlos Gomez-Roca, Carlos Eduardo de Andrea, David Spigel, Thomas Wu, Lelia Delamarre, Johannes Schöneberg, Zora Modrusan, Richard Price, Shannon J Turley, Ira Mellman, Christine Moussion.
      The immune phenotype of a tumour is a key predictor of its response to immunotherapy1-4. Patients who respond to checkpoint blockade generally present with immune-inflamed5-7 tumours that are highly infiltrated by T cells. However, not all inflamed tumours respond to therapy, and even lower response rates occur among tumours that lack T cells (immune desert) or that spatially exclude T cells to the periphery of the tumour lesion (immune excluded)8. Despite the importance of these tumour immune phenotypes in patients, little is known about their development, heterogeneity or dynamics owing to the technical difficulty of tracking these features in situ. Here we introduce skin tumour array by microporation (STAMP)-a preclinical approach that combines high-throughput time-lapse imaging with next-generation sequencing of tumour arrays. Using STAMP, we followed the development of thousands of arrayed tumours in vivo to show that tumour immune phenotypes and outcomes vary between adjacent tumours and are controlled by local factors within the tumour microenvironment. Particularly, the recruitment of T cells by fibroblasts and monocytes into the tumour core was supportive of T cell cytotoxic activity and tumour rejection. Tumour immune phenotypes were dynamic over time and an early conversion to an immune-inflamed phenotype was predictive of spontaneous or therapy-induced tumour rejection. Thus, STAMP captures the dynamic relationships of the spatial, cellular and molecular components of tumour rejection and has the potential to translate therapeutic concepts into successful clinical strategies.
    DOI:  https://doi.org/10.1038/s41586-023-06132-2
  12. Sci Adv. 2023 Jun 02. 9(22): eadg4993
    ULK1-mediated metabolic reprogramming regulates Vps34 lipid kinase activity by its lactylation.
    Mengshu Jia, Xiao Yue, Weixia Sun, Qianjun Zhou, Cheng Chang, Weihua Gong, Jian Feng, Xie Li, Ruonan Zhan, Kemin Mo, Lijuan Zhang, Yajie Qian, Yuying Sun, Aoxue Wang, Yejun Zou, Weicai Chen, Yan Li, Li Huang, Yi Yang, Yuzheng Zhao, Xiawei Cheng.
      Autophagy and glycolysis are highly conserved biological processes involved in both physiological and pathological cellular programs, but the interplay between these processes is poorly understood. Here, we show that the glycolytic enzyme lactate dehydrogenase A (LDHA) is activated upon UNC-51-like kinase 1 (ULK1) activation under nutrient deprivation. Specifically, ULK1 directly interacts with LDHA, phosphorylates serine-196 when nutrients are scarce and promotes lactate production. Lactate connects autophagy and glycolysis through Vps34 lactylation (at lysine-356 and lysine-781), which is mediated by the acyltransferase KAT5/TIP60. Vps34 lactylation enhances the association of Vps34 with Beclin1, Atg14L, and UVRAG, and then increases Vps34 lipid kinase activity. Vps34 lactylation promotes autophagic flux and endolysosomal trafficking. Vps34 lactylation in skeletal muscle during intense exercise maintains muscle cell homeostasis and correlates with cancer progress by inducing cell autophagy. Together, our findings describe autophagy regulation mechanism and then integrate cell autophagy and glycolysis.
    DOI:  https://doi.org/10.1126/sciadv.adg4993
  13. Development. 2023 Jun 01. pii: dev201103. [Epub ahead of print]150(11):
    Maturing differentiated human pluripotent stem cells in vitro: methods and challenges.
    Daniele Ottaviani, Menno Ter Huurne, David A Elliott, Milena Bellin, Christine L Mummery.
      Human pluripotent stem cells (hPSCs), derived from individuals or genetically modified with disease-related mutations and variants, have revolutionised studies of human disease. Researchers are beginning to exploit the extraordinary potential of stem cell technology to screen for new drugs to treat intractable diseases, ideally without side-effects. However, a major problem is that the differentiated cell types on which these models are based are immature; they resemble fetal and not adult cells. Here, we discuss the nature and hurdles of hPSC maturation, using cardiomyocytes as an example. We review methods used to induce cardiomyocyte maturation in culture and consider remaining challenges for their integration into research on human disease and drug development pipelines.
    Keywords:  Cardiac maturation; Cardiac microtissues; Cardiac organoids; Engineered heart tissue; hiPSC-derived cardiomyocytes
    DOI:  https://doi.org/10.1242/dev.201103
  14. Development. 2023 Oct 15. pii: dev199961. [Epub ahead of print]150(20):
    Nutrient regulation of development and cell fate decisions.
    William B Tu, Heather R Christofk, Kathrin Plath.
      Diet contributes to health at all stages of life, from embryonic development to old age. Nutrients, including vitamins, amino acids, lipids and sugars, have instructive roles in directing cell fate and function, maintaining stem cell populations, tissue homeostasis and alleviating the consequences of aging. This Review highlights recent findings that illuminate how common diets and specific nutrients impact cell fate decisions in healthy and disease contexts. We also draw attention to new models, technologies and resources that help to address outstanding questions in this emerging field and may lead to dietary approaches that promote healthy development and improve disease treatments.
    Keywords:  Cell fate decision; Dietary nutrient; Metabolism; Stem cell
    DOI:  https://doi.org/10.1242/dev.199961
  15. iScience. 2023 Jun 16. 26(6): 106853
    Visualizing gene expression changes in time, space, and single cells with expressyouRcell.
    Martina Paganin, Toma Tebaldi, Fabio Lauria, Gabriella Viero.
      The last decade has witnessed massive advancements in high-throughput techniques capable of producing increasingly complex gene expression datasets across time and space and at the resolution of single cells. Yet, the large volume of big data available and the complexity of experimental designs hamper an easy understanding and effective communication of the results. We present expressyouRcell, an easy-to-use R package to map the multi-dimensional variations of transcript and protein levels in dynamic cell pictographs. expressyouRcell visualizes gene expression variations as pictographic representations of cell-type thematic maps. expressyouRcell visually reduces the complexity of displaying gene expression and protein level changes across multiple measurements (time points or single-cell trajectories) by generating dynamic representations of cellular pictographs. We applied expressyouRcell to single cell, bulk RNA sequencing (RNA-seq), and proteomics datasets, demonstrating its flexibility and usability in the visualization of complex variations in gene expression. Our approach improves the standard quantitative interpretation and communication of relevant results.
    Keywords:  Computational bioinformatics
    DOI:  https://doi.org/10.1016/j.isci.2023.106853
  16. Nat Commun. 2023 May 27. 14(1): 3064
    Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets.
    Shilu Zhang, Saptarshi Pyne, Stefan Pietrzak, Spencer Halberg, Sunnie Grace McCalla, Alireza Fotuhi Siahpirani, Rupa Sridharan, Sushmita Roy.
      Cell type-specific gene expression patterns are outputs of transcriptional gene regulatory networks (GRNs) that connect transcription factors and signaling proteins to target genes. Single-cell technologies such as single cell RNA-sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq), can examine cell-type specific gene regulation at unprecedented detail. However, current approaches to infer cell type-specific GRNs are limited in their ability to integrate scRNA-seq and scATAC-seq measurements and to model network dynamics on a cell lineage. To address this challenge, we have developed single-cell Multi-Task Network Inference (scMTNI), a multi-task learning framework to infer the GRN for each cell type on a lineage from scRNA-seq and scATAC-seq data. Using simulated and real datasets, we show that scMTNI is a broadly applicable framework for linear and branching lineages that accurately infers GRN dynamics and identifies key regulators of fate transitions for diverse processes such as cellular reprogramming and differentiation.
    DOI:  https://doi.org/10.1038/s41467-023-38637-9
  17. BMC Genomics. 2023 May 29. 24(1): 289
    ssDNA is not superior to dsDNA as long HDR donors for CRISPR-mediated endogenous gene tagging in human diploid RPE1 and HCT116 cells.
    Akira Mabuchi, Shoji Hata, Mariya Genova, Chiharu Tei, Kei K Ito, Masayasu Hirota, Takuma Komori, Masamitsu Fukuyama, Takumi Chinen, Atsushi Toyoda, Daiju Kitagawa.
       BACKGROUND: Recent advances in CRISPR technology have enabled us to perform gene knock-in in various species and cell lines. CRISPR-mediated knock-in requires donor DNA which serves as a template for homology-directed repair (HDR). For knock-in of short sequences or base substitutions, ssDNA donors are frequently used among various other forms of HDR donors, such as linear dsDNA. However, partly due to the complexity of long ssDNA preparation, it remains unclear whether ssDNA is the optimal type of HDR donors for insertion of long transgenes such as fluorescent reporters in human cells.
    RESULTS: In this study, we established a nuclease-based simple method for the preparation of long ssDNA with high yield and purity, and comprehensively compared the performance of ssDNA and dsDNA donors with 90 bases of homology arms for endogenous gene tagging with long transgenes in human diploid RPE1 and HCT116 cells. Quantification using flow cytometry revealed lower efficiency of endogenous fluorescent tagging with ssDNA donors than with dsDNA. By analyzing knock-in outcomes using long-read amplicon sequencing and a classification framework, a variety of mis-integration events were detected regardless of the donor type. Importantly, the ratio of precise insertion was lower with ssDNA donors than with dsDNA. Moreover, in off-target integration analyses using donors without homology arms, ssDNA and dsDNA were comparably prone to non-homologous integration.
    CONCLUSIONS: These results indicate that ssDNA is not superior to dsDNA as long HDR donors with relatively short homology arms for gene knock-in in human RPE1 and HCT116 cells.
    Keywords:  CRISPR-Cas; Knock-in; Long ssDNA; Repair template
    DOI:  https://doi.org/10.1186/s12864-023-09377-3
  18. STAR Protoc. 2023 May 29. pii: S2666-1667(23)00253-8. [Epub ahead of print]4(2): 102286
    Protocol for biallelic tagging of an endogenous gene using CRISPR-Cas9 in human cells.
    Nannan Kong, Ying Wai Chan.
      We present here a protocol for biallelic tagging of an endogenous gene in human cells using CRISPR-Cas9 editing technology. Using RIF1 as an example, we describe tagging the gene with a mini-auxin-inducible degron and a green fluorescent protein at its C terminus. We detail steps for preparing and designing the sgRNA and homologous repair template, and clone selection and verification. For complete details on the use and execution of this protocol, please refer to Kong et al.1.
    Keywords:  CRISPR; Cell Biology
    DOI:  https://doi.org/10.1016/j.xpro.2023.102286
  19. J Vis Exp. 2023 05 12.
    Robust Tissue Fabrication for Long-Term Culture of iPSC-Derived Brain Organoids for Aging Research.
    Lena Sophie Koch, David Choy Buentello, Kerensa Broersen.
      The currently available animal and cellular models do not fully recapitulate the complexity of changes that take place in the aging human brain. A recent development of procedures describing the generation of human cerebral organoids, derived from human induced pluripotent stem cells (iPSCs), has the potential to fundamentally transform the ability to model and understand the aging of the human brain and related pathogenic processes. Here, an optimized protocol for generating, maintaining, aging, and characterizing human iPSC-derived cerebral organoids is presented. This protocol can be implemented to generate brain organoids in a reproducible manner and serves as a step-by-step guide, incorporating the latest techniques that result in improved organoid maturation and aging in culture. Specific issues related to organoid maturation, necrosis, variability, and batch effects are being addressed. Taken together, these technological advances will allow the modeling of brain aging in organoids derived from a variety of young and aged human donors, as well as individuals afflicted with age-related brain disorders, allowing the identification of physiologic and pathogenic mechanisms of human brain aging.
    DOI:  https://doi.org/10.3791/64586
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