Epithelial Cell Types Research Articles

The spatial distribution of CFTR-rich Ionocytes cells in the postnatal mouse airway development

Ionocytes are a new type of rare airway epithelial cells expressing Ascl3 and Foxi1 transcription factors, as well as 50% of Cftr-transcripts in mouse airways. However, their role and precise location remain mostly unexplored. This research aimed to shed light on ionocyte ontogeny and distribution within the mouse airway epithelium. Mice were bred in the C57Bl6/J background and maintained in the Specific Pathogen Free mouse facility of Centro de Estudios Científicos (CECs) with access to food and water ad libitum. We used 1,7, 10, 14,21 and 28-days-old wild-type mice, 6 and 8-week-old, and 1 year wild-type and 14-days-old 6 and 8-week-old CftrΔF508/ΔF508 animals. The tracheas were sliced in frontal sections, and the ionocytes were identified by immunofluorescence against the FOXI1 transcription factor. All values were expressed as mean ± S.E.M. All animal procedures were approved by the institutional IACUC (CECS-2022-03). We found that FOXI1+cells had a triangular shape with a basolateral process. Unexpectedly, we observed that FOXI1+cells appear postnatally close to the submucosal glands (SMG), and its number increases drastically between 6 and 8-week-old wild type mice. The quantity of FOXI1+cells cells in the adult trachea decreased towards the distal part (proximal=11.2±1.2 vs distal=4.0±0.9 FOXI1+cells/mm basal lamina, n=7, P=<0,001, t-test), and we did not find significative differences between WT and CftrΔF508/ΔF508 adult mouse. FOXI1+cells were often observed in the epithelia around the collecting duct exit and in the collecting duct epithelium of the SMG. In conclusion, our study provides new insights into the localization and distribution of ionocytes in the mouse airway epithelium. Our results indicate that ionocytes may play a role in regulating mucus composition in upper airways. We suggest that age-dependent changes in cell quantity might reflect the need of increased CFTR function in adult stages. Further research is needed to fully understand the function of ionocytes in the airway and their potential role in respiratory diseases such as cystic fibrosis. Proyecto Postdoctoral 3220672 Proyecto FONDECYT 1221257. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Divergent coactivator usage and CREB1 activity controls tuft lineage commitment

Abstract The precise coordination of co-activators and transcription factors in shaping distinct intestinal epithelial cell types during intestinal stem cell (ISC) differentiation, especially the roles of CBP and P300, remains poorly understood despite extensive gene regulation studies. Here using conditional and inducible genetic models, we identify P300 but not CBP as a specific repressor of tuft and goblet lineages. Both ISC- and IEC-specific deletion of P300 elicited selective expansion of tuft and goblet cells with upregulation of gene modules that orchestrate their differentiation without affecting Paneth and enteroendocrine linages. Intestinal organoids that lack P300 more robustly upregulated tuft cell marker genes in response to IL13, a cytokine that drives type-II immunity and tuft cell expansion. Because P300 often acts as co-activator of TFs that regulate lineage specific gene expression, we hypothesized that lack of P300 repressed a repressor of tuft cell lineage. Among TFs that associate with P300, we tested whether CREB1 regulates P300 mediated restriction of tuft lineage. Surprisingly, we found that CREB1 is necessary for tuft cell commitment in vivo and expansion in response to IL13 treatment in organoids. Overall, these results contribute to our understanding of the complex regulatory mechanisms underlying the ISC differentiation to form specialized cell types in the intestinal epithelium.

Cell cycle variants during Drosophila male accessory gland development.

The Drosophila melanogaster male accessory gland (AG) is a functional analog of the mammalian prostate and seminal vesicles containing two secretory epithelial cell types, termed main and secondary cells. This tissue is responsible for making and secreting seminal fluid proteins and other molecules that contribute to successful reproduction. The cells of this tissue are binucleate and polyploid, due to variant cell cycles that include endomitosis and endocycling during metamorphosis. Here, we provide evidence of additional cell cycle variants in this tissue. We show that main cells of the gland are connected by ring canals that form after the penultimate mitosis, and we describe an additional post-eclosion endocycle required for gland maturation that is dependent on juvenile hormone signaling. We present evidence that the main cells of the D. melanogaster AG undergo a unique cell cycle reprogramming throughout organ development that results in step-wise cell cycle truncations culminating in cells containing two octoploid nuclei with under-replicated heterochromatin in the mature gland. We propose this tissue as a model to study developmental and hormonal temporal control of cell cycle variants in terminally differentiating tissues.

A promoter-dependent upstream activator augments CFTR expression in diverse epithelial cell types

The cystic fibrosis transmembrane conductance regulator (CFTR) gene encodes an anion-selective channel found in epithelial cell membranes. Mutations in CFTR cause cystic fibrosis (CF), an inherited disorder that impairs epithelial function in multiple organs. Most men with CF are infertile due to loss of intact genital ducts. Here we investigated a novel epididymis-selective cis-regulatory element (CRE), located within a peak of open chromatin at -9.5 kb 5′ to the CFTR gene promoter. Activation of the -9.5 kb CRE alone by CRISPRa had no impact on CFTR gene expression. However, CRISPRa co-activation of the -9.5 kb CRE and the CFTR gene promoter in epididymis cells significantly augmented CFTR mRNA and protein expression when compared to promoter activation alone. This increase was accompanied by enhanced chromatin accessibility at both sites. Furthermore, the combined CRISPRa strategy activated CFTR expression in other epithelial cells that lack open chromatin at the -9.5 kb site and in which the locus is normally inactive. However, the -9.5 kb CRE does not function as a classical enhancer of the CFTR promoter in transient reporter gene assays. These data provide a novel mechanism for activating/augmenting CFTR expression, which may have therapeutic utility for mutations that perturb CFTR transcription.

In vivo assessment of human corneal epithelial cells in orthokeratology lens wearers: A pilot study.

Central corneal epithelial thinning associated with midperipheral epithelial thickening has been reported as the main factor contributing to the effectiveness of orthokeratology (ortho-k) in myopia control. Yet, the cellular mechanism governing the regional change in refractive power remains elusive. This study aimed to evaluate the correlation between the regional change in corneal epithelial thickness and cell density in ortho-k wearers. A new human prototype of a polarization-dependent optical coherence microscope was developed to enable noncontact and noninvasive in vivo imaging of corneal epithelial cells in ortho-k wearers with and without their ortho-k lens. The epithelial thickness and cell density were evaluated at the central and midperipheral corneal locations in four ortho-k wearers and four spectacle wearers serving as controls. Polarization-dependent optical coherence microscope achieved in vivo volumetric imaging of all epithelial cell types in ortho-k wearers with and without their lens over a field of view of 0.5 × 0.5 mm2 with an isotropic resolution of ~2.2 mm. The central epithelial thinning and midperipheral epithelial thickening were consistent across all ortho-k wearers. However, the inconsistency in their regional epithelial cell density highlighted a great variability in individual response to ortho-k treatment. There was no strong correlation between epithelial thickness and cell density, especially at the midperipheral cornea, in ortho-k participants. This study constitutes our first step toward uncovering the cellular mechanism underlying the effectiveness of ortho-k in myopia control. Future studies will focus on the longitudinal evaluation of epithelial cells before and during ortho-k treatment to identify factors governing individual response to ortho-k treatment and ultimately inform the dynamics of epithelial cells taking place during the ortho-k treatment.

Abstract NG08: Dissecting and quantifying pancreatic cancer plasticity using single-cell multiomics, lineage tracing and functional genomics reveals novel mediators of therapy resistance

Abstract NG08: Dissecting and quantifying pancreatic cancer plasticity using single-cell multiomics, lineage tracing and functional genomics reveals novel mediators of therapy resistance

Tracing the origin of alveolar stem cells in lung repair and regeneration

Alveolar type 2 (AT2) cells are stem cells of the alveolar epithelia. Previous genetic lineage tracing studies reported multiple cellular origins for AT2 cells after injury. However, conventional lineage tracing based on Cre-loxP has the limitation of non-specific labeling. Here, we introduced a dual recombinase-mediated intersectional genetic lineage tracing approach, enabling precise investigation of AT2 cellular origins during lung homeostasis, injury, and repair. We found AT1 cells, being terminally differentiated, did not contribute to AT2 cells after lung injury and repair. Distinctive yet simultaneous labeling of club cells, bronchioalveolar stem cells (BASCs), and existing AT2 cells revealed the exact contribution of each to AT2 cells post-injury. Mechanistically, Notch signaling inhibition promotes BASCs but impairs club cells' ability to generate AT2 cells during lung repair. This intersectional genetic lineage tracing strategy with enhanced precision allowed us to elucidate the physiological role of various epithelial cell types in alveolar regeneration following injury.

A New Immortalized Human Lacrimal Gland Cell Line.

The lacrimal gland is crucial for maintaining ocular health by producing the aqueous component of the tear film, which hydrates and nourishes the ocular surface. Decreased production of this component results in dry eye disease, a condition affecting over 250 million people worldwide. However, the scarcity of primary human material for studying its underlying mechanisms and the absence of a cell model for human lacrimal gland epithelial cells present significant challenges. Here, we describe the generation of immortalized human lacrimal gland cell lines through the introduction of an SV40 antigen. We successfully isolated and characterized three cell clones from a female lacrimal gland donor, confirming their epithelial identity through genomic and protein analyses, including PCR, RNAseq, immunofluorescence and cultivation in a 3D spheroid model. Our findings represent a significant advancement, providing improved accessibility to investigate the molecular pathogenesis mechanisms of dry eye disease and potential therapeutic interventions. We identified the expression of typical epithelial cell marker genes and demonstrated the cells' capability to form 2D cell sheets and 3D spheroids. This establishment of immortalized human lacrimal gland cells with epithelial characteristics holds promise for future comprehensive studies, contributing to a deeper understanding of dry eye disease and its cellular mechanisms.

Comprehensive analysis of human tissues reveals unique expression and localization patterns of HSF1 and HSF2.

Heat shock factors (HSFs) are the main transcriptional regulators of the evolutionarily conserved heat shock response. Beyond cell stress, several studies have demonstrated that HSFs also contribute to a vast variety of human pathologies, ranging from metabolic diseases to cancer and neurodegeneration. Despite their evident role in mitigating cellular perturbations, the functions of HSF1 and HSF2 in physiological proteostasis have remained inconclusive. Here, we analyzed a comprehensive selection of paraffin-embedded human tissue samples with immunohistochemistry. We demonstrate that both HSF1 and HSF2 display distinct expression and subcellular localization patterns in benign tissues. HSF1 localizes to the nucleus in all epithelial cell types, whereas nuclear expression of HSF2 was limited to only a few cell types, especially the spermatogonia and the urothelial umbrella cells. We observed a consistent and robust cytoplasmic expression of HSF2 across all studied smooth muscle and endothelial cells, including the smooth muscle cells surrounding the vasculature and the high endothelial venules in lymph nodes. Outstandingly, HSF2 localized specifically at cell-cell adhesion sites in a broad selection of tissue types, such as the cardiac muscle, liver, and epididymis. To the best of our knowledge, this is the first study to systematically describe the expression and localization patterns of HSF1 and HSF2 in benign human tissues. Thus, our work expands the biological landscape of these factors and creates the foundation for the identification of specific roles of HSF1 and HSF2 in normal physiological processes.

Telocytes: current methods of research, challenges and future perspectives.

Telocytes (TCs) are CD34-positive interstitial cells that have long cytoplasmic projections, called telopodes; they have been identified in several organs and in various species. These cells establish a complex communication network between different stromal and epithelial cell types, and there is growing evidence that they play a key role in physiology and pathology. In many tissues, TC network impairment has been implicated in the onset and progression of pathological conditions, which makes the study of TCs of great interest for the development of novel therapies. In this review, we summarise the main methods involved in the characterisation of these cells as well as their inherent difficulties and then discuss the functional assays that are used to uncover the role of TCs in normal and pathological conditions, from the most traditional to the most recent. Furthermore, we provide future perspectives in the study of TCs, especially regarding the establishment of more precise markers, commercial lineages and means for drug delivery and genetic editing that directly target TCs.

Abstract 860: Pan-tissue master regulator inference reveals mechanisms of MHC alterations in cancers

Abstract Introduction: Major histocompatibility complex (MHC) genes are an integral part of the adaptive immune system. The T-cells can detect and kill cancer cells through the recognition of mutant peptides on the cell surface via the MHC. As a result, many cancers evade the immune system by altering their MHC regulation which can also lead to resistance to immune checkpoint blockade (ICB). Therefore, understanding MHC regulation in both baseline (normal state) and cancer is critical for uncovering mechanisms behind MHC alterations. Here, we have undertaken a pan-tissue evaluation to comprehensively decode MHC transcriptional regulation in healthy tissues and various cancers using a large compendium of single-cell RNA-seq (scRNA-seq) datasets. Methods: To study MHC class I (MHC-I) and MHC class II (MHC-II) transcriptional regulation at baseline we leveraged a large-scale scRNA-seq dataset encompassing 18 tissues and 124 epithelial cell types. Upon re-clustering and annotation, we investigated MHC expression across cell types and tissues and quantified its heterogeneity using the Gini coefficient. Next, we sought to identify transcription factors (TF) predictive of MHC-I and MHC-II expression, for that, we employed a master regulator inference that utilizes uni- and multi- regression models. Further, to investigate MHC and nominated TFs dysregulation in cancer, we curated a compendium of scRNA-seq datasets comprising 43 datasets, 20 cancer types, across 538 patients. Results: In normal epithelial cell types, we observed a large range (~8 fold) in MHC-I expression. We also detected MHC-II expression in unexpected cell types such as club cells in the prostate. We found that lung epithelial cells showed elevated MHC-II expression. Immunohistochemistry was performed to validate these findings. Using master regulator inference, we nominated 104 and 107 TFs which predict MHC-I and MHC-II expression, respectively. The nominated TFs showed significant enrichment (p < 0.001) for known TFs, alongside putative novel transcriptional regulators such as YBX1 (MHC-I p < 2e-16, MHC-II p = 8e-07) and XBP1 (MHC-I p < 2e-16, MHC-II p = 7e-04). Using our single-cell compendium of 20 cancer types we also observed a pan-cancer repression in MHC genes (p < 0.001). Next, we utilized an ICB cohort to identify specific TFs that could predict therapeutic benefits. Interestingly, XBP1 (p < 1e-16) and SP100 (p < 2.2e-08) were strong predictors of patients' survival. We also observed a large heterogeneity in MHC-II expression among colon cancer patients. Upon investigation, we found that patients with high MHC-II expression were mismatch repair deficient, this implicates MHC-II upregulation as an immune evasion mechanism. Conclusion: In conclusion, we have comprehensively evaluated MHC expression in 124 epithelial cell types and across 20 cancers identifying TFs predictive of MHC-I and MHC-II expression and their effects on patient outcomes. Citation Format: Mahnoor N. Gondal, Rahul Mannan, Yi Bao, Jing Hu, Marcin Cieslik, Arul M. Chinnaiyan. Pan-tissue master regulator inference reveals mechanisms of MHC alterations in cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 860.

Abstract 5323: Inflammation drives lineage plasticity and a club cell-like phenotype in prostate epithelial cells

Abstract Background: Club cells are a type of bronchiolar epithelial cell that serve a protective and antimicrobial function in the lung. An epithelial cell population in adult human prostates was recently identified as sharing a similar transcriptomic profile and morphology to lung club cells. Club-like epithelial cells were identified in the prostatic urethra, collecting ducts, and rarely in the peripheral zone of normal organ donor prostates. However, we recently reported that cells expressing club cell markers (CP, LTF, MMP7, PIGR, SCGB1A1) are present in the peripheral zone of radical prostatectomy specimens. Here, expression of club cell markers was restricted to luminal epithelial cells in an inflammation-associated lesion termed proliferative inflammatory atrophy (PIA). We also demonstrated that these club-like cells within PIA express the same markers as intermediate cells, a proposed prostate cancer progenitor cell. We now aim to identify exogenous factors that drive the club cell phenotype in vitro. Our ultimate goal is to understand how club cell gene expression affects the oncogenic and metastatic potential of prostate epithelial cells. Methods: We characterized the expression of club cell genes in prostate cell lines (LNCaP, PREC, and PREC-AR-Myc) following exposure to inflammatory stimuli (TNFα, hydrogen peroxide, uropathogenic Escherichia coli) in vitro. We performed quantitative reverse transcription PCR (RT-qPCR) to measure expression of club cell markers (LTF, MMP7, PIGR) and intermediate cell markers (AR, NKX3.1, SMOX). Additionally, we used chromogenic RNA in situ hybridization (RISH) to visualize LTF, MMP7, and PIGR expression following exposure to inflammatory stimuli. Results: We report that TNFα exposure in vitro increased expression of club cell genes (LTF, MMP7, PIGR). Surprisingly, TNFα exposure induced LTF expression in LNCaP cells, despite prior findings that LTF is silenced by CpG island hypermethylation in prostate cancer and in LNCaP cells. This finding was confirmed by both RT-qPCR and RISH. Additionally, we found that TNFα exposure altered intermediate cell markers (AR, NKX3.1, SMOX) expression consistent with the previously reported gene expression pattern of luminal epithelial cells in PIA. Conclusions: Overall, our results suggest that TNFα-mediated signaling drives the expression of club cell markers associated with lineage plasticity. Our next step will be to analyze inflammation-driven alterations to methylation and chromatin accessibility around loci associated with club cell genes, proton-oncogenes, and tumor suppressor genes. Citation Format: Megan Hess, Hanbing Song, Jessica Hicks, Luke Mummert, Angelo De Marzo, Franklin W. Huang, Karen Sfanos. Inflammation drives lineage plasticity and a club cell-like phenotype in prostate epithelial cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5323.

Disease-related non-muscle myosin IIA D1424N rod domain mutation, but not R702C motor domain mutation, disrupts mouse ocular lens fiber cell alignment and hexagonal packing.

The mouse ocular lens is an excellent vertebrate model system for studying hexagonal cell packing and shape changes during tissue morphogenesis and differentiation. The lens is composed of two types of cells, epithelial and fiber cells. During the initiation of fiber cell differentiation, lens epithelial cells transform from randomly packed cells to hexagonally shaped and packed cells to form meridional row cells. The meridional row cells further differentiate and elongate into newly formed fiber cells that maintain hexagonal cell shape and ordered packing. In other tissues, actomyosin contractility regulates cell hexagonal packing geometry during epithelial tissue morphogenesis. Here, we use the mouse lens as a model to study the effect of two human disease-related non-muscle myosin IIA (NMIIA) mutations on lens cellular organization during fiber cell morphogenesis and differentiation. We studied genetic knock-in heterozygous mice with NMIIA-R702C motor domain or NMIIA-D1424N rod domain mutations. We observed that while one allele of NMIIA-R702C has no impact on lens meridional row epithelial cell shape and packing, one allele of the NMIIA-D1424N mutation can cause localized defects in cell hexagonal packing. Similarly, one allele of NMIIA-R702C motor domain mutation does not affect lens fiber cell organization while the NMIIA-D1424N mutant proteins disrupt fiber cell organization and packing. Our work demonstrates that disease-related NMIIA rod domain mutations (D1424N or E1841K) disrupt mouse lens fiber cell morphogenesis and differentiation.

Abstract 6108: Investigation of breast tumor biology and microenvironment in women of African descent using a single cell multiomic approach

Abstract Women of African descent are at an increased risk of developing and dying from aggressive subtypes of breast cancer. A connection between aggressive disease and Western Sub-Saharan African ancestry has been postulated, but it remains largely unknown to what extent breast cancer in Africa is reminiscent of breast cancer in U.S. African American (AA) women who experience disproportionately high mortality rates. We performed ATAC- and RNA-sequencing on 9 human triple-negative breast cancer cell lines of U.S. origin and discovered that African ancestry influences the chromatin landscape, leading to disparate transcription factor (TF) activity and downstream gene expression patterns indicative of an aggressive tumor biology. Here, we describe an ambitious study that employs single-nucleus (sn) ATAC- and RNA-sequencing (snMultiome) of frozen breast tumors to characterize chromatin accessibility and gene expression patterns with single-cell resolution in AA (n=33), Kenyan (n=25), and European American (EA, n=24) women in relation to genetic ancestry, risk factor exposures, clinical characteristics, and 5-year survival. To achieve this, we successfully isolated intact, high-quality single nuclei from archival frozen breast tumor tissue through an optimized combination of enzymatic digestion and automated tissue homogenization. We performed snMultiome sequencing of 82 tumors using the 10x Genomics platform. Following filtering, normalization (SCT for snRNA; LSI for snATAC), peak calling (MACS2), and integration (Harmony), our dataset includes a total of 296,557 nuclei. Cancerous (163,419 nuclei) and non-cancerous (133,138 nuclei) cells were distinguished based on DNA copy number (CopyKat). Within the microenvironment, 11 major immune, epithelial, and stromal cell types were successfully annotated, exhibiting distinct patterns by population group (e.g. AA tumors showed markedly increased abundance of myeloid and T-cells, while Kenyan tumors showed increased abundance of pericytes and fibroblasts). A large number of enriched TFs within each cell type varied significantly by population group, suggesting distinct chromatin accessibility patterns related to genetic ancestry. Within cancerous cells, striking intra- and inter-tumoral heterogeneity was observed by genetic ancestry even within molecular subtype groups. Current efforts focus on in-depth molecular characterization of ancestry- and risk factor-related differences in the tumor epithelium and microenvironment and distinct signatures present in lethal disease. This project holds the potential to yield crucial insights into how ancestry or other factors may influence the etiology of different breast cancer subtypes, as well as produce clinically actionable biomarkers and therapeutic targets to enhance precision medicine within patient populations at high risk for aggressive disease. Citation Format: Alexandra R. Harris, Huaitian Liu, Brittany Jenkins-Lord, Tiffany H. Dorsey, Francis Makokha, Shahin Sayed, Gretchen Gierach, Stefan Ambs. Investigation of breast tumor biology and microenvironment in women of African descent using a single cell multiomic approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6108.

Abstract 1403: The role of Dclk1-expression cells in normal pancreas and in pancreatic tumor progression

Abstract Background: Tuft cells, marked by Doublecortin-like kinase-1 (Dclk1), are rare in the healthy pancreas but increase markedly during pancreatic tumorigenesis. While Group 2 innate lymphoid cells (ILC2s) are known to modulate inflammation and immunity, their specific roles in cancer-related immunity and immunotherapy interactions with pancreatic tuft cells remain unknown. Methods: To investigate tuft cells during early pancreatic neoplasia, we used a Dclk1 reporter mouse model and single-cell RNA-seq to study Dclk1-expressing cells in normal pancreas and neoplasia using Mist1/Kras mouse. We treated mice with IL-13 peptides and anti-IL-13 antibodies to explore the IL-13-ILC2 axis in tuft cell regulation. Results: Within the normal pancreas, Dclk1 expression marked several specialized epithelial cell types, including tuft-like cells, neuroendocrine cells, and a small number of acinar progenitor cells. A notable increase in Dclk1-expressing cells was observed at the onset of early PanIN lesions, with a subsequent decline in advanced PanIN stages and PDAC. Using flow cytometric analysis, we observed an increase in ILC2 cells in the Mist1/Kras pancreas in response to IL33 produced by pancreatic cancer-associated fibroblasts (CAFs). Blocking ILC2 activation with anti-IL33 antibodies reduced Dclk1 cell hyperplasia during PanIN progression. Given the known association between tuft cells, ILC2 cells, and the IL13/IL4 signaling pathways in the intestine, we discovered that Dclk1-expressing cells highly expressed the IL4 receptor (IL4ra). IL-13 levels increased during PanIN progression, and we found that ILC2s comprised the primary source of IL-13 within pancreatic tumors. In vitro, studies showed that the presence of IL-13 maintained the expansion of Dclk1-expressing tuft-like cells in pancreatic organoids derived from Dclk1-DTR-ZsGreen mice. Correspondingly, the in vivo administration of anti-IL-13 resulted in reduced Dclk1 expression. Conclusion: Previous studies have shown that pancreatic tuft cells inhibit pancreatic cancer progression. Our study reveals a novel regulatory mechanism wherein IL-13 secreted by ILC2s modulates Dclk1 tuft cell expression during pancreatic tumorigenesis. The IL13-ILC2 axis appears to be a potential therapeutic target to regulate Dclk1 cell activity, which could influence the course of pancreatic tumorigenesis. Future investigations will further explore the interaction between the IL13/ILC2 axis and Dclk1 in pancreatic cancer development. Citation Format: Giovanni Valenti, Pasquale Laise, Feijing Wu, Hiroki Kobayashi, Quin T. Waterbury, Ryota Takahashi, Tuo Ruan, Zhengyu Jiang, Yosuke Ochiai, Leah B. Zamechek, Timothy C. Wang. The role of Dclk1-expression cells in normal pancreas and in pancreatic tumor progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1403.

Abstract 5863: Double-negative prostate cancer emerges through a mixed basal, club, and hillock cell identity driven by KLF5

Abstract The purpose of this study was to characterize the phenotypes and drivers of therapy-induced lineage plasticity during the development of castration resistant prostate cancer (CRPC). While the majority of localized prostate cancer can be cured with surgery or radiation, metastatic disease is lethal. Therapies targeting the androgen receptor (AR) are initially effective, but eventually men will develop CRPC. About 70-75% of CRPC displays restored AR signaling (ARPC), while the remaining 25-30% display lineage plasticity evidenced by the emergence of AR-negative subtypes including those that display neuroendocrine (NE) markers, or double negative CRPC (DNPC) lacking both AR and NE markers. AR independent manifestations of CRPC represent a clinical challenge because no effective therapies are available and therapeutic targets are largely unknown. We analyzed publicly available bulk and single-cell RNA-seq datasets derived from clinical CRPC specimens to characterize the cellular identity of AR-negative tumors. Using a database of all known transcriptional regulators, we identified potential drivers of these phenotypes. We performed siRNA-mediated knockdown experiments in a model of DNPC to explore the extent to which the candidate regulators maintain AR-negative cell identity and sustain growth of DNPC prostate cancer cells. We identified a subset of CRPC tumors that co-express gene sets defining basal, club, and hillock cells in the benign prostate. This data supports the existence of epithelial cell lineage plasticity manifesting within CRPC tumors, as well as individual CRPC tumor cells, wherein AR-positive tumor cells transform to a phenotype encompassing basal, club, and hillock cell identities. We nominated the stem cell transcription factor KLF5 as a regulator of basal, club, and hillock cell identities in CRPC. In cell line models of DNPC, knock down of KLF5 inhibited cell growth and reduced the expression of genes defining basal, club, and hillock cell identities. This work links a prevalent and poorly-defined subtype of AR-negative CRPC to AR-negative epithelial cell types in benign prostate tissue. Inhibition of KLF5 and its downstream effectors could represent a therapeutic strategy to prevent or delay lineage plasticity and thereby extend patient response to AR-targeted therapies. Citation Format: Samuel Pitzen, Yinjie Qiu, Sarah Munro, Scott Dehm. Double-negative prostate cancer emerges through a mixed basal, club, and hillock cell identity driven by KLF5 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5863.

Abstract 4347: Cell-type specific transcriptional regulation of APOBEC3A in cancers

Abstract APOBEC3s (A-H) are a family of seven cytosine deaminases that inactivate viruses as part of the innate immune response. However, APOBEC3A and APOBEC3B have been found to mediate mutagenesis in tumor genomes by deaminating ssDNA that transiently arise during transcription and DNA replication. The mechanisms that trigger these enzymes to generate high mutation burdens in some cancers and affect disease progression and clinical outcomes are largely unknown. Here, we explored cell-type-specific transcriptional regulation of APOBEC3s using single-nucleus/cell RNA-seq (sn/scRNA-seq) data (>100 samples and >300,000 cells) from four tumor types - bladder, lung, breast, and kidney - that display different levels of APOBEC-induced mutation burden. Our analyses revealed that among seven members of the APOBEC3 family, APOBEC3A is expressed in a cell-type-specific manner. The expression was predominant in KRT13 and CDH12 epithelial cell-types and inflamed macrophages. The APOBEC3A+ epithelial cell populations were abundant in the bladder, moderate in the lung and breast, and nearly absent in the kidney tumors. APOBEC3A expression correlated with interferon and pro-inflammatory signaling in KRT13+ cells. Transcription factors ELF3 and ATF3 were significantly upregulated in APOBEC3A+ KRT13 cells. Pseudotime analysis of sn/scRNA-seq data revealed that APOBEC3A cells are in epithelial-mesenchymal transition. Finally, several gene markers defining APOBEC3A+ KRT13 cell types were identified. Ongoing analyses include investigations into clinical correlates, cell-type-specific mutation burdens, and validation through in vitro functional approaches. Our results propose that APOBEC3A is turned on in specific epithelial cell types by multiple signaling pathways during tumorigenesis, thereby driving tumor heterogeneity, particularly in high mutation-burden cancers. Citation Format: Dhanusha Yesudhas, Bilal Lone, Kelly Butler, Arup Chakraborty, Abdul Rouf Banday. Cell-type specific transcriptional regulation of APOBEC3A in cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4347.

Abstract 196: In vitro modeling of pediatric solid tumor lung metastases

Abstract Metastasis remains the main cause of death in pediatric cancer patients with the lung being one of the most common affected organs. Our inability to cure these patients is largely due to insufficient knowledge about tumor and metastatic niche plasticity, while existing models are not fully effective in mirroring the response seen in clinical setting. Our goal is to overcome these limitations by establishing in vitro lung metastasis models using tumor/lung organoid co-cultures to study lung infiltration of pediatric solid tumors. We successfully established patient-derived lung organoids from pediatric lung tissue and characterized them according to the presence and the localization of the respective lung epithelial cell types. Co-culture conditions of lung organoids with PDX-derived Ewing sarcoma and osteosarcoma cells were optimized and models established, while the establishment of models for other pediatric solid tumor entities is ongoing. We have observed infiltration of the lung organoids by tumor cells, and our preliminary findings suggest distinct patterns of infiltration among different tumor entities. Furthermore, we have performed single-cell RNA sequencing analysis on these co-cultures in comparison to the parental lung organoids and tumor cells, aiming to uncover the specific signaling pathways activated in the lung metastatic niche in response to tumor cell invasion. Additionally, experiments using conditioned medium suggest that the lung organoid secretome is sufficient to induce homing of osteosarcoma and Ewing sarcoma cells to the organoids, with the CXCL12/CXCR4 signaling axis as a prime candidate driver. To ascertain the extent to which our in vitro model recapitulates the in vivo lung metastatic niche, we performed spatial transcriptomics (using VISIUM/10X Genomics) on formalin-fixed paraffin-embedded (FFPE) tissue blocks of paired primary tumors and lung metastasis samples for Ewing sarcoma and osteosarcoma. Comprehensive data analysis is currently ongoing, which will instruct a stepwise incorporation of additional factors into our modular organoid co-culture model, resulting in a better representation of the lung metastatic niche. Further, the analysis of patient-derived material will elucidate the spatial organization of solid tumor lung metastases and contribute to the identification of signaling pathways implicated in lung infiltration. In conclusion, our study not only unravels the complexities of pediatric solid tumor metastasis, but also lays the foundation for exploring the anti-metastatic potential of pathway-specific compounds targeting tumor/lung interactions using the established in vitro lung metastasis models. This study is supported by grant 35353-B of the Austrian Science Fund. Citation Format: Martha Zylka, Christoph Hafemeister, Lukas Watzke, Ulrike Mann, Didier Surdez, E. Alejandro Sweet-Cordero, Bernadette Liegl-Atzwanger, Matthias Dettmer, Matthias Farlik, Florian Halbritter, Martin Metzelder, Heinrich Kovar, Branka Radic-Sarikas. In vitro modeling of pediatric solid tumor lung metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 196.

A map of signaling responses in the human airway epithelium

Receptor-mediated signaling plays a central role in tissue regeneration, and it is dysregulated in disease. Here, we build a signaling-response map for a model regenerative human tissue: the airway epithelium. We analyzed the effect of 17 receptor-mediated signaling pathways on organotypic cultures to determine changes in abundance and phenotype of epithelial cell types. This map recapitulates the gamut of known airway epithelial signaling responses to these pathways. It defines convergent states induced by multiple ligands and diverse, ligand-specific responses in basal cell and secretory cell metaplasia. We show that loss of canonical differentiation induced by multiple pathways is associated with cell-cycle arrest, but that arrest is not sufficient to block differentiation. Using the signaling-response map, we show that a TGFB1-mediated response underlies specific aberrant cells found in multiple lung diseases and identify interferon responses in COVID-19 patient samples. Thus, we offer a framework enabling systematic evaluation of tissue signaling responses. A record of this paper's transparent peer review process is included in the supplemental information.

Bacillus amyloliquefaciens SC06 Relieving Intestinal Inflammation by Modulating Intestinal Stem Cells Proliferation and Differentiation via AhR/STAT3 Pathway in LPS-Challenged Piglets.

Bacillus amyloliquefaciens is a well-accepted probiotic, with many benefits for both humans and animals. The ability of intestinal stem cells (ISCs) to develop into several intestinal epithelial cell types helps accelerate intestinal epithelial regeneration. Limited knowledge exists on how bacteria regulated ISCs proliferation and regeneration. Our study investigated the effects of Bacillus amyloliquefaciens supplementation on ISC proliferation and regeneration and intestinal mucosal barrier functions in piglets exposed to lipopolysaccharide (LPS). Eighteen piglets (male, 21 days old) were randomly split into 3 clusters: CON cluster, LPS cluster, and SC06+LPS cluster. On day 21, 100 μg/kg body weight of LPS was intraperitoneally administered to the SC06+LPS and LPS groups. We found SC06 supplementation maintained the intestinal barrier integrity, enhanced intestinal antioxidant capacity, reduced generation of inflammatory response, and suppressed enterocyte apoptosis against the deleterious effects triggered by LPS. In addition, our research indicated that the SC06 supplementation not only improved the ISC regeneration, but also resulted in upregulation of aryl hydrocarbon receptor (AhR) in LPS-challenge piglets. Further studies showed that SC06 also induced ISC differentiation toward goblet cells and inhibited their differentiation to intestinal absorptive cells and enterocytes. The coculture system of SC06 and ileum organoids revealed that SC06 increased the growth of ISCs and repaired LPS-induced organoid damage through activating the AhR/STAT3 signaling pathway. These findings showed that SC06, possibly through the AhR/STAT3 pathway, accelerated ISC proliferation and promoted epithelial barrier healing, providing a potential clinical treatment for IBD. Our research demonstrated that SC06 is effective in preventing intestinal epithelial damage after pathological injury, restoring intestinal homeostasis, and maintaining intestinal epithelial regeneration.