Biology subjects

Loriot, A.

Publications and source records attributed to Loriot, A..

14 recordsLinked to original sources

bioRxiv2026

Mitochondrial dysfunction as a hallmark of brain senescence in telomerase-deficient mice

Neurodegenerative diseases, including Alzheimer's disease (AD), are strongly associated with aging. However, the molecular mechanisms underlying pathological brain aging remain incompletely understood. In this study, we used a mouse model of telomere attrition, a major driver of cellular senescence, to perform an unbiased analysis of how telomere-driven senescence affects cellular physiology and contributes to processes relevant to neurodegenerative conditions. After validating the presence of senescence hallmarks in telomerase-deficient brains, we characterized their transcriptomic and proteomic profiles. Mitochondrial function and associated energy metabolism emerged as the major dysregulated pathways, driven predominantly by proteomic rather than transcriptomic changes. Functional biochemical analyses on isolated brain mitochondria demonstrated impaired electron transport chain (ETC) complex activity and reduced energetic status, despite preserved ETC complex integrity and mitochondrial content. Further analyses in senescent primary neurons indicated an accumulation of dysfunctional mitochondria, characterized by increased reactive oxygen species (ROS) production and reduced ATP levels, although basal cellular respiration was maintained. At the tissue level, these alterations were associated with moderate reductions in neuronal density in the subiculum and cortical layer V, indicating region-specific vulnerability rather than widespread neurodegeneration. We propose that a major consequence of telomere dysfunction associated with pathological brain aging is the downregulation of mitochondrial activity, which contributes to the selective vulnerability of specific brain regions. These findings highlight mitochondrial pathways as attractive targets for interventions aimed at preserving brain health during aging.

neuroscience↗

bioRxiv2026

Beige/brown fat-mediated cardiac protection from high-fat diet is dependent on adipocyte beta3-adrenergic receptor

Cardiometabolic diseases associated with obesity are continuously increasing worldwide. Yet, current therapeutic strategies remain insufficient to improve patient outcomes. The beta3-adrenergic receptor ({beta}3AR) promotes lipolysis in adipose tissue (AT) and thermogenesis specifically in brown adipose tissue (BAT). In mice, BAT activation also improves systemic metabolism and limits cardiometabolic damage. While BAT is limited in humans (e.g., with ageing and obesity), {beta}3AR activation induces beige adipocytes within white adipose depots with similar thermogenic properties. To study the role of adipocyte {beta}3AR in the regulation of cardiac metabolism and remodeling, mice with/without adipocyte-specific {beta}3AR genetic deletion were fed a high-fat-sucrose (HF-S) diet and treated with the selective {beta}3AR agonist CL316,243 (CL). The metabolic and cardiac protection following {beta}3AR activation was abrogated upon {beta}3AR deletion in adipocytes, together with the beiging of the epididymal (visceral) AT, highlighting a critical role of adipose {beta}3AR signalling in mediating these benefits. Multi-omic analysis of AT and cardiac samples identified CL-induced secreted mediators of the crosstalk between AT and the heart. Therefore, adipocyte {beta}3AR is critical for the adipose-cardiac communication and supports the therapeutic potential of targeting {beta}3AR for the management of obesity-related cardiometabolic diseases.

systems biology↗

bioRxiv2026

Mixed acid fermentation products from Lachnospira eligens counteract myotube atrophy

IntroductionAcute myeloid leukemia (AML) is a hematological malignancy associated with muscle wasting. As the relative abundance of Lachnospira eligens was reduced in patients with AML compared to healthy individuals and correlated positively with muscle strength, we hypothesized that L. eligens positively impacts the muscle through the production of small metabolites reaching the systemic circulation. MethodsL. eligens levels were analyzed in two additional independent cohorts. Six L. eligens isolates were characterized through whole-genome sequencing to select clinically relevant strains. The composition of their culture supernatant was analyzed by metabolomics. The impact of L. eligens supernatant on dexamethasone- and interleukin-6-atrophied murine myotubes was assessed. Bioactive metabolites and their production mechanism were identified using among others bioactivity-guided fractionation. The underlying mechanism was also explored on the host side through myotubes transcriptome analysis and metabolic flux analysis. The relevance of bioactive metabolites and their production mechanism was evaluated through clinical data and samples analyses and in a mouse model of leukemia. ResultsThe levels of L. eligens are reduced in independent cohorts of patients with AML and its supernatant counteracts myotube atrophy. This anti-atrophic effect, conserved between strains of the same species, depends on the occurrence of mixed acid fermentation (MAF) in anoxic culture conditions and the presence of its acid end-products acetate, formate and D-lactate. Consistent with those results, blood levels of acetate are decreased and the relative abundance of fecal bacteria capable of performing aerobic respiration is increased in patients with AML. However, bacterial supernatant failed to prevent muscle atrophy and weakness in leukemic mice, likely due to insufficient sustained elevation of acid end-products in the blood. ConclusionThis work reveals the anti-atrophic effect of MAF end-products on myotubes and suggests the importance of considering gut electron acceptor levels (e.g. O2) in disorders affecting muscle health. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/729780v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@112529eorg.highwire.dtl.DTLVardef@1ee1929org.highwire.dtl.DTLVardef@b5f389org.highwire.dtl.DTLVardef@187bc40_HPS_FORMAT_FIGEXP M_FIG Mixed acid fermentation products from Lachnospira eligens counteract myotube atrophy. Our study suggests that gut anaerobiosis is disrupted in treatment-naive patients with acute myeloid leukemia (AML), leading to decreased circulating acetate levels and a reduced relative abundance of L. eligens, which significantly correlated with muscle strength. In line with this framework, in vitro experiments demonstrate that the culture supernatant of L. eligens, which contains mixed acid fermentation (MAF) end-products such as acetate, effectively counteracts C2C12 myotube atrophy in the presence of pro-atrophying stimuli. Further mechanistic experiments indicate a causal role for MAF end-products in this anti-atrophying effect. Created with BioRender.com. Legend: solid frames: experimental results; dashed frames: hypothetical conclusions derived from results; black solid arrow: established correlation; black dashed arrows: hypothetical causation. C_FIG

microbiology↗

bioRxiv2026

Alzheimer's disease-associated Presenilin 2 N141I mutation impairs neuronal lipid homeostasis and mitochondrial dynamics through selective downregulation of the Golgi exchange factor Gbf1

Presenilin 2 (PS2) mutations cause familial Alzheimers disease, yet their effects beyond amyloid processing remain poorly understood. Here, we investigated how PS2 deletion and the N141I mutation affect neuronal lipid homeostasis and mitochondrial dynamics in mouse primary neurons. Both PS2 deletion and N141I mutation reduced neuronal lipid content. However, exogenous lipid supplementation rescued this deficit only in N141I-expressing neurons, indicating a partial loss-of-function effect. N141I neurons also displayed reduced OPA1, a mitochondrial fusion regulator, restored by lipid supplementation. RNA-sequencing identified Gbf1, a Golgi-specific guanine nucleotide exchange factor, as selectively downregulated in N141I but not knockout tissue, which was confirmed at the protein level in mouse brain and primary neurons. Gbf1 knockdown in mouse embryonic fibroblasts (MEFs) recapitulated the N141I lipid profile. Together, these findings reveal a PS2-GBF1-lipid-mitochondria axis disrupted specifically by the N141I mutation, suggesting an amyloid-independent pathway contributing to neurodegeneration and identifying potential therapeutic targets for familial Alzheimers disease.

neuroscience↗

bioRxiv2026

Ciliogenic pancreatopathy reveals a link between ciliopathies and exocrine pancreatic disease

BackgroundWhile pancreatic cysts have been described in syndromic ciliopathies, the pancreas is not commonly recognized as a target organ. However, several ciliary gene knockout mouse models develop a pancreatic phenotype combining acinar atrophy and adipocyte accumulation, hereby called adipopancreatosis, suggesting a link between ciliary dysfunction and pancreatic disease. ObjectiveWe investigated whether mutations in ciliopathy-associated genes are linked to pancreatic dysfunction in humans. DesignWe analyzed a cohort of 341 patients with pediatric-onset pancreatic anomalies and characterized the pancreatic phenotype of new mouse models with conditional Nphp3 inactivation or bearing Nphp3 mutations recapitulating human mutations. In patients, pancreatic fat content was quantified using Dixon-MRI. ResultsMutations in the cilium-related HNF1B and NPHP3 were identified in patients presenting with both renal and pancreatic dysfunction. Nphp3 mutant mice developed acinar atrophy, adipopancreatosis, and moderate inflammation. Adipocytes in the pancreas exhibited a white adipocyte-like profile and likely originated from mesothelial-derived fibroblasts. Reduced numbers and altered length of ductal cilia were monitored. Interestingly, secretory canaliculi, typically unnoticed structures found within and between acinar cells and connected to the acinar lumen, exhibited a microcystic morphology. Consistent with the mouse phenotype, Dixon-MRI revealed significantly increased pancreatic fat content in patients with HNF1B and NPHP3 mutations. ConclusionWe describe a previously unrecognized pancreatic manifestation of ciliopathies, which we name ciliogenic pancreatopathy. Patients with known ciliopathy-causing mutations should be evaluated for this pancreatic condition, particularly those with kidney disease, as concomitant exocrine pancreatic insufficiency may further compromise renal function or the outcome of kidney graft. What is already known on this topicO_LICiliopathies, resulting from defects in primary cilia, are genetic disorders primarily affecting the kidney and liver. C_LIO_LIPancreatic cysts have been sporadically reported in syndromic ciliopathies. C_LIO_LIThe pancreas is not currently recognized as a major target organ of ciliary dysfunction. C_LIO_LIA clear link between ciliary gene mutations and pancreatic anomalies is still unknown. C_LIO_LIAnimal studies have suggested a possible association between ciliary dysfunction and pancreatic anomalies. C_LI What this study addsO_LIIdentifies HNF1B and NPHP3 mutations as genetic causes of a pancreatic phenotype characterized by acinar atrophy and adipose replacement (adipopancreatosis). C_LIO_LIDemonstrates the presence of defective ductal cilia and moderate inflammation in the pancreas of Nphp3 mutant mice. C_LIO_LIReveals that secretory canaliculi in the exocrine pancreas of Nphp3 mutant mice acquire a microcystic morphology. C_LIO_LIShows that patients with HNF1B or NPHP3 mutations have significantly increased pancreatic fat content by Dixon-MRI. C_LIO_LIDefines a new disease entity, ciliogenic pancreatopathy, as a pancreatic manifestation of ciliopathies. C_LI How this study might affect research, practice or policyO_LIEstablishes the pancreas as a novel and clinically relevant target of ciliopathies. C_LIO_LIExpands the phenotypic spectrum of HNF1B- and NPHP3-related diseases to include exocrine pancreatic dysfunction. C_LIO_LISuggests that patients with ciliopathy-causing mutations should be evaluated for exocrine pancreatic insufficiency. C_LIO_LIHighlights the need to consider pancreatic function monitoring in kidney disease and transplant settings. C_LIO_LIOpens new research avenues into the role of primary cilia in pancreatic homeostasis and disease. C_LI

cell biology↗

bioRxiv2025

SRF fusion oncogenes encode constitutively activated chimeric transcription factors in myoid soft tissue tumors

SRF fusion genes drive the pathogenesis of muscle-related soft tissue tumors, including subsets of perivascular tumors, inflammatory myofibroblastic tumor, and rhabdomyosarcoma. SRF encodes Serum Response Factor, a well-characterized transcription factor that regulates muscle development. We characterized four fusion genes: SRF::RELA, SRF::FOXO1, SRF::ICA1L, and SRF::PDGFRB. All localized to the nucleus and dimerized through the SRF MADS box. SRF::RELA, SRF::FOXO1, and SRF::ICA1L acted as constitutively active transcription factors independent of canonical cofactors, binding SRF target promoters and driving transcription via the partner transactivation domain (TAD). A cryptic TAD was uncovered in ICA1L. These fusions promoted mesenchymal cell growth and upregulated muscle-related genes in mesenchymal stem cells, recapitulating transcriptional signatures of human tumors. In contrast, SRF::PDGFRB acted through its kinase domain, was imatinib-sensitive, activated STAT1 and stimulated inflammation genes, consistent with its tumor phenotype. SRF fusions thus define a novel family of oncogenes in human myoid soft tissue tumors. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/676997v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@621647org.highwire.dtl.DTLVardef@1a496b1org.highwire.dtl.DTLVardef@a1643corg.highwire.dtl.DTLVardef@1bbca8c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

A survey of human cancer-germline genes: linking X chromosome localization, DNA methylation and sex-biased expression in early embryos

Human cancer-germline (CG) genes are a group of testis-specific genes that become aberrantly activated in various tumors. Ongoing studies aim to understand their functions in order to evaluate their potential as anti-cancer therapeutic targets. Evidence suggests the existence of subcategories of CG genes, depending on location on autosomal or sex chromosomes, reliance on DNA methylation for transcriptional regulation, and profile of expression during gametogenesis and early embryogenesis. To clarify this issue, we developed CTexploreR, a R/Bioconductor package that integrates an up-to-date reference list of human CG genes (n=146) with multiple bulk and single-cell methylomic and transcriptomic datasets. Based on promoter methylation profiles and responsiveness to a DNA methylation inhibitor, 74% of the CG genes were classified as DNA methylation dependent (Methdep). Intriguingly, most X-linked CG genes (69/70) fell into this category, thereby implicating DNA methylation dependency in the well-documented over-representation of testis-specific genes on the X chromosome. We further observed that, whereas X-linked Methdep CG genes become demethylated and activated in pre-spermatogonia in the fetal testis, most of them resist DNA demethylation in female germ cells and remain therefore silent in fetal and adult oocytes. Importantly, a number of X-linked Methdep CG genes (e.g. FMR1NB, GAGE2A, MAGEB2/C2, PAGE2, VCX3A/B) maintained this maternal-specific imprinting after fertilization, and were expressed exclusively in female preimplantation embryos, which inherit a paternal X chromosome. Together, our study using the CTexploreR package has allowed us to show that X-linked CG genes undergo transient maternal imprinting and contribute therefore to transcriptional sexual dimorphism in early embryos. Author SummaryCancer-germline (CG) genes include a set of genes that are normally active only in the testis but become aberrantly switched on in different types of tumor, making them potential targets for new anti-cancer treatments. We developed a new analytical tool called CTexploreR, to study these genes, and observed that a large subset of CG genes reside on the X chromosome and use DNA methylation as a mechanism of repression in non-testicular tissues. In fetal testis, these genes lose methylation and become activated in early spermatogenic cells, while in female ovaries they stay methylated and remain silent. Notably, we demonstrate that several CG genes keep this methylation pattern after fertilization, and are therefore expressed in female but not male embryos, which inherit only one X chromosome of maternal origin. CG genes carrying this transient maternal imprinting appear therefore as main contributors of sex-biased mRNA expression in preimplantation embryos. Our Jindings therefore open up new Jields of investigation into the functions of CG genes, the sexual dimorphism of early embryos, and the intergenerational transmission of epigenetic imprints.

genomics↗

bioRxiv2025

Constitutive cGAS-STING activation in ALT+ cells

Stimulator of interferon genes (STING) is a pivotal mediator of anti-tumor immunity, activated downstream of cytoplasmic DNA recognition by cyclic GMP-AMP synthase (cGAS). In cells that employ the alternative lengthening of telomeres (ALT) pathway, extrachromosomal telomeric repeats (ECTRs) act as potent activators of the cGAS-STING pathway. Although ALT+ cells were previously thought to evade this pathway through epigenetic silencing, our findings reveal more nuanced adaptive mechanisms that involve the spatial regulation of STING and the clearance of immunostimulatory ECTR species. In the vast majority of ALT+ cells, ongoing ECTR production drives sustained 2'3'-cGAMP synthesis, directing STING to the Golgi apparatus for immune signaling before lysosomal degradation. Lysosomal degradation of STING relies largely on interferon regulatory factor 3 (IRF3), with minimal involvement of TANK-binding kinase 1 (TBK1), pointing at a novel role for IRF3 in STING trafficking in ALT+ cells. Another adaptive mechanism involves the removal of immunogenic cytoplasmic ECTRs through STING-mediated lysosomal degradation. These mechanisms likely cooperate to restrict chronic interferon signaling that might otherwise prevent ALT+ cancers from emerging. These findings refine our understanding of immune sensing in ALT+ cancers, revealing how ALT+ cells respond to continuous ECTR production and suggesting a potential therapeutic target to modulate the microenvironment of ALT+ tumors.

cell biology↗

bioRxiv2024

Spatial transcriptomics profiling of gallbladder adenocarcinoma: a detailed two-case study of progression from precursor lesions to cancer

BackgroundMost studies on tumour progression from precursor lesion toward gallbladder adenocarcinoma investigate lesions sampled from distinct patients, providing an overarching view of pathogenic cascades. Whether this reflects the tumourigenic process in individual patients remains insufficiently explored. Genomic and epigenomic studies suggest that a subset of gallbladder cancers originate from biliary intraepithelial neoplasia (BilIN) precursor lesions, whereas others form independently from BilINs. Spatial transcriptomic data supporting these conclusions are missing. Moreover, multiple areas with precursor or adenocarcinoma lesions can be detected within the same pathological sample. Yet, knowledge about intra-patient variability of such lesions is lacking. MethodsTo characterise the spatial transcriptomics of gallbladder cancer tumourigenesis in individual patients, we selected two patients with distinct cancer aetiology and whose samples simultaneously displayed multiple areas of normal epithelium, BilINs and adenocarcinoma. Using GeoMx digital spatial profiling, we characterised the whole transcriptome of a high number of regions of interest (ROIs) per sample in the two patients (24 and 32 ROIs respectively), with each ROI covering approximately 200 cells of normal epithelium, low-grade BilIN, high-grade BilIN or adenocarcinoma. Human gallbladder organoids and cell-ine derived tumours were used to investigate the tumour-promoting role of genes. ResultsSpatial transcriptomics revealed that each type of lesion displayed limited intra-patient transcriptomic variability. Our data further suggest that adenocarcinoma derived from high-grade BilIN in one patient and from low-grade BilIN in the other patient, with co-existing high-grade BilIN evolving via a distinct process in the latter case. The two patients displayed distinct sequences of signalling pathway activation during tumour progression, but Semaphorin 4A (SEMA4A) expression was repressed in both patients. Using human gallbladder-derived organoids and cell line-derived tumours, we provide evidence that repression of SEMA4A promotes pseudostratification of the epithelium and enhances cell migration and survival. ConclusionGallbladder adenocarcinoma can develop according to patient-specific processes, and limited intra-patient variability of precursor and cancer lesions was noticed. Our data suggest that repression of SEMA4A can promote tumour progression. They also highlight the need to gain gene expression data in addition to histological information to avoid understimating the risk of low-grade preneoplastic lesions.

cancer biology↗

bioRxiv2023

An abundance of brain-expressed genes show ectopic activation in lung adenocarcinoma

Tumoral transformation processes sometimes include activation of unscheduled gene expression programs in the cancer cells. This is best exemplified by the so-called cancer-testis (CT) genes, a group of genes expressed in testicular germ cells that become activated in tumors of various somatic origins, through a process of DNA demethylation. Here, we explored the possibility that other tissue-specific gene clusters may become ectopically activated in tumors. Lung adenocarcinoma (LUAD) was used as a model, as all necessary transcriptomic datasets were available, including that of AT2 cells, the cell-of- origin of LUAD. We found that besides CT genes, an abundant group of genes expressed in the brain (CB genes, n=63) or in both brain and testis (CBT genes, n=28) become aberrantly activated in LUAD cell lines and tissues. Interestingly, activation of CB and CBTgene clusters was also detected in various other tumor types. Most CB/CBT genes appeared to exert neuronal functions. Moreover, a significant number of them encode antigens involved in neurological paraneoplastic syndromes. Neither neuroendocrine transdifferentiation, which occurs in 10-20% LUAD, nor DNA demethylation appeared to be responsible of the ectopic activation of CB and CBTgene clusters. Instead, prediction tools and depletion experiments identified the REST repressor as a regulator of a number of CB/CBT genes. Conclusion: Together, our data indicate that tumor development is associated with aberrant activation of a brain gene expression program, supporting the assumption that acquisition of neuronal functions might contribute to malignancy.

cancer biology↗

bioRxiv2022

BRAFV600E expression in thyrocytes causes recruitment of immunosuppressive STABILIN-1 macrophages

Papillary thyroid carcinoma (PTC) is the most frequent histological subtype of thyroid cancers (TC), and BRAFV600E genetic alteration is found in 60% of this endocrine cancer. This oncogene is associated with poor prognosis, resistance to radioiodine therapy and tumor progression. Histological follow-up by anatomo-pathologists reveals that 2/3 of surgically-removed thyroids do not present malignant lesions. Continued fundamental research into the molecular mechanisms of TC downstream of BRAFV600E remains thus central to better understand the clinical behavior of these tumors. To study PTC, we used a mouse model in which expression of BRAFV600E is specifically switched on in thyrocytes by doxycycline administration. Upon daily intraperitoneal doxycycline injection, thyroid tissue rapidly acquired histological features mimicking human PTC. Transcriptomic analysis revealed major changes in immune signaling pathways upon BRAFV600E induction. Multiplex immunofluorescence confirmed the abundant recruitment of macrophages, among which a population of LYVE-1+/CD206+/STABILIN-1+ was dramatically increased. By genetically inactivating the gene coding for the scavenger receptor STABILIN-1, we showed an increase of CD8+ T cells in this in situ BRAFV600E dependent TC. Finally, we demonstrated the presence of CD206+/STABILIN-1+ macrophages in human thyroid pathologies. Altogether, we revealed the recruitment of immunosuppressive STABILIN-1 macrophages a PTC mouse model and the relevance of these observations in human thyroid tissues.

cancer biology↗

bioRxiv2021

Transcriptional overlap links DNA hypomethylation with DNA hypermethylation at adjacent promoters in cancer

DNA methylation is an epigenetic mark associated with gene repression. It is now well established that tumor development involves alterations in DNA methylation patterns, which include both gains (hypermethylation) and losses (hypomethylation) of methylation marks in different genomic regions. The mechanisms underlying these two opposite, yet co-existing, alterations in tumors remain unclear. While studying the human MAGEA6/GABRA3 gene locus, we observed that DNA hypomethylation in tumor cells can lead to the activation of a long transcript (CT-GABRA3) that overlaps downstream promoters (GABRQ and GABRA3) and triggers their hypermethylation. Overlapped promoters displayed increases in H3K36me3, a histone mark known to be deposited during progression of the transcription machinery and to stimulate de novo DNA methylation. Consistent with such a processive mechanism, increases in H3K36me3 and DNA methylation were observed over the entire region covered by the CT-GABRA3 overlapping transcript. Importantly, experimental induction of CT-GABRA3 by depletion of DNMT1 DNA methyltransferase, resulted in a similar pattern of increased DNA methylation in the MAGEA6/GABRA3 locus. Bioinformatics analyses in lung cancer datasets identified other genomic loci displaying this process of coupled DNA hypo- and hypermethylation. In several of these loci, DNA hypermethylation affected tumor suppressor genes, e.g. RERG and PTPRO. Together, our work reveals that focal DNA hypomethylation in tumors can indirectly contribute to hypermethylation of nearby promoters through activation of overlapping transcription, and establishes therefore an unsuspected connection between these two opposite epigenetic alterations.

cancer biology↗

bioRxiv2019

A novel mouse model designed for studying cholangiocarcinoma tumorigenesis uncovers a role for a SOX17-Tensin 4 pathway

Background & AimsAlthough earlier diagnosis and treatment of intrahepatic cholangiocarcinoma (iCCA) is necessary to improve therapy, there is still limited information available about initiation and evolution of iCCA precursor lesions. Therefore, there is a need to identify mechanisms driving formation of precancerous lesions and their progression towards invasive tumor using experimental models that faithfully recapitulate human tumorigenesis. MethodsWe generated a new mouse model which combines cholangiocyte-specific expression of KrasG12D with 3,5-diethoxycarbonyl-1,4-dihydrocollidine diet-induced inflammation to mimic iCCA development in patients with cholangitis. Histological and transcriptomic analyses of the mouse precursor lesions and iCCA were performed and compared with human analyses. The function of genes overexpressed during tumorigenesis was investigated in human cell lines. ResultsMice expressing KrasG12D in cholangiocytes and fed a DDC diet developed cholangitis, ductular proliferations, intraductal papillary neoplasms of bile ducts (IPNBs) and eventually iCCAs. The histology of mouse and human IPNBs were highly similar, and mouse iCCAs displayed histological characteristics of human mucin-producing large duct type iCCA. Signaling pathways activated in human iCCA were activated in mice. The identification of transition zones between IPNB and iCCA on tissue sections, combined with RNA-sequencing analyses of the lesions supported that iCCAs derive from IPNBs. We provide evidence that a gene cascade which comprises KRASG12D, SRY-related HMG box transcription factor 17 (SOX17) and Tensin 4 (TNS4), and which is activated by epidermal growth factor, promotes tumor progression. ConclusionsWe developed a novel mouse model that faithfully recapitulates human iCCA tumorigenesis and identified a gene cascade promoting tumor progression.

cancer biology↗

bioRxiv2018

Dynamics and predicted drug response of a gene network linking dedifferentiation with beta-catenin dysfunction in hepatocellular carcinoma

Alterations of individual genes variably affect development of hepatocellular carcinoma (HCC), prompting the need to characterize the function of tumor-promoting genes in the context of gene regulatory networks (GRN). Here, we identify a GRN which functionally links LIN28B-dependent dedifferentiation with dysfunction of CTNNB1 ({beta}-CATENIN). LIN28B and CTNNB1 form a functional GRN with SMARCA4 (BRG1), Let-7b, SOX9, TP53 and MYC. GRN activity is detected in HCC and gastrointestinal cancers; it negatively correlates with HCC prognosis and contributes to a transcriptomic profile typical of the proliferative class of HCC. Using data from The Cancer Genome Atlas and from transcriptomic, transfection and mouse transgenic experiments, we generated and validated a quantitative mathematical model of the GRN. The model predicts how the expression of GRN components changes when the expression of another GRN member varies or is inhibited by a pharmacological drug. The dynamics of GRN component expression reveal distinct cell states that can switch reversibly in normal condition, and irreversibly in HCC. We conclude that identification and modelling of the GRN provides insight into prognosis, mechanisms of tumor-promoting genes and response to pharmacological agents in HCC.

cancer biology↗