Metastatic Cohort Research Articles

Deep learning model accurately classifies metastatic tumors from primary tumors based on mutational signatures

Metastatic propagation is the leading cause of death for most cancers. Prediction and elucidation of metastatic process is crucial for the treatment of cancer. Even though somatic mutations have been linked to tumorigenesis and metastasis, it is less explored whether metastatic events can be identified through genomic mutational signatures, which are concise descriptions of the mutational processes. Here, we developed MetaWise, a Deep Neural Network (DNN) model, by applying mutational signatures as input features calculated from Whole-Exome Sequencing (WES) data of TCGA and other metastatic cohorts. This model can accurately classify metastatic tumors from primary tumors and outperform traditional machine learning (ML) models and a deep learning (DL) model, DiaDeL. Signatures of non-coding mutations also have a major impact on the model’s performance. SHapley Additive exPlanations (SHAP) and Local Surrogate (LIME) analyses identify several mutational signatures which are directly correlated to metastatic spread in cancers, including APOBEC-mutagenesis, UV-induced signatures, and DNA damage response deficiency signatures.

A robust gene prognostic index composed of GZMB, IRF1, and TP63 can stratify the risk of two metastatic urothelial carcinoma cohorts based on immune checkpoint blockade therapy.

Immune checkpoint blockade (ICB) therapy has become a first-line treatment option for metastatic urothelial carcinoma (mUC) patients who do not meet the criteria of cisplatin. Still, only a few people can benefit from it, so useful predictive markers are needed. Download the ICB-based mUC and chemotherapy-based bladder cancer cohorts, and extract the expression data of pyroptosis-related genes (PRG). The LASSO algorithm was used to construct the PRG prognostic index (PRGPI) in the mUC cohort, and we verified the prognostic ability of PRGPI in two mUC and two bladder cancer cohorts. Most of the PRG in the mUC cohort were immune-activated genes, and a few were immunosuppressive genes. The PRGPI composed of GZMB, IRF1, and TP63 can stratify the risk of mUC. In IMvigor210 and GSE176307 cohorts, the P-values of Kaplan Meier analysis was < 0.01 and 0.002, respectively. PRGPI could also predict ICB response, and the chi-square test of the two cohorts had P-values of 0.002 and 0.046, respectively. In addition, PRGPI can also predict the prognosis of two bladder cancer cohorts without ICB therapy. The PRGPI and the expression of PDCD1/CD274 had a high degree of synergistic correlation. The Low PRGPI group showed prominent characteristics of immune infiltration and was enriched in the immune signal activation pathway. The PRGPI we constructed can effectively predict the treatment response and overall survival rate of mUC patients treated with ICB. The PRGPI can help mUC patients achieve individualized and accurate treatment in the future.

Guidance on Therapeutic Strategies for Metastatic Urothelial Cancer

Guidance on Therapeutic Strategies for Metastatic Urothelial Cancer

Molecular Profiling Provides Clinical Insights Into Targeted and Immunotherapies as Well as Colorectal Cancer Prognosis

Tumor genetic testing is indispensable in the management of primary and metastatic colorectal cancer (mCRC), yet the indications for genomics-guided precision medicine and immunotherapy need to be better understood and defined. We prospectively sequenced tumors from 869 Chinese colorectal cancer patients by a large panel and evaluated the clinical significance of single gene somatic mutations and co-occurring events in mCRC, as well as their functional effects and tumorigenic mechanisms. We systematically assessed the heterogeneity of the tumor immune microenvironment in different genomic contexts through the combined analysis of Immunoscore, multiplex immunostaining, whole-exome sequencing, transcriptome, and single-cell sequencing. Single-gene somatic mutations in BRAF or RBM10 were associated with shorter progression-free survival (PFS) in mCRC patients. Functional studies suggested RBM10 acts as a tumor suppressor in CRC development. Co-mutations of KRAS/AMER1 or KRAS/APC were enriched in the metastatic cohort, which had poor PFS and did not benefit from bevacizumab due to accelerated drug metabolism. Forty patients (4.6%) carried pathogenic or likely pathogenic germline alterations in the DNA damage repair pathway, and 37.5% of these tumors had secondary-hit events with loss of heterozygosity or biallelic alterations. A high tumor indel burden with MSI-high suggested immunogenicity with numerous activated tumor-infiltrating lymphocytes, whereas POLE-mutation with TMB-ultrahigh indicated a relatively quiescent immunophenotype. The heterogeneous genomic-immunological interactions were reflected in the divergent neoantigen presentation and depletion, immune checkpoint expression, PD-1/PD-L1 interaction, and T-cell responsiveness to pembrolizumab. Our integrated analysis provides insights into CRC prognostic stratification, drug response, and personalized genomics-guided targeted and immunotherapies.

The T1 Ratio of Marrow (TROM) as a Novel Tool to Identify Metastatic from Nonmalignant Marrow Lesions of the Spine: A Pilot Study.

Objective The purpose of this study was to analyze quantitative values of normal and abnormal marrow on T1-weighted images of spine, to propose a ratio for T1 values of abnormal to normal vertebrae, and to assess whether this ratio could be helpful in predicting presence of neoplastic lesions in the spine. Materials and Methods One-hundred randomly selected magnetic resonance imagings of lumbar spine without infection, fracture, and tumor were selected to form normal cohort. A second cohort of 100 metastasis of lumbar spine was identified. Ratio of T1 value of vertebral body to the T1 value of the inferior vertebral body was performed for normal cohort from D11 to L5. Ratio of T1 value of metastasis to adjacent normal vertebral body was done for metastatic cohort. Data was analyzed using standard t -test and kappa was performed for intra- and inter-observer reliability. Results A decline in T1 value of abnormal to normal marrow was seen in patients with metastasis that was statistically significant. We call this the T1 ratio of marrow (TROM). The sensitivity and accuracy with the cutoff value of TROM at 0.7 (92% sensitivity, 97.1% accuracy) are better than at 0.6 (75% sensitivity, 96.2% accuracy) or 0.5 (47% sensitivity, 93.2% accuracy). A subset analysis of the other T1 hypointense benign lesions including atypical hemangiomas and focal marrow hyperplasia, however, revealed overlapping TROM values with the metastatic cohort. Conclusion Using the TROM on T1-weighted images could not confidently differentiate malignant from benign T1 hypointense lesions of the spine.

Novel Generative Recurrent Neural Network Framework to Produce Accurate, Applicable, and Deidentified Synthetic Medical Data for Patients With Metastatic Cancer

Sensitive patient data cannot be easily shared/analyzed, severely limiting the innovative progress of research, specifically for marginalized/under-represented populations. Existing methods of deidentification are subject to data breaches. The objective of this study was to develop a neural network capable of generating a synthetic version of data for patients with novel postoperative metastatic cancer. We analyzed a metastatic cancer patient cohort of 167,474 patients obtained from the National Surgical Quality Improvement Program. Twenty-seven clinical features were analyzed. We created a volume-matched synthetic cohort of 167,474 patients and a reduced-size synthetic cohort of 5,000 patients. The volume-matched and reduced-size synthetic cohorts were compared against the ground truth data to analyze differences in principal component distribution, underlying statistical properties/associations, intervariable correlations, and machine learning classifier performance when developed on the synthetic data. Among 167,474 patients with metastatic cancer in the original data, 50,669 (30.3%) died within 30 days of their index surgery. Our model was able to accurately capture underlying statistical properties, principal components, and intervariable correlations within the ground truth data, yielding an accuracy of 93.2% with a loss of 0.21%, and develop synthetic data capable of training accurate machine learning classifiers. The reduced-size synthetic data accurately replicated all categorical variables and every continuous variable with statistically similar records (P > .05), with the sole exception of preoperative albumin (P < .05). The volume-matched synthetic data frame was able to accurately replicate all categorical variables (P > .05). This described methodology can be applied to any structured medical data from any setting, significantly expedite scientific analysis/innovation, and be used to develop improved predictive classifiers with boosted tree-based algorithms, serving as the potential new gold standard of medical data sharing and data augmentation.

Different risk and prognostic factors for liver metastasis of breast cancer patients with de novo and relapsed distant metastasis in a Chinese population.

The present study aimed to identify clinicopathological characteristics of breast cancer liver metastasis (BCLM) as well as to characterize the risk and prognostic factors for the liver metastasis (LM) of breast cancer patients with de novo and relapsed distant metastasis in a Chinese population. Patients with metastatic breast cancer (MBC) who were hospitalized in the Breast Cancer Center at Chongqing University between January 2011 and December 2019 were included in the present study. Logistic regression analyses were conducted to identify risk factors for the presence of BCLM. Cox proportional hazard regression models were performed to determine the prognostic factors for the survival of BCLM patients. The correlation between LM and overall survival was assessed by the Kaplan-Meier method. In total, 1,228 eligible MBC patients, including 325 cases (26.5%) with de novo metastasis (cohort A) and 903 cases (73.5%) with relapsed metastasis (cohort B), were enrolled in the present study. In cohort A and cohort B, 81 (24.9%) and 226 (25.0%) patients had BCLM, respectively. Patients in these two cohorts had different clinicopathological features. Logistic regression analysis identified that the human epidermal growth factor receptor 2 (HER2) status in cohort A as well as the HER2 status and invasive ductal carcinoma histology in cohort B were risk factors for BCLM. The median OS of patients with LM was inferior to that of non-LM patients (17.1 vs. 37.7 months, P = 0.0004 and 47.6 vs. 84.0 months, P < 0.0001, respectively). Cox analysis identified that the primary T stage, Ki67 level, and breast surgery history were independent prognostic factors for cohorts A and B, respectively. De novo and relapsed MBC patients have different risk and prognostic factors for LM. Patients with BCLM have an unfavorable prognosis.

Abstract 6635: Lipid and glycolipid antigen presentation faults as a mechanism of resistance to immune checkpoint therapy in poorly immunogenic melanomas

Abstract Introduction: Cold tumors are characterized by lacking infiltration of antitumor T cells. These tumors are universally refractory to immune checkpoint therapies (ICT). While poor T cell infiltration has been partly ascribed to low tumor mutational burden (TMB), TMB doesn’t necessarily exclude immunogenic responses nor ensure a response to ICT. Mechanisms of T cell exclusion in tumors with sufficient TMB may be caused by molecular failure of the antigen processing and presentation (APP), which impacts T cell generation. It was previously described that loss of heterozygosity (LOH) of an essential component of the MHC class I molecule, the beta-2-microglobulin (B2M), is associated with low antigen presentation, tumor T cell infiltration, and ICT resistance in melanoma. Here we provide further insight into APP and ICT response in melanoma. Methods: Transcriptomic analysis and visualization of genomic data from the GDC-TCGA skin cutaneous melanoma (SKCM) study were performed using the Xena platform. Four anti-PD1 metastatic melanoma cohorts were normalized with transcripts per million units. STRING protein-protein interaction analysis was performed in the human database with 11 nodes and 39 edges. Nanostring transcriptomic data from metastatic uveal melanoma (mUM) was revisited from our previous publications for Spearman’s correlational and group analysis of APP signatures amongst ICT responders and non-responders. Results: In an expanded analysis of 4 normalized anti-PD1 treated metastatic melanoma cohorts (n=272), we confirmed that transcriptomic levels of B2M are significantly reduced in non-responders. Moreover, STRING protein-protein interaction analysis of B2M revealed CD1D as a potential molecular partner of B2M. We, therefore, observed that CD1D transcriptomic expression is not only reduced in anti-PD1 poor responders but is a survival prognosticator in primary tumors from the GDC-TCGA study. Interestingly, CD1D expression is also significantly reduced in poorly immunogenic mUM tumors, a cancer type regarded as universally refractory to ICT. Conclusions: These findings suggest that APP faults in ICT-resistant tumors are not restricted to faults in peptide presentation to T lymphocytes (via B2M) but may also impact the presentation of tumor-associated lipid and glycolipid antigens via CD1d, which can impact antitumor responses of natural killer T cells (NKT). Adjuvant therapies that restore MHC-I and CD1d-mediated antigen presentation may unleash the response to ICT via NKT. Understanding CD1d expression faults locally and systemically may provide valuable prognostication information likely to impact how cancer is treated by optimally selecting patients for ICT and validating novel therapeutic targets for immunotherapy development. Citation Format: Carlos Rogerio Figueiredo. Lipid and glycolipid antigen presentation faults as a mechanism of resistance to immune checkpoint therapy in poorly immunogenic melanomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6635.

Abstract 1157: Uncovering a novel role of peroxisomal β-oxidation in advanced, treatment-resistant prostate cancer

Abstract Background and Aims: Prostate cancer (PCa) is highly reliant on lipids for energy, hence targeting fatty acid oxidation (FAO) is a highly promising approach to the treatment of PCa. Recent work by our group and others have shown that FAO is critical for cell viability and survival, and is one of the key drivers of treatment resistance. Although FAO occurs in both the mitochondria and peroxisomes, the functional relevance and therapeutic exploitability of peroxisomal FAO (perFAO) in PCa has not been extensively explored compared to the mitochondria. Herein, we aim to investigate the therapeutic efficacy of targeting perFAO in clinical prostate tumors and PCa cells, and explore its role in PCa progression. Methods and Results: Pharmacological inhibition of perFAO using the clinical agent, thioridazine, significantly suppressed proliferation, migration, and colony formation of a range of advanced and treatment-resistant PCa cells. Further, we evaluated the therapeutic efficacy of thioridazine in a more clinically relevant setting using patient-derived tissues and showed a significant inhibition of cell proliferation (n = 11, p &amp;lt; 0.05). Next, we performed a bioinformatics analysis of clinical RNAseq datasets composed of primary and metastatic PCa tissues and identified DECR2, the auxiliary enzyme of perFAO, as a key target of perFAO in PCa. DECR2 is overexpressed in metastatic castrate-resistant PCa (CRPC) tissues compared to primary PCa and benign tissues, and is significantly associated with shorter relapse-free survival (p &amp;lt; 0.01). DECR2 knockdown significantly suppressed proliferation and migration of CRPC and enzalutamide-resistant PCa cells, and markedly reduced LNCaP tumor growth in vivo. In contrast, overexpression of DECR2 in LNCaP cells significantly increased tumor growth in vivo. Interestingly, analysis of a published proteomics dataset of PCa cells that are either androgen-dependent or resistant to androgen receptor (AR) inhibitors revealed a significant correlation of peroxisomal genes (MSigDB) with acquired resistance to AR inhibition. Notably, DECR2 overexpression was significantly associated with shorter overall survival (p &amp;lt; 0.05) in a metastatic CRPC cohort treated with AR inhibitors. We further showed that DECR2 overexpression in LNCaP cells significantly reduced sensitivity to AR inhibitor treatments and androgen-deprivation, suggesting a role for perFAO in promoting survival and treatment resistance. Conclusion: Our study has revealed a novel role for perFAO in PCa progression and treatment resistance. Importantly, this study also identified DECR2 as a key regulator of tumor cell proliferation and lipid metabolism, representing a potential novel therapeutic target for advanced, treatment-resistant PCa that currently lacks effective targeted therapies. Citation Format: Chui Yan Mah, An D. Nguyen, Takuto Niijima, Madison Helm, Jonas Dehairs, Feargal J. Ryan, Natalie Ryan, Ian G. Mills, Johannes V. Swinnen, David J. Lynn, Zeyad D. Nassar, Lisa M. Butler. Uncovering a novel role of peroxisomal β-oxidation in advanced, treatment-resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1157.

Abstract 5773: A forward genetic screen identifies SIRT1 as a driver of neuroendocrine prostate cancer

Abstract Neuroendocrine prostate cancer (NEPC) is a deadly variant of prostate cancer for which no cure is yet available. Up to 20 percent of the patients with castration resistant prostate cancer (CRPC), will progress to NEPC after treatment with standard-of-care therapies, such as abiraterone and enzalutamide, that target the androgen receptor (AR) pathway. However, the molecular mechanisms that drive the emergence of NEPC are largely unknown, contributing to a lack of treatment options for patients with NEPC. We implemented a forward genetic approach to identify novel drivers of NEPC, by using the Sleeping Beauty (SB) transposon-based forward genetic mutagenesis screening system in our Pten-, Trp53-deficient mouse model that is primed to develop NEPC at a low frequency. We generated a mouse strain (NPp53-SB) in which the Nkx3.1 promoter regulates the expression of tamoxifen-inducible Cre specifically in the mouse prostate epithelium, resulting in transposition of the T2Onc2 transposable element and conditional deletion of Pten and Trp53 in mouse prostate epithelium. We observed an increased NEPC incidence in our NPp53-SB mouse model compared to control mice without the transposon T2Onc2, suggesting that the SB-mediated insertional mutagenesis events are driving the development of NEPC. To elucidate the genetic events that are driving the observed NEPC phenotype, we identified the common insertion sites (CISs) of the transposon insertions, which revealed a total of 330 CIS-associated genes. We further performed an integrative analysis using RNA-seq data from our SB cohort, a second mouse dataset and a metastatic CRPC patient cohort, which allowed us to identify the Master Regulator (MR) proteins that are associated with NEPC, as well as the upstream genomic events that modulate these MRs and the emergence of NEPC. Our integrative analysis identified the deacetylase Sirt1 as a candidate driver of NEPC. Using CRISPR activation (CRISPRa) technology in vivo we observed that SIRT1 activation induced an NEPC-like phenotype in the adenocarcinoma LNCaP cell line, while Sirt1 drug-mediated inhibition in an NEPC cell line resulted in less aggressive tumors.In summary, we have developed a Sleeping Beauty forward genetic screen in our mouse model of CRPC, which not only accelerates disease progression, but also increases the incidence of NEPC. Our integrative analysis identified a panel of CIS-associated genes that are likely to be functionally involved in progression to NEPC. In particular, Sirt1 was shown to be a promising candidate, which may shed light on mechanisms that this aggressive disease uses to evade treatments and may inform the development of novel therapies. Citation Format: Francisca Nunes de Almeida, Alessandro Vasciaveo, Min Zou, Matteo Di Bernardo, Andrea Califano, Cory Abate-Shen. A forward genetic screen identifies SIRT1 as a driver of neuroendocrine prostate cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5773.

Abstract 2098: Molecular based blood screening assay for metastatic adenoid cystic carcinoma

Abstract Adenoid cystic carcinoma (ACC) is a rare, yet highly lethal, tumor that originates in the excretory glands of the head and neck. It is a locally aggressive disease, with more than half of patients presenting with perineural invasion and/or bone erosion. The current standard of care consists of surgical excision followed by radiation. Many healthy patients are left with positive margins after surgery and receive systemic therapy in addition to adjuvant radiation without evidence showing added benefit for that approach. Despite extensive surgery, long-term survival rates remain low due to a high incidence of locoregional disease progression and metastatic disease to the lung, liver, brain, or bones, sometimes several years after definitive treatment. Extensive genome analysis of ACC has uncovered a high mutation rate of the proto-oncogene MYB, typically as a genomic translocation resulting in an MYB fusion event with one of the following gene loci: nuclear factor I/B (NFIB), transforming growth factor beta 3 (TGFBR3) or RAD51B. The translocation approximates an enhancer to the MYB regulatory element which can be transactivated by the MYB fusion product, thus leading to the overexpression of MYB via a positive feedback mechanism. Currently, detection of systemic disease relies on diagnostic imaging, which can be imprecise, costly and time-consuming. Years of routine imaging is very impractical, attrition rates are high, and patients often present years later with symptomatic metastatic disease. A rapid and sensitive molecular-based blood screening tool would allow for continuous monitoring and earlier detection of metastatic ACC, ideally improving survival outcomes for these patients. In this study, we hypothesized that the dysregulation in MYB, and the reliance of ACC cells on MYB for survival and progression could be harnessed to develop a molecular screening tool to monitor for metastatic disease of ACC. We developed a blood-based PCR screening probes for metastatic disease in patients with a history of ACC. By analyzing blood samples from four cohorts: healthy individuals (no history of cancer) (n=6), patients with a history of ACC but with no evidence of disease for longer than 3yrs (NED) (n=16), patients with newly diagnosed local disease (n=8), and patients with confirmed metastatic disease (n=7), we demonstrate that our assay was able to detect significantly elevated levels of aberrant MYB expression in all blood specimens from our metastatic disease cohort (p &amp;lt; 0.01). Additionally, our probes were able to detect aberrant levels of MYB in the blood of a patient 11 months before imaging techniques identified metastatic lung lesions. These findings indicate that we can harness a specific ACC genetic trait to develop a sensitive, rapid, and inexpensive molecular screening assay from blood to detect metastatic ACC. We continue to expand and validate these findings by screening existing and new ACC patients every 6 months. Citation Format: Acadia H. Moeyersoms, Ryan A. Gallo, Zoukaa B. Sargi, Jason M. Leibowitz, Andrew J. Rong, David T. Tse, Daniel Pelaez. Molecular based blood screening assay for metastatic adenoid cystic carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2098.

Abstract 6430: Single-cell transcriptomic and epigenomic landscapes of innate and adaptive immune cells in metastatic melanoma treated with immunotherapy

Abstract Immune checkpoint inhibitors (ICIs) have revolutionized the care for cancer and extended survival for advanced cancer patients. While ICIs have shown astonishing clinical benefits, less than 50% of patients experience a durable response. To find better biomarkers for ICI response and understand the diverse cellular players in the tumor microenvironment (TME), we performed single-cell RNA sequencing (scRNA; 222,351 cells; 39 samples), single-nucleus transposase-accessible chromatin sequencing (scATAC; 45,478 cells; 15 samples), and bulk RNA sequencing (39 samples) on a metastatic melanoma cohort with rich phenotypic and molecular data. In ICI resistant tumors, we revealed how cell-adhesion and ribosomal activity changes in adaptive immune cells can reflect tumor-level therapeutic failure. We characterized T cell diversity in the TME and discovered an early activated state and a terminally exhausted state. Among the innate immune cells, we detected a mature dendritic cell (DC) state as a strong prognostic predictor of progression-free survival associated with ICI treatment. We studied its differentiation trajectory, transcriptome signatures, epigenome landscape and interactome with T-cells, in comparison to conventional dendritic cell types 1 and 2. We also showed that CRISPR deactivation of the enhancers induced by the mature DC state compromised DCs’ antigen-presentation capabilities and their interactions with antigen-specific T-cells. Lastly, we identified genes and functional modules associated with ICI response (e.g. cell-adhesion) and resistance (e.g. oxidative phosphorylation). Given their functional roles in strengthening immune response to cancer, the molecular and cellular mediators discovered here can help predict ICI regimen efficacy, guide therapeutic development and drug combinations, and pave the path to targeted therapies with long-term effects and new immunotherapies. Citation Format: Jiekun Yang, Doris Fu, Kyriakitsa Galani, Li-Lun Ho, Emily J. Robitschek, Dennie T. Frederick, Sandeep K. Yadav, Wentao Deng, Anand K. Singh, Kelly P. Burke, Cassia Wang, Tatyana Sharova, David Liu, Kunal Rai, Genevieve M. Boland, Manolis Kellis. Single-cell transcriptomic and epigenomic landscapes of innate and adaptive immune cells in metastatic melanoma treated with immunotherapy. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6430.

Abstract 6071: Whole-exome RNA sequencing of metastatic synovial sarcomas reveals heterogeneous transcriptomic profile and targetable co-alterations: Cohort study from the French Sarcoma Group

Abstract Introduction: Synovial Sarcoma (SS) is a rare and aggressive disease that predominantly occurs in young adult. SS are characterized by a pathognomonic t(X:18) translocation leading SS18: SSX1/2/4 fusion. Small studies (n&amp;lt;100) described molecular background beyond this fusion in patients and the transcriptomic profile of SS remains poorly known. The aim of our study is to provide a large cohort analyzing transcriptomic and co-alterations to better understand and treat SS. Methods: We present a clinico-biological cohort study including all adult patients with histologically confirmed diagnosis of afvanced SS from January 2000, registered in the French Sarcoma database (NETSARC+) and with available formalin-fixed paraffin embedded (FFPE) archival tumor samples and clinical data. FFPE tumor samples were analyzed by dedicated whole-exome RNA-sequencing (WERS) to assess transcriptomic, small nucleotide variation (SNV) and fusions. Results: 122 patients (133 samples) met the study criteria, including 11 patients with paired primary-metastatic tumor samples. Clinical characteristics (age, sex, tumor grade, primary and metastasis site distribution) were consistent with expected SS population. The SS18:SSX1/2/4 fusion was found in all patient (90% by WERS and if negative, by FISH). Unsupervised analyses of transcriptomic data by principal component analyses, hierarchical sample clustering or UMAP revealed heterogeneity in gene expression. Clinical factors (age, sex, grade, tumor type, complete response to treatment, survival) did not correlate with transcriptomic profiles. Immune cell analyses confirmed a low infiltration of immune cells, notably poor in CD8+ T cells. Cancer testis antigens such as NYESO-1, MAGE-A4 were both expressed with a heterogeneous co-expression of other CTAs across samples. In the 11 primary-metastatic paired- samples, no gene pathway was found differentially expressed between primary and metastatic samples cohort with the exception of lung tissue specific genes. Comparing chemotherapy-naïve versus pre-treated samples did not identify differential expression of specific genes across samples. Single Nucleotide Variant analyses was reliable on 84% FFPE samples and revealed an overall low Tumor Mutational Burden with some samples harboring canonical oncogene pathogenic mutations of BTK, RAS, NF1, RB1 as well as in DNA repair pathway(15% spanning over ATM ATR,CHK2, BRCA1/2 PALB2 CHK2, FANCM, RAD51), PI3K pathways (PI3KCA E545K) and other poorly described in SS. Conclusion: Investigating the largest cohort of metastatic SS by whole-exome RNA-sequencing, revealed Synovial Sarcoma, usually classified as “simple genomic sarcoma” is a translocation-related sarcoma harboring heterogeneous transcriptomic and numerous SNV co-alterations including targetable mutations. Citation Format: Helene Vanacker, Mehdi Brahmi, Yannick Le Meitour, Julien Bollard, Valery Attignon, Alexandra Meurgey, Myriam Jean-Denis, Laurie Tonon, Shibani Pokras, Erika Klohe, Michael Nathenson, Kristin Blouch, Ioanna Eleftheriadou, Jean-Yves Blay, Franck Tirode, Armelle Dufresne. Whole-exome RNA sequencing of metastatic synovial sarcomas reveals heterogeneous transcriptomic profile and targetable co-alterations: Cohort study from the French Sarcoma Group. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6071.

Epigenetic control of CD1D expression as a mechanism of resistance to immune checkpoint therapy in poorly immunogenic melanomas.

Immune Checkpoint Therapies (ICT) have revolutionized the treatment of metastatic melanoma. However, only a subset of patients reaches complete responses. Deficient β2-microglobulin (β2M) expression impacts antigen presentation to T cells, leading to ICT resistance. Here, we investigate alternative β2M-correlated biomarkers that associate with ICT resistance. We shortlisted immune biomarkers interacting with human β2M using the STRING database. Next, we profiled the transcriptomic expression of these biomarkers in association with clinical and survival outcomes in the melanoma GDC-TCGA-SKCM dataset and a collection of publicly available metastatic melanoma cohorts treated with ICT (anti-PD1). Epigenetic control of identified biomarkers was interrogated using the Illumina Human Methylation 450 dataset from the melanoma GDC-TCGA-SKCM study. We show that β2M associates with CD1d, CD1b, and FCGRT at the protein level. Co-expression and correlation profile of B2M with CD1D, CD1B, and FCGRT dissociates in melanoma patients following B2M expression loss. Lower CD1D expression is typically found in patients with poor survival outcomes from the GDC-TCGA-SKCM dataset, in patients not responding to anti-PD1 immunotherapies, and in a resistant anti-PD1 pre-clinical model. Immune cell abundance study reveals that B2M and CD1D are both enriched in tumor cells and dendritic cells from patients responding to anti-PD1 immunotherapies. These patients also show increased levels of natural killer T (NKT) cell signatures in the tumor microenvironment (TME). Methylation reactions in the TME of melanoma impact the expression of B2M and SPI1, which controls CD1D expression. These findings suggest that epigenetic changes in the TME of melanoma may impact β2M and CD1d-mediated functions, such as antigen presentation for T cells and NKT cells. Our hypothesis is grounded in comprehensive bioinformatic analyses of a large transcriptomic dataset from four clinical cohorts and mouse models. It will benefit from further development using well-established functional immune assays to support understanding the molecular processes leading to epigenetic control of β2M and CD1d. This research line may lead to the rational development of new combinatorial treatments for metastatic melanoma patients that poorly respond to ICT.

Prevalence and Morbidity of Local Treatment-Related Side Effects in Metastatic Prostate Cancer Patients.

Treatment toxicity from surgery radical prostatectomy (RP) or radiation therapy (RT) has been well studied in patients with localized prostate cancer. However, little is known about lingering toxicities in patients who develop metastatic recurrence. We aimed to compare the prevalence of local treatment-related side effects in patients with metastatic recurrence and those in remission, and to explore to what extent medical oncologists address this morbidity. This was a single site, cross-sectional study evaluating patient-reported outcomes using the Expanded Prostate Cancer Index Clinical Practice (EPIC-CP) instrument, which measures Health-Related Quality of Life (HRQoL) across urinary, bowel, sexual, and hormonal domains, with higher scores reflecting increased symptom burden. The primary endpoint was differences in overall and domain-specific EPIC-CP scores between the metastatic and localized cohorts, with secondary endpoints evaluating provider interventions for symptom alleviation. Median total EPIC-CP scores were higher in the metastatic cohort (18.0, IQR 13.0-24.0) compared to the localized cohort (10.0, 6.0-15.0) (P < 0.001). This difference was mostly driven by worsening symptoms in the sexual (8.0, 8.0-9.0 vs. 6.0, 3.0-8.0) (P < 0.001) and hormonal domains (2.0, 1.0-6.0 vs. 0.0, 0.0-2.0) (P < 0.001), although there were also differences in the urinary irritation/obstruction (3.0, 0.0-3.0 vs. 1.0, 0.0-2.0) (P < 0.001) and bowel domains (1.0, 0.0-3.0 vs. 0.0, 0.0-0.0) (P < 0.001). There was a trend towards higher scores in patients that had received RT as primary treatment. Medical oncologists rarely changed management in response to local symptoms. Prostate cancer patients with metastatic recurrence suffer from a higher burden of localized treatment-related symptoms compared with patients in remission, with primary RT associated with more prevalent toxicity than radical prostatectomy. There is an unmet need for more intensive management of local symptoms. Further studies should focus on factors that portend long term worse morbidity.

Carbon Fiber-Reinforced Polyetheretherketone Spinal Implants for Treatment of Spinal Tumors: Perceived Advantages and Limitations.

Carbon-fiber reinforced polyetheretherketone (CFRP)-based spinal implants are an alternative to titanium, offering less image artifact as their metallic counterparts while maintaining similar biomechanical and biocompatibility properties. Its use in the management of spinal tumors has been reported, however the perceived advantages related to improved imaging quality, radiation treatment planning, and detection of tumor recurrence have not been fully assessed. We performed a retrospective review of medical records amongst oncologic patients treated at MD Anderson Cancer Center with CFRP implants. Histology, tumor location, construct features, time of follow-up, adjuvant radiation, recurrences, overall survival, and hardware-related complications were recorded. Sixty-nine consecutive patients were assessed (22 primary tumors, 47 metastases) and the median time for follow-up was 5.4 months. Amongst the cohort, a total of 491 CFRP pedicle screws were implanted. Hardware complications were observed in 5 cases (7.04%). Adjuvant radiation was completed in 8 patients with primary tumors and 29 patients with spinal metastases. A total of 28 patients (40.5%) from the combined primary and metastatic cohorts experienced systemic disease progression, with 12 patients (17.3%) demonstrating local recurrences. Amongst primary and metastatic tumors, overall survival (p = 0.363) and rate of local recurrence (p = 0.112) were similar. This largest series of CFRP implants demonstrates safe and effective spinal stabilization for patients with both primary and metastatic tumors. Enhanced postoperative imaging led to minimal imaging artifacts which facilitated postoperative radiation planning and the ability to detect local recurrence.

Association of smoking with the survival of patients with brain metastasis of lung cancer.

Smoking is associated with increased mortality in patients with cancer. However, there are limited data on the impact of smoking on the survival of patients with brain metastases. Therefore, this study aimed to evaluate whether smoking was associated with survival and whether smoking cessation was beneficial to these patients. This study used lung cancer with a brain metastasis cohort of the West China Hospital of Sichuan University from 2013 to 2021. Patients were stratified according to smoking history; the distribution, clinical characteristics, and survival data of each group were estimated. Kaplan-Meier analysis and risk analysis were performed for the survival endpoint. Of the 2,647 patients included in the analysis, the median age was 57.8 years, and 55.4% were men. Among them, 67.1% had no smoking history, 18.9% still smoked, and 14% reported quitting smoking. Compared with never smokers, current smokers [HR, 1.51 (95% CI, 1.35-1.69), p < 0.01] and former smokers [HR, 1.32 (95% CI, 1.16-1.49), p<0.01] had an increased risk of death. However, quitting smoking was not associated with improved survival [HR, 0.90 (95% CI, 0.77-1.04), p = 0.16]. The overall survival increased with the increase of smoking cessation years. In lung cancer patients with brain metastases, smoking was associated with an increased risk of death, but quitting smoking was not associated with improved survival.

Differential Expression and Clinical Relevance of C-X-C Motif Chemokine Receptor 4 (CXCR4) in Renal Cell Carcinomas, Benign Renal Tumors, and Metastases

C-X-C Motif Chemokine Receptor 4 (CXCR4) is part of the human chemokine system and involved in progression and metastasis in renal cell carcinoma (RCC). However, the role of CXCR4 protein expression in RCC remains controversial. In particular, data regarding the subcellular distribution of CXCR4 in RCC and RCC metastasis as well as CXCR4 expression in renal tumors of variant histology are limited. The aim of the present study was the evaluation of the differential CXCR4 expression in RCC primary tumor and metastatic tissue as well as in variant renal histologies. In addition, the prognostic capacity of CXCR4 expression in organ-confined clear cell RCC (ccRCC) was evaluated. Three independent renal tumor cohorts (primary ccRCC cohort n1 = 64; cohort of various histological entities n2 = 146; metastatic RCC tissue cohort n3 = 92) were evaluated using tissue microarrays (TMA). After immunohistochemical staining for CXCR4, nuclear and cytoplasmic expression patterns were evaluated. CXCR4 expression was correlated with validated pathologic prognosticators, clinical data, and overall and cancer-specific survival. Positive cytoplasmic staining was observed in 98% of the benign and 38.9% of the malignant samples. Nuclear staining was positive for 94.1% of the benign samples and 83% of the malignant samples. The median cytoplasmic expression score was found to be higher in benign tissue than in ccRCC (130.00 vs. 0.00); median nuclear expression score analysis indicated the opposite (56.0 vs. 71.0). Within malignant subtypes, the highest expression score was seen in papillary renal cell carcinomas (cytoplasmic: 117.50, nuclear: 41.50). Within benign renal tumors, high cytoplasmic and nuclear CXCR4 expression scores were seen for oncocytomas (cytoplasmic: 100.00, nuclear: 31.00). Expression scores in RCC metastasis ranked between benign renal tissue and ccRCC in cytoplasmic and nuclear expression. Cytoplasmic CXCR4 expression was identified as a prognostic factor for OS and CSS (p = 0.042; p = 0.019). Multivariate analysis including clinicopathological parameters did not reveal an independent prognostic character of CXCR4 expression. CXCR4 expression differs significantly within benign lesions and renal neoplasms. Cytoplasmic and nuclear expression of CXCR4 could be detected across all RCC subtypes. The prognostic value of CXCR4 in ccRCC was confirmed in univariate analysis.

Association between homologous recombination deficiency and outcomes with platinum and platinum-free chemotherapy in patients with triple-negative breast cancer.

The choice of chemotherapeutic regimen for triple-negative breast cancer (TNBC) remains controversial. Homologous recombination deficiency (HRD) has attracted increasing attention in informing chemotherapy treatment. This study was aimed at investigating the feasibility of HRD as a clinically actionable biomarker for platinum-containing and platinum-free therapy. Chinese patients with TNBC who received chemotherapy between May 1, 2008 and March 31, 2020 were retrospectively analyzed with a customized 3D-HRD panel. HRD positivity was defined by an HRD score ≥ 30 or deleterious BRCA1/2 mutation. A total of 386 chemotherapy-treated patients with TNBC were screened from a surgical cohort (NCT01150513) and a metastatic cohort, and 189 patients with available clinical and tumor sequencing data were included. In the entire cohort, 49.2% (93/189) of patients were identified as HRD positive (40 with deleterious BRCA1/2 mutations and 53 with BRCA1/2 intact with an HRD score of ≥ 30). In the first-line metastatic setting, platinum therapy was associated with longer median progression-free survival (mPFS) than platinum-free therapy [9.1 vs. 3.0 months; hazard ratio (HR), 0.43; 95% confidence interval 0.22-0.84; P = 0.01]. Among HRD-positive patients, the mPFS was significantly longer in those treated with platinum rather than platinum-free therapy (13.6 vs. 2.0 months; HR, 0.11; P = 0.001). Among patients administered a platinum-free regimen, HRD-negative patients showed a PFS significantly superior to that of HRD-positive patients (P = 0.02; treatment-biomarker P-interaction = 0.001). Similar results were observed in the BRCA1/2-intact subset. In the adjuvant setting, HRD-positive patients tended to benefit more from platinum chemotherapy than from platinum-free chemotherapy (P = 0.05, P-interaction = 0.02). HRD characterization may guide decision-making regarding the use of platinum treatment in patients with TNBC in both adjuvant and metastatic settings.

Are we delivering high-quality medical oncology care? A national comparison of severe acute toxicity from systemic anti-cancer therapy

BackgroundIn the precision medicine era the complexity of systemic anti-cancer therapy (SACT) delivery and their associated toxicities have also increased. However, there has been little systematic assessment of the quality of care associated with systemic anti-cancer therapy delivery across national healthcare systems. We evaluated hospital-level severe acute toxicity rates during SACT treatment as a means of identifying variation in care quality. MethodsAll colorectal cancer (CRC) patients receiving SACT within 106 English National Health Service (NHS) hospitals between 2016 and 2019 were included.Severe acute toxicity rates were derived from hospital administrative data using a validated coding framework. Toxicity rates were adjusted for age, sex, comorbidity, performance status, tumour site, and TNM staging. Variation in hospital-level toxicity rates was assessed separately in the adjuvant and first-line metastatic settings. Results8,173 patients received SACT in the adjuvant setting, and 7,683 patients in the first-line metastatic setting. Adjusted severe acute toxicity rates varied between hospitals from 11% to 49% for the adjuvant cohort, and from 25% to 67% for the metastatic cohort.Compared to the national mean toxicity rate in the adjuvant cohort, six hospitals were more than 2 standard deviations (2SD) above, and four hospitals were more than 2SD below. In the metastatic cohort, six hospitals were more than 2SD above, and seven hospitals were more than 2SD below the national mean toxicity rate.Overall, 12 hospitals (12%) had toxicity rates more than 2SD above the national mean, and 11 (10%) had rates more than 2SD below. ConclusionThere is substantial variation in hospital-level severe acute toxicity rates in both the adjuvant and metastatic settings, despite risk-adjustment. Ongoing national public reporting of this performance indicator can be used investigate reasons for variation in toxicity rates and stimulate quality improvement initiatives to improve care. This may include increasing centralisation of SACT care delivery to minimise variation. This approach can be applied across different cancer types and in many different countries where similar regional or national clinical and administrative hospital datasets are available.