bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract B008: Investigating the evolution of undifferentiated soft tissue sarcomas in a genetically engineered mouse model
Authors: Chan Jason E. , Rub Jonathan , Sussman Carleigh , Grbovic-huezo Olivera , Tap William D. , Antonescu Cristina , Singer Sam , Betel Doron , Tammela Tuomas 
Published: September 2022

Abstract
Undifferentiated soft tissue sarcomas (USTS) are an aggressive class of sarcomas with few effective treatment options. Because of the rarity of these sarcomas and the paucity of representative disease models, little is known about how they develop. We used single cell transcriptomics to study the initiation and evolution of an USTS in an autochthonous genetically engineered mouse model. We profiled multiple stages of tumor development and identified intermediary cell states that define sarcomagenesis. Interestingly, we identify two discrete evolutionary pathways that arise in parallel in the mouse model. To determine the human relevance of our findings, we are developing machine learning approaches to compare cell states between the mouse model with single-cell transcriptomes that we generated from patient-derived xenografts. This cross-species comparison will uncover core USTS cell states and define their ancestral state transitions. Our ultimate goal is to identify essential molecular features of USTS, which may represent entry points for future therapeutic strategies.
Citation Format: Jason E. Chan, Jonathan Rub, Carleigh Sussman, Olivera Grbovic-huezo, William D. Tap, Cristina Antonescu, Sam Singer, Doron Betel, Tuomas Tammela. Investigating the evolution of undifferentiated soft tissue sarcomas in a genetically engineered mouse model [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B008.
Abstract B013: STEAP1 facilitates iron transport in ewing sarcoma to support mitochondrial activity
Authors: Shyp Taras , Mousavizadeh Rouhollah , Negri Gian Luca , Zhang Hai-Feng , Lizardo Michael , Sorensen Poul 
Published: September 2022

Abstract
Ewing sarcoma (EwS) is a highly aggressive bone-associated tumor of children and young adults with strong propensity to progress and dismal outcome for patients with advanced stages of the disease. EwS is defined by a pathognomonic recurrent potent transcription factor, in 85-90% of cases EWSR1-FLI1. One of the previously described transcriptional targets of EWSR1-FLI1 is six-transmembrane epithelial antigen of the prostate 1 (STEAP1). STEAP1 is a member of the STEAP membrane-bound protein family involved in reduction of iron and copper which is a crucial step for metal transport and overexpressed in various malignancies. However, a precise functional role of STEAP1 in cancers including EwS remains elusive. EwS cell lines with knockout (KO) or knockdown (KD) of STEAP1 were created to perform functional studies for elucidating the functions of STEAP1 in EwS, including transient metal measurements. Additionally, the measurement of functional mitochondrial activity was performed by an extracellular flux analyzer. The activity of the mitochondrial electron transport chain complexes was measured by blue native PAGE. We showed that STEAP1 functions as a metalloreductase and STEAP1 KO cells have lower intracellular iron levels. Furthermore, we discovered that STEAP1 KO cells have significantly lower levels of the mitochondrial labile iron pool. Consequently, EwS cells with STEAP1 KO demonstrated impaired mitochondrial respiration and increased glycolysis rates. Additionally, the functional activity of iron-sulfur containing proteins and the the assembly of subunits of the mitochondrial electron transport chain complexes were decreased. This study is the first to demonstrate in vitro involvement of STEAP1 in transitional metal homeostasis and mitochondrial activity. These discoveries unveil alternative therapeutic strategies for EwS patients such as using compounds that promote an iron-dependent form of cell death, ferroptosis, or drugs that decrease metabolic adaptability.
Citation Format: Taras Shyp, Rouhollah Mousavizadeh, Gian Luca Negri, Hai-Feng Zhang, Michael Lizardo, Poul Sorensen. STEAP1 facilitates iron transport in ewing sarcoma to support mitochondrial activity [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B013.
Abstract B026: Expression levels of chaperonin containing TCP1 in cancer are among the highest in sarcomas
Authors: Cox Amanda J. , Khaled Annette 
Published: September 2022

Abstract
Protein folding complexes are essential for oncogenesis. Of these, the multi-subunit complex, Chaperonin-Containing TCP-1 (CCT or TRiC), is upregulated across a spectrum of cancers and folds many of the oncoproteins that drive cancer growth. Using the UCSC Xena online database, which includes datasets from TCGA, TARGET, GTEx, and KidsFirst, we found significant increases in gene expression of the subunits (CCT1-8) that form the chaperonin complex in sarcomas, both adult and pediatric, as compared to other cancers like invasive breast carcinoma, lung carcinoma, glioblastoma multiforme, or prostate cancer. Most notably was the high expression of the second subunit (CCT2) in Rhabdomyosarcoma compared to other pediatric cancers. These findings were confirmed with other databases (e.g., Oncomine). Expression of CCT subunits, like CCT2, was decreased in normal tissues, such as muscle, kidney, and uterus, as compared to sarcoma tissues. Bioinformatic data was confirmed by finding detectable staining of CCT2 protein in sarcoma tissues. This was supported by data from the human protein atlas showing minimal staining for CCT2 in normal smooth and skeletal muscle. Cancer adjacent tissues from a metastatic breast cancer patient study had minimal staining for CCT2 in muscle, fat, and bone. These data show that CCT is increased in sarcomas, while decreased in normal tissues, and has potential for further study as a driver of sarcoma development and a target for therapeutic intervention.
Citation Format: Amanda J. Cox, Annette Khaled. Expression levels of chaperonin containing TCP1 in cancer are among the highest in sarcomas [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B026.
Abstract IA004: Mesenchymal progenitors and sarcomagenesis
Authors: Underhill T. Michael 
Published: September 2022

Abstract
Synovial sarcoma (SS) is an aggressive soft-tissue malignancy that can arise in any area of the body, and most frequently affects adolescents and young adults. The 10-year survival rate has been estimated at 50%. SS is characterized by a pathognomonic t(X;18)(p11.2;q11.2) translocation which produces a fusion oncogene named SS18-SSX. In mouse models, expression of SS18-SSX is sufficient to drive the development of SS-like tumors. Despite recent advancements in our understanding of SS biology, the cell of origin remains undefined. In most instances, it is likely mesenchymal in nature. We previously generated a mesenchymal progenitor (MP) specific Cre line that has enabled us to identify MPs within the embryo [MOU1], and characterize and define their lineage trajectories through development into the adult. This line has been used to generate a unique mouse model of SS where the human SS18-SSX fusion oncogene with an EGFP marker is conditionally expressed in adult MPs. This model shows 100% penetrant SS tumor formation with a median latency period of 16 weeks. Histologic analyses of tumors reveal characteristic cellular morphology and the expression of common markers of SS. Single-cell (sc) RNA-seq gene expression profiles of murine tumors recapitulate those observed in human SS samples and highlight genetic programs involved in sarcomagenesis. Using this model, we can identify and isolate neoplastic lesions prior to the development of grossly visible tumors and trace these cells through the complete transformation continuum. By comparing tumor cells to normal MPs, we aim to better understand the mechanisms underlying the SS18-SSX induced transformation of MPs. Together, this model identifies a cell of origin for SS and provides us with a unique opportunity to address the molecular and cellular drivers of SS.
Citation Format: T. Michael Underhill. Mesenchymal progenitors and sarcomagenesis [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA004.
Abstract IA005: On the use of stem cells to generate sarcomas in vitro models
Authors: Boveé Judith V.M.G. 
Published: September 2022

Abstract
Sarcomas are rare cancers arising in soft tissue and bone. They are difficult to diagnose and treat, with 38-48% mortality for this often young age group. It is now generally accepted that molecular changes in cancer open avenues for personalized medicine. However, to achieve this for sarcoma there are several challenges, as representative model systems are scarce. Moreover, sarcomas are heterogeneous and &gt;70 sarcoma types are recognized. A simple dichotomy based on molecular pathways of simple versus complex genomics is often used as a conceptual framework. My group has used mesenchymal stem cells to generate a model for complex genome sarcomas such as osteosarcoma. Murine and canine mesenchymal stem cells (MSCs) can be used to model spontaneous malignant transformation towards sarcomas with complex genomics. These MSCs have an abnormal karyotype, many structural variants and point mutations at whole genome sequencing analysis, and form sarcomas (osteosarcoma, undifferentiated pleomorphic and spindle cell sarcoma) after injection into mice. Cross-species analysis reveals that p53 loss is an early event in sarcomagenesis, and MSCs with a knockout in Trp53 transform earlier compared to wild-type MSCs. In addition, loss of p16Ink4a is shown to be a driver of osteosarcomagenesis: the majority of spontaneously transformed murine MSCs has alterations in p15Ink4b, p16Ink4a, or p19Arf and knockout of these genes in MSCs results in accelerated transformation. Of interest, osteosarcoma cells with defective p16INK4A are sensitive to the CDK4/CDK6 inhibitor Palbociclib, suggesting that a subset of osteosarcoma patients with intact Rb, but defective p16 or overexpression of CDK4 and/or CDK6 (in total 20-23%) might benefit from CDK4/CDK6 inhibition. Bone and soft tissue tumors with a simple genome often carry chromosomal translocations. We have generated a model for pseudomyogenic hemangioendothelioma (PHE), a rare locally aggressive vascular tumor. PHE has a tumor-specific t(7;19)(q22;q13) translocation resulting in a SERPINE1-FOSB fusion. We used CRISPR/Cas9 to generate this fusion in induced pluripotent stem cells (hiPSCs), which were subsequently differentiated into ECs (hiPSC-ECs) to address this. Comparison of parental with PHE hiPSC-ECs shows invasive growth in mice after transplantation, and transcriptome analysis identifies PI3K-Akt and MAPK signaling pathways as possible therapeutic targets. The modified hiPSC-ECs thus recapitulate functional features of PHE and demonstrate how these stem cell based translocation models can be used to understand tumorigenic mechanisms and identify therapeutic targets.
Citation Format: Judith V.M.G. Boveé. On the use of stem cells to generate sarcomas in vitro models [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA005.
Abstract IA006: Immunobiology of sarcomas and therapeutic implications
Authors: Llosa Nicolas J. 
Published: September 2022

Abstract
Undoubtedly, the greatest breakthrough in cancer treatment over the past decade has been immunotherapy. However, the immunosuppressive nature of the tumor microenvironment (TME) remains the biggest obstacle to increasing the number of patients that respond to immunotherapy. Unfortunately, initial trials of immune checkpoint inhibitors in patients with soft tissue sarcoma (STS) have achieved very limited success, and the reasons for this are crudely unappreciated. Hence, it is critical to move beyond the current focus on targeting individual cell types of interest and rather adopt a more comprehensive systems-level approach in which we analyze and integrate all the TME components to identify and disable the critical nodes. Our team has characterized the immunobiology of STS via cutting–edge high-dimensional mapping platforms that we have established and standardized for analyzing specimens from patients with STS. We have discovered that tumor infiltrating myeloid cells (TIM) penetrate and dominate the TME of STS provoking the suppression of effective antitumoral T cell immune responses. Using a set of sophisticated multiscale techniques, we deconvoluted the TME of various STS creating a comprehensive map of all immune cell populations present and dissected out chemokine gradients of specific histological regions relevant for the recruitment and development of TIM in the TME of STS. STS TIM are regulated by tumor-derived cytokines to acquire a polarized immunosuppressive phenotype, which in turn de-activates the T cell compartment in the TME. In this way, we elucidated unique myeloid populations as key facilitators of STS progression and mediators of local tumor immunosuppression. Furthermore, we defined metabolic pathways utilized by TIM that contribute to their immunosuppressive properties in STS and manipulated them via glutamine antagonism in our mouse model of STS. Our intervention generated a TME that was less acidic, less hypoxic and more replete with nutrients leading to an intratumoral influx of T cells, both CD4+ and CD8+ cells, along with B cells. These modifications in the TME in combination with anti PD-1 therapy induced better endogenous anti-tumor responses and repurposed TIM markedly thereby reducing the tumor size and improving the survival of mice. Thus, we propose a metabolic strategy to therapeutically target the TME of STS and reprogram their immunosuppressive myeloid niche as a means of enhancing immunotherapy.
Citation Format: Nicolas J. Llosa. Immunobiology of sarcomas and therapeutic implications [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA006.
Abstract IA007: B cell immunity generation in tertiary lymphoid structures, a major determinant of sarcoma immune response to immunotherapy
Authors: Fridman Wolf H. 
Published: September 2022

Abstract
The presence of tertiary lymphoid structures (TLSs) and a high intratumoral density of B lymphocytes have been associated with improved survival in several tumor types. We investigated the impact of TLS on responses to immunotherapy and, analyzing a large-scale retrospective analysis of three independent cohorts of patients with cancer, including sarcomas, who were treated with anti-PD-1 or anti-PD-L1 antibodies, we showed that the presence of mature TLSs was associated with improved objective response rates, progression-free survival and overall survival, independent of PD-L1 expression status and CD8+T cell density. To decipher the role of B cells in such responses, we performed spatial transcriptomics and examined the nature of B cell responses within TLS structure. B cells were enriched in TLS, and therein we could identify all B cell maturation stages toward plasma cell (PC) formation. B cell repertoire analysis revealed clonal diversification, selection, expansion in TLS and the presence of full mature clonotypes at distance. In TLS+ tumors, IgG producing PCs disseminated into the tumor beds along fibroblastic tracks. TLS+ tumors exhibited high frequencies of IgG-producing PCs and IgG-stained and apoptic malignant cells, suggestive of anti-tumor effector activity. We validated these findings in a prospective trial in metastatic Soft Tissue Sarcoma (STS) bearing patients. PEMBROSARC is a multi-cohort phase II study of pembrolizumab combined with low-dose cyclophosphamide in patients with advanced STS. The 6-months non-progressive rate (NPR) and the objective response rates previously reported in cohorts including all comers were 4.9% and 2.4%, respectively. In the cohort enrolling patients selected based on the presence of TLS, the 6-month NPR was 40% and the objective response rate was 30%. Exploratory analyses reveled that infiltration by IgG antibody-producing plasma cells was associated with improved clinical outcome as well as the presence of IgG antibodies on tumor cells. Altogether, these results establish that maturation, selection and amplification of B cells in intratumoral TLSs results in Plasma Cells generation which may produce anti-tumor antibodies. The latter may amplify in situ antitumor immune responses leading to better therapeutic responses to immunotherapy.
Citation Format: Wolf H. Fridman. B cell immunity generation in tertiary lymphoid structures, a major determinant of sarcoma immune response to immunotherapy [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA007.
Abstract IA009: Oncogenic transcription factors drive highly tumor-specific LincRNA
Authors: Delattre Olivier , Vibert Julien , Saulnier Olivier , Waterfall Joshua 
Published: September 2022

Abstract
Many cancers are characterized by gene fusions encoding oncogenic chimeric transcription factors (TFs) such as EWS::FLI1 in Ewing sarcoma (EwS). EWS::FLI1 induces a complete reprogramming of mesenchymal stem cells, the putative cell of origin of Ewing sarcoma, through binding and subsequent generation of thousands of neoenhancers at GGAA microsatellite repeats. We show that EWS::FLI1 induces the robust expression of a specific set of novel spliced and polyadenylated transcripts within otherwise transcriptionally silent regions of the genome. These neo-genes (NGs) are virtually undetectable in large collections of normal tissues or non-EwS tumors and can be silenced by CRISPR interference at regulatory EWS::FLI1-bound microsatellites. Ribosome profiling and proteomics further show that some NGs are translated into highly EwS-specific peptides. More generally, hundreds of NGs can be detected in diverse cancers characterized by chimeric TFs. Altogether, we identify the transcription, processing, and translation of novel, specific, highly expressed multi-exonic transcripts from otherwise silent regions of the genome as a new activity of aberrant TFs in cancer. These neotranscripts, which can be classified as LincRNAs, or neopeptides may have specific functions in the tumor cells. The latter may also constitute ideal neoepitopes as they are tumor-specific, clonally expressed in sarcoma cells, induced by the driver genetic alterations and public for a given sarcoma.
Citation Format: Olivier Delattre, Julien Vibert, Olivier Saulnier, Joshua Waterfall. Oncogenic transcription factors drive highly tumor-specific LincRNA [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA009.
Abstract IA019: How to target lung metastasis: dynamic changes in chromatin accessibility during osteosarcoma lung metastasis expose vulnerabilities
Authors: Scacheri Peter C. 
Published: September 2022

Abstract
The metastatic cascade describes the series of steps required for a cancer cell to successfully spread from its primary tumor to a secondary organ. Despite knowing that metastasis is a fluid process, almost all studies to date have relied on end-point assays. As a result, little is known about the continuum of molecular events required for successful growth within the secondary organ. By profiling accessible chromatin in osteosarcoma cells grown in vitro and isolated from an early and late timepoint during lung metastasis, we identify temporally distinct epigenomic reprogramming events that occur as tumors form and grow within the metastatic microenvironment. Furthermore, these data pinpoint key upstream transcription factors responsible for the dynamic chromatin changes. Through paired in vivo and in vitro CRISPR drop-out screens, we show a subset of these putative pro-metastatic transcription factors are essential for lung metastasis, but dispensable for in vitro growth. Targeting the same factors with chemical probes in vitro and ex vivo demonstrated similar context-dependent essentiality. Altogether, our study demonstrates the epigenomes of metastasizing cancer cells are tightly regulated in a dynamic and context-specific manner, and the transcription factors controlling this process may serve as novel vulnerabilities.
Citation Format: Peter C. Scacheri. How to target lung metastasis: dynamic changes in chromatin accessibility during osteosarcoma lung metastasis expose vulnerabilities [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA019.
Abstract IA029: The origins of leiomyosarcoma: implications for prognosis and defining new therapeutic options
Authors: Gladdy Rebecca A. 
Published: September 2022

Abstract
Introduction: Leiomyosarcomas (LMS) are genetically heterogenous tumors differentiating along smooth muscle lines. Currently, LMS treatment is not informed by molecular subtyping and is associated with highly variable survival. While disease site continues to dictate clinical management, the contribution of genetic factors to LMS subtype, origins, and timing are unknown. Here we analyze 70 genomes and 130 transcriptomes of LMS, including multiple tumor regions and paired metastases, with the goal of defining the molecular origins of LMS and using both computational analysis and functional genomics to define new therapeutic arenas for metastatic disease. Results: Molecular profiling highlight the very early origins of LMS. We uncover three specific subtypes of LMS that likely develop from distinct lineages of smooth muscle cells. Of these, dedifferentiated LMS with high immune infiltration and tumors primarily of gynecological origin harbor genomic dystrophin deletions and/or loss of dystrophin expression, acquire the highest burden of genomic mutation, and are associated with worse survival. Homologous recombination defects lead to genome-wide mutational signatures, and a corresponding sensitivity to PARP trappers and other DNA damage response inhibitors, suggesting a promising therapeutic strategy for LMS. Finally, by phylogenetic reconstruction, we present evidence that clones seeding lethal metastases arise decades prior to LMS diagnosis. Conclusions: In summary, LMS, the catch all-label for any primary malignant smooth muscle neoplasm, encompasses at least three distinct entities. We report that the utility of DNA damage response inhibitors is promising and warrants further exploration. Finally, the molecular evolution and timing of LMS provide a broad window for early intervention and risk stratification for these patients.
Citation Format: Rebecca A. Gladdy. The origins of leiomyosarcoma: implications for prognosis and defining new therapeutic options [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA029.