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@ARTICLE{Stanifer:176912,
      author       = {M. L. Stanifer and S. Boulant$^*$},
      title        = {{A}dapting {G}astrointestinal {O}rganoids for {P}athogen
                      {I}nfection and {S}ingle {C}ell {S}equencing under
                      {B}iosafety {L}evel 3 ({BSL}-3) {C}onditions.},
      journal      = {JoVE},
      volume       = {175},
      issn         = {1940-087X},
      address      = {[S.l.]},
      publisher    = {JoVE},
      reportid     = {DKFZ-2021-02154},
      pages        = {62857},
      year         = {2021},
      note         = {#LA:F140#},
      abstract     = {Human intestinal organoids constitute the best cellular
                      model to study pathogen infections of the gastrointestinal
                      tract. These organoids can be derived from all sections of
                      the GI tract (gastric, jejunum, duodenum, ileum, colon,
                      rectum) and, upon differentiation, contain most of the cell
                      types that are naturally found in each individual section.
                      For example, intestinal organoids contain nutrient-absorbing
                      enterocytes, secretory cells (Goblet, Paneth, and
                      enteroendocrine), stem cells, as well as all
                      lineage-specific differentiation intermediates (e.g., early
                      or immature cell types). The greatest advantage in using
                      gastrointestinal tract-derived organoids to study infectious
                      diseases is the possibility of precisely identifying which
                      cell type is targeted by the enteric pathogen and to address
                      whether the different sections of the gastrointestinal tract
                      and their specific cell types similarly respond to pathogen
                      challenges. Over the past years, gastrointestinal models, as
                      well as organoids from other tissues, have been employed to
                      study viral tropism and the mechanisms of pathogenesis.
                      However, utilizing all the advantages of using organoids
                      when employing highly pathogenic viruses represents a
                      technical challenge and requires strict biosafety
                      considerations. Additionally, as organoids are often grown
                      in three dimensions, the basolateral side of the cells is
                      facing the outside of the organoid while their apical side
                      is facing the inside (lumen) of the organoids. This
                      organization poses a challenge for enteric pathogens as many
                      enteric infections initiate from the apical/luminal side of
                      the cells following ingestion. The following manuscript will
                      provide a comprehensive protocol to prepare human intestinal
                      organoids for infection with enteric pathogens by
                      considering the infection side (apical vs. basolateral) to
                      perform single-cell RNA sequencing to characterize
                      cell-type-specific host/pathogen interactions. This method
                      details the preparation of the organoids as well as the
                      considerations needed to perform this work under biosafety
                      level 3 (BSL-3) containment conditions.},
      cin          = {F140},
      ddc          = {570},
      cid          = {I:(DE-He78)F140-20160331},
      pnm          = {316 - Infektionen, Entzündung und Krebs (POF4-316)},
      pid          = {G:(DE-HGF)POF4-316},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:34570087},
      doi          = {10.3791/62857},
      url          = {https://inrepo02.dkfz.de/record/176912},
}