Underlying Tumor Biology Research Articles

Abstract ED4-3: Inflammatory Breast Cancer

Abstract Inflammatory Breast Cancer (IBC) has an incidence of 1-5% among all breast cancers diagnosed within the USA, yet it accounts for a disproportionately high rate of mortality, leading to up to 10% of all breast cancer related deaths. Although IBC can present with any receptor status in terms of estrogen, progesterone, and human epidermal growth factor 2 (HER2), there is a higher proportion of HER2 positive cases compared to non-IBC. Given the distinct difference in outcome, it is important to differentiate IBC from more indolent locally advanced non-IBC with secondary inflammatory features. Despite ongoing efforts to identify molecular markers specific for IBC, the underlying tumor biology and genomic drivers of progression remain largely unknown. In this session we will review tumor-intrinsic signaling pathways, the role of the tumor microenvironment and clinical trials with combination therapies to inform future biomarkers of disease progression in IBC. Citation Format: Filipa Lynce. Inflammatory Breast Cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr ED4-3.

Abstract P3-05-48: Prediction of disease recurrence in low risk Oncotype Dx breast cancers from digital H&E-stained whole slide images of pre-treatment resections alone

Abstract Background Breast cancer patients with estrogen receptor (ER)+/HER2- (and usually node-negative) tumors can avail themselves of Oncotype DX Breast Recurrence Score (ODXRS) testing to predict their risk of distant recurrence within 9 years and, consequently, putative chemotherapy benefit. However, ODXRS testing requires sufficient tumour availability and specimen shipping, which imposes time and financial burdens to testing which have to be met by healthcare systems. The advent of digital pathology offers a potential avenue for exploring computer-aided diagnostic solutions which may overcome these hurdles by extracting the requisite information from hematoxylin and eosin (H&E)-stained tissue whole slide images (WSIs) alone. In turn, this technology could significantly reduce diagnostic turnaround times and cost, and improve accessibility and test reproducibility, thereby enabling healthcare systems to run more efficiently and offer patients more timely results. Ideally, such a platform should incorporate a measure of the underlying tumor biology to provide a fully explainable, white box solution, and may offer further insights into the identification of early recurrence events. Aims The aim of this study was to establish whether our computer-aided solution’s (Q-Plasia OncoReader Breast, QPORB) digital biomarker representing G1/S cell cycle deformations extracted from H&E WSIs was prognostic for disease-free survival (DFS) and could predict disease recurrence, particularly in the setting of low risk ODXRS breast cancers. Methods Primary breast cancer resection/excision specimens (n=70 cases) sent for ODXRS testing from St James’s University Hospital, UK (2016-2019) were collected. Anonymised diagnostic glass slides (n=198 slides) of H&E-stained tumors were scanned at x20 magnification on an Aperio AT2 scanner. In parallel, relevant clinical and histological data were collected from pathology reports and electronic patient records, including both ODXRS and recurrence events during follow-up. The QPORB recurrence scale (QPORB-RS), which combines statistical physics and tumor biology to identify image-based malignant cell cycle deformation, extracts prognostic information from WSIs. The contribution of potential confounders (age, stage, grade, lesion size, Nottingham prognostic index and Charlson score) were accounted for. Results The QPORB-RS was prognostic for DFS for patients with predominantly node-negative (including node micro-metastases) HR+/HER2- tumors over a median follow-up period of 5 years (P=0.02; dichotomized Kaplan Meyer with median cut-off). The QPORB-RS concurred with ODXRS’s high vs. low recurrence risk in 73% (19/26) and 61% (27/44) of cases, respectively, with an overall agreement of 66% (46/70). Moreover, the QPORB-RS identified all 5 patients who had recurrences (with ODXRS of 6, 9, 10, 21 and 26, and ages of 55, 66, 42, 35 and 50 years, respectively) as being high risk in the subset of those given a low (including historically intermediate) ODXRS and who did not receive chemotherapy. Conclusion The QPORB-RS is a good prognostic test of risk of disease recurrence in breast cancer patients with predominantly node-negative (including node micro-metastases) HR+/HER2- tumors within a median 5-year follow-up period. Our efforts are now focussed on extending this cohort and establishing the prognostic value of the QPORB-RS across all breast carcinomas, regardless of molecular subtype, stage/node positivity and menopausal status. Citation Format: Satabhisa Mukhopadhyay, Tathagata Dasgupta, Elizabeth Walsh, Rebecca Millican-Slater, Andrew hanby, Joanne Stephenson, Craig A. Bunnell, Nicolas M. Orsi. Prediction of disease recurrence in low risk Oncotype Dx breast cancers from digital H&E-stained whole slide images of pre-treatment resections alone [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-05-48.

Pre-diagnostic delay among patients with curative esophageal and gastric cancer during the COVID-19 pandemic.

302 Background: The majority of esophageal and gastric cancers are diagnosed at an advanced stage with poor overall survival (OS), leading some to propose screening, even in countries with a low incidence. Whether diagnostic delay from symptom onset has any impact on OS is unclear. We investigated this question in the peri-COVID19 pandemic era. Methods: We retrospectively analyzed a cohort of 308 patients with esophageal, gastroesophageal junction, or gastric carcinoma treated with curative intent at the Princess Margaret Cancer Centre from January 2017 to December 2021. Clinical details pertaining to the initial presentation were determined through a retrospective chart review. OS was estimated using the Kaplan-Meier method. Cox proportional hazards regression models were used to assess the association between pre-diagnostic interval with OS adjusting for baseline patient characteristics. Results: The median interval from symptom onset to diagnosis was 98 days (IQR 47-169 days). Using a cox proportional hazard model, prolonged pre-diagnostic interval was not associated with worse OS (HR 1.00, P=0.62). Comparing patients diagnosed before and during the COVID19 pandemic, there was a notable increase in diagnostic delay with median pre-diagnostic interval increasing from 92 to 126 days (P=0.007). Median age at time of diagnosis was 69.6 during the pandemic vs 64.7 before the pandemic. Linear regression showed squamous cell histology was significantly associated with increasing time to initial diagnosis (P=0.04). Looking at other delay metrics, there were no changes in time interval from diagnosis to treatment during versus before the pandemic (median = 1.7 weeks for both), and there was no change in time from diagnosis to resection in those patients who underwent surgery. Conclusions: The COVID19 pandemic caused significant diagnostic delay for patients presenting with curative esophageal and gastric cancer. We found no evidence of pandemic-related health system delays in treatment, once a diagnosis was made. The lack of correlation of pre-diagnostic interval with OS may reflect underlying tumour biology as the driving force that determines prognosis.

Combined 70- and 80-gene signatures identify tumors with genomically luminal biology responsive to neoadjuvant endocrine therapy and are prognostic of 5-year outcome in early-stage breast cancer

BackgroundAs more patients with early-stage breast cancer receive neoadjuvant endocrine therapy (NET), there is a need for reliable biomarkers that can identify patients with HR+ HER2- tumors who are likely to benefit from NET. NBRST (NCT01479101) compared the prognostic value of the 70-gene risk classification and 80-gene molecular subtyping signatures with conventional pathological classification methods in response to neoadjuvant therapy. We evaluated the association of these signatures with clinical response and 5-year outcome of patients treated with NET. Methods1091 patients with early-stage breast cancer scheduled to receive neoadjuvant therapy were prospectively enrolled into NBRST, and a sub-analysis of 67 patients treated with NET was performed. Patients received standard of care genomic testing using the 70-gene and 80-gene signatures and were treated with NET, per physician's discretion. The primary endpoint was pathologic partial response (pPR) and secondary endpoints were distant metastasis-free survival (DMFS) and overall survival (OS). Clinical benefit was defined as having a pPR or stable disease (SD) with NET. ResultsOverall, 94.4% of patients with genomically (g) Luminal A-Type (50.0% pPR and 44.4% SD) and 95.0% with Luminal B-Type tumors (55.0% pPR and 40.0% SD) exhibited clinical benefit. At 5 years, patients with gLuminal B tumors had significantly worse DMFS (75.6%, 95% CI 50.8–89.1) than patients with gLuminal A (91.1%; 95% CI 74.8–97.1; p = 0.047), with a similar trend for OS, albeit not significant (81.0%, 95% CI 56.9–92.4 and 91.1%, 95% CI 74.8–97.1, respectively; p = 0.13). ConclusionsGenomic assays offer a broader understanding of the underlying tumor biology, which adds precision to pathology as a preoperative risk classifier. Patients with 70-gene signature Low Risk, gLuminal A tumors treated with endocrine therapy alone have excellent 5-year outcomes. Most patients with genomically-defined Luminal A- and B-Type tumors respond well to NET, suggesting these patients may be safely treated with NET, while those with gLuminal B tumors will also require post-operative chemotherapy or CDK4/6 inhibitors to improve long-term outcomes. Overall, these findings demonstrate that genomic classification, defined by the combined 70- and 80-gene signatures, is associated with tumor response and prognostic of long-term outcomes.

EPCO-12. SEX-SPECIFIC PATTERNS CONNECTING LOCOREGIONAL MRI FEATURES AND IMMUNOHISTOCHEMISTRY OF IMAGE-LOCALIZED BIOPSIES OF GLIOBLASTOMA

Abstract Glioblastoma (GBM) is the most aggressive primary brain tumor with a median survival of 14 months. GBMs are challenging to treat due to their heterogeneous nature. It has also been seen that these tumors have sex differences in their cellular subtypes as well as imaging. Radiomics has the potential to provide a non-invasive, spatial understanding of genetic and epigenetic diversity in these complex tumors and to aid in treatment planning. We have an ongoing study to obtain image-localized biopsies from GBM patients, allowing us to complete radiomic analysis and make connections between immunohistochemistry (IHC) and magnetic resonance imaging (MRI) features. We sought to determine if the patterns on imaging were correlated with underlying tumor biology. We focused on immunohistochemistry (IHC) markers of key features of tumor biology including SOX2 for stem-like tumor cells, CD68 for immune response and Ki67 for proliferation kinetics. Our study included 38 patients with a total of 99 biopsies (bxs): 27 males with 77 bxs and 11 females with 22 bxs. Biopsies were sectioned and stained for the SOX2, CD68, and KI67 markers. We computed 18 first-order radiomic features at each biopsy location for patients’ multimodal MRIs: T1W, T1Gd, T2W, FLAIR, apparent diffusion coefficient, diffusion weighted imaging (DWI) and susceptibility weighted imaging. We then performed correlation analysis between each radiomic feature and marker abundance for each IHC stain. Overall, we found sex-distinct patterns connecting imaging with these IHC markers. For example, amongst female patients, DWI held more prominent correlations with SOX2 than in males. Whereas there were more correlations between CD68 IHC abundance and T1Gd imaging features in males compared to females. Taken together, the overall patterns connecting locoregional imaging features to these IHC markers showed sex-distinct patterns suggesting the potential for sex to be an important biological variable when interpreting the biology underlying imaging changes.

Molecular Classification of Hepatocellular Carcinoma Using Wnt-Hippo Signaling Pathway-Related Genes.

Simple SummaryThe characters of Taiwanese hepatocellular carcinoma (HCC) are different from other parts of the world. We characterized the molecular features of HCC using a newly developed classification system based on the expression of the Wnt–Hippo signaling pathway-related genes. We analyzed the data in terms of prognostic value, transcriptome features, immune infiltration, and clinical characteristics, and compared the resulting subclasses with previously published classifications. A new molecular classification method based on a 272 gene panel of Wnt–Hippo pathways that may provide a new target for the treatment.In Taiwan, a combination of hepatitis B and C infection, economic boom-related food and alcohol overconsumption, and Chinese medicine prescriptions has led to a high rate of hepatocellular carcinoma (HCC). However, the causative factors and underlying tumor biology for this unique HCC environment have not been identified. Wnt and Hippo signaling pathways play an important regulatory role in HCC development, and their functions are generally considered as positive and negative regulators of cell proliferation, respectively. In this study, we characterized the molecular features of HCC using a newly developed classification system based on the expression of the Wnt–Hippo signaling pathway-related genes. RNA sequencing (RNA-Seq) was performed on liver tumor tissues from 100 patients with liver cancer. RNA-Seq data for 272 previously characterized Wnt–Hippo signaling pathway-related genes were used for hierarchical clustering. We analyzed the data in terms of prognostic value, transcriptome features, immune infiltration, and clinical characteristics, and compared the resulting subclasses with previously published classifications. Four subclasses of HCC (HCCW1–4) were identified. Subclass HCCW1 displayed the highest PCDHB4 expression. Subclass HCCW2 displayed lower Edmondson–Steiner grades (I and II) and CTNNB1 mutation frequencies. Subclass HCCW3 was associated with a good prognosis, the highest PCDHGB7 expression, high CD8+ naïve T cells abundance, and relatively low TP53 mutation rates. Subclass HCCW4 was associated with a poor prognosis, the highest PCDHB2 and PCDHB6 expression, a relatively high abundance of Th1 cells, NKT and class-switched memory B cells, relatively low enrichment of cDC, iDC, and CD4+ memory T cells, and high Edmondson–Steiner grades (III and IV). We also identified Wnt–Hippo signaling pathway-related genes that may influence immune cell infiltration. We developed a panel of 272 Wnt–Hippo signaling pathway-related genes to classify HCC into four groups based on Taiwanese HCC and The Cancer Genome Atlas Liver Hepatocellular Carcinoma datasets. This novel molecular classification system may aid the treatment of HCC.

Cytoreductive Surgery and Hyperthermic Intraperitoneal Chemotherapy for Colorectal Peritoneal Metastases: A Summary of Key Clinical Trials.

The peritoneal cavity is a common site of metastatic spread from colorectal cancer (CRC). Patients with peritoneal metastases (PM) often have aggressive underlying tumor biology and poor survival. While only a minority of patients with CRC have potentially resectable disease, the high overall incidence of CRC makes management of PM a common clinical problem. In this population, cytoreductive surgery (CRS)-hyperthermic intraperitoneal chemotherapy (HIPEC) is the only effective therapy for appropriately selected patients. In this narrative review, we summarize the existing literature on CRS-HIPEC in colorectal PM. Recent prospective clinical trials have shown conflicting evidence regarding the benefit of HIPEC perfusion in addition to CRS. Current strategies to prevent PM in those at high-risk have been shown to be ineffective. Herein we will provide a framework for clinicians to understand and apply these data to treat this complex disease presentation.

Nasopharyngeal Carcinoma and Its Microenvironment: Past, Current, and Future Perspectives.

Nasopharyngeal carcinoma (NPC) is an epithelial malignancy that raises public health concerns in endemic countries. Despite breakthroughs in therapeutic strategies, late diagnosis and drug resistance often lead to unsatisfactory clinical outcomes in NPC patients. The tumor microenvironment (TME) is a complex niche consisting of tumor-associated cells, such as fibroblasts, endothelial cells, leukocytes, that influences tumor initiation, progression, invasion, and metastasis. Cells in the TME communicate through various mechanisms, of note, exosomes, ligand-receptor interactions, cytokines and chemokines are active players in the construction of TME, characterized by an abundance of immune infiltrates with suppressed immune activities. The NPC microenvironment serves as a target-rich niche for the discovery of potential promising predictive or diagnostic biomarkers and the development of therapeutic strategies. Thus, huge efforts have been made to exploit the role of the NPC microenvironment. The whole picture of the NPC microenvironment remains to be portrayed to understand the mechanisms underlying tumor biology and implement research into clinical practice. The current review discusses the recent insights into the role of TME in the development and progression of NPC which results in different clinical outcomes of patients. Clinical interventions with the use of TME components as potential biomarkers or therapeutic targets, their challenges, and future perspectives will be introduced. This review anticipates to provide insights to the researchers for future preclinical, translational and clinical research on the NPC microenvironment.

Role of Virus-Directed Therapy in Soft Tissue Sarcoma.

Bone and soft tissue sarcoma are rare cancers of mesenchymal origin with the characteristics of heterogeneity and diversity that account for less than 1% of solid malignant cancers. Conventional chemotherapy remains standard of care with response rates of 10-15% that are usually dependent on histologic subtype as some subtypes are chemotherapy resistant. There remains a large unmet clinical need for new and novel options promoting the development of promising therapeutic options such as immunotherapy. With more than 80 different subtypes, the heterogeneity of sarcoma requires thoughtful clinical trial design. In the sarcoma field, recent breakthroughs have occurred in the context of histology-specific approach based on underlying tumor biology. To that end, immunotherapy approaches will need to take a similar approach. Oncolytic viruses (OVs) have emerged as a promising treatment for many solid tumors and shown encouraging results in sarcoma. This review mainly focuses on collective clinical data highlighting the role of OVs as immunotherapy being used in soft tissue sarcoma (STS) and bone sarcomas. Combining OVs with T cell-activating checkpoint inhibition, adoptive cell therapy or targeted therapies may yield increased potency, improve antitumor efficacy of oncolytic virotherapy, and offer a new prospect for the treatment of sarcoma.

Abstract GS4-07: The Breast PreCancer Atlas DCIS genomic signatures define biology and correlate with clinical outcomes: An analysis of TBCRC 038 and RAHBT cohorts

Abstract Background. DCIS consists of a molecularly heterogeneous group of premalignant lesions, with variable risk of invasive progression. Understanding biomarkers for invasive progression could help individualize treatment recommendations based upon tumor biology. As part of the NCI Human Tumor Atlas Network (HTAN), we conducted comprehensive genomic analyses on two large DCIS case-control cohorts. Methods. We performed smart3-seq and low-pass whole genome sequencing on two independent, retrospective, longitudinally sampled DCIS case-control cohorts. TBCRC 038 was a multicenter cohort diagnosed with DCIS between 1998 and 2016 at one of the Translational Breast Cancer Research sites; the RAHBT (Resource of Archival Human Breast Tissue) cohort included women identified through the St. Louis Breast Tissue Repository, and the Women’s Health Repository diagnosed between 1997 and 2001. We studied the spectrum of molecular changes present and sought genomic predictors of subsequent ipsilateral breast events (iBEs: DCIS recurrence or invasive progression) in both DCIS epithelium and stroma in formalin fixed paraffin embedded tissue. We generated de novo tumor and stroma-centric subtypes for DCIS that represents fundamental transcriptomic organization. Copy number analysis was performed using low-pass DNA sequencing. Non-negative matrix factorization (NMF) was applied to the RNA expression of all coding genes to identify clusters. A negative-binomial regression model was used to identify differentially expressed genes. Results. We analyzed 677 DCIS samples from 481 patients with 7.1 years median follow-up. In TBCRC samples, we identified three clusters via NMF in TBCRC referred to as ER low, quiescent, and ER high. The ER-low cluster had significantly higher levels of ERBB2 and lower levels of ESR1 compared to quiescent and ER-high clusters. Quiescent cluster lesions were less proliferative and less metabolically active than ER high and ER low subtypes. These findings were replicated in the RAHBT cohort. Focusing on the stromal component of DCIS from laser capture microdissection in RAHBT samples, we identified four distinct DCIS-associated stromal clusters. A “normal-like” stromal cluster with ECM organization and PI3K-AKT signaling; a “collagen-rich” stromal cluster; a “desmoplastic” stromal cluster with high fibroblast and total myeloid abundance, mostly associated with macrophages and myeloid dendritic cells (mDC); and an “immune-dense” stromal cluster. Further, we compared differentially expressed genes in patients with or without subsequent iBEs within 5 years of diagnosis. Hypothesizing that the resulting 812 DE genes (DESeq2) represent multiple routes to subsequent iBEs, we leveraged NMF to identify paths to progression. In both TBCRC and RAHBT cohorts, poor outcome groups exhibited increased ER, MYC signaling, and oxidative phosphorylation, supporting that these pathways are important for DCIS recurrence and progression. Conclusion. Comprehensive genomic profiling in two independent DCIS cohorts with longitudinal outcomes shows distinct DCIS stromal expression patterns and immune cell composition. RNA expression profiles reveal underlying tumor biology that is associated with later iBEs in both cohorts. These studies provide new insight into DCIS biology and will guide the design of diagnostic strategies to prevent invasive progression. Citation Format: Siri H Strand, Belén Rivero-Gutiérrez, Kathleen E Houlahan, Jose A Seoane, Lorraine M King, Tyler Risom, Lunden Simpson, Sujay Vennam, Aziz Khan, Timothy Hardman, Bryan E Harmon, Fergus J Couch, Kristalyn Gallagher, Mark Kilgore, Shi Wei, Angela DeMichele, Tari King, Priscilla F McAuliffe, Julie Nangia, Joanna Lee, Jennifer Tseng, Anna Maria Storniolo, Alastair Thompson, Gaorav Gupta, Robyn Burns, Deborah J Veis, Katherine DeSchryver, Chunfang Zhu, Magdalena Matusiak, Jason Wang, Shirley X Zhu, Jen Tappenden, Daisy Yi Ding, Dadong Zhang, Jingqin Luo, Shu Jiang, Sushama Varma, Cody Straub, Sucheta Srivastava, Christina Curtis, Rob Tibshirani, Robert Michael Angelo, Allison Hall, Kouros Owzar, Kornelia Polyak, Carlo Maley, Jeffrey R Marks, Graham A Colditz, E Shelley Hwang, Robert B West. The Breast PreCancer Atlas DCIS genomic signatures define biology and correlate with clinical outcomes: An analysis of TBCRC 038 and RAHBT cohorts [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr GS4-07.

Landmark Series: Importance of Pancreatic Resection Margins.

An important goal of cancer surgery is to achieve negative surgical margins and remove all disease completely. For pancreatic neoplasms, microscopic margins may remain positive despite gross removal of the palpable mass, and surgeons must then consider extending resection, even to the point of completion pancreatectomy, an option that renders the patient with significant adverse effects related to exocrine and endocrine insufficiency. Counterintuitively, extending resection to ensure clear margins may not improve patient outcome. Furthermore, the goal of improving survival by extending the resection may not be achieved, as an initial positive margin may indicate more aggressive underlying tumor biology. There is a growing body of literature on this topic, and this landmark series review will examine the key publications that guide our management for resection of pancreatic ductal adenocarcinoma, intraductal papillary mucinous neoplasms, and pancreatic neuroendocrine tumors.

EXTH-73. PROTEASOME INHIBITION EXPOSES SELECTIVE VULNERABILITY IN CENTRAL NERVOUS SYSTEM LYMPHOMA

Abstract Central nervous system lymphoma (CNSL), including primary and secondary CNSL, has a poor prognosis despite standard intensive chemotherapy. Since the majority of CNSL tumors are highly dependent on NF-κB signaling pathway for survival, Bruton’s kinase inhibitors, which target upstream in the NF-κB pathway, have demonstrated favorable clinical response in PCNSL patients. However, early recurrence is frequently observed. Therefore, novel therapeutic strategies are required in this progressive CNS disease. To understand the underlying tumor biology and explore a novel therapeutic strategy of CNSL, we previously established a panel of patient-derived xenograft (PDX) models, from both immunocompetent and Epstein-Barr virus (EBV)-positive CNSL patients. We confirmed that these PDX models highly recapitulated the phenotypic and genetic features of patient tumors. Using 19 PDX models, including 17 originally established PDXs, we found that NF-κB pathway related genomic alterations and AKT/mTOR signaling did not correlate with sensitivity to BTK inhibitors. We also found that RelA/p65 dephosphorylation as a biomarker of CNSL cells, which are responding to ibrutinib. Through high-throughput and NF-κB pathway-targeted drug screenings, we discovered that proteasome inhibitors suppressed cell viability across all CNSL models. The therapeutic effect, observed at a lower nanomolar range, was mediated by inhibition of the canonical NF-κB and AKT/mTOR pathways and was reversed by silencing of MYD88/CD79B in immunocompetent CNSL or LMP1 in EBV-positive CNSL. The second-generation proteasome inhibitor marizomib prolonged overall survival in CNSL orthotopic xenograft models through simultaneous suppression of RelA/p65 and AKT/mTOR signaling. Proteasome inhibition deregulated Mcl-1 and mediated caspase-dependent apoptosis, which was further enhanced by Bcl-2 family inhibition. Our results demonstrate the potential of proteasome inhibition as a novel therapeutic strategy in patients with immunocompetent and EBV-positive CNSL.

Independent somatic evolution underlies clustered neuroendocrine tumors in the human small intestine

Small intestine neuroendocrine tumor (SI-NET), the most common cancer of the small bowel, often displays a curious multifocal phenotype with several tumors clustered together in a limited intestinal segment. SI-NET also shows an unusual absence of driver mutations explaining tumor initiation and metastatic spread. The evolutionary trajectories that underlie multifocal SI-NET lesions could provide insight into the underlying tumor biology, but this question remains unresolved. Here, we determine the complete genome sequences of 61 tumors and metastases from 11 patients with multifocal SI-NET, allowing for elucidation of phylogenetic relationships between tumors within single patients. Intra-individual comparisons revealed a lack of shared somatic single-nucleotide variants among the sampled intestinal lesions, supporting an independent clonal origin. Furthermore, in three of the patients, two independent tumors had metastasized. We conclude that primary multifocal SI-NETs generally arise from clonally independent cells, suggesting a contribution from a cancer-priming local factor.

Context and Approach to Metastatic Bone Disease

Metastatic bone disease (MBD) commonly heralds the final progression of many cancers. Skeletal-related events (SRE) represent symptomatic bone metastases and usually present as pain, fracture, spinal cord compression, and hypercalcemia of malignancy. As patients with advanced disease live longer due to therapeutic advances, the number of patients with metastatic bone disease is increasing. The optimal management of MBD and SRE requires a coordinated team effort including specialists from surgical and nonsurgical disciplines. MBD management is far from a one-size-fits-all approach. Each patient must be evaluated within the context of their expectations and disease status. An appreciation of the underlying tumor biology combined with life expectancy estimates helps guide appropriate treatment. This article attempts to provide a framework in which to evaluate and treat patients with metastatic bone disease. In addition, an ask is made for orthopedic surgeons to develop an awareness for the need of an integrated multidisciplinary approach and consider assuming the lead role of the musculoskeletal team.

Prostate-specific membrane antigen (PSMA)-based imaging in localized and advanced prostate cancer: a narrative review.

Combined molecular and morphologic imaging modalities have emerged in recent years as an alternative to conventional imaging in prostate cancer (PC). In particular, novel prostate-specific membrane antigen (PSMA) radiotracers have demonstrated increased sensitivity and specificity for the initial staging of men with clinically localized PC, as well as for PC detection in the setting of biochemical recurrence (BCR). Molecular imaging is increasingly used to guide treatment decisions in these patients—though its impact on survival has yet to be established. Improved PC detection in men with BCR has also helped to identify a subset of patients with oligometastatic disease. The optimal management of oligometastatic PC and the role of metastasis-directed therapies (MDT) are the subjects of ongoing studies. In comparison to clinically localized or biochemically recurrent PC, the role of molecular imaging in men with advanced disease is less established. In metastatic castration-resistant PC (mCRPC), PSMA-based imaging has primarily been investigated as a companion diagnostic tool to predict and monitor response to PSMA-targeted radioligand therapy (RLT). More recent efforts have focused on using molecular imaging to monitor treatment response to conventional chemohormonal therapies. However, despite promising early results, several barriers remain to the widespread use of PSMA-based imaging in metastatic PC: temporary flares in PSMA uptake have been described in a subset of patients after initiation of therapy, and the underlying mechanism and clinical implications of this phenomenon are still poorly understood. Furthermore, whereas PSMA is invariably expressed in hormone-sensitive PC, loss of PSMA expression is increasingly recognized in a subset of mCRPC patients with aggressive disease. Although this may limit the use of PSMA-based imaging as a standalone modality in advanced PC, loss of PSMA uptake may also provide non-invasive and clinically relevant molecular insight on patients’ underlying tumor biology.

Abstract 2756: A toolbox enabling a data-driven selection of regions of interest in tumor tissue sections for imaging mass cytometry analysis

Abstract Highly multiplexed imaging technologies are increasingly applied in biomedical research to identify underlying patterns of disease. As part of an IMI-funded project, the IMMUcan (Integrated immunoprofiling of large adaptive cancer patients cohorts) consortium will generate single-cell resolved molecular profiles for thousands of cancer patients from hospitals across Europe. Patient tissues will be profiled using two imaging modalities, multispectral immunofluorescence (mIF) and Imaging Mass Cytometry (IMC), in junction with data from different omics techniques. IMC enables highly multiplexed tissue imaging, but its current throughput only enables to image a fraction of large/whole-slide tumor tissue sections. The selection of regions of interest for IMC analysis is of critical importance with respect to the cells present in an area and the antibody panel used for the analysis of such an area. To target areas of interest in tumor tissue sections, e.g. with immune cell infiltration or tertiary lymphoid structures, we have developed a data driven approach based on mIF imaging analyses from consecutive sections to select such regions of interest for analysis with IMC. A mIF panel was designed to stain T cells, B cells, macrophages, neutrophils, dendritic cells and tumor cells to have an overview of immune cell populations within the whole tissue. After quantification, mIF images and data are hosted on a webserver and regions that contain cell-types of interest are annotated with the help of a web-based tool. mIF images are used for alignment with brightfield whole slide scans of the consecutive FFPE sections which are used for IMC. After alignment, the annotated regions of interest are acquired in IMC. The mean positional offset from IF to IMC for regions of interest was roughly 120 µm and the overall cell-type numbers across both technologies were well correlated. The approach presented here has the great advantage to allow us to reproducibly target similar areas for IMC across thousands of samples based on mIF within the IMMUcan consortium and will enable single-cell analysis for whole tumor sections based on mIF and IMC to gain a deeper understanding of the underlying tumor biology. Funding: IMI2 JU grant agreement 821558, supported by EU's Horizon 2020 and EFPIA. Citation Format: Daniel Schulz, Stephanie Renaud-Tissot, Robin Liechti, Nils Eling, Michelle Daniel, Jonas Windhager, Yervand Karapetyan, Thomas Mrowiec, Sylvie Rusakiewicz, Henoch S. Hong, Marie Morfouace, Bernd Bodenmiller. A toolbox enabling a data-driven selection of regions of interest in tumor tissue sections for imaging mass cytometry analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2756.

Abstract 260: Application of integrated analysis of whole genome sequencing and RNA sequencing to personalized therapy decision making in pediatric and young adult cancer

Abstract The use of comprehensive personal genomic data to guide cancer treatment decisions has demonstrated success in recent years. However, its application to pediatric cancer remains challenging. Most pediatric cancer genomes have relatively few somatic aberrations and the recognized oncogenic drivers are often not targetable. Here we describe a whole genome and transcriptome analysis approach to elucidate the impact of currently un-targetable disease drivers on pathways and regulatory networks within cancer cells, in an effort to identify aberrations that can be targeted therapeutically. In the pediatric personalized oncogenomics (PedsPOG) project, we have analyzed 81 pediatric and young adult cases representing diverse types of relapsed, refractory or very poor prognosis cancers (17 primary central nervous system (CNS), 5 hematopoietic and lymphoid malignancies, and 59 from a variety of non-CNS solid cancers). Patients' ages ranged from 0.4-20.7 years at enrollment, with a median of 11.5 years. For each patient, genomic sequencing data from tumour and normal samples were analysed to detect germline and somatic variants including simple mutations to more complex alterations such as gene fusions, mutation burden and mutation signatures. Tumour transcriptome data was analyzed to identify aberrant gene expression and calculate immune-related signatures such as presence and composition of T cells in the tumour sample. Combined interpretation of germline and somatic variants was used to understand the underlying tumour biology and provide rationale for treatment options. Using the integrated analysis of genomic and transcriptomic data, actionable targets were identified in 80 out of 81 patients (98%), while therapeutic targets would have been identified in only 32-50% of the patients if individual genomic variants were used separately (such as mutation, fusion, and copy number changes). RNA expression data appears to be highly informative, from which targets were detected in 90% of the patients, albeit at lower levels of evidence. In particular, prediction of outlier T-cell presence based on expression data was identified as a potential biomarker which led to favorable response to immune checkpoint inhibition. Twenty-four cases received PedsPOG-informed therapy and disease response was evaluated by RECIST or RANO criteria. Complete response was observed in four patients, and thirteen patients demonstrated partial response or stable disease. In conclusion, the use of whole genome sequencing and transcriptome sequencing has yielded novel findings and therapeutic options in children and adolescents with poor prognosis cancer. Citation Format: Yaoqing Shen, Melika Bonakdar, Laura Williamson, Erin Pleasance, Karen Mungall, Richard A. Moore, Andrew J. Mungall, Stephen Yip, Anna F. Lee, Christopher Dunham, Janessa Laskin, Marco M. Marra, Steven J. Jones, Shahrad R. Rassekh, Rebecca J. Deyell. Application of integrated analysis of whole genome sequencing and RNA sequencing to personalized therapy decision making in pediatric and young adult cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 260.

IgD Myeloma: Clinical Features and Outcome from a Multicenter Retrospective Study in Chinese and Korean of 308 Patients from Asian Myeloma Network (AMN) Project

IgD myeloma is a rare hematologic malignancy for which clinical and biological features and patient outcomes have not been extensively studied. However, previous studies found 3.1% IgD myeloma prevalence in Asian myeloma patients, and with the high incidence of 6%, especially for younger than 50 years with 10.3% in Chinese myeloma patients (Kim K. et al. Am J Hematol. 2014, Lu J. et al. Drug Des Devel Ther. 2016). Therefore, to further assess the frequency and the specific characteristics and evaluate the outcome of patients with IgD myeloma, we carried out a multicenter retrospective study in Chinese and Korean patients from AMN project with diagnosis of IgD myeloma.A total of 308 patients from 22 centers were included in this analysis. The median age at diagnosis was 56 years with a male predominance (65.70%). Anemia and renal dysfunction were found in 86.7% and 46.2%, respectively. Renal failure is more common at presentation with an increase in serum creatinine (> 2 mg/dL) in more than 10% various series of IgD MM. The bias for λ light chain expression with a reversed light chain ratio is a characteristic feature of IgD MM, which showed 95.79% of patients with IgD λ light chain in Asian patients. DS stage 1, 2, and 3 were showed in 1.30%, 5.84%, and 92.86%, respectively. The chromosomal aberration accounted in 58.14% and t(11;14) was the most common cytogenetic finding (40.57%). Median overall survival (OS) was 39.2 months (95% CI 31.56-41.43). Higher International Staging System (ISS) stages III (62.62%) might be associated with worse survival (P = 0.02), while ISS stages I and II were seen in 16.39% and 20.98%. Patents received with stem cell transplantation showed better survival rates. New drugs including bortezomib, thalidomide, and lenalidomide were used in more than 60% of all patients and affected OS when used as a first-line treatment.In this multicenter retrospective study from Chinese and Korean IgD myeloma patients, we found that IgD MM more likely presented at advanced stage and showed a more aggressive clinical course. The underlying tumor biology responsible for these differences remains to be determined. DisclosuresNo relevant conflicts of interest to declare.

A prospective validation of the genomic classifier to define high-metastasis risk in a subset of African American men with early localized prostate cancer: VanDAAM study.

5005 Background: Risk stratification of prostate cancer (PC) using routine clinical variables remains suboptimal as they do not account for underlying tumor biology. The genomic classifier provides information on underlying biology and independently predicts an individual patient’s risk of metastasis. Although the performance of the genomic classifier has been tested across different cohorts primarily comprised of White men, its validation as an optimal genomic risk classifier for African American men (AAM) is thus far lacking in a prospective trial. We report the initial results on the prospective validation of the genomic classifier in a matched cohort of AAM and non-AAM (NAAM). Methods: This was a multisite, prospective validation trial of the genomic classifier i.e. Decipher score in AAM. Participants were recruited on a 1:1 enrollment ratio of AAM to NAAM diagnosed with low-intermediate risk PC. Patient on active surveillance were ineligible. NAAM were matched to AAM on PSA, age, biopsy Gleason score, clinical stage, and percent positive biopsy cores. Diagnostic biopsy specimens were processed at a CLIA certified laboratory and Decipher score was assessed using whole transcriptome profiling platform. Total target accrual was 250 men treated for low-intermediate PC over three years. Statistical analyses include categorical comparison of race dependent risk group migration between NCCN risk group and genomic classifier. Relative risk of metastasis was estimated using negative binomial model. Results: Final analytical cohort included 207 evaluable cases (AAM = 102 and NAAM = 107) with comprehensive genomic information. Risk of metastasis was determined based on pretreatment biopsy Decipher score, and patients were classified as low, favorable-, and unfavorable intermediate risk. Despite achieving a robustly matched clinical cohort, we observed significant genomic heterogeneity between AAM and NAAM across NCCN risk groups. In a comparative analysis, 49% of low-favorable intermediate risk AAM harbored high genomic risk tumors as compared to only 10% NAAM, p = 0.02. Similarly, using the modified clinico-genomic risk classifier (cGC), comprised of both Decipher score and clinical variables, AAM experienced an extreme deviation of risk status (difference [δ] between cGC and NCCN ≥ 2) as compared to NAAM (26.8% vs 8.1%, p = 0.03). In a binomial model, low-favorable NCCN risk AAM were 3.9 times more likely to be reclassified as high genomic risk for distant metastasis compared to NAAM (RR = 3.99, 95% CI, 1.15 – 13.86, p = 0.02). Conclusions: Clinical NCCN risk classification is an inadequate surrogate of tumor biology and offers suboptimal risk stratification for AAM with PC. Integration of patient specific genomic classifier into standard of care will improve accuracy in disease risk classification and treatment recommendations for AAM. Clinical trial information: NCT02723734.

New Treatment Strategies for the Inflammatory Breast Cancer.

Inflammatory breast cancer (IBC) remains the most aggressive type of breast cancer. During the past decade, enormous progress has been made to refine diagnostic criteria and establish multimodality treatment strategies as keys for the improvement of survival outcomes. Multiple genomic studies enabled a better understanding of underlying tumor biology, which is responsible for the complex and aggressive nature of IBC. Despite these important achievements, outcomes for this subgroup of patients remain unsatisfactory compared to locally advanced non-IBC counterparts. Global efforts are now focused on identifying novel strategies that will improve treatment response, prolong survival for metastatic patients, achieve superior local control, and possibly increase the cure rate for locally advanced disease. Genomic technologies constitute the most important tool that will support future clinical progress. Gene-expressing profiling of the tumor tissue and liquid biopsy are important parts of the everyday clinical practice aiming to guide treatment decisions by providing information on tumor molecular drivers or primary and acquired resistance to treatment. The International IBC expert panel and IBC International Consortium made a tremendous effort to define IBC as a distinct entity of BC, and they will continue to lead and support the research for this rare and very aggressive disease. Finally, a uniform platform is now required to develop and lead large, multi-arm, proof-of-concept clinical trials that perform rapid, focused, and cost-effective evaluations of potential novel therapeutics in IBC.