Tumor Heterogeneity Evolution Research Articles

Multiscale Tissue Modeling Reveals Impact of Cancer Treatment to Tumor Heterogeneity

In the last decade models of cell interactions have allowed allow more and more insight into the dynamics and properties of single cells and their influence on the properties of tissues. Especially in systems that are hard to experimentally access, computational simulations excel in isolating effects and predicting emerging biological properties. Many of these simulations either concentrate on a high-resolution description of a limited number of cells or large numbers of cells at the cost of resolution. In contrast, we developed a highly scalable model that for the first time incorporates a sub-cellular resolution of each single cell while allowing simulating the interplay of millions of cells. Thus, we can investigate the pivotal role of single cells in the progression of the macroscopic tumor. Technically, our model is based on a cellular Potts model that has been expanded to include such as tumor initiation, malignancy transformation, mutations based on single cell alterations and tumor stem cells (TSCs) driving tumor renewal as well as treatment resistivity. We observe the emergence and evolution of tumor heterogeneity and analyze the local neighborhood and clustering of cell types. Different treatment protocols of pulsed chemo- and or radiotherapy show a large influence on the development of the tumor composition. A small amount of TSCs in the tumor significantly alters its properties and especially boosts post-treatment heterogeneity as well as regrowth. We scan the reproducibility and stochasticity of tumor development and treatment outcome in relation to the cell parameters.

Abstract SY38-02: Personalized adaptive therapy for metastatic cancer: An integrated approach

Abstract SY38-02: Personalized adaptive therapy for metastatic cancer: An integrated approach

Abstract 498: Meta-analysis of genomic aberrations identified in CTCs andctDNA in triple negative breast cancer

Abstract Technological innovation and scientific advances in understanding cancer at the molecular level have accelerated the discovery and development of both diagnostics and therapeutics. Circulating tumor cells (CTCs) and plasma circulating tumor DNA (ctDNA) are non-invasive prognostic markers that have been associated with metastatic and aggressive disease. Both CTCs and ctDNA allow molecular characterization of a tumor that is inaccessible or too risky to biopsy. The analysis of genomic aberrations in both sample types provides insights into drug resistance and can help determine appropriate, targeted cancer treatments. Mutations found in the primary or metastatic tumor can be identified in both CTCs and ctDNA as well as novel mutations that may reflect intratumoral and intermetastatic heterogeneity. When collected and evaluated over an extended period of time, changes in the CTC and/or ctDNA mutational profile can offer guidance into the effectiveness of a treatment, indicate the progression of disease, and detect recurrence of disease earlier. We have performed whole exome sequencing of CTCs and ctDNA from a metastatic triple negative breast cancer (TNBC) patient to better understand the evolution of tumor heterogeneity during therapy. The patient was enrolled in the Intensive Trial of OMics in Cancer clinical Trial (ITOMIC-001) and initially received weekly cisplatin infusions followed by additional targeted therapy. Longitudinal peripheral blood samples were collected over a period of 272 days following enrollment in the clinical trial. CTCs were identified using the AccuCyte-CyteFinder system (RareCyte, Seattle WA). We used next generation sequencing, and computational biology tools to analyze genomic DNA from multiple CTCs, white blood cells (WBCs) and ctDNA from various time points. We observed similar genomic aberrations in both CTCs and ctDNA that could be classified into three groups: a) a static group that remains unchanged during the course of therapy, b) a sample-specific group that is unique to each time point and c) an intermediate group that has variants that are short-lived but are present across multiple time points. Variants identified in the liquid biopsy samples were compared with variants observed in primary breast tumor, metastatic bone marrow tumor and publically available pan-cancer datasets. We then performed meta-analysis on somatic variants to identify changes in affected networks in response to therapy over time. Several key nodes were identified that could rationally have been targeted for therapy using compounds currently in clinical trials. We then compared and combined the perturbed networks obtained from the CTCs and ctDNA to better understand the etiology of TNBC. These studies represent the first step of a synergistic partnership between the genetic information obtained from the analysis of CTCs and ctDNA with innovative health care for patients with metastatic breast cancer. Citation Format: Kellie Howard, Sharon Austin, Fang Yin Lo, Arturo Ramirez, Debbie Boles, John Pruitt, Elisabeth Mahen, Heather Collins, Amanda Leonti, Lindsey Maassel, Christopher Subia, Tuuli Saloranta, Nicole Christopherson, Kerry Deutsch, Jackie Stilwell, Eric Kaldjian, Michael Dorschner, Sibel Blau, Anthony Blau, Marcia Eisenberg, Steven Anderson, Anup Madan. Meta-analysis of genomic aberrations identified in CTCs andctDNA in triple negative breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 498.

Abstract 2383: Multiregional RNA sequencing identifies intratumor transcriptomic heterogeneity in a subset of early-stage hepatocellular carcinoma

Abstract BACKGROUND: Hepatocellular carcinoma (HCC) is known to have histological intra-tumor heterogeneity. Little is known about the underlying molecular contributions to this observation, or its potential impact on resistance to therapies. AIMS: 1) To evaluate intra-tumoral molecular heterogeneity of primary HCCs using multi-regional RNA-seq; 2) to correlate molecular alterations with histological features at distinct areas. METHODS: We analyzed 55 fresh-frozen tissues from 10 patients with BCLC-A HCC treated with surgical resection. Multi-regional sampling included 38 HCCs and 16 adjacent non-tumoral tissues (average 5.4 samples per patient). We performed H&E staining and RNA-seq on all samples. Each sequenced section was evaluated for a panel of 11 histological features. Data analyses included clustering (consensus and multidimensional scaling (MDS)), sample ordering via linear graph modeling of expression, pathogen quantitation, gene set enrichment analysis (GSEA), and nearest template method (NTP) for gene signature prediction. RESULTS: Patients enrolled were mostly males (70%), with an average age of 59, all with single-nodule HCC, and a median tumor size of 5.3 cm (range 3-16 cm). Background liver disease was HBV in 50% of cases without histological cirrhosis in 80%. MDS and consensus clustering identified heterogeneity in 40% (4/10) of patients as defined by at least one sample not clustering with their counterparts. Sample ordering uncovered dominant tumor heterogeneity evolution paths, including HBV specific ones. GSEA revealed differential enrichment (FDR<0.05) of Cancer Hallmark Gene Sets in the 4 heterogeneous tumors. Indeed, these 4 tumors showed concordant gene set enrichment (FDR<.05) in all regions only 19% of the time compared to 83% in homogenous tumors on average. NTP further confirmed heterogeneity in molecular classification predictions in 2/4 heterogeneous tumors (e.g., Proliferation class). There were no significant differences in size or regions sequenced between heterogeneous and homogenous tumors. Molecular outliers show distinct histological features such as high mitotic rate and poorer differentiation. CONCLUSION: Transcriptomic intra-tumor heterogeneity is frequent in a subset of surgically resected HCC, and it correlates with histological features. Integrative analysis of CNVs, expressed mutations, allele specific expression, and gene fusions is ongoing. Citation Format: Amanda Craig, Mehmet E. Ahsen, Ismail Labgaa, Ashley Stueck, Delia D’Avola, Stephen C. Ward, Maria Isabel Fiel, Ganesh Gunasekaran, Josep Llovet, Swan Thung, Myron Schwartz, Bojan Losic, Gustavo Stolovitzky, Augusto Villanueva. Multiregional RNA sequencing identifies intratumor transcriptomic heterogeneity in a subset of early-stage hepatocellular carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2383.

Abstract A31: Combination therapies guided by evolution of tumor heterogeneity.

Abstract Successful treatment of hematologic malignancies is challenged by genetic heterogeneity of tumors and the dynamic evolution of the heterogeneity in response to targeted drugs as well as chemotherapeutics. We are applying an integrated computational/experimental approach to elucidating principles which can guide selection of effective combination therapies by mathematical analysis of how tumors evolve with respect to drug sensitivity and resistance during treatment. In an initial pharmacological screen of targeted drugs and chemotherapeutics on murine Bcr-Abl; p19Arf-/- ALL cells, we found that crizotinib was particularly effective (IC50 = ~500 nM) with comparable efficacy to that for imatinib (IC50 = ~200 nM). Moreover, in a derivative cell line bearing spontaneous Bcr-AblT315I mutation, crizotinib exhibited efficacy comparable to that of the Bcr-AblWT parental cell line. This same Bcr-AblT315I cell line showed strong resistance to Abl inhibitors imatinib, dasatinib, nilotinib, and bosutinib. Imatinib and crizotinib also exhibited comparable in vivo efficacy, based on overall survival of syngeneic immunocompetent recipient mice transplanted with Bcr-Abl; p19Arf-/- ALL cells. Cell cycle profiles and signaling analyses suggest that crizotinib induces G2/M arrest and subsequently bim-dependent caspase-mediated apoptosis. This phenotype has been subsequently validated in the human K562 Ph+ CML and murine Baf3 Bcr-AblWT and Bcr-AblT315I cell lines. Resistant populations were also derived through dose escalation treatments with imatinib, dasatinib, nilotinib, foretinib, and crizotinib. Bcr-Abl; p19Arf-/- ALL cells were treated at IC90, and recovered populations were subsequently split into: [a] no-drug media, with sensitivity to different sets of drugs assessed at specific time points post-recovery; and [b] new media with drug concentration at 2x the previous dose (e.g., IC90 2x). Cell populations that were resistant to dasatinib at 1x and 2x IC90 became even more sensitive to crizotinib and foretinib. The drug sensitivity does not appear to be a transient behavior as a result of intracellular rewiring, but rather a change in the tumor heterogeneity via selection of particular subpopulations, as evidenced by sustained sensitivity when these populations were analyzed 24h, 48h, 72h, 5 days, and 9 days post drug selection in no-drug media. The sensitivity was abrogated at IC90 4x and above. Cell populations resistant at these higher doses of dasatinib also became cross-resistant to imatinib and foretinib. This potentially suggests particular stages in the tumor evolution under continued drug selection for which they are extremely sensitive to other pharmacological agents. These findings suggest a novel combination treatment strategy taking into account the evolutionary trajectories of tumor heterogeneity, with drugs dosed sequentially in a multi-course regimen. The sequential treatment is not to exploit vulnerabilities of intracellular rewiring induced by the first drug, but rather vulnerabilities of resulting expanded subpopulations upon selection by the first drug. Citation Format: Boyang Zhao, Michael T. Hemann, Douglas A. Lauffenburger. Combination therapies guided by evolution of tumor heterogeneity. [abstract]. In: Proceedings of the AACR Special Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(17 Suppl):Abstract nr A31.

Abstract 4819: Differential evolution of tumor heterogeneity in leiomyosarcomas and liposarcomas suggested by genomic profiling

Abstract Sarcomas represent a heterogeneous set of malignant tumors originating from mesenchymal cells. Liposarcomas (LPS) and Leiomyosarcomas (LMS) are two of the most common histotypes, accounting for approximately 25% and 30% of all soft tissue sarcomas, respectively. The most frequent form of LPS is represented by a spectrum of disease including well-differentiated LPS (WDLPS), a non-metastasizing but locally recurrent disease with adipocytic differentiation, and de-differentiated LPS (DDLPS), an aggressive, frequently metastasizing high grade sarcoma which can arise in conjunction with elements of WDLPS. Besides the known oncogenic KIT or PDGFRA driver mutations in GIST, somatic alterations in RB1, deletions in PTEN, MDM2 amplifications in LPS, and TP53 mutations in LMS are the most commonly reported genomic aberrancies identified in sarcomas. Both WDLPS and DDLPS share amplification of 12q13-15, a genomic region containing the MDM2 and CDK4 loci, yet little is understood about the other genetic processes that yield such different phenotypes. In LMS, recurrent mutations in TP53 have been identified, but a detailed analysis of primary and metastatic tumors has not previously been described. To evaluate genetic events in these transitions, we performed whole exome sequencing (WES) on trios comprising normal tissue, WDLPS, and DDLPS obtained from individual patients (n = 19), as well as on trios of normal tissue, primary and metastatic LMS tumors obtained from separate individual patients (n = 8). Consistent with prior reports of the molecular characterization of LPS, we observed arm-level amplifications in Chr 12 in all LPS samples, and Chr 17 amplification in many LMS cases. There were no shared somatic alterations across paired WDLPS and DLPS pairs from individual patients aside from the common Chr 12 amplification (MDM2 & CDK4). A higher mutation rate was observed in LMS, and there were many clonal somatic alterations shared between the primary and metastatic lesions of individuals. This study demonstrates the heterogeneity of evolution between different subtypes of sarcomas using whole exome sequencing of clinical specimens. This finding has implications for better understanding of the molecular drivers of these tumors and opportunities to identify subtype-specific therapeutic targets. Citation Format: Ali Amin-Mansour, Stefano Sioletic, Scott L. Carter, Levi A. Garraway, George D. Demetri, Suzanne George, Eliezer M. Van Allen, Andrew J. Wagner. Differential evolution of tumor heterogeneity in leiomyosarcomas and liposarcomas suggested by genomic profiling. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4819. doi:10.1158/1538-7445.AM2015-4819