Biology subjects

Ferrone, C. R.

Publications and source records attributed to Ferrone, C. R..

4 recordsLinked to original sources

bioRxiv2024

Generation of a biliary tract cancer cell line atlas reveals molecular subtypes and therapeutic targets

Biliary tract cancers (BTCs) are a group of deadly malignancies encompassing intrahepatic and extrahepatic cholangiocarcinoma, gallbladder carcinoma, and ampullary carcinoma. Here, we present the integrative analysis of 63 BTC cell lines via multi-omics clustering and genome- scale CRISPR screens, providing a platform to illuminate BTC biology and inform therapeutic development. We identify dependencies broadly enriched in BTC compared to other cancers as well as dependencies selective to the anatomic subtypes. Notably, cholangiocarcinoma cell lines are stratified into distinct lineage subtypes based on biliary or dual biliary/hepatocyte marker signatures, associated with dependency on specific lineage survival factors. Transcriptional analysis of patient specimens demonstrates the prognostic significance of these lineage subtypes. Additionally, we delineate strategies to enhance targeted therapies or to overcome resistance in cell lines with key driver gene mutations. Furthermore, clustering based on dependencies and proteomics data elucidates unexpected functional relationships, including a BTC subgroup with partial squamous differentiation. Thus, this cell line atlas reveals potential therapeutic targets in molecularly defined BTCs, unveils biologically distinct disease subtypes, and offers a vital resource for BTC research.

cancer biology↗

bioRxiv2024

Disrupting CD38-driven T cell dysfunction restores sensitivity to cancer immunotherapy

A central problem in cancer immunotherapy with immune checkpoint blockade (ICB) is the development of resistance, which affects 50% of patients with metastatic melanoma1,2. T cell exhaustion, resulting from chronic antigen exposure in the tumour microenvironment, is a major driver of ICB resistance3. Here, we show that CD38, an ecto-enzyme involved in nicotinamide adenine dinucleotide (NAD+) catabolism, is highly expressed in exhausted CD8+ T cells in melanoma and is associated with ICB resistance. Tumour-derived CD38hiCD8+ T cells are dysfunctional, characterised by impaired proliferative capacity, effector function, and dysregulated mitochondrial bioenergetics. Genetic and pharmacological blockade of CD38 in murine and patient-derived organotypic tumour models (MDOTS/PDOTS) enhanced tumour immunity and overcame ICB resistance. Mechanistically, disrupting CD38 activity in T cells restored cellular NAD+ pools, improved mitochondrial function, increased proliferation, augmented effector function, and restored ICB sensitivity. Taken together, these data demonstrate a role for the CD38-NAD+ axis in promoting T cell exhaustion and ICB resistance, and establish the efficacy of CD38 directed therapeutic strategies to overcome ICB resistance using clinically relevant, patient-derived 3D tumour models.

cancer biology↗

bioRxiv2023

Dysregulated Repeat Element Viral-like Immune Response in Hepatocellular Carcinoma

PurposeHepatocellular carcinoma (HCC) is a lethal malignancy driven by complex interactions between cancer cells, immune cells, and additional stromal cells in the tumor microenvironment (TME). The LINE1 retrotransposon is a ubiquitous repeat RNA whose de-repression leads to significant cancer cell-intrinsic and TME changes that promote aggressive tumor characteristics. We leveraged single cell spatial transcriptomic profiling to characterize the relationship between LINE1 and differences in the heterogeneous HCC TME. Experimental DesignWe applied our profiling methodology to a cohort of 23 tissue specimens collected from patients who had undergone liver resection or transplantation and validated it in a partially-overlapping similar cohort of 39 specimens using RNA in-situ hybridization (RNA-ISH). ResultsWe found that LINE1-high tumors and LINE1-high single HCC cells exhibited a de-differentiated, stem-like, and inflammatory phenotype. Furthermore, within individual tumors, LINE1 high cancer cells associated spatially with one another and excluded the larger, organized immune cell conglomerates seen in LINE1 low tumors. Finally, we found that LINE1 RNA expression correlated with worse overall survival in the larger expanded retrospective cohort. ConclusionsOur study is the first to show a clearly disorganized immune TME in HCC driven by LINE1 expression, and this observation correlated with poor survival for patients whose tumors expressed large amounts of the LINE1 repeat RNA. These results provide further evidence of how effective anti-tumor immune responses contribute to cures after definitive surgery and may lead to novel biomarkers or drug targets in HCC. TRANSLATIONAL RELEVANCEThe viral-like LINE1 retrotransposon is known to influence tumor cell state and the immune response in a variety of cancer. Here, we have used single cell spatial transcriptomic profiling to resolve repeat and coding gene RNA expression in a cohort of hepatocellular carcinoma (HCC) patients. LINE1 RNA expression in HCC tumor cells was correlated with an undifferentiated stem-like cancer state and a disorganized, sparse immune infiltrate. Using in situ hybridization on an expanded validation cohort, we noted significantly worsened survival in the LINE1 high group. Altogether, LINE1 repeat RNA is a tumor intrinsic biomarker of more aggressive features that can be used for risk stratification and a potential biomarker for response to immunotherapies that merits further investigation.

cancer biology↗

bioRxiv2020

Single-nucleus and spatial transcriptomics of archival pancreatic cancer reveals multi-compartment reprogramming after neoadjuvant treatment

Pancreatic ductal adenocarcinoma (PDAC) remains a treatment-refractory disease. Characterizing PDAC by mRNA profiling remains particularly challenging. Previously identified bulk expression subtypes were influenced by contaminating stroma and have not yet informed clinical management, whereas single cell RNA-seq (scRNA-seq) of fresh tumors under-represented key cell types. Here, we developed a robust single-nucleus RNA-seq (snRNA-seq) technique for frozen archival PDAC specimens and used it to study both untreated tumors and those that received neoadjuvant chemotherapy and radiotherapy (CRT). Gene expression programs learned across untreated malignant cell and fibroblast profiles uncovered a clinically relevant molecular taxonomy with improved prognostic stratification compared to prior classifications. Moreover, in the increasingly-adopted neoadjuvant treatment context, there was a depletion of classical-like phenotypes in malignant cells in favor of basal-like phenotypes associated with TNF-NFkB and interferon signaling as well as the presence of novel acinar and neuroendocrine classical-like states, which may be more resilient to cytotoxic treatment. Spatially-resolved transcriptomics revealed an association between malignant cells expressing these basal-like programs and higher immune infiltration with increased lymphocytic content, whereas those exhibiting classical-like programs were linked to sparser macrophage-predominant microniches, perhaps pointing to susceptibility to distinct therapeutic strategies. Our refined molecular taxonomy and spatial resolution can help advance precision oncology in PDAC through informative stratification in clinical trials and insights into differential therapeutic targeting leveraging the immune system.

genomics↗