bims-gerecp Biomed News
on Gene regulatory networks of epithelial cell plasticity
Issue of 2024–09–29
thirteen papers selected by
Xiao Qin, University of Oxford
  1. Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution.
  2. Coordinated, multicellular patterns of transcriptional variation that stratify patient cohorts are revealed by tensor decomposition.
  3. Vitessce: integrative visualization of multimodal and spatially resolved single-cell data.
  4. Self-sustaining long-term 3D epithelioid cultures reveal drivers of clonal expansion in esophageal epithelium.
  5. Designing realistic regulatory DNA with autoregressive language models.
  6. Droplet-based functional CRISPR screening of cell-cell interactions by SPEAC-seq.
  7. Tumor-associated mesenchymal stromal cells modulate macrophage phagocytosis in stromal-rich colorectal cancer via PD-1 signaling.
  8. A Ctnnb1 enhancer transcriptionally regulates Wnt signaling dosage to balance homeostasis and tumorigenesis of intestinal epithelia.
  9. An ILK/STAT3 pathway controls glioblastoma stem cell plasticity.
  10. Benchmarking algorithms for single-cell multi-omics prediction and integration.
  11. Expanding the genome editing toolbox with designer CRISPR-Cas-like transposons.
  12. It took a long, long time: Ras and the race to cure cancer.
  13. Single cell genome and epigenome co-profiling reveals hardwiring and plasticity in breast cancer.
  1. Nat Genet. 2024 Sep 24.
    Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution.
    Joshua S Schiffman, Andrew R D'Avino, Tamara Prieto, Yakun Pang, Yilin Fan, Srinivas Rajagopalan, Catherine Potenski, Toshiro Hara, Mario L Suvà, Charles Gawad, Dan A Landau.
      Single-cell sequencing has characterized cell state heterogeneity across diverse healthy and malignant tissues. However, the plasticity or heritability of these cell states remains largely unknown. To address this, we introduce PATH (phylogenetic analysis of trait heritability), a framework to quantify cell state heritability versus plasticity and infer cell state transition and proliferation dynamics from single-cell lineage tracing data. Applying PATH to a mouse model of pancreatic cancer, we observed heritability at the ends of the epithelial-to-mesenchymal transition spectrum, with higher plasticity at more intermediate states. In primary glioblastoma, we identified bidirectional transitions between stem- and mesenchymal-like cells, which use the astrocyte-like state as an intermediary. Finally, we reconstructed a phylogeny from single-cell whole-genome sequencing in B cell acute lymphoblastic leukemia and delineated the heritability of B cell differentiation states linked with genetic drivers. Altogether, PATH replaces qualitative conceptions of plasticity with quantitative measures, offering a framework to study somatic evolution.
    DOI:  https://doi.org/10.1038/s41588-024-01920-6
  2. Nat Biotechnol. 2024 Sep 23.
    Coordinated, multicellular patterns of transcriptional variation that stratify patient cohorts are revealed by tensor decomposition.
    Jonathan Mitchel, M Grace Gordon, Richard K Perez, Evan Biederstedt, Raymund Bueno, Chun Jimmie Ye, Peter V Kharchenko.
      Tissue-level and organism-level biological processes often involve the coordinated action of multiple distinct cell types. The recent application of single-cell assays to many individuals should enable the study of how donor-level variation in one cell type is linked to that in other cell types. Here we introduce a computational approach called single-cell interpretable tensor decomposition (scITD) to identify common axes of interindividual variation by considering joint expression variation across multiple cell types. scITD combines expression matrices from each cell type into a higher-order matrix and factorizes the result using the Tucker tensor decomposition. Applying scITD to single-cell RNA-sequencing data on 115 persons with lupus and 83 persons with coronavirus disease 2019, we identify patterns of coordinated cellular activity linked to disease severity and specific phenotypes, such as lupus nephritis. scITD results also implicate specific signaling pathways likely mediating coordination between cell types. Overall, scITD offers a tool for understanding the covariation of cell states across individuals, which can yield insights into the complex processes that define and stratify disease.
    DOI:  https://doi.org/10.1038/s41587-024-02411-z
  3. Nat Methods. 2024 Sep 27.
    Vitessce: integrative visualization of multimodal and spatially resolved single-cell data.
    Mark S Keller, Ilan Gold, Chuck McCallum, Trevor Manz, Peter V Kharchenko, Nils Gehlenborg.
      Multiomics technologies with single-cell and spatial resolution make it possible to measure thousands of features across millions of cells. However, visual analysis of high-dimensional transcriptomic, proteomic, genome-mapped and imaging data types simultaneously remains a challenge. Here we describe Vitessce, an interactive web-based visualization framework for exploration of multimodal and spatially resolved single-cell data. We demonstrate integrative visualization of millions of data points, including cell-type annotations, gene expression quantities, spatially resolved transcripts and cell segmentations, across multiple coordinated views. The open-source software is available at http://vitessce.io .
    DOI:  https://doi.org/10.1038/s41592-024-02436-x
  4. Nat Genet. 2024 Sep 23.
    Self-sustaining long-term 3D epithelioid cultures reveal drivers of clonal expansion in esophageal epithelium.
    Albert Herms, David Fernandez-Antoran, Maria P Alcolea, Argyro Kalogeropoulou, Ujjwal Banerjee, Gabriel Piedrafita, Emilie Abby, Jose Antonio Valverde-Lopez, Inês S Ferreira, Irene Caseda, Maria T Bejar, Stefan C Dentro, Sara Vidal-Notari, Swee Hoe Ong, Bartomeu Colom, Kasumi Murai, Charlotte King, Krishnaa Mahbubani, Kourosh Saeb-Parsy, Alan R Lowe, Moritz Gerstung, Philip H Jones.
      Aging epithelia are colonized by somatic mutations, which are subjected to selection influenced by intrinsic and extrinsic factors. The lack of suitable culture systems has slowed the study of this and other long-term biological processes. Here, we describe epithelioids, a facile, cost-effective method of culturing multiple mouse and human epithelia. Esophageal epithelioids self-maintain without passaging for at least 1 year, maintaining a three-dimensional structure with proliferative basal cells that differentiate into suprabasal cells, which eventually shed and retain genomic stability. Live imaging over 5 months showed that epithelioids replicate in vivo cell dynamics. Epithelioids support genetic manipulation and enable the study of mutant cell competition and selection in three-dimensional epithelia, and show how anti-cancer treatments modulate competition between transformed and wild-type cells. Finally, a targeted CRISPR-Cas9 screen shows that epithelioids recapitulate mutant gene selection in aging human esophagus and identifies additional drivers of clonal expansion, resolving the genetic networks underpinning competitive fitness.
    DOI:  https://doi.org/10.1038/s41588-024-01875-8
  5. Genome Res. 2024 Sep 25.
    Designing realistic regulatory DNA with autoregressive language models.
    Avantika Lal, David Garfield, Tommaso Biancalani, Gokcen Eraslan.
      Cis-regulatory elements (CREs), such as promoters and enhancers, are DNA sequences that regulate the expression of genes. The activity of a CRE is influenced by the order, composition, and spacing of sequence motifs that are bound by proteins called transcription factors (TFs). Synthetic CREs with specific properties are needed for biomanufacturing as well as for many therapeutic applications including cell and gene therapy. Here, we present regLM, a framework to design synthetic CREs with desired properties, such as high, low, or cell type-specific activity, using autoregressive language models in conjunction with supervised sequence-to-function models. We used our framework to design synthetic yeast promoters and cell type-specific human enhancers. We demonstrate that the synthetic CREs generated by our approach are not only predicted to have the desired functionality but also contain biological features similar to experimentally validated CREs. regLM thus facilitates the design of realistic regulatory DNA elements while providing insights into the cis-regulatory code.
    DOI:  https://doi.org/10.1101/gr.279142.124
  6. Nat Protoc. 2024 Sep 26.
    Droplet-based functional CRISPR screening of cell-cell interactions by SPEAC-seq.
    Camilo Faust Akl, Mathias Linnerbauer, Zhaorong Li, Hong-Gyun Lee, Iain C Clark, Michael A Wheeler, Francisco J Quintana.
      Cell-cell interactions are essential for the function and contextual regulation of biological tissues. We present a platform for high-throughput microfluidics-supported genetic screening of functional regulators of cell-cell interactions. Systematic perturbation of encapsulated associated cells followed by sequencing (SPEAC-seq) combines genome-wide CRISPR libraries, cell coculture in droplets and microfluidic droplet sorting based on functional read-outs determined by fluorescent reporter circuits to enable the unbiased discovery of interaction regulators. This technique overcomes limitations of traditional methods for characterization of cell-cell communication, which require a priori knowledge of cellular interactions, are highly engineered and lack functional read-outs. As an example of this technique, we describe the investigation of neuroinflammatory intercellular communication between microglia and astrocytes, using genome-wide CRISPR-Cas9 inactivation libraries and fluorescent reporters of NF-κB activation. This approach enabled the discovery of thousands of microglial regulators of astrocyte NF-κB activation important for the control of central nervous system inflammation. Importantly, SPEAC-seq can be adapted to different cell types, screening modalities, cell functions and physiological contexts, only limited by the ability to fluorescently report cell functions and by droplet cultivation conditions. Performing genome-wide screening takes less than 2 weeks and requires microfluidics capabilities. Thus, SPEAC-seq enables the large-scale investigation of cell-cell interactions.
    DOI:  https://doi.org/10.1038/s41596-024-01056-1
  7. iScience. 2024 Sep 20. 27(9): 110701
    Tumor-associated mesenchymal stromal cells modulate macrophage phagocytosis in stromal-rich colorectal cancer via PD-1 signaling.
    Niamh A Leonard, Shania M Corry, Eileen Reidy, Hannah Egan, Grace O'Malley, Kerry Thompson, Emma McDermott, Aoise O'Neill, Norashikin Zakaria, Laurence J Egan, Thomas Ritter, Daniela Loessner, Keara Redmond, Margaret Sheehan, Aoife Canney, Aisling M Hogan, Sean O Hynes, Oliver Treacy, Philip D Dunne, Aideen E Ryan.
      CMS4 colorectal cancer (CRC), based on the consensus molecular subtype (CMS), stratifies patients with the poorest disease-free survival rates. It is characterized by a strong mesenchymal stromal cell (MSC) signature, wound healing-like inflammation and therapy resistance. We utilized 2D and 3D in vitro, in vivo, and ex vivo models to assess the impact of inflammation and stromal cells on immunosuppression in CMS4 CRC. RNA sequencing data from untreated stage II/III CRC patients showed enriched TNF-α signatures in CMS1 and CMS4 tumors. Secretome from TNF-α treated cancer cells induced an immunomodulatory and chemotactic phenotype in MSC and cancer-associated fibroblasts (CAFs). Macrophages in CRC tumours migrate and preferentially localise in stromal compartment. Inflammatory CRC secretome enhances expression of PD-L1 and CD47 on both human and murine stromal cells. We demonstrate that TNF-α-induced inflammation in CRC suppresses macrophage phagocytosis via stromal cells. We show that stromal cell-mediated suppression of macrophage phagocytosis is mediated in part through PD-1 signaling. These data suggest that re-stratification of CRC by CMS may reveal patient subsets with microsatellite stable tumors, particularly CMS4-like tumors, that may respond to immunotherapies.
    Keywords:  Cancer; Immunology; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2024.110701
  8. Elife. 2024 Sep 25. pii: RP98238. [Epub ahead of print]13
    A Ctnnb1 enhancer transcriptionally regulates Wnt signaling dosage to balance homeostasis and tumorigenesis of intestinal epithelia.
    Xiaojiao Hua, Chen Zhao, Jianbo Tian, Junbao Wang, Xiaoping Miao, Gen Zheng, Min Wu, Mei Ye, Ying Liu, Yan Zhou.
      The β-catenin-dependent canonical Wnt signaling is pivotal in organ development, tissue homeostasis, and cancer. Here, we identified an upstream enhancer of Ctnnb1 - the coding gene for β-catenin, named ieCtnnb1 (intestinal enhancer of Ctnnb1), which is crucial for intestinal homeostasis. ieCtnnb1 is predominantly active in the base of small intestinal crypts and throughout the epithelia of large intestine. Knockout of ieCtnnb1 led to a reduction in Ctnnb1 transcription, compromising the canonical Wnt signaling in intestinal crypts. Single-cell sequencing revealed that ieCtnnb1 knockout altered epithelial compositions and potentially compromised functions of small intestinal crypts. While deletion of ieCtnnb1 hampered epithelial turnovers in physiologic conditions, it prevented occurrence and progression of Wnt/β-catenin-driven colorectal cancers. Human ieCTNNB1 drove reporter gene expression in a pattern highly similar to mouse ieCtnnb1. ieCTNNB1 contains a single-nucleotide polymorphism associated with CTNNB1 expression levels in human gastrointestinal epithelia. The enhancer activity of ieCTNNB1 in colorectal cancer tissues was stronger than that in adjacent normal tissues. HNF4α and phosphorylated CREB1 were identified as key trans-factors binding to ieCTNNB1 and regulating CTNNB1 transcription. Together, these findings unveil an enhancer-dependent mechanism controlling the dosage of Wnt signaling and homeostasis in intestinal epithelia.
    Keywords:  Ctnnb1; canonical Wnt signaling; cell biology; colorectal cancer; enhancer; intestinal epithelial homeostasis; mouse
    DOI:  https://doi.org/10.7554/eLife.98238
  9. Dev Cell. 2024 Sep 20. pii: S1534-5807(24)00531-8. [Epub ahead of print]
    An ILK/STAT3 pathway controls glioblastoma stem cell plasticity.
    Alexander E P Loftus, Marianna S Romano, Anh Nguyen Phuong, Ben J McKinnel, Morwenna T Muir, Muhammad Furqan, John C Dawson, Lidia Avalle, Adam T Douglas, Richard L Mort, Adam Byron, Neil O Carragher, Steven M Pollard, Valerie G Brunton, Margaret C Frame.
      Glioblastoma (GBM) is driven by malignant neural stem-like cells that display extensive heterogeneity and phenotypic plasticity, which drive tumor progression and therapeutic resistance. Here, we show that the extracellular matrix-cell adhesion protein integrin-linked kinase (ILK) stimulates phenotypic plasticity and mesenchymal-like, invasive behavior in a murine GBM stem cell model. ILK is required for the interconversion of GBM stem cells between malignancy-associated glial-like states, and its loss produces cells that are unresponsive to multiple cell state transition cues. We further show that an ILK/STAT3 signaling pathway controls the plasticity that enables transition of GBM stem cells to an astrocyte-like state in vitro and in vivo. Finally, we find that ILK expression correlates with expression of STAT3-regulated proteins and protein signatures describing astrocyte-like and mesenchymal states in patient tumors. This work identifies ILK as a pivotal regulator of multiple malignancy-associated GBM phenotypes, including phenotypic plasticity and mesenchymal state.
    Keywords:  STAT3; adhesion; astrocytes; cancer; glioblastoma; integrin-linked kinase; plasticity; stem cells
    DOI:  https://doi.org/10.1016/j.devcel.2024.09.003
  10. Nat Methods. 2024 Sep 25.
    Benchmarking algorithms for single-cell multi-omics prediction and integration.
    Yinlei Hu, Siyuan Wan, Yuanhanyu Luo, Yuanzhe Li, Tong Wu, Wentao Deng, Chen Jiang, Shan Jiang, Yueping Zhang, Nianping Liu, Zongcheng Yang, Falai Chen, Bin Li, Kun Qu.
      The development of single-cell multi-omics technology has greatly enhanced our understanding of biology, and in parallel, numerous algorithms have been proposed to predict the protein abundance and/or chromatin accessibility of cells from single-cell transcriptomic information and to integrate various types of single-cell multi-omics data. However, few studies have systematically compared and evaluated the performance of these algorithms. Here, we present a benchmark study of 14 protein abundance/chromatin accessibility prediction algorithms and 18 single-cell multi-omics integration algorithms using 47 single-cell multi-omics datasets. Our benchmark study showed overall totalVI and scArches outperformed the other algorithms for predicting protein abundance, and LS_Lab was the top-performing algorithm for the prediction of chromatin accessibility in most cases. Seurat, MOJITOO and scAI emerge as leading algorithms for vertical integration, whereas totalVI and UINMF excel beyond their counterparts in both horizontal and mosaic integration scenarios. Additionally, we provide a pipeline to assist researchers in selecting the optimal multi-omics prediction and integration algorithm.
    DOI:  https://doi.org/10.1038/s41592-024-02429-w
  11. Nat Methods. 2024 Sep 23.
    Expanding the genome editing toolbox with designer CRISPR-Cas-like transposons.
      
    DOI:  https://doi.org/10.1038/s41592-024-02460-x
  12. Cell. 2024 Sep 19. pii: S0092-8674(24)01028-6. [Epub ahead of print]
    It took a long, long time: Ras and the race to cure cancer.
    Robert A Weinberg.
      
    DOI:  https://doi.org/10.1016/j.cell.2024.09.010
  13. bioRxiv. 2024 Sep 10. pii: 2024.09.06.611519. [Epub ahead of print]
    Single cell genome and epigenome co-profiling reveals hardwiring and plasticity in breast cancer.
    Kaile Wang, Yun Yan, Heba Elgamal, Jianzhuo Li, Chenling Tang, Shanshan Bai, Zhenna Xiao, Emi Sei, Yiyun Lin, Junke Wang, Jessica Montalvan, Changandeep Nagi, Alastair M Thompson, Nicholas Navin.
      Understanding the impact of genetic alterations on epigenomic phenotypes during breast cancer progression is challenging with unimodal measurements. Here, we report wellDA-seq, the first high-genomic resolution, high-throughput method that can simultaneously measure the whole genome and chromatin accessibility profiles of thousands of single cells. Using wellDA-seq, we profiled 22,123 single cells from 2 normal and 9 tumors breast tissues. By directly mapping the epigenomic phenotypes to genetic lineages across cancer subclones, we found evidence of both genetic hardwiring and epigenetic plasticity. In 6 estrogen-receptor positive breast cancers, we directly identified the ancestral cancer cells, and found that their epithelial cell-of-origin was Luminal Hormone Responsive cells. We also identified cell types with copy number aberrations (CNA) in normal breast tissues and discovered non-epithelial cell types in the microenvironment with CNAs in breast cancers. These data provide insights into the complex relationship between genetic alterations and epigenomic phenotypes during breast tumor evolution.
    DOI:  https://doi.org/10.1101/2024.09.06.611519
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