Late-stage Tumors Research Articles

TTK, CDC25A, and ESPL1 as Prognostic Biomarkers for Endometrial Cancer.

Objective Endometrial cancer (EC) is one of the most common malignant gynaecological tumours worldwide. This study was aimed at identifying EC prognostic genes and investigating the molecular mechanisms of these genes in EC. Methods Two mRNA datasets of EC were downloaded from the Gene Expression Omnibus (GEO). The GEO2R tool and Draw Venn Diagram were used to identify differentially expressed genes (DEGs) between normal endometrial tissues and EC tissues. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID). Next, the protein-protein interactions (PPIs) of these DEGs were determined by the Search Tool for the Retrieval of Interacting Genes (STRING) tool and Cytoscape with Molecular Complex Detection (MCODE). Furthermore, Kaplan-Meier survival analysis was performed by UALCAN to verify genes associated with significantly poor prognosis. Next, Gene Expression Profiling Interactive Analysis (GEPIA) was used to verify the expression levels of these selected genes. Additionally, a reanalysis of the KEGG pathways was performed to understand the potential biological functions of selected genes. Finally, the associations between these genes and clinical features were analysed based on TCGA cancer genomic datasets for EC. Results In EC tissues, compared with normal endometrial tissues, 147 of 249 DEGs were upregulated and 102 were downregulated. A total of 64 upregulated genes were assembled into a PPI network. Next, 14 genes were found to be both associated with significantly poor prognosis and highly expressed in EC tissues. Reanalysis of the KEGG pathways found that three of these genes were enriched in the cell cycle pathway. TTK, CDC25A, and ESPL1 showed higher expression in cancers with late stage and higher tumour grade. Conclusion In summary, through integrated bioinformatics approaches, we found three significant prognostic genes of EC, which might be potential therapeutic targets for EC patients.

Epidemiological and Survival Analysis of Primary Intestinal Non-Hodgkin's Lymphoma Patients from SEER Database

Introduction: Gastrointestinal tract is the most common site of extranodal non-Hodgkin's lymphoma (EN-NHL). Most of the data published so far has been on the gastric NHL and very limited data is available on primary intestinal - Non-Hodgkin's Lymphoma (PI-NHL). Here, we are presenting the epidemiological and survival data for PI-NHL from the SEER 21 database. Methods: Data for all the EN-NHL and Intestinal NHL are collected for the period 2000-2015 from the SEER 21 database based on the WHO ICD-O3 classification. PI-NHL data has been extracted from EN- NHL and intestinal datasets and then cross-matched for accuracy of the desired patient subset selection. A total of 9,290 PI-NHL cases common to both the lists were selected and used for analysis. Patients with incomplete staging and survival data were excluded from the survival analysis. Survival analysis variables include gender (male or female), ethnicity (white or non-white), early age of onset (≤ 50 years), late age of onset (>50 years), location (small or large intestine), the staging of the tumor as early-stage (stage 1 and stage 2) or late-stage tumors (stage 3 and stage 4), and history of prior malignancy (first primary tumor or second/later primary tumor). Survival analysis is done using a cox-proportional hazard regression model. Results: The percentage of PI-NHL of all the intestinal cancers and extranodal non-Hodgkin's lymphoma is 1.42% (1.40 - 1.45, 95% CI) and 10.52% (10.32 - 10.72, 95% CI) respectively. The demographic and clinical characteristics of the patients are described in Figure 1. In the survival analysis (Figure 2), the risk of overall mortality is higher in the late-onset cancers (HR - 1.16, 1.08 -1.24, P-value<0.001), non-white population (HR- 1.13, 1.05 - 1.22, P-value 0.002) and second or later primary tumors (HR - 1.10, 1.01 - 1.20, P-Value - 0.036). Gender, site, and stage are not significantly related to mortality but the trend towards higher mortality is seen in the late-stage tumor (HR - 1.04, 0.97 - 1.12, P-Value - 0.29). Conclusion: PL-NHL is a rare type of intestinal malignancy. Our study showed that the risk of overall mortality is higher in late-onset cancer, non-white population, and in second or later primary tumors. Gender, site, and stage are not significantly related to mortality. The analysis was done for overall survival and this may have affected the outcome of the survival variables. Therefore, a survival analysis of cause-specific mortality data will give a more elaborate picture of the relationship between the mortality data and these variables. Disclosures No relevant conflicts of interest to declare.

Presentation, Management, and Outcomes Across the Rural-Urban Continuum for Hepatocellular Carcinoma.

BackgroundHepatocellular carcinoma is 1 of few cancers with rising incidence and mortality in the United States. Little is known about disease presentation and outcomes across the rural-urban continuum.MethodsUsing the population-based Surveillance, Epidemiology, and End Results registry, we identified adults with incident hepatocellular carcinoma between 2000 and 2016. Urban, suburban, and rural residence at time of cancer diagnosis were categorized by the Census Bureau’s percent of the population living in nonurban areas. We examined association between place of residence and overall survival. Secondary outcomes were late tumor stage and receipt of therapy.ResultsOf 83 368 incident cases of hepatocellular carcinoma, 75.8%, 20.4%, and 3.8% lived in urban, suburban, and rural communities, respectively. Median survival was 7 months (interquartile range = 2-24). All stage and stage-specific survival differed by place of residence, except for distant stage. In adjusted models, rural and suburban residents had a respective 1.09-fold (95% confidence interval [CI] = 1.04 to 1.14; P < .001) and 1.08-fold (95% CI = 1.05 to 1.10; P < .001) increased hazard of overall mortality as compared with urban residents. Furthermore, rural and suburban residents had 18% (odds ratio [OR] = 1.18, 95% CI = 1.10 to 1.27; P < .001) and 5% (OR = 1.05, 95% CI = 1.02 to 1.09; P = .003) higher odds of diagnosis at late stage and were 12% (OR = 0.88, 95% CI = 0.80 to 0.94; P < .001) and 8% (OR = 0.92, 95% CI = 0.88 to 0.95; P < .001) less likely to receive treatment, respectively, compared with urban residents.ConclusionsResidence in a suburban and rural community at time of diagnosis was independently associated with worse indicators across the cancer continuum for liver cancer. Further research is needed to elucidate the primary drivers of these rural-urban disparities.

Impact of Matrix Metalloproteinase-11 Gene Polymorphisms on Biochemical Recurrence and Clinicopathological Characteristics of Prostate Cancer.

Prostate cancer is among the most common malignant tumors worldwide. Matrix metalloproteinase (MMP)-11 is involved in extracellular matrix degradation and remodeling and plays an essential role in cancer development and metastasis. This study investigated the association of MMP-11 polymorphisms with the clinicopathological characteristics and biochemical recurrence of prostate cancer. Five single-nucleotide polymorphisms (SNPs) of the MMP-11 were analyzed in 578 patients with prostate cancer through real-time polymerase chain reaction analysis. A prostate-specific antigen level of >10 ng/mL, Gleason grade groups 4 + 5, advanced tumor stage, lymph node metastasis, invasion, and high-risk D’Amico classification were significantly associated with biochemical recurrence in the patients (p < 0.001). MMP-11 rs131451 “TC + CC” polymorphic variants were associated with advanced clinical stage (T stage; p = 0.007) and high-risk D’Amico classification (p = 0.015) in patients with biochemical recurrence. These findings demonstrate that MMP-11 polymorphisms were not associated with prostate cancer susceptibility; however, the rs131451 polymorphic variant was associated with late-stage tumors and high-risk D’Amico classification in prostate cancer patients with biochemical recurrence. Thus, the MMP-11 SNP rs131451 may contribute to the tumor development in prostate cancer patients with biochemical recurrence.

Molecular Profiling Reveals Common and Specific Development Processes in Different Types of Gynecologic Cancers.

BackgroundGynecologic cancers have become a major threat to women’s health. The molecular biology of gynecologic cancers is not as well understood as that of breast cancer, and precision targeting is still new. Although viewed collectively as a group of cancers within the female reproductive system, they are more often studied separately. A comprehensive within-group comparison on molecular profiles is lacking.MethodsWe conducted a whole-exome sequencing study of cervical/endometrial/ovarian cancer samples from 209 Chinese patients. We combined our data with genomic and transcriptomic data from relevant TCGA cohorts to identify and verify common/exclusive molecular changes in cervical/endometrial/ovarian cancer.ResultsWe identified shared molecular features including a COSMIC signature of deficient mismatch repair (dMMR), four recurrent copy-number variation (CNV) events, and extensive alterations in PI3K-Akt-mTOR signaling and cilium component genes; we also identified transcription factors and pathways that are exclusively altered in cervical/endometrial/ovarian cancer. The functions of the commonly/exclusively altered genomic circuits suggest (1) a common reprogramming process during early tumor initiation, which involves PI3K activation, defects in mismatch repair and cilium organization, as well as disruption in interferon signaling and immune recognition; (2) a cell-type specific program at late-stage tumor development that eventually lead to tumor proliferation and migration.ConclusionThis study describes, from a molecular point of view, how similar and how different gynecologic cancers are, and it provides a hypothesis about the causes of the observed similarities and differences.

Integrative network analysis identifies an immune-based prognostic signature as the determinant for the mesenchymal subtype in epithelial ovarian cancer.

Epithelial ovarian cancer (EOC) has been classified into four molecular subtypes, of which the mesenchymal subtype has the poorest survival. Our goal is to develop an immune-based prognostic signature by incorporating molecular subtypes for EOC patients. The gene expression profiles of EOC samples were collected from seven public datasets as well as an internal retrospective validation cohort, containing 1192 EOC patients. Network analysis was applied to integrate the mesenchymal modalities and immune signature to establish an immune-based prognostic signature for EOC (IPSEOC). The signature was trained and validated in eight independent datasets. Seven immune genes were identified as key regulators of the mesenchymal subtype and were used to construct the IPSEOC. The IPSEOC significantly divided patients into high- and low-risk groups in discovery (OS: P < .0001), 6 independent public validation sets (OS: P = .04 to P = .002), and an internal retrospective validation cohort (OS: P = .025). Furthermore, pathway analysis revealed that differences between risk groups were mainly activation of mesenchymal-related signalling. Moreover, a significant correlation existed between the IPSEOC values versus clinical phenotypes including late tumor stages, drug resistance. We propose an immune-based signature, which is a promising prognostic biomarker in ovarian cancer. Prospective studies are needed to further validate its analytical accuracy and test the clinical utility.

Association of the Implant Surface Texture Used in Reconstruction With Breast Cancer Recurrence

The potential association between breast implant-related anaplastic large cell lymphoma (BIA-ALCL) and implant texture has raised concerns about the additional unexpected adverse effects of textured implants, including potentially adverse outcomes for other cancers. In addition to the risk of developing BIA-ALCL, breast cancer survivors may worry about whether the type of implant inserted is associated with recurrence of their original cancer-an issue for which little evidence currently exists. To evaluate the oncologic outcomes of breast cancer according to the surface type of implants used for reconstruction and to identify the independent factors associated with breast cancer recurrence and survival, including implant surface type. This cohort study was conducted at Samsung Medical Center, a single tertiary referral center in Seoul, South Korea. Patients with breast cancer who underwent total mastectomy and immediate 2-stage tissue expander/implant reconstruction between January 1, 2011, and December 31, 2016, were identified from a prospectively maintained database. Patients were categorized into 2 groups according to the surface type of implant used for their reconstruction (smooth or textured implant). These patients were followed up for at least 2 years after insertion of the implant. Data analysis was performed from February 15, 2020, to March 5, 2020. Use of smooth implants vs textured implants at the second-stage operation. The main outcomes of interest were local and regional recurrence-free survival (LRRFS) and disease-free survival (DFS) rates. Cumulative incidence of oncologic events in the smooth implant and textured implant groups and their respective hazard ratios (HRs) were collected and updated regularly. In total, 650 patients (all women, with a mean [SD] age of 43.5 [7.4] years), representing 687 cases, met the inclusion criteria and were followed up for a median (range) duration of 52 (31-106) months. Of the 687 cases, 274 (39.9%) received a smooth implant and 413 (60.1%) received a textured implant. Patients in these 2 surface texture groups had similar characteristics, including tumor staging (stage I: 102 [37.2%] vs 173 [41.9%]; stage II: 93 [33.9%] vs 119 [28.8%]; stage III: 14 [5.1%] vs 20 [4.8%]; P = .50) and rates of adjuvant radiotherapy (42 [15.3%] vs 49 [11.9%]; P = .19) and chemotherapy (113 [41.2%] vs 171 [41.4%]; P = .97). The 5-year LRRFS was 96.7%, and the 5-year DFS was 95.2%. Compared with the use of a smooth implant, textured implant use was statistically significantly associated with lower DFS, and this difference remained significant after adjusting for estrogen receptor (ER) status and tumor stage (HR, 3.054; 95% CI, 1.158-8.051; P = .02). Similar statistically significant associations were observed on multivariable analysis of patients with ER-positive cancer (HR, 3.130; 95% CI, 1.053-9.307; P = .04) and those with invasive cancer (HR, 3.044; 95% CI, 1.152-8.039; P = .03). The association of textured implant use with recurrence (lower DFS) was more prominent in cases with late-stage (stage II or III) tumor (HR, 8.874; 95% CI, 1.146-68.748; P = .04). The LRRFS did not differ statistically significantly according to implant surface texture. This cohort study found that use of textured implants in reconstruction appears to be associated with recurrence of breast cancer. Further investigation is required to verify these results.

TCEAL2 as a Tumor Suppressor in Renal Cell Carcinoma is Associated with the Good Prognosis of Patients.

BackgroundRenal cell carcinoma (RCC) is one of the most common tumors in urinary tract tumors. However, the mechanism that supports renal cell carcinoma is unclear. The function of transcription elongation factor A (SII)-like 2 (TCEAL2) and its association with human cancer have not been reported.Materials and MethodsTo explore the role of TCEAL2 in carcinogenesis of clear cell renal cell carcinoma (ccRCC), we performed bioinformatics analysis to determine the expression levels of TCEAL2 in ccRCC specimens and normal kidney tissue and then verified findings with our samples by qPCR, Western blot and immunohistochemistry staining. Furthermore, the lentiviral vectors were used to increase the expression of TCEAL2 in ccRCC cell lines. The immunofluorescence assay was taken to observe the subcellular location of TCEAL2 in ccRCC cells, and CCK-8 and flow cytometry were introduced for assessing cell proliferation and cell cycle of ccRCC cells, respectively.ResultsCompared with adjacent normal kidney tissue and human proximal tubular epithelial cells, the expression of TCEAL2 in ccRCC tissues and cell lines was down-regulated. Patients who had low expression of TCEAL2 had a statistically significant late tumor stage. Restore of TCEAL2 in ccRCC cells inhibited cell proliferation and induced cell cycle arrest in S phase of ccRCC cells.ConclusionTo our knowledge, this is the first report of TCEAL2 expression changes in ccRCC. We found that the decrease of TCEAL2 expression may be related to the occurrence of ccRCC. Further research is needed to clarify the molecular mechanism of TCEAL2 in progress of ccRCC.

Expression of MTDH and IL-10 Is an Independent Predictor of Worse Prognosis in ER-Negative or PR-Negative Breast Cancer Patients.

(1) Background: Tumor hypoxia leads to metastasis and certain immune responses, and interferes with normal biological functions. It also affects glucose intake, down-regulates oxidative phosphorylation, and inhibits fatty-acid desaturation regulated by hypoxia-inducible factor 1α (HIF-1α). Although tumor hypoxia has been found to promote tumor metastasis, the roles of HIF-1α-regulated genes and their application are not completely integrated in clinical practice. (2) Methods: We examined the correlation between HIF-1α, metadherin (MTDH), and interleukin (IL)-10 mRNA expression, as well as their expression patterns in the prognosis of breast cancer using the Gene Expression Profiling Interactive Analysis (GEPIA) databases via a web interface; tissue microarrays (TMAs) were stained for MTDH and IL-10 protein expression using immunohistochemistry. (3) Results: HIF-1α, MTDH, and IL-10 mRNA expression are highly correlated and strongly associated with poor prognosis. MTDH and IL-10 protein expression of breast cancer patients usually harbored negative estrogen receptor (ER) or progesterone receptor (PR) status, and late-stage tumors have higher IL-10 expression. With regard to MTDH and IL-10 protein expression status for using univariate and multivariate analysis, the results showed that the protein expression of MTDH and IL-10 in ER-negative or PR-negative breast cancer patients have the worse prognosis. (4) Conclusions: we propose a new insight into hypoxia tumors in the metabolism and immune evidence for breast cancer therapy.

Inflection of Akt/mTOR/STAT-3 cascade in TNF-α induced protein 8 mediated human lung carcinogenesis

Lung cancer is the leading cause of cancer-related death across the globe. Despite the marked advances in detection and therapeutic approaches, management of lung cancer patients remains a major challenge to oncologists which can be mainly attributed to late stage diagnosis, tumor recurrence and chemoresistance. Therefore, to overthrow these limitations, there arises a vital need to develop effective biomarkers for the successful management of this aggressive cancer type. Notably, TNF-alpha induced protein 8 (TIPE), a nuclear factor-kappa B (NF-κB)-inducible, oncogenic molecule and cytoplasmic protein which is involved in the regulation of T lymphocyte-mediated immunity and different processes in tumor cells such as proliferation, cell death and evasion of growth suppressors, might serve as one such biomarker which would facilitate effective management of lung cancer. Expression studies revealed this protein to be significantly upregulated in different lung cancer types, pathological conditions, stages and grades of lung tumor compared to normal human lung tissues. In addition, knockout of TIPE led to the reduced proliferation, survival, invasion and migration of lung cancer cells. Furthermore, TIPE was found to function through modulation of Akt/mTOR/STAT-3 signaling cascade. This is the first report which shows the involvement of TIPE in tobacco induced lung carcinogenesis. It positively regulated nicotine, NNK, NNN, and BaP induced proliferation, survival and migration of lung cancer cells possibly via Akt/STAT-3 signaling. Thus, this protein possesses important role in the pathogenesis of lung tumor and hence it can be targeted for developing newer therapeutic interventions for the clinico-management of lung cancer.

Clinicopathological significance of Sox10 expression in triple-negative breast carcinoma.

BackgroundThis study aimed to investigate the SRY-related higll-mobility-group box 10 (Sox10) expression in the pathological diagnosis of triple-negative breast cancer (TNBC). Furthermore, its correlation with the clinicopathological characteristics and disease-free survival rate in patients with TNBC was also evaluated to identify the diagnostic utility of Sox10 as a reliable biomarker for the diagnosis and prognosis of TNBC.MethodsUsing immunohistochemistry (IHC), we identified the expression of Sox10, GATA binding protein 3 (GATA-3), forkhead box protein A1 (FOXA1), gross cystic disease fluid protein (GCDFP15), and mammaglobin (MGB) in 376 cases of primary invasive breast cancer, and 77 cases of metastatic breast cancer. The expression of Sox10 in different molecular subtypes of primary invasive breast cancer and metastatic breast cancer were also compared. Furthermore, the correlation between Sox10 expression and clinicopathological parameters and disease-free survival (DFS) of patients with primary TNBC were also analyzed.ResultsExpression of Sox10 was only detected in the myoepithelial cells of normal breast tissue, but not in any other types of cells, including luminal cells and fibroblasts. The positive rate of Sox10 in primary and metastatic TNBC was significantly higher than that in luminal types and human epidermal growth factor receptor 2 (HER2) overexpressed type. The sensitivity and specificity of Sox10 expression in primary TNBC and metastatic TNBC were significantly lower than GATA-3, significantly higher than FOXA1, GCDFP15, and MGB (P<0.001, P=0.0004, P=0.0064, P=0.0229, respectively). In 71 cases of primary TNBC, a higher expression rate of Sox10 was significantly associated with high-grade tumors, late-stage tumors, and tumors with involvement of four or more lymph node metastases (P=0.0145, P=0.0105, P=0.0249, respectively).ConclusionsSox10 may be used as a novel reliable putative marker for the diagnosis of TNBC. Notably, Sox10 combined with GATA-3 expression may serve as a supplementary differential diagnostic biomarker for primary and metastatic TNBC. Besides, Sox10 may be a good predictor of the prognosis of primary and metastatic TNBC. This study also highlights the significance of targeting Sox10 as a promising potential therapeutic target gene for TNBC therapy.

1924P Diagnostic demographics of radioiodine-refractory differentiated thyroid cancer (RR-DTC) and usage patterns of local and systemic therapies (ERUDIT study)

Advanced differentiated thyroid carcinoma (aDTC), herein defined as locally unresectable or metastatic disease, frequently develops into RR-DTC, one of the most common late-stage endocrine tumours. However, available data about its evolution is limited. ERUDIT is a multicentre, observational, retrospective study of patients diagnosed with aDTC in Spain and Portugal. The study describes its natural history from the initial diagnosis until the advanced stages of disease. This communication is focused on the RR-DTC subpopulation, its diagnosis, treatment patterns, and specialties involved in its management. Clinical records from patients ≥18 y-o diagnosed with aDTC (including poorly differentiated DTC) with first evidence of advanced disease documented between January 2007 and August 2017 were retrospectively reviewed until death or lost to follow-up. 213 patients were identified in 23 centres. Median age at initial diagnosis was 63 y-o, 59% were females. aDTC presented de novo in 54% of the cases. In all, 77.5% were initially diagnosed or developed into RR-DTC along study follow-up. Median (Q1-Q3) time to RR-DTC from first radioiodine dose was 27.6 (9.5-50.6) months. Computed (CT) and fluorodeoxygucose positron emission tomography (FDG PET-CT) were the most used methods to follow refractory disease (41% and 27%, respectively). Management was multimodal, with surgery (15%), watchful waiting (48%), locoregional (35%), and systemic therapies (ST) (37%) being used. Median (Q1-Q3) time from RR-DTC diagnosis to start of ST was 8.9 (1.4-34.7) months, while median overall survival (95%CI) reached 4.7 (3.4-8.0) years in this subpopulation. Endocrinology (59%) and Oncology (33%) were the leading medical specialties responsible for patient monitoring, while two thirds of the patients were evaluated by multidisciplinary committees. Most of aDTC tumours either present or become RR-DTC in around 2.3 years and are treated multidisciplinarily. Survival expectancy of this group nears 5 years, confirming an unfavourable evolution of most aDTC at their late treatment stages.

Abstract 5585: RealTVac - a novel strategy to treat advanced, late-stage tumors with real-time tumor vaccination

Abstract Novel anti-cancer immune therapeutic strategies, like various new antibody formats and/or tumor vaccines, show promising results in patients. However, due to the “immune-escape phenomenon” driven by tumor-secreted Transforming Growth Factor-beta (TGF-beta), the host immune system of cancer bearing patients frequently fails to control tumor re-growth. Real-Time Tumor Vaccincation (RealTVac) approach aims at avoiding this “immune-escape phenomenon” by intratumoral inhibition of active TGF-beta isotypes while simultanously and synergistically inducing an efficient immune response by a highly potent combination of immune stimulating factors. The synergistic effects of the proposed combination of a TGF-beta inhibitor with immunostimulating cytokines upon human immune cell activation are demonstrated in in-vitro experiments. Both, immune cell proliferation and tumor cell cytotoxicity were significantly enhanced. Initial experiments in a syngenic B16 melanoma xenograft model in immunocompetent mice indicate that Real-Time Tumor Vaccination of established subcutaneous B16 tumor xenografts reduced local tumor growth compared to untreated controls. To summarize, the goal of the local application of RealTVac is to allow the host immune system to scan in real-time all Tumor Associated Antigens (TAAs) being currently expressed by those tumor cells that are exposed to sufficient TGF-beta inhibition. The repetitive administration of the RealTVac approach is furthermore expected to provide a continuous update of the immune response, reflecting the changing pattern of currently expressed TAAs related to the dynamic intratumoral heterogeneity in malignant tumors. Thus, intratumoral immunization as applied for RealTVac may create a new paradigm for cancer therapy in the future. Citation Format: Piotr Jachimczak, Andreas Mitsch, Achim Aigner. RealTVac - a novel strategy to treat advanced, late-stage tumors with real-time tumor vaccination [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5585.

Abstract CT153: SDX-7320 elicits improvements in tumor-related and metabolic biomarkers: Results of a phase 1 dose-escalation study in patients with advanced refractory or late-stage solid tumors

Abstract Background and Rationale: Metabo-oncology is the study of specific tumor types whose growth and/or metastasis is accelerated by metabolic dysfunction, often associated with hyper-adiposity. In this setting the metabolic hormones leptin, adiponectin and insulin are potential mediators. SDX-7320 is a novel methionine aminopeptidase type 2 inhibitor (MetAP2) being developed for use in combination with other anti-cancer agents to treat the metabo-oncology patient population. Study Design: This first-in-human study used a 3+3 design with dose expansion at the RP2D. Measurements included standard assessments of safety, tolerability, as well as inhibition of MetAP2 in whole blood, plasma levels of protein biomarkers and drug exposure. Tumor response was measured using RECIST v.1.1. Results: 32 patients with an average of 5.3 prior treatment regimens were dosed. Sub-cutaneous dosing of SDX-7320 began at 1.7 mg/m2 once per week (Q7D, 28 days/cycle) and was escalated to 49 mg/m2. Repeated Q7D administration at 49 mg/m2 resulted in dose-limiting (G3-G4) thrombocytopenia. Expansion at 49 mg/m2 confirmed thrombocytopenia as the dose-limiting toxicity (DLT), reversible upon cessation of dosing. Dose-escalation was re-initiated at 36 mg/m2 every two weeks (Q14D). Repeated dosing at 65 mg/m2 (Q14D) resulted in G3 reversible thrombocytopenia. Expansion at 49 mg/m2 (Q14D) confirmed that this was the maximum tolerated dose (MTD) on a Q14D schedule. No deaths or Grade 5 TEAEs attributable to SDX-7320 were reported. Six patients had a combined total of 9 Grade 3/4 TEAEs considered by the Investigator to be at least possibly SDX-7320-related: thrombocytopenia (4 patients) and single cases of anemia, anorexia, fatigue, QTc prolonged, and vasculitis. Fourteen patients (44% had stable disease &amp;gt2 cycles and three patients had stable disease for ≥6 cycles. Inhibition of MetAP2 in whole blood was 100% at all doses evaluated while the time to reach 100% inhibition was inversely related to dose. When stratified for elevated baseline levels, the following biomarkers declined after initiating SDX-7320 (average of each patient's maximum % change relative to baseline +/- SD): bFGF (-53 +/- 76%), VEGF-C (-35 +/- 39%), and insulin (-55 +/- 30%). Without stratification, leptin levels declined (-51 +/-29%) and levels of adiponectin increased after SDX-7320 (+74 +/- 63% relative to baseline). Conclusions and Next Steps : SDX-7320 was well-tolerated with prolonged stable disease in an open-label, phase I first-in-human study. Improvements were observed in both tumor-related and metabolic biomarkers. Additional studies of SDX-7320 (in combination with other anti-cancer agents) in patients with solid tumors sensitive to metabolic hormones are scheduled. SDX-7320 is the first novel agent in clinical development to treat the metabo-oncology patient population. Citation Format: Monica M. Mita, Johanna Bendell, Alain C. Mita, Michael Gordon, Jasgit Sachdev, Bradley J. Carver, James Shanahan, Benjamin Mayes, Kris Awerkamp, David Browning, Neal Salomon, Kimberly Sullivan, Alfred Anderson-Villaluz, Joe Johnson, John S. Petersen, David J. Turnquist, Peter Cornelius. SDX-7320 elicits improvements in tumor-related and metabolic biomarkers: Results of a phase 1 dose-escalation study in patients with advanced refractory or late-stage solid tumors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr CT153.

Abstract 829: Global tumor transcriptional activity reveals aggressiveness across multiple cancers

Abstract Background: At present, conventional clinical and histopathological evaluations are not sufficient to distinguish biologically indolent cancers from those that will exhibit aggressive behavior. We hypothesize that global transcriptomic activity of tumor cells reflects the end cumulative result of somatic, germline, and epigenetic alterations, as well as additional transcriptional regulatory events. Therefore, it may be more directly associated with clinical outcomes. However, the total number of mRNA molecules is not directly measurable, either in bulk or single-cell RNA sequencing data. To this end, we develop a novel metric: the transcriptional activity score (TAS), to measure the relative global tumor-cell specific transcriptional activity in heterogeneous tumor samples. Materials and Methods: We propose TAS as the ratio of average total transcript proportion over the count proportion of tumor cells versus surrounding non-tumor cells. The transcript proportions are estimated using RNAseq deconvolution method DeMixT and the count proportions are estimated using DNAseq deconvolution methods such as ASCAT and ABSOLUTE. Using matching bulk RNA and DNA sequencing data from the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), we calculated TAS for a total of 5,031 patient samples across 15 cancer types. For validation, we obtained TAS for two genomic studies: 1) from patients with early-onset prostate cancer (n=99) as part of the ICGC, and 2) from patients with localized prostate cancer as part of the Canadian Prostate Cancer Genome Network (CPC-GENE, n=144). Results: We found that higher TAS corresponds to a more aggressive state of cancer, as characterized by MYC dysregulation, genome instability, known marker genes, and molecular subtypes. By examining the association between TAS and survival outcomes across cancer types, we also found that TAS refines the prognostic ability of pathologic stage, identifying aggressive early-stage tumors associated with poor survival as well as late-stage tumors with favorable outcomes. In prostate cancer, TAS is linearly associated with progression-free probabilities, useful to rank patients within the median risk group (Gleason score = 7). This added prediction power is consistent in TCGA and two independent validation data (ICGC and CPC-GENE). Conclusion: We have developed a new summary metric using matched DNA and RNA sequencing data from tumor samples, to compute, in vivo and using deconvolution, the relative global gene expression level of tumor cells. The TAS metric evaluates global transcriptional activity, an intrinsic behavior of cells that is well-known, but now for the first time is shown through TAS to be associated with prognosis. TAS may serve as a tractable phenotype to help elucidate the biology that underlies metastasis, prognosis and response to treatment in cancer patients. Citation Format: Shaolong Cao, Jennifer R. Wang, Jonas Demeulemeester, Jingxiao Chen, Kaixian Yu, Peng Yang, Bora Lim, Alfonso Urbanucci, Peter Campbell, Hongtu Zhu, Peter Van loo, Wenyi Wang. Global tumor transcriptional activity reveals aggressiveness across multiple cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 829.

Abstract 5463: Accuracy improvements in somatic whole-genome small-variant calling with the DRAGEN platform

Abstract Introduction: Next-generation whole-genome sequencing promises to enable dramatic expansion of precision oncology and personalized cancer care. To support this effort, it is critical to develop computational tools that can analyze sequence data accurately and with rapid turn-around-time. One particularly challenging problem is the calling of somatic variants in matched tumor and normal samples. We present the DRAGENTM 3.5 somatic pipeline that performs 110x/40x whole-genome end-to-end analysis in under two hours with accuracy superior to that of all other tools we have benchmarked, including Mutect2/GATK4 and Strelka2. In addition, DRAGEN 3.5 is robust against variations in coverage, sequencing platform, sample preparation chemistry, and tumor purity. It also tolerates tumor-in-normal contamination, thereby making the pipeline applicable to late-stage solid tumors or hematological cancers. Methods: DRAGEN 3.5 replaces the legacy genotyping model (originally developed as part of MuTect2) with that of Strelka2. Whereas the MuTect2 model performs separate analyses on the tumor and normal samples, the Strelka2 model performs a joint analysis, allowing (1) detection of systematic errors that affect both samples simultaneously and (2) modeling of tumor-in-normal contamination, where the amount of contamination in the normal sample depends on the allele frequency observed in the tumor sample at the locus in question. In addition, we improved the probabilistic model of systematic error by incorporating models of strand bias and mismapping. Results: We benchmarked DRAGEN against Mutect2 (included in GATK 4.1.2) and Strelka2 (version 2.9.9) on five public synthetic and real datasets with known truth sets. DRAGEN greatly outperformed the other methods on all five datasets, producing 14-67% and 22-91% fewer false SNV calls, and 35-86% and 48-89% fewer false indel calls than Strelka2 and Mutect2 respectively. DRAGEN also exhibits higher tolerance to tumor-in-normal (TiN) contamination than Strelka2 which is already equipped with a model tolerating TiN contamination. The average end-to-end workflow runtime of the DRAGEN somatic pipeline was 77 minutes, 75% and 830% faster than Strelka2 and Mutect2 taking DRAGEN alignments as input. Conclusion: The DRAGEN pipeline enables reliable whole-genome analysis that can be scaled to large numbers of samples, leading to better tumor characterization and improved interpretation. We anticipate that it will ultimately fuel progress in oncology, cancer research and precision medicine. The DRAGEN 3.5 somatic pipeline can be run either locally on a DRAGEN server or remotely in the cloud via https://basespace.illumina.com. Citation Format: Konrad Scheffler, Sangtae Kim, Varun Jain, Jeffrey Yuan, Westley Sherman, Taylor O'Connell, Eric Ojard, Lisa Murray, Rami Mehio, Severine Catreux. Accuracy improvements in somatic whole-genome small-variant calling with the DRAGEN platform [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5463.

Abstract 5233: Towards patient-centric drug discovery: Analyzing drug action in malignant pleural effusions and ascites using high content imaging and deep learning

Abstract Introduction: A vast majority of investigational anticancer drugs found to be active in preclinical development later do not show the desired effect in the clinic (Wong et al., Biostatistics 2019). This suggests that currently used preclinical models do not fully recapitulate the complexity of the human disease. The study of drug activity in primary human tissue samples, by contrast, could provide a more immediate picture of the activity of a molecule's effect in a patient. Factors that have so far hampered the use of primary tissue samples for drug discovery and development include access in sufficient quantity as well as robust analytical methods. We hypothesised that malignant pleural effusions and ascites (MPAs) of solid tumour patients are a promising model system to study drug activity in a preclinical setting. They are easily accessible in large quantities and contain cancer cells as well as major recruited immune populations. The latter could render them interesting model systems for studying I/O drug activity. Following previous successes in studying drug action in primary human tissues of haematological cancer patients with automated microscopy (Snijder et al 2017, Lancet Haem, NCT03096821) we here describe advances in using high content imaging and deep learning-based image analysis to study drug action in MPAs of solid tumour patients. Methods: MPAs from patients with metastatic breast, pancreatic, lung and ovarian cancer (at least n=10 of each) were collected under appropriate ethics approval. The response of EpCam+/CD45− and CD45+ cells against small molecule drugs was evaluated using high content microscopy. Drug response was quantified with single cell resolution using regional convolutional neural networks (R-CNNs) comprising an object detection and a single cell classification stage. EpCam+ and live/dead cell classification accuracies on the validation set were &amp;gt;94%. Results: MPAs contain both cancer cells (range: 1-37%) and recruited myeloid and lymphoid immune populations with varying activation states (e.g. CD69+/PD-1+ CD8+ T-cells). Ex vivo drug responses from each patient sample were measured and combined to form an overall map of drug susceptibility across the patient population, pan-indication. Sensitivity mirrors drug approvals and also reveals drugs with potential off label use. Conclusions: Single-cell phenotypic analysis of MPAs enables the study of anticancer drug action in a setting that is one step closer to the clinic than cell line or outgrown organoid models of solid tumor. While initial response patterns can be observed that mirror current approvals, further biological and clinical validation must occur to understand in how far these data can be used for drug discovery and translational research purposes. Application as a functional tool for selecting salvage therapies for late-stage solid tumor patients (“functional prevision medicine”) can also be envisioned. Citation Format: Robert Sehlke, Christina Taubert, Isabella Alt, Florian Rohrer, Elisabeth Fuchs, Bojan Vilagos, Nikolaus Krall, Minichsdorfer Christoph, Michael Schumacher, Dominik Maurer, Klaus Hackner, Judith Lafleur, Lukas Hefler, Thorsten Fureder, Gregory Ian Vladimer. Towards patient-centric drug discovery: Analyzing drug action in malignant pleural effusions and ascites using high content imaging and deep learning [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5233.

Abstract 2485: RNA editing by APOBEC3s in lung cancer tumors largely occurs in infiltrating immune cells

Abstract Introduction: APOBEC3 enzymes contribute significantly to DNA mutagenesis in cancer. Our recent studies show that these enzymes are also capable of converting C bases at specific positions (sites) of RNAs to U. By examining primary non-small cell lung cancer (NSCLC) tumors of The Cancer Genome Atlas (TCGA) project, we have demonstrated that such APOBEC3-mediated C-to-U RNA editing occurs in lung cancer tumors. While we could detect editing events in the tumors, their cellular origin remains unclear. Here, we investigated if the editing occurs in cancerous or stromal cells of lung cancer tumors. Methods: Immune-related features of the TCGA lung cancer tumors (n = 1,009) were obtained from various TCGA studies to examine their association with APOBEC3-mediated RNA editing that we had determined previously. Freshly resected late-stage NSCLC tumors of five patients were mechanically and enzymatically dissociated into single cells using a cocktail of collagenase, elastase, and DNAse enzymes. Antibodies conjugated to magnetic beads were then used to isolate cancerous epithelial (EpCAM+) and stromal pan-immune (EpCAM-/CD45+) and macrophage/monocyte (EpCAM-/CD14+) subsets of cells from the single-cell suspensions. RNA (depleted of rRNA) and genomic DNA of the cell isolations were subjected to total RNA and whole exome sequencing. Sequencing data was examined to identify C-to-U RNA editing at 5,208 known APOBEC3-mediated editing sites. Results: TCGA lung tumors with higher RNA editing levels had stronger tumoral immune response. Particularly, they had about 25% more infiltrating leukocytes, CD8 T cell fraction, and immune cytolytic activity compared to tumors with low editing level (P &amp;lt; 0.01 in all t tests). As expected, expression of genes that are markers of epithelial (such as EPCAM and MUC1), pan-immune (CD45, ITGAL), and macrophage/monocyte (CD14, FCGR3A) cells were dramatically higher among the corresponding cell subsets that were isolated from lung tumors. Whereas expression of APOBEC3B and F were similar among the three subsets, the expression of APOBEC3A, C, D, G and H were 2-4-fold higher in pan-immune and macrophage/monocyte compared to epithelial cells. Concordantly, while editing events were seen in the epithelial cells at average 7% of examined sites, editing was more frequent in the pan-immune and macrophage/monocyte cells (17% and 22%, respectively). Conclusions: RNA editing by APOBEC3s reflects a heightened immune response in lung cancer. A large proportion of RNA editing by APOBEC3s in tumors occurs in immune cells such as macrophages. Further investigations are needed to understand RNA editing in various other immune cells, as well as the relevance of RNA editing of specific genes in cancer and immune cell biology. Citation Format: Mariko Asaoka, Eric Kannisto, Takashi Ishikawa, Sai Yendamuri, Santosh Kumar Patnaik. RNA editing by APOBEC3s in lung cancer tumors largely occurs in infiltrating immune cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2485.

Abstract 5999: The Warburg Effect suggests a palliative care approach to cancer therapy

Abstract Introduction: Otto Warburg discovered in 1924 that cancer cells needed a lot more glucose than normal cells. Today, the “Warburg Effect” is not only recognized as a “hallmark of cancer” but also served as the scientific basis for cancer detection using fluorodeoxyglucose (FDG) Positron emission tomography (PET-scans). Warburg suggested in 1927 that treating cancer patients with insulin can deprive glucose to the cancer cells by lowering the blood glucose levels and may inhibit tumor growth. Although at least six peer-reviewed publications so far have provided support for the feasibility of this approach, no clinical trial has ever been done. We have previously presented an analysis of the data from hospitals in China suggesting that insulin can be safely administered for patients receiving a small dosage of standard chemotherapy drugs as palliative treatments for late-stage cancer patients. Here, we report additional data from more patients and medical facilities. Experimental procedures: Patients diagnosed with multiple types of late-stage solid tumors were treated with regular insulin (Humulin R) administered intravenously, and small doses of standard chemotherapy drugs (approximately 10% of the standard dosages). Blood glucose levels were monitored throughout the course of treatment. Hypoglycemia was reversed by ingestion of food and drink or injection of glucose solution. Depending on how well the patients tolerated the treatments, 5-30 units of insulin were used. No permanent side effects were observed or reported. Summary of data: Over 400 treatments have been performed on over 30 patients ranging from 30 to 76 years old, and diagnosed with 14 types of cancer. The average age of the patients was 56.2 years old. Symptoms of hypoglycemia were observed in all 30+ patients, and readily reversed by intravenous infusions of glucose or ingestion of food and drink. The insulin treatments were well tolerated and no longer -term side effects were observed. Conclusions: Our analysis supports the feasibility of using regular insulin as a reproducibly safe method to achieve glucose deprivation in patients with advanced stages of multiple types of cancer receiving palliative and hospice care. These and additional future studies could form the basis for eventually conducting a clinical trial testing whether regular insulin, which is inexpensive and available over the counter, can be an alternative therapeutic option for palliative and hospice care in some patients. Citation Format: Linda C. Meade-Tollin, Tom C. Tsang. The Warburg Effect suggests a palliative care approach to cancer therapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5999.

Oral cancer: Clinicopathological features and associated risk factors in a high risk population presenting to a major tertiary care center in Pakistan.

Oral squamous cell carcinoma (OSCC) has the highest prevalence in head and neck cancers and is the first and second most common cancer in males and females of Pakistan respectively. Major risk factors include peculiar chewing habits like areca nut, betel quid, and tobacco. The majority of OSCC presents at an advanced stage with poor prognosis. On the face of such a high burden of this preventable cancer, there is a relative lack of recent robust data and its association with known risk factors from Pakistan. The aim of this study was to identify the socioeconomic factors and clinicopathological features that may contribute to the development of OSCC. A total of 186 patients diagnosed and treated at a tertiary care hospital, Karachi Pakistan were recruited. Clinicopathological and socioeconomic information was obtained on a structured questionnaire. Descriptive analysis was done for demographics and socioeconomic status (SES) while regression analysis was performed to evaluate the association between SES and chewing habits, tumor site, and tumor stage. The majority of patients were males and the mean age of OSCC patients was 47.62±12.18 years. Most of the patients belonged to low SES (68.3%) and 77.4% were habitual of chewing. Gender (male) and SES were significantly associated with chewing habits (p<0.05). Odds of developing buccal mucosa tumors in chewers (of any type of substance) and gutka users were 2 and 4 times higher than non-chewers respectively. Middle age, chewing habits, and occupation were significantly associated with late stage presentation of OSCC (p<0.05). In conclusion, male patients belonging to low SES in their forties who had chewing habits for years constituted the bulk of OSCC. Buccal mucosa was the most common site in chewers and the majority presented with late stage tumors.