Biology subjects

Pauli, C.

Publications and source records attributed to Pauli, C..

11 recordsLinked to original sources

bioRxiv2026

High regeneration-associated stress defines a distinct HCC subgroup with therapeutically exploitable vulnerabilities

Background: To date, no precision oncology approach has been established for HCC. Despite the diverse underlying causes, HCC development exhibits a uniform pathophysiology characterised by chronic hyper-proliferation, resulting from hepatocyte apoptosis and compensatory liver regeneration. This chronic hyper-proliferative pressure, termed regeneration stress, drives genomic instability during HCC onset, yet its therapeutic potential remains poorly explored. This study aimed to identify targetable vulnerabilities tied to regeneration stress and establish clinically applicable markers for treatment stratification. Methods: Weighted gene co-expression network analysis (WGCNA) was applied on external bulk RNA-seq datasets to define a LIVer REgeneration Stress Signature (LIVRESS). The signature was functionally validated using HCC patient-derived organoids (HCC-Org), and vulnerabilities were mapped using mid-throughput drug screening, single-molecule and single-cell assays, and multi-omic integration. Results: High LIVRESS scores, characterised by enrichment in replication, mitotic and DNA damage repair pathways, identified a subset of HCC patients with aggressive disease and poorer survival across aetiologies. HCC-Org with high LIVRESS scores displayed exquisite sensitivity to multiple inhibitors of the checkpoint kinase ATR. Although HCC-Org models exhibited a baseline reduction in replication fork speed, sensitivity to ATR inhibitor (ATRi) was decoupled from replication fork dynamics and rather linked to intrinsic mitotic instability. ATR inhibition triggers mitotic failure and apoptosis in LIVRESSHigh HCC-Org. This killing effect was significantly potentiated by combining ATRi with PARPi or WEE1i. Multi-omic integration identified KPNA2 as a surrogate biomarker of ATRi sensitivity. Conclusion: Our findings demonstrate that a subset of HCC-Org, characterised by high liver regeneration-associated stress, is vulnerable to ATRi-based therapies. By focusing on a comprehensive regenerative stress model, we establish a framework to stratify HCC patients and implement biomarker-driven, ATR-based therapies for HCC patients with advanced disease. Impact and implications: Regeneration stress is a key factor that drives genomic instability in HCC, providing a basis for the LIVRESS to identify patients dependent on ATR-mediated checkpoints. These findings reveal a conceptual shift for researchers and trialists: ATRi efficacy is decoupled from replication fork dynamics and instead leverages mitotic fragility. Practically, the LIVRESS and its IHC surrogate marker (KPNA2) offer a scalable roadmap for physicians to improve patient stratification in ATRi-based precision oncology trials. While requiring prospective validation, these results pave the way toward biomarker-driven therapies for advanced HCC.

cancer biology↗

bioRxiv2026

Synovitis in systemic sclerosis is an interferon-driven stromal condition distinct from rheumatoid arthritis

Joint involvement is a major driver of disability in systemic sclerosis (SSc), yet its pathophysiology remains poorly understood. In the absence of specific evidence, SSc synovitis is treated by analogy with rheumatoid arthritis (RA). Here, we present the first comprehensive molecular characterization of SSc synovitis, integrating histology, single-cell RNA sequencing, and spatial multi-omics of synovial biopsies from SSc patients, RA patients, and non-inflammatory controls with in vitro validation. We show that SSc synovitis is characterized by distinct pathomechanisms from RA. Histologically, most SSc biopsies displayed a pauci-immune pathotype with sparse immune infiltrates and predominant stromal cells. At molecular level, synovial fibroblasts in SSc were characterized by a disease-specific type I interferon (IFN) response program, in contrast to the TNF-dominant profile of RA, accompanied by dysregulation of the complement cascade. This IFN program extended across multiple synovial cell types, including monocyte-derived macrophages and endothelial cells, and was spatially organized into focal myeloid niches and a diffuse stromal program. Systemically, elevated serum IFN-2a levels were associated with the presence of clinical synovitis in an independent cohort of SSc patients. We furthermore show that similar IFN-driven programs are shared between skin and synovium in SSc. Genes downregulated by IFNAR1 blockade in SSc skin were enriched in SSc synovium, supporting IFN receptor blockade as a multi-organ target therapeutic strategy. These findings reframe SSc synovitis as a less destructive, IFN-driven stromal condition distinct from RA and provide a mechanistic basis for dedicated clinical trials for joint inflammation in SSc. One Sentence SummarySSc synovitis is a pauci-immune, IFN-driven stromal condition distinct from RA, supporting IFNAR1 blockade as a therapeutic strategy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/733140v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@d85bb5org.highwire.dtl.DTLVardef@6cffe6org.highwire.dtl.DTLVardef@148eb4org.highwire.dtl.DTLVardef@1a4cd83_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

MTAP deficiency is a novel biomarker in neuroendocrine neoplasms of the lung

IntroductionMTAP emerges as potential predictive biomarker for MTA-cooperative PRMT5-inhibitors. Although MTAP attracts increasing attention in non-small cell lung cancer, its role in pulmonary neuroendocrine neoplasms (NENs) remains largely unexplored. MethodsHere, we assessed the prevalence of MTAP deficiency in 209 pulmonary NENs using immunohistochemistry (IHC). Additionally, we performed fluorescence in situ hybridization (FISH), whole exome sequencing (WES), deep proteomic profiling, transcriptomic, and methylation analyses of selected MTAP deficient and proficient carcinoids to further elucidate the underlying mechanisms of MTAP expression pattern. ResultsMTAP deficiency by IHC was detected in all neuroendocrine precursor lesions (n=17), 92% of typical carcinoids (n=51), 86% of atypical carcinoids (n=21), and 10% of large cell neuroendocrine carcinomas (LCNEC) (n=30). In contrast, all small cell lung cancers (SCLC) were MTAP proficient (n=90). In MTAP deficient carcinoids, FISH and WES did not detect homozygous 9p21 deletions, and methylation analysis showed no evidence of MTAP promoter hypermethylation. Comparing MTAP deficient and MTAP proficient carcinoids, proteomic data showed a clear separation between the two groups. Further, there was an inverse correlation between the expression of MTAP and OTP (orthopedia homeobox protein), which is known as a strong prognostic marker in pulmonary carcinoids. DiscussionMTAP deficiency is a novel hallmark of neuroendocrine precursors and most pulmonary carcinoids, clearly distinguishing the latter from SCLC and most LCNEC. It is neither caused by 9p21 deletion, nor by MTAP promoter hypermethylation. MTAP deficiency is a group-defining feature of carcinoids that might pave the way for new therapeutic approaches.

pathology↗

bioRxiv2025

Exploiting pair correlation function to describe biological tissue structure

Multiplexed imaging technologies now enable the simultaneous profiling of hundreds to thousands of molecular targets in intact tissues, providing unprecedented insight into cellular heterogeneity and spatial organization. While data generation has rapidly matured, the quantitative analysis of spatial structure remains challenging and poorly standardized, particularly across biological length scales. Existing approaches, such as distance-based metrics, neighborhood analyses and graph neural networks, either capture only local interactions or sacrifice interpretability for predictive power. Here we introduce PCF-SiM (Pair Correlation Function Sigmoid Modeling), a scalable and interpretable framework that leverages parametric modeling of the pair correlation function to quantify spatial organization in multiplexed imaging data. PCF-SiM compresses complex spatial patterns into a small set of biologically meaningful parameters, enabling robust comparisons across cell types, samples and conditions. Applying PCF-SiM to diverse public spatial transcriptomics datasets, we demonstrate its ability to detect condition-dependent tissue remodeling in a mouse colitis model. We further extend the framework with a co-scaling strategy that identifies cell types participating in shared spatial structures. Using newly generated clinical datasets from Hashimotos thyroiditis and uveal melanoma liver metastases, PCF-SiM reveals hierarchical organization of autoimmune infiltrates and coordinated spatial interactions between lymphatic endothelial cells and tumor-infiltrating lymphocytes. Finally, we show that reliable inference of tissue-scale architecture requires whole-slide imaging, exposing intrinsic limitations of tumor microarray-based spatial analyses. Together, PCF-SiM provides a principled and interpretable approach for spatial analysis of multiplexed imaging data.

bioinformatics↗

bioRxiv2025

Disease-specific fibroblast-myeloid interactions in rheumatoid arthritis synovium

Rheumatoid arthritis (RA) is characterized by profound remodeling of the synovial microenvironment. Here we show that enhanced fibroblast-macrophage cross-talk distinguishes RA from psoriatic arthritis (PsA). MerTK-SPP1 macrophages represent the dominant inflammatory myeloid population in RA, interacting with expanded fibroblast subsets through SPP1-mediated signaling. Lining fibroblasts display induction of antigen-presentation and IL-6/JAK-STAT pathways, while a CHI3L1-producing fibroblast population arises specifically in RA and may act as a source of autoantigens. These stromal populations interact closely with FABP5 iDC3 cells and T cells within a disrupted synovial lining, creating a niche driving adaptive immune activation. In contrast, PsA exhibits increased fibroblast- endothelial interactions without major endothelial transcriptional changes. Our data identify SPP1 signaling and fibroblast-myeloid-dendritic interactions as core drivers of RA synovial inflammation that links innate immune activation to the initiation of autoimmunity. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/688477v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@c76e39org.highwire.dtl.DTLVardef@11563a9org.highwire.dtl.DTLVardef@141f3fborg.highwire.dtl.DTLVardef@f90742_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Dynamic Ribosomal RNA Methylation Regulates Translation in the Hematopoietic System and is Essential for Stem Cell Fitness

Self-renewal and differentiation are at the basis of hematopoiesis. While it is known that tight regulation of translation is vital for hematopoietic stem cells (HSCs) biology, the mechanisms underlying translation regulation across the hematopoietic system remain obscure. Here we reveal a novel mechanism of translation regulation in the hematopoietic hierarchy, which is mediated by ribosomal RNA (rRNA) methylation dynamics. Using ultra-low input ribosome-profiling, we characterized cell-type-specific translation capacity during erythroid differentiation. We found that translation efficiency changes progressively with differentiation and can distinguish between discrete cell populations as well as to define differentiation trajectories. To reveal the underlying mechanism, we performed comprehensive mapping of the most abundant rRNA modification - 2-O-methyl (2OMe). We found that, like translation efficiency, 2OMe dynamics followed a distinct trajectory during erythroid differentiation. Genetic perturbation of individual 2OMe sites demonstrated their distinct roles in modulating proliferation and differentiation. By combining CRISPR screening, molecular and functional analyses, we identified a specific methylation site, 28S-Gm4588, which is progressively lost during differentiation, as a key regulator of HSC self-renewal. We showed that low methylation at this site led to translational skewing, mediated mainly by codon frequency, which promoted differentiation. Functionally, HSCs with diminished 28S-Gm4588 methylation exhibited impaired self-renewal capacity ex-vivo, and loss of fitness in-vivo in bone marrow transplantations. Extending our findings beyond the hematopoietic system, we also found distinct dynamics of 2OMe profiles during differentiation of non-hematopoietic stem cells. Our findings reveal rRNA methylation dynamics as a general mechanism for cell-type-specific translation, required for cell function and differentiation. KEY POINTSO_LIHematopoietic differentiation is associated with rRNA methylation dynamics to control cell-type-specific translation. C_LIO_LITranslation efficiency can distinguish discrete cell types and define differentiation trajectories. C_LIO_LIHSC fitness is regulated by a single rRNA methylation. C_LI

molecular biology↗

bioRxiv2024

Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures

Mammalian ribosomal RNA (rRNA) molecules are highly abundant RNAs, decorated with over 220 rRNA modifications. Previous works have shown that some rRNA modification types can be dynamically regulated; however, how and when the mammalian rRNA modification landscape is remodeled remains largely unexplored. Here, we employ direct RNA nanopore sequencing to chart the human and mouse rRNA epitranscriptome across tissues, developmental stages, cell types and disease. Our analyses reveal multiple rRNA sites that are differentially modified in a tissue- and/or developmental stage-specific manner, including previously unannotated modified sites. We demonstrate that rRNA modification patterns can be used for tissue and cell type identification, which we hereby term epitranscriptomic fingerprinting. We then explore rRNA modification patterns in normal-tumor matched samples from lung cancer patients, finding that epitranscriptomic fingerprinting accurately classifies clinical samples into normal and tumor groups from only 250 reads per sample, demonstrating the potential of rRNA modifications as diagnostic biomarkers.

molecular biology↗

bioRxiv2024

Unbiased functional genetic screens reveal essential RNA modifications in human cancer and drug resistance

RNA modification pathways are mis-regulated in multiple types of human cancer. To comprehensively identify cancer-relevant RNA modifications and their regulators, we screened all 150 annotated human RNA modifying proteins across 18 different normal and cancer cell lines using a CRISPR-based genetic knockout system. Fifty RNA modifying proteins were essential for survival of at least one cell type. A third of these essential genes were amplified in 38 different human primary cancer types and potentially drive cancer growth. Unexpectedly, the number of essential genes per cell line varied considerably, and this variation was not due to tissue of origin. Instead, we found that cancer cell-specific mitochondrial metabolic plasticity was responsible for the unique requirement of certain RNA modifications. For example, leukemia cells with high intrinsic drug tolerance required mitochondrial flexibility to survive treatment with the anti-leukemic drugs cytarabine and venetoclax. Synthetic lethality screens revealed that drug-resistance is abolished by deleting the mitochondrial methyltransferase TRMT5, which is responsible for the formation of N1-methylguanosine (m1G) in the tRNA anticodon loop. In summary, our study identifies cancer-relevant RNA modifying enzymes, and reveals a novel promising drug target for therapy-resistant acute myeloid leukemia.

cell biology↗

bioRxiv2024

Differential Expression Analysis of Cannabis sativa response to thermotherapy of Hops Latent Viroid (HLVd) infection and clearance of the viroid in Tissue Culture Micropropagation

Increased farming and cultivation of Cannabis sativa is rapidly pushing Cannabis (Cannabis sativa L.) towards becoming a commercial agricultural commodity. Large-scale cultivation facilities maintain thousands of clonal varieties of recreational and medicinal cannabis and there is a strong market-driven motivation to maintain a commercial pipeline of clean healthy vigorously growing plants free of pathogens. However, mass production and high-capacity cultivation create an environment that is susceptible to highly transmissible pathogens and infectious entities such as Hop Latent Viroid (HLVd). From nurseries to cultivation facilities, its become increasingly important to maintain a routine testing regimen and ensure cultivation facilities are HLVd-free environments. One method to address the problem of infected plants is to perform thermotherapy on C. sativa explants under tissue culture conditions and isolate clean tissue to multiply productive and healthy mature plants. We carried out a novel thermotherapy method using tissue culture in 5 varieties of type III cannabis that were HLVd positive to document the degree of success of the treatment at the RNA level. We observed that following thermotherapy treatment we were able to decrease the level of HLVd positive tests in select varieties and observed some varieties were highly susceptible and unable to clear the viroid. Plants were tested using a one-step RT-qPCR method, developed and validated, in part, along with this work, and present the results as well as an exploratory transcriptome analysis of an internally developed variety, AnnaLee, which tested negative for HLVd following thermotherapy treatment, and explore possible genes of interest for viroid infection, clearance, and mitigation. Author SummaryRT-qPCR and transcriptome analysis of Hops latent viroid (HLVd) in infected and non-infected Cannabis varieties. A thermotherapy procedure was conducted on HLVd infected Cannabis sativa meristem tissue maintained through tissue culture micropropagation techniques. Total RNA was isolated from the cultured plantlet stocks and evaluated by a real-time reverse transcriptase assay for HLVd. Infection status post thermotherapy was assessed, and viroid-free plants were maintained and subsequently tested. A single thermotherapy-treated cultivar, Anna Lee was selected for transcriptomics, and an analysis of the genes that were differentially regulated in infected and non-infected treated plants is discussed.

plant biology↗

bioRxiv2022

A comprehensive single-cell atlas of freshly dissociated human synovium in inflammatory arthritis with an optimized dissociation protocol for prospective fresh synovial biopsy collection

Single-cell RNA-sequencing is advancing our understanding of synovial pathobiology in inflammatory arthritis. Here, we optimized the protocol for the dissociation of fresh synovial biopsies and created a reference single-cell map of fresh human synovium in inflammatory arthritis. We utilized the published method for dissociating cryopreserved synovium and optimized it for dissociating small fresh synovial biopsies. The optimized protocol enabled the isolation of a good yield of consistently highly viable cells, minimizing the dropout rate of prospectively collected biopsies. Our reference synovium map comprised over 100000 unsorted single-cell profiles from 25 synovial tissues of patients with inflammatory arthritis. Synovial cells formed 11 lymphoid, 15 myeloid and 16 stromal cell clusters, including IFITM2+ synovial neutrophils. Using this reference map, we successfully annotated published synovial scRNA-seq datasets. Our dataset uncovered endothelial cell diversity and identified SOD2highSAA1+SAA2+ and SERPINE1+COL5A3+ fibroblast clusters, expressing genes linked to cartilage breakdown (SDC4) and extracellular matrix remodelling (LOXL2, TGFBI, TGFB1), respectively. We broadened the characterization of tissue resident FOLR2+COLEC12high and LYVE1+SLC40A1+ macrophages, inferring their extracellular matrix sensing and iron recycling activities. Our research brings an efficient synovium dissociation protocol and a reference annotation resource of fresh human synovium, while expanding the knowledge about synovial cell diversity in inflammatory arthritis.

genomics↗

bioRxiv2020

SF3B1 promotes tumor malignancy through splicing-independent co-activation of HIF1α

Mutations in the splicing factor SF3B1 are frequently occurring in various cancers and drive tumor progression through the activation of cryptic splice sites in multiple genes. Recent studies also demonstrate a positive correlation between expression levels of wildtype SF3B1 and tumor malignancy, but underlying mechanisms remain elusive. Here, we report that SF3B1 acts as an activator of HIF signaling through a splicing-independent mechanism. We demonstrate that SF3B1 forms a heterotrimer with HIF1 and HIF1{beta}, facilitating binding of the HIF1 complex to hypoxia response elements (HREs) to activate target gene expression. We further validate the relevance of this mechanism for tumor progression. Monoallelic deletion of Sf3b1 impedes formation and progression of hypoxic pancreatic cancer via impaired HIF signaling, but is well tolerated in normoxic chromophobe renal cell carcinoma. Our work uncovers an essential role of SF3B1 in HIF1 signaling, providing a causal link between high SF3B1 expression and aggressiveness of solid tumors.

cell biology↗