Advertisement
Cell Reports Methods
All content is freely available to readers and supported through open access

Sep 27, 2021

Volume 1Issue 5
Open Access
On the cover: There is a growing need to develop technologies that provide quantitative information on the spatial location of RNAs and proteins on a single-cell level. In this issue, Savulescu et al. present DypFISH, a versatile toolbox of analytical techniques to interrogate single-molecule RNA FISH data in combination with protein immunolabeling. The cover image represents the localization patterns of various RNAs and proteins, generated by using the DypFISH technique and compacted into one representative micropatterned cell resembling a kite. Cover image by Robyn Brackin, Advanced Medical Bioimaging, Charité – Universitätsmedizin, Berlin, Germany....
On the cover: There is a growing need to develop technologies that provide quantitative information on the spatial location of RNAs and proteins on a single-cell level. In this issue, Savulescu et al. present DypFISH, a versatile toolbox of analytical techniques to interrogate single-molecule RNA FISH data in combination with protein immunolabeling. The cover image represents the localization patterns of various RNAs and proteins, generated by using the DypFISH technique and compacted into one representative micropatterned cell resembling a kite. Cover image by Robyn Brackin, Advanced Medical Bioimaging, Charité – Universitätsmedizin, Berlin, Germany.

Preview

Review

  • Global approaches for profiling transcription initiation

    • Robert A. Policastro,
    • Gabriel E. Zentner
    Transcription start site (TSS) selection influences transcript stability and diversity in development and disease. In this Protocol Review, Policastro and Zentner comprehensively discuss molecular and computational techniques for global profiling of TSSs, providing a practical resource for researchers.

Reports

  • Single-cell intracellular epitope and transcript detection reveals signal transduction dynamics

    • Francesca Rivello,
    • Erik van Buijtenen,
    • Kinga Matuła,
    • Jessie A.G.L. van Buggenum,
    • Paul Vink,
    • Hans van Eenennaam,
    • Klaas W. Mulder,
    • Wilhelm T.S. Huck
    Rivello et al. develop QuRIE-seq for high-throughput quantification of single-cell mRNA levels in combination with extra- and intracellular protein levels via immunostaining with 80 DNA-conjugated antibodies. This method shows the cellular response over time to external perturbations at the surface marker, (phospho)proteome, or gene expression level.
  • An object-oriented framework for evolutionary pangenome analysis

    • Ignacio Ferrés,
    • Gregorio Iraola
    Ferrés and Iraola develop a software package in R to integrate and analyze bacterial pangenome data. This allows creating a single programming object that stores all the data, as well as methods to produce standard analyses and visualizations for comparative genomics.

Articles

  • Tools for efficient analysis of neurons in a 3D reference atlas of whole mouse spinal cord

    • Felix Fiederling,
    • Luke A. Hammond,
    • David Ng,
    • Carol Mason,
    • Jane Dodd
    Fiederling et al. provide tools for efficient analysis of neurons and their processes within the entire mouse spinal cord. A 3D reference atlas puts images into anatomical context and allows integration of data from different studies. They demonstrate the usefulness of this methodology, analyzing known and previously unknown neuronal distributions.
  • Interrogating RNA and protein spatial subcellular distribution in smFISH data with DypFISH

    • Anca F. Savulescu,
    • Robyn Brackin,
    • Emmanuel Bouilhol,
    • Benjamin Dartigues,
    • Jonathan H. Warrell,
    • Mafalda R. Pimentel,
    • Nicolas Beaume,
    • Isabela C. Fortunato,
    • Stephane Dallongeville,
    • Mikaël Boulle,
    • Hayssam Soueidan,
    • Fabrice Agou,
    • Jan Schmoranzer,
    • Jean-Christophe Olivo-Marin,
    • Claudio A. Franco,
    • Edgar R. Gomes,
    • Macha Nikolski,
    • Musa M. Mhlanga
    Savulescu et al. present DypFISH, a method to quantitatively investigate the subcellular spatial localization of RNA and proteins. DypFISH introduces a range of analytical techniques and statistics to interrogate single-molecule RNA FISH data in combination with protein immunolabeling.
  • An image analysis method for regionally defined cellular phenotyping of the Drosophila midgut

    • Arto Viitanen,
    • Josef Gullmets,
    • Jack Morikka,
    • Pekka Katajisto,
    • Jaakko Mattila,
    • Ville Hietakangas
    The intestine is divided into functionally distinct regions along its anteroposterior axis. Here, Viitanen and co-workers develop a quantitative image analysis approach to map and compare cellular phenotypes of Drosophila midgut with subregional resolution.
  • A mouse model for the study of anti-tumor T cell responses in Kras-driven lung adenocarcinoma

    • Brittany Fitzgerald,
    • Kelli A. Connolly,
    • Can Cui,
    • Eric Fagerberg,
    • Dylan L. Mariuzza,
    • Noah I. Hornick,
    • Gena G. Foster,
    • Ivana William,
    • Julie F. Cheung,
    • Nikhil S. Joshi
    Fitzgerald et al. develop a mouse model of LUAD that generates an endogenous CD8 T cell response against lung tumors. Tumors from this model respond to immunotherapy, providing a new tool for researchers to use to investigate the processes that underlie immunotherapy responses.
  • Systematic discovery and validation of T cell targets directed against oncogenic KRAS mutations

    • Jaewon Choi,
    • Scott P. Goulding,
    • Brandon P. Conn,
    • Christopher D. McGann,
    • Jared L. Dietze,
    • Jessica Kohler,
    • Divya Lenkala,
    • Antoine Boudot,
    • Daniel A. Rothenberg,
    • Paul J. Turcott,
    • John R. Srouji,
    • Kendra C. Foley,
    • Michael S. Rooney,
    • Marit M. van Buuren,
    • Richard B. Gaynor,
    • Jennifer G. Abelin,
    • Terri A. Addona,
    • Vikram R. Juneja
    T cell-based therapies for cancer rely on targets that are both presented on specific HLA molecules and are immunogenic. Choi et al. establish a systematic pipeline to evaluate both aspects sensitively and apply it to common KRAS mutations to broadly explore T cell targets from this oncogene.
  • Systematic detection of m6A-modified transcripts at single-molecule and single-cell resolution

    • Kyung Lock Kim,
    • Peter van Galen,
    • Volker Hovestadt,
    • Gilbert J. Rahme,
    • Ekaterina N. Andreishcheva,
    • Abhijeet Shinde,
    • Elizabeth Gaskell,
    • Daniel R. Jones,
    • Efrat Shema,
    • Bradley E. Bernstein
    Kim et al. develop a microscopy-based platform for epitranscriptome profiling, compatible with low-input samples and single cells. The platform provides multi-modal measurements of cell surface markers, gene expression, and m6A RNA modification. The system is flexible and can be applied to study various RNA modifications and their dynamics in heterogeneous cell mixtures.
  • A mixture-of-experts deep generative model for integrated analysis of single-cell multiomics data

    • Kodai Minoura,
    • Ko Abe,
    • Hyunha Nam,
    • Hiroyoshi Nishikawa,
    • Teppei Shimamura
    Minoura et al. report the development of scMM, a multimodal deep generative model-based framework for analyzing single-cell multiomics data. scMM extracts biologically interpretable joint representations from high-dimensional multimodal data that can be used for downstream analyses. In addition, it learns relationships among single-cell modalities, enabling many-to-many prediction of missing modalities.
  • In situ functional cell phenotyping reveals microdomain networks in colorectal cancer recurrence

    • Samantha A. Furman,
    • Andrew M. Stern,
    • Shikhar Uttam,
    • D. Lansing Taylor,
    • Filippo Pullara,
    • S. Chakra Chennubhotla
    Furman et al. present an unbiased spatial analytics approach, LEAPH, to derive functional cell phenotypes on a continuum from spatial proteomics data. LEAPH was applied to a hyperplexed colorectal cancer image dataset to discover microdomains and signaling networks associated with, and potentially driving, colorectal cancer recurrence.
Advertisement
Advertisement