Primary Patient-derived Xenograft Research Articles

TMOD-10. ESTABLISHMENT OF ADULT AND PEDIATRIC BRAZILIAN PRE-CLINICAL MODELS FOR HIGH-GRADE GLIOMAS

Abstract High-grade gliomas (HGG) are the most aggressive brain tumors, necessitating robust and representative preclinical models for therapeutic research. We established primary cultures and patient-derived xenograft models from three pediatric high-grade gliomas (pHGG) and one adult IDH wild-type glioblastoma (GBM IDHwt) Brazilian patients. The first pHGG case, from an 11-year-old with PDGFRA (c.1977C>G) and TP53 (c.637C>T) mutations, led to the development of the HCB570 primary culture, PDX and patient-derived orthotopic xenograft (PDOX) OXP9. The second pHGG, from an 11-year-old with CMMRD syndrome and MSH6 germline mutation, resulted in the HCB589 primary culture, PDX and PDOX OXP22. The third pHGG case, from a 14-year-old with diffuse midline glioma harboring an H3F3A mutation, established the HCB604 primary culture and PDX OXP32. The HCB612 primary culture and PDX GBM1, were established from an adult patient with GBM IDHwt, TERT mutated, with no MGMT promoter methylated. The primary cultures showed varied proliferative rates, with an average doubling time of 55 hours. All cultures demonstrated colony-formating capability, with an average IC50 of 750µM for temozolomide (TMZ) exposure. Immunohistochemical and EPIC methylation profiles confirmed that the PDX models closely resemble the patient features. Our establishment of diverse preclinical models, including those derived from patients with rare genetic conditions such as CMMRD, provides valuable insights into HGG pathogenesis and potential therapeutic strategies. The present Brazilian patient-derived models enrich glioma research inclusion diversity and foster future personalized treatment approaches.

THOC1 complexes with SIN3A to regulate R-loops and promote glioblastoma progression.

Glioblastoma (GBM), the most common and aggressive malignant brain tumor in adults, has a median survival of 21 months. To identify drivers of GBM proliferation, we conducted a CRISPR-knockout screen, which revealed THO Complex 1 (THOC1) as a key driver. Knocking down THOC1 significantly reduced GBM cell viability across patient-derived xenograft (PDX) lines, enhancing survival (p<0.01) in primary PDX models. Conversely, overexpressing THOC1 in non-cancerous cells bolstered viability, decreasing survival and causing tumor engraftment in vivo (p<0.01). Further investigation revealed THOC1's robust interaction with SIN3A, a histone deacetylase complex. Histone deacetylation has been previously shown to prevent the buildup of R-loops, structures that form normally during transcription but can be lethal in excess. We found that THOC1-knockdown leads to elevated R-loop levels and reduced histone deacetylation levels. Next, to understand the networks specifically regulated by THOC1-mediated R-loop prevention, we conducted unbiased RNA-sequencing on control and THOC1-knockdown GBM cells. We found that THOC1's role in R-loop prevention primarily affects telomeres, critical regions for cell replication. We further show that THOC1-knockdown results in significantly increased telomeric R-loop levels and shortened telomeres. Ultimately, this study suggests that targeting THOC1 shows promise as a therapeutic strategy to disrupt the delicate R-loop landscape and undermine GBM's replicative potential.

Abstract B012: Predicting targetable paralog synthetic lethalities and functional redundancies in cancer genomes

Abstract Paralogs are prevalent in the human genome and are considered a rich source of synthetic lethality due to functional redundancy. For a cancer cell carrying a gene with Loss-Of-Function (LOF) mutation, inactivation of its paralog using gene editing can induce a selective decrease in viability, leaving normal cells that do not harbor the mutation unharmed. Previous studies have exploited this vulnerability of cancer genomes. However, the cancer-specificity of such synthetic lethality limits its application across different cancer types. Furthermore, the role of functional redundancy which can explain the cancer specificity has remained largely unexplored. In this study, we computationally predicted synthetic lethal paralogs along with mechanistically important functional redundancies between them in a cancer-specific manner. We applied our prediction method to publicly available data for an aggressive subtype of breast cancer called triple-negative breast cancer (TNBC), which lacks the expression key biomarkers and hence has the worst prognosis among other breast cancer subtypes. TNBC is characterized by the highest mutational load and the largest fraction of genome altered among the breast cancer subtypes providing a rich mutational landscape to identify LOF genes. Using the CRISPR inactivation screen data for cancer cell lines obtained from the Cancer Dependency Map (DepMap) project, we predicted sets of synthetic lethal paralogs that show a significantly greater viability decrease if a gene carries LOF and its paralog is inactivated, compared to the viability decrease due to the inactivation of only one of the paralogs. Consistent with previous findings of context-dependent synthetic lethality, we found that a relatively small fraction of TNBC-specific synthetic lethal paralogs overlapped with those found across other cancer types. To uncover the mechanistically important functional redundancies between paralogs, we analyzed the genomics and transcriptomics data from multiple sources: TNBC panel of primary tumors and patient-derived xenografts, Pan-Cancer Analysis of Whole Genomes (PCAWG), and the Cancer Cell Line Encyclopedia (CCLE). The functional redundancies varied across cancer types based on (1) mutual exclusivity of LOFs, (2) backup compensation of deleterious mutations, (3) backup upregulation, and (4) dosage balance. Overall, our findings show a strong context-dependency of synthetic lethal paralogs and estimates of functional redundancy, emphasizing the importance of such cancer-specific predictions in identifying targetable paralog synthetic lethalities. Collectively, the computational method and sets of targetable paralogs are a unique resource for developing precision oncology therapeutic strategies against TNBC and other cancers more broadly. Citation Format: Rohan Dandage, Elena Kuzmin. Predicting targetable paralog synthetic lethalities and functional redundancies in cancer genomes [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B012.

Development and validation of AI-assisted transcriptomic signatures to personalize adjuvant chemotherapy in patients with resectable pancreatic ductal adenocarcinoma.

4015 Background: Adjuvant chemotherapies for PDAC include modified FOLFIRINOX (mFFX) or gemcitabine-based regimen in fit patients and gemcitabine or 5FU single agents in other patients. While more effective, mFFX is associated with a greater toxicity than other options. Moreover, therapeutic decisions still rely mainly on the patient's performance status rather than tailored to tumor-based criteria. Our study aims to personalize treatments by developing transcriptomic signatures specific to commonly used drugs for pancreatic cancer. Methods: We analyzed the response to drugs (5-fluorouracil, oxaliplatin, and irinotecan) in three types of preclinical models (primary cell cultures, tumoroids, and patient-derived xenografts in immunodeficient mice). We then associated the detected sensitivities to drugs with transcriptomic data from each model. We also incorporated the previously developed gemcitabine signature. Finally, we used a machine learning method, the "Least Absolute Shrinkage and Selection Operator-random forest," to improve the signatures, integrating the tumor microenvironment master regulators. The learning cohort were GemPred for gemcitabine (1) and COMPASS (2) for mFFX. The resulting transcriptomic predictive tool was called Pancreas-View. We validated these signatures in the PRODIGE-24/CCTG PA6 trial cohort comprising 343 patients (3). Results: The signatures may allow to identify responsive patients to specific drugs and showed a significant improvement in their cancer-specific survival (CSS) and disease-free survival (DFS) when they received a matched therapy (mFFX or gemcitabine). Additionally, a positive association was observed between the number of drugs for which tumors predict to be sensitive and patient’s survival when appropriately treated. Patients who received “appropriate” drugs (n = 164; 47.8%) displayed a longer DFS : 50.1 months (stratified HR: 0.31; 95% CI, 0.21-0.44; p &lt; 0.001) in the mFFX arm, and 33.7 months (stratified HR: 0.40; 95% CI, 0.17-0.59; p &lt; 0.001) in the gemcitabine arm, respectively. Conversely, patients that received a treatment not matched with the signature prediction (n = 86; 25.1%) and those predicted to be resistant to all drugs (n = 93; 27.1%) had the poorest DFS results (10.6 and 10.8 months, respectively). Conclusions: By integrating preclinical models and machine learning, we developed a comprehensive predictive tool based on the transcriptome that may help to identify tumors sensitivity to mFFX components and gemcitabine. Crucially, these transcriptomic signatures can also lead to reduce toxicity by avoiding the unnecessary administration of drugs predicted as ineffective for a given tumor. Nicolle R, et al. Ann Oncol 2021;32:250-260. Aung K, et al Clin Cancer Res 2018;24:1344–1354. Conroy T, et al. N Engl J Med 2018; 379:2395-2406.

Creation and Validation of Patient-Derived Cancer Model Using Peritoneal and Pleural Effusion in Patients with Advanced Ovarian Cancer: An Early Experience.

Background: The application of personalized cancer treatment based on genetic information and surgical samples has begun in the field of cancer medicine. However, a biopsy may be painful for patients with advanced diseases that do not qualify for surgical resection. Patient-derived xenografts (PDXs) are cancer models in which patient samples are transplanted into immunodeficient mice. PDXs are expected to be useful for personalized medicine. The aim of this study was to establish a PDX from body fluid (PDX-BF), such as peritoneal and pleural effusion samples, to provide personalized medicine without surgery. Methods: PDXs-BF were created from patients with ovarian cancer who had positive cytology findings based on peritoneal and pleural effusion samples. PDXs were also prepared from each primary tumor. The pathological findings based on immunohistochemistry were compared between the primary tumor, PDX, and PDX-BF. Further, genomic profiles and gene expression were evaluated using DNA and RNA sequencing to compare primary tumors, PDXs, and PDX-BF. Results: Among the 15 patients, PDX-BF was established for 8 patients (5 high-grade serous carcinoma, 1 carcinosarcoma, 1 low-grade serous carcinoma, and 1 clear cell carcinoma); the success rate was 53%. Histologically, PDXs-BF have features similar to those of primary tumors and PDXs. In particular, PDXs-BF had similar gene mutations and expression patterns to primary tumors and PDXs. Conclusions: PDX-BF reproduced primary tumors in terms of pathological features and genomic profiles, including gene mutation and expression. Thus, PDX-BF may be a potential alternative to surgical resection for patients with advanced disease.

Nuclear KRT19 is a transcriptional corepressor promoting histone deacetylation and liver tumorigenesis.

Epigenetic reprogramming and escape from terminal differentiation are poorly understood enabling characteristics of liver cancer. Keratin 19 (KRT19), classically known to form the intermediate filament cytoskeleton, is a marker of stemness and worse prognosis in liver cancer. This study aimed to address the functional roles of KRT19 in liver tumorigenesis and to elucidate the underlying mechanisms. Using multiplexed genome editing of hepatocytes in vivo, we demonstrated that KRT19 promoted liver tumorigenesis in mice. Cell fractionation revealed a previously unrecognized nuclear fraction of KRT19. Tandem affinity purification identified histone deacetylase 1 and REST corepressor 1, components of the corepressor of RE-1 silencing transcription factor (CoREST) complex as KRT19-interacting proteins. KRT19 knockout markedly enhanced histone acetylation levels. Mechanistically, KRT19 promotes CoREST complex formation by enhancing histone deacetylase 1 and REST corepressor 1 interaction, thus increasing the deacetylase activity. ChIP-seq revealed hepatocyte-specific genes, such as hepatocyte nuclear factor 4 alpha ( HNF4A ), as direct targets of KRT19-CoREST. In addition, we identified forkhead box P4 as a direct activator of aberrant KRT19 expression in liver cancer. Furthermore, treatment of primary liver tumors and patient-derived xenografts in mice suggest that KRT19 expression has the potential to predict response to histone deacetylase 1 inhibitors especially in combination with lenvatinib. Our data show that nuclear KRT19 acts as a transcriptional corepressor through promoting the deacetylase activity of the CoREST complex, resulting in dedifferentiation of liver cancer. These findings reveal a previously unrecognized function of KRT19 in directly shaping the epigenetic landscape in cancer.

Abstract 5120: Direct targeting of the COMPASS complex inhibits neuroblastoma growth by inhibiting cancer stem cells

Abstract Epigenetic regulator COMPASS Complex, a histone H3K4 methyltransferase has recently been shown to be involved in multiple cancers and attaining focus as a novel therapeutic target. High-risk neuroblastoma (NB) is a heterogeneous pediatric cancer with high mortality and relapse rates. The relapse of refractory cancer is shown to be driven by cancer stem cells (CSCs), which are maintained by epigenetic malfunctions. In the present study, we determined the effects of inhibiting the COMPASS complex on NB CSCs and overall NB growth. A high-throughput shRNA screening of methyltransferases and demethylases reveals the role of COMPASS complex partners MLL1 and Menin in NB proliferation. We found that both MLL1 and Menin are overexpressed in our previously identified CD114+ NB CSCs. Further, MEN1 (gene coding Menin) expression showed an inverse correlation with overall NB patient survival and cancer progression in a comprehensive analysis of 1235 primary NB patient data. Our ChIP results show that the CSF3R gene which codes for CD114 and maintains CD114+ NB CSCs, is regulated by the presence of high H3K4me3 activating marks. Further, we used MI-503 to inhibit MLL1-Menin interaction and also developed MEN1 stable knockdown and found that both strategies significantly inhibit H3K4me3 activity in NB, particularly at the CSF3R gene promoter. This led to decreased CSF3R expression and NB CSC levels. MI-503 significantly inhibits proliferation in different NB cell lines and primary patient-derived xenograft (PDX) lines, with minimal effect on non-cancerous fibroblasts. MI-503 significantly inhibits NB cell cycle progression at the S phase, induces apoptosis, and inhibits NB 3D spheroid growth and development. Interestingly, we overserved differential selectivity of MI-503 in inducing apoptosis and in blocking the cell cycle in NB CSCs in contrast to non-CSCs. MEN1 knockdown also inhibits NB proliferation and 3D spheroid growth. Furthermore, MI-503 in a dose-dependent manner synergistically sensitizes NB to chemotherapy doxorubicin and significantly inhibits NB proliferation and spheroid growth compared to either agent alone. Further, by using the NB xenograft in vivo tumor model, we established that MI-503 significantly inhibits NB tumor growth and tumor metastasis by directly inhibiting tumor NB CSCs, without any observed toxicities. Similar results of significantly reduced tumor growth, metastasis, and NB CSCs were shown by the MEN1 knockdown in vivo. Overall, our data show that the MLL1-Menin of the COMPASS complex directly activates the CSF3R gene to maintain NB CSCs and drive NB pathogenesis. Our data show that MI-503 or MEN1 knockdown leads to significant inhibition of NB growth by directly inhibiting NB CSCs in both in vitro and in vivo tumor models. Further developing these epigenetic-based therapeutic strategies and combining them with current therapies will pave the way for effectively managing NB. Citation Format: Rameswari Chilamakuri, Saurabh Agarwal. Direct targeting of the COMPASS complex inhibits neuroblastoma growth by inhibiting cancer stem 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 5120.

Abstract 5434: A novel combination therapy for lung squamous cell carcinoma

Abstract Lung cancer is the leading cause of cancer deaths in the US. Non-small cell lung cancer (NSCLC) accounts for ~80% of lung cancer cases and is further classified into adenocarcinoma (LUAD), squamous cell carcinoma (LUSC), and large cell carcinoma. New approaches targeting pathways in NSCLC have emerged, resulting in encouraging new treatments that benefit LUAD patients, but very few advances have been made in the treatment options for LUSC which accounts for ~30% of lung cancer cases. NSCLCs, including LUSCs, contain a sub-population of cells that exhibit properties of cancer stem cells (CSCs) and are responsible for tumor initiation, maintenance, therapeutic resistance, and relapse. Therefore, CSCs must be effectively targeted to elicit long lasting therapeutic results in LUSC patients. Our studies have shown that: 1) PKCι is an oncogene and prognostic marker in LUSC; 2) copy number gains (CNGs) of the PKCι gene (PRKCI) drives overexpression of PKCι in 90% of LUSCs; 3) PKCι phosphorylates SOX2, and controls SOX2-mediated transcriptional activation of Hedgehog Acyl Transferase, resulting in Hedgehog (Hh) pathway activation that drives a CSC phenotype in LUSC cells; and 4) the FDA approved compound Auranofin (ANF) is a potent inhibitor of oncogenic PKCι. In this study, we assessed the effect of ANF in combination with the Hh pathway inhibitor, LDE225, on LUSC CSCs and tumor growth. Cell viability, sphere formation and soft agar assays were used to assess the effects of ANF and LDE225 alone or in combination on the growth of LUSC CSCs with PRKCI CNGs or LUAD and LUSC CSCs without PRKCI CNG to determine if PRKCI CNG can be used to predict response to ANF and LDE225 and test the selectivity of response for LUSC. The effects of ANF and LDE225 on the levels of PKCι-Hh signaling components was assessed by qPCR and western blotting. Finally, the efficacy of ANF and LDE225 in combination was evaluated in human primary LUSC patient-derived xenograft (PDX) models that harbor PRKCI CNGs and the ability of PKCι-Hh signaling intermediates to serve as biomarkers of PKCι-Hh pathway inhibition was validated in vivo. We observed a dose-dependent decrease in cell proliferation, clonal expansion and transformed growth in CSCs treated with ANF and LDE225 alone. ANF and LDE225 combined treatment of LUSC CSCs with PRKCI CNGs (but not LUAD or LUSC CSCs without PRKCI CNG) synergistically inhibited CSC phenotypes based on results of combination index analysis. Furthermore, treatment of LUSC PDX models with ANF and LDE225 in combination had a synergistic effect on tumor growth inhibition. Lastly, ANF and LDE225 treatment led to inhibition of PKCι-Hh signaling intermediates demonstrating the on-target effects of treatment. Our data indicate that a PKCι-Hh vertical blockade strategy of combined ANF and LDE225 effectively targets LUSC CSCs and blocks tumor growth in vivo and provides compelling rationale to develop this novel combination strategy further in clinical trials. Citation Format: Dania Alqasrawi, Ryan Argo, Christine Ratliff Rang, Prita Pandya, Skyeler Klinge, Jennifer Lindemann, Nyla Searl, Alan Fields, Verline Justilien. A novel combination therapy for lung squamous cell carcinoma [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 5434.

Dynamic evolution of bone marrow adipocyte in B cell acute lymphoblastic leukemia: insights from diagnosis to post-chemotherapy

ABSTRACT Adipocyte is a unique and versatile component of bone marrow microenvironment (BMM). However, the dynamic evolution of Bone Marrow (BM) adipocytes from the diagnosis of B cell Acute Lymphoblastic Leukemia (B-ALL) to the post-treatment state, and how they affect the progression of leukemia, remains inadequately explicated. Primary patient-derived xenograft models (PDXs) and stromal cell co-culture system are employed in this study. We show that the dynamic evolution of BM adipocytes from initial diagnosis of B-ALL to the post-chemotherapy phase, transitioning from cellular depletion in the initial leukemia niche to a fully restored state upon remission. Increased BM adipocytes retards engraftment of B-ALL cells in PDX models and inhibits cells growth of B-ALL in vitro. Mechanistically, the proliferation arrest of B-ALL cells in the context of adipocytes-enrichment niche, might attribute to the presence of adiponectin secreted by adipocytes themselves and the absence of cytokines secreted by mesenchymal stem cell (MSCs). In summary, our findings offer a novel perspective for further in-depth understanding of the dynamic balance between BMM and B-ALL.

ETV6::ACSL6 translocation-driven super-enhancer activation leads to eosinophilia in acute lymphoblastic leukemia through IL-3 overexpression.

ETV6::ACSL6 represents a rare genetic aberration in hematopoietic neoplasms and is often associated with severe eosinophilia, which confers an unfavorable prognosis requiring additional anti-inflammatory treatment. However, since the translocation is unlikely to produce a fusion protein, the mechanism of ETV6::ACSL6 action remains unclear. Here, we performed multi-omics analyses of primary leukemia cells and patient-derived xenografts from an acute lymphoblastic leukemia (ALL) patient with ETV6::ACSL6 translocation. We identified a super-enhancer located within the ETV6 gene locus, and revealed translocation and activation of the super-enhancer associated with the ETV6::ACSL6 fusion. The translocated super-enhancer exhibited intense interactions with genomic regions adjacent to and distal from the breakpoint at chromosomes 5 and 12, including genes coding inflammatory factors such as IL-3. This led to modulations in DNA methylation, histone modifications, and chromatin structures, triggering transcription of inflammatory factors leading to eosinophilia. Furthermore, the bromodomain and extraterminal domain (BET) inhibitor synergized with standard-of-care drugs for ALL, effectively reducing IL-3 expression and inhibiting ETV6::ACSL6 ALL growth in vitro and in vivo. Overall, our study revealed for the first time a cis-regulatory mechanism of super-enhancer translocation in ETV6::ACSL6ALL, leading to an ALL-accompanying clinical syndrome. These findings may stimulate novel treatment approaches for this challenging ALL subtype.

Abstract A060: Organoid Culture as a Unique Resource for Studying Aggressive Triple Negative Breast Cancer in African American

Abstract Introduction Triple negative breast cancer (TNBC) among women with African ancestry has been shown to be more aggressive than in women of European ancestry. However, the root cause for this disparity is not fully understood. In our previous studies, we show that the gene expression in the breast cancer stem cells of TNBC tumors was differential based on Western sub-Saharan ancestry. To study the role of African ancestry in the biology of TNBC, we have developed patient-derived organoids (PDO) from African (Ghanaian) and African American tumors that will be available for research. Organoid culture has the capacity to mimic the physiological tissue organization and functionality and has been used as an invaluable tool for disease modeling and drug discovery. Objective The objective is to develop and characterize PDOs based on African TNBC that will serve as a renewable source of African tumors for breast cancer research. Methods Through our international collaboration called Precision Medicine for Aggressive Breast Cancers (PMABC), we obtained fresh patient tumors from continental Africa (Ghana) and African American tumors from Henry Ford Health. PDOs were developed form both primary tumors and patient-derived xenografts (PDX). Tissues were processed using the Miltenyi Gentle Mac. The cells were seeded in a 12-well plate coated with Matrigel. Developed organoids are characterized using single cell RNA sequencing as well as 10X spatial sequencing Results We have successfully developed organoids using frozen tissues from both West African and African American breast patients. We have successfully established four (4) organoid lines from individual primary breast cancer tissues and one PDX. The organoids are passaged after every 7-14 days, and the highest passage so far is passage number 12 for the organoids from primary tissues and passage number 15 for the PDXs. We are in the process of characterizing the developed organoids using single-cell assay in comparisons to their primary tumor of origin. Conclusion Establishment of organoids has helped us have a renewable source of tumor for studying the aggressive TNBC among Women with African ancestry. We aim to use the organoids to identify tumor biomarkers for treating aggressive TNBC that disproportionately affects women of western sub Saharan ancestry. Citation Format: Moses Kamita, Kurt Fernando, Sylvester Antwi, Forster Amponsah-Manu, Josephine Nsaful, Kafui Akakpo, Jessica Bensenhaver, Kwabena Agbedinu, Michael Nortey, Nelson Affram, Mohammed Sheriff, Cassandra Mills, Alex Mremi, Jieoma Aja, Moses Dokurugu, Haythem Ali, Eleanor Walker, Max Wicha, Evelyn Jiagge. Organoid Culture as a Unique Resource for Studying Aggressive Triple Negative Breast Cancer in African American [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A060.

Patient-derived organoids: a promising tool for breast cancer research.

Breast cancer (BC) is the most prevalent malignancy among women worldwide. Traditional research models such as primary cancer cell and patient-derived tumor xenografts (PDTXs) have limitations. Cancer cells lack a tumor microenvironment (TME) and genetic diversity, whereas PDTXs are expensive and have a time-consuming preparation protocol. Therefore, alternative research models are warranted. Patient-derived organoids (PDOs) are a promising in vitro model. They mimic the TME, gene expression, and cell types of original cancer tissues. PDOs have been successfully developed from various cancers, including BC. In this review, we focused on the value and limitations of PDOs in BC research, including their characteristics and potential in drug development, personalized therapy, immunotherapy, and the application prospects of PDOs in drug testing and prognosis.

Splicing modulators impair DNA damage response and induce killing of cohesin-mutant MDS and AML.

Splicing modulation is a promising treatment strategy pursued to date only in splicing factor-mutant cancers; however, its therapeutic potential is poorly understood outside of this context. Like splicing factors, genes encoding components of the cohesin complex are frequently mutated in cancer, including myelodysplastic syndromes (MDS) and secondary acute myeloid leukemia (AML), where they are associated with poor outcomes. Here, we showed that cohesin mutations are biomarkers of sensitivity to drugs targeting the splicing factor 3B subunit 1 (SF3B1) H3B-8800 and E-7107. We identified drug-induced alterations in splicing, and corresponding reduced gene expression, of a number of DNA repair genes, including BRCA1 and BRCA2, as the mechanism underlying this sensitivity in cell line models, primary patient samples and patient-derived xenograft (PDX) models of AML. We found that DNA damage repair genes are particularly sensitive to exon skipping induced by SF3B1 modulators due to their long length and large number of exons per transcript. Furthermore, we demonstrated that treatment of cohesin-mutant cells with SF3B1 modulators not only resulted in impaired DNA damage response and accumulation of DNA damage, but it sensitized cells to subsequent killing by poly(ADP-ribose) polymerase (PARP) inhibitors and chemotherapy and led to improved overall survival of PDX models of cohesin-mutant AML in vivo. Our findings expand the potential therapeutic benefits of SF3B1 splicing modulators to include cohesin-mutant MDS and AML.

Molecular characterization of metastatic progression in patient derived xenograft models of malignant uveal melanoma

Aims/Purpose: It has been observed that large UM lesions with significant infiltration of macrophages and CD8+ T cells exhibit specific genetic profiles that increase the risk of liver metastasis. Additionally, recent discoveries of DNA methylation changes in Class 2 tumours undergoing metastasis suggest a potential role of epigenetic alterations in UM progression.Methods: To identify factors involved in UM metastasis, we implanted 25 viable UM tumours (consisting of 11 Class 1 tumours with a good prognosis and 14 Class 2 tumours with a poor prognosis) subcutaneously into immunodeficient NSG mice. From these, we successfully established ten patient‐derived xenografts (PDXs) using Class 2 tumour tissues. Two metastatic PDXs were derived from liver (UM50) and peritoneal (UM58) metastases spontaneously developed on mice.Results: Comprehensive characterization of both primary tumours and PDX tissues was performed using bulk transcriptomics and methylomics techniques. Among the enriched metabolic pathways identified in the liver metastasis‐derived PDX tissue of sample UM50 compared to the PDX tissue from the primary tumour, four were related to epigenetic regulation, including the activation of rRNA expression by ERCC6 and EHMT2, methylation of histones and DNA by Polycomb Repressive Complex 2 (PRC2), regulation of rRNA expression by NAD‐dependent Deacetylase Sirtuin‐1, and the DNA methylation pathway.Conclusions: These findings highlight the potential importance of epigenetic deregulation in UM progression and provide a foundation for future investigations. Further analysis using the Chromium Single Cell ATAC platform to examine chromatin accessibility at the single‐cell level in primary and metastatic PDX tissues of UM50 and UM58 that are ongoing can contribute to unravelling the precise role of epigenetic alterations in UM metastasis. Continued research in this area may lead to the development of novel therapeutic strategies targeting epigenetic mechanisms and improving outcomes for patients with metastatic UM.

Comparative RNA-Seq Analysis Revealed Tissue-Specific Splicing Variations during the Generation of the PDX Model

Tissue-specific gene expression generates fundamental differences in the function of each tissue and affects the characteristics of the tumors that are created as a result. However, it is unclear how much the tissue specificity is conserved during grafting of the primary tumor into an immune-compromised mouse model. Here, we performed a comparative RNA-seq analysis of four different primary-patient derived xenograft (PDX) tumors. The analysis revealed a conserved RNA biotype distribution of primary−PDX pairs, as revealed by previous works. Interestingly, we detected significant changes in the splicing pattern of PDX, which was mainly comprised of skipped exons. This was confirmed by splicing variant-specific RT-PCR analysis. On the other hand, the correlation analysis for the tissue-specific genes indicated overall strong positive correlations between the primary and PDX tumor pairs, with the exception of gastric cancer cases, which showed an inverse correlation. These data propose a tissue-specific change in splicing events during PDX formation as a variable factor that affects primary−PDX integrity.

The tumor-enriched small molecule gambogic amide suppresses glioma by targeting WDR1-dependent cytoskeleton remodeling

Glioma is the most prevalent brain tumor, presenting with limited treatment options, while patients with malignant glioma and glioblastoma (GBM) have poor prognoses. The physical obstacle to drug delivery imposed by the blood‒brain barrier (BBB) and glioma stem cells (GSCs), which are widely recognized as crucial elements contributing to the unsatisfactory clinical outcomes. In this study, we found a small molecule, gambogic amide (GA-amide), exhibited the ability to effectively penetrate the blood-brain barrier (BBB) and displayed a notable enrichment within the tumor region. Moreover, GA-amide exhibited significant efficacy in inhibiting tumor growth across various in vivo glioma models, encompassing transgenic and primary patient-derived xenograft (PDX) models. We further performed a genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) knockout screen to determine the druggable target of GA-amide. By the combination of the cellular thermal shift assay (CETSA), the drug affinity responsive target stability (DARTS) approach, molecular docking simulation and surface plasmon resonance (SPR) analysis, WD repeat domain 1 (WDR1) was identified as the direct binding target of GA-amide. Through direct interaction with WDR1, GA-amide promoted the formation of a complex involving WDR1, MYH9 and Cofilin, which accelerate the depolymerization of F-actin to inhibit the invasion of patient-derived glioma cells (PDCs) and induce PDC apoptosis via the mitochondrial apoptotic pathway. In conclusion, our study not only identified GA-amide as an effective and safe agent for treating glioma but also shed light on the underlying mechanisms of GA-amide from the perspective of cytoskeletal homeostasis.

STI-8591, a Novel Tyrosine Kinase Inhibitor, Shows Excellent Antileukemic Activity in FLT3-Mutated (mut) Acute Myeloid Leukemia (AML)

FMS-related tyrosine kinase 3 ( FLT3) mutations, including internal tandem duplications ( FLT3-ITD) and tyrosine kinase domain ( FLT3-TKD), are found in approximately 30% of AML patients. FLT3 has emerged as a promising molecular target in therapy of AML. Herein, we report on the activity of STI-8591, a novel kinase inhibitor developed by Hangzhou ACEA Pharmaceutical Research Co, in AML models carrying FLT3 mut, including those associated with TKI resistance [e.g., FLT3-ITD(F691L)]. We first determined the in vitro antileukemic effects of STI-8591 in FLT3mut human AML cell lines (MV4-11, MOLM-13), a murine cell line Ba/F3 transduced with FLT3-TKD(D835Y)[Ba/F3 FLT3-TKD(D835Y)] or FLT3-ITD-TKD(D835Y) [Ba/F3 FLT3-ITD-TKD(D835Y)] or FLT3-ITD/F691L [Ba/F3 FLT3-ITD(F691L), which has been associated with drug-resistant, and primary blasts from FLT3mut AML patients. STI-8591 effectively inhibited cell proliferation and induced apoptosis in FLT3-ITD/TKDmut cell lines (IC 50: 0.33 to 9.19nM at 24 hours). Of note, STI-8591 demonstrates 4-7-fold higher antileukemic activity on otherwise resistant Ba/F3 FLT3-ITD(F691L) cells than the currently available FLT3 inhibitors, Gilteritinib and Quizartinib. Similar antileukemic activity of STI-8591 was observed on primary FLT3mut AML blasts (median IC 50: 13.67nM, n=5). The antileukemic mechanism of STI-8591 is associated with inhibition of the phosphorylation of the mutated FLT3 protein and its downstream targets (i.e., STAT5, AKT, and ERK) as shown by western blot analysis. To test the in vivo antileukemic activity of STI-8591, we utilized 4 FLT3mut AML murine and human models, obtained by transplanting: 1. BM mononuclear cells (MNCs) from CD45.2 MLLPTD/WTFLT3ITDITD AML mice congenic CD45.1 B6 mice; 2. murine cell lines [i.e. Ba/F3 FLT3-TKD(D835Y) , Ba/F3 FLT3-ITD-TKD(D835Y), or Ba/F3 FLT3-ITD(F691L), 3. Luciferase-expressing FLT3mut MOLM13 cells (MOLM13 Luci) into NCG mice; 4. primary blasts from FLT3 mut AML patients into NSGS mice. We treated these mice for 3-4 weeks [3 to 30mg/kg/day(d), oral gavage]. For the MLLPTD/WTFLT3ITDITD model (n=10 mice/group), compared with Vehicle(V)-treated mice [median survival: 44 d], we observed significantly lower engraftment and longer overall survival (OS) in mice treated with STI-8591 10mg/kg (52 d, p&amp;lt;0.0001) or 30mg/kg (57 d, p&amp;lt;0.0001) or Gilteritinib 10mg/kg (49 d, p=0.0029). At 10mg/kg dosage, STI-8591-treated mice lived longer than Gilteritinib-treated mice (p=0.0195). Treatment of STI-8591 also demonstrated significant benefits to mice transplanted with FLT3mut Ba/F3 cells. For the TKI-resistant Ba/F3 FLT3-ITD(F691L) model (n=10/group), STI-8591 (median:19 and 37 d for 10 and 30 mg/kg) and Gilteritinib (17 and 24 d for 10 and 30 mg/kg) -treated mice had longer OS than V-treated (12 d) mice. At equivalent dosage (10 and 30mg/kg), STI-8591-treated mice lived longer than Gilteritinib-treated mice (p=0.0013 and p&amp;lt;0.0001). For the MOLM13 Luci+ model (n=5/group), mice receiving STI-8591 or Gilteritinib treatment demonstrated a significant reduction in disease burden as observed by bioluminescence imaging (BLI), and prolonged OS. Compared with V-treated mice (median: 23 d), we observed longer OS in Gilteritinib (10mg/kg, 33 d, p=0.0023) and STI-8591 (3mg/kg, 27 d, p=0.0179; 10mg/kg, 34 d, p=0.0023; and 30mg/kg, 35 d, p=0.0023) -treated mice. At 10 mg/kg dosage, STI-8591- and Gilteritinib- treated mice showed no significant difference in OS (p=0.2411). Similar experiments are ongoing in FLT3 mut primary AML patient-derived xenografts (PDXs) and will be reported at the ASH meeting. To evaluate antileukemic activity of STI-8591 in mice bearing disease in central nervous system (CNS), we implanted 5×10 5 /3 µL MOLM13 cells intracranially into SCID mice to construct the CNS leukemia model (n=9/group). Compared with V-treated mice (median: 11 d), we observed a longer OS in mice treated with Gilteritinib (10 mg/kg, 18 d, p=0.0004) or STI-8591 (10 mg/kg, 23 d, p&amp;lt;0.0001; and 30 mg/kg, 26 d, p&amp;lt;0.0001). At 10 mg/kg dosage, STI-8591-treated mice lived longer than Gilteritinib-treated mice (p=0.005). In conclusion, STI-8591, a novel TKI exhibited a potent antileukemic activity in various FLT3mut AML models, including those carrying FLT3 mut associated with drug resistance. These results supported further clinical development of STI-8591 for treatment of AML.

Establishment of a patient-derived xenograft humanized mouse model for hepatoblastoma in children

Objective: To establish a patient-derived xenograft (PDX) humanized mouse model for hepatoblastoma in children. In addition, compare the biological consistency between successfully modeled PDX tumors and primary tumors in children while comparing and analyzing the influence of PDX model modeling success as a key factor. Methods: A PDX tumor model was constructed from fresh tumor tissue samples from 39 children with hepatoblastoma. The tumor growth time and volume size were recorded in detail. Simultaneously, 39 children's data were collected for experimental and clinical analysis. The difference in tumorigenesis rate between different parameters was analyzed by χ (2) test (categorical variable). Continuous variables with a normal distribution were compared using the t-test. Results: After cell passage and pathological diagnosis, 21 cases of hepatoblastoma PDX models were successfully constructed, with a success rate of 53.8% (21/39). Tumor samples from each generation of successfully modeled PDX models had pathology results that were consistent with those of the corresponding primary tumors. The analysis of the key factors affecting the tumor formation rate of PDX revealed that the metastasis rate was more successful in primary tumors than in liver in situ tumors (7/8 vs. 14/31, P = 0.049). However, there was no significant difference between tumor formation rates and pathological subtypes. According to the PDX tumor formation group comparison between the primary tumor and the metastatic tumor, there was no statistically significant difference between the two groups in terms of tumor formation time and tumor volume. Hematoxylin-eosin staining in hepatoblastoma's PDX mouse was consistent with the primary tumor. Immunohistochemistry positivity rates of four proteins, namely hepatocyte antigen (Hepatocyte), phosphatidylinositol glycan 3, β-catenin, and alpha-fetoprotein, in primary tumor tissues and PDX mouse models were 100% vs. 100%, 100% vs. 95.24%, 100% vs. 100%, and 95.24% vs. 85.71%, respectively. Conclusion: A PDX mouse model for hepatoblastoma has been successfully established in children. The tumor formation rate is high, with metastatic tumors having a higher tumor formation rate than primary tumors and transplanted tumors retaining the biological characteristics of primary tumors.

Abstract A066: Molecular phenotyping in single cell RNA sequencing allows for identification of common populations across studies and platforms

Abstract Single cell RNA sequencing (scRNA seq) has become a prominent tool towards understanding models of prostate cancer. However, there are limited approaches geared towards collating these experiments into a unified framework for understanding discoveries across studies. In our lab, we have performed scRNA seq on multiple organoid models, across a spectrum of phenotypes including amphicrine, adenocarcinoma, and neuroendocrine disease, as well as performed lineage barcode tracing in a subset of these experiments as a means of identifying lineage transitions. Additionally, we have scRNA seq on a robust patient-derived xenograft (PDX) model of metastasis, consisting of experiments from primary and metastatic PDX models collected from multiple tissues including both intact and castrated backgrounds. Along with data generated by our lab, we accessed published scRNA seq studies from other labs which broadened the pool of experiments to include data from cell lines and multiple single cell analysis platforms. In order to perform computational molecular phenotyping of the scRNA seq experiments, we curated gene sets from the literature and applied principal components analysis (PCA) to them as our molecular phenotyping scoring approach which is widely used by previous studies. Because of the diverse background of the studies being incorporated into our molecular phenotyping, we used the bioconductor stack of single cell analysis tools to perform quality control and removal of batch effects. We observe that molecular phenotyping of samples across different backgrounds shows common populations typically associated with proliferation and stemness, and that unique populations present in each sample are usually more associated with terminal differentiation and senescence. In addition to identifying common and unique populations across samples and platforms, we also can assess individual genes on their importance in the molecular phenotyping approach. The use of PCA to generate our molecular phenotyping score allows the rotation matrix to be used as an additional metric when ranking genes for biological importance in concert with commonly used metrics such as variability and deviance. When combining the global metrics with the rotation matrix for each gene set, genes can be arranged in a network to determine key genes for molecular phenotyping, allowing for more concise gene sets that decrease the computational overhead for performing the molecular phenotyping. Overall, our work suggests that a unified framework of analysis can yield new insights into scRNA seq studies by identifying common populations present across sample backgrounds and different scRNA seq technologies. Additionally, genes can be arranged into networks based on biological significance derived from global statistical analysis as well as molecular phenotyping to identify more concise gene signatures, decreasing computational overhead and highlighting genes with excessive contribution to biological state. Citation Format: Brian Capaldo, Michael Beshiri, Juan Yin, Kathy Kelly. Molecular phenotyping in single cell RNA sequencing allows for identification of common populations across studies and platforms [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A066.

Establishment of Pancreatic Cancer-Derived Tumor Organoids and Fibroblasts From Fresh Tissue.

Tumor organoids are three-dimensional (3D) ex vivo tumor models that recapitulate the biological key features of the original primary tumor tissues. Patient-derived tumor organoids have been used in translational cancer research and can be applied to assess treatment sensitivity and resistance, cell-cell interactions, and tumor cell interactions with the tumor microenvironment. Tumor organoids are complex culture systems that require advanced cell culture techniques and culture media with specific growth factor cocktails and a biological basement membrane that mimics the extracellular environment. The ability to establish primary tumor cultures highly depends on the tissue of origin, the cellularity, and the clinical features of the tumor, such as the tumor grade. Furthermore, tissue sample collection, material quality and quantity, as well as correct biobanking and storage are crucial elements of this procedure. The technical capabilities of the laboratory are also crucial factors to consider. Here, we report a validated SOP/protocol that is technically and economically feasible for the culture of ex vivo tumor organoids from fresh tissue samples of pancreatic adenocarcinoma origin, either from fresh primary resected patient donor tissue or patient-derived xenografts (PDX). The technique described herein can be performed in laboratories with basic tissue culture and mouse facilities and is tailored for wide application in the translational oncology field.