Cell volume expansion and local contractility drive collective invasion of the basement membrane in breast cancer

Breast cancer becomes invasive when carcinoma cells invade through the basement membrane (BM)-a nanoporous layer of matrix that physically separates the primary tumour from the stroma. Single cells can invade through nanoporous three-dimensional matrices due to protease-mediated degradation or force-mediated widening of pores via invadopodial protrusions. However, how multiple cells collectively invade through the physiological BM, as they do during breast cancer progression, remains unclear. Here we developed a three-dimensional in vitro model of collective invasion of the BM during breast cancer. We show that cells utilize both proteases and forces-but not invadopodia-to breach the BM. Forces are generated from a combination of global cell volume expansion, which stretches the BM, and local contractile forces that act in the plane of the BM to breach it, allowing invasion. These results uncover a mechanism by which cells collectively interact to overcome a critical barrier to metastasis.

Spatial transcriptomics identifies candidate stromal drivers of benign prostatic hyperplasia

Benign prostatic hyperplasia (BPH) is the nodular proliferation of the prostate transition zone in older men, leading to urinary storage and voiding problems that can be recalcitrant to therapy. Decades ago, John McNeal proposed that BPH originates with the "reawakening" of embryonic inductive activity by adult prostate stroma, which spurs new ductal proliferation and branching morphogenesis. Here, by laser microdissection and transcriptional profiling of the BPH stroma adjacent to hyperplastic branching ducts, we identified secreted factors likely mediating stromal induction of prostate glandular epithelium and coinciding processes. The top stromal factors were insulin-like growth factor 1 (IGF1) and CXC chemokine ligand 13 (CXCL13), which we verified by RNA in situ hybridization to be coexpressed in BPH fibroblasts, along with their cognate receptors (IGF1R and CXCR5) on adjacent epithelium. In contrast, IGF1 but not CXCL13 was expressed in human embryonic prostate stroma. Finally, we demonstrated that IGF1 is necessary for the generation of BPH-1 cell spheroids and patient-derived BPH cell organoids in 3D culture. Our findings partially support historic speculations on the etiology of BPH and provide what we believe to be new molecular targets for rational therapies directed against the underlying processes driving BPH.

CD142 Identifies Neoplastic Desmoid Tumor Cells, Uncovering Interactions Between Neoplastic and Stromal Cells That Drive Proliferation

The interaction between neoplastic and stromal cells within a tumor mass plays an important role in cancer biology. However, it is challenging to distinguish between tumor and stromal cells in mesenchymal tumors because lineage-specific cell surface markers typically used in other cancers do not distinguish between the different cell subpopulations. Desmoid tumors consist of mesenchymal fibroblast-like cells driven by mutations stabilizing beta-catenin. Here we aimed to identify surface markers that can distinguish mutant cells from stromal cells to study tumor-stroma interactions. We analyzed colonies derived from single cells from human desmoid tumors using a high-throughput surface antigen screen, to characterize the mutant and nonmutant cells. We found that CD142 is highly expressed by the mutant cell populations and correlates with beta-catenin activity. CD142-based cell sorting isolated the mutant population from heterogeneous samples, including one where no mutation was previously detected by traditional Sanger sequencing. We then studied the secretome of mutant and nonmutant fibroblastic cells. PTX3 is one stroma-derived secreted factor that increases mutant cell proliferation via STAT6 activation. These data demonstrate a sensitive method to quantify and distinguish neoplastic from stromal cells in mesenchymal tumors. It identifies proteins secreted by nonmutant cells that regulate mutant cell proliferation that could be therapeutically.

Significance

Distinguishing between neoplastic (tumor) and non-neoplastic (stromal) cells within mesenchymal tumors is particularly challenging, because lineage-specific cell surface markers typically used in other cancers do not differentiate between the different cell subpopulations. Here, we developed a strategy combining clonal expansion with surface proteome profiling to identify markers for quantifying and isolating mutant and nonmutant cell subpopulations in desmoid tumors, and to study their interactions via soluble factors.

Abstract PD2-09: Characterization of the lymphovascular invasion microenvironment reveals immune response dichotomy

Background: Metastasis is the leading cause of cancer related deaths in breast cancer patients. Lymphovascular invasion represents one of the earliest stages of metastasis wherein the cells are introduced to a very different and distinct microenvironment. Methods: We leveraged spatial techniques developed for limited specimens in archival tissue to study patient matched cross-sectional tumor samples from different stages of breast neoplasia including normal breast, ductal carcinoma in situ (DCIS), primary invasive carcinoma (IBC), lymphovascular invasion (LVI) and regional lymph node metastasis. We selected a set of 21 patients with ER+ breast cancer to generate cross-sectional samples of each of these stages, for a total of 331 samples. The areas of LVI were identified by a combination of H&E review and immunohistochemistry for podoplanin. We performed smart-3SEQ for gene expression profiling and light pass whole genome sequencing for DNA copy number alterations. Results: We profiled the spectrum of neoplasia for transcriptome-wide gene expression. Principal component analysis of all 252 DCIS, LVI, IBC, or metastasis samples using the top 500 genes with the highest variance demonstrated that clustering was roughly based on the diagnostic stage (i.e. DCIS, LVI, IBC, or metastasis). Differential gene expression profiling identified thousands of genes increased or decreased in expression across the transitional stages with the largest change in gene expression being the transition from normal breast to DCIS, dominated by gene expression down regulation. We next performed NMF clustering on 62 samples of LVI from 18 cases and identified two patterns of gene expression which define two subgroups. Gene ontology analysis revealed that one cluster was associated with increased proliferation and metabolism, whereas the second cluster was dominated by an immune response. When we analyzed the immune and proliferative LVI subgroups separately, we found that the immune profiles in the patient matched IBC and LVI samples from the LVI Immune cluster were similar, whereas the immune profiles in the patient matched IBC and LVI samples from the Proliferative cluster were significantly different. At the LVI stage, all immune cell populations estimated by CibersortX were decreased in the Proliferative LVI cluster. These changes were validated using immunofluorescence for proliferation (Ki67), T cells (CD3) and macrophages (CD68) on the same samples. Using the LVI centroids, we built a model that could predict the same clusters in the METABRIC IBC. Kaplan-Meier analysis showed a significant difference between groups, with the Proliferative-like IBC group having a worse prognosis than the Immune-like IBC group. Conclusions: We observed a dichotomy at the LVI stage with a more proliferative cluster that may escape the immune response and an immune cluster which has a microenvironment with a similar pattern to its primary IBC. The recognition of two groups of LVI, differing in immune association and proliferation, raises the possibility that the risk of metastasis could be different in these two groups, leading to different biological pathways of progression.

Citation Format: Belén Rivero-Gutiérrez, Diego Mallo, Almudena Espín-Pérez, Sujay Vennam, Chunfang Zhu, Sushama Varma, Greg Scott, Joseph Foley, E Shelley Hwang, Carlo Maley, Robert West. Characterization of the lymphovascular invasion microenvironment reveals immune response dichotomy [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 PD2-09.

Diagnostic utility of FOXO1 immunohistochemistry for rhabdomyosarcoma classification

AIMS

Rhabdomyosarcomas currently are classified into one of four subtypes (alveolar, embryonal, spindle cell/sclerosing, or pleomorphic) according to their morphological, immunohistochemical, and molecular genetic features. The alveolar subtype is characterised by a recurrent translocation involving PAX3 or PAX7 and FOXO1; identification of this translocation is important for appropriate classification and prognostication. In this study, we aimed to explore the diagnostic utility of FOXO1 immunohistochemistry for rhabdomyosarcoma classification.

METHODS/RESULTS

A monoclonal antibody targeting a FOXO1 epitope retained in the fusion oncoprotein was used to study 105 rhabdomyosarcomas. FOXO1 was positive for expression by immunohistochemistry in all 25 alveolar rhabdomyosarcomas, with 84% showing diffuse expression in greater than 90% of neoplastic cells; the remainder of alveolar rhabdomyosarcomas displayed at least moderate staining in a minimum of 60% of lesional cells. Apart from three spindle cell rhabdomyosarcomas showing heterogeneous nuclear immunoreactivity in 40-80% of tumour cells, the 80 cases of embryonal, pleomorphic, and spindle cell/sclerosing rhabdomyosarcoma were negative for FOXO1 expression (96.3% specific) when using a threshold of nuclear staining in 20% of neoplastic cells to determine positivity. Variable cytoplasmic staining was present in a fraction of all rhabdomyosarcoma subtypes. Nonneoplastic lymphocytes, endothelial cells, and Schwann cells also showed variably intense nuclear anti-FOXO1 immunoreactivity.

CONCLUSION

Taken together, our findings suggest that FOXO1 immunohistochemistry is a highly sensitive and relatively specific surrogate marker of the PAX3/7::FOXO1 fusion oncoprotein in rhabdomyosarcoma. Cytoplasmic immunoreactivity, expression in nonneoplastic tissues, and limited nuclear staining of nonalveolar rhabdomyosarcomas represent potential pitfalls in interpretation.

Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts

Ductal carcinoma in situ (DCIS) is the most common precursor of invasive breast cancer (IBC), with variable propensity for progression. We perform multiscale, integrated molecular profiling of DCIS with clinical outcomes by analyzing 774 DCIS samples from 542 patients with 7.3 years median follow-up from the Translational Breast Cancer Research Consortium 038 study and the Resource of Archival Breast Tissue cohorts. We identify 812 genes associated with ipsilateral recurrence within 5 years from treatment and develop a classifier that predicts DCIS or IBC recurrence in both cohorts. Pathways associated with recurrence include proliferation, immune response, and metabolism. Distinct stromal expression patterns and immune cell compositions are identified. Our multiscale approach employed in situ methods to generate a spatially resolved atlas of breast precancers, where complementary modalities can be directly compared and correlated with conventional pathology findings, disease states, and clinical outcome.

Interactions in CSF1-Driven Tenosynovial Giant Cell Tumors

PURPOSE

A major component of cells in tenosynovial giant cell tumor (TGCT) consists of bystander macrophages responding to CSF1 that is overproduced by a small number of neoplastic cells with a chromosomal translocation involving the CSF1 gene. An autocrine loop was postulated where the neoplastic cells would be stimulated through CSF1R expressed on their surface. Here, we use single-cell RNA sequencing (scRNA-seq) to investigate cellular interactions in TGCT.

EXPERIMENTAL DESIGN

A total of 18,788 single cells from three TGCT and two giant cell tumor of bone (GCTB) samples underwent scRNA-seq. The three TGCTs were additionally analyzed using long-read RNA sequencing. Immunofluorescence and IHC for a range of markers were used to validate and extend the scRNA-seq findings.

RESULTS

Two recurrent neoplastic cell populations were identified in TGCT that are highly similar to nonneoplastic synoviocytes. We identified GFPT2 as a marker that highlights the neoplastic cells in TCGT. We show that the neoplastic cells themselves do not express CSF1R. We identified overlapping MAB features between the giant cells in TGCT and GCTB.

CONCLUSIONS

The neoplastic cells in TGCT are highly similar to nonneoplastic synoviocytes. The lack of CSF1R on the neoplastic cells indicates they may be unaffected by current therapies. High expression of GFPT2 in the neoplastic cells is associated with activation of the YAP1/TAZ pathway. In addition, we identified expression of the platelet-derived growth factor receptor in the neoplastic cells. These findings suggest two additional pathways to target in this tumor.

BTEX (benzene, toluene, ethylbenzene, and xylene) and risk of cancer - a study from Centers for Disease Control and Prevention's National Health and Nutrition Examination Survey

Introduction/Objective

BTEX (benzene, toluene, ethylbenzene, and xylene) is well know for its toxicity via through environmental, occupational and recreational exposures. However, there is limited literature about the carcinogenic effect of BTEX. Hence, we aim to study the prevalence and association of cancer amongst individuals with exposure of BTEX.

Methods/Case Report

A retrospective cross-sectional study was performed between 2013 and 2018 utilizing the NHANES database. Adult individuals having data on socio-demographic questionnaires and lab findings on exposure to BTEX were included. Prevalence of cancer was identified amongst exposure to BTEX (vs no-BTEX). Univariate (chi-squre test and Mann–Whitney U test) and Multivariate (survey logistic regression) analysis was performed to evaluate the epidemiologic characteristics of individuals exposred to BTEX and association of cancer with BTEX exposure in comparison to no BTEX exposure.The p value of <0.05 considered statistically significant.

Results (if a Case Study enter NA)

124,162 participants were identified with BTEX exposure. Individuals with BTEX exposure were young (40 vs 51 year old), male (91% vs female: 87%), and Mexican American (92% vs Non-Hispanic Black: 89% vs Non-Hispanic White: 89% vs other Hispanic: 87%). Univariate analysis showed higher total prevalence of cancer in BTEX (9.3% vs. 1.3%; p<0.0001) compared to no BTEX. Individuals with BTEX exposure had higher prevalnece of blood cancer (0.47% vs 0.00; p<0.0001), leukemia (0.56% vs 0.00; p<0.001), and lymphoma (1.72% vs 0.39%; p<0.0001) in comparison with no exposure. Multivaritate analysis showed participants with BTEX exposure had 10% higher risk of cancer (aOR: 1.10; 95%CI: 1.10-1.10; p<0.0001) compared to no BTEX exposure. Additionally, exposure to individual components of benzene (aOR: 1.24; 95%CI: 1.24; p<0.0001), ethylbenzene (aOR: 1.08; 95%CI: 1.08-1.08; p<0.0001), and o-xylene (aOR: 1.19; 95%CI: 1.19-1.19; p<0.0001) had higher risk of cancer compared to no exposure participants.

Conclusion

Our study conclude higher risk of cancer among participants with exposure to benzene, ethylbenzene and o-xylene. Future studies are warranted to evaluate the association of various types of cancers in BTEX exposure.

GRM1 Immunohistochemistry Distinguishes Chondromyxoid Fibroma From its Histologic Mimics

Chondromyxoid fibroma (CMF) is a rare benign bone neoplasm that manifests histologically as a lobular proliferation of stellate to spindle-shaped cells in a myxoid background, exhibiting morphologic overlap with other cartilaginous and myxoid tumors of bone. CMF is characterized by recurrent genetic rearrangements that place the glutamate receptor gene GRM1 under the regulatory control of a constitutively active promoter, leading to increased gene expression. Here, we explore the diagnostic utility of GRM1 immunohistochemistry as a surrogate marker for GRM1 rearrangement using a commercially available monoclonal antibody in a study of 230 tumors, including 30 CMF cases represented by 35 specimens. GRM1 was positive by immunohistochemistry in 97% of CMF specimens (34/35), exhibiting moderate to strong staining in more than 50% of neoplastic cells; staining was diffuse (>95% of cells) in 25 specimens (71%). Among the 9 CMF specimens with documented exposure to acid decalcification, 4 (44%) exhibited diffuse immunoreactivity (>95%) for GRM1, whereas all 15 CMF specimens (100%) with lack of exposure to decalcification reagents were diffusely immunoreactive ( P =0.003). High GRM1 expression at the RNA level was previously observed by quantitative reverse transcription polymerase chain reaction in 9 CMF cases that were also positive by immunohistochemistry; low GRM1 expression was observed by quantitative reverse transcription polymerase chain reaction in the single case of CMF that was negative by immunohistochemistry. GRM1 immunohistochemistry was negative (<5%) in histologic mimics of CMF, including conventional chondrosarcoma, enchondroma, chondroblastoma, clear cell chondrosarcoma, giant cell tumor of the bone, fibrous dysplasia, chondroblastic osteosarcoma, myoepithelial tumor, primary aneurysmal bone cyst, brown tumor, phosphaturic mesenchymal tumor, CMF-like osteosarcoma, and extraskeletal myxoid chondrosarcoma. These results indicate that GRM1 immunohistochemistry may have utility in distinguishing CMF from its histologic mimics.

Abstract B015: Targeting hexosamine biosynthesis pathway for the treatment of desmoid tumors

Cancer cells rewire metabolic pathways and energy production to support the enhanced proliferation, invasion and resistance to treatment. The three main glucose metabolism pathways that support growth of cancer cells are: a) the glycolysis pathway for energy production; b) the pentose phosphate pathway for biomass production; and c) the hexosamine biosynthesis pathway (HBP) for protein glycosylation. It is known that the activation of HBP leads to altered glycosylation of oncogenes, transcription factors and kinases in many types of cancer. These aberrations may lead to increased proliferation and survival of tumor cells, and may be associated with resistance to therapy. A better understanding of the role of HBP in malignancies has the potential for clinical implications. Several studies demonstrated that pharmacological inhibition of GFPT2 (glutamine-fructose-6-phosphate transaminase 2, the first and rate-limiting enzyme in HBP) and the enzymes that act downstream of HBP may exhibit anti-tumorigenic effect both in vitro and in vivo, and may modulate sensitivity to chemo-, radio- and immunotherapy. Most of these studies focused on carcinomas and the role of HPB in sarcoma has not been studied. We recently reported a remarkable enrichment of genes involved in HBP in a subset of leiomyosarcoma (LMS) and demonstrated that expression of GFPT2 in LMS is associated with poor clinical outcome. We identified the c-Myc oncoprotein as a potential target of HPB that may be stabilized by aberrant glycosylation in LMS. Here we show the results of a large-scale screening of 260 primary specimens of 33 types of soft tissue lesions. In addition to expression in a subset of LMS, we observed near universal expression of GFPT2 in 34 of 35 desmoid type fibromatosis (DTF), independent of the mutation type of the CTNNB1 gene. Gene Set Enrichment Analysis of a previously published 3SEQ transcriptomic dataset composed of DTF and 9 other types of fibrotic lesions identified significant enrichment of other genes implicated in HBP and multiple glycosylation-associated pathways in DTF compared to the other types of fibrotic lesions. Our analysis identified ATF6 (activating transcription factor 6) as a possible target regulated by aberrant glycosylation as a consequence of HBP activation in DTF. ATF6 is a glycoprotein that has been demonstrated to underlie the resistance to chemotherapy in osteosarcoma, to have a pro-oncogenic role in primary liver cancers and has been proposed as a therapeutic target in cystic fibrosis. Others have shown that targeting HBP can provide therapeutic benefit in a number of preclinical models of carcinoma. Our studies offer new insights into the mechanisms of DTF tumorigenesis and, when confirmed by in vitro studies, will provide a rationale to explore the potential of therapeutic targeting of HBP in DTF.

Citation Format: Joanna Przybyl, Angela Tolwani, Sushama Varma, Matt van de Rijn. Targeting hexosamine biosynthesis pathway for the treatment of desmoid tumors [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B015.

Examining the association between socio-demographic factors, catheter use and antibiotic prescribing in Northern Ireland primary care: a cross-sectional multilevel analysis

Inappropriate use of antibiotics is among the key drivers of antimicrobial resistance (AMR). Antibiotic use in Northern Ireland (NI) is the highest in the UK and approximately 80% is prescribed in primary care. Little information however exists about the patient and prescriber factors driving this. We described the trend in NI primary care total antibiotic prescribing 2010–2019 and conducted a cross-sectional study using a random sample of individuals registered with an NI GP on 1st January 2019. We used multilevel logistic regression to examine how sociodemographic factors and urinary catheter use was associated with the likelihood of being prescribed an antibiotic during 2019, adjusting for clustering at GP practice and GP federation levels. Finite mixture modelling (FMM) was conducted to determine the association between the aforementioned risk factors and quantity of antibiotic prescribed (defined daily doses). The association between age and antibiotic prescription differed by gender. Compared to males 41–50 years, adjusted odds of prescription were higher for males aged 0–10, 11–20 and 51 + years, and females of any age. Catheter use was strongly associated with antibiotic prescription (aOR = 6.82, 95% CI 2.50–18.64). Socioeconomic deprivation and urban/rural settlement were not associated in the multilevel logistic analysis. GP practices and federations accounted for 1.24% and 0.12% of the variation in antibiotic prescribing respectively. FMM showed associations between larger quantities of antibiotics and being older, male and having a catheter. This work described the profile of individuals most likely to receive an antibiotic prescription in NI primary care and identified GP practice as a source of variation; suggesting an opportunity for reduction from effective interventions targeted at both individuals and general practices.

The microdissected gene expression landscape of nasopharyngeal cancer reveals vulnerabilities in FGF and noncanonical NF-κB signaling

Nasopharyngeal cancer (NPC) is an Epstein-Barr virus (EBV)-positive epithelial malignancy with an extensive inflammatory infiltrate. Traditional RNA-sequencing techniques uncovered only microenvironment signatures, while the gene expression of the tumor epithelial compartment has remained a mystery. Here, we use Smart-3SEQ to prepare transcriptome-wide gene expression profiles from microdissected NPC tumors, dysplasia, and normal controls. We describe changes in biological pathways across the normal to tumor spectrum and show that fibroblast growth factor (FGF) ligands are overexpressed in NPC tumors, while negative regulators of FGF signaling, including SPRY1, SPRY2, and LGALS3, are down-regulated early in carcinogenesis. Within the NF-κB signaling pathway, the critical noncanonical transcription factors, RELB and NFKB2, are enriched in the majority of NPC tumors. We confirm the responsiveness of EBV-positive NPC cell lines to targeted inhibition of these pathways, reflecting the heterogeneity in NPC patient tumors. Our data comprehensively describe the gene expression landscape of NPC and unravel the mysteries of receptor tyrosine kinase and NF-κB pathways in NPC.

694 IMPROVING OPIATE PRESCRIBING IN OLDER ADULTS WITH HIP FRACTURES TO COMBAT THE IATROGENIC FALLOUT

Background

The number of opioid prescriptions in older patients has increased dramatically and it is recognised that opioids are the fourth most likely drug to cause preventable hospital admissions. The adverse effects of opioids occur more frequently in the geriatric population. Little is known about the impact of postoperative pain in older adults. NICE recommends paracetamol with additional opioids if there is insufficient postoperative pain relief. Multidisciplinary management with early and then daily physiotherapy is critical. We have assessed pre-morbid, immediate and prolonged use of opioids in patients following hip fracture. Local problem Pre-intervention analysis identified 79% (57/72) of all patients being discharged on opiates. At 4-months, 37% (17/46) of those were still using them. This represents 28% (17/61) of all patients.

Methods

Analysis of all patients (excluding poly-trauma) with hip fractures over the age of 60 years admitted to St Mary’s Hospital. Interventions Development of local guideline on analgesia prescribing; particularly focusing senior geriatrician led decision making. Prescribing oxycodone for first 72-hours and initially using nerve block. Avoidance of transdermal preparations and withdrawing stronger opioids prior to discharge. Clear instructions for GP’s on a stop date and need for community review. Patient information leaflet dispensed with all discharge opioid prescriptions.

Results

Post-intervention cycle; 17% (11/63) of patients were taking prescribed opioids prior to admission (similar to the pre-cohort). 52% (33/63) were discharged on opiates, down from 79%. At 4-months, of those discharged on opioids, 30% (9/30) were still using them; lower than in the first cycle (37%). Overall reduction from 28% to 16% of patients on opioids at 4-months.

Conclusion

The use of specific hip fracture analgesia guideline, senior geriatrician decision-making and support to community colleagues can reduce in-patient and community opiate prescribing, and stem the growing problem of opioid addiction, misuse and iatrogenic re-admission.

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

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.

Multiomics Analysis of Spatially Distinct Stromal Cells Reveals Tumor-Induced O-Glycosylation of the CDK4-pRB Axis in Fibroblasts at the Invasive Tumor Edge

The invasive leading edge represents a potential gateway for tumor metastasis. The role of fibroblasts from the tumor edge in promoting cancer invasion and metastasis has not been comprehensively elucidated. We hypothesize that cross-talk between tumor and stromal cells within the tumor microenvironment results in activation of key biological pathways depending on their position in the tumor (edge vs. core). Here we highlight phenotypic differences between tumor-adjacent-fibroblasts (TAF) from the invasive edge and tumor core fibroblasts from the tumor core, established from human lung adenocarcinomas. A multiomics approach that includes genomics, proteomics, and O-glycoproteomics was used to characterize cross-talk between TAFs and cancer cells. These analyses showed that O-glycosylation, an essential posttranslational modification resulting from sugar metabolism, alters key biological pathways including the cyclin-dependent kinase 4 (CDK4) and phosphorylated retinoblastoma protein axis in the stroma and indirectly modulates proinvasive features of cancer cells. In summary, the O-glycoproteome represents a new consideration for important biological processes involved in tumor-stroma cross-talk and a potential avenue to improve the anticancer efficacy of CDK4 inhibitors.

SIGNIFICANCE

A multiomics analysis of spatially distinct fibroblasts establishes the importance of the stromal O-glycoproteome in tumor-stroma interactions at the leading edge and provides potential strategies to improve cancer treatment. See related commentary by De Wever, p. 537.

Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma

Ductal carcinoma in situ (DCIS) is a pre-invasive lesion that is thought to be a precursor to invasive breast cancer (IBC). To understand the changes in the tumor microenvironment (TME) accompanying transition to IBC, we used multiplexed ion beam imaging by time of flight (MIBI-TOF) and a 37-plex antibody staining panel to interrogate 79 clinically annotated surgical resections using machine learning tools for cell segmentation, pixel-based clustering, and object morphometrics. Comparison of normal breast with patient-matched DCIS and IBC revealed coordinated transitions between four TME states that were delineated based on the location and function of myoepithelium, fibroblasts, and immune cells. Surprisingly, myoepithelial disruption was more advanced in DCIS patients that did not develop IBC, suggesting this process could be protective against recurrence. Taken together, this HTAN Breast PreCancer Atlas study offers insight into drivers of IBC relapse and emphasizes the importance of the TME in regulating these processes.

The correlated expression of COX-2 and keratin 15 in radicular cysts

Background

The expression of cyclooxygenase-2 (COX-2) and Keratin-15 (K15) in radicular cysts (RCs) is poorly understood. Identifying the expression of these two markers may modify the current treatment of RC. The objective of this study was to evaluate the expression of COX-2 and its relationship to K15 expression in the odontogenic epithelial cells of the RC.

Material and Methods

A total of 18 RCs were immunohistochemically analyzed for COX-2 and K15 expression. The cellular inflammatory reaction in the cyst wall was also assessed by measuring the percentage of inflammatory cells to the total number of cells.

Results

COX-2 expression in the odontogenic epithelium of RC was absent in 11.1 % (n=2), mild in 27.8 % (n=5), moderate in 22.2% (n=4) and strong in 38.9% (n=7). Meanwhile, K15 expression was absent in 27.8% (n=5), mild in 16.7% (n=3), moderate in 44.4% (n=8), and strong in 11.1% (n=2) of the cases. The inflammatory infiltrate was mild in 2 cases (11.1%), moderate in 6 cases (33.3%), and high in 10 cases (55.6%). Spearman’s correlation test revealed significant correlation (rho= .533; p= .023) between COX-2 and K15 expression in the odontogenic epithelium of RC. However, no correlation was noted between inflammation and expression of COX-2 (rho= 0.248, p=.321) or K15 (rho= -0.162, p= .520).

Conclusions

There is high and correlated expression of COX-2 and K15 in the odontogenic epithelium of RC. COX-2 could therefore be involved in epithelial cell differentiation of the cyst. Additionally, the expression of K15 in RC may be an indicator of epithelial cell differentiation.

Key words:Cyclooxygenase, COX-2, Keratin-15, K15, Radicular cyst.

Tyrosine kinase domain mutations in chronic myelogenous leukemia patients: A single center experience

Introduction:

Despite the impressive responses achieved with tyrosine kinase inhibitor (TKI) therapy, treatment resistance develops in 16–33% of patients of chronic myelogenous leukemia (CML). Of the BCR-ABL1 dependent mechanisms, mutations in the tyrosine kinase domain (TKD) are the commonest cause of resistance.

Material and Methods:

Allele specific oligonucleotide - polymerase chain reaction (ASO-PCR) was done for testing the six common TKD mutations, T315I, G250E, E255K, M244V, M351T, and Y253F.

Results and Conclusion:

TKD mutation study was done on 83 patients. Of these 44 (53%) were positive for one or more mutations. On analyzing specific mutations, E255K was the commonest mutation seen in 24 (29%) cases, followed by T315I in 23(28%) cases. Y253F mutation was not seen in the present study sample. In the present cohort of 83 patients, 29 (35%) cases were positive for single mutation, 12 (14%) had two mutations and 3 (4%) had three mutations.

Self-Organizing Maps for Cellular In Silico Staining and Cell Substate Classification

Cellular composition and structural organization of cells in the tissue determine effective antitumor response and can predict patient outcome and therapy response. Here we present Seg-SOM, a method for dimensionality reduction of cell morphology in H&E-stained tissue images. Seg-SOM resolves cellular tissue heterogeneity and reveals complex tissue architecture. We leverage a self-organizing map (SOM) artificial neural network to group cells based on morphological features like shape and size. Seg-SOM allows for cell segmentation, systematic classification, and in silico cell labeling. We apply the Seg-SOM to a dataset of breast cancer progression images and find that clustering of SOM classes reveals groups of cells corresponding to fibroblasts, epithelial cells, and lymphocytes. We show that labeling the Lymphocyte SOM class on the breast tissue images accurately estimates lymphocytic infiltration. We further demonstrate how to use Seq-SOM in combination with non-negative matrix factorization to statistically describe the interaction of cell subtypes and use the interaction information as highly interpretable features for a histological classifier. Our work provides a framework for use of SOM in human pathology to resolve cellular composition of complex human tissues. We provide a python implementation and an easy-to-use docker deployment, enabling researchers to effortlessly featurize digitalized H&E-stained tissue.

Atlas of clinically distinct cell states and ecosystems across human solid tumors

Determining how cells vary with their local signaling environment and organize into distinct cellular communities is critical for understanding processes as diverse as development, aging, and cancer. Here we introduce EcoTyper, a machine learning framework for large-scale identification and validation of cell states and multicellular communities from bulk, single-cell, and spatially resolved gene expression data. When applied to 12 major cell lineages across 16 types of human carcinoma, EcoTyper identified 69 transcriptionally defined cell states. Most states were specific to neoplastic tissue, ubiquitous across tumor types, and significantly prognostic. By analyzing cell-state co-occurrence patterns, we discovered ten clinically distinct multicellular communities with unexpectedly strong conservation, including three with myeloid and stromal elements linked to adverse survival, one enriched in normal tissue, and two associated with early cancer development. This study elucidates fundamental units of cellular organization in human carcinoma and provides a framework for large-scale profiling of cellular ecosystems in any tissue.

Acceptability of Neuroscientific Interventions in Education

Researchers are increasingly applying neuroscience technologies that probe or manipulate the brain to improve educational outcomes. However, their use remains fraught with ethical controversies. Here, we investigate the acceptability of neuroscience applications to educational practice in two groups of young adults: those studying bioscience who will be driving future basic neuroscience research and technology transfer, and those studying education who will be choosing among neuroscience-derived applications for their students. Respondents rated the acceptability of six scenarios describing neuroscience applications to education spanning multiple methodologies, from neuroimaging to neuroactive drugs to brain stimulation. They did so from two perspectives (student, teacher) and for three recipient populations (low-achieving, high-achieving students, students with learning disabilities). Overall, the biosciences students were more favorable to all neuroscience applications than the education students. Scenarios that measured brain activity (i.e., EEG or fMRI) to assess or predict intellectual abilities were deemed more acceptable than manipulations of mental activity by drug use or stimulation techniques, which may violate body integrity. Enhancement up to the norm for low-achieving students and especially students with learning disabilities was more favorably viewed than enhancement beyond the norm for high-achieving students. Finally, respondents rated neuroscientific applications to be less acceptable when adopting the perspective of a teacher than that of a student. Future studies should go beyond the acceptability ratings collected here to delineate the role that concepts of access, equity, authenticity, agency and personal choice play in guiding respondents' reasoning.

Transcriptome and genome evolution during HER2-amplified breast neoplasia

Background

The acquisition of oncogenic drivers is a critical feature of cancer progression. For some carcinomas, it is clear that certain genetic drivers occur early in neoplasia and others late. Why these drivers are selected and how these changes alter the neoplasia’s fitness is less understood.

Methods

Here we use spatially oriented genomic approaches to identify transcriptomic and genetic changes at the single-duct level within precursor neoplasia associated with invasive breast cancer. We study HER2 amplification in ductal carcinoma in situ (DCIS) as an event that can be both quantified and spatially located via fluorescence in situ hybridization (FISH) and immunohistochemistry on fixed paraffin-embedded tissue.

Results

By combining the HER2-FISH with the laser capture microdissection (LCM) Smart-3SEQ method, we found that HER2 amplification in DCIS alters the transcriptomic profiles and increases diversity of copy number variations (CNVs). Particularly, interferon signaling pathway is activated by HER2 amplification in DCIS, which may provide a prolonged interferon signaling activation in HER2-positive breast cancer. Multiple subclones of HER2-amplified DCIS with distinct CNV profiles are observed, suggesting that multiple events occurred for the acquisition of HER2 amplification. Notably, DCIS acquires key transcriptomic changes and CNV events prior to HER2 amplification, suggesting that pre-amplified DCIS may create a cellular state primed to gain HER2 amplification for growth advantage.

Conclusion

By using genomic methods that are spatially oriented, this study identifies several features that appear to generate insights into neoplastic progression in precancer lesions at a single-duct level.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13058-021-01451-6.

115 Multi-Disciplinary Simulation Training on Delirium

Introduction

Delirium is still perceived as a “geriatric medicine competency”, despite its high prevalence across most specialties. Collective multi-disciplinary team performance in implementation of multi-component interventions is key. Simulation training incorporates the complex interplay of non-technical factors, specifically, role recognition and empowerment, inter-personal skills and teamwork that are pivotal in delivering effective delirium care.

Methods

Funding was approved by Health Education England. 2 pilot teaching sessions were arranged in the simulation ward. 3 scenarios were developed, each requiring a facilitator, an actor and three participants- a foundation-year doctor, a nurse/healthcare assistant and a therapist. Scenario 1 dealt with a patient with hypoactive delirium with focus on identification and multidisciplinary optimisation. Scenario 2 challenged participants with management of an agitated patient. Scenario 3 involved discharging a patient with resolving delirium and a reluctant relative, with emphasis on mental capacity assessment. Communication, patient risk assessment and challenging perceived role barriers were global themes. Participant feedback was captured using unstructured interviews and pre- and post-session 5-point Likert confidence scale in various learning outcomes.

Results

16 participants were included- 4 foundation year doctors, 3 therapists, 2 healthcare assistants and 7 nurses. There was an average improvement in Likert confidence scales in all measured learning outcomes. All participants would recommend the course to their colleagues (average Likert scale 4.9). Qualitative feedback appraised the course for demonstration of de-escalation communication strategies, the application of mental capacity and recognition of early discharge planning.

Conclusion

Simulation training targeted at multi-disciplinary groups is an effective way to deliver teaching on delirium. It contextualises synergistic operation of different skills and personal accountability in influencing patient management. The challenge to its potential remains its adoption as mandatory training for various disciplines involved in care of older adults and its implementation at a wider-scale, to assure cost effectiveness.

Abstract PD5-08: The human tumor atlas network (HTAN) breast pre cancer atlas: A multi-omic integrative analysis of ductal carcinoma in situ (DCIS) and correlation with clinical outcomes

Introduction. As nonobligate precursors of invasive disease, pre-cancers provide a unique vantage point from which to study the molecular pathways and evolutionary dynamics that lead to the development of life-threatening cancers. Ductal carcinoma in situ (DCIS) is the most commonly diagnosed precursor of breast cancer, with variable propensity for invasive progression. In order to address the problems of over- and under-treatment, we performed a multimodal, integrated profile of DCIS with clinical outcomes with which to develop and validate predictors of invasive progression. Methods. We present observations on DNA, RNA, and protein expression on two independent patient cohorts of DCIS, diagnosed from 1981 to 2014, from the Translational Breast Cancer Research Consortium (TBCRC 038) and the Washington University Repository of Archival Human Breast Tissue (RAHBT). Patients initially diagnosed with DCIS, with either DCIS or invasive recurrence (cases; mean follow up 5.8 years) were matched to those without recurrence (controls; mean follow up 10.3 years), based upon age at diagnosis and year of diagnosis. Results. We present genomic and cellular changes that correlate with both disease states and patient outcomes in DCIS. DCIS can be clustered by classification systems developed for IBC. Specific immune cell types and pathways correlate with longitudinal outcome. Luminal cell adhesion and metabolism pathways are upregulated in controls and cases, respectively. Highly multiplexed ion beam imaging (MIBI) was used to validate RNA seq findings, and to provide single cell-level spatial context for molecular alterations.Conclusion. We have performed an integrated multi-omic analysis of DCIS and associated tumor micorenvironment. Our multi-scale approach employs in situ methods to generate a spatially resolved atlas of breast precancers where different modalities can be directly compared to each other, and correlated with conventional pathology findings and clinical outcome. The PreCancer Atlas represents a complex multi-modal database for DCIS study, whose design allows for future discovery and hypothesis generation.

Table 1. Breast Pre-cancer Atlas Multi-scale Characterization AssaysAssayScaleType of DataIntegration and validation with other assaysRNA-seq (Single duct, single cell, TME)Cell, duct, organ, normal tissue1. Whole transcriptome gene expression profiling per single duct (also enabling CNV and cell type prediction)2. Whole transcriptome gene expression profiling per single duct1. Prediction of CNV confirmed by DNA-seq (single duct) and FISH (single cell)2. Prediction of cell type composition (Cibersort) confirmed by multiplex IHC and multicolor flow cytometryLow-pass whole genome DNA-seqDuct and adjacent normalCNV profiling per single ductAnalysis of CNV supported by RNA-seq (single duct) and MIBI (single cell)Whole genome sequencingDuct and adjacent normalMutation status per single ductMutational analysis confirmed by RNA-seqMultiplex IHC (MIBI & Cyclic multicolor)Cell1. Cell type2. Proteomic analysisAnalysis of cell type supported by RNA-seq of ducts (Cibersort) and single cellsH&E MorphometricsCell, duct, organSpatial location of cell types, organization of ductsAnalysis of H&E images correlated with FISH data

Citation Format: Shelley Hwang, Siri H Strand, Belen Rivero, Lorraine King, Tyler Risom, Bryan Harmon, Fergus Couch, Kristalyn Gallagher, Mark Kilgore, Shi Wei, Angela DeMichele, Tari King, Priscilla McAuliffe, Julie Nangia, Ana Maria Storniolo, Alastair Thompson, Gaorav Gupta, Joanna Lee, Jennifer Tseng, Robyn Burns, ChunFang Zhu, Magda Matusiak, Shirley X Zhu, Jason Wang, Jose Seoane, Jen Tappenden, Daisy Ding, Dadong Zhang, Jingqin Luo, Sujay Vennam, Sushama Varma, Lunden Simpson, Luis Cisneros, Timmothy Hardman, Lauren Anderson, Cody Straub, Sucheta Srivastava, Deb J Veis, Christina Curtis, Rob Tibshirani, Robert Michael Angelo, Allison Hall, Kouros Owzar, Kornelia Polyak, Carlo Maley, Jeff Marks, Graham Colditz, Robert B West. The human tumor atlas network (HTAN) breast pre cancer atlas: A multi-omic integrative analysis of ductal carcinoma in situ (DCIS) and correlation with clinical outcomes [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD5-08.

DDIT3 Immunohistochemistry Is a Useful Tool for the Diagnosis of Myxoid Liposarcoma

Myxoid liposarcoma is a malignant adipogenic neoplasm characterized by prominent arborizing capillaries, occasional lipoblasts, and primitive-appearing spindle cells in a myxoid background. A recurrent translocation in myxoid liposarcoma results in an oncoprotein consisting of full-length DDIT3 (CHOP) fused to an N-terminal segment of either FUS (TLS) or, less often, EWSR1. Here, we explore the diagnostic significance of DDIT3 expression in myxoid liposarcoma using a mouse monoclonal antibody recognizing an epitope in the N-terminal region. Studying a total of 300 tumors, we find diffuse, moderate-to-strong nuclear-localized anti-DDIT3 immunoreactivity in all 46 cases of myxoid liposarcoma representing 36 unique tumors, including 6 cases with high-grade (round cell) morphology. DDIT3 immunohistochemistry also highlighted a distinctive vasculocentric growth pattern in 7 myxoid liposarcomas treated with neoadjuvant radiation. In contrast, the vast majority of other examined lipomatous and myxoid neoplasms exhibited no DDIT3 expression; limited, weak immunoreactivity in <10% of cells was infrequently observed in dedifferentiated liposarcoma (6/39, 15%), solitary fibrous tumor (3/12, 25%), pleomorphic liposarcoma (1/15, 7%), and high-grade myxofibrosarcoma (2/17, 12%). Although this minimal DDIT3 expression did not correlate with DDIT3 amplification or myxoid liposarcoma-like morphology in dedifferentiated liposarcoma, there was evidence among sarcomas (excluding myxoid liposarcoma) of a relationship between expression and exposure to neoadjuvant radiation or cytotoxic chemotherapy. The constellation of findings indicates that DDIT3 immunohistochemistry may have utility in the evaluation of myxoid and lipomatous neoplasms to support the diagnosis of myxoid liposarcoma.

Origins and clonal convergence of gastrointestinal IgE+ B cells in human peanut allergy

B cells in human food allergy have been studied predominantly in the blood. Little is known about IgE⁺ B cells or plasma cells in tissues exposed to dietary antigens. We characterized IgE⁺ clones in blood, stomach, duodenum, and esophagus of 19 peanut-allergic patients, using high-throughput DNA sequencing. IgE⁺ cells in allergic patients are enriched in stomach and duodenum, and have a plasma cell phenotype. Clonally related IgE⁺ and non-IgE-expressing cell frequencies in tissues suggest local isotype switching, including transitions between IgA and IgE isotypes. Highly similar antibody sequences specific for peanut allergen Ara h 2 are shared between patients, indicating that common immunoglobulin genetic rearrangements may contribute to pathogenesis. These data define the gastrointestinal tract as a reservoir of IgE⁺ B lineage cells in food allergy.

Abstract PR05: Mapping the tumor and microenvironmental evolution underlying DCIS progression through multiplexed ion beam imaging

Ductal Carcinoma in Situ (DCIS) is a pre-invasive lesion that accounts for nearly 20% of new breast cancer diagnoses. Of these cases, about half will progress to invasive breast cancer (IBC) within ten years. However, because diagnostic criteria for delineating low risk lesions from those likely to progress to IBC have not been identified, many patients are receiving unnecessary chemotherapy and surgery that can result in therapy-related morbidity and death. With this in mind, we used Multiplexed Ion Beam Imaging by time of flight (MIBI-TOF) and RNA-seq laser-capture microdissection (SMART-3SEQ) to construct a comprehensive spatial atlas describing the structure, function, and cellular composition of DCIS. MIBI-TOF and SMART-3SEQ were used to compare lesions from patients that later developed IBC with those from age- and history matched DCIS controls without recurrence. Using a 37-marker staining panel to interrogate 137 lesions, we identified 30 distinct cell populations of the epithelial, stromal, and immune lineages that were arranged in recurrent cellular microenvironments specific for DCIS or invasive disease. We observe a coordinated shift in the immune and stromal compartments as invasive disease arises, including an expansion of immune cell diversity and transition to reactive stromal phenotypes in synchronous DCIS + IBC, which was distinct from the macrophage-dominant microenvironment of recurrent IBC. Single-cell segmentation using a deep learning model was combined with pixel-level coexpression analysis to determine how thickness, continuity, and phenotype of ductal myoepithelium changes as tumors progress from a pre-invasive state. These data were incorporated into a comprehensive model which was subsequently used to identify a subset of features that correlate with disease-free survival following DCIS tumor resection. Taken together, these features represent important prognostic metrics that can be used to separate pre-invasive from indolent DCIS tumors, and allow for tailored therapy that improves patient outcomes and quality of life in this disease.

Citation Format: Tyler Risom, Belen Rivero, Candace Liu, Alex Baranski, Siri Strand, Noah Greenwald, Erin McCaffrey, Sushama Varma, Leeat Keren, Sucheta Srivastava, Chunfang Zhu, Sujay Vennam, Shelley Hwang, Graham Colditz, Sean Bendall, Robert West, Michael Angelo. Mapping the tumor and microenvironmental evolution underlying DCIS progression through multiplexed ion beam imaging [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PR05.

Abstract B28: ERAP2 overexpression is a marker for reduced anti-PD-1 response in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is an EBV-associated epithelial cancer common in the Southern Chinese population. Patients with recurrent or metastatic NPC treated with PD-1 blockade showed a response rate of 20.5%, with no correlation observed between the expression of PD-L1 and treatment response. In an effort to identify biomarkers for anti-PD-1 treatment response, we evaluated a cohort of 10 NPC patients with recurrent or metastatic NPC treated with nivolumab or pembrolizumab. Laser capture microdissection was performed on pretreatment biopsies, with tumor and microenvironment compartments separately microdissected. Nasopharyngeal epithelium from normal nasopharyngeal biopsies were also microdissected as controls. Smart-3SEQ, a novel 3´ end RNA-Seq technique that allows for the accurate quantification of transcript abundance in FFPE samples, was performed to obtain gene expression libraries. ERAP2, a zinc metalloaminopeptidase that performs N-terminal trimming of antigenic epitopes for presentation by MHC class I, was among the most highly upregulated genes in the tumor compartment of nonresponders (adjusted p = 0.033). ERAP2 overexpression was also observed in NPC tumors compared to normal controls. Immunohistochemistry validated the overexpression of ERAP2 in nonresponders, while responders had similar expression to normal controls. In conclusion, ERAP2 is overexpressed in NPC tumors and is a promising biomarker for reduced anti-PD-1 response in NPC.

Citation Format: Joshua K. Tay, Brigette B.Y. Ma, Sushama Varma, Yaw Chyn Lim, Chee Seng Tan, Kwok Wai Lo, John B. Sunwoo, Kevin J. Cullen, Boon Cher Goh, Robert B. West. ERAP2 overexpression is a marker for reduced anti-PD-1 response in nasopharyngeal carcinoma [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr B28.

National survey of UK Dermatologists demonstrates significant variation in how to obtain consent for dermatological procedures

Consent must be undertaken prior to any dermatological procedure; however, in doing this, the clinician needs to ensure consent is valid and satisfies the principles of determining material risk. We aimed to assess variations in obtaining consent in the UK and understanding of material risk through a nationally distributed survey to members of the British Society for Dermatological Surgery and British Association of Dermatologists. Of 165 responses, we found that written consent was being obtained for all procedures in 73.9% of cases and typically at the time of procedure in the operating room/theatre (78.8%). Fifty-seven per cent of respondents were not familiar with the term 'material risk' and almost one-third were not aware of the Montgomery vs. Lanarkshire ruling, which replaced the Bolam test in 2015. We would encourage readers to be aware of these changes to consent law in the UK and how it might affect their approach to obtaining consent.

Genomic landscape of ductal carcinoma in situ and association with progression

PURPOSE

The detection rate of breast ductal carcinoma in situ (DCIS) has increased significantly, raising the concern that DCIS is overdiagnosed and overtreated. Therefore, there is an unmet clinical need to better predict the risk of progression among DCIS patients. Our hypothesis is that by combining molecular signatures with clinicopathologic features, we can elucidate the biology of breast cancer progression, and risk-stratify patients with DCIS.

METHODS

Targeted exon sequencing with a custom panel of 223 genes/regions was performed for 125 DCIS cases. Among them, 60 were from cases having concurrent or subsequent invasive breast cancer (IBC) (DCIS + IBC group), and 65 from cases with no IBC development over a median follow-up of 13 years (DCIS-only group). Copy number alterations in chromosome 1q32, 8q24, and 11q13 were analyzed using fluorescence in situ hybridization (FISH). Multivariable logistic regression models were fit to the outcome of DCIS progression to IBC as functions of demographic and clinical features.

RESULTS

We observed recurrent variants of known IBC-related mutations, and the most commonly mutated genes in DCIS were PIK3CA (34.4%) and TP53 (18.4%). There was an inverse association between PIK3CA kinase domain mutations and progression (Odds Ratio [OR] 10.2, p < 0.05). Copy number variations in 1q32 and 8q24 were associated with progression (OR 9.3 and 46, respectively; both p < 0.05).

CONCLUSIONS

PIK3CA kinase domain mutations and the absence of copy number gains in DCIS are protective against progression to IBC. These results may guide efforts to distinguish low-risk from high-risk DCIS.

Detection of Circulating Tumor DNA in Patients With Uterine Leiomyomas

PURPOSE

The preoperative distinction between uterine leiomyoma (LM) and leiomyosarcoma (LMS) is difficult, which may result in dissemination of an unexpected malignancy during surgery for a presumed benign lesion. An assay based on circulating tumor DNA (ctDNA) could help in the preoperative distinction between LM and LMS. This study addresses the feasibility of applying the two most frequently used approaches for detection of ctDNA: profiling of copy number alterations (CNAs) and point mutations in the plasma of patients with LM.

PATIENTS AND METHODS

By shallow whole-genome sequencing, we prospectively examined whether LM-derived ctDNA could be detected in plasma specimens of 12 patients. Plasma levels of lactate dehydrogenase, a marker suggested for the distinction between LM and LMS by prior studies, were also determined. We also profiled 36 LM tumor specimens by exome sequencing to develop a panel for targeted detection of point mutations in ctDNA of patients with LM.

RESULTS

We identified tumor-derived CNAs in the plasma DNA of 50% (six of 12) of patients with LM. The lactate dehydrogenase levels did not allow for an accurate distinction between patients with LM and patients with LMS. We identified only two recurrently mutated genes in LM tumors (MED12 and ACLY).

CONCLUSION

Our results show that LMs do shed DNA into the circulation, which provides an opportunity for the development of ctDNA-based testing to distinguish LM from LMS. Although we could not design an LM-specific panel for ctDNA profiling, we propose that the detection of CNAs or point mutations in selected tumor suppressor genes in ctDNA may favor a diagnosis of LMS, since these genes are not affected in LM.

MYB-activated models for testing therapeutic agents in adenoid cystic carcinoma

OBJECTIVE

There are no effective systemic therapies for adenoid cystic cancer (ACC) and lack of tumor lines and mouse models have hindered drug development.We aim to develop MYB-activated models for testing new therapeutic agents.

MATERIALS AND METHODS

We studied new ACC patient-derived xenograft (PDX) models and generated a matched cell line from one patient. In addition, we generated a genetically-engineered MYB-NFIB mouse model (GEMM) that was crossed with Ink4a^+/-/Arf^+/- mice to study tumor spectrum and obtain tumor lines. Using human and murine ACC-like tumor lines, we analyzed MYB expression by RNA-Seq and immunoblot and tested efficacy of new MYB inhibitors.

RESULTS

We detected MYB-NFIB transcripts in both UFH1 and UFH2 PDX and observed tumor inhibition by MYB depletion using shRNA in vivo. We observed rapid loss of MYB expression when we cultured UFH1 in vitro, but were able to generate a UFH2 tumor cell line that retained MYB expression for 6 months. RNA-Seq expression detected an ACC-like mRNA signature in PDX samples and we confirmed an identical KMT2A/MLL variant in UFH2 PDX, matched cell line, and primary biopsy. Although the predominant phenotype of the MYB-NFIB GEMM was B-cell leukemia, we also generated a MYB-activated ACC-like mammary tumor cell line. We observed tumor inhibition using a novel MYB peptidomimetic in both human and murine tumor models.

CONCLUSIONS

We generated and studied new murine and human MYB-activated tumor samples and detected growth inhibition with MYB peptidomimetics. These data provide tools to define treatment strategies for patients with advanced MYB-activated ACC.

Cell cycle progression in confining microenvironments is regulated by a growth-responsive TRPV4-PI3K/Akt-p27Kip1 signaling axis

In tissues, cells reside in confining microenvironments, which may mechanically restrict the ability of a cell to double in size as it prepares to divide. How confinement affects cell cycle progression remains unclear. We show that cells progressed through the cell cycle and proliferated when cultured in hydrogels exhibiting fast stress relaxation but were mostly arrested in the G0/G1 phase of the cell cycle when cultured in hydrogels that exhibit slow stress relaxation. In fast-relaxing gels, activity of stretch-activated channels (SACs), including TRPV4, promotes activation of the phosphatidylinositol 3-kinase (PI3K)/Akt pathway, which in turn drives cytoplasmic localization of the cell cycle inhibitor p27Kip1, thereby allowing S phase entry and proliferation. Cell growth during G1 activated the TRPV4-PI3K/Akt-p27Kip1 signaling axis, but growth is inhibited in the confining slow-relaxing hydrogels. Thus, in confining microenvironments, cells sense when growth is sufficient for division to proceed through a growth-responsive signaling axis mediated by SACs.

Genomic analysis of benign prostatic hyperplasia implicates cellular re-landscaping in disease pathogenesis

Benign prostatic hyperplasia (BPH) is the most common cause of lower urinary tract symptoms in men. Current treatments target prostate physiology rather than BPH pathophysiology and are only partially effective. Here, we applied next-generation sequencing to gain new insight into BPH. By RNAseq, we uncovered transcriptional heterogeneity among BPH cases, where a 65-gene BPH stromal signature correlated with symptom severity. Stromal signaling molecules BMP5 and CXCL13 were enriched in BPH while estrogen regulated pathways were depleted. Notably, BMP5 addition to cultured prostatic myofibroblasts altered their expression profile towards a BPH profile that included the BPH stromal signature. RNAseq also suggested an altered cellular milieu in BPH, which we verified by immunohistochemistry and single-cell RNAseq. In particular, BPH tissues exhibited enrichment of myofibroblast subsets, whilst depletion of neuroendocrine cells and an estrogen receptor (ESR1)-positive fibroblast cell type residing near epithelium. By whole-exome sequencing, we uncovered somatic single-nucleotide variants (SNVs) in BPH, of uncertain pathogenic significance but indicative of clonal cell expansions. Thus, genomic characterization of BPH has identified a clinically-relevant stromal signature and new candidate disease pathways (including a likely role for BMP5 signaling), and reveals BPH to be not merely a hyperplasia, but rather a fundamental re-landscaping of cell types.

YAP-independent mechanotransduction drives breast cancer progression

Increased tissue stiffness is a driver of breast cancer progression. The transcriptional regulator YAP is considered a universal mechanotransducer, based largely on 2D culture studies. However, the role of YAP during in vivo breast cancer remains unclear. Here, we find that mechanotransduction occurs independently of YAP in breast cancer patient samples and mechanically tunable 3D cultures. Mechanistically, the lack of YAP activity in 3D culture and in vivo is associated with the absence of stress fibers and an order of magnitude decrease in nuclear cross-sectional area relative to 2D culture. This work highlights the context-dependent role of YAP in mechanotransduction, and establishes that YAP does not mediate mechanotransduction in breast cancer.

Incidence of sleep problems and their mediating role on depression and anxious preoccupation in patients with resected, non-advanced cancer: data from NEOcoping study

BACKGROUND

Our study analyzes the incidence of sleep problems and their mediating role on depression and anxious preoccupation in patients with resected, non-advanced cancer.

METHODS

A multi-institutional, prospective, observational study was conducted with 750 participants of 14 hospitals in Spain. Participants' socio-demographic and clinical characteristics were collected using a standardized self-report form and using EORTC QoL-QLQ-C30, BSI, Mini-MAC questionnaires.

RESULTS

In women, sleep problems, depression and anxious preoccupation were observed in 65, 41 and 21%, respectively. In men, sleep problems, depression and anxious preoccupation were reported in 51, 29 and 61%, respectively. More sleep problems, depression and anxious preoccupation were found among women than males. Depression was a significant predictor of anxious preoccupation. In males, sleep problems partially mediated this association. This was not confirmed in women.

CONCLUSION

Our findings point toward the importance of developing interventions that decrease depression and sleep problems in cancer.

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

The immune system is critical in modulating cancer progression, but knowledge of immune composition, phenotype, and interactions with tumor is limited. We used multiplexed ion beam imaging by time-of-flight (MIBI-TOF) to simultaneously quantify in situ expression of 36 proteins covering identity, function, and immune regulation at sub-cellular resolution in 41 triple-negative breast cancer patients. Multi-step processing, including deep-learning-based segmentation, revealed variability in the composition of tumor-immune populations across individuals, reconciled by overall immune infiltration and enriched co-occurrence of immune subpopulations and checkpoint expression. Spatial enrichment analysis showed immune mixed and compartmentalized tumors, coinciding with expression of PD1, PD-L1, and IDO in a cell-type- and location-specific manner. Ordered immune structures along the tumor-immune border were associated with compartmentalization and linked to survival. These data demonstrate organization in the tumor-immune microenvironment that is structured in cellular composition, spatial arrangement, and regulatory-protein expression and provide a framework to apply multiplexed imaging to immune oncology.

Abstract 185: p300 and STAT3 drive YAP-independent mechanotransduction during breast cancer invasion

83% of non-invasive breast cancers are diagnosed as ductal carcinoma in situ (DCIS). While some DCIS tumors remain confined in the mammary duct, about half progress into invasive ductal carcinoma (IDC), when carcinoma cells break through the basement membrane (BM) into the type-1 collagen (col-1) rich stroma, a key first step towards metastasis. As 90% of cancer-related deaths are due to metastasis, preventing progression to invasive disease could significantly reduce cancer mortality. However there are no established biomarkers for invasive potential and current diagnostic methods cannot predict which DCIS cases will progress to IDC. Interestingly, increased tissue stiffness correlates with invasion and the transcriptional regulator YAP has been implicated as a mechanotransducer, largely based on 2D culture studies. To identify the drivers of DCIS progression, we encapsulated mammary epithelial cells (MECs) in 3D hydrogels with a range of stiffness and that presented either BM-ligands or col-1 containing microenvironments to the cells. RNA-seq identified the global gene expression changes induced by increased 3D culture stiffness in BM-like environments. 3SEQ analysis of breast cancer patient samples revealed that genes regulated by 3D culture stiffness were upregulated in breast cancer patients, demonstrating the relevance of 3D culture models and suggesting expression of S100A7 as a potential biomarker of breast cancer progression. Interestingly gene expression changes induced by increased 3D stiffness in BM-like environments were distinct from col-1 like environments. Col-1 exposure in stiff gels promotes expression of genes whose protein products remodel the col-1 network including FN1 and LOX. As col-1 remodeling promotes cell dissemination, this suggests that col-1 exposure following BM invasion induces pro-metastatic changes in carcinoma phenotype. Surprisingly, enhanced stiffness induced invasion in MECs independently of YAP activation in both BM-like and col-1 rich 3D hydrogels. Instead, bioinformatic analysis identified transcriptional regulators p300 and STAT3 as mediators of 3D mechanosensing. Inhibition of p300 and STAT3 in stiff 3D BM-like environments and, conversely, overexpression in soft 3D BM-like environments confirm a role during stiffness-induced proliferation. This suggests p300 and STAT3 as possible targets for preventing progression to invasive disease. While genetic alterations initiate transformation, these results reveal the miroenvironment events that initiate breast cancer invasion.

Citation Format: Joanna Y. Lee, Jessica Chang, Sungmin Nam, Hong-pyo Lee, Antonia A. Dominguez, Sushama Varma, Lei S. Qi, Robert B. West, Ovijit Chaudhuri. p300 and STAT3 drive YAP-independent mechanotransduction during breast cancer invasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 185.

Abstract 3411: Biological subtypes of nasopharyngeal carcinoma by genomic profiling

Objective:

Nasopharyngeal carcinoma (NPC) is a common Epstein-barr virus-associated epithelial malignancy in several parts of the world including Southeast Asia. While the majority of patients are treated uniformly with a combination of chemo and radiation therapy, 20% of patients experience recurrence, most commonly in the form of distant metastasis. NPC subtypes based on underlying differences in biology are unexplored and are likely responsible for the heterogeneous clinical response. As NPC biopsies are small and have significant stromal infiltrate, obtaining pure epithelial cells for genomic profiling is a challenge. We aim to overcome these limitations to identify biological subtypes and dysregulated molecular pathways in NPC.

Methods:

We first evaluated 217 whole exomes sequences, including 102 microdissected tumors, from three previous studies for single nucleotide variants and copy number changes, following GATK standards and using next generation sequencing copy number callers. We then applied a novel method for gene expression profiling developed in our lab to a new cohort of EBV-positive primary NPC cases from our institution. We performed laser capture microdissection, separately dissecting tumor, normal and microenvironment for each case. We applied Smart-3SEQ, a novel 3' end RNA-Seq technique which allows for the accurate quantification of transcript abundance in dissected FFPE samples comprising only a few hundred cells.

Results:

We achieved a per-base concordance of 80.4% between copy number profiles by SNP array and whole exome sequencing. Unsupervised clustering identified three distinct copy-number groups of NPC tumors, with a low copy-number group demonstrating an 18.7% better 5-year disease-specific survival, not attributable to stage. Apart from broad cytogenetic changes, narrow regions of amplifications (e.g. 1q21, 11q13) and deletions (e.g. 9p21, 11q22) were important for defining copy-number subtypes.

Preliminary differential gene expression analysis showed that genes involved in cell cycle and cellular differentiation were significantly dysregulated in tumor cells (p &lt; 0.001 and p = 0.03 respectively), while genes involved in cilia assembly and flagella transport were upregulated in normal cells (p &lt; 0.001 for both). Our further analysis includes defining tumor subtypes based on gene expression, identifying key driver pathways, and correlating with EBV-latent gene expression, the immune environment, as well as clinical outcome.

Conclusion:

NPC tumors are biologically heterogeneous and can be classified based on their mutational and gene expression profiles. This provides an important basis for the consideration of escalation and de-escalation of therapy in selected patient groups.

Citation Format: Kai Xun Joshua Tay, Chunfang Zhu, Sujay Vennam, Sushama Varma, Quynh-Thu Le, John Sunwoo, Robert West. Biological subtypes of nasopharyngeal carcinoma by genomic profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3411.