Biology subjects

Kranenburg, O.

Publications and source records attributed to Kranenburg, O..

11 recordsLinked to original sources

bioRxiv2025

ATR inhibitors synergize with mitomycin C to enhance cytotoxicity in patient-derived non-muscle invasive bladder cancer organoids

Background and ObjectiveThere is a high recurrence rate in non-muscle invasive bladder cancer (NMIBC) patients treated with intravesical chemotherapy or BCG, indicating the need for novel treatment options. Synergy between DNA damage response inhibitors and chemotherapy has been shown for different solid tumors. In this study, we explore whether combining chemotherapeutic agents with Ataxia telangiectasia and Rad3-related (ATR) kinase inhibitors is a suitable strategy to reduce recurrence in NMIBC. MethodsNMIBC patient-derived organoids (PDOs; n=6) were exposed to mitomycin C (MMC), gemcitabine, or epirubicin for 2h, to mimic intravesical instillation, and subsequently to ATR inhibitors (berzosertib, ceralasertib, tuvusertib) for 72h. Cell viability and PDO regrowth potential was determined by microscopy and CellTiter-Glo(R) luminescence assays, during a period of 6 weeks post-treatment. Key Findings and LimitationsPDO viability was severely impaired (1-22% viable cells at t=6 weeks) after combination treatment with MMC and ATR inhibitors. This effect was observed directly after treatment and maintained during 6 weeks after drug exposure. In contrast, PDOs treated with only chemotherapy or ATR inhibitors showed similar proliferation rates as untreated controls in week 6. LimitationsPDO models were all chemotherapy naive (either BCG or no pre-treatment). It would be interesting to confirm these findings in MMC-resistant models. Conclusions and Clinical ImplicationsThis study demonstrates synergy between different ATR inhibitors and MMC in a panel of six NMIBC PDOs. We propose that combining intravesical chemotherapy instillations with DNA damage response inhibitors should be further evaluated as a promising strategy to reduce recurrence rates for NMIBC. Plain English summaryIn this report we looked at new treatment options for non-muscle invasive bladder cancer. We discovered that tumor cells are killed very efficiently if chemotherapy is combined with drugs that prevent cells from repairing DNA damage.

cancer biology↗

bioRxiv2025

Functional γδT-omics pipeline reveals compartmentalization of Vδ1⁺ T cell migration, tumor-reactivity, and clonality in human colorectal cancer

{gamma}{delta}T cells play a pivotal role in cancer immune surveillance, yet the current knowledge of their function across the compartments in solid tumors is meager. To address this gap, we developed a comprehensive {gamma}{delta}T-omics platform that integrates functional screening, biomimetic migration assays, {gamma}{delta}TCR repertoire analysis, and transcriptomic profiling. Using matched samples from 31 patients with microsatellite-stable colorectal cancer (CRC), we analyzed {gamma}{delta}T cells from peripheral blood (PBLs{gamma}{delta}), adjacent colon (LPLs{gamma}{delta}), primary tumors (pTILs{gamma}{delta}), and liver metastases (mTILs{gamma}{delta}). This approach uncovered striking compartmentalization of {gamma}{delta}T cell phenotypes, clonality, and function. Tumor-reactive, clonally expanded V{delta}1 {gamma}{delta}T cells were enriched in primary tumors and shared transcriptional and functional features with lamina propria lymphocytes (LPLs). In contrast, V{delta}1 {gamma}{delta}T cells from liver metastases lacked tumor reactivity, exhibited distinct {gamma}{delta}TCR repertoires, and expressed transcriptional signatures associated with TGF-{beta}-mediated suppression and cellular quiescence, suggesting they are shaped by tissue-specific environmental cues. CXCL16 secretion by tumor cells initiated V{delta}1 LPLs{gamma}{delta} migration, which was further amplified by {gamma}{delta}TCR-mediated CCL5 induction from pTILs{gamma}{delta}, leading to CCR5 downregulation and subsequent entrapment of pTILs{gamma}{delta} within the tumor microenvironment. Accordingly, our clinical data from an independent second cohort of 69 patients showed that infiltration by pTILs{gamma}{delta}, but not mTILs{gamma}{delta}, is associated with a protective effect against CRC progression. In summary, our study offers a compartment-resolved perspective on {gamma}{delta}T cell behavior in CRC, revealing key trafficking and functional mechanisms, and enabling the identification of novel tumor-reactive {gamma}{delta}TCRs and migratory cues to inform immunotherapeutic strategies for both primary and metastatic CRC. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/671055v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@ff3bborg.highwire.dtl.DTLVardef@14a7e1forg.highwire.dtl.DTLVardef@19e4de4org.highwire.dtl.DTLVardef@bc600_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Site-dependent Treg cell transcriptional reprograming in a metastatic colorectal cancer model holds prognostic significance

In colorectal cancer (CRC), tumor-infiltrating regulatory T (Treg) cells suppress anti-tumor immunity, promoting immune evasion and tumor progression. Effective therapies require selectively targeting tumor-infiltrating Treg (TI-Treg) cells while preserving systemic Treg cells, necessitating insight into their adaptations within the tumor microenvironment. Here, CRC-organoids were implanted in the liver of Foxp3eGFP mice to investigate location-specific phenotypic differences in TI-Treg cells. Tumor tissue exhibited an increased proportion of Treg cells and a decrease of effector CD4 and CD8 T cells compared to matched healthy tissue. RNA sequencing of Treg cells isolated from the spleen, primary liver tumor transplant, or metastases identified gene expression profiles previously associated with CRC-related Treg cells in patients. Location-specific differences included elevated expression of WNT-pathway genes in peritoneal TI-Treg cells compared to liver counterparts. Higher expression of genes upregulated in liver TI-Treg cells correlated with poor CRC prognosis. Splenic Treg cells from tumor-bearing mice displayed distinct transcriptional profiles from both their healthy counterparts and TI-Treg cells, suggesting they represent a distinct CD4+ population. Taken together, these findings highlight TI-Treg cells heterogeneity across different tumor sites and the distinct nature of splenic Treg cells in tumor-bearing hosts.

immunology↗

bioRxiv2024

Basement membrane hydrogels dampen CAR-T cell activation: nanofibrillar cellulose gels as alternative to preserve T cell function in 3D cell cultures.

BackgroundHydrogel-based 3D culture systems are emerging as a valuable tool for preclinical screening of cell-based immunotherapies against solid and hematological malignancies, such as chimeric antigen receptor T (CAR-T) cells. Hydrogels can influence T cell function in a non-desired manner due to their mechanical properties and chemical composition, potentially skewing results in preclinical testing of novel immunotherapeutic compounds. MethodsIn this study, we assess CD4+ T and CAR-T cell activation and proliferation in chemically-undefined matrices (Matrigel and basement membrane extract, BME) and compare them to a synthetic nanofibrillar cellulose (NFC) hydrogel. ResultsRheometric analyses show that NFC is more rigid than Matrigel and BME. Murine CD4+ T cells acquire a regulatory T cell (Treg) phenotype in Matrigel and BME, while this is not observed in NFC. Proliferation and activation of human T cells are higher in NFC than in Matrigel or BME. Similarly, we show that CAR-T cell activation and proliferation is significantly impaired in Matrigel and BME, in contrast to NFC. ConclusionsOur findings highlight the impact of hydrogel choice on (CAR-)T cell behavior, with direct implications for preclinical immunotherapy testing. In contrast to Matrigel and BME, NFC offers a chemically-defined 3D environment where T cell function is preserved. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSIn 3D (preclinical) tumor-killing assays for evaluating engineered T cell cytotoxicity, the surrounding matrix can influence immune cell phenotype and function, potentially skewing T cell activity. Basement membrane hydrogels such as Matrigel and basement membrane extract (BME), widely used as scaffolds for 3D culture, are inherently heterogeneous and contain extracellular matrix components that can influence lymphocyte function. What this study addsHere, we show that (CAR-)T cell function is significantly reduced in Matrigel and BME as compared to standard (2D) culture conditions. In contrast, (CAR-)T cell activity is preserved in synthetic nanofibrillar cellulose (NFC) gels. Importantly, murine T cells spontaneously acquire a Treg phenotype in Matrigel and BME. T cell proliferation and cytokine secretion are >10-fold lower in Matrigel than in NFC. Similarly, CAR-T cell survival and expansion are 10-fold higher in NFC than in Matrigel or BME. How this study might affect research, practice or policyWe report that the intrinsic cytotoxic and proliferative potential of (CAR-)T cells can be underestimated when performing assays in 3D cultures based on Matrigel or BME. As an alternative, we suggest the use of chemically defined synthetic gels, and we show that nanofibrillar cellulose hydrogels are suitable 3D matrices for preserving T cell phenotype and activation.

immunology↗

bioRxiv2024

A unique interplay of access and selection shapes peritoneal metastasis evolution in colorectal cancer

Whether metastasis in humans can be accomplished by most primary tumor cells or requires the evolution of a specialized trait remains an open question. To evaluate whether metastases are founded by non-random subsets of primary tumor lineages requires extensive, difficult-to-implement sampling. We have realized an unusually dense multi-region sampling scheme in a cohort of 26 colorectal cancer patients with peritoneal metastases, reconstructing the evolutionary history of on average 28.8 tissue samples per patient with a microsatellite-based fingerprinting assay. To assess metastatic randomness, we evaluate inter- and intra-metastatic heterogeneity relative to the primary tumor and find that peritoneal metastases are more heterogeneous than liver metastases but less diverse than locoregional metastases. Metachronous peritoneal metastases exposed to systemic chemotherapy show significantly higher inter-lesion diversity than synchronous, untreated metastases. Projection of peritoneal metastasis origins onto a spatial map of the primary tumor reveals that they often originate at the deep-invading edge, in contrast to liver and lymph node metastases which exhibit no such preference. Furthermore, peritoneal metastases typically do not share a common subclonal origin with distant metastases in more remote organs. Synthesizing these insights into an evolutionary portrait of peritoneal metastases, we conclude that the peritoneal-metastatic process imposes milder selective pressures onto disseminating cancer cells than the liver-metastatic process. Peritoneal metastases unique evolutionary features have potential implications for staging and treatment.

genetics↗

bioRxiv2024

Tumor-derived colorectal cancer organoids induce a unique Treg cell population through direct modulation of CD4+ T cell differentiation.

In colorectal cancer (CRC), increased numbers of tumor-infiltrating CD4+ regulatory T (Treg) cells correlate with tumor development and immunotherapy failure, leading to poor prognosis. However, the molecular and cellular mechanisms governing Treg recruitment, expansion, or differentiation remain unclear. Here, we developed an in vitro co-culture system to assess the capacity of CRC tumors to directly modulate Treg cell differentiation. CD4+ T cells from Foxp3eGFP mice were co-cultured with murine tumor-derived CRC organoids, resulting in a significant increase in Treg cell numbers. This induction of Treg cells was not due to increased proliferation, but rather through differentiation of CD4+ T cells in a TGF{beta}-dependent manner. Human CRC tumor organoids similarly induced Treg cells that exhibited enhanced suppressive capacity compared to TGF{beta}-induced Treg cells. RNA-sequencing analysis identified distinct transcriptional profiles between CRC organoid-induced Treg cells and TGF{beta}-induced Treg cells, with upregulation of key functional signature genes linked to CRC Treg cells in vivo. High expression of genes upregulated in CRC organoid-induced Treg cells correlates with shorter progression free interval and overall survival of CRC patients, highlighting their prognostic potential. Taken together, CRC tumor organoids drive CD4+ differentiation to Treg cells with a phenotype resembling tumor-infiltrating Treg cells. This model can be applied to both understand the molecular mechanisms by which tumors can directly modulate CD4+ T cell differentiation and identify approaches to disrupt Treg cell function and stimulate anti-tumor immunity.

immunology↗

bioRxiv2023

Pre-existing Subclones Determine Radioresistance in Rectal Cancer Organoids

More than half of all cancer patients receive radiation therapy, but resistance is commonly observed. Currently, it is unknown whether resistance to radiation therapy is acquired or inherently present. Here, we employed organoids derived from rectal cancer and single-cell whole genome sequencing to investigate the long-term evolution of subclones in response to radiation. Comparing single-cell whole genome karyotypes between unirradiated and irradiated organoids revealed three patterns of subclonal evolution: (i) subclonal persistence, (ii) subclonal extinction, and (iii) subclonal expansion. Only organoids in which subclonal shifts occurred (i.e., expansion or extinction) became more resistant to radiation. Although radioresistant subclones did not share recurrent copy number alterations that could explain their radioresistance, resistance was associated with reduced chromosomal instability; an association that was also observed in 529 human cancer cell lines. These data suggest resistance to radiation is inherently present and associated with reduced chromosomal instability.

cancer biology↗

bioRxiv2023

Stromal localization of inactive CD8+ T cells in metastatic mismatch repair deficient colorectal cancer

BackgroundThe determinants of metastasis in mismatch repair deficiency with high levels of microsatellite instability (MSI-H) in colorectal cancer (CRC) are poorly understood. Here, we hypothesized that distinct immune and stromal microenvironments in primary tumors may discriminate between non-metastatic MSI-H CRC and metastatic MSI-H CRC. MethodsWe profiled 46,727 single cells using high-plex imaging mass cytometry and analyzed both differential cell type abundance, and spatial distribution of stromal and immune cells in primary CRC tumors with or without metastatic capacity. We validated our findings in a second independent cohort using immunohistochemistry. ResultsHigh-plex imaging mass cytometry and hierarchical clustering based on microenvironmental markers separated primary MSI-H CRC tumors with and without metastatic capacity. Primary tumors with metastatic capacity displayed a high stromal content and low influx of CD8+ T cells, which expressed significantly lower levels of markers reflecting proliferation (Ki67) and antigen-experience (CD45RO) compared to CD8+ T cells in non-metastatic tumors. CD8+ T cells showed intra-epithelial localization in non-metastatic tumors, but stromal localization in metastatic tumors, which was validated in a second cohort. ConclusionWe conclude that localization of phenotypically distinct CD8+ T cells within stroma may predict metastasis formation in MSI-H CRC.

cancer biology↗

bioRxiv2023

Mechanical regulation of cell fate transitions underlying colorectal cancer metastasis formation

Colorectal cancer (CRC) cells exhibit high plasticity and transition between different cellular states during the development of metastasis. Lgr5-expressing cancer stem cells fuel the growth of the primary tumor and metastasis, yet disseminated tumor cells arriving at the metastatic site are devoid of Lgr5 expression. It is currently unknown how CRC cell fate transitions are regulated during the metastatic process and how tumor cells give rise to metastatic lesions despite being Lgr5neg. Here, we show that the reprogramming of disseminating CRC cells is driven by mechanical interactions with the Collagen I-rich interstitial matrix. Collagen I-induced pulling forces are sensed by integrins and mechanosensitive calcium channels, which together direct the transition of CRC cells into a fetal-like state. The fetal-like state is maintained after reaching the blood circulation and promotes metastasis-initiation of disseminated CRC cells in the liver. Our findings indicate a key contribution of mechanical signals in controlling cell fate transitions that underlie the metastatic potential of CRC, involving an interplay between different mechanosensitive mechanisms.

cancer biology↗

bioRxiv2022

RNF43 mutations facilitate mucinous colorectal cancer metastasis via formation of a tumour-intrinsic niche

Colorectal cancer (CRC) progression is characterised by a remarkable increase in plasticity and cellular heterogeneity. The ability of cells to shift states and adopt mixed lineage potential exacerbates during metastasis and associates with poor patient survival. How these atypical differentiated states emerge and drive cancer progression however has remained unclear. Here, we investigate this issue for BRAF-mutant CRC that commonly arise via the serrated pathway and are linked to poor prognosis via incompletely understood progression steps. Using patient-derived organoids, gene editing and murine tumour models, we show that mutations in RNF43, a regulator of WNT receptor abundance, endow BRAF-mutant CRC with metastatic capacity by driving a non-dividing tumour-intrinsic niche cell (TINC) state that provides growth factor self-sufficiency to the cancer tissue. TINCs are enriched in RNF43-mutant, mucinous and metastatic samples of human CRC, and ablation of TINCs lead to re-acquired external growth factor dependency during CRC organoid outgrowth. Together, our findings uncover a mechanism by which tumours leverage cellular plasticity to mediate self-organised stem- and niche-cell interactions. Our results argue that formation of a tumour-intrinsic niche is a prerequisite for BRAF-mutant CRC seeding to distant organs and that interference with niche formation may help avoid metastatic relapse.

cancer biology↗

bioRxiv2020

Phenotypic plasticity and partial EMT underlie local invasion and distant metastasis in colon cancer

Phenotypic plasticity represents the most relevant hallmark of the carcinoma cell as it bestows it with the capacity of transiently altering its morphologic and functional features while en route to the metastatic site. However, the study of phenotypic plasticity is hindered by the rarity of these events within primary lesions and by the lack of experimental models. Here, we identified a subpopulation of phenotypic plastic colon cancer cells: EpCAMlo cells are motile, invasive, chemo-resistant, and highly metastatic. EpCAMlo bulk and single-cell RNAseq analysis indicated 1. enhanced Wnt/{beta}-catenin signaling, 2. a broad spectrum of degrees of EMT activation including hybrid E/M states (partial EMT) with highly plastic features, and 3. high correlation with the CMS4 subtype, accounting for colon cancer cases with poor prognosis and a pronounced stromal component. Of note, a signature of genes specifically expressed in EpCAMlo cancer cells is highly predictive of overall survival in tumors other than CMS4, thus highlighting the relevance of quasi-mesenchymal tumor cells across the spectrum of colon cancers. Enhanced Wnt and the downstream EMT activation represent key events in eliciting phenotypic plasticity along the invasive front of primary colon carcinomas. Distinct sets of epithelial and mesenchymal genes define transcriptional trajectories through which state transitions arise. pEMT cells, often earmarked by the extracellular matrix glycoprotein SPARC together with nuclear ZEB1 and {beta}-catenin along the invasive front of primary colon carcinomas, are predicted to represent the origin of these (de)differentiation routes through biologically-distinct cellular states, and to underlie the phenotypic plasticity of colon cancer cells.

cancer biology↗