bims-instec 2023-07-16 papers

Sci Adv. 2023 Jul 14. 9(28): eadg4055

An organoid-based CRISPR-Cas9 screen for regulators of intestinal epithelial maturation and cell fate.

Stine L Hansen, Hjalte L Larsen, Laura M Pikkupeura, Grzegorz Maciag, Jordi Guiu, Iris Müller, Ditte L Clement, Christina Mueller, Jens Vilstrup Johansen, Kristian Helin, Mads Lerdrup, Kim B Jensen.

Generation of functionally mature organs requires exquisite control of transcriptional programs governing cell state transitions during development. Despite advances in understanding the behavior of adult intestinal stem cells and their progeny, the transcriptional regulators that control the emergence of the mature intestinal phenotype remain largely unknown. Using mouse fetal and adult small intestinal organoids, we uncover transcriptional differences between the fetal and adult state and identify rare adult-like cells present in fetal organoids. This suggests that fetal organoids have an inherent potential to mature, which is locked by a regulatory program. By implementing a CRISPR-Cas9 screen targeting transcriptional regulators expressed in fetal organoids, we establish Smarca4 and Smarcc1 as important factors safeguarding the immature progenitor state. Our approach demonstrates the utility of organoid models in the identification of factors regulating cell fate and state transitions during tissue maturation and reveals that SMARCA4 and SMARCC1 prevent precocious differentiation during intestinal development.

DOI: https://doi.org/10.1126/sciadv.adg4055

Sci Adv. 2023 Jul 14. 9(28): eadf9460

Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation.

Laura M Pikkupeura, Raul B Bressan, Jordi Guiu, Yun Chen, Martti Maimets, Daniela Mayer, Pawel J Schweiger, Stine L Hansen, Grzegorz J Maciag, Hjalte L Larsen, Kadi Lõhmussaar, Marianne Terndrup Pedersen, Joji M Yap Teves, Jette Bornholdt, Vladimir Benes, Albin Sandelin, Kim B Jensen.

During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for lifelong maintenance of the tissue. While the morphological changes associated with the transition are well characterized, the molecular mechanisms underpinning the maturation process are not fully understood. Here, we leverage intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation, and three-dimensional (3D) chromatin conformation landscapes in fetal and adult epithelial cells. We observed prominent differences in gene expression and enhancer activity, which are accompanied by local changes in 3D organization, DNA accessibility, and methylation between the two cellular states. Using integrative analyses, we identified sustained Yes-Associated Protein (YAP) transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization and likely to be coordinated by changes in extracellular matrix composition. Together, our work highlights the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue maturation.

DOI: https://doi.org/10.1126/sciadv.adf9460

Clin Cancer Res. 2023 Jul 13. pii: CCR-22-3964. [Epub ahead of print]

Transcriptomic Signatures of MSI-high Metastatic Colorectal Cancer Predict Efficacy of Immune Checkpoint Inhibitors.

PURPOSE: Microsatellite instability (MSI) is currently the only predictive biomarker of efficacy of immune checkpoint inhibitors (ICI) in metastatic colorectal cancers (mCRC). However, 10-40% of patients with MSI mCRC will experience a primary resistance to ICI.
EXPERIMENTAL DESIGN: In 2 cohorts of patients with MSI mCRC treated with ICI (exploratory: N=103, validation: N=35), 3'RNAseq was performed from primary tumors. Previously described single-cell transcriptomic signatures of tumor microenvironment (TME) were analysed.
RESULTS: In the exploratory cohort, the unsupervised clustering allowed the identification of three clusters of tumors with distinct transcriptional profiles: cluster A ("stromalHIGH-proliferationLOW"), cluster B ("stromalHIGH-proliferationMED"), and cluster C ("stromalLOW-proliferationHIGH"), with an enrichment of patients progressing at first disease assessment under ICI in the cluster A (30% vs 12% in cluster B and 8.1% in cluster C, p=0.074). Progression-free survival (PFS) was also significantly shorter in patients belonging to cluster A, compared to clusters B or C (p<0.001) with 2-year PFS rates of 33.5%, 80.5% and 78.3%, respectively. In multivariate analysis, PFS was still significantly longer in patients belonging to cluster B (HR: 0.19 95%CI 0.08-0.45, p<0.001) and cluster C (HR: 0.25 95%CI 0.10-0.59, p=0.02), compared to patients belonging to cluster A. The association of this clustering with PFS under ICI was confirmed in the validation cohort. PFS related to non-ICI-based regimens was not significantly different according to cluster.
CONCLUSION: This unsupervised transcriptomic classification identified three groups of MSI mCRCs with different compositions of TME cells and proliferative capacities of TME/tumor cells. The "stromalHIGH-proliferationLOW" cluster is associated with a poorer prognosis with ICI treatment.

DOI: https://doi.org/10.1158/1078-0432.CCR-22-3964