Biology subjects

Hawinkels, L. J. A. C.

Publications and source records attributed to Hawinkels, L. J. A. C..

6 recordsLinked to original sources

bioRxiv2026

Bulk RNA sequencing deconvolution of pancreatic ductal adenocarcinoma identifies cancer-associated fibroblast subsets associated with survival and tumor microenvironment composition

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer characterized by a high abundance of cancer-associated fibroblasts (CAFs), which influence therapy response, tumor biology and tumor aggressiveness. CAFs are a heterogeneous cell type and previous single-cell RNA sequencing (scRNAseq) of PDAC tumors identified three main CAF subtypes: myofibroblastic, inflammatory and antigen-presenting CAFs (myCAF, iCAF, apCAF, respectively). However, scRNAseq on large patient cohorts is often not feasible due to costs and technical constraints. Therefore, bulk RNAseq deconvolution can be used to identify cell types within the heterogeneous tumor microenvironment. Here, Statescope deconvolution was used to identify different cell types of the tumor microenvironment within an early onset PDAC cohort, comprising 74 patients aged under 60. Three CAF populations were identified (iCAFs, myCAFs and desmoplastic CAFs), and their correlations with tumor microenvironment components, mutational signatures and survival were examined. iCAFs were associated with classical-like tumor cells, whereas myCAFs and desmoplastic CAFs correlated with basal-like tumor cells. Desmoplastic CAFs are associated with inflammatory granulocytes/neutrophils, while negatively associating with monocyte-derived macrophages and immature/transitional B cells. No associations were observed between mutational signatures and the abundance of CAF and epithelial tumor subtypes. Interestingly, a high abundance of CAFs, and specifically increased iCAF abundance, was associated with improved survival. This iCAF-mediated survival effect was predominantly apparent in female patients. All in all, deconvolution of bulk RNA sequencing data, followed by its integration with clinical and biological parameters, reveals the heterogeneity and prognostic implications of CAF subpopulations in the tumor microenvironment of early onset PDAC patients.

cancer biology↗

bioRxiv2025

Divergent Therapeutic and Prognostic Impacts of Immunogenic Features in Undifferentiated Soft Tissue Sarcoma and Myxofibrosarcoma

Myxofibrosarcoma and undifferentiated soft tissue sarcoma (USTS) are genetically complex soft tissue sarcomas with distinct morphological features. Treatment typically involves surgery, often combined with neoadjuvant chemo- or radiotherapy. To better understand the immunobiology of these sarcomas and its associations with treatment response and prognosis, we performed transcriptomic and immunophenotypic profiling. RNA sequencing was performed on 13 USTS and 10 myxofibrosarcomas and immunological profiles were compared with soft tissue sarcoma data from The Cancer Genome Atlas (n = 206 including 44 USTS and 17 myxofibrosarcomas). Immune contextures were further evaluated in 16 USTS and 11 myxofibrosarcomas using imaging mass cytometry. Characterization of T cell and macrophage infiltration in tumors was further assessed in 23 USTS and 22 myxofibrosarcomas through multispectral immunofluorescence and immunohistochemical analysis. USTS and myxofibrosarcomas demonstrated immunogenic features compared to other soft tissue sarcomas, with subsets of USTS and myxofibrosarcomas demonstrating high T cell infiltration while USTS demonstrated a higher infiltration by myeloid cells as compared to myxofibrosarcoma. Prognostically, T cells and CD68+CD163+ macrophages were associated with metastasis-free survival in USTS but not in myxofibrosarcomas. Notably, in USTS, neoadjuvant radiotherapy appeared to induce cytotoxic T cell infiltration and depletion of myeloid cells, whereas these effects were not observed in myxofibrosarcomas. These findings highlight important differences in the immunobiology of USTS and myxofibrosarcomas with therapeutic and prognostic implications. These differences should be taken into account given the growing availability of immunotherapeutic options for treating patients with soft tissue sarcomas.

cancer biology↗

bioRxiv2025

ZEB1, a novel regulator of Junctional Adhesion Molecule A, impacts sensitivity of pancreatic cancer-associated fibroblasts to oncolytic reovirus

Oncolytic virus (OV) therapy is a promising treatment for various tumors. However, in pancreatic ductal adenocarcinoma (PDAC), the high abundance of cancer-associated fibroblasts (CAFs) can limit OV therapy efficacy by impairing viral spread and anti-tumor immunity. We have previously shown that oncolytic reovirus infection of CAFs depends on expression of the reovirus entry receptor Junctional Adhesion Molecule A (JAM-A), which is not or lowly expressed in most PDAC CAFs. We propose that increasing JAM-A expression on CAFs will boost viral spread in a tumor. However, there are currently no known regulators of JAM-A expression. Therefore, we performed a genome-wide CRISPR/Cas9 knock-out screen to identify regulators of JAM-A expression. Ablation of the top negative regulator, Zinc Finger E-Box binding Homeobox 1 (ZEB1), in pancreatic fibroblasts led to strong JAM-A upregulation. We show that ZEB1 directly regulates JAM-A expression by binding to the E-box regions located within the JAM-A promotor. Importantly, ZEB1 ablation increased the sensitivity of fibroblasts to reovirus infection and subsequent cell death. Our work provides a novel overview of genes regulating JAM-A expression and provides a rational approach of combining ZEB1 inhibition with reovirus therapy to target both CAFs and tumor cells in stroma-rich tumors such as PDAC.

cancer biology↗

bioRxiv2024

TGFβ signaling in cancer-associated fibroblasts drives a hepatic gp130-dependent pro-metastatic inflammatory program in CMS4 colorectal cancer subtype

Current molecular classification of colorectal cancer (CRC), the Consensus Molecular Subtypes (CMS), has highlighted the biological heterogeneity of CRC and enables patient stratification based on the molecular subtype of their tumor. The CMS4 subtype shows the worst prognosis and is linked to the highest occurrence of hepatic metastasis but the underlying molecular mechanisms remain unclear. In this study, we show that the molecular features that largely define CMS4 classification, i.e. abundance of cancer-associated fibroblasts (CAFs) in the tumor microenvironment (TME) and active TGF{beta} signaling, converge to promote liver metastasis. Studying TGF{beta} signaling in CRC patient-derived CAFs from the primary tumor revealed that all three TGF{beta} isoforms induce expression of different IL-6 cytokine family members, particularly IL-6 and IL-11. This primary tumor-derived IL-6 and IL-11 in turn induce upregulation of myeloid chemoattractants, including SAA1, in hepatocytes. Chemical inhibition and genetic ablation experiments revealed that gp130, the IL-6 family of cytokine co-receptor, through JAK/STAT signaling is crucial for the induction of neutrophil chemoattractants by hepatocytes and mediates the migration of potential pro-metastatic neutrophils towards the liver. This IL-6 family-JAK/STAT stromal signaling axis is active in both a murine model of CMS4 as well as in human CRC patients in vivo. Combined, our data reveal that TGF{beta} signaling in CAFs actively contributes to the formation of a neutrophil-dependent, pre-metastatic hepatic niche and that this mechanism might play a role in the metastatic phenotype of CMS4 subtype CRC.

cancer biology↗

bioRxiv2021

Revisiting colorectal cancer tumorigenesis with spatially-resolved gene expression profiling

Early detection and treatment are paramount to the clinical outcome of patients with colorectal cancer (CRC). Deciphering the dynamic interactions that occur between epithelial cells and stromal cells during tumorigenesis requires in-depth analyses of early-stage CRC lesions in spatial context. Here we employed spatially-resolved gene expression profiling to dissect molecular processes that associate with malignant transformation in CRC. We provide the transcriptional landscapes of colorectal cancer tumorigenesis from healthy mucosa, through different degrees of dysplasia, to cancer. The complementary examination of epithelial and stromal fractions allowed us to define whether specific oncogenic processes involved cancer cells, stromal cells, or the tumor microenvironment as a whole. We identified several genes that were consistently deregulated during CRC onset that could serve as clinical biomarkers for early-stage CRC. Furthermore, we uncovered an essential role for the innate immune system during CRC tumorigenesis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/462502v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@c24d1forg.highwire.dtl.DTLVardef@554113org.highwire.dtl.DTLVardef@1236f99org.highwire.dtl.DTLVardef@173ac8c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2018

Prostaglandin F2α-induced TGFβ-PMEPA1 pathway is a critical mediator of epithelial plasticity and ovarian carcinoma progression.

Prostaglandin (PG) F2 has been scarcely studied in cancer. We have identified a new role for PGF2 in ovarian cancer, stimulating the production of TGF{beta} and the consequent induction of PMEPA1. We show that this induction increases cell plasticity and proliferation, enhancing tumor growth through PMEPA1. Thus, PMEPA1 overexpression in ovarian carcinoma cells, significantly increased cell proliferation rates, whereas PMEPA1 silencing decreased proliferation. In addition, PMEPA1 overexpression buffered TGF{beta} signaling, via reduction of SMAD-dependent signaling. PMEPA1 overexpressing cells acquired an epithelial morphology, associated to higher E-cadherin expression levels while {beta}-catenin nuclear translocation was inhibited. Interestingly, in mouse xenografts, PMEPA1 overexpressing ovarian cells had a clear survival and proliferative advantage, resulting in higher metastatic capacity, while PMEPA1 silencing had the opposite effect. Furthermore, high PMEPA1 expression in a cohort of advanced ovarian cancer patients was observed, correlating with E-cadherin expression. Most importantly, high PMEPA1 mRNA levels were associated with lower patient survival.\n\nSignificanceThis work identifies Prostaglandin F2 as an inducer, through NFAT, of TGF{beta} and together with this up-regulate PMEPA1, which is identified both as a drug target and as a prognostic biomarker in ovarian tumors, potentially useful in clinical practice.

cancer biology↗