Drive Tumor Heterogeneity Research Articles

Abstract C165: Interrogating the Tumor and Immune Microenvironment of Endometrial Cancers Among a Diverse Cohort of Cases

Abstract Endometrial cancer (EC) is the sixth most common gynecological malignancy, with an increasing incidence worldwide over the last two decades. African American women are more likely to be diagnosed with endometrial cancer than Caucasian women. Unfortunately, African American women are more frequently diagnosed with high-grade EC, which occurs 2-3 times more often compared to their white and Hispanic counterparts. Additionally, African American women have higher mortality rates from EC than Caucasian women, highlighting a significant cancer disparity among these patients. Uterine EC disparities are induced by complex ecosystems composed of cellular niches with distinct genotypes, phenotypes, and spatial transcriptomic landscapes. In estrogen-dependent EC tumorigenesis, the endometrium undergoes uncontrollable proliferation, progressing from normal to atypical hyperplasia and ultimately to carcinoma. The heterogeneity of EC tumors complicates therapeutic targeting, rendering EC a challenging disease to cure. This study aims to investigate the genetic and transcriptomic features found in the tumor microenvironment of African American patients with EC. Previous research has shown that the molecular classification of EC tumors can be categorized as estrogen-driven, hypermutant, microsatellite instable, or lacking a specific molecular profile. Current models do not adequately reflect the oncogenic origin and pathological progression in patients. The cohort of EC cases includes primary, metastatic, and normal tumor tissues classified as Uterine Endometrial Adenocarcinoma, along with two Serous Papillary cases with varying tumor grades (low to high grade). Spatial transcriptomics and whole exome sequencing were performed on these samples. Spatial transcriptomics will identify the alterations in gene expression and the spatial landscape of the cell neighborhoods driving tumor heterogeneity. Whole exome sequencing will provide insight into the germline and somatic variants present in EC, offering a deeper understanding of the potential genetic drivers in African American patients. The genes expressed across the EC tumor landscape are implicated in cell proliferation, epithelial- mesenchymal transition, DNA damage response, and immune response. The analysis will also show the transition of normal to malignant endometrium harboring high tumor mutational burden and microsatellite instability when comparing paired samples. This comprehensive approach aims to elucidate the genetic and transcriptomic underpinnings contributing to the disparities observed in African American patients with EC, ultimately informing better-targeted therapies and improving outcomes. Citation Format: Danyelle Paine, John Carpten. Interrogating the Tumor and Immune Microenvironment of Endometrial Cancers Among a Diverse Cohort of Cases [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C165.

STEM-07. CONSERVATION AND FAITHFUL REPRESENTATION OF CIRCULAR EXTRACHROMOSOMAL DNA IN ORTHOTOPIC PATIENT-DERIVED MEDULLOBLASTOMA XENOGRAFTS

Abstract BACKGROUND Extrachromosomal DNA (ecDNA) drives tumor heterogeneity and correlates with poor survival across various cancer types. Patient-derived xenograft (PDX) models facilitate preclinical drug testing in vivo, enabling tumor growth analysis and molecular tumor profiling. These models, combined with single-cell profiling, offer insights into intratumoral heterogeneity under therapeutic pressure and the emergence of drug resistance. We investigate the abundance and conservation of ecDNA in PDX models to assess the faithful representation of ecDNA compared to their corresponding primary tumors. METHODS Whole-genome sequencing (WGS) was applied to 27 medulloblastoma (MB) PDX models and their tumors of origin using Amplicon Architect. ecDNA frequency in these models was also compared to that in the MB patient population. Optical genome mapping enabled accurate and reliable ecDNA sequence reconstructions. Multiome single-cell RNA and ATAC-sequencing of a PDX tumor enabled analysis of ecDNA conservation and intratumoral heterogeneity compared to similar data previously obtained from the primary tumor. RESULTS ecDNA is largely conserved in PDX models, emphasizing their relevance as faithful models of the primary tumors. MB PDX models exhibit significant higher ecDNA frequency (16 out of 27 tumors) as compared to their frequency in the overall patient population (~18%), suggesting ecDNA as a driver for successful establishment of MB PDX models. Single-cell analysis revealed that ecDNA is omnipresent in almost all PDX tumor cells, contrasting with only ~9% of tumor cells in the primary tumor. CONCLUSIONS ecDNA analysis in medulloblastoma primary tumors and in PDX models revealed that ecDNA is preserved in PDX models. These findings emphasize the relevance of PDX models in preclinical in vivo studies aimed at analyzing the role of ecDNA under therapeutic pressure and for analyzing clonal selection along with molecular evolution of ecDNA during the development of therapeutic resistance.

A potassium-chloride co-transporter with altered genome architecture functions as a suppressor in glioma.

Gliomas, the most lethal tumours in brain, have a poor prognosis despite accepting standard treatment. Limited benefits from current therapies can be attributed to genetic, epigenetic and microenvironmental cues that affect cell programming and drive tumour heterogeneity. Through the analysis of Hi-C data, we identified a potassium-chloride co-transporter SLC12A5 associated with disrupted topologically associating domain which was downregulated in tumour tissues. Multiple independent glioma cohorts were included to analyse the characterization of SLC12A5 and found it was significantly associated with pathological features, prognostic value, genomic alterations, transcriptional landscape and drug response. We constructed two SLC12A5 overexpression cell lines to verify the function of SLC12A5 that suppressed tumour cell proliferation and migration invitro. In addition, SLC12A5 was also positively associated with GABAA receptor activity and negatively associated with pro-tumour immune signatures and immunotherapy response. Collectively, our study provides a comprehensive characterization of SLC12A5 in glioma and supports SLC12A5 as a potential suppressor of disease progression.

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

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

Abstract B085: Carcinoma-associated mesenchymal stem cells promote high-grade serous ovarian cancer metastasis and drive tumor heterogeneity at the metastatic site through direct mitochondrial transfer

Abstract High-grade serous ovarian cancer (HGSC) is the most common and lethal form of ovarian cancer, accounting for over 70% of ovarian cancer cases. HGSC mortality is largely driven by early and diffuse transcoelomic spread from the primary site throughout the peritoneal cavity, resulting in roughly three-quarters of cases presenting with advanced stage disease at time of diagnosis. Following detachment from the primary tumor, disseminated ovarian cancer cells are spread by the peritoneal fluid and ascites where they must adapt to their new microenvironment to survive and successfully form metastases. Crucial to this spread is the formation of multicellular aggregates containing both cancer and non-malignant stromal cells, which enhance cancer cell survival and are associated with poor clinical outcome. While most studies on HGSC multicellular aggregates have focused on ovarian cancer cells alone, the interactions between ovarian cancer cells and other non-malignant cells have yet to be fully elucidated. Prior work by our group have shown that stromal-progenitor cells, termed carcinoma-associated mesenchymal stem/stromal cells (CA-MSCs), enhance HGSC metastasis through direct cellular interaction and formation of heterocellular CA-MSC:cancer cell complexes. Here we demonstrate CA-MSCs enhance metastasis by preferentially donating their mitochondria to cancer cells with the least amount of endogenous mitochondria content (‘mito poor’ cancer cells), increasing their ability to survive and driving tumor heterogeneity at the metastatic site in vivo. Mito poor cancer cells were shown to have decreased proliferative capacity, increased sensitivity to platinum-based chemotherapy and display decreased oxidative phosphorylation (OXPHOS) compared to ‘mito rich’ cancer cells. Primary patient-derived CA-MSCs rescue this vulnerable phenotype by increasing proliferation, chemoresistance and OXPHOS in mito poor cancer cells. These findings were validated in a fully autologous system using CA-MSCs and cancer cells derived from the same patient to prevent confounding effects of cellular response to foreign organelle/DNA. Through lentiviral knockdown of the mitochondrial motor protein MIRO1 we further demonstrate mitochondrial transfer is necessary for CA-MSC-mediated rescue of mito poor cancer cells. Further, we developed a haplotype-specific quantification of mitochondrial DNA to differentiate CA-MSC from endogenous cancer cell mitochondria which was used to quantify the amount of CA-MSC mitochondrial donation and demonstrate donated mitochondria persist in cancer cells up to 14 days. Importantly, CA-MSC mitochondrial donation occurred in vivo and was associated with decreased survival in an orthotopic ovarian cancer murine model. Genomic barcoding was used to quantify tumor cell clonal heterogeneity; using this system we demonstrate CA-MSC mitochondrial donation significantly enhance tumor cell heterogeneity at the metastatic site in vivo. Collectively, we report CA-MSC mitochondrial transfer as a driver of HGSC progression, heterogeneity and metastasis. Citation Format: Leonard G. Frisbie, Catherine A. Pressimone, Roja Baruwal, Geyon L. Garcia, Zanib Javed, Claudette St. Croix, Simon Watkins, Michael Calderone, Huda I. Atiya, Nadine Hempel, Alexander Pearson, Lan G. Coffman. Carcinoma-associated mesenchymal stem cells promote high-grade serous ovarian cancer metastasis and drive tumor heterogeneity at the metastatic site through direct mitochondrial transfer [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr B085.

Oncolytic herpes simplex viruses for the treatment of glioma and targeting glioblastoma stem-like cells.

Glioblastoma (GBM) is one of the most lethal cancers, having a poor prognosis and a median survival of only about 15 months with standard treatment (surgery, radiation, and chemotherapy), which has not been significantly extended in decades. GBM demonstrates remarkable cellular heterogeneity, with glioblastoma stem-like cells (GSCs) at the apex. GSCs are a subpopulation of GBM cells that possess the ability to self-renew, differentiate, initiate tumor formation, and manipulate the tumor microenvironment (TME). GSCs are no longer considered a static population of cells with specific markers but are quite flexible phenotypically and in driving tumor heterogeneity and therapeutic resistance. In light of these features, they are a critical target for successful GBM therapy. Oncolytic viruses, in particular oncolytic herpes simplex viruses (oHSVs), have many attributes for therapy and are promising agents to target GSCs. oHSVs are genetically-engineered to selectively replicate in and kill cancer cells, including GSCs, but not normal cells. Moreover, oHSV can induce anti-tumor immune responses and synergize with other therapies, such as chemotherapy, DNA repair inhibitors, and immune checkpoint inhibitors, to potentiate treatment effects and reduce GSC populations that are partly responsible for chemo- and radio-resistance. Herein, we present an overview of GSCs, activity of different oHSVs, clinical trial results, and combination strategies to enhance efficacy, including therapeutic arming of oHSV. Throughout, the therapeutic focus will be on GSCs and studies specifically targeting these cells. Recent clinical trials and approval of oHSV G47Δ in Japan for patients with recurrent glioma demonstrate the efficacy and promise of oHSV therapy.

Coordinated cancer chaos

Stochastic processes, such as genetic instability and microenvironment evolution, drive tumor heterogeneity, thereby creating the chaotic appearance of tumors in histopathology. In this issue of Cell, Lin etal. reveal that tumors are surprisingly spatially organized from a molecular to tissue scale, indicating that cancers evolve as autonomously patterned systems.

Unraveling tumor microenvironment heterogeneity in malignant pleural mesothelioma identifies biologically distinct immune subtypes enabling prognosis determination.

BackgroundMalignant pleural mesothelioma (MPM) is a rare and intractable disease exhibiting a remarkable intratumoral heterogeneity and dismal prognosis. Although immunotherapy has reshaped the therapeutic strategies for MPM, patients react with discrepant responsiveness.MethodsHerein, we recruited 333 MPM patients from 5 various cohorts and developed an in-silico classification system using unsupervised Non-negative Matrix Factorization and Nearest Template Prediction algorithms. The genomic alterations, immune signatures, and patient outcomes were systemically analyzed across the external TCGA-MESO samples. Machine learning-based integrated methodology was applied to identify a gene classifier for clinical application.ResultsThe gene expression profiling-based classification algorithm identified immune-related subtypes for MPMs. In comparison with the non-immune subtype, we validated the existence of abundant immunocytes in the immune subtype. Immune-suppressed MPMs were enriched with stroma fraction, myeloid components, and immunosuppressive tumor-associated macrophages (TAMs) as well exhibited increased TGF-β signature that informs worse clinical outcomes and reduced efficacy of anti-PD-1 treatment. The immune-activated MPMs harbored the highest lymphocyte infiltration, growing TCR and BCR diversity, and presented the pan-cancer immune phenotype of IFN-γ dominant, which confers these tumors with better drug response when undergoing immune checkpoint inhibitor (ICI) treatment. Genetically, BAP1 mutation was most commonly found in patients of immune-activated MPMs and was associated with a favorable outcome in a subtype-specific pattern. Finally, a robust 12-gene classifier was generated to classify MPMs with high accuracy, holding promise value in predicting patient survival.ConclusionsWe demonstrate that the novel classification system can be exploited to guide the identification of diverse immune subtypes, providing critical biological insights into the mechanisms driving tumor heterogeneity and responsible for cancer-related patient prognoses.

Abstract 1686: Characterizing tumor heterogeneity through label-free, morphology-based live cell sorting

Abstract The complexity of cancer is compounded by the continuous emergence of malignant cell populations that drive tumor heterogeneity and challenges diagnostic and therapeutic advances. Methods to study cancer at the single cell level are important to better understand tumor heterogeneity. Isolation of tumor cells from tissue typically relies on targeting biomarkers overexpressed in tumor cells, such as EpCAM, resulting in cells that may express common markers with morphologic and molecular heterogeneity. We developed a platform termed Computational Sorting and Mapping of Single cells (COSMOS) that uses high-dimensional morphology analysis of single cells using artificial intelligence, microfluidics and high resolution bright-field imaging to identify and enrich target cells. We used COSMOS to train a deep convolutional neural network (ConvNet) classifier to identify and enrich malignant cells from non-small cell lung cancer (NSCLC) dissociated tumor cell (DTC) samples. The enriched population of NSCLC cells are label-free, unperturbed and viable, making them amenable to many downstream analysis methods but importantly also contain single cell high-dimensional morphology profiles. We verified enrichment of malignant cells by performing RNA and DNA analysis on the enriched sample. Single cell RNA-seq (scRNA-Seq) analysis shows high levels of EpCAM expression in sorted cells. Copy number variation (CNV) analysis demonstrated increased amplitude of deletion and amplification peaks relative to the pre-sorted DTC sample. Further, mutational analysis show increased allele frequency of mutations including P53 and KRAS in post-sorted compared to pre-sorted samples. Morphological heterogeneity within the malignant population is observed by UMAP analysis with the presence of multiple clusters of morphologically unique tumor cell populations detected. We further trained the classifier to detect and enrich for each subpopulation; CNV, mutation, bulk RNASeq, and scRNA-Seq analysis revealed molecular differences between the morphology subgroups. Further work is planned to evaluate the link between the morphological, molecular and functional characteristics of each subpopulation. We demonstrate a platform that can enrich malignant cells based on morphology, yielding a population of cells that are label-free, viable and unperturbed, making them compatible with downstream molecular assays commonly used to study heterogeneity. Additionally the cells can be morphologically profiled at the single cell level yielding a high-dimensional morphological profile that reveals heterogeneous populations of cells that can be further characterized by molecular analysis and could offer a new dimension to understand heterogeneity and biomarker discovery. Citation Format: Andreja Jovic, Kiran Saini, Michael Phelan, Ryan Chow, Simo Zhang, Chassidy Johnson, Nianzhen Li, Thomas J. Musci, Mahyar Salek, Maddison (Mahdokht) Masaeli. Characterizing tumor heterogeneity through label-free, morphology-based live cell sorting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1686.

Primary Founder Mutations in the PRKDC Gene Increase Tumor Mutation Load in Colorectal Cancer.

The clonal composition of a malignant tumor strongly depends on cellular dynamics influenced by the asynchronized loss of DNA repair mechanisms. Here, our aim was to identify founder mutations leading to subsequent boosts in mutation load. The overall mutation burden in 591 colorectal cancer tumors was analyzed, including the mutation status of DNA-repair genes. The number of mutations was first determined across all patients and the proportion of genes having mutation in each percentile was ranked. Early mutations in DNA repair genes preceding a mutational expansion were designated as founder mutations. Survival analysis for gene expression was performed using microarray data with available relapse-free survival. Of the 180 genes involved in DNA repair, the top five founder mutations were in PRKDC (n = 31), ATM (n = 26), POLE (n = 18), SRCAP (n = 18), and BRCA2 (n = 15). PRKDC expression was 6.4-fold higher in tumors compared to normal samples, and higher expression led to longer relapse-free survival in 1211 patients (HR = 0.72, p = 4.4 × 10−3). In an experimental setting, the mutational load resulting from UV radiation combined with inhibition of PRKDC was analyzed. Upon treatments, the mutational load exposed a significant two-fold increase. Our results suggest PRKDC as a new key gene driving tumor heterogeneity.

Tumor heterogeneity reshapes the tumor microenvironment to influence drug resistance.

Tumor heterogeneity is one of the hallmarks of cancer and a challenge in the field of oncology. Tumor heterogeneity is the main cause of drug resistance, leading to therapeutic failure. Mechanically, tumor heterogeneity either directly affects therapeutic targets or shapes the tumor microenvironment (TME) by defining transcriptomic and phenotypic profiles to influence drug resistance. Tumor heterogeneity evolves spatially and temporally during tumor development, leading to the constant reprogramming of the TME. Advances in molecular profiling technologies and precision oncology platforms have allowed us to uncover the impact of tumor heterogeneity on drug resistance in the context of the TME. In this review, we focus on the processes during which genomic mutations drive tumor heterogeneity and the mechanisms through which tumor heterogeneity reprograms the TME to affect drug resistance and patient prognosis.

Single-Cell Transcriptomic Analysis Revealed a Critical Role of SPP1/CD44-Mediated Crosstalk Between Macrophages and Cancer Cells in Glioma.

High-grade glioma is one of the most lethal human cancers characterized by extensive tumor heterogeneity. In order to identify cellular and molecular mechanisms that drive tumor heterogeneity of this lethal disease, we performed single-cell RNA sequencing analysis of one high-grade glioma. Accordingly, we analyzed the individual cellular components in the ecosystem of this tumor. We found that tumor-associated macrophages are predominant in the immune microenvironment. Furthermore, we identified five distinct subpopulations of tumor cells, including one cycling, two OPC/NPC-like and two MES-like cell subpopulations. Moreover, we revealed the evolutionary transition from the cycling to OPC/NPC-like and MES-like cells by trajectory analysis. Importantly, we found that SPP1/CD44 interaction plays a critical role in macrophage-mediated activation of MES-like cells by exploring the cell-cell communication among all cellular components in the tumor ecosystem. Finally, we showed that high expression levels of both SPP1 and CD44 correlate with an increased infiltration of macrophages and poor prognosis of glioma patients. Taken together, this study provided a single-cell atlas of one high-grade glioma and revealed a critical role of macrophage-mediated SPP1/CD44 signaling in glioma progression, indicating that the SPP1/CD44 axis is a potential target for glioma treatment.

Abstract PO-033: The angiotensin II type 1 receptor blocker telmisartan inhibits the development of transient tumour hypoxia and improves response to ionizing radiation therapy

Abstract Poorly oxygenated (hypoxic) cells are key components of the solid tumour microenvironment that drive tumour heterogeneity. Hypoxia regulates a variety of processes that promote tumour cell survival and metastasis, and hypoxic tumour cells are resistant to therapy. Patients with tumours that contain hypoxic cells have worse outcome after radiotherapy, chemotherapy, and even surgery, underscoring the therapeutic relevance of hypoxia in driving more aggressive tumour phenotypes. Hypoxic tumour cells result from deficiencies in the delivery of oxygen relative to the high oxygen demand of tumour cells. “Chronic” hypoxia develops due to the limited diffusion distance of oxygen through tumour tissue, while “transient” hypoxia occurs due to fluctuations in microregional tumour perfusion and oxygen delivery over time. Transiently hypoxic cells are more resistant to radiation therapy and are more metastatic than chronically hypoxic cells although, despite decades of work in this area, there are no effective long-term strategies to specifically target transiently hypoxic cells in solid tumours. Angiotensin II type 1 receptor (AT1R) blockers (ARBs) are widely prescribed anti-hypertensive agents that can also exhibit anti-fibrotic activity. Recent evidence indicates that the ARB losartan can inhibit collagen I (Col1) deposition in tumours by cancer-associated fibroblasts (CAFs), reduce blood vessel constriction, and increase net tumour blood flow, although the influence of losartan or other ARBs on transient hypoxia and tumour radiation response is unknown. We hypothesized that ARB-mediated inhibition of Col1 deposition from CAFs increases tumour blood flow by stabilizing microregional fluctuations in tumour perfusion and that ARBs will reduce transient tumour hypoxia. We tested the ARBs losartan and telmisartan in human tumour xenografts using positron emission tomography and intravenously injected fluorescent perfusion dyes to quantify tumour perfusion, and a combination of exogenous hypoxia markers and the hemorheological agent pentoxifylline to assess transient tumour hypoxia. We found that CAF-containing tumours had reduced Col1 levels in response to telmisartan, but not losartan, consistent with the improved pharmacokinetics and AT1R binding affinity of telmisartan. Telmisartan increased net tumour blood flow and stabilized microregional fluctuations in tumour perfusion. Importantly, telmisartan decreased overall hypoxia in the tumours by specifically targeting transient tumour hypoxia, which translated into a significant improvement in radiation response. These data indicate that telmisartan reduces a therapeutically-relevant population of transiently hypoxic tumour cells. Understanding how the solid tumour microenvironment influences cancer therapy is central to improving treatment outcome. Our work underscores the importance of transient tumour hypoxia and supports future clinical studies to evaluate telmisartan as a neoadjuvant for radiation therapy. Citation Format: Brennan J. Wadsworth, Rachel A. Cederberg, Che-Min Lee, Natalie S. Firmino, S. Elizabeth Franks, Jinhe Pan, Nadine Colpo, Kuo-Shyan Lin, Francois Benard, Kevin L. Bennewith. The angiotensin II type 1 receptor blocker telmisartan inhibits the development of transient tumour hypoxia and improves response to ionizing radiation therapy [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-033.

Cancer-associated mutations in the condensin II subunit CAPH2 cause genomic instability through telomere dysfunction and anaphase chromosome bridges.

Genome instability in cancer drives tumor heterogeneity, undermines the success of therapies, and leads to metastasis and recurrence. Condensins are conserved chromatin‐binding proteins that promote genomic stability, mainly by ensuring proper condensation of chromatin and mitotic chromosome segregation. Condensin mutations are found in human tumors, but it is not known how or even if such mutations promote cancer progression. In this study, we focus on condensin II subunit CAPH2 and specific CAPH2 mutations reported to be enriched in human cancer patients, and we test how CAPH2 cancer‐specific mutations may lead to condensin II complex dysfunction and contribute to genome instability. We find that R551P, R551S, and S556F mutations in CAPH2 cause genomic instability by causing DNA damage, anaphase defects, micronuclei, and chromosomal instability. DNA damage and anaphase defects are caused primarily by ataxia telangiectasia and Rad3‐related‐dependent telomere dysfunction, as anaphase bridges are enriched for telomeric repeat sequences. We also show that these mutations decrease the binding of CAPH2 to the ATPase subunit SMC4 as well as the rest of the condensin II complex, and decrease the amount of CAPH2 protein bound to chromatin. Thus, in vivo the R551P, R551S, and S556F cancer‐specific CAPH2 mutant proteins are likely to impair condensin II complex formation, impede condensin II activity during mitosis and interphase, and promote genetic heterogeneity in cell populations that can lead to clonal outgrowth of cancer cells with highly diverse genotypes.

Adipose-derived mesenchymal stem cells differentiate into pancreatic cancer-associated fibroblasts invitro.

Cancer-associated fibroblasts (CAFs) are key components of the dense, proliferating stroma observed in pancreatic ductal adenocarcinoma (PDAC), and CAF subpopulations drive tumor heterogeneity and play a major role in PDAC progression and drug resistance. CAFs consist of heterogenous subpopulations such as myoblastic CAF (myCAF) and inflammatory CAF (iCAF), and each has distinct essential roles. However, it is not clear how CAF subpopulations are formed in PDAC. Adipose-derived MSCs (AD-MSCs), which possess a high multilineage potential and self-renewal capacity, are reported to be one of the invivo CAF sources. Here, we aimed to investigate whether AD-MSCs can act as precursors for CAFs invitro. We recorded morphological features and collected omics data from two invitro co-culture models for recapitulating clinical PDAC. Additionally, we tested the advantages of the co-culture model in terms of accurately modeling morphology and CAF heterogeneity. We showed that AD-MSCs differentiate into two distinct CAF subpopulations: Direct contact co-culture with PDAC cell line Capan-1 induced differentiation into myCAFs and iCAFs, while indirect co-culture induced differentiation into only iCAFs. Using these co-culture systems, we also identified novel CAF markers that may be helpful for elucidating the mechanisms of CAFs in the tumor microenvironment (TME). In conclusion, AD-MSCs can differentiate into distinct CAF subtypes depending on the different co-culture conditions invitro, and the identification of potential CAF markers may aid in future investigations of the mechanisms underlying the role of CAFs in the TME.

Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia

Acute myeloid leukemia (AML) is characterised by a series of genetic and epigenetic alterations that result in deregulation of transcriptional networks. One understudied source of transcriptional regulators are transposable elements (TEs), whose aberrant usage could contribute to oncogenic transcriptional circuits. However, the regulatory influence of TEs and their links to AML pathogenesis remain unexplored. Here we identify six endogenous retrovirus (ERV) families with AML-associated enhancer chromatin signatures that are enriched in binding of key regulators of hematopoiesis and AML pathogenesis. Using both locus-specific genetic editing and simultaneous epigenetic silencing of multiple ERVs, we demonstrate that ERV deregulation directly alters the expression of adjacent genes in AML. Strikingly, deletion or epigenetic silencing of an ERV-derived enhancer suppresses cell growth by inducing apoptosis in leukemia cell lines. This work reveals that ERVs are a previously unappreciated source of AML enhancers that may be exploited by cancer cells to help drive tumour heterogeneity and evolution.

Abstract B19: Role of cell-cell communication in endocrine therapy-resistant breast cancer

Abstract Endocrine therapy is the mainstay for the treatment of estrogen-receptor positive (ER+) breast cancer. However, frequent emergence of endocrine resistance is a major clinical challenge. Cell-cell cooperation in the tumor microenvironment plays a vital role in acquiring resistance, but its role is poorly understood. We studied the interactions among endocrine-resistant (R) and -sensitive (S) breast cancer cells in the presence and absence of ER-targeted endocrine therapy. We measured changes in admixed cell population remodeling by dual fluorescent labeling of LCC1 (S) with eGFP (green fluorescent protein) and their derived resistant variant (selected against the antiestrogen fulvestrant) LCC9 (R) with mCherry (red fluorescent protein), respectively. Thus, unlike most prior studies, these are genetically related cells, rather than ER+ and ER- cell lines obtained from different patients. Our results revealed that “S”cells (LCC1) acquired the phenotype of “R” cells when cultured in a mixed population. A ratio of 5:1 of S:R cells in mixed population was sufficient to confer resistance to fulvestrant to the S cells within a six-day period. Furthermore, we show that acquirement of this resistant phenotype for the S cells was partially blocked by inhibition of either gap junctions or exosome secretion, suggesting a role of cell-cell contact as well as extracellular vesicles. Global proteomic analysis of pure and admixed S and R cell populations showed that R and S can alter key molecular features of each other when present in mixed cell populations. We used a Bayesian approach to fit single culture cell populations to infer density-dependent growth parameters (growth rate, carrying capacity) and a generalized Lotka-Volterra model to understand how S and R coculture populations may be depressing or supporting growth of the other. Our results identify a net mutualistic interaction between the susceptible and resistant cancer strains, demonstrating that there are ecological dynamics to cancer resistance. In some tumors, ecological dynamics may be more mechanistically relevant than simple Darwinian-based clonal selection in driving tumor heterogeneity and determining response to treatment. Our study strongly indicates that different tumor cell types that may exist in tumors are able to influence each other, which leads to alteration of phenotype. Note: This abstract was not presented at the conference. Citation Format: Surojeet Sengupta, Rong Hu, Zachary Susswein, Adeola Fagunloye, Shweta Bansal, Robert Clarke. Role of cell-cell communication in endocrine therapy-resistant breast cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr B19.

Accumulation of DNA methylation alterations in paediatric glioma stem cells following fractionated dose irradiation

BackgroundRadiation is an important therapeutic tool. However, radiotherapy has the potential to promote co-evolution of genetic and epigenetic changes that can drive tumour heterogeneity, formation of radioresistant cells and tumour relapse. There is a clinical need for a better understanding of DNA methylation alterations that may follow radiotherapy to be able to prevent the development of radiation-resistant cells.MethodsWe examined radiation-induced changes in DNA methylation profiles of paediatric glioma stem cells (GSCs) in vitro. Five GSC cultures were irradiated in vitro with repeated doses of 2 or 4 Gy. Radiation was given in 3 or 15 fractions. DNA methylation profiling using Illumina DNA methylation arrays was performed at 14 days post-radiation. The cellular characteristics were studied in parallel.ResultsFew fractions of radiation did not result in significant accumulation of DNA methylation alterations. However, extended dose fractionations changed DNA methylation profiles and induced thousands of differentially methylated positions, specifically in enhancer regions, sites involved in alternative splicing and in repetitive regions. Radiation induced dose-dependent morphological and proliferative alterations of the cells as a consequence of the radiation exposure.ConclusionsDNA methylation alterations of sites with regulatory functions in proliferation and differentiation were identified, which may reflect cellular response to radiation stress through epigenetic reprogramming and differentiation cues.

Epigenomic Profiling Discovers Trans-lineage SOX2 Partnerships Driving Tumor Heterogeneity in Lung Squamous Cell Carcinoma.

Molecular characterization of lung squamous cell carcinoma (LUSC), one of the major subtypes of lung cancer, has not sufficiently improved its nonstratified treatment strategies over decades. Accumulating evidence suggests that lineage-specific transcriptional regulators control differentiation states during cancer evolution and underlie their distinct biological behaviors. In this study, by investigating the super-enhancer landscape of LUSC, we identified a previously undescribed "neural" subtype defined by Sox2 and a neural lineage factor Brn2, as well as the classical LUSC subtype defined by Sox2 and its classical squamous partner p63. Robust protein-protein interaction and genomic cooccupancy of Sox2 and Brn2, in place for p63 in the classical LUSC, indicated their transcriptional cooperation imparting this unique lineage state in the "neural" LUSC. Forced expression of p63 downregulated Brn2 in the "neural" LUSC cells and invoked the classical LUSC lineage with more squamous/epithelial features, which were accompanied by increased activities of ErbB/Akt and MAPK-ERK pathways, suggesting differential dependency. Collectively, our data demonstrate heterogeneous cell lineage states of LUSC featured by Sox2 cooperation with Brn2 or p63, for which distinct therapeutic approaches may be warranted. SIGNIFICANCE: Epigenomic profiling reveals a novel subtype of lung squamous cell carcinoma with neural differentiation.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/24/6084/F1.large.jpg.

ES17.03 Heterogeneity & Immune Checkpoint Expression

Mesothelioma is a spatially complex malignancy. Morphologic heterogeneity is commonly identified, especially with surgical resection that can unmask distinct histologic components across sites of disease. Molecular analyses of HUMARA methylation patterns on the X-chromosome, CDKN2A deletions, and single nucleotide variants from multiple tumor sites all suggest that mesothelioma is polyclonal with multiple genetic subclones within each tumor. Temporal histologic heterogeneity has also been reported with sarcomatoid differentiation during progression of disease. The selective pressures of the microenvironment and therapies may further drive tumor heterogeneity. With the application of immune checkpoint inhibitors for the treatment of this disease, the expression of immune checkpoints and the immunologic milieu of mesothelioma has been increasingly investigated. Whereas most studies report immune checkpoint expression from a single site of disease obtained from a single time point, distinct immunologic patterns have been observed within tumors from different sites. The molecular and immunologic heterogeneity of mesothelioma may have prognostic and therapeutic implications. PD-L1, Mesothelioma, Heterogeneity