Aberrant cell state plasticity mediated by developmental reprogramming precedes colorectal cancer initiation

Bala, Pratyusha; Rennhack, Jonathan; Aitymbayev, Daulet; Morris, Clare X; Moyer, Sydney M.; Duronio, Gina N.; Doan, Paul; Li, Zhixin; Liang, Xiaoyan; Hornick, Jason L.; Yurgelun, Matthew B.; Hahn, William C.; Sethi, Nilay

doi:10.1126/sciadv.adf0927

Cited by 17 publications

(20 citation statements)

References 80 publications

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“…5a). Not surprisingly, CTNNB1 and SOX9 showed the strongest dependency across CRC cell lines, consistent with previous findings 27,30,33,41 .…”

Section: Smarcb1 Suppression Impairs Crc Growth In Vitro and In Vivosupporting

confidence: 92%

“…2b). To biologically validate the system, we asked whether disrupting SOX9 induced differentiation reporter activity based on our previous results 27,33 . HT-29 KRT20-GFP reporter line stably expressing a shRNA against SOX9 led to a shift in the number of GFP+ cells (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Aberrant stem cell-like activity imparts differentiation defects in CRC development 27,29,31,33 . Given that unrestricted WNT activation is a critical initiating event in CRC pathogenesis, most frequently via lossof-function APC mutations [17][18][19] , it is natural that therapeutic discovery efforts and screening approaches have been directed towards disrupting this potent developmental pathway 30,[49][50][51] .…”

Section: Discussionmentioning

confidence: 99%

“…SOX9 functionally blocks differentiation by activating an aberrant stem cell-like transcriptional program in human CRC 27,33 . SOX9 suppression induces differentiation and impairs CRC growth.…”

Section: Development Of An Endogenous Reporter By Genome Editing Sox9...mentioning

confidence: 99%

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Utilizing a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation activity in colorectal cancer

Spisák

Chen

Likasitwatanakul

et al. 2023

Preprint

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Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators that regulate these key cellular programs in CRC, we developed an endogenous reporter system by genome-editing human CRC cell lines with knock-in fluorescent reporters at the SOX9 and KRT20 locus to report aberrant stem cell-like activity and differentiation respectively in pooled CRISPR screening formats. We then constructed a dual reporter system that simultaneously monitors aberrant stem cell-like and differentiation activity in the same CRC cell line, improving our signal to noise discrimination. Using a focused-library CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs, we identified factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominated SMARCB1 of the SWI/SNF BAF complex as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency in CRC and required for human CRC cell line and patient-derived organoid growth in vivo. These studies highlight the utility of a biologically designed endogenous reporter system to uncover novel therapeutic targets for drug development.

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“…5a). Not surprisingly, CTNNB1 and SOX9 showed the strongest dependency across CRC cell lines, consistent with previous findings 27,30,33,41 .…”

Section: Smarcb1 Suppression Impairs Crc Growth In Vitro and In Vivosupporting

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Development Of An Endogenous Reporter By Genome Editing Sox9...mentioning

confidence: 99%

See 2 more Smart Citations

Utilizing a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation activity in colorectal cancer

Spisák

Chen

Likasitwatanakul

et al. 2023

Preprint

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“…Persistent fetal gene signatures in childhood malignancies are typically explained by their prenatal origins 2–6 . In contrast, reactivation of fetal gene expression is considered a consequence of oncofetal reprogramming (OFR) in adult malignancies and is associated with aggressive disease 7–10 . To date, OFR has not been described in the context of childhood malignancies.…”

mentioning

confidence: 99%

Oncogenic RAS-Pathway Activation Drives Oncofetal Reprogramming and Creates Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia

Hartmann,

Schönung,

Rajak

et al. 2023

Preprint

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Aberrant fetal gene expression facilitates tumor-specific cellular plasticity by hijacking molecular programs of embryogenesis1. Persistent fetal gene signatures in childhood malignancies are typically explained by their prenatal origins2–6. In contrast, reactivation of fetal gene expression is considered a consequence of oncofetal reprogramming (OFR) in adult malignancies and is associated with aggressive disease7–10. To date, OFR has not been described in the context of childhood malignancies. Here, we performed a comprehensive multi-layered molecular characterization of juvenile myelomonocytic leukemia (JMML) and identified OFR as a hallmark of aggressive JMML. We observed that hematopoietic stem cells (HSCs) aberrantly express mixed developmental programs in JMML. Expression of fetal gene signatures combined with a postnatal epigenetic landscape suggested OFR, which was validated in a JMML mouse model, demonstrating that postnatal activation of RAS signaling is sufficient to induce fetal gene signatures. Integrative analysis identified the fetal HSC maturation marker CD52 as a novel therapeutic target for aggressive JMML. Anti-CD52 treatment depleted human JMML HSCs and disrupted disease propagationin vivo. In summary, this study implicates OFR, defined as postnatal acquisition of fetal transcription signatures, in the pathobiology of a childhood malignancy. We provide evidence for the direct involvement of oncogenic RAS signaling in OFR. Finally, we demonstrate how OFR can be leveraged for the development of novel treatment strategies.Highlights▪ Epigenomic and transcriptomic landscape of juvenile myelomonocytic leukemia (JMML) in the context of hematopoietic development.▪ The presence of fetal transcription signatures in childhood malignancies is not indicative of a developmental maturation block.▪ High-risk JMML is characterized by oncofetal reprogramming of postnatal hematopoietic stem cells (HSCs).▪ RAS-pathway mutations induce fetal-like gene expression signatures in murine postnatal HSCs.▪ The fetal maturation marker CD52 is a novel therapeutic target in high-risk JMML.

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Cellular and molecular characteristics of stromal Lkb1 deficiency‐induced gastrointestinal polyposis based on single‐cell RNA sequencing

Cai,

Jiang,

Tong

et al. 2024

The Journal of Pathology

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Liver kinase B1 (Lkb1), encoded by serine/threonine kinase (Stk11), is a serine/threonine kinase and tumor suppressor that is strongly implicated in Peutz–Jeghers syndrome (PJS). Numerous studies have shown that mesenchymal‐specific Lkb1 is sufficient for the development of PJS‐like polyps in mice. However, the cellular origin and components of these Lkb1‐associated polyps and underlying mechanisms remain elusive. In this study, we generated tamoxifen‐inducible Lkb1flox/flox;Myh11‐Cre/ERT2 and Lkb1flox/flox;PDGFRα‐Cre/ERT2 mice, performed single‐cell RNA sequencing (scRNA‐seq) and imaging‐based lineage tracing, and aimed to investigate the cellular complexity of gastrointestinal polyps associated with PJS. We found that Lkb1flox/+;Myh11‐Cre/ERT2 mice developed gastrointestinal polyps starting at 9 months after tamoxifen treatment. scRNA‐seq revealed aberrant stem cell‐like characteristics of epithelial cells from polyp tissues of Lkb1flox/+;Myh11‐Cre/ERT2 mice. The Lkb1‐associated polyps were further characterized by a branching smooth muscle core, abundant extracellular matrix deposition, and high immune cell infiltration. In addition, the Spp1–Cd44 or Spp1–Itga8/Itgb1 axes were identified as important interactions among epithelial, mesenchymal, and immune compartments in Lkb1‐associated polyps. These characteristics of gastrointestinal polyps were also demonstrated in another mouse model, tamoxifen‐inducible Lkb1flox/flox;PDGFRα‐Cre/ERT2 mice, which developed obvious gastrointestinal polyps as early as 2–3 months after tamoxifen treatment. Our findings further confirm the critical role of mesenchymal Lkb1/Stk11 in gastrointestinal polyposis and provide novel insight into the cellular complexity of Lkb1‐associated polyp biology. © 2024 The Pathological Society of Great Britain and Ireland.

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Aberrant cell state plasticity mediated by developmental reprogramming precedes colorectal cancer initiation

Cited by 17 publications

References 80 publications

Utilizing a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation activity in colorectal cancer

Utilizing a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation activity in colorectal cancer

Oncogenic RAS-Pathway Activation Drives Oncofetal Reprogramming and Creates Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia

Cellular and molecular characteristics of stromal Lkb1 deficiency‐induced gastrointestinal polyposis based on single‐cell RNA sequencing

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