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Furth, E.

Publications and source records attributed to Furth, E..

3 recordsLinked to original sources

E2f coordinates the proliferation and transdifferentiation of a Sox9+bile duct cell to initiate hepatocellular carcinoma

Disruption of the Rb/E2f interaction is one of the six original hallmarks of cancer and is thought to confer unrestricted proliferative potential to tumor cells. Although E2f is active in almost all cancer cases as a result of this disruption, the consequence of its unrestricted activity for cancer initiation remains mostly unknown. To address this question, we genetically inactivated the entire Rb family of genes (Triple Knock Out, TKO) in specific cell lineages in the liver. Strikingly, this unbiased approach reveals that Rb family inactivation initiates a phenotypically similar hepatocellular carcinoma (HCC) from either periportal hepatocytes or Sox9+ bile duct cells. In the latter population, Rb family inactivation results in unrestricted proliferation as well as the E2f-driven transactivation of the pioneer factor Foxa3, which activates a "periportal hepatocyte-like" metabolic program to ensure transdifferentiation into hepatocytes. Notably, single or compound inactivation of E2f1 and E2f3 in the TKO background is sufficient to suppress Foxa3 expression and HCC initiation, without altering the proliferative status of Sox9+ bile duct cells. Collectively, our results reveal that derepression of a cell cycle gene program and activation of non-cell cycle oncogenic features by E2f are distinct consequences of disrupting the Rb/E2f interaction, and that coordinated activation of these two functions are essential for HCC initiation from a founder liver bile duct cell lineage.

cancer biology↗

Long Noncoding RNAs Enforce Pancreatic Cancer Identity and Block Reprogramming

The Yamanaka factors (OCT4, SOX2, KLF4, and MYC; OSKM) can rejuvenate aging phenotypes in somatic cell types by resetting the epigenetic landscape. Curiously, most solid tumor cells remain largely resistant to reprogramming despite their well-documented plasticity, and the underlying mechanisms are unclear. Here, we combined genomic profiling and in vivo assays to investigate OSKM-mediated reprogramming of pancreatic ductal adenocarcinoma (PDAC). In the initial stages, we found that cancer-specific genes were refractory while mesodermal/ECM programs, normally silenced by PRC2, were aberrantly upregulated. A CRISPR interference screen for OSKM reprogramming coupled with functional analyses revealed that suppression of cancer-associated long noncoding RNAs (lncRNAs) erased malignant epithelial programs, restored tumor suppressor activity, and impaired tumorigenicity in vivo. We further identified that ATXN7L3-AS1 lncRNA sustains the PDAC malignant identity through its association with active epithelial oncogenic programs and poised PRC2-targeted developmental genes, thereby supporting both plasticity and memory. Thus, by exploring why cancer cells are resistant to reprogramming, we identify lncRNAs as gatekeepers of malignant identity, suggesting that targeting lncRNAs could be a generalizable therapeutic strategy in treating solid tumors.

cancer biology↗

Niche differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

Single cells influence, and are shaped by, their local spatial niche. Technologies for in situ measurement of gene expression at the transcriptome scale have enabled the detailed profiling of the spatial distributions of cell types in tissue as well as the interrogation of local signaling patterns between cell types [1]. Towards these goals, we propose a new statistical procedure called niche-differential expression (niche-DE) analysis. Niche-DE identifies cell-type specific niche-associated genes, defined as genes whose expression within a specific cell type is significantly up- or down-regulated, in the context of specific spatial niches. We develop effective and interpretable measures for global false discovery control and show, through the analysis of data sets generated by myriad protocols, that the method is robust to technical issues such as over-dispersion and spot swapping. Niche-DE can be applied to low-resolution spot- and ROI-based spatial transcriptomics data as well as data that is single-cell or subcellular in resolution. Based on niche-DE, we also develop a procedure to reveal the ligand-receptor signaling mechanisms that underlie niche-differential gene expression patterns. When applied to 10x Visium data from liver metastases of colorectal cancer, niche-DE identifies marker genes for cancer-associated fibroblasts and macrophages and elucidates ligand-receptor crosstalk patterns between tumor cells, macrophages and fibroblasts. Co-detection by indexing (CODEX) was performed on the same patient samples, to corroborate the niche-DE results.

bioinformatics↗