HIF1A signaling selectively supports proliferation of breast cancer in the brain

Blood-borne metastasis to the brain is a major complication of breast cancer, but cellular pathways that enable cancer cells to selectively grow in the brain microenvironment are poorly understood. We find that cultured circulating tumor cells (CTCs), derived from blood samples of women with advanced breast cancer and directly inoculated into the mouse frontal lobe, exhibit striking differences in proliferative potential in the brain. Derivative cell lines generated by serial intracranial injections acquire selectively increased proliferative competency in the brain, with reduced orthotopic tumor growth. Increased Hypoxia Inducible Factor 1A (HIF1A)-associated signaling correlates with enhanced proliferation in the brain, and shRNA-mediated suppression of HIF1A or drug inhibition of HIF-associated glycolytic pathways selectively impairs brain tumor growth while minimally impacting mammary tumor growth. In clinical specimens, brain metastases have elevated HIF1A protein expression, compared with matched primary breast tumors, and in patients with brain metastases, hypoxic signaling within CTCs predicts decreased overall survival. The selective activation of hypoxic signaling by metastatic breast cancer in the brain may have therapeutic implications.

The Lipogenic Regulator SREBP2 Induces Transferrin in Circulating Melanoma Cells and Suppresses Ferroptosis

Circulating tumor cells (CTC) are shed by cancer into the bloodstream, where a viable subset overcomes oxidative stress to initiate metastasis. We show that single CTCs from patients with melanoma coordinately upregulate lipogenesis and iron homeostasis pathways. These are correlated with both intrinsic and acquired resistance to BRAF inhibitors across clonal cultures of BRAF-mutant CTCs. The lipogenesis regulator SREBP2 directly induces transcription of the iron carrier Transferrin (TF), reducing intracellular iron pools, reactive oxygen species, and lipid peroxidation, thereby conferring resistance to inducers of ferroptosis. Knockdown of endogenous TF impairs tumor formation by melanoma CTCs, and their tumorigenic defects are partially rescued by the lipophilic antioxidants ferrostatin-1 and vitamin E. In a prospective melanoma cohort, presence of CTCs with high lipogenic and iron metabolic RNA signatures is correlated with adverse clinical outcome, irrespective of treatment regimen. Thus, SREBP2-driven iron homeostatic pathways contribute to cancer progression, drug resistance, and metastasis. SIGNIFICANCE: Through single-cell analysis of primary and cultured melanoma CTCs, we have uncovered intrinsic cancer cell heterogeneity within lipogenic and iron homeostatic pathways that modulates resistance to BRAF inhibitors and to ferroptosis inducers. Activation of these pathways within CTCs is correlated with adverse clinical outcome, pointing to therapeutic opportunities.This article is highlighted in the In This Issue feature, p. 521.

Abstract IA-02: Pancreatic cancer heterogeneity and plasticity: The mix of seed and soil

A series of transcriptomic analyses of human pancreatic ductal adenocarcinoma (PDAC) have consistently demonstrated multiple cancer subtypes with different functional behavior in preclinical models and patient outcomes in clinical studies. The two major molecular subtypes described in PDAC are the classical epithelial (E) and the quasi-mesenchymal (QM) subtypes, otherwise known as the basal-like or squamous subtype. Although a model of E and QM subtypes to dichotomize PDAC tumor behavior affords the simplicity of use in biomarker and functional studies, there has been increasing evidence of epithelial mesenchymal transition (EMT) transcriptional plasticity of PDAC cells in model systems as well as evidence from single cell RNA-seq studies. This suggests that the E and QM states are on a continuum that can result in interconverting cell types. We have utilized single cell technologies, functional model systems, and human tumor analysis to characterize the landscape of PDAC heterogeneity and the factors involved with cellular plasticity between E and QM states. Initial single cell RNA-seq studies in PDAC mouse models revealed that partial EMT is enriched in circulating tumor cells (CTCs) compared to primary tumor cells (Ting DT et al. Cell Reports 2014). These CTCs were also highly enriched for extracellular matrix (ECM) gene expression that were shared with stromal fibroblasts in the primary tumor indicating that the “seeds” of metastasis produce their own “soil”. Functional studies in patient derived PDAC cell lines and cancer associated fibroblasts (CAFs) revealed EMT heterogeneity was partially driven by the relative amounts of stromal CAFs (Ligorio M*, Sil S* et al. Cell 2019). Using RNA in situ hybridization (RNA-ISH) in human primary PDAC tumors and high content digital image analysis, we classified individual tumor cells for EMT and proliferative (PRO) phenotypes that were linked with relative stromal content and characterize the significant inter- and intra-tumoral heterogeneity of these cell types within distinct tumor glands. In addition, analysis of PDAC tumorspheres revealed a significant induction of EMT changes in response to FOLFIRINOX, which was also found in patient tumors that were resected after neoadjuvant FOLFIRINOX (Porter RL et al. PNAS 2019). Finally, we have recently characterized human PDAC CTCs that has identified 4 different stem cell genes (WNT5A/KLF4, LGALS3, LIN28B) that are enriched in these metastatic precursors and cluster separately between patients (Franses JW*, Philipp J* et al. Nature Communications 2020). Each of these CTC phenotypes are all associated with EMT features suggestive of different pathways that can achieve similar metastatic behavior. Altogether, single cell heterogeneity of PDAC is functionally linked with tumor stromal interactions, response to chemotherapy, and the ability to seed distant metastases.

Citation Format: David T. Ting. Pancreatic cancer heterogeneity and plasticity: The mix of seed and soil [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr IA-02.

Glioblastoma-Associated Microglia Reprogramming Is Mediated by Functional Transfer of Extracellular miR-21

Gliomas are primary, diffusely infiltrating brain tumors. Microglia are innate immune cells in the CNS and make up a substantial portion of the tumor mass. Glioma cells shape their microenvironment, communicating with and reprogramming surrounding cells, resulting in enhanced angiogenesis, immune suppression, and remodeling of the extracellular matrix. Glioma cells communicate with microglia, in part by releasing extracellular vesicles (EVs). Mouse glioma cells stably expressing a palmitoylated GFP to label EVs were implanted intracranially into syngeneic miR-21-null mice. Here, we demonstrate functional delivery of miR-21, regulating specific downstream mRNA targets in microglia after uptake of tumor-derived EVs. These findings attest to EV-dependent microRNA delivery as studied in an in vivo-based model and provide insight into the reprograming of microglial cells by tumor cells to create a favorable microenvironment for cancer progression.

Neoplastic-Stromal Cell Cross-talk Regulates Matrisome Expression in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is characterized by a highly desmoplastic reaction, warranting intense cancer-stroma communication. In this study, we interrogated the contribution of the BET family of chromatin adaptors to the cross-talk between PDAC cells and the tumor stroma. Short-term treatment of orthotopic xenograft tumors with CPI203, a small-molecule inhibitor of BET proteins, resulted in broad changes in the expression of genes encoding components of the extracellular matrix (matrisome) in both cancer and stromal cells. Remarkably, more than half of matrisome genes were expressed by cancer cells. In vitro cocultures of PDAC cells and cancer-associated fibroblasts (CAF) demonstrated that matrisome expression was regulated by BET-dependent cancer-CAF cross-talk. Disrupting this cross-talk in vivo resulted in diminished growth of orthotopic patient-derived xenograft tumors, reduced proliferation of cancer cells, and changes in collagen structure consistent with that of patients who experienced better survival. Examination of matrisome gene expression in publicly available data sets of 573 PDAC tumors identified a 65-gene signature that was able to distinguish long- and short-term PDAC survivors. Importantly, the expression of genes predictive of short-term survival was diminished in the cancer cells of orthotopic xenograft tumors of mice treated with CPI203. Taken together, these results demonstrate that inhibiting the activity BET proteins results in transcriptional and structural differences in the matrisome are associated with better patient survival. IMPLICATIONS: These studies highlight the biological relevance of the matrisome program in PDAC and suggest targeting of epigenetically driven tumor-stroma cross-talk as a potential therapeutic avenue.

IDH-mutant gliomas harbor fewer regulatory T cells in humans and mice

The metabolic gene isocitrate dehydrogenase 1 (IDH1) is commonly mutated in lower grade glioma (LGG) and secondary glioblastoma (GBM). Regulatory T cells (Tregs) play a significant role in the suppression of antitumor immunity in human glioma. Given the importance of Tregs in the overall framework of designing immune-based therapies, a better understanding on their association with IDH mutational status remains of critical clinical importance. Using multispectral imaging analysis, we compared the incidence of Tregs in IDH-mutant and IDH wild-type glioma from patient tumor samples of LGG. An orthotopic IDH-mutant murine model was generated to evaluate the role of mutant IDH on Treg infiltration by immunohistochemistry. When compared to IDH wild-type controls, Tregs are disproportionally underrepresented in mutant disease, even when taken as a proportion of all infiltrating T cells. Our findings suggest that therapeutic agents targeting Tregs may be more appropriate in modulating the immune response to wild-type disease.

Abstract LB-350: Robust correlation of Galectin-9 expression with immunological tumor features and outcome in multiple tumor types establishes it as both a novel therapeutic target and a biomarker

Galectin-9 (gal-9) is a powerful biological target for cancer immunotherapy and acts as pivotal immuno-suppressor disabling immune-mediated cancer attack and cancer susceptibility to cytotoxic T cell-induced death. We have developed a fully human, anti-gal-9 mAb (LYT-200), aimed for a first in human clinical trial in 2020 in difficult-to-treat cancers. The current study provides compelling evidence of gal-9 significance as a biomarker and a target for therapy.

Tissue sources: >1000 breast (BC) and 500 colorectal cancers (CRC) from Nottingham University and 150 pancreatic ductal adenocarcinoma (PDA) and 100 cholangiocarcinoma (CCA) from the Massachusetts General Hospital. Clinicopathological information were available for correlative analyses. Anti-gal-9 mAb (1G3, Sigma) was used for tissue staining. Independent pathologists assigned intensity score: 0, 1, 2, 3 for gal-9. The following was used: Pearson correlation for two variables; Log-rank test for Kaplan-Meier survival curves; Cox models were fit using the R-function ‘coxph' from the ‘survival' package.

Gal-9 was highly expressed in BC, CRC, PDA, CCA, and in patients' blood compared to healthy controls, indicating its biomarker and therapeutic target potential. High gal-9 in BC correlated with worse 5-year distant metastases free (DMFS; p=0.007) and disease free survival (DFS; p<0.001). High gal-9 retained independent prognostic potential in multivariate analyses with BC stage, grade and size (p=0.006). In PDL-1 positive versus PDL-1 negative tumors, high gal-9 correlated with worse DMFS and DFS (p<0.001). High gal-9 correlated with high tumor grade and mitotic score (p<0.001;p=0.006), triple negative receptor status (p=0.007), and features of an immunosuppressed microenvironment: tumor excluded CD8+ T cells (p=0.02) and intra-tumoral and stromal FOXP3+ cells (p<0.007). Correlative analyses of gal-9 expression with CCR7, CD1a, CD24, CD56, granzyme B, IFNγ, IL17, IL1β, IL23, TGFβ, MHC II, RORγ; and of CRC, PDA and CCA series with comprehensive clinicopathological and molecular tumor characteristics, are under way.

The current study features large, comprehensive cancer patient cohorts providing compelling evidence that gal-9 may be a valuable cancer biomarker and a therapeutic target. BC data collectively confirm the relevance of gal-9 immuno-biology and function in this disease. This study reinforces the importance of considering gal-9 as a theranostic and investigating targeting gal-9 to impede tumor growth through immune rescue in multiple tumor types.

Citation Format: Aleksandra Filipovic, Shohei Koide, Linxiao Chen, David T. Ting, Mohammad Ilyas, Wakkas Fadhil, Emad Rakha, Andrew Green. Robust correlation of Galectin-9 expression with immunological tumor features and outcome in multiple tumor types establishes it as both a novel therapeutic target and a biomarker [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-350.

Abstract 6073: The lipogenic regulator SREBP induces Transferrin in circulating melanoma cells, suppressing their susceptibility to ferroptosis

Circulating tumor cells (CTCs) are shed by cancers into the bloodstream, where a viable subset overcomes oxidative stress to initiate metastatic outgrowth. Clonally derived cultured CTCs from patients with BRAF-mutant melanoma reveal upregulation of lipogenesis and iron homeostasis pathways, correlated with their baseline and acquired drug resistance. In CTCs, the lipogenesis regulator SREBP directly induces transcription of the iron carrier Transferrin (TF), thereby reducing intracellular reactive oxygen species (ROS) and lipid peroxidation, and conferring resistance to BRAF inhibitors and inducers of ferroptosis. Knockdown of endogenous TF impairs tumorigenesis by melanoma CTCs; their associated soft agar clonogenic defect is rescued by the lipophilic anti-oxidants Ferrostatin-1 or Vitamin E, and by cholesterol. Single cell RNA-seq of patient-derived melanoma CTCs identifies a subset with high lipogenic, iron metabolic and proliferative signatures, correlated with adverse clinical outcome. Together, the coordinated regulation of these SREBP-driven pathways contributes to cancer progression, drug resistance and metastasis.

Citation Format: Xin Hong, Whijae Roh, Ryan J. Sullivan, Keith H. Wong, Ben S. Wittner, HongShan Guo, Taronish D. Dubash, Moshe Sade-Feldman, Ben K. Wesley, Genevieve M. Boland, Dieuwke L. Marvin, Todd Bonesteel, Chenyue Lu, Elad Horwitz, François Aguet, Samuel S. Freeman, Katherine Calhoun, Michelle K. Jewett, Linda T. Nieman, Nir Hacohen, Anders M. Näär, David T. Ting, Mehmet Toner, Shannon L. Stott, Gad Getz, Shyamala Maheswaran, Daniel A. Haber. The lipogenic regulator SREBP induces Transferrin in circulating melanoma cells, suppressing their susceptibility to ferroptosis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6073.

Abstract LB-011: Patient-derived organoids may facilitate precision medicine in pancreatic cancer: Demonstrating feasibility in the context of a multi-center clinical trial

Background: Systemic disease control is the principle driver of prognosis in patients with pancreatic cancer (PDAC). Currently, there are no predictive biomarkers of clinical response to guide selection of an optimal treatment approach. Our work explores the logistics and feasibility of generating patient tumor-derived models to serve as biomarkers. Methods: Patients with borderline resectable or locally advanced PDAC enrolled to participate in a multi-institutional prospective, randomized, trial were eligible. Pretreatment core needle biopsies from diagnostic endoscopy were shipped via commercial post to a centralized organoid laboratory. Patient-specific organoids (PDO) were established as previously described by our group. Putative predictive biomarkers of clinical treatment response, including whole-exome sequencing (WES), RNA-sequencing, and pharmacotyping (chemotherapeutic sensitivity testing) were performed prospectively. Putative predictive biomarkers will be compared to clinical outcomes when approved by the trial's Data Safety Monitoring Board. Results: Approximately 40% (42/98) of patients participated in tissue acquisition for organoid development. Culture maturation can be described in three relevant phases: establishment, expansion, and characterization. The establishment phase describes the emergence of viable ductal organoid development in the setting of a culture being cleared of other components of the tumor microenvironment. During these first 3-5 passages, there are numerous potential pitfalls, including technical and logistical challenges. Out of 42, 26 (62%) PDOs were successfully established. Notably, the establishment phase appears to be an area of the greatest improvement, as the rates of successful establishment improve while the collaborative team builds experience. Expansion involves biomass accumulation in clean culture. Of those that succeeded in establishment, 77% (20/26) entered in expansion phase. We can currently report 15 PDOs having reached the characterization phase (WES, RNA-seq with subtyping, and/or pharmacotyping). Based on RNA expression profile, 10/14 were classified as classical and 4 as basal-like subtype. Mean time to pharmacotyping was 179 days. The PDOs showed a variable population distribution of sensitivity to standard-of-care chemotherapeutics (gemcitabine, paclitaxel, irinotecan, 5-FU, oxaliplatin). Conclusions: Developing a living organoid biobank from PDAC biopsies in a multi-center trial setting is a tractable approach in precision medicine initiatives. Amongst a collaborative team of physician scientists, the establishment phase is critical. PDOs from pre-treatment biopsies can be individually characterized within a clinically relevant time frame and unique tumor-specific ex vivo-derived therapeutic sensitivities can be assessed.

Citation Format: Toni T. Seppälä, Jacquelyn W. Zimmerman, Noah Rozich, Alex Blair, Ammar Javed, John L. Cameron, William R. Burns, Jin He, David Tuveson, Christopher L. Wolfgang, David P. Ryan, Alec Kimmelman, Joseph M. Herman, Wells Messersmith, Theodore S. Hong, David T. Ting, Richard Andrew Burkhart. Patient-derived organoids may facilitate precision medicine in pancreatic cancer: Demonstrating feasibility in the context of a multi-center clinical trial [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-011.

Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection

The relationship of SARS-CoV-2 lung infection and severity of pulmonary disease is not fully understood. We analyzed autopsy specimens from 24 patients who succumbed to SARS-CoV-2 infection using a combination of different RNA and protein analytical platforms to characterize inter- and intra- patient heterogeneity of pulmonary virus infection. There was a spectrum of high and low virus cases that was associated with duration of disease and activation of interferon pathway genes. Using a digital spatial profiling platform, the virus corresponded to distinct spatial expression of interferon response genes and immune checkpoint genes demonstrating the intra-pulmonary heterogeneity of SARS-CoV-2 infection.

Pancreatic circulating tumor cell profiling identifies LIN28B as a metastasis driver and drug target

Pancreatic ductal adenocarcinoma (PDAC) lethality is due to metastatic dissemination. Characterization of rare, heterogeneous circulating tumor cells (CTCs) can provide insight into metastasis and guide development of novel therapies. Using the CTC-iChip to purify CTCs from PDAC patients for RNA-seq characterization, we identify three major correlated gene sets, with stemness genes LIN28B/KLF4, WNT5A, and LGALS3 enriched in each correlated gene set; only LIN28B CTC expression was prognostic. CRISPR knockout of LIN28B-an oncofetal RNA-binding protein exerting diverse effects via negative regulation of let-7 miRNAs and other RNA targets-in cell and animal models confers a less aggressive/metastatic phenotype. This correlates with de-repression of let-7 miRNAs and is mimicked by silencing of downstream let-7 target HMGA2 or chemical inhibition of LIN28B/let-7 binding. Molecular characterization of CTCs provides a unique opportunity to correlated gene set metastatic profiles, identify drivers of dissemination, and develop therapies targeting the "seeds" of metastasis.

Abstract A66: Repeatome profiling in high-grade serous ovarian cancer reveals abundant repeat noncoding RNA expression

The lack of consensus on clinically relevant molecular subtypes by gene expression in high-grade serous ovarian carcinoma (HGSOC) creates a barrier to subtype-based clinical investigation for the development of targeted therapies. We previously discovered aberrant expression of noncoding repeat RNAs across epithelial cancers including ovarian (Ting, Science 2011), which can invoke innate immune responses in tumors (Chiappinelli, Cell 2015). Epigenetic alterations and loss of tumor suppressor function, especially p53, can derepress endogenous repetitive elements in cancer. Further, BRCA1 deficiency induces satellite repeat RNAs, which promote genomic instability via interacting with the BRCA1 complex (Zhu, Mol Cell 2018), highlighting their potential significance in HGSOC. Here we aim to comprehensively define the as yet uncharacterized “repeatome” in HGSOC to refine molecular subtypes and identify novel biomarkers and therapeutic targets. We developed a Total RNASeq platform and novel computational pipelines to quantify the repeatome (Solovyov, Cell Rep 2018). Results from RNASeq are validated in cell lines and human tumors with RNA in situ hybridization (RNA-ISH) using probes to specific repeat RNAs, and combined IHC is performed to quantify intratumoral immune subpopulations. Whole-exome sequencing is performed to link the repeatome with somatic mutations. To obtain a global landscape of the ovarian cancer repeatome, Total RNASeq was performed on 32 patient-derived ovarian cancer cell lines, 11 HGSOC PDX, and 11 additional ovarian cancer cell lines. We detect abundant repeat RNA expression from all major subclasses including retrotransposons, endogenous retroviruses, and satellites. HGSOC are enriched for satellite repeats compared with other cancers, most notably in BRCA-mutant HGSOC. Human satellite II (HSATII), a cancer-specific satellite, is strongly upregulated in HGSOC compared with fallopian tube epithelial cells and displays highly variable expression across different models. RNA-ISH for HSATII on human ovarian cancer tissue microarrays confirms the abundance and variation of HSATII. Additionally, the repeatome is altered in HGSOC following exposure to in vitro chemotherapy and epigenetic agents with distinct patterns of expression linked to specific agents. Additional RNAseq analysis using hierarchical clustering and principal component analysis are being used to understand the relationship of repeatome expression patterns with coding gene expression, somatic mutations, in vitro drug sensitivity, and clinical outcomes. Digital image analysis of repeat RNA-ISH expression and immune cell infiltrate quantitation will determine the link between tumor cell repeat RNA levels and the responding immune tumor microenvironment. Overall, these studies will define the undiscovered repeatome in HGSOC and provide a foundation for discovery of novel biomarkers and potential therapeutic strategies, particularly those to increase efficacy of immunotherapies.

Citation Format: Rebecca L. Porter, Anna Szabolcs, Niyati Desai, Vishal Thapar, Raghav Mohan, Alexander Solovyov, David Pepin, Joyce Liu, Benjamin Greenbaum, David T. Ting. Repeatome profiling in high-grade serous ovarian cancer reveals abundant repeat noncoding RNA expression [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr A66.

Pancreatic ductal adenocarcinoma: tumour regression grading following neoadjuvant FOLFIRINOX and radiation

AIMS

In the adjuvant setting, when compared to gemcitabine, patients with pancreatic ductal adenocarcinoma (PDAC) treated with FOLFIRINOX (Folinic Acid, Fluorouracil, Irinotecan, and Oxaliplatin) show superior survival. In this study, we quantitatively assess the pathological tumour response to chemoradiation in pancreatectomy specimens and reassess guidelines for tumour regression grading.

METHODS AND RESULTS

We evaluated 92 patients with borderline resectable/locally advanced PDAC following pancreatectomy and neoadjuvant treatment with FOLFIRINOX and radiation. Demographic data, CAP tumour regression grade (TRG) and overall survival (OS) were recorded. A quantitative analysis of residual tumour was performed on the slide with the highest tumour burden to derive a tumour-to-tumour bed ratio. On univariate analysis, only lymph node status (P = 0.043) and CAP TRG (P = 0.038) correlated with OS. Sixteen per cent of patients showed a complete pathological response. The optimal tumour-to-tumour bed ratio cut-point was 11.6%, and on a multivariate model was the only pathological parameter that correlated with OS (P = 0.016) (hazard ratio = 2.27).

CONCLUSIONS

The high proportion of patients with PDAC showing complete and near-complete pathological responses supports the use of FOLFIRINOX and radiation in the neoadjuvant setting. Several traditional pathology parameters fail to predict OS in patients treated with chemoradiation, while a quantitative tumour-to-tumour bed ratio is a powerful predictor of OS. The data support a two-tiered approach to TRG based on tumour-to-tumour bed ratio, and quantitative analysis merits further consideration.

Glioblastoma hijacks microglial gene expression to support tumor growth

BACKGROUND

Glioblastomas are the most common and lethal primary brain tumors. Microglia, the resident immune cells of the brain, survey their environment and respond to pathogens, toxins, and tumors. Glioblastoma cells communicate with microglia, in part by releasing extracellular vesicles (EVs). Despite the presence of large numbers of microglia in glioblastoma, the tumors continue to grow, and these neuroimmune cells appear incapable of keeping the tumor in check. To understand this process, we analyzed gene expression in microglia interacting with glioblastoma cells.

METHODS

We used RNASeq of isolated microglia to analyze the expression patterns of genes involved in key microglial functions in mice with glioblastoma. We focused on microglia that had taken up tumor-derived EVs and therefore were within and immediately adjacent to the tumor.

RESULTS

We show that these microglia have downregulated expression of genes involved in sensing tumor cells and tumor-derived danger signals, as well as genes used for tumor killing. In contrast, expression of genes involved in facilitating tumor spread was upregulated. These changes appear to be in part EV-mediated, since intracranial injection of EVs in normal mice led to similar transcriptional changes in microglia. We observed a similar microglial transcriptomic signature when we analyzed datasets from human patients with glioblastoma.

CONCLUSION

Our data define a microglia_Glioblastoma specific phenotype, whereby glioblastomas have hijacked gene expression in the neuroimmune system to favor avoiding tumor sensing, suppressing the immune response, clearing a path for invasion, and enhancing tumor propagation. For further exploration, we developed an interactive online tool at http://www.glioma-microglia.com with all expression data and additional functional and pathway information for each gene.

Total Neoadjuvant Therapy With FOLFIRINOX in Combination With Losartan Followed by Chemoradiotherapy for Locally Advanced Pancreatic Cancer: A Phase 2 Clinical Trial

Importance

Patients with locally advanced pancreatic cancer have historically poor outcomes. Evaluation of a total neoadjuvant approach is warranted.

Objective

To evaluate the margin-negative (R0) resection rate of neoadjuvant FOLFIRINOX (fluorouracil, leucovorin, oxaliplatin, and irinotecan) and losartan followed by chemoradiotherapy for locally advanced pancreatic cancer.

Design, Setting, and Participants

A single-arm phase 2 clinical trial was conducted at a large academic hospital from August 22, 2013, to May 22, 2018, among 49 patients with previously untreated locally advanced unresectable pancreatic cancer as determined by multidisciplinary review. Patients had Eastern Cooperative Oncology Group performance status 0 or 1 and adequate hematologic, renal, and hepatic function. Median follow-up for the analysis was 17.1 months (range, 5.0-53.7) among 27 patients still alive at study completion.

Interventions

Patients received FOLFIRINOX and losartan for 8 cycles. Patients with radiographically resectable tumor after chemotherapy received short-course chemoradiotherapy (5 GyE × 5 with protons) with capecitabine. Patients with persistent vascular involvement received long-course chemoradiotherapy (50.4 Gy with a vascular boost to 58.8 Gy) with fluorouracil or capecitabine.

Main Outcomes and Measures

R0 resection rate.

Results

Of the 49 patients (26 women and 23 men; median age 63 years [range, 42-78 years]), 39 completed 8 cycles of FOLFIRINOX and losartan; 10 patients had fewer than 8 cycles due to progression (5 patients), losartan intolerance (3 patients), and toxicity (2 patients). Seven patients (16%) had short-course chemoradiotherapy while 38 (84%) had long-course chemoradiotherapy. Forty-two (86%) patients underwent attempted surgery, with R0 resection achieved in 34 of 49 patients (69%; 95% CI, 55%-82%). Overall median progression-free survival was 17.5 months (95% CI: 13.9-22.7) and median overall survival was 31.4 months (95% CI, 18.1-38.5). Among patients who underwent resection, median progression-free survival was 21.3 months (95% CI, 16.6-28.2), and median overall survival was 33.0 months (95% CI, 31.4 to not reached).

Conclusions and Relevance

Total neoadjuvant therapy with FOLFIRINOX, losartan, and chemoradiotherapy provides downstaging of locally advanced pancreatic ductal adenocarcinoma and is associated with an R0 resection rate of 61%.

Trial Registration

ClinicalTrials.gov identifier: NCT01821729.

Deregulation of ribosomal protein expression and translation promotes breast cancer metastasis

Circulating tumor cells (CTCs) are shed into the bloodstream from primary tumors, but only a small subset of these cells generates metastases. We conducted an in vivo genome-wide CRISPR activation screen in CTCs from breast cancer patients to identify genes that promote distant metastasis in mice. Genes coding for ribosomal proteins and regulators of translation were enriched in this screen. Overexpression of RPL15, which encodes a component of the large ribosomal subunit, increased metastatic growth in multiple organs and selectively enhanced translation of other ribosomal proteins and cell cycle regulators. RNA sequencing of freshly isolated CTCs from breast cancer patients revealed a subset with strong ribosome and protein synthesis signatures; these CTCs expressed proliferation and epithelial markers and correlated with poor clinical outcome. Therapies targeting this aggressive subset of CTCs may merit exploration as potential suppressors of metastatic progression.

Abstract B26: Targeted and sustained drug delivery therapy for localized pancreatic cancer: In vivo validation in porcine models

As systemic therapy improves, local control of nonmetastatic pancreatic adenocarcinoma (PDAC) remains a major challenge. Up to 40% of patients present with locally advanced and borderline resectable anatomy, for whom enhanced local downsizing of disease could improve resection rates and thus overall survival (OS). Additionally, for the 20% of PDAC patients who undergo resection, improved postoperative local control may translate into improved local disease-free intervals. Targeted therapies with reduced systemic toxicity are needed for the treatment of PDAC since current therapies have not provided meaningful advances. PanTher is developing a novel locally targeted drug delivery product (PTM-101) to treat localized PDAC by directly delivering chemotherapeutic agents to the primary tumor. PTM-101 is a bioresorbable polymeric patch containing paclitaxel surgically placed onto the tumor. The ingredients biodegrade over time, resulting in sustained release of drug, thereby providing localized treatment. In murine orthotopic patient-derived xenograft models, we showed that PTM-101 is 12 times more effective in controlling tumor progression compared to the same agent given via systemic route, without the toxicity of systemic therapy. In addition, increase in OS and inhibition of metastasis have been achieved after single treatment. Here we describe testing the implantation of clinically sized product in large animal models in preparation of our first-in-man study. To understand feasibility and safety of implant of PTM-101, two pilot studies were conducted in porcine models. In the first study, PTM-101 was sterilely implanted onto the peritoneum laparoscopically. In the second, it was placed in an open technique directly onto the ventral surface of a healthy porcine pancreas. In both cases, PTM-101 was designed to deliver drug locally over a 30-day period. Study parameters included body weights, hematology, urinalyses, drug levels in the blood and at the implantation site, and histomorphologic evaluation of major organs. In these models, we demonstrated that surgical implantation of PTM-101 can be achieved without complication and our approach ensures localized delivery of a large amount of encapsulated drug, resulting in higher drug concentration and retention in the area underneath the implant. More importantly, no detectable levels of the drug were present in the blood at any point during the 30-day treatment, validating once more the ability of PTM-101 to direct delivery only at the intended site. By changing the route of administration to target just the area of interest, PTM-101 is designed to increase the amount of drug reaching the tumor with the aim to enhance therapeutic efficacy. This could open the door to clinically relevant applications in patients with localized PDAC: (i) preoperatively as neoadjuvant treatment to control progression and downsize locally advanced and borderline anatomy to improve resectability, or (ii) post-resection to reduce the rate of local recurrence.

Citation Format: Margaret Lashof-Sullivan, Amanda L. McSweeney, David T. Ting, Michael P. Kim, Ching-Wei D. Tzeng, Laura Indolfi. Targeted and sustained drug delivery therapy for localized pancreatic cancer: In vivo validation in porcine models [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr B26.

Author Correction: Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Global Cancer Transcriptome Quantifies Repeat Element Polarization between Immunotherapy Responsive and T Cell Suppressive Classes

It has been posited that anti-tumoral innate activation is driven by derepression of endogenous repeats. We compared RNA sequencing protocols to assess repeat transcriptomes in The Cancer Genome Atlas (TCGA). Although poly(A) selection efficiently detects coding genes, most non-coding genes, and limited subsets of repeats, it fails to capture overall repeat expression and co-expression. Alternatively, total RNA expression reveals distinct repeat co-expression subgroups and delivers greater dynamic changes, implying they may serve as better biomarkers of clinical outcomes. We show that endogenous retrovirus expression predicts immunotherapy response better than conventional immune signatures in one cohort yet is not predictive in another. Moreover, we find that global repeat derepression, including the HSATII satellite repeat, correlates with an immunosuppressive phenotype in colorectal and pancreatic tumors and validate in situ. In conclusion, we stress the importance of analyzing the full spectrum of repeat transcription to decode their role in tumor immunity.

Abstract LB-257: Liquid biopsy versus tissue biopsy to assess acquired resistance and tumor heterogeneity in gastrointestinal cancers

The inevitable emergence of acquired resistance is a major limitation to the clinical benefit of precision medicine strategies. Single-lesion tumor biopsies have long been the mainstay of understanding acquired resistance, but recent data suggest tumor biopsies may under-represent the molecular heterogeneity of acquired resistance. Alternatively, studies have suggested that liquid biopsy approaches analyzing cell-free DNA (cfDNA) may offer significant advantages, but extensive prospective comparisons of matched liquid vs. tumor biopsies obtained at the time of acquired resistance are lacking. Here, we assess systematic liquid biopsy upon acquired resistance to targeted therapy in 44 patients across seven molecularly defined subtypes of gastrointestinal cancers. Liquid biopsy at disease progression identified at least one functionally validated molecular mechanism of resistance in 75% of patients, wherein 52% exhibited >1 resistance alteration (range 2-9, median 3 per patient). In 23 patients in whom a matched post-progression tumor biopsy could be obtained, tumor biopsy was less effective than liquid biopsy in identifying resistance mechanisms, with resistance alterations detected in only 48% of patients, and multiple resistance mechanisms detected in only 9% of cases. In matched cases, liquid biopsy detected at least one resistance alteration not detected in tumor biopsy in 78% of cases. Targeted analysis and whole-exome sequencing of serial cfDNA, multiple post-progression biopsies, and rapid autopsy specimens from select cases revealed key insights into the geographic and complex characteristics of heterogeneity captured by liquid biopsy in the setting of acquired resistance. These data illustrate that acquired resistance is characterized by frequent and profound tumor heterogeneity, and suggests that liquid biopsy may more effectively identify heterogeneous clinically relevant resistance alterations compared to standard tumor biopsy.

Citation Format: Aparna R. Parikh, Ignaty Leshchiner, Liudmila Elagina, Lipika Goyal, Chaya Levovitz, Giulia Siravegna, Dimitri Livitz, Kahn Rhrissorrakrai, Liz Martin, Emily E. Van Seventer, Megan Hanna, Kara Slowik, Filippo Utro, Christopher J. Pinto, Alicia Wong, Brian P. Danysh, Ferran Fece de la Cruz, Isobel J. Fetter, Brandon Nadres, Heather A. Shahzade, Jill N. Allen, Lawrence S. Blaszkowsky, Jeffrey W. Clark, Bruce Giantonio, Janet E. Murphy, Ryan D. Nipp, Eric Roeland, David P. Ryan, Colin D. Weekes, Eunice L. Kwak, Jason E. Faris, Francois Aguet, Ipsita Guha, Mehlika Hazar-Rethinam, Dora Dias-Santagata, David T. Ting, Andrew X. Zhu, Theodore S. Hong, Todd R. Golub, A J. Iafrate, Viktor Adalsteinsson, Alberto Bardelli, Laxmi Parida, Dejan Juric, Gad Getz, Ryan B. Corcoran. Liquid biopsy versus tissue biopsy to assess acquired resistance and tumor heterogeneity in gastrointestinal cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-257.

Quasimesenchymal phenotype predicts systemic metastasis in pancreatic ductal adenocarcinoma

Metastasis following surgical resection is a leading cause of mortality in pancreatic ductal adenocarcinoma. Epithelial-mesenchymal transition is thought to play an important role in metastasis, although its clinical relevance in metastasis remains uncertain. We evaluated a panel of RNA in-situ hybridization probes for epithelial-mesenchymal transition-related genes expressed in circulating tumor cells. We assessed the predictive value of this panel for metastasis in pancreatic ductal adenocarcinoma and, to determine if the phenotype is generalizable between cancers, in colonic adenocarcinoma. One hundred fifty-eight pancreatic ductal adenocarcinomas and 205 colonic adenocarcinomas were classified as epithelial or quasimesenchymal phenotype using dual colorimetric RNA-in-situ hybridization. SMAD4 expression on pancreatic ductal adenocarcinomas was assessed by immunohistochemistry. Pancreatic ductal adenocarcinomas with quasimesenchymal phenotype had a significantly shorter disease-specific survival (P = 0.031) and metastasis-free survival (P = 0.0001) than those with an epithelial phenotype. Pancreatic ductal adenocarcinomas with SMAD4 loss also had lower disease-specific survival (P = 0.041) and metastasis-free survival (P = 0.001) than those with intact SMAD4. However, the quasimesenchymal phenotype proved a more robust predictor of metastases-area under the curve for quasimesenchymal = 0.8; SMAD4 = 0.6. The quasimesenchymal phenotype also predicted metastasis-free survival (P = 0.004) in colonic adenocarcinoma. Epithelial-mesenchymal transition defined two phenotypes with distinct metastatic capabilities-epithelial phenotype tumors with predominantly organ-confined disease and quasimesenchymal phenotype with high risk of metastatic disease in two epithelial malignancies. Collectively, this work validates the relevance of epithelial-mesenchymal transition in human gastrointestinal tumors.

Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer

Single-cell technologies have described heterogeneity across tissues, but the spatial distribution and forces that drive single-cell phenotypes have not been well defined. Combining single-cell RNA and protein analytics in studying the role of stromal cancer-associated fibroblasts (CAFs) in modulating heterogeneity in pancreatic cancer (pancreatic ductal adenocarcinoma [PDAC]) model systems, we have identified significant single-cell population shifts toward invasive epithelial-to-mesenchymal transition (EMT) and proliferative (PRO) phenotypes linked with mitogen-activated protein kinase (MAPK) and signal transducer and activator of transcription 3 (STAT3) signaling. Using high-content digital imaging of RNA in situ hybridization in 195 PDAC tumors, we quantified these EMT and PRO subpopulations in 319,626 individual cancer cells that can be classified within the context of distinct tumor gland "units." Tumor gland typing provided an additional layer of intratumoral heterogeneity that was associated with differences in stromal abundance and clinical outcomes. This demonstrates the impact of the stroma in shaping tumor architecture by altering inherent patterns of tumor glands in human PDAC.