Gene Expression In Tumor Cells Research Articles

IMMU-16. ANTI-VEGF TREATMENT EFFECT AGAINST GLIOMA IS IMMUNE DEPENDENT AND MEDIATED BY ENHANCED T CELL ACTIVITY

Abstract Immunotherapy trials in glioblastoma patients increasingly avoid immunosuppressive steroids and consider bevacizumab as alternative anti-edema treatment. Since VEGF is also a potent immunosuppressive factor, we explored the dimension and mechanisms of immune-mediated effects of anti-VEGF treatment. Murine glioma cells were injected intracerebrally into C57BL/6 wild-type mice or immunodeficient Pfp/Rag2 knockout mice and animals were treated with B20 (anti-murine VEGF) or dexamethasone. Immune cells were profiled by flow cytometry, and RNAseq was performed on sorted tumor and immune cells at different timepoints. B20 prolonged the survival of immunocompetent mice but not of Pfp/Rag2 knockout mice, indicating that the immune system is essential for its effect. At an early timepoint when controls became symptomatic, B20 “early” tumors (B20-ea) showed increased infiltration with T cells and myeloid cells, and decreased vascularization, whereas B20 tumors at the survival endpoint resembled IgG-controls. Gene expression in B20-ea tumor cells was dominated by hypoxia, neural development, invasion, TGF-β, Notch and Wnt signatures as well as concerted upregulation of Kmt2 H3K4 methyltransferases. In CD11b+ myeloid cells from B20-ea tumors, M1 hallmark genes and T cell activation genes were upregulated, while M2 genes were downregulated. Deconvolution revealed a transient shift towards pro-immune microglia/macrophages as well as increased NK cells and DCs. In CD8+ and CD4+ T cells, B20 increased the expression of S1pr1 and α/β TCR genes. The proportion of progenitor-like exhausted CD8+ cells, which are responsive to PD-1 blockade, was increased in B20-ea. In CD4+ cells, B20 caused skewing towards TFH, while dexamethasone increased TH2 cytokine expression. Depletion experiments demonstrated that CD8+ and CD4+ T cells but not NK cells were necessary for the survival-prolonging effect of B20. To conclude, anti-VEGF therapy has significant immunostimulatory effects which are, however, largely transient, so that an early treatment window of opportunity may exist during which it could actively support immunotherapy.

Construction of a tumor mutational burden-derived LncRNA prognostic computational framework associated with therapy sensitivity in skin cutaneous melanoma

BackgroundSkin cutaneous melanoma (SKCM) poses a significant public health challenge due to its aggressive nature and limited treatment options. To address this, the study introduces the Tumor Mutational Burden-Derived Immune lncRNA Prognostic Index (TILPI) as a potential prognostic tool for SKCM.MethodsTILPI was developed using a combination of gene set variation analysis, differential expression analysis, and COX regression analysis. Additionally, functional experiments were conducted to validate the findings, focusing on the effects of STARD4-AS1 knockdown on SKCM tumor cell behavior. These experiments encompassed assessments of tumor cell proliferation, gene and protein expression, migration, invasion, and in vivo tumor growth.ResultsThe results demonstrated that knockdown of STARD4-AS1 led to a significant reduction in tumor cell proliferation and impaired migration and invasion abilities. Moreover, it resulted in the downregulation of ADCY4, PRKACA, and SOX10 gene expression, as well as decreased protein expression of ADCY4, PRKACA, and SOX10. In vivo experiments further confirmed the efficacy of STARD4-AS1 knockdown in reducing tumor growth.ConclusionsThis study elucidates the mechanistic role of STARD4-AS1 and its downstream targets in SKCM progression, highlighting the importance of the ADCY4/PRKACA/SOX10 pathway. The integration of computational analysis with experimental validation enhances the understanding of TILPI and its clinical implications. Overall, the findings underscore the potential of novel computational frameworks like TILPI in predicting and managing SKCM, particularly through targeting the ADCY4/PRKACA/SOX10 pathway.

Poly (ADP-Ribose) Polymerase 1 Induces Cyclic GMP-AMP Synthase-stimulator of Interferon Genes Pathway Dysregulation to Promote Immune Escape of Colorectal Cancer Cells

Colorectal cancer (CRC) ranks third globally in cancer incidence and mortality, posing a significant human concern. Recent advancements in immunotherapy are noteworthy. This study explores immune modulation for CRC treatment. Initially targeting poly (ADP-ribose) polymerase 1 (PARP-1), a gene overexpressed in CRC tissues per The Cancer Genome Atlas, we examined its correlation with immune cell infiltration using the Tumor Immune Estimation Resource tool. Quantitative reverse transcription polymerase chain reaction assessed PARP-1 mRNA and inflammation-related gene expression in tumor tissues and cells. Assessing CD8+ T-cell proliferation and cytotoxicity towards HCT116 cells involved carboxyfluorescein diacetate succinimidyl ester and lactate dehydrogenase kits. Chemotaxis was gauged using a Transwell system in a CD8+ T-cell coculture setup, with immunofluorescence revealing cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING) levels in HCT116 cells. Enzyme-linked immunosorbent assay kits measured CD8+ T-cell cytokine secretion. The findings suggested that PARP-1 was overexpressed in CRC tissues and cells and this overexpression was positively correlated with Treg cell infiltration. Overexpression of PARP-1 could significantly reduce the proportion of cGAS and STING-positive cells in HCT116 cells, dampen the proliferation, tumor-killing capacity, and chemotaxis of CD8+ T cells, and inhibit the secretion of related cytokines. The introduction of STING agonists could reverse the effects caused by overexpressed PARP-1. In vivo experiments affirmed the independent anti-tumor effects of PARP-1 inhibitors and STING agonists, synergistically inhibiting tumor growth. Silencing PARP-1 in HCT116 cells potentially boosts CD8+ T-cell activity against these cells through the cGAS-STING pathway.

PYCR1 promotes liver cancer cell growth and metastasis by regulating IRS1 expression through lactylation modification.

Liver cancer (LC) is among the deadliest cancers worldwide, with existing treatments showing limited efficacy. This study aimed to elucidate the role and underlying mechanisms of pyrroline-5-carboxylate reductase 1 (PYCR1) as a potential therapeutic target in LC. Immunohistochemistry and Western blot were used to analyse the expression of PYCR1 in LC cells and tissues. EdU assays, colony-forming assays, scratch wound healing assays, Transwell assays, nude mouse xenograft models and nude mouse lung metastasis models were used to detect the growth and metastasis abilities of LC cells. Transcriptome sequencing was used to search for downstream target genes regulated by PYCR1, and metabolomics was used to identify the downstream metabolites regulated by PYCR1. ChIP assays were used to analyse the enrichment of H3K18 lactylation in the IRS1 promoter region. We found that the expression of PYCR1 was significantly increased in HCC and that this high expression was associated with poor prognosis in HCC patients. Knockout or inhibition of PYCR1 inhibited HCC cell proliferation, migration and invasion both in vivo and in vitro. In addition, we revealed that knocking out or inhibiting PYCR1 could inhibit glycolysis in HCC cells and reduce H3K18 lactylation of the IRS1 histone, thereby inhibiting IRS1 expression. Our findings identify PYCR1 as a pivotal regulator of LC progression that influences tumour cell metabolism and gene expression. By demonstrating the potential of targeting PYCR1 to inhibit LC cell proliferation and metastasis, this study identified PYCR1 as a promising therapeutic target for LC. Pyrroline-5-carboxylate reductase 1 (PYCR1) promotes the proliferation and metastasis of liver cancer (LC) cells. The expression of PYCR1 in LC is regulated by DNA methylation. Knocking down or inhibiting PYCR1 inhibits glycolysis as well as the PI3K/AKT/mTOR and MAPK/ERK pathways in LC cells. PYCR1 regulates the transcriptional activity of IRS1 by affecting H3K18 lactylation in its promoter region.

Role and Mechanism of Lactylation in Cancer

Post translational modifications (PTMs) can change the properties of a protein by covalent addition of functional groups to one or more amino acids, and influence almost all aspects of normal cell biology and pathogenesis. Lactylation is a novel identified PTM, and has been found in both histone and non-histone proteins. Since associated with the end product of glycolysis-- lactate, lactylation modification could provide a new perspective for understanding the relationship between metabolic reprogramming and epigenetic modifications. Accumulated evidences suggest that lactylation play important roles in tumor progression and links to poor prognosis in clinical studies. Histone lactylation can affect gene expression in tumor cells and immunological cells, further promoting tumor progression and immune suppression. Lactylation on non-histone proteins can also regulate tumor progression and drug resistance. In this review, we aimed to summarize the roles of lactylation in cancer progression, microenvironment interactions and immune suppression, try to identify new molecular targets for cancer therapy and provide a new direction for combined targeted therapy and immunotherapy. .

CircRNA hsa_circ_0069,399 as a potential clinical prognostic marker in laryngeal squamous cell carcinoma

ObjectiveCircular RNAs (circRNAs) significantly influence the invasion, metastasis, gene expression, proliferation, and apoptosis of tumor cells. However, the roles of circRNAs in laryngeal squamous cell carcinoma (LSCC) remain largely unexplored. This study aims to examine circRNA expression patterns in LSCC and adjacent non-tumorous tissues, with the goal of uncovering potential biomarkers for LSCC. MethodsTissue samples were collected from both the tumor and adjacent normal tissues of ten patients who had undergone surgical resection. The profiling of circRNAs was conducted through transcriptomic sequencing and analytical bioinformatics approaches. A ternary regulatory network based on the competitive endogenous RNA (ceRNA) hypothesis was established, linking target circRNAs to clinical immunohistochemical parameters for comparison. Verification of target circRNAs in LSCC tissues was performed using quantitative real-time PCR (RT-qPCR), whereas target mRNAs were analyzed through immunohistochemistry. ResultsA total of 126 significantly different circRNAs were identified, including 40 up-regulated genes and 86 down-regulated genes. Furthermore, 92 circRNA-miRNA-mRNA regulatory relationship axes related to clinical immunohistochemical indicators were found based on 5 candidate circRNAs. Interestingly, all axes related to the target genes MKI67 and TP53 were found to compete with the same circRNA: hsa_circ_0069,399. Further verification confirmed that the hsa_circ_0069,399 expression was overtly upregulated in tumor tissues from LSCC patients, which was consistent with the sequencing results. Conclusionhsa_circ_0069,399 could be a potential prognostic marker for LSCC.

Longitudinal molecular profiling elucidates immunometabolism dynamics in breast cancer

Although metabolic reprogramming within tumor cells and tumor microenvironment (TME) is well described in breast cancer, little is known about how the interplay of immune state and cancer metabolism evolves during treatment. Here, we characterize the immunometabolic profiles of tumor tissue samples longitudinally collected from individuals with breast cancer before, during and after neoadjuvant chemotherapy (NAC) using proteomics, genomics and histopathology. We show that the pre-, on-treatment and dynamic changes of the immune state, tumor metabolic proteins and tumor cell gene expression profiling-based metabolic phenotype are associated with treatment response. Single-cell/nucleus RNA sequencing revealed distinct tumor and immune cell states in metabolism between cold and hot tumors. Potential drivers of NAC based on above analyses were validated in vitro. In summary, the study shows that the interaction of tumor-intrinsic metabolic states and TME is associated with treatment outcome, supporting the concept of targeting tumor metabolism for immunoregulation.

Abstract RF01-02: A randomized Phase I pre-operative window trial of transdermal endoxifen in women planning mastectomy: evaluation of dermal safety, intra-mammary drug distribution, and biologic effects

Abstract Background: Breast cancer prevention requires only local exposure of the breast to active drug but oral preventive agents entail systemic exposure, with resultant adverse effects, limiting acceptance by high-risk women. Drug-delivery through the breast skin is an attractive option, but requires demonstration of dermal safety and drug distribution throughout the breast. We formulated the tamoxifen metabolite (E/Z)-endoxifen in a hydroalcoholic/oleic acid gel for transdermal delivery. We tested this in a placebo-controlled, double-blinded Phase I trial with dose escalation from 10 to 20 mg daily and evaluated dermal safety, intra-mammary drug distribution, and biologic effects in DCIS or invasive cancers. Methods: Women planning mastectomy for therapy for Stage 0-III breast cancer, or surgical risk reduction (N=32) were randomized (2:1) to placebo-gel or endoxifen-gel applied to the skin of both breasts for 3-5 weeks. Our primary endpoint, dermal safety was evaluated using the modified NCI Common Terminology Criteria for Adverse Events version 4. Endoxifen concentration, and modulation of circulating tamoxifen biomarkers were evaluated to demonstrate minimal systemic effects. Plasma and tissue concentration of endoxifen were determined using Liquid Chromatography – Tandem Mass Spectrometry. Tamoxifen-responsive circulating markers, insulin-like growth factor 1 (IGF1) and sex hormone-binding globulin (SHBG), were measured with enzyme-linked immunosorbent assays. Finally, we explored anti-cancer efficacy in tumors by measuring the modulation of tumor cell proliferation (Ki67 labeling index) and gene expression associated with tamoxifen response in proliferation (BIRC5, MKI67, MYBL2, CCNB1, AURKA), cell cycle (UBE2C, PLK1, CEP55, CDK1, RRM2, TOP2A, PTTG1), cancer-associated stromal genes of invasion (FN1, SERPINH1, PLOD2, PDGFA, ITGAV) and extracellular matrix (COL11A1, SPP1, COMP, BGN). Within-participant changes between baseline and post-treatment were assessed using the Wilcoxon signed rank test. Differences between treatment arms were assessed using the Wilcoxon rank sum test and the Kruskal-Wallis test. Results: endoxifen-gel at both doses incurred no dermal or systemic toxicity nor change in circulating biomarkers (IGF1, SHBG) compared to placebo. All treated breasts contained endoxifen at each of five sampling locations; the median per-person tissue concentration in the treated participants was 0.6 ng/g (IQR 0.4-1.6), significantly higher (p < 0.001) than the median plasma concentration (0.2 ng/mL, IQR 0.2-0.2). The median ratio of the more potent (Z)-isomer to (E)-isomer at each breast location was 1.5 (IQR 0.96-2.54, p < 0.05). We observed non-significant overall reduction in tumor Ki67 LI (median change -1.7 with IQR -5.8, 3.6) and gene expression of MKI67 and the genes associated with proliferation, and cell cycle. However, downregulation of invasion signature genes (FN1, SERPINH1, PLOD2, PDGFA, ITGAV) was significant (p=0.03) and a cluster of six participants demonstrated a consistent reduction of MKI67 and multiple gene signatures suggesting the possibility that their tumors might be early responders to low endoxifen exposure within 3 to 4 weeks of treatment. Conclusions: our evaluation of transdermal (E/Z) endoxifen 10 and 20 mg in hydroalcoholic/oleic acid formulation demonstrates lack of early dermal toxicity, and good tolerability over a month or so of therapy. Our findings warrant development of transdermal formulations of (Z)-endoxifen with better dermal permeation for a Phase 2 breast cancer prevention trial compared to low-dose oral SERMs so that women at high-risk for breast cancer may have a range of cancer prevention options available to them. Citation Format: Oukseub Lee, Latifa Bazzi, Yanfei Xu, Erik Pearson, Minhua Wang, Omid Hosseini, Azza Akasha, Jennifer Choi, Masha Kocherginsky, Kelly Benante, Thomas Helland, Gunnar Mellgren, Eileen Dimond, Marjorie Perloff, Brandy Heckman-Stoddard, Seema Khan, Scott Karlan, Melissa Pilewskie. A randomized Phase I pre-operative window trial of transdermal endoxifen in women planning mastectomy: evaluation of dermal safety, intra-mammary drug distribution, and biologic effects [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr RF01-02.

Abstract 3985: Immune-competent “NoGlow” transgenic mice overcome restrictive tolerance to multiple xenoantigens and simultaneously permit identification, tracking, and temporal gene expression in tumor cells

Abstract The ability to temporally regulate gene expression and track labeled cells make animal models powerful biomedical tools. However, sudden exposure to xenobiotic genes (e.g. GFP, luciferase (luc), or rtTA3) triggers inadvertent immune responses that can significantly suppress foreign gene expression or result in complete rejection of transplanted cells. Although germline expression of foreign genes somewhat addresses these challenges, native fluorescence and bioluminescence abrogates their utility as cellular reporters and spatiotemporally restricted expression can lead to suboptimal xenoantigen tolerance. Even in endogenous cancer models, we find that the means of tissue-directed expression of the same foreign gene yield significant differences in overall tolerance. Thus, the degree of tolerance to foreign genes strongly impacts the utility of different genetic modification and can strongly influence experimental outcomes and interpretations. To overcome these unwanted immune responses and enable reliable cell tracking/gene regulation, we developed a novel mouse model that selectively expresses antigen-intact but non-functional forms of GFP, luc, and rtTA3. These "NoGlow" mice possess no detectable background fluorescence or luminescence and mount limited adaptive immune responses against transgenic xenoantigens even after vaccination. Furthermore, we demonstrate that NoGlow mice allow tracking and tetracycline inducible gene regulation of triple-transgenic cells expressing GFP/luc/rtTA3, in contrast to transgene-negative immune competent mice which completely eliminate these cells. Notably, this model enables de novo metastasis from orthotopically implanted, triple-transgenic tumor cells, despite high xenoantigen expression. Finally, we observed model and sex-based differences in immune tolerance to the encoded xenoantigens after activation by different tissue-specific CREs, illustrating the obstacles of tolerizing animals to foreign genes and validating the utility of NoGlow mice to dissect the mechanisms of central and peripheral tolerance. Altogether, the NoGlow model provides a critical resource for in vivo studies across multiple disciplines, including oncology, developmental biology, infectious disease, autoimmunity, and transplantation. Citation Format: Timothy N. Trotter, Andrea Wilson, Jason McBane, Carina Dagotto, Xiao Yang, Junping Wei, Gangjun Lei, Hannah Thrash, H. Kim Lyerly, Zachary Hartman. Immune-competent “NoGlow” transgenic mice overcome restrictive tolerance to multiple xenoantigens and simultaneously permit identification, tracking, and temporal gene expression in tumor 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 3985.

Abstract 293: Distinctive roles of mammary adipomes in breast cancer progression: Insights from functional analysis and differential gene expression

Abstract Breast Cancer (BC) is a heterogeneous disease that impacts treatment response. This is due in part to the tumor microenvironment (TME), which contributes significantly to BC pathogenesis, including metastasis. Women with higher breast density and reduced breast fat face an increased BC risk across multiple tumor subtypes. This is exemplified by the correlation between increased tumor progression, the appearance of fibrosis and the loss of mature adipocytes. While the role of adipokines in this process has been studied extensively, the contribution of adipocyte-derived extracellular vesicles (EV) or "adipomes" in tumorigenesis and metastasis remains poorly understood. To address this question, we developed a novel technique for isolating intact adipomes from normal mammary fat (MF) obtained from wild-type C57BL/6 mice as well as from tumor-associated MF (TAMF) obtained from mice inoculated orthotopically with EO771 mammary tumor cells. Adipome isolation involved high-speed centrifugation to separate macro- and micro-vesicles, purification using the ExoQuick EV isolation system, and immunomagnetic capture of adipomes. Characterization of adipomes by transmission electron microscopy revealed two adipome populations, large L-adipomes of ~350 nm, and small S-adipomes of ~40 nm. Notably, the quantity of L-adipomes in tumor-associated mammary fat (TAMF) was 10-fold greater than the amount of L-adipomes in the MF of non-tumor-bearing mice. To identify possible functional roles of L-adipomes in the pathogenesis of BC, lipidomic profiling was undertaken. L-Adipomes from TAMF showed significantly altered lipid species in comparison to MF-derived L-adipomes. Adipomes were further characterized by treating EO771 cells for 72 hr with TAMF- or MF-derived adipomes at a cell to adipome ratio of 1:10, followed by RNAseq analysis. Differentially upregulated genes in TAMF-derived L-adipomes included Esr1, Erbb2, Tgfb1, Bcl2, MMP2, and Notch associated with fibrosis, EMT, angiogenesis and invasion and downregulation of genes linked to tumor suppression, apoptosis, and mitochondrial metabolism. Overall, our study illustrates the importance of tumor-associated adipomes in regulating gene expression in tumor cells, which emphasizes the specificity of adipome content relating to the cell-of-origin and the host's pathologic and metabolic state and in modulating signaling pathways involved in BC progression. Citation Format: Hariprasad Thangavel, Kezia Lizardo, Robert I. Glazer, Jyothi F. Nagajyothi. Distinctive roles of mammary adipomes in breast cancer progression: Insights from functional analysis and differential gene expression [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 293.

Abstract 2660: CXCL9/10 is critical for immunotherapeutic efficacy by recruiting and activating T lymphocytes in tumor microenvironment

Abstract Background: Tumor immunotherapies targeting PD-(L)1 exhibit anti-tumor efficacy in only about 20% of patients with a variety of cancers. Literature has demonstrated that “hot tumor” which contains high T lymphocytes in tumor microenvironment exhibits a better response to immunotherapies than “cold tumor”. Therefore, we hypothesize that T lymphocyte-recruited factors play the roles determining the immunotherapeutic efficacy, including CXCL9, 10, and 11, which are located in human chromosome 4 with consistent co-expression and protein structure. Aims: The aim of this study is to investigate whether CXCL9/10 is critical in determining the anti-PD-(L)1 immunotherapeutic efficacy. Methods: GEPIA, cBioPortal, and Kaplan-Meier Plotter were used to investigate the gene expression, co-expression, and immunotherapeutic association for CD274 (PD-L1), ICAM1, and CXCL9/10 in lung, colon, and liver cancers. qPCR and flow cytometry were used to detect the gene expression in tumor cells and T lymphocytes, particularly comparing the differences between LL/2 and CT26 cells whereas LL/2 is immunotherapy-resistant and CT26 is immunotherapy-sensitive. CD8+ T cell transwell assay and qPCR were used to measure the function of CXCL10 on CD8+ T cell migration and activation, whereas IFNγ and IL-2 as the activation markers. Results: We found that CXCL9/10 overexpressed in a variety of tumors, including lung, colon, and liver tumors with a correlation with PD-L1. However, PD-L1 was not overexpressed in most tumors. High PD-L1 and CXCL10 are basically associated with better survival rates in tumor patients receiving immunotherapies. Correlation analysis revealed that IRF-1 and STAT1 were correlated with PD-L1 and CXCL10 expression in lung cancer. Since literature has indicated that LL/2-derived syngeneic tumor exhibits immunotherapy-resistant and CT26 exhibits immunotherapy-sensitive, we further compared the gene expression between them. We found that IFNA, IFNG, CXCL10, and PD-L1 all expressed higher levels in CT26 cells than LL/2. Moreover, we found that T lymphocytes specifically expressed high CXCR3, a receptor of CXCL9/10, including CD4+ T and CD8+ T cells by flow cytometry. As expected, CD8+ T cells can be recruited in a transwell assay by IFNα and CXCL9. In addition, we found that IFNα induced CXCL10 expression in monocytes and CXCL10 increased activation markers IFNγ and IL-2 in CD4+ T and CD8+ T cells. Conclusions: This study revealed that CXCL9/10 expression is correlated with PD-L1 in tumors, resulting in better immunotherapeutic efficacy. The evidence demonstrated that CT26 intrinsically exhibited higher IFNs and CXCL9/10 compared to LL/2. Therefore, CXCL9/10 potentially recruits and activates CD8+ T cells to tumor microenvironment, transferring “cold tumor” to “hot tumor”. This study indicates that CXCL9/10 is critical for immunotherapeutic efficacy. Citation Format: Chun-Chia Cheng, Jungshan Chang, Zong-Lin Sie, Ai-Sheng Ho, Cheng-Liang Peng, Chun-Chao Chang. CXCL9/10 is critical for immunotherapeutic efficacy by recruiting and activating T lymphocytes in tumor microenvironment [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 2660.

Abstract 5493: Digital spatial profiling of MC38 colon carcinoma following checkpoint inhibition

Abstract Immunotherapy aims to bolster the immune response within the tumor microenvironment (TME). However, checkpoint inhibitors utilized in the treatment of colon carcinoma have demonstrated efficacy only in certain patients. To develop more effective therapeutics, strategies that navigate the heterogeneous nature of the TME must be employed. The MC38 tumor model, known for its immunologically active characteristics and responsiveness to certain immunotherapies, is widely used for preclinical drug development. Furthermore, elevated levels of pan-cytokeratin (PanCK) expression in tumors have shown an association with diminished survival rates among colon carcinoma patients. In this study, we used the GeoMx® DSP platform (NanoString Technologies) to investigate the spatial expression profile of PanCK in MC38 tumors and analyze the impact that PanCK expression exerts on anti-PD-1 induced gene expression in tumor and immune cells. To this end, C57BL/6J female mice were implanted with MC38 cells, enrolled into groups, and treated with anti-PD-1 antibody. Tumor growth was monitored by caliper measurements and anti-PD-1 produced minimal responses with a Day 22 median % Delta T/C value of 88%. For DSP analysis, tumors were collected 10 days post-treatment, formalin fixed for paraffin embedding, and then sectioned for PanCK and CD45 protein visualization. Regions of interest were drawn to create a matrix analysis that defined regions with high or low PanCK expression, that were proximal or distal to CD45+ immune rich regions of the tumor. A segmentation algorithm was applied to examine gene expression within each region using the GeoMx Mouse Whole Transcriptome Atlas. Cluster analysis revealed an enrichment of apoptosis and autophagy gene sets in tumor cells that were proximal to immune rich regions. In the CD45+ segment, immune cells adjacent to high PanCK-expressing cells contained 318 genes with significantly increased expression levels when compared to low PanCK-expressing cells, and only 11 genes with decreased expression levels. The upregulated genes were enriched for numerous biomarkers of T cell recruitment and activation, including cd3, cd8, cxcr3, ccl5, cxcl9, icos, and cd27. Next, we conducted a linear mixed model analysis to examine the impact of PanCK expression on anti-PD-1 induced gene regulation. Notably, an enrichment of genes that code for T cell exhaustion biomarkers was observed in immune cells near PanCK high expressing cells, including ctla4, slamf7, tigit, and lag3. In summary, the most pronounced transcriptomic changes occurred within immune cells situated near tumor cells displaying high PanCK expression and suggest that PanCK expression correlates directly with T cell recruitment and activation but also exhaustion. Furthermore, these data emphasize the significance of spatial analysis as a valuable component of preclinical research, as demonstrated in MC38 tumor model. Citation Format: Priyanka Singh, Daniel Saims, Sheri Barnes, David Draper. Digital spatial profiling of MC38 colon carcinoma following checkpoint inhibition [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 5493.

Abstract 1577: Cancer associated fibroblast - tumor cell crosstalk enhances epithelial to mesenchymal transition and promotes a classical to basal switch in human pancreatic ductal adenocarcinoma

Abstract Introduction: Cancer associated fibroblasts (CAF) drive a complex tumor microenvironment (TME) in pancreatic ductal adenocarcinoma (PDAC) through incompletely understood interactions. Two major CAF subtypes, myofibroblastic (myCAF) and inflammatory (iCAF), dominate the tumor landscape and have been defined by gene expression profiles. There is significant plasticity between subtypes and alterations in CAF behavior likely drive changes in tumorigenicity and immune evasion. Additionally, PDAC tumor cells usually present with a predominant classical or basal phenotype that is associated with clinical outcomes. We hypothesized that CAF phenotype impacts tumor cell gene expression and alters the clinically-relevant tumor subtyping. Methods: We interrogated cellular crosstalk in the PDAC TME using a novel three-dimensional, patient-matched coculture system of patient-derived organoids (PDO) and CAFs, established from 12 patients undergoing surgical resection. Molecular characterization included bulk RNA sequencing, proteome profiling (107 factor), flow cytometry, multiplex RNA Scope, imaging mass cytometry (IMC), and RT-qPCR. Results: PDO gene expression analysis from bulk RNAseq demonstrated CAF coculture induced phenotypic shifts in the Moffitt subtype from a classical to a basal phenotype. Further, CAF coculture enhanced epithelial to mesenchymal transition (EMT) across all patients, even those with a baseline basal phenotype. We hypothesized this could be due to both cell-cell crosstalk and secreted factors. We therefore treated PDO with CAF-conditioned media (CM) and demonstrated that CM is sufficient to drive the observed classical-to-basal shift by RT-qPCR. Secretome analysis of CM derived from 3 CAF lines identified HGF, FGF19, and IL-8 as factors contributing to this transcriptional change. Next, we used spatial - omics (transcriptomics and proteomics) to examine the validity of these findings in source patient tissue. Using RNA Scope, we discovered distinct tumor neighborhoods expressing basal mRNAs KRT17 and KRT6a surrounded by CAFs compared to those expressing classical genes TFF1 and GATA6. We then used IMC to further explore CAF subtypes in patient tumors and found FAP+ myCAF regions corresponded to basal tumor regions, while CXCL12+ iCAFs were found in classical regions. Conclusions: PDAC tumor biology is likely driven by interactions between cancer cells and CAFs. Potential mediators of these interactions include both cell-cell contact and secreted factors. We introduce a novel approach combining in vitro coculture with tissue-based assays, demonstrating that modern culture techniques preserve cell type heterogeneity and plasticity. Together, these data demonstrate that a CAF-rich TME drives tumor cell plasticity not only towards EMT but also a more basal disease phenotype. Citation Format: Samantha Guinn, Brayan Perez, Jignasha Patel, Jae Lee, Daniel Zabransky, Won Ho, Elana J. Fertig, Emma Kartalia, Joseph Tandurella, Richard Burkhart, Jacquelyn W. Zimmerman, Elizabeth Jaffee. Cancer associated fibroblast - tumor cell crosstalk enhances epithelial to mesenchymal transition and promotes a classical to basal switch in human pancreatic ductal adenocarcinoma [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 1577.

Increased stiffness of extracellular matrix enhanced chemoresistance in 3D-bioprinted ovarian cancer model

Ovarian cancer is a gynecological malignancy with a high mortality rate. The ovarian cancer microenvironment is a crucial factor affecting the overall and progression-free survival rates of patients with ovarian cancer. The biophysical factors of the tumor microenvironment, such as stiffness, can affect the gene expression and behavior of tumor cells. In this study, we utilized 3D bioprinting technology to construct ovarian cancer tumor models with varying levels of stiffness in vitro to investigate the effect of extracellular matrix stiffness on drug resistance of tumor cells. Our findings indicate that increasing the stiffness of extracellular matrix can attenuate the sensitivity of tumor cells to chemotherapeutic agents. Additionally, the increased stiffness of 3D tumor model may promote malignant phenotypes, such as tumor stemness and tumor progression.

Influences of probiotics and gut microbiota on immunomodulation for the treatment of patients with cancer: a systematic review

Introduction: Immunomodulation and immunostimulation are the main mechanisms of action of probiotics in the fight against cancer. Objective: It was to carry out a systematic review of the influences of probiotics and gut microbiota on immunomodulation for the treatment of cancer patients. Methods: The PRISMA Platform systematic review rules were followed. The research was carried out from September to October 2023 in the Web of Science, Scopus, PubMed, Science Direct, Scielo, and Google Scholar databases. The quality of the studies was based on the GRADE instrument and the risk of bias was analyzed according to the Cochrane instrument. Results and Conclusion: A total of 125 articles were found, and 35 articles were evaluated in full and 18 were included and developed in the present systematic review study. Considering the Cochrane tool for risk of bias, the overall assessment resulted in 45 studies with a high risk of bias and 15 studies that did not meet GRADE and AMSTAR-2. Most studies showed homogeneity in their results, with X2=55.4%>50%. It was concluded that probiotics suppress inflammation by inhibiting several signaling pathways and reducing the global activation of NF-κβ and the production of pro-inflammatory cytokines. Probiotics influence receptor antagonism, receptor expression, binding and expression of adapter proteins, expression of negative regulatory signal molecules, and mainly the induction of microRNAs. These microRNAs can modulate the gene expression of tumor cells together with regulatory T cells that have important functions in the tumor microenvironment, mainly in inducing immune evasion. Some modulatory effects of probiotics include the production of cytokines by epithelial cells, increased mucin secretion and phagocytosis and NK cell activity, activation of T and NKT cells, stimulation of IgA production, and decreased proliferation of T cells. The gut microbiota has a major impact on the systemic immune system. The specific microbiota controls cell differentiation in which CD4+ T cells (Th17 cells) secrete IL-17. The presence of Th17 cells and regulatory T cells is associated with the gut microbiota.

TIE1 promotes cervical cancer progression via Basigin-matrix metalloproteinase axis.

Background: Tyrosine kinase with immunoglobulin and EGF-like domains 1 (TIE1) is known as an orphan receptor prominently expressed in endothelial cells and participates in angiogenesis by regulating TIE2 activity. Our previous study demonstrated elevated TIE1 expression in cervical cancer cells. However, the role of TIE1 in cervical cancer progression, metastasis and treatment remains elusive. Methods: Immunohistochemistry staining for TIE1 and Basigin was performed in 135 human cervical cancer tissues. Overexpressing vectors and siRNAs were used to manipulate gene expression in tumor cells. Colony formation, wound healing, and transwell assays were used to assess cervical cancer cell proliferation and migration in vitro. Subcutaneous xenograft tumor and lung metastasis mouse models were established to examine tumor growth and metastasis. Co-Immunoprecipitation and Mass Spectrometry were applied to explore the proteins binding to TIE1. Immunoprecipitation and immunofluorescence staining were used to verify the interaction between TIE1 and Basigin. Cycloheximide chase assay and MG132 treatment were conducted to analyze protein stability. Results: High TIE1 expression was associated with poor survival in cervical cancer patients. TIE1 overexpression promoted the proliferation, migration and invasion of cervical cancer cells in vitro, as well as tumor growth and metastasis in vivo. In addition, Basigin, a transmembrane glycoprotein, was identified as a TIE1 binding protein, suggesting a pivotal role in matrix metalloproteinase regulation, angiogenesis, cell adhesion, and immune responses. Knockdown of Basigin or treatment with the Basigin inhibitor AC-73 reversed the tumor-promoting effect of TIE1 in vitro and in vivo. Furthermore, we found that TIE1 was able to interact with and stabilize the Basigin protein and stimulate the Basigin-matrix metalloproteinase axis. Conclusion: TIE1 expression in cervical cells exerts a tumor-promoting effect, which is at least in part dependent on its interaction with Basigin. These findings have revealed a TIE2-independent mechanism of TIE1, which may provide a new biomarker for cervical cancer progression, and a potential therapeutic target for the treatment of cervical cancer patients.

Spatial transcriptomic interrogation of the tumour-stroma boundary in a 3D engineered model of ameloblastoma

Stromal cells are key components of the tumour microenvironment (TME) and their incorporation into 3D engineered tumour-stroma models is essential for tumour mimicry. By engineering tumouroids with distinct tumour and stromal compartments, it has been possible to identify how gene expression of tumour cells is altered and influenced by the presence of different stromal cells. Ameloblastoma is a benign epithelial tumour of the jawbone. In engineered, multi-compartment tumouroids spatial transcriptomics revealed an upregulation of oncogenes in the ameloblastoma transcriptome where osteoblasts were present in the stromal compartment (bone stroma). Where a gingival fibroblast stroma was engineered, the ameloblastoma tumour transcriptome revealed increased matrix remodelling genes. This study provides evidence to show the stromal-specific effect on tumour behaviour and illustrates the importance of engineering biologically relevant stroma for engineered tumour models. Our novel results show that an engineered fibroblast stroma causes the upregulation of matrix remodelling genes in ameloblastoma which directly correlates to measured invasion in the model. In contrast the presence of a bone stroma increases the expression of oncogenes by ameloblastoma cells.

The Role of microRNAs in Gene Expression and Signaling Response of Tumor Cells to an Acidic Environment

Many tumors are characterized by marked extracellular acidosis due to increased glycolytic metabolism, which affects gene expression and thereby tumor biological behavior. At the same time, acidosis leads to altered expression of several microRNAs (Mir7, Mir183, Mir203, Mir215). The aim of this study was to analyze whether the acidosis-induced changes in cytokines and tumor-related genes are mediated via pH-sensitive microRNAs. Therefore, the expression of Il6, Nos2, Ccl2, Spp1, Tnf, Acat2, Aox1, Crem, Gls2, Per3, Pink1, Txnip, and Ypel3 was examined in acidosis upon simultaneous transfection with microRNA mimics or antagomirs in two tumor lines in vitro and in vivo. In addition, it was investigated whether microRNA expression in acidosis is affected via known pH-sensitive signaling pathways (MAPK, PKC, PI3K), via ROS, or via altered intracellular Ca2+ concentration. pH-dependent microRNAs were shown to play only a minor role in modulating gene expression. Individual genes (e.g., Ccl2, Txnip, Ypel3) appear to be affected by Mir183, Mir203, or Mir215 in acidosis, but these effects are cell line-specific. When examining whether acid-dependent signaling affects microRNA expression, it was found that Mir203 was modulated by MAPK and ROS, Mir7 was affected by PKC, and Mir215 was dependent on the intracellular Ca2+ concentration. Mir183 could be increased by ROS scavenging. These correlations could possibly result in new therapeutic approaches for acidotic tumors.

Important Role for Glutamine in Human and Mouse TME Models of CLL ; Towards Development of a PET Tracer As a Novel Diagnostic Tool

The amino acid transporter ASCT2, encoded by the gene SLC1A5, is the main glutamine importer in proliferating human and mouse cells. We recently showed that glutamine is the main fuel of the tricarboxylic acid (TCA) cycle in cells from chronic lymphocytic leukemia (CLL) patients, and that blocking its import attenuated CD40/BCR-induced venetoclax (VEN) resistance 1. In the current study, we have investigated the role of ASCT2 and the consequences of its inhibition in human and mouse CLL cells and in healthy lymphocytes by flow cytometry, gene expression analysis, extracellular flux analysis, metabolomics, CRISPR/Cas9 gene editing and adoptive-cell transfer experiments. To enable in vivo assessment of ASCT2 in the future with Positron Emission Tomography (PET), we have explored the potential use of 18F-labelelled ( 2S,2R)-4-fluoroglutamine (4- 18F]FGln) 2 as PET tracer. Increased expression of ASCT2 upon PMA/ionomycin stimulation was observed in healthy B and T cells. In BCR/CD40-stimulated CLL cells, the increased expression was irrespective of IGHV status. We dissected the main routes of glutamine usage in CD40- and BCR-stimulated CLL cells and found that in addition to its role in the TCA cycle, glutamine import is linked to mTOR signaling. The ASCT2 inhibitor V9302 impaired mTOR signaling and decreased translation of new proteins, including the anti-apoptotic proteins Bcl-XL and Mcl-1. Of relevance for therapeutic approaches, the effector and proliferative capacity of human T cells was preserved upon V9302 treatment. This suggests that blocking ASCT2 will not affect immune responses. The SLC1A5 gene was deleted by CRISPR/Cas9 technique in murine TCL1 cells 3. Adoptive cell transfer experiments of SLC1A5-KO and WT TCL1 cells injected at 50-50% ratio in recipient mice showed selective outgrowth of SLC1A5-WT cells, with no detection of the SLC1A5-KO in the spleen of overt leukemic mice. This indicates that TCL1 leukemic cells rely on SLC1A5/ASCT2 for growth. Finally, we explored the high expression of ASCT2 and glutamine addiction in CLL from the diagnostic perspective. With the aim of improving the currently suboptimal [ 18F]FDG PET for imaging of CLL LN sites 4, we successfully synthesized 4-[ 18F]FGln. We observed uptake in CD40-stimulated CLL cells, which was decreased in the presence of V9302. Experiments to perform PET with 4-[ 18F]FGln in TCL1 mice to demonstrate an in vivo proof of concept are ongoing. Overall, these data support a crucial role for ASCT2 and glutamine in leukemia development and VEN resistance in CLL. This provides a basis for targeting the transporter for therapeutic options and/or taking advantage of its function for diagnostic approaches using 4-[ 18F]FGln as PET tracer. 1. Chen, Z. et al. Characterization of metabolic alterations of chronic lymphocytic leukemia in the lymph node microenvironment. Blood140, 630-643, doi:10.1182/blood.2021013990 (2022). 2. Qu, W. et al. Synthesis of optically pure 4-fluoro-glutamines as potential metabolic imaging agents for tumors. J Am Chem Soc133, 1122-1133, doi:10.1021/ja109203d (2011). 3. Nardi, F. et al. Assessing gene function in human B cells: CRISPR/Cas9-based gene editing and mRNA-based gene expression in healthy and tumor cells. Eur J Immunol52, 1362-1365, doi:10.1002/eji.202149784 (2022). 4. Rhodes, J. M. & Mato, A. R. PET/Computed Tomography in Chronic Lymphocytic Leukemia and Richter Transformation. PET Clin14, 405-410, doi:10.1016/j.cpet.2019.03.007 (2019).

SCAR: Single-cell and Spatially-resolved Cancer Resources.

Advances in sequencing and imaging technologies offer a unique opportunity to unravel cell heterogeneity and develop new immunotherapy strategies for cancer research. There is an urgent need for a resource that effectively integrates a vast amount of transcriptomic profiling data to comprehensively explore cancer tissue heterogeneity and the tumor microenvironment. In this context, we developed the Single-cell and Spatially-resolved Cancer Resources (SCAR) database, a combined tumor spatial and single-cell transcriptomic platform, which is freely accessible at http://8.142.154.29/SCAR2023 or http://scaratlas.com. SCAR contains spatial transcriptomicdata from 21 tumor tissues and single-cell transcriptomic data from 11 301 352 cells encompassing 395 cancer subtypes and covering a wide variety oftissues, organoids, and cell lines. This resource offers diverse functional modules to address key cancer research questions at multiple levels, including the screening of tumor cell types, metabolic features, cell communication and gene expression patterns within the tumor microenvironment. Moreover, SCAR enables the analysis of biomarker expression patterns and cell developmental trajectories. SCAR also provides a comprehensive analysis of multi-dimensional datasets based on 34 state-of-the-art omics techniques, serving as an essential tool for in-depth mining and understanding of cell heterogeneity and spatial location. The implications of this resource extend to both cancer biology research and cancer immunotherapy development.