Biology subjects

Biffi, G.

Publications and source records attributed to Biffi, G..

14 recordsLinked to original sources

bioRxiv2026

Time-calibrated phylogenomics reveals relationships and parallel evolution of neoteny within Elateriformia (Coleoptera) despite pervasive homoplasy

The controversy over Elateriformia relationships hampers understanding of the evolution of disparate soft-bodied and fully sclerotized phenotypes, bioluminescence, and the ontogenetic reprogramming that leads to larviform females. Elateriformia contains >50,000 species in 34 families, including fireflies, jewel, and click beetles. We sample 31 families and 195 ingroup taxa, each with up to 4,224 orthologs. Through explicit hypothesis testing, coalescent-based approaches, and evaluation of dataset properties, we resolve backbone relationships. We reconfirm the monophyly of Byrrhoidea sensu lato, rejecting the recent resurrection of Dryopoidea, and verify the reciprocally monophyletic lampyroid and elaterid clades. We characterize short internodes and gene-tree discordance, both of which are indicative of ancient rapid radiations. Counterintuitively, signals from moderately variable genes are crucial for resolving certain splits, suggesting that even subtle rate differences distinguish phylogenetically informative loci from overly conserved, less informative markers. Time-calibrated phylogenies indicate the early origin of Elateriformia (281-287 Mya), with superfamilies diverging at the Permian-Triassic boundary and diversifying throughout the Jurassic. We identify 15 independent origins of soft-bodiedness and neotenic modifications spanning the Mid Jurassic to the present. Our hypothesis provides a foundation for investigating the genetic mechanisms underlying ontogenetic reprogramming and bioluminescence.

evolutionary biology↗

bioRxiv2026

TGF-β- and IL-1-dependent fibroblast states differentially shape pancreatic cancer microenvironments and metastasis

Pancreatic ductal adenocarcinoma (PDAC) contains heterogeneous cancer-associated fibroblast (CAF) populations, including interleukin 1 (IL-1)-dependent inflammatory CAFs (iCAFs) and transforming growth factor beta (TGF-{beta})-dependent myofibroblastic CAFs (myCAFs), whose functions at primary and metastatic sites remain incompletely defined. Here, we genetically disrupted IL-1 or TGF-{beta} signalling in fibroblast activation protein (FAP)-expressing CAFs arising from a shared cellular origin to determine how myCAF and iCAF states shape PDAC progression and microenvironments. Depletion of TGF-{beta}-dependent myCAFs, but not IL-1-dependent iCAFs, did not alter primary tumour growth or local metastatic dissemination but significantly reduced liver and lung metastases. Matched primary tumours and liver metastasis analyses also revealed site-specific stromal responses to TGF-{beta} signalling disruption. Experimental models of liver metastasis colonisation and outgrowth indicated that the reduced metastatic phenotype was linked primarily to alterations within pancreatic tumours rather than to impaired malignant cell outgrowth at metastatic sites. Single-cell RNA-sequencing of myCAF-depleted primary tumours revealed extensive transcriptional reprogramming across fibroblast, immune and malignant compartments, highlighting the complexity of assigning myCAF-to-malignant cell signalling mechanisms in vivo. To resolve this crosstalk, we co-cultured PDAC organoids with pancreatic stellate cells engineered to remain in myCAF or iCAF states. Cross-model transcriptomic analyses, together with genetic and pharmacological perturbation studies, showed that myCAF-derived TGF-{beta} directly promotes epithelial-to-mesenchymal transition signalling in PDAC malignant cells, providing a candidate mechanism for the reduced metastasis observed upon myCAF depletion in vivo. These findings reveal distinct, context-dependent roles for TGF-{beta}- and IL-1-dependent CAF states and identify myCAF-derived TGF-{beta} signalling as a stromal mechanism promoting malignant cell plasticity.

cancer biology↗

bioRxiv2026

scFLAME: a unified generative model for interpretable clustering, hierarchical structure discovery and marker-gene identification in single-cell RNA-seq data

Identifying cell types from single-cell RNA sequencing (scRNA-seq) data typically requires several separate and often uninterpretable steps: dimensionality reduction, batch-correction, clustering, marker-gene identification and the discovery of finer-grained structure. Here we introduce scFLAME (single-cell Factor Latent Analysis with Mixture Embeddings), a probabilistic generative model that unifies these tasks: a negative binomial factor analysis of the raw counts - which can be adjusted for batch - is coupled to a Gaussian mixture prior over the latent space, learning the embedding and clustering jointly, while a shared linear decoder provides cluster-specific marker genes directly from the fitted model, and a merging procedure recovers a probabilistic hierarchy of finer-grained partitions. On simulated and real data, scFLAME matches or exceeds state-of-the-art clustering accuracy, is robust across sequencing platforms, and scales near-linearly to hundreds of thousands of cells. scFLAME thus replaces a chain of separate tools with a single, interpretable model for single-cell analysis.

bioinformatics↗

bioRxiv2026

IL-1-activated cancer-associated fibroblasts promote STAT1-driven transcriptional reprogramming of pancreatic tumour cells

Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest cancers, with limited treatment options and poor survival rates. It is characterised by strong driver mutations, epigenetic reprogramming, and a dense tumour microenvironment (TME). A defining feature of the PDAC TME is its fibrotic stroma, which is largely composed of cancer-associated fibroblasts (CAFs). Distinct CAF populations have been implicated in PDAC progression, but the mechanisms that govern their crosstalk with the cancer cells are poorly understood. We generated genetically engineered pancreatic stellate cells (PSCs) modelling interleukin-1 (IL-1)-dependent inflammatory CAFs (iCAFs) and transforming growth factor-{beta} (TGF-{beta})-dependent myofibroblastic CAFs (myCAFs) to investigate how distinct stromal populations shape the epigenetic landscape of pancreatic ductal adenocarcinoma (PDAC). We found that iCAFs, but not myCAFs, promoted gemcitabine resistance in epithelial tumour cells and identified STAT1 as a critical mediator of iCAF-tumour cell crosstalk. Mechanistically, STAT1 drove the induction of interferon (IFN)-responsive genes, while blockade of IFN-{beta} attenuated iCAF-mediated transcriptional reprogramming. Genetic ablation of STAT1 in tumour cells abolished iCAF-induced chemoresistance and associated transcriptional changes. In an orthotopic in vivo model, STAT1 knockout significantly prolonged survival following gemcitabine treatment, supporting a central role for STAT1 signalling in stromal-driven therapy resistance. We provide a comprehensive analysis on how IL-1-dependent iCAFs contribute to epigenetic reprogramming in PDAC and uncover a previously undescribed role for STAT1 in stromal-epithelial interactions. These findings reveal distinct, non-overlapping mechanisms by which CAF subtypes modulate tumour behaviour and identify STAT1 as a therapeutic vulnerability that can be exploited to sensitise PDAC to standard chemotherapy. Significance statementThis study establishes that the epigenetic landscape of PDAC is differentially shaped by iCAF- and myCAF-like PSCs and defines STAT1 as a mediator of iCAF-induced chemoresistance and transcriptional reprogramming. We demonstrate that genetic ablation of STAT1 sensitises tumours to gemcitabine in vivo, extending survival and positioning STAT1 as an actionable target to overcome stromal-mediated therapy resistance in PDAC.

cancer biology↗

bioRxiv2026

Cross-species graph-embedding unmasks the ageing microenvironment as a key determinant of pancreatic cancer malignant cell biology and therapy response

Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis and is characterised by an extensive pro-tumorigenic stroma. Although most PDAC cases occur in older patients, the impact of ageing on malignant-stromal interactions and therapy response remains poorly understood. Here, we established orthotopically-grafted organoid-derived PDAC models across three murine age groups to characterise changes in the PDAC stroma and malignant cells with ageing. Cross-species analyses of tumour transcriptomes using a graph-embedding approach showed that integrating mouse models of different ages better captures the diversity of human PDAC, and that aged models more faithfully recapitulate the biology of older patients with PDAC. We also demonstrated that aged PDAC models have a more inflammatory stroma than that of younger tumours, shaping the malignant cell transcriptome. Finally, graph-embedding identified IRAK4 as a candidate therapeutic vulnerability in aged, but not young, KRAS- and p53-mutant PDAC, which we validated in preclinical drug studies. These findings highlight how ageing is a critical determinant of PDAC biology and associated therapeutic vulnerabilities, which should be an important consideration when designing disease models for preclinical development of precision therapies.

cancer biology↗

bioRxiv2025

Multi-stromal organoid co-cultures model pancreatic cancer and pancreatitis epithelial cell-fibroblast heterogeneity

Malignant cell-fibroblast cross-talks modulate disease progression and therapy response of pancreatic ductal adenocarcinoma (PDAC). Our knowledge of the heterogeneous nature of PDAC cancer-associated fibroblasts (CAFs) has significantly increased over the last few years. Yet, whether CAFs in PDAC differ from fibroblasts in pancreatic inflammation remains poorly understood. Chronic pancreatitis - a prolonged inflammatory state of the pancreas - is a risk factor for PDAC and is characterised by abundant fibroblasts. Thus, dissecting pancreatic fibroblast and epithelial cell reprogramming in malignancy relative to inflammation could inform new preventative, diagnostic and therapeutic strategies for PDAC. Here, we studied how pancreatic malignancy and inflammation differently shape fibroblast heterogeneity and their crosstalk with epithelial cells. We analysed human samples and mouse models of pancreatitis and PDAC and leveraged new murine pancreatitis-derived epithelial organoids to establish pancreatitis and PDAC organoid/multi-stroma co-cultures comprising pancreatic stellate cells, fibroblasts and mesothelial cells. We demonstrate that a combination of in vitro and in vivo models better captures epithelial cell and fibroblast markers of human pancreatitis and PDAC compared to mouse models alone. Finally, we identify PDAC and pancreatitis epithelial cell-specific reprogramming of stromal cells of different origin, and we infer the contribution of these distinct stromal cell types to fibroblasts in PDAC and pancreatitis in vivo. Together, our study highlights different epithelial cell-fibroblast heterogeneity in PDAC and pancreatitis, and provides new platforms for the identification of markers and epithelial-stromal interdependencies of these diseases.

cancer biology↗

bioRxiv2024

SMAD4 and KRAS status shape malignant-stromal crosstalk in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) contains an extensive stroma that modulates response to therapy, contributing to the dismal prognosis associated with this cancer. Evidence suggests that the stromal composition of PDAC is shaped by mutations within malignant cells; however, most pre-clinical models of PDAC are driven by KrasG12D and mutant Trp53 and have not assessed the contribution of other known oncogenic drivers, including KRASG12V and alterations in CDKN2A and SMAD4. To increase understanding of malignant cell-stroma crosstalk in PDAC, we analyzed Trp53-mutant mouse models driven by KrasG12D or KrasG12V in which Smad4 was wild-type or deleted. KrasG12D; Smad4-deleted PDAC developed a fibro-inflammatory rich stroma with increased JAK/STAT malignant cell signaling and an enhanced therapeutic response to JAK/STAT inhibition. In stark contrast, the stroma of Smad4-deleted KrasG12V PDAC was differently altered, and the malignant compartment lacked JAK/STAT signaling dependency. Thus, malignant cell genotype impacts malignant-stromal phenotype in PDAC, directly affecting therapeutic efficacy. STATEMENT OF SIGNIFICANCEUnderstanding malignant cell-stroma crosstalk in PDAC has focused on models containing KrasG12D and mutant Trp53. Here, we show that PDAC driven by KrasG12D or KrasG12Vin which Smad4 is deleted display differences in malignant-stromal signaling and treatment sensitivity, highlighting the importance of understanding genotype-phenotype relationships for precision PDAC therapy.

cancer biology↗

bioRxiv2024

Tissue-resident regulatory T cells exert dualistic anti-tumour and pro-repair function in the exocrine pancreas

Regulatory T cells are fundamentally important for maintaining immune homeostasis, and their potent immune-suppressive roles make them attractive immunotherapeutic targets in cancer. Recent work suggests potential functions of tissue-resident Tregs (trTregs) in tissue-repair and epithelial cell homeostasis. Here, we describe a rare population of trTreg in the exocrine pancreas. We show that these cells share common features of trTregs, including expression of the IL-33 receptor ST2 and production of the epithelial growth factor Amphiregulin, and display an oligoclonal T cell receptor repertoire. Using a mouse model of acute pancreatitis, we show that pancreatic Tregs rapidly expand upon release of IL-33 by fibroblasts. Moreover, depletion of Tregs after initiation of pancreatic injury impairs the regeneration of the exocrine parenchyma. This effect is due, in part, through a direct effect of Tregs on acinar cell proliferation. Finally, we show that transient Treg depletion in established orthotopic pancreatic tumours leads to tumour rejection yet provokes long-lasting damages to surrounding exocrine parenchyma. In all, our results demonstrate the tissue-repair capacity of pancreatic Tregs, and highlight a dualistic role of these cells in the pancreatic tumour ecosystem, with their harmful immune-suppressive function in the tumour coupled to a beneficial tissue-repair function in the surrounding tissue.

immunology↗

bioRxiv2023

Differential Activity of MAPK signalling Defines Fibroblast Subtypes in Pancreatic Cancer

Fibroblast heterogeneity is increasingly recognised across cancer conditions. Given their important contribution to disease progression, mapping out fibroblasts heterogeneity is critical to devise effective anti-cancer therapies. Cancer-associated fibroblasts (CAFs) represent the most abundant cell population in pancreatic ductal adenocarcinoma (PDAC). Whether CAF phenotypes are differently specified by PDAC cell lineages remains to be elucidated. Here, we reveal an important role for the MAPK signalling pathway in the definition of PDAC CAF phenotypes. We identify the myCAF transcriptional phenotype as uniquely dependent on proficient MAPK signalling. In addition, CAFs displaying elevated MAPK activity are specifically anchored to basal-like/squamous PDAC cells and define tumour subdomains with reduced frequency of CD8+ T cells. We characterize the single-cell transcriptome of mouse PDAC tumours in response to MAPK inhibition and identify gene expression signatures of MAPKhigh CAFs, which suggest immunoregulatory functions. Accordingly, a gene expression signature of MAPKhigh CAFs correlates with poor prognosis in several human cancer conditions, including PDAC, and with reduced response to immune checkpoint inhibition in immune-reactive solid tumours. Altogether, our data expand our knowledge on CAF phenotype heterogeneity and reveal a new strategy for targeting of myofibroblastic CAFs in vivo.

cancer biology↗

bioRxiv2022

ERBB-activated myofibroblastic cancer-associated fibroblasts promote local metastasis of pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis. Cancer-associated fibroblasts (CAFs) are recognized potential therapeutic targets, but poor understanding of these heterogeneous cell populations has limited the development of effective treatment strategies. We previously identified TGF-{beta} as a main driver of myofibroblastic CAFs (myCAFs). Here, we show that EGFR/ERBB2 signaling is induced by TGF-{beta} in myCAFs through an autocrine process mediated by the ERBB ligand amphiregulin. Inhibition of this ERBB-signaling network in PDAC organoid-derived cultures and mouse models impacts distinct CAF subtypes, providing insights into mechanisms underpinning their heterogeneity. Remarkably, ERBB-activated myCAFs promote local PDAC metastasis in mice, unmasking functional significance in myCAF heterogeneity. Finally, analyses of other cancer datasets suggest these processes might operate in other malignancies. These data provide functional relevance to CAF heterogeneity and identify a potential target for preventing local tumor invasion in PDAC.

cancer biology↗

bioRxiv2022

Single-cell transcriptomic analysis of human pleura reveals stromal heterogeneity and informs in vitro models of mesothelioma

The pleural lining of the thorax regulates local immunity, inflammation and repair. A variety of conditions, both benign and malignant including pleural mesothelioma, can affect this tissue. A lack of knowledge concerning the mesothelial and stromal cells comprising the pleura has hampered the development of targeted therapies. Here we present the first comprehensive single cell transcriptomic atlas of the human parietal pleura and demonstrate its utility in elucidating pleural biology. We confirm the presence of known universal fibroblasts and describe novel, potentially pleural-specific, fibroblast subtypes. We also present transcriptomic characterisation of multiple in vitro models of benign and malignant mesothelial cells, and characterise these through comparison with in vivo transcriptomic data. While bulk pleural transcriptomes have been reported previously, this is the first study to provide resolution at single cell level. We expect our pleural cell atlas will prove invaluable to those studying pleural biology and disease. For example, it has already enabled us to shed light on the transdifferentiation of mesothelial cells allowing us to develop a simple method for prolonging mesothelial cell differentiation in vitro.

cancer biology↗

bioRxiv2020

DETECTION OF INCIPIENT PANCREATIC CANCER WITH NOVEL TUMOR-SPECIFIC ANTIBODIES IN MOUSE MODELS

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy, as 90% of patients do not survive beyond five years from diagnosis. This dismal prognosis is largely due to the advanced stage of the disease at diagnosis, which precludes potentially curative surgical resection. Although early detection strategies hold significant promise for improving patient outcomes, there is still no accurate diagnostic tool to detect incipient PDAC. Here, we sought to develop antibodies for the early detection of PDAC by positron-emission tomography (PET) imaging. Accordingly, we establish a pipeline to generate novel tumor-specific monoclonal antibodies (mAbs) against cell-surface proteins of PDAC patient-derived organoids (PDOs). We identify a panel of 16 tumor organoid-binding antibodies (TOBi-bodies) that display high reactivity to human PDAC tissues but not to matched adjacent normal pancreas. We then employ biochemical, flow cytometric, mass spectrometric, and CRISPR/Cas9-mediated knockout methods to determine the cognate antigens of these TOBi-bodies. We identify two mAbs that bind to tumor-specific variants of the surface protein CEACAM6 and show minimal binding to normal tissues. PET imaging in mouse models using these TOBi-bodies enables the detection of incipient human organoid-derived PDAC tumors that are rather undetectable by palpation or high-resolution ultrasound imaging techniques. We propose that further development of these mAbs as PET radiotracers could facilitate the early detection and accurate staging of PDAC.

cancer biology↗

bioRxiv2020

Dissecting cell type-specific metabolism in pancreatic ductal adenocarcinoma

Tumors are composed of many different cell types including cancer cells, fibroblasts, and immune cells. Dissecting functional metabolic differences between various cell types within a mixed population can be limited by the rapid turnover of metabolites relative to the time needed to isolate cells. To overcome this challenge, we traced isotope-labeled nutrients into macromolecules that turn over more slowly than metabolites. This approach was used to assess differences between cancer cell and fibroblast metabolism in pancreatic cancer organoid-fibroblast co-cultures and in pancreatic tumors. In these contexts, we find pancreatic cancer cells exhibit increased pyruvate carboxylation relative to fibroblasts, and that this flux depends on both pyruvate carboxylase and malic enzyme 1 activity. Consequently, expression of both enzymes in cancer cells is necessary for organoid and tumor growth, demonstrating that dissecting the metabolism of specific cell populations within heterogeneous systems can identify dependencies that may not be evident from studying isolated cells in culture or bulk tumor tissue.

cancer biology↗

bioRxiv2019

Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation

A highly aggressive subset of pancreatic ductal adenocarcinomas undergo trans-differentiation into the squamous lineage during disease progression. While the tumorigenic consequences of this aberrant cell fate transition are poorly understood, recent studies have identified a role for the master regulator TP63 in this process. Here, we investigated whether squamous trans-differentiation of pancreatic cancer cells can influence the phenotype of non-neoplastic cells in the tumor microenvironment. Conditioned media experiments revealed that squamous-subtype pancreatic cancer cells secrete factors that convert quiescent pancreatic stellate cells into a specialized subtype of cancer-associated fibroblasts (CAFs) that express inflammatory genes at high levels. We use gain- and loss-of-function approaches in vivo to show that squamous-subtype pancreatic tumor models become enriched with inflammatory CAFs and neutrophils in a TP63-dependent manner. These non cell-autonomous effects occur, at least in part, through TP63-mediated activation of enhancers at pro-inflammatory cytokine loci, which includes IL1A as a key target. Taken together, our findings reveal enhanced tissue inflammation as a consequence of squamous trans-differentiation in pancreatic cancer, thus highlighting an instructive role of tumor cell lineage in reprogramming the stromal microenvironment.

cancer biology↗