Biology subjects

Rift, C. V.

Publications and source records attributed to Rift, C. V..

2 recordsLinked to original sources

bioRxiv2025

Regulatory elements of pancreas development license the initiation of pancreatic ductal adenocarcinoma

Cellular plasticity and transitional cellular states are crucial for tissue regeneration across multiple organs. In the pancreas, oncogenic Kras hijacks this program, acting on tissue-specific enhancers to prevent the resolution of acinar-to-ductal metaplasia (ADM) and lock regeneration into a pro-inflammatory state that progresses to cancer. Enhancer transcription, an early event during cellular state transitions, can generate stable enhancer-associated long noncoding RNAs (lncRNAs) positioned near key transcription factors and chromatin contact boundaries, often enriched for disease-associated variants. While enhancer-associated lncRNAs have been implicated in transcriptional regulation and genome organization, their role in pancreas regeneration and cancer initiation has remained unexplored. In this study, we investigated the expression of epithelial long noncoding RNAs (lncRNAs) and their target genes in PDAC precursor lesion formation. We focus on lncRNAs transcribed from enhancer elements near cell identity transcription factors. We demonstrate that LINC00673, expressed from a Sox9-associated super-enhancer during pancreatic development, is reactivated in PDAC. Conditional deletion of LINC00673 in the murine pancreatic epithelium accelerates resolution of ADM and significantly impairs PDAC initiation. Notably, LINC00673 harbors a variant associated with risk of developing PDAC. Our study identifies a critical function of LINC00673 in regulating both cell-autonomous and non-cell-autonomous processes during pancreas regeneration and Kras-driven cancer initiation. Furthermore, we highlight a previously unrecognized role of transcribed super-enhancers in facilitating long-range gene regulation during pancreatic cancer initiation. These findings reveal a novel regulatory layer linking developmental enhancer activity, cellular plasticity and pancreatic disease progression. TeaserLong noncoding RNAs from developmental enhancers play a role in long-range gene regulation with crucial biological impacts in development and cancer. Grant supportThis project has been supported by the Danish Cancer Society (R302-A17481). LA is supported by core funding of the Biotech Research and Innovation Center, the Danish Cancer Society (R302-A17481, R322-A17.350), The Novo Nordisk Foundation (NNF21OC0070884) and The Innovation Fund (Eurostars 2807). The Novo Nordisk Foundation Center for Stem Cell Biology was supported by Novo Nordisk Foundation grants NNF17CC0027852.

cell biology↗

bioRxiv2024

Refining Spatial Proteomics by Mass Spectrometry: An Efficient Workflow Tailored for Archival Tissue

BackgroundFormalin-fixed, paraffin-embedded (FFPE) tissue remains the gold standard for extensively archiving biological specimens, providing biobanks with large repositories of retrospective potential. However, while formalin crosslinking is effective at preserving tissue, it poses significant challenges for extracting molecular information, including the proteome. Traditionally, this process required high levels of input material, which, in turn, limited the ability to preserve cell-type heterogeneity and spatial information. To address these limitations, we developed an easily adaptable and highly efficient workflow for extracting deep proteomes from low-input materials, such as biopsies used in routine histopathological diagnostics. MethodsWe compared the extraction efficiency of pancreatic acinar cells identified in FFPE tissue samples stained with conventional hematoxylin-eosin (H&E) against that of cells isolated from tissue samples immunostained for the epithelial cell adhesion molecule (EpCAM) across material inputs ranging from 1,166 to 800,000 {micro}m2 (estimated to 2 to 1,310 cells in volume). Cells were isolated using laser capture microdissection and subsequently analyzed using Liquid Chromatography-Tandem Mass Spectrometry. ResultsSimilar yields for both methods were observed, with EpCAM-positive cells yielding slightly higher results--approximately 1,200 unique protein groups at the lowest input and up to 5,900 at the highest. In cells isolated from H&E-stained tissue, [~]900 to [~]5,200 protein groups were identified. We decided that the optimal balance for our workflow, ensuring maximum protein identification while minimizing input material, lies within the range of approximately 50,000 to 100,000 {micro}m2. With these results, we tested spatial capabilities and biological relevance by isolating cancer cells from biopsies of pancreatic cancer, lung cancer, or glioblastoma, with the first two being stained with EpCAM and the latter being stained against the tumor-suppressor protein p53. We successfully identified tissue-specific protein expressions and observed prominent clustering of all cell populations. DiscussionOur results highlight the feasibility of performing spatial proteomics on FFPE tissue using minimal input material. This adaptable methodology opens up possibilities for investigating cell-type-specific biology while preserving spatial and histological information.

bioengineering↗