Tumor Slices Research Articles

The Impact of Spliceosome Inhibition in SF3B1-Mutated Uveal Melanoma.

Unfortunately, treatment of patients with uveal melanoma (UM) with metastatic disease is limited. Twenty percent of patients with UM harbor a mutation in the splicing factor gene SF3B1, suggesting that aberrant spliceosome function plays a vital role in tumorigenesis. Splicing inhibitors exploit the preferential sensitivity of spliceosome-compromised leukemic cells to these compounds. We studied the effect of the splicing inhibitor E7107 using two UM cell lines and ex vivo cultured SF3B1- and BAP1-mutated primary UM tumor slices. These UM cell lines and ex vivo tumor slices were exposed for 24 hours to different concentrations of E7107. Tumor slices were stained with hematoxylin and eosin (H&E) and incubated with BAP1, MelanA, MIB-1, and caspase-3 antisera. The E7107-exposed UM cell lines exhibited decreased cell viability and increased apoptosis, with the greatest effect on SF3B1-mutated UM cells. A similar effect on UM tumor slices was observed upon exposure to E7107. Additionally, RNA was isolated for differential isoform expression analysis. No significant difference in isoform usage was found genome-wide. However, specific genes were differentially expressed after E7107 treatment in the SF3B1-mutated samples. Moreover, E7107 had the greatest effect on intron retention. This study indicates/suggests that mutated SF3B1 UM cells are more sensitive to the splicing inhibitor E7107 than wild-type SF3B1 UM cells.

Abstract A056: Pancreatic ductal adenocarcinoma derived cancer-associated fibroblasts suppress tumor infiltrating lymphocytes in the tumor microenvironment

Abstract Patients with pancreatic ductal adenocarcinoma (PDAC) have a poor prognosis due to late presentation of disease and frequent resistance to therapy. Immunotherapy regimens have uniformly failed in PDAC, which has long been considered an immunologically cold tumor. It is believed that immunotherapy has been unsuccessful in PDAC due to its dense, fibrotic, and immunosuppressive microenvironment. Cancer-associated fibrosis may account for up to 90% of the PDAC microenvironment, thus further study of this immunosuppressive component is urgently needed. Methods Human PDAC surgical specimens were procured, sectioned, and allocated for histology, flow cytometry, tumor-infiltrating lymphocyte (TIL) expansion, and fibroblast culture. For histology, tumor slices were saved in 10% formalin and wax embedded. Histological PDAC slides were stained against fibroblasts markers alpha smooth muscle actin, fibroblast activation protein; and T-cell markers CD3, CD69, CD25, FOXP3. First, tumor sections were digested using mechanical and chemical techniques. For flow cytometry, digested tumor cells were stained with fluorescent conjugated antibodies targeting CD45, CD3, CD4, CD8, CD25, CD69, PD-1 and ICAM. For TIL isolation and expansion, resultant single-cells were bead-isolated for CD3 positive cells, cultured and expanded with 2000 IU interleukin-2 and 1.5 mg/mL anti-CD3/CD28 antibodies. For fibroblast culture, fibroblasts were bead isolated and sub-cultured in RPMI supplemented with FGF. TILs were co-cultured with patient-derived fibroblasts/fibroblast media with the PD-L1 inhibitor Atezolizumab. TILs were then analyzed by flowcytometry, and media from co-culture was analyzed via ELISA for gamma interferon release. Results TILs isolated from PDAC (N=5) co-cultured with patient-matched fibroblasts or media were phenotypically compared using flow cytometry and measure for gamma interferon release. Interestingly, TILs co-cultured with fibroblasts or fibroblast media showed improved expansion over peripheral blood derived control T-cells, but both groups showed highly impaired gamma interferon release. Co-cultured TILs had high levels of PD-1 and low levels of CD69, compared to control TILs, indicating a suppressed phenotype. TILs co-cultured with fibroblasts and Atezolizumab resulted in significantly increased CD69 expression and gamma interferon release (P>0.05), indicating an activated phenotype. Histological PDAC slides showed abundant T-cell infiltrates with minimal CD69 expression. CD25+ T-cells were identified throughout fibrotic areas of the TME. Conclusion Here, we challenge the long-held belief that PDAC is immunologically cold as our tumor cross-sections (N=5) were rich in T-cells. More importantly, our results show that tumor-derived fibroblasts appear to play a role in suppression of TIL function, which is partially reversible with immunomodulatory techniques (e.g., anti-PDL1therapy). Our results warrant further investigation into targeting CAFs in PDAC microenvironment to improve patient response to immunotherapy. Citation Format: Charles Bailey, Hannah Mcdonald, Anna Reagan, Michael Cavnar, Mautin Barry-Hundeyin, Prakash Pandalai, Joseph Kim. Pancreatic ductal adenocarcinoma derived cancer-associated fibroblasts suppress tumor infiltrating lymphocytes in the tumor microenvironment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A056.

Proteo-metabolomics and patient tumor slice experiments point to amino acid centrality for rewired mitochondria in fibrolamellar carcinoma

Fibrolamellar carcinoma (FLC) is a rare, lethal, early-onset liver cancer with a critical need for new therapeutics. The primary driver in FLC is the fusion oncoprotein, DNAJ-PKAc, which remains challenging to target therapeutically. It is critical, therefore, to expand understanding of the FLC molecular landscape to identify druggable pathways/targets. Here, we perform the most comprehensive integrative proteo-metabolomic analysis of FLC. We also conduct nutrient manipulation, respirometry analyses, as well as key loss-of-function assays in FLC tumor tissue slices from patients. We propose a model of cellular energetics in FLC pointing to proline anabolism being mediated by ornithine aminotransferase hyperactivity and ornithine transcarbamylase hypoactivity with serine and glutamine catabolism fueling the process. We highlight FLC's potential dependency on voltage-dependent anion channel (VDAC), a mitochondrial gatekeeper for anions including pyruvate. The metabolic rewiring in FLC that we propose in our model, with an emphasis on mitochondria, can be exploited for therapeutic vulnerabilities.

XSiGra: explainable model for single-cell spatial data elucidation.

Recent advancements in spatial imaging technologies have revolutionized the acquisition of high-resolution multichannel images, gene expressions, and spatial locations at the single-cell level. Our study introduces xSiGra, an interpretable graph-based AI model, designed to elucidate interpretable features of identified spatial cell types, by harnessing multimodal features from spatial imaging technologies. By constructing a spatial cellular graph with immunohistology images and gene expression as node attributes, xSiGra employs hybrid graph transformer models to delineate spatial cell types. Additionally, xSiGra integrates a novel variant of gradient-weighted class activation mapping component to uncover interpretable features, including pivotal genes and cells for various cell types, thereby facilitating deeper biological insights from spatial data. Through rigorous benchmarking against existing methods, xSiGra demonstrates superior performance across diverse spatial imaging datasets. Application of xSiGra on a lung tumor slice unveils the importance score of cells, illustrating that cellular activity is not solely determined by itself but also impacted by neighboring cells. Moreover, leveraging the identified interpretable genes, xSiGra reveals endothelial cell subset interacting with tumor cells, indicating its heterogeneous underlying mechanisms within complex cellular interactions.

Radiosynthesis and Preclinical Evaluation of 18F-Labeled Estradiol Derivatives with Different Lipophilicity for PET Imaging of Breast Cancer.

About 75% of breast tumors show an overexpression of the estradiol receptor (ER), making it a valuable target for tumor diagnosis and therapy. To date, 16α-[18F]fluoroestradiol (FES) is the only FDA-approved imaging probe for the positron emission tomography (PET) imaging of ER-positive (ER+) breast cancer. However, FES has the drawback of a high retention in the liver. Therefore, the aim of this study was the development and preclinical evaluation of estradiol (E2) derivatives with different lipophilicity. Three 18F-labeled prosthetic groups (two glycosyl and one PEG azide) were chosen for conjugation with ethinyl estradiol (EE) by 18F-CuAAC (Cu-catalyzed azide-alkyne cycloaddition). The cellular uptake in ER+ MCF-7 tumor cells was highest for the less hydrophilic derivative (18F-TA-Glyco-EE). In nude mice bearing different breast tumors (ER+ MCF-7 and T47D versus ER- MDA-MB-231), 18F-TA-Glyco-EE revealed a high uptake in the liver (13%ID/g, 30 min p.i.), which decreased over 90 min to 1.2%ID/g, indicating fast hepatobiliary clearance. The statistically significant difference of 18F-TA-Glyco-EE uptake in T47D compared to MDA-MB-231 tumors at 60-90 min p.i. indicated ER-specific uptake, whereas in vivo PET imaging did not provide evidence for specific uptake of 18F-TA-Glyco-EE in MCF-7 tumors, probably due to ER occupation by E2 after E2-dependent MCF-7 tumor growth in mice. However, in vitro autoradiography revealed a high specific binding of 18F-TA-Glyco-EE to ER+ tumor slices. We conclude that 18F-TA-Glyco-EE, with its increased hydrophilicity after deacetylation in the blood and thus rapid washout from non-target tissues, may be a viable alternative to FES for the PET imaging of breast cancer.

Spatial correlation between in vivo imaging and immunohistochemical biomarkers: A methodological study

In this study, we present a method that enables voxel-by-voxel comparison of in vivo imaging to immunohistochemistry (IHC) biomarkers. As a proof of concept, we investigated the spatial correlation between dynamic contrast enhanced (DCE-)CT parameters and IHC biomarkers Ki-67 (proliferation), HIF-1α (hypoxia), and CD45 (immune cells). 54 whole-mount tumor slices of 15 laryngeal and hypopharyngeal carcinomas were immunohistochemically stained and digitized. Heatmaps of biomarker positivity were created and registered to DCE-CT parameter maps. The adiabatic approximation to the tissue homogeneity model was used to fit the following DCE parameters: Ktrans (transfer constant), Ve (extravascular and extracellular space), and Vi (intravascular space). Both IHC and DCE maps were downsampled to 4 × 4 × 3 mm[3] voxels. The mean values per tumor were used to calculate the between-subject correlations between parameters. For the within-subject (spatial) correlation, values of all voxels within a tumor were compared using the repeated measures correlation (rrm). No between-subject correlations were found between IHC biomarkers and DCE parameters, whereas we found multiple significant within-subject correlations: Ve and Ki-67 (rrm = -0.17, P < .001), Ve and HIF-1α (rrm = -0.12, P < .001), Ktrans and CD45 (rrm = 0.13, P < .001), Vi and CD45 (rrm = 0.16, P < .001), and Vi and Ki-67 (rrm = 0.08, P = .003). The strongest correlation was found between IHC biomarkers Ki-67 and HIF-1α (rrm = 0.35, P < .001). This study shows the technical feasibility of determining the 3 dimensional spatial correlation between histopathological biomarker heatmaps and in vivo imaging. It also shows that between-subject correlations do not reflect within-subject correlations of parameters.

Development of human pancreatic cancer avatars as a model for dynamic immune landscape profiling and personalized therapy.

Pancreatic ductal adenocarcinoma (PDAC) is the most common form of pancreatic cancer, a disease with dismal overall survival. Advances in treatment are hindered by a lack of preclinical models. Here, we show how a personalized organotypic "avatar" created from resected tissue allows spatial and temporal reporting on a complete in situ tumor microenvironment and mirrors clinical responses. Our perfusion culture method extends tumor slice viability, maintaining stable tumor content, metabolism, stromal composition, and immune cell populations for 12 days. Using multiplexed immunofluorescence and spatial transcriptomics, we identify immune neighborhoods and potential for immunotherapy. We used avatars to assess the impact of a preclinically validated metabolic therapy and show recovery of stromal and immune phenotypes and tumor redifferentiation. To determine clinical relevance, we monitored avatar response to gemcitabine treatment and identify a patient avatar-predictable response from clinical follow-up. Thus, avatars provide valuable information for syngeneic testing of therapeutics and a truly personalized therapeutic assessment platform for patients.

BRCA1 foci test as a predictive biomarker of olaparib response in ovarian cancer patient-derived xenograft models.

Standard therapy for high-grade ovarian carcinoma includes surgery followed by platinum-based chemotherapy and poly-ADP ribose polymerase inhibitors (PARPis). Deficiency in homologous recombination repair (HRD) characterizes almost half of high-grade ovarian carcinomas and is due to genetic and epigenetic alterations in genes involved in HR repair, mainly BRCA1/BRCA2, and predicts response to PARPi. The academic and commercial tests set up to define the HRD status of the tumor rely on DNA sequencing analysis, while functional tests such as the RAD51 foci assay are currently under study, but have not been validated yet and are available for patients. In a well-characterized ovarian carcinoma patient-derived xenograft platform whose response to cisplatin and olaparib, a PARPi, is known, we assessed the association between the BRCA1 foci score, determined in formalin-fixed paraffin-embedded tumor slices with an immunofluorescence technique, and other HRD biomarkers and explored the potential of the BRCA1 foci test to predict tumors' response to cisplatin and olaparib. The BRCA1 foci score was associated with both tumors' HRD status and RAD51 foci score. A low BRCA1 foci score predicted response to olaparib and cisplatin, while a high score was associated with resistance to therapy. As we recently published that a low RAD51 foci score predicted olaparib sensitivity in our xenobank, we combined the two scores and showed that the predictive value was better than with the single tests. This study reports for the first time the capacity of the BRCA1 foci test to identify HRD ovarian carcinomas and possibly predict response to olaparib.

Histogram analysis of multiple diffusion models for predicting advanced non-small cell lung cancer response to chemoimmunotherapy

BackgroundThere is an urgent need to find a reliable and effective imaging method to evaluate the therapeutic efficacy of immunochemotherapy in advanced non-small cell lung cancer (NSCLC). This study aimed to investigate the capability of intravoxel incoherent motion (IVIM) and diffusion kurtosis imaging (DKI) histogram analysis based on different region of interest (ROI) selection methods for predicting treatment response to chemoimmunotherapy in advanced NSCLC.MethodsSeventy-two stage III or IV NSCLC patients who received chemoimmunotherapy were enrolled in this study. IVIM and DKI were performed before treatment. The patients were classified as responders group and non-responders group according to the Response Evaluation Criteria in Solid Tumors 1.1. The histogram parameters of ADC, Dslow, Dfast, f, Dk and K were measured using whole tumor volume ROI and single slice ROI analysis methods. Variables with statistical differences would be included in stepwise logistic regression analysis to determine independent parameters, by which the combined model was also established. And the receiver operating characteristic curve (ROC) were used to evaluate the prediction performance of histogram parameters and the combined model.ResultsADC, Dslow, Dk histogram metrics were significantly lower in the responders group than in the non-responders group, while the histogram parameters of f were significantly higher in the responders group than in the non-responders group (all P < 0.05). The mean value of each parameter was better than or equivalent to other histogram metrics, where the mean value of f obtained from whole tumor and single slice both had the highest AUC (AUC = 0.886 and 0.812, respectively) compared to other single parameters. The combined model improved the diagnostic efficiency with an AUC of 0.968 (whole tumor) and 0.893 (single slice), respectively.ConclusionsWhole tumor volume ROI demonstrated better diagnostic ability than single slice ROI analysis, which indicated whole tumor histogram analysis of IVIM and DKI hold greater potential than single slice ROI analysis to be a promising tool of predicting therapeutic response to chemoimmunotherapy in advanced NSCLC at initial state.

LinG3D: visualizing the spatio-temporal dynamics of clonal evolution.

Cancers are spatially heterogenous, thus their clonal evolution, especially following anti-cancer treatments, depends on where the mutated cells are located within the tumor tissue. For example, cells exposed to different concentrations of drugs, such as cells located near the vessels in contrast to those residing far from the vasculature, can undergo a different evolutionary path. However, classical representations of cell lineage trees do not account for this spatial component of emerging cancer clones. Here, we propose routines to trace spatial and temporal clonal evolution in computer simulations of the tumor evolution models. The LinG3D (Lineage Graphs in 3D) is an open-source collection of routines (in MATLAB, Python, and R) that enables spatio-temporal visualization of clonal evolution in a two-dimensional tumor slice from computer simulations of the tumor evolution models. These routines draw traces of tumor clones in both time and space, and may include a projection of a selected microenvironmental factor, such as the drug or oxygen distribution within the tumor, if such a microenvironmental factor is used in the tumor evolution model. The utility of LinG3D has been demonstrated through examples of simulated tumors with different number of clones and, additionally, in experimental colony growth assay. This routine package extends the classical lineage trees, that show cellular clone relationships in time, by adding the space component to show the locations of cellular clones within the 2D tumor tissue patch from computer simulations of tumor evolution models.

Octyl itaconate enhances VSVΔ51 oncolytic virotherapy by multitarget inhibition of antiviral and inflammatory pathways

The presence of heterogeneity in responses to oncolytic virotherapy poses a barrier to clinical effectiveness, as resistance to this treatment can occur through the inhibition of viral spread within the tumor, potentially leading to treatment failures. Here we show that 4-octyl itaconate (4-OI), a chemical derivative of the Krebs cycle-derived metabolite itaconate, enhances oncolytic virotherapy with VSVΔ51 in various models including human and murine resistant cancer cell lines, three-dimensional (3D) patient-derived colon tumoroids and organotypic brain tumor slices. Furthermore, 4-OI in combination with VSVΔ51 improves therapeutic outcomes in a resistant murine colon tumor model. Mechanistically, we find that 4-OI suppresses antiviral immunity in cancer cells through the modification of cysteine residues in MAVS and IKKβ independently of the NRF2/KEAP1 axis. We propose that the combination of a metabolite-derived drug with an oncolytic virus agent can greatly improve anticancer therapeutic outcomes by direct interference with the type I IFN and NF-κB-mediated antiviral responses.

Transcriptomic analysis-guided assessment of precision-cut tumor slices (PCTS) as an ex-vivo tool in cancer research

With cancer immunotherapy and precision medicine dynamically evolving, there is greater need for pre-clinical models that can better replicate the intact tumor and its complex tumor microenvironment (TME). Precision-cut tumor slices (PCTS) have recently emerged as an ex vivo human tumor model, offering the opportunity to study individual patient responses to targeted therapies, including immunotherapies. However, little is known about the physiologic status of PCTS and how culture conditions alter gene expression. In this study, we generated PCTS from head and neck cancers (HNC) and mesothelioma tumors (Meso) and undertook transcriptomic analyses to understand the changes that occur in the timeframe between PCTS generation and up to 72 h (hrs) in culture. Our findings showed major changes occurring during the first 24 h culture period of PCTS, involving genes related to wound healing, extracellular matrix, hypoxia, and IFNγ-dependent pathways in both tumor types, as well as tumor-specific changes. Collectively, our data provides an insight into PCTS physiology, which should be taken into consideration when designing PCTS studies, especially in the context of immunology and immunotherapy.

Abstract PO4-18-03: Combined Treatment with Pyrotinib and Chrysin Synergistically Improve the Autophagy Level in HER2-Positive Breast Cancer by Regulating the miR-16-5p/ZBTB16/G6PD Axis

Abstract Human epidermal growth factor receptor 2 (HER2)-positive breast cancer (BC) has been the most challenging subtype of BC, which consists of 20% of BC with an apparent correlation with poor prognosis. Despite that pyrotinib, a new HER2 inhibitor, has led to dramatic improvements in prognosis outcome, the efficacy of pyrotinib as monotherapy remain largely restricted due to its acquired resistance. Therefore, we aim at identifying a potent antitumor drug incorporated with pyrotinib for amplifying therapeutic efficacy for treating HER2-positive BC. Here, we reported a novel incorporation of pyrotinib in combination with chrysin, and explored its antitumor efficacy and the underlying mechanisms on HER2+ breast cancer. We determined that pyrotinib combined with chrysin yielded a potent synergistic effect to induce apoptosis and inhibit BT-474 and SK-BR-3 tumor cells, and suppressed in vivo tumor growth in tumor-bearing mice models. This may be mechanistically attributed to the induction of enhanced endoplasmic reticulum stress to increase the autophagy level. Furthermore, it was demonstrated that the combined treatment with pyrotinib and chrysin induced ubiquitination and G6PD degradation by regulating zinc finger and BTB/POZ domain-containing family protein 16 (ZBTB16) in tumorigenesis of BC. Besides, we identified that miR-16-5p is a potential upstream regulatory target of ZBTB16. Blocking miR-16-5p overexpression could inhibit HER2-positive tumorigenesis and significantly potentiate the efficacy of pyrotinib in combination with chrysin. Together, these findings demonstrate the utility of combined treatment with pyrotinib and chrysin as a potential option in the target treatment of HER2-positive BC through an unrecognized miR-16-5p/ZBTB16/G6PD axis. The miR-16-5p/ZBTB16/G6PD axis plays a crucial role in the pyrotinib plus chrysin-enabled anti HER2-positive BC Fig.1 a Cell viability of SK-BR-3 cells received various treatments. b Detection of cell cycle arrest of SK-BR-3 cells after various treatments. c Schematic diagram of the established protocol of the animal models. Photograph of resected tumor tissues, tumor volume (d), and tumor weight (e) of mice in different treatment groups during the whole testing period. f H&amp;E, Ki67, and Tunel immunohistochemical staining of tumor sections of mice in various treatment groups. g Autophagy flux of SK-BR-3 cells labeled with mRFP-GFP-LC3 in the different treatment groups. h Expression level of ER stress markers in SK-BR-3 cells after various treatments via RT-qPCR and western blot. *P &amp;lt;0.05, compared with control group (DMSO), #P &amp;lt;0.05, compared with chrysin group, &amp; P&amp;lt;0.05, compared with pyrotinib group. i Western blot analysis of the expression of G6PD in different treatment groups. j Fluorescence images of SK-BR-3 cells subjected to G6PD overexpression for the detection of autophagy level. k Ubibrowser database predicting the E3 ubiquitin ligases that may be involved in the regulation of G6PD ubiquitination. l Western blot analysis of G6PD protein half-life in SK-BR-3 cells with ZBTB16 silence. Cells were co-incubated with cycloheximide (CHX, 50μg/ml) for the indicated time. m Determination of the ubiquitination of G6PD in cells pretreated with 10 μM MG-132 for 3 h. Cells were transfected with ubiquitin after different treatments. The ubiquitinated G6PD was subjected to immunoprecipitation before western blot with ubiquitin antibody. n Dual-luciferase report verifying the targeting of ZBTB16 and miR-16-5p. o Transmission electron microscopy images of autophagosomes of tumors in various treatment groups (× 20000). p Immunohistochemical staining images of tumor slices for the determination of G6PD. q Schematic diagram for the underlying mechanism of pyrotinib combined chrysin against HER2-positive BC. Citation Format: Ting Luo, Xiaorong Zhong, Ping He, Dan Zheng, Yan Cheng, Kunrui Zhu. Combined Treatment with Pyrotinib and Chrysin Synergistically Improve the Autophagy Level in HER2-Positive Breast Cancer by Regulating the miR-16-5p/ZBTB16/G6PD Axis [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 PO4-18-03.

Ultrabright quantum dots assisted in vivo NIR-II fluorescence microscopic imaging for brain metastases in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is an aggressive and often fatal disease, especially since the brain metastasis of TNBC has been a particularly severe manifestation. However, brain metastasis in TNBC at early stages often lacks noticeable symptoms, making it challenging to detect. Near-infrared II (NIR-II) fluorescence microscopic imaging obtains long wavelength, which enables reduced scattering, high spatial resolution and minimal autofluorescence, it is also a favorable imaging method for tumor diagnosis. PbS@CdS quantum dots (QDs) are one of the popular NIR-II fluorescence nanoprobes for well brightness. In this study, NIR-II emissive PbS@CdS QDs were utilized and further encapsulated with thiol-terminated poly(ethylene oxide) (SH-PEG, MW = 5000) to form PbS@CdS@PEG QDs nanoparticles (NPs). The obtained PbS@CdS@PEG QDs NPs were then characterized and further studied in detail. The PbS@CdS@PEG QDs NPs had large absorption spectra, exhibited strong NIR-II fluorescence emission at approximately 1300[Formula: see text]nm, and possessed good NIR-II fluorescence properties. Then, the mice model of early-stage brain metastases of TNBC was established, and the PbS@CdS@PEG QDs NPs were injected into the tumor-bearing mice for NIR-II fluorescence microscopic bioimaging. The brain vessels and tumors of the living mice were detected with high spatial resolution under the NIR-II fluorescence microscopic imaging system with irradiation of 808[Formula: see text]nm laser. The tumor tissues were further restricted and prepared as thin slices. The NIR-II fluorescence signals were collected from the tumor slices with high spatial resolution and signal-to-background ratio (SBR). Thus, the PbS@CdS@PEG QDs NPs-assisted NIR-II fluorescence microscopic system can effectively achieve targeting brain metastases of TNBC imaging, offering a novel and promising approach for TNBC-specific diagnosis.

Abstract LB172: A cytosolic complex between exportin-7(XPO7) and ste20-like kinase (SLK) regulates PI3K-AKT-mTOR signaling in cholangiocarcinoma

Abstract Cholangiocarcinoma (CCA) is a deadly malignancy with an evolving therapeutic landscape. Although nucleic acid-based evaluations have unveiled some druggable targets, limited options are available for the majority of patients with this disease. We therefore evaluated biliary exosomes by mass spectrometry from 16 patients with CCA, which revealed a 17-fold enhancement of the nuclear export protein XPO7 in CCA-derived biliary exosomes. IHC analysis of XPO7 expression in CCA tumors from 170 patients unexpectedly demonstrated intense cytoplasmic staining in 30% of the samples, which correlated with abbreviated survival. Within the cytosol, we demonstrate that XPO7 exists in a molecular complex with the serine/threonine kinase SLK. shRNA-mediated knockdown of either XPO7 or SLK abrogated tumor organoid formation in vitro, and reduced orthotopic tumor formation and substantially altered tumor morphology using athymic mice. A kinome screen of FDA-approved drugs revealed tivozanib inhibits SLK (IC50= 81.8 nM), which we confirmed using crystallography. Tivozanib treatment reduced tumor organoid formation in vitro and induced tumor regression in vivo using murine xenografts with resulting morphology similar to XPO7 and SLK knockdown tumors. Importantly, site-directed mutagenesis of SLK was used to confirm the observed phenotypic alterations secondary to SLK inhibition. Signal transduction studies with SLK knockdown in CCA cell lines demonstrated downregulation of PI3K-AKT-mTOR signaling with further effects on DNA damage resulting in G2 cell cycle arrest. Moreover, tivozanib demonstrated anti-tumor activity and increased apoptosis in established CCA patient-derived xenografts with cytoplasmic XPO7 expression. Using ex vivo tumor slice cultures, tivozanib significantly increased tumor cell apoptosis in XPO7/SLK-expressing tumors (N=3) but not in tumors without this expression pattern (N=6). Further evaluation of these tivozanib-treated tumor slice cultures demonstrated a reduction in the expression of phosphorylated mTOR (S2448), AKT (T308), S6 (S235/236) in the high XPO7/SLK-expressing tumors but not in tumors without this expression pattern. Lastly, tivozanib monotherapy demonstrated in vivo efficacy with arrest of tumor progression (RECIST stable disease) in an ongoing clinical trial (NCT04645160). Citation Format: Priyanka P. Desai, Tahsin M. Khan, Reed I. Ayabe, Emily Smith, Surajit Sinha, Ashley Rainey, Yuri Lin, Tracey Pu, Kenneth Lubrice, Leila Sarvestani, Sarfaraz Akmal, Shahyan Rehman, Kirsten Remmert, Michael Yaffe, Craig Thomas, John Brognard, Jonathan M. Hernandez. A cytosolic complex between exportin-7(XPO7) and ste20-like kinase (SLK) regulates PI3K-AKT-mTOR signaling in cholangiocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB172.

Abstract 4440: Topographical investigation of metabolites in excised squares (TIMES2): Comprehensive cross-sectional metabolite quantification of pancreatic cancer in vivo

Abstract Purpose: Pancreatic cancer is a lethal malignancy characterized by complex intratumoral metabolic reprogramming and intercellular nutrient sharing between cells in the tumor microenvironment (TME) that promote pancreatic cancer progression. However, this crosstalk, as well as regional variation in perfusion and oxygenation, can lead to metabolic heterogeneity that has not been appreciated by metabolomics of whole tumors. Here we quantify amino acids and tricarboxylic acid cycle (TCA) intermediates using a novel methodology that allows us to portray global tumor metabolite heterogeneity in a tumor. Methods: Human PaTu-8902 or murine HY19636 (from female KPC mice LSL-KrasG12D; p53 L/+, Ptf1a-Cre+) pancreatic cancer cell lines were orthotopically injected into pancreata of NCr nude mice (n=3) or C57BL/6 mice (n=2). Mice were euthanized after 3-5 weeks and tumors were harvested. Tumor slices were further sectioned into 1mm x 1mm x 1mm cubes using a custom-made multisectional slicing device and each cube location was recorded. Each cube was extracted using methanol, water, and chloroform with labelled amino acid standards, derivitized, and resolved using gas chromatography-mass spectrometry (DB-35MS column with Agilent 7890B gas chromatograph coupled to a single quadrupole 5977B mass spectrometer). 22 metabolites (15 amino acids, 5 TCA intermediates, lactate, and pyruvate) were identified by unique fragments and retention time compared to known standards. Peaks were picked using OpenChrom and analyzed using MATLAB. Data was analyzed using Graphpad Prism. Principal Component Analysis (PCA) was visualized using Python on a Jupyter notebook. Results: Both orthotopic human and murine pancreatic tumors demonstrated striking levels of intratumoral metabolite heterogeneity. Glycine, glutamine, and proline were the amino acids with the highest coefficient of variance, while leucine, isoleucine, and serine had the lowest coefficient of variance. α-ketoglutarate and succinate were the TCA intermediates with highest coefficient of variance. Lactate had the lowest coefficient of variance among all examined metabolites. Spatial mapping of each metabolite demonstrated distinct regions with varying abundance levels of metabolites. PCA demonstrated 75% of variance was carried by PC1 and 10% carried by PC2. Conclusions: This study reveals insights into the degree of intratumoral heterogeneity present in pancreatic tumors that illustrate the difficulty of in vivo metabolomics analysis and suggest that high-resolution (single cell) metabolomics techniques will be critical to study metabolism in the complex TME. Citation Format: Peter Yu, Robert Banh, Albert Sohn, Stephen Martis, Douglas Biancur, Keisuke Yamamoto, Elaine Lin, Alec Kimmelman. Topographical investigation of metabolites in excised squares (TIMES2): Comprehensive cross-sectional metabolite quantification of pancreatic cancer in vivo [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 4440.

Abstract 6777: An ex-vivo organotypic culture platform of mucinous carcinomatosis peritonei identifies CDK4-6 inhibition as a novel treatment

Abstract Concomitant mutations in KRAS and GNAS have been linked to mucinous histology in gastrointestinal neoplasms of the appendix, colon, and pancreas (IPMN). Upon progression, these tumors are characterized by metastasis which favors the peritoneal surface, resulting in mucinous carcinomatosis peritonei (MCP). Recently we have described a novel technique which allows for long term culture and drug intervention of human MCP tumors ex-vivo. With evidence of durable clinical benefit of CDK4-6 inhibition in a single patient with chemo refractory MCP of appendiceal origin, we sought to further investigate anti-tumor responses using CDK4-6 inhibition in ex-vivo tumor slices, in order to identify candidates for a personalized clinical therapy trial. Here, in a comparison of ex-vivo patient tumor slices from 18 individual donors, treatment using CDK4-6 inhibitors revealed a significant reduction in cancer cell specific proliferation in mucinous GNAS-mut tumors compared to non-mucinous cancers. Anti-tumor responses of CDK4-6 were determined to be tumor-cell intrinsic, as CDK4-6 inhibition blocked proliferation of stromal cells in the TME independently of patient tumor mutational and mucin status. Based on these finding a personalized clinical trial was conducted where we report that 13 of 16 patients (81%) enrolled with MCP treated with palbociclib had at least a 10% decrease in CEA, as compared to historical chemotherapy responses rates reported from 14-30%. These results indicate that CDK4/6 inhibition is a novel and efficacious treatment for patients with MCP. Citation Format: Jonathan Weitz, Daisuke Nishizaki, Jay Patel, Isabella Ng, Siming Sun, Dana Ramms, Jingjing Zou, Joel Baumgartner, Kaitlyn Kelly, Hitendra Patel, Rebekah White, Jula Veerapong, Peter Vu, Silvio Gutkind, Herve Tiriac, Shumei Kato, Andrew Lowy. An ex-vivo organotypic culture platform of mucinous carcinomatosis peritonei identifies CDK4-6 inhibition as a novel treatment [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 6777.

Abstract 1272: Spatial profiling of human colorectal cancer brain metastasis identifies chromosomal instability with adaptive niche cellular reorganization and reprograming

Abstract Brain metastasis in colorectal cancer (mCRC) poses a significant clinical challenge with poor outcomes. Our study, the largest spatial analysis reported to date, aimed to uncover unique cellular and genomic features facilitating metastatic lesion development. Employing spatial transcriptomics on 60 patients' surgical resections, we validated our findings with single-cell RNA sequencing (scRNA-seq), whole-genome sequencing (WGS), and ex vivo functional studies in tumor slice cultures. We obtained spatially distinct gene expression profiles of metastatic tumor cells, tumor microenvironment (TME) and brain parenchymal lineages. Our analysis identified spatially heterogenous upregulation of PI3K, MAPK, EGFR, p53, and TGFβ signaling in metastatic tumor cells. Tumor cells had high levels of chromosomal instability (CIN) marked by recurrent amplifications in chromosomes 6, 7, 17, and 20. WGS from three independent cohorts revealed significantly higher CIN in mCRC brain compared to primary CRC or mCRC from other organs. Spatial neighborhood analysis identified an immune desert phenotype with lack of proximity between lymphocytes and metastatic tumor cells. However, mCRC brain contained abundant plasma cells identifying a unique TME niche feature. Significant proximity between tumor cells and endothelial cells underscored their potential role in tumor seeding and growth. Spatially aware differential expression analysis demonstrated adaptive responses in the brain parenchyma. This included increased Golgi-ER processing and Rho GTPase signaling in neurons and astrocytes adjacent to metastatic tumor cells, respectively. Macrophages were characterized by high expression of pro-fibrogenic genes. Increased SPP1 ligand expression from these macrophages interacted with corresponding receptors on spatially proximal fibroblasts, identifying a key niche reorganization feature that can promote metastatic lesion growth. To evaluate the translational potential of our findings, we examined the effects of perturbating the metastatic niche using scRNA-seq. We established a tumor slice culture from a mCRC brain surgical resection, which maintained all original cell states. Despite elevated signaling pathway activity, metastatic tumor cells were resistant to regorafenib, a multi-receptor tyrosine kinase inhibitor. In contrast, pirfenidone, an anti-fibrotic and anti-inflammatory small molecule, successfully reduced extracellular matrix-associated gene expression programs in fibroblasts in the TME. Our analysis identified distinct properties of mCRC brain that can serve as therapeutic targets, including high levels of chromosomal instability, remodeling of brain parenchyma, lymphocyte evasion, plasma cell abundance and macrophage-fibroblast interactions. Citation Format: Anuja Sathe, Aparajita Khan, Ji In Kang, Rithika Meka, Susan M. Grimes, Andrew S. Luksik, Michael Lim, Claudia Petrisch, Christopher M. Jackson, Hannes Vogel, Melanie Gephart, Summer Han, Hanlee P. Ji. Spatial profiling of human colorectal cancer brain metastasis identifies chromosomal instability with adaptive niche cellular reorganization and reprograming [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 1272.

Abstract 6658: TcE armed oncolytic virus VSV-GP combines oncolysis and T-cell retargeting for improved efficacy

Abstract Background: Oncolytic viruses, such as the chimeric vesicular stomatitis virus variant VSV-GP have dual modes of action, direct tumor-cell killing, and activation of tumor-specific immunity. While tumor cells deficient in type I interferon (IFN) response are permissive to VSV-GP replication and killing, IFN competent tumor cells are protected from VSV-GP-mediated oncolysis. Our previous data demonstrated that VSV-GP therapy turns immunologically ‘cold’ tumors ‘hot’ by increasing infiltration of T cells into the tumor. The aim of this study was to use the VSV-GP platform to locally express a T cell engager (TcE) molecule to redirect these T cells to destroy non-permissive IFN competent tumor cells expressing the target of the TcE on their cell surface. Methods: We selected EpCAM as the target antigen and used a bispecific EpCAM-TcE molecule consisting of two variable single chain fragments against EpCAM and CD3, respectively. VSV-GP encoding EpCAM-TcE (VSV-GP-EpCAM-TcE) or an invariant control TcE (VSV-GP-TNP-TcE) were generated as previously described. T cells were co-cultured with human target cells expressing EpCAM on their cell surface, either infected with the VSV-GP-EpCAM-TcE virus or with supernatant from VSV-GP-EpCAM-TcE infected cells. T cell activation, proliferation, degranulation and cytokine secretion were analyzed by flow cytometry and multiplex cytokine assays as a measure of TcE mediated cross-linking of T cells to their target on cancer cells. Patient-derived head and neck squamous cell carcinoma (HNSCC) tumors were sectioned into approximately 200 µM slices and infected with the virus. T cell activation was measured by cytokine secretion. The therapeutic potential of VSV-GP-EpCAM-TcE was tested in vivo in cell-line derived xenograft (CDX) models implanted in immunodeficient mice humanized with donor-derived PBMCs or CD34+ cells. Results: Virus fitness was maintained for VSV-GP encoding the TcE molecule. Using co-culture assays, we demonstrated that EpCAM-TcE molecule is successfully expressed by VSV-GP and can activate both CD4+ and CD8+ T cells resulting in proliferation, degranulation, and cytokine secretion. Furthermore, we validated the concept using patient-derived HNSCC tumor slices which are representative of complex human tumor ecosystems. We could confirm that cancer cells infected by VSV-GP-EpCAM-TcE virus express functional TcE molecule and activates T cells to secrete IFNγ and TNFα. Finally, we tested the concept in two different CDX models where VSV-GP-EpCAM-TcE showed improved tumor growth inhibition due to a combined effect of oncolysis and T cell activation by EpCAM-CD3 TcE. Summary: The oncolytic virus VSV-GP can be successfully armed with a TcE to redirect tumor-infiltrating T cells to destroy tumor cells which are not permissive to viral replication. This resulted in an enhanced therapeutic efficacy compared to just the oncolytic effect. Citation Format: Aparna Ponnurangam, Theresa Schwaiger, Sophie Walter, Simone Bartl, Melissa Mayr, Monika Petersson, Tanja Schoenberger, Fabian Heinemann, Peter Gross, Wolfgang Rist, Srinath Kasturirangan, Charlotte Lempp, Jutta Petschenka, Krishna Das, Nolden Tobias. TcE armed oncolytic virus VSV-GP combines oncolysis and T-cell retargeting for improved efficacy [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 6658.

Abstract 2710: Combination CXCR4 and PD-1 blockade increases T cell infiltration and effector function in fibrolamellar carcinoma (FLC)

Abstract Introduction: Fibrolamellar carcinoma (FLC), a rare liver cancer affecting young patients without cirrhosis, has a poor prognosis and few systemic therapy options. Current evidence implicates an immunosuppressive tumor microenvironment (TME), including our preliminary data suggesting preferential localization of T cells in stromal bands. We hypothesized that dual blockade of C-X-C chemokine receptor type 4 (CXCR4) and programmed cell death protein (PD-1) would enhance T cell infiltration and activation, respectively, and thereby increase tumor killing. Methods: Flow cytometry and single-nuclear RNA sequencing (snRNA-seq) were used to analyze immune cells and evaluate gene expression, respectively, in patient-derived FLC and non-tumor liver (NTL). Immunohistochemistry (IHC) was used to assess CD3+ T cell localization in relation to CXCL12, the chemokine ligand of CXCR4. Tumor slice cultures (TSCs) from fresh FLC resection specimens (n=11) were treated with control (IgG1), a small molecule CXCR4 inhibitor (AMD3100), anti-PD-1 blocking antibody (αPD-1), or combination CXCR4 and PD-1 blockade (AMD3100/αPD-1). IHC, RNA expression (Nanostring), and live microscopy were used to evaluate T cell mobilization and function. Results: Flow cytometry analysis demonstrated fewer CD45+ cells (16% vs 54% of live cells, p=0.01) and heterogenous PD-1 expression on T cells in FLC compared with NTL. SnRNA-seq analysis showed that CXCR4 expression is upregulated in FLC lymphocyte and macrophage populations relative to NTL (15% vs 10% and 20% vs 5% expressed), and CXCL12 is expressed primarily in stellate cells. CD3+ T cells colocalized with CXCL12 in the FLC stroma on IHC. Multiplex IHC of treated TSCs revealed more T cells in the carcinoma (CK7+) than the stromal (SMA+) compartment after AMD3100 compared with IgG1 (63% vs 34% T cells in CK7+ compartment, p=0.05). Nanostring indicated upregulation of effector pathways (apoptosis, cytotoxicity, lymphocyte activation) after AMD3100/αPD-1 compared with IgG1. Time-lapse live microscopy revealed a greater percentage of apoptotic carcinoma cells (SR-FLICA+CK7+) colocalized with CD3+ T cells (37% vs 18%, p=0.005) and longer CD3+ T cell track length (27 vs 22 μm, p=0.03) after AMD3100/αPD-1 than before treatment. Cleaved caspase-3 (CC3) IHC demonstrated significantly increased tumor apoptosis after AMD3100/αPD-1 compared with IgG1 and monotherapy (53% vs 32% (IgG1), 39% (AMD3100), and 42% (αPD-1) CC3+ cells, p=0.002, p=0.03, p=0.04). Conclusion: The CXCR4/CXCL12 axis mediates T cell exclusion in the FLC TME. Combination CXCR4 and PD-1 blockade overcomes immunosuppression in FLC by mobilizing T cells into the carcinoma compartment and activating their effector function, with resultant tumor apoptosis. These findings support consideration of clinical trials testing drugs targeting CXCR4 and PD-1 in FLC. Citation Format: Lindsay K. Dickerson, Renske van den Bijgaart, Xiuyun Jiang, Sara K. Daniel, Jason A. Carter, Alaa Farghli, Kevin M. Sullivan, Yongjun Liu, Heidi L. Kenerson, Raymond S. Yeung, Teresa S. Kim, Ian N. Crispe, Praveen Sethupathy, Kevin C. Barry, Venu G. Pillarisetty. Combination CXCR4 and PD-1 blockade increases T cell infiltration and effector function in fibrolamellar carcinoma (FLC) [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 2710.