bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4266: Proteomics for precision oncology: Profiling the proteome of matching tumor and adjacent normal tissue using data-independent acquisition
Authors: Vowinckel Jakob , Novy Karel , Corwin Thomas , Treiber Tobias , Bruderer Roland , Reiter Lukas , von Leitner Eike , Rinner Oliver , Escher Claudia
Published: September 2020

Precision oncology requires a deep understanding of the molecular mechanism in cancer biology. The predominant approach today focuses on genome structure and gene expression data, which have become available with the rise of next-gen sequencing technology. On a phenotypic level, however, protein expression and activation are arguably more directly related to cellular function. The availability of combined genome and proteome level data from the same tumor is therefore expected to provide a much more complete picture of a tumor in a particular state. Until recently, proteomics technology could not match the scale of next-gen sequencing and consequently, precision medicine research has almost exclusively been based on gene-level data. Here we show the first truly large-scale data set for protein expression and protein phosphorylation for a large collection of biospecimens derived from the IndivuType cohort of Indivumed, Germany. Matching fresh-frozen tumor and adjacent normal tissue samples from thousands of patients including various cancer entities were obtained from Indivumed's network of partner hospitals Enabled by the novel data-independent acquisition (DIA) workflow, a mass spectrometric method that obtains peptide fragmentation data in a highly parallelized way with high reproducibility and sensitivity, more than 7,000 proteins in the whole proteome (WP) and 20,000 phospho-peptides in the phospho-proteome (PP) workflow were analyzed. Sample processing from 5 mg of tissue per sample was performed on 96-well plates with the help of a liquid handling robot. Phospho-peptide enrichment was carried out using a Kingfisher Flex device and MagReSyn Ti-IMAC magnetic beads (ReSyn Biosciences). Data-independent acquisition (DIA) LC-MS/MS was performed on multiple platforms consisting of a Thermo Scientific Q Exactive HF-X mass spectrometer coupled to a Waters M-Class LC. Chromatography was operating at 5 µL/min, and separation was achieved using 45 min (WP) and 60 min (PP) gradients. With a throughput of 850 WP and 650 PP samples per month, thousands of samples were analyzed to date. The resulting proteome data is integrated into Indivumed's IndivuType multi-omics database, supporting the identification and validation of new molecular cancer drug targets and biomarkers.

Citation Format: Jakob Vowinckel, Karel Novy, Thomas Corwin, Tobias Treiber, Roland Bruderer, Lukas Reiter, Eike von Leitner, Oliver Rinner, Claudia Escher. Proteomics for precision oncology: Profiling the proteome of matching tumor and adjacent normal tissue using data-independent acquisition [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 4266.
Abstract 427: A mouse model for studying oncogenesis of HPV-associated oropharyngeal cancer
Authors: McGhee Eva , Lin Yi-Ling , Vadgama Jay , Lang Khadijah , Okoro Judith , Vidal Victoria , Long Naomi , Li Mengtao
Published: September 2020

The human papillomavirus (HPV) causes 70% of oropharyngeal cancers in the United States. While the molecular and cellular mechanisms and the stepwise progression of HPV-related cervical cancer have been well studied, oropharyngeal HPV carcinogenesis remains to be unraveled since an equivalent HPV premalignant stage has never been identified in clinical oropharyngeal tissues. In this study, a series of keratinocyte cell lines derived from the base of the tongue of C3H mice were established. These cells formed varying degrees of malignancy in the syngenetic mice and are used to study the biology of HPV-related oropharyngeal cancer in an immunocompetent host. Keratinocytes from the base of the tongue were isolated from C3H newborns and were subsequently retrovirally immortalized with TERT or HPV16 E6E7 oncoproteins, with or without oncogene H-ras. They are designated MOKT1 (TERT), MOKT1/H-ras (TERT/H-ras), MOKE2 (E6E7), or MOKE2/H-ras (E6E7/H-ras). These cells were injected in the masseter muscle of syngeneic mice and the developing lesions were harvested for histological analysis over a time course of 1 month. E6E7 transformed MOKE2 cells exhibited features of HPV associated cancer cells. We found that p63 and phosphorylated STAT3 were upregulated in MOKE2 cells in comparison to MOKT1 cells. MOKE2 cells obtained growth advantages with increased cell proliferation and decreased apoptosis. In addition, MOKE2 cells showed increased cell migration activity in wound healing assays. While all cell lines grew indefinitely in vitro, MOKT1 and MOKT1/H-ras failed to show any sign of malignancy when implanted in vivo. MOKE2 demonstrated features of malignancy, but the phenotype was transient. Host immunity does not appear to be the determining factor for suppressing tumor growth as MOKE2 regressing also occurred when implanted in immunodeficient NSG mice. Only MOKE2/H-ras cells were capable of progressing and establishing permanent cancer. Ourdata suggest that differentiation induced cell growth arrest may contribute to tumor regression and a second hit is required to overcome such arrest. The MOKE2 cells can be used in syngeneic mice to study secondary oncogenic factors in the development of HPV-related oropharyngeal cancer.

Citation Format: Eva McGhee, Yi-Ling Lin, Jay Vadgama, Khadijah Lang, Judith Okoro, Victoria Vidal, Naomi Long, Mengtao Li. A mouse model for studying oncogenesis of HPV-associated oropharyngeal cancer [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 427.
Abstract 4304: Radio-chemotherapy efficacy is predicted by intra-tumor CD8+FoxP3+ double positive T cell density in locally advanced non-small cell lung carcinoma
Authors: Velut Yoan , Boulle Geoffroy , Lupo Audrey Mansuet , Gibault Laure , Blons Hélène , Tredaniel Jean , Fournel Ludovic , Boni Aurélie , Cremer Isabelle , Wislez Marie , Duchatelle Veronique , Hammond Scott , Alifano Marco , Giraud Philippe , Damotte Diane
Published: September 2020

Background: radiotherapy is a standard of care for locally advanced stage III (N2) non-small cell lung cancer (NSCLC) combined with surgery and/or chemotherapy. Radiotherapy is hypothesized to induce intra-tumoral immune infiltration via neoantigen release from dying tumor cells sometimes resulting in an abscopal effect. However, intra-tumoral immune cell characteristics that predict radiotherapy efficacy have not been identified.

Patients and Methods: we retrospectively analyzed tumor samples and clinical data from 113 patients, 89 resected) and 24 non-resected stage III (N2) NSCLC treated within the same radiotherapy department (2002 to 2015). We performed multiplex staining (CD8, FoxP3, PD-L1, pan-keratin) in order to correlate immune environment (density and location) to overall survival (OS) and disease free survival (DFS).

Results: high density of CD8+ T cells was associated with DFS (p=0.0036, HR=2.42 [1.31 - 4.47]) and OS (p=0.049, HR=1.93 [0.99 - 3.78]) in resected group only. High density of CD8+/FoxP3+ double positive T cells was associated with OS (p=0.017, HR= 1.97 [1.11 - 3.48]) in the global population; and in resected group for OS (p=0.05, HR=1.92 [0.98 - 3.74]) and PFS (p=0.03, HR=1.83 [1.03 - 3.23]), with a trend of significance for OS and PFS in the non-resected group (p=0.06, HR=2.84 [0.88 - 9.13] and p=0.05, HR=3.03 [0.91 - 10.10], respectively). Intermediate PD-L1 expression in tumor cells (TPS=1-49%) was associated with a higher survival in the resected group.

Conclusions: we demonstrated that intra-tumoral CD8+ T cell and particularly the CD8+/FoxP3+ cell density predict radiotherapy efficacy and survival in stage III N2 NSCLC. Thus, it suggests that radiotherapy rather improves than promotes tumor immunogenicity.

Citation Format: Yoan Velut, Geoffroy Boulle, Audrey Mansuet Lupo, Laure Gibault, Hélène Blons, Jean Tredaniel, Ludovic Fournel, Aurélie Boni, Isabelle Cremer, Marie Wislez, Veronique Duchatelle, Scott Hammond, Marco Alifano, Philippe Giraud, Diane Damotte. Radio-chemotherapy efficacy is predicted by intra-tumor CD8+FoxP3+ double positive T cell density in locally advanced non-small cell lung carcinoma [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 4304.
Abstract 4345: Environmental determinants for lung cancer mortality among Black men in Berrien County, Michigan: A Multi-media analysis
Authors: Uppala Padma P. Tadi , Wong Brian , Berman Laurel , Caudill Motria , Cadet Jean
Published: September 2020

Environmental risk factors such as air, water, soil pollution, chemical exposures, climate change, and radiation contribute to more than 100 diseases. Understanding the connection of the environment to health is a critical pathway to address health disparities and poor health outcomes in communities. Purpose: This study investigates environmental determinants for lung cancer mortality among Black men in Berrien County, Michigan. Methods: We examined environmental contaminants in the land, air, and water. Environmental data was obtained from toxic release Inventories (TRI) and brownfields from the US EPA's TRI databases, My Environment, Environmental justice SCREEN websites, ATSDR public health assessment information for contaminated sites in Berrien County and ATSDR Toxicological Profiles and ToxFAQs for common environmental contaminants and associated health concerns. We created GIS maps overlaid with all-cause mortality data. Using the TOXMAP database, we generated Environmental Health Toxmaps for cancer mortality in Berrien County and overlaid with TRI facilities. Results: Age-adjusted mortality among black males for all malignant cancers (208.90) and cancer of the lung and bronchus (110.70) were high compared to national data. An important observation from this analysis indicated that cancer of the lung and bronchus was 110.70 among black males and was 60.20 among white males in Benton Harbor. According to the overlaid GIS maps, zip codes surrounding the Benton harbor area seems to have the highest number of contaminated sites and high mortality rates. Benton Harbor in Berrien County had the second-highest level of summer Action Days (10 days) in the state. We reviewed the Action Days reported on the Michigan Department of Environmental Quality website (2019) and found that Benton Harbor typically was in the "top" tier for Action Days for several years. Although health disparities were observed among Black and White males for lung cancer, smoking rates were not elevated among black males as compared to the general population. In conclusion, we suggest that in addition to smoking, environmental, and socioeconomic factors may contribute to high lung cancer rates among Black men in Benton Harbor in Berrien County.

Citation Format: Padma P. Tadi Uppala, Brian Wong, Laurel Berman, Motria Caudill, Jean Cadet. Environmental determinants for lung cancer mortality among Black men in Berrien County, Michigan: A Multi-media analysis [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 4345.
Abstract 4349: Comparison of Psychosocial Wellbeing among African American and Caucasian Metastatic Cancer Survivors
Authors: Caffey Jayla M. , Bail Jennifer
Published: September 2020

Introduction:

Approximately 5 million Americans are living with metastatic cancer and are at an increased risk for psychosocial distress (e.g., hopelessness). Hope is vital to life and is essential for effectively coping with illness. Among early-stage cancer survivors, previous studies indicate that African Americans (AA) experience greater cancer burden than Caucasians (CAU). The aim of this study was to compare psychosocial wellbeing between AA and CAU MCS residing in the Deep South.

Methods:

MCS were identified via UAB Cancer Registry and I2B2.Using a modified Dilman's method, eligible MCS (>21 years and physician permission to contact) were mailed a survey. Psychosocial wellbeing (i.e. physical and mental wellbeing, anxiety, depression, social isolation, emotional support, and hopefulness) of MCS were assessed via PROMIS® measures. Returned surveys were double-key entered into REDCap®. Data were analyzed using Excel. Descriptive statistics were used to characterize the study sample and instrument scores. Between group difference, between AA and CAU MCS, was examined via independent-samples t-test.

Results:

To date, 100 surveys have been returned (AA=18; CAU=82; Mage=67 years; Msurvivorship=3 years) with a broad representation of primary cancer sites (breast=23%; prostate=10%; gynecological=16%; colorectal=13%; lung=10%; kidney=11%; other=17%). Mean instrument scores were similar between AA and CAU MCS for physical wellbeing (44.57 vs 44.81), mental wellbeing (48.1 vs 48.46), anxiety (45.76 vs 48.45), depression (44.85 vs 46.77), social isolation (39.96 vs 40.89), and emotional support (39.96 vs 40.89). However, AA MCS reported significantly better feelings of hopefulness than CAU MCS (61.34 vs 55.39, p>0.01, d=0.73).

Discussion:

Findings suggest that AA MCS may be more hopeful than CAU MCS. These preliminary findings warrant further analysis after data collection is complete (an additional 300 returned surveys are anticipated).

Citation Format: Jayla M. Caffey, Jennifer Bail. Comparison of Psychosocial Wellbeing among African American and Caucasian Metastatic Cancer Survivors [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 4349.
Abstract 4355: Different strategies for peritoneal lavage cytology testing in the staging of gastric cancer: A cost-effectiveness analysis
Authors: He Qifei , Zhu Jinyi , Wang Anqiang , Li Xia , Bu Zhaode , Ji Jiafu
Published: September 2020

Background & Aims: The positive peritoneal cytology (PCY) indicates metastasis disease in patients with gastric cancer (GC); thus, the cytology testing is directly related to subsequent treatments, patients' prognoses, and medical costs. However, the cost-effectiveness of PCY testing remains unclear. We aim to evaluate the cost-effectiveness of PCY testing by comparing two active testing strategies of a guideline-recommended intraoperative laparoscopic peritoneal lavage (ILPL) and a newly proposed preoperative percutaneous peritoneal lavage (PPPL), and a third strategy of exploratory laparotomy with no cytology testing (ELNC) among GC patients.

Methods: We developed a decision-analytic Markov model to compare the cost-effectiveness of the above three strategies for a hypothetical cohort of GC patients with curative intent after initial imaging, from the perspective of Chinese society. Quality-adjusted life-years (QALYs), transition probabilities and costs were modeled using data mainly from published literature. We performed base case analysis and measured incremental cost-effectiveness ratios (ICERs) for various strategies, which were compared to a willingness-to-pay (WTP) threshold that was set to a three-fold of Chinese gross domestic product (GDP) per capita, $29,313/QALY gained. Furthermore, we conducted both one-way and probabilistic sensitivity analyses to investigate the model's robustness.

Results: In the base case analysis, we found that ELNC was dominated (i.e., more expensive and less effective) by PPPL and ILPL. ILPL was the most cost-effective method, with an ICER of US $16,673/QALY compared to PPPL. One-way sensitivity analyses demonstrated that the exploratory laparotomy mortality following ILPL and the peritoneal cytology prevalence were the only two influential parameters within their plausible range when assessing the cost-effectiveness of PPPL and ILPL. In the probabilistic sensitivity analyses, the probability of ILPL being cost-effective was 71.3% at the WTP threshold of $29,313/QALY; however, PPPL was more likely to be cost-effective when the willing-to-pay (WTP) threshold was below $17,020/QALY gained.

Conclusion: Cytology testing for GC staging through either ILPL or PPPL dominated ELNC in patients with curative intent. Moreover, ILPL was the most cost-effective modality at the current WTP threshold, while PPPL could potentially be cost-effective in lower-income areas.

Citation Format: Qifei He, Jinyi Zhu, Anqiang Wang, Xia Li, Zhaode Bu, Jiafu Ji. Different strategies for peritoneal lavage cytology testing in the staging of gastric cancer: A cost-effectiveness analysis [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 4355.
Abstract 4362: Combination of conventional therapies and antiandrogenic treatments as a succesful tool for triple negative breast cancer (TNBC) treatment
Authors: Caceres Sara , Diez Angela Alonso , Silvan Gema , Illera Maria J. , Illera Juan C.
Published: September 2020

Triple negative breast cancer (TNBC) patients do not benefit from conventional hormonal therapies due to the loss of expression of ER, PR, and HER2. Therefore, the usual adjuvant treatments for breast cancer, are not applied to TNBC. Recently, it has been found that approximately one third of TNBC tumours express androgen receptor (AR) and it is associated with better response to endocrine therapies. However, the prognostic value of AR expression in TNBC is still unclear. Therefore, in this preliminary study we evaluate the effectiveness of an anti-androgen treatment (bicalutamide) respect to conventional treatments (doxorubicin and lapatinib) in TNBC human cell lines and their corresponding xenografts. Briefly, SUM149, SUM159 and MDAMB231 TNBC cell lines were cultured in supplemented medium. Cells were plated in 96-well plates and a serial dilution of Doxorubicin, Lapatinib, Bicatulamide and respective combinations were added. In addition, 106 cells were implanted subcutaneosly into five female mice (Balb/C SCID). When tumors developed, mice were treated with doxorubicin, bicalutamide, doxorubicin + bicalutamide and doxorubicin + bicalutamide + lapatinib. Every treatment was perfomed every 3 days during 15 days and tumor reduction and appearance of metastases were evaluated. Results from cell culture showed that neoplasic cells from each cell line were high sensitive to bicalutamide treatment (SUM149 EC50: 9,860e009; MDAMB231 EC50: 9,454e009; SUM159 EC50: 2,170e009). Also, viability decreased when we added an anti-androgen (bicalutamide) to the conventional treatments (doxorubicin + lapatinib). In vivo experiments revealed a greater percentage of tumour reduction (around 70%) in mice treated with combination of treatments and a lower appearance of metastasis was observed in this group respect to control group (SUM149: 40% vs 60%; MDA-MB-231: 20% vs 75%; SUM159: 20% vs 60%). Therefore, our preliminary findings suggest that the addition of an anti-androgenic agent to treatments currently in use can reduce the tumour considerably, defining anti-androgenic treatments as a novel effective therapeutic target.

Citation Format: Sara Caceres, Angela Alonso Diez, Gema Silvan, Maria J. Illera, Juan C. Illera. Combination of conventional therapies and antiandrogenic treatments as a succesful tool for triple negative breast cancer (TNBC) treatment [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 4362.
Abstract 440: Dual role of epithelial MyD88 inApc-mutant intestinal tumors
Authors: Kajino-Sakamoto Rie , Fujishita Teruaki , Taketo Makoto Mark , Aoki Masahiro
Published: September 2020

Mutational activation of the Wnt/β-catenin signaling plays essential roles in initiating the adenoma-carcinoma sequence for the majority of colorectal cancers (CRCs) as well as in maintaining the transformed phenotypes of progressed CRCs. However, the Wnt/β-catenin signaling itself is not easy to target for therapy. Here we addressed the roles of MyD88, a critical adaptor protein in the interleukin (IL)-1β and Toll-like receptor (TLR) pathways, in intestinal epithelial cells (IECs) during intestinal tumor formation in Apc+/Δ716 mice, a mouse model of familial adenomatous polyposis as well as the early-stage spontaneous colorectal cancer. Conditional knockout of MyD88 in IECs significantly reduced the number of intestinal tumors in Apc+/Δ716 mice. Although suppression of tumor formation in Apc mutant mice by IEC-specific knockout of MyD88 was previously reported by others, our mechanistic studies uncovered the downstream molecular pathways of MyD88 involved in tumor formation. (1) IEC-specific MyD88 loss induced inactivation of the JNK/mTORC1 signaling, a pathway we previously demonstrated to be essential in the growth of Apc+/Δ716 tumors, leading to decreased proliferation of tumor cells in vivo. (2) IEC-specific MyD88 loss reduced the level of NF-κB p65 and attenuated the Wnt/β-catenin signaling, leading to apoptosis of intestinal tumor cells in vivo. (3) Induction of MyD88 deletion in the intestinal tumor-derived organoids, but not in the normal IEC-derived organoids, caused apoptotic cell death and suppressed their growth in vitro. (4) Knockdown of MYD88 in colorectal cancer cell lines harboring mutations in the Wnt/β-catenin signaling reduced their proliferation and induced apoptosis. These results demonstrate a novel mechanism by which epithelial MyD88 contributes to intestinal tumorigenesis, and also suggest synthetic lethality between MyD88 deficiency and mutations in the Wnt/β-catenin signaling in CRCs.

Citation Format: Rie Kajino-Sakamoto, Teruaki Fujishita, Makoto Mark Taketo, Masahiro Aoki. Dual role of epithelial MyD88 inApc-mutant intestinal 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 440.
Abstract 4401: GABA system expression level changes persist across cancers of many organ systems
Authors: Knott Erika Lynn , Leidenheimer Nancy J.
Published: September 2020

The gamma-aminobutyric acid (GABA) system is evolutionarily conserved and, in mammals, is comprised of 30 genes encoding 4 enzymes, 21 receptor subunits, and 5 transporters. The GABA system has primarily been studied for its role in inhibitory neurotransmission in the brain; however, the physiological importance of this system in peripheral tissues is less well-recognized. Although a few GABA system components have been linked to cancer progression, this information is disparate, limited, and largely unsupervised. Here, we undertook a systematic bioinformatics investigation. To this end, we accessed RNA-seq / microarray transcript data and mass spectrometry / immunohistochemistry protein data from patient tumor datasets within The Cancer Genome Atlas (TCGA), NCBI's Gene Expression Omnibus (GEO), and the NCI's Clinical Proteomic Tumor Analysis Consortium (CPTAC). In order to visualize / analyze data, bioinformatics user-interface platforms were used, including cBioPortal, the Human Protein Atlas, UALCAN, and KM-Plotter. Kaplan-Meier survival curves, differential gene expression between tumor vs. normal samples (across cancer subtypes and stages), and targeted gene set enrichment / correlations were assessed. Several GABA system genes - such as ABAT, GABRP, and GABBR1 - were commonly altered across the >13 cancer types examined (including reproductive, digestive, and secretory and solid organ tumors). Unexpectedly, other transcripts such as ALDH5A1 were highly expressed across all cancers (RNA-seq log2 RSEM median value ~9). Based on Kaplan-Meier survival curve analysis, 11 GABA system genes were identified as prognostic markers for at least one type of cancer (log-rank P value < 0.001 when analyzed using optimized cutoff values; average FKPM > 1). Furthermore, 19 of the 30 investigated genes showed significant alterations in transcript levels between normal adjacent vs. tumor tissues (p < 0.05; minimum median expression = 1 TPM) in at least one cancer type. Interestingly, unique transcript expression patterns of GABA system genes were found among cancer subtypes, such as between triple-negative vs. ER+ breast cancers. Our efforts seek both to identify cancers that leverage the GABA system for their progression, and also to provide a basis for subsequent hypothesis-driven experimentation. Additionally, the data analyzed herein may reveal opportunities to repurpose drugs for cancer treatment, as there are a variety of GABA system-targeting therapeutic agents used to treat neurological and psychiatric disorders.

We thank the LSU Health School of Graduate Studies and Feist-Weiller Cancer Center for support.

Citation Format: Erika Lynn Knott, Nancy J. Leidenheimer. GABA system expression level changes persist across cancers of many organ systems [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 4401.
Abstract 4421: Development of a clinical-genomic database to study tumor evolution and molecular biomarkers of drug resistance in a real-world setting
Authors: Kumar Naveen , Kucharlapati Rajesh , Hardin Aaron , Raymond Victoria M. , Fairclough Stephen , Lang Kathryn
Published: September 2020

Background: Real-world evidence (RWE), specifically the integration of clinical and molecular data, plays an increasingly important role in elucidating the molecular landscape of advanced solid tumors, at diagnosis and at progression, and furthering precision oncology research. However, reliance on tissue genomic testing results within these RWE databases significantly limits our understanding of tumor evolution as tissue profiles are typically limited to a single time point, generally at diagnosis, and biopsies are not routinely completed at progression. Circulating tumor DNA (ctDNA) analysis at diagnosis and progression is an alternative to serial tissue testing. Studying the real-world data derived from ctDNA testing results can provide additional information, specifically around tumor evolution and mechanisms of innate and acquired resistance in response to intervening therapies (targeted and non-targeted).

Methods: Anonymized results from patients consecutively tested with Guardant360®, a CLIA-certified, CAP-accredited, NYSDOH-approved ctDNA test indicated for patients with advanced and metastatic solid tumor cancers (Guardant Health, Redwood City, California) were analyzed. Using a secure and HIPAA-compliant methodology, these results were then linked to a de-identified encounters database containing medical and pharmacy claims to provide a longitudinal view of patients' journeys, including diagnosis, treatments, and real-world outcomes.

Results: Of 85,874 patients, the disease groups most highly represented were lung, breast, colorectal, prostate, and pancreas cancers. 48,317 patients (56.3%) had a record of treatment with an antineoplastic treatment (i.e. chemo, hormonal, small molecule, or immuno-therapy). Of patients with a record of therapy, 14,608 (30.2%) had a record of therapy following, but none prior to, the Guardant360 test date, 14,493 (30.0%) had a record of therapy prior to, but not following theGuardant360 test date, and 19,216 (39.8%) had a record of therapy both before and after Guardant360 test date.

Conclusions: In a cohort of patients who underwent ctDNA testing and for whom treatment information was available, post-therapy molecular results were available in 69.8%. The availability of genomic information following systemic therapy suggest that this dataset is a viable resource to study drug resistance and tumor evolution in the real-world setting.

Citation Format: Naveen Kumar, Rajesh Kucharlapati, Aaron Hardin, Victoria M. Raymond, Stephen Fairclough, Kathryn Lang. Development of a clinical-genomic database to study tumor evolution and molecular biomarkers of drug resistance in a real-world setting [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 4421.
Abstract 4432: scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens
Authors: Yang Lin , Zhu Yuqing , Yu Hua , Cheng Xiaolong , Chen Sitong , Chu Yulan , Huang He , Zhang Jin , Li Wei
Published: September 2020

We present scMAGeCK, a computational framework to identify genomic elements associated with multiple expression-based phenotypes in CRISPR/Cas9 functional screening that uses single-cell RNA-seq as readout. scMAGeCK outperforms existing methods, identifies genes and enhancers with known and novel functions in cell proliferation, and enables an unbiased construction of genotype-phenotype network. Single-cell CRISPR screening on mouse embryonic stem cells identifies key genes associated with different pluripotency states. Applying scMAGeCK on multiple datasets, we identify key factors that improve the power of single-cell CRISPR screening. Collectively, scMAGeCK is a novel tool to study genotype-phenotype relationships at a single-cell level.

Citation Format: Lin Yang, Yuqing Zhu, Hua Yu, Xiaolong Cheng, Sitong Chen, Yulan Chu, He Huang, Jin Zhang, Wei Li. scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens [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 4432.
Abstract 4436: Combination therapy with an antibody specific for transferrin receptor 1 (ch128.1/IgG1) and bortezomib or lenalidomide results in increased survival in an in vivo model of human multiple myeloma
Authors: Candelaria Pierre V. , Nava Miguel , Martinez-Maza Otoniel , Daniels-Wells Tracy R. , Penichet Manuel L.
Published: September 2020

Multiple myeloma (MM) is a B-cell proliferative disorder of monoclonal malignant plasma cells. It is the second most common hematologic malignancy in the United States, after non-Hodgkin lymphoma (NHL). Clinical manifestations of MM include osteolytic bone lesions, hypercalcemia, renal failure, anemia, recurrent infections, and neuropathy. Standard treatments for MM include the proteasome inhibitor bortezomib, as well as lenalidomide, a thalidomide analog with immunomodulatory and antiangiogenic properties. Although the use of these two agents in combination with other therapies have significantly improved MM survival, the disease remains incurable. We previously developed a mouse/human chimeric antibody (ch128.1/IgG1) specific for human transferrin receptor 1 (TfR1). TfR1, also known as CD71, is a meaningful target for antibody-based cancer therapy, given its high expression on malignant cells and relevant role in cancer cell pathology. We have reported that treatment of SCID-Beige mice bearing disseminated human KMS-11, MM.1S, or MM.1R myeloma tumors with ch128.1/IgG1 results in significant antitumor activity in early and late disease stages. The mechanism of antitumor activity is Fc-mediated in which macrophages are considered to play a relevant role. Since combining multiple treatments with differing mechanisms of action is an effective antitumor strategy, and given the relevance of bortezomib and lenalidomide in MM therapy, we decided to explore, for the first time, the combination of these two agents with ch128.1/IgG1. We found that treatment with a single dose of ch128.1/IgG1, or multiple doses of bortezomib or lenalidomide used as single agents, results in significant antitumor activity in SCID-Beige mice bearing late stage disseminated human MM.1S tumors. However, this antitumor activity is superior when ch128.1/IgG1 was combined with bortezomib or lenalidomide, showing significantly longer survival compared to each therapy used alone. These results suggest that the addition of a ch128.1/IgG1 therapy arm in a combinatorial treatment regimen involving bortezomib and/or lenalidomide is a promising strategy against human B-cell malignancies such as MM.

Citation Format: Pierre V. Candelaria, Miguel Nava, Otoniel Martinez-Maza, Tracy R. Daniels-Wells, Manuel L. Penichet. Combination therapy with an antibody specific for transferrin receptor 1 (ch128.1/IgG1) and bortezomib or lenalidomide results in increased survival in an in vivo model of human multiple myeloma [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 4436.
Abstract 4451: Combination of local mRNA immunotherapy with systemic immune checkpoint blockade demonstrates anti-tumor activity across a diverse range of preclinical syngeneic tumor models
Authors: Malkova Natalia V. , Tolstykh Tatiana , Levit Mikhail , Theilhaber Joachim , Hebert Andrew , Atchison Kevin , Maisonet Adalis , Hotz Christian , Sahin Ugur , Protopopov Alexei , Pollard Jack , Sidhu Sukhvinder , Wiederschain Dmitri , Wagenaar Timothy R.
Published: September 2020

Cancer immunotherapies with anti-PD-1/PD-L1 checkpoint blockade antibodies have revolutionized the treatment of a wide variety of malignancies. However, immunotherapy is ineffective in a significant subset of patients, or eventually results in the development of resistance with relapsed disease. Therefore, the future of immuno-oncology is identification of new agents that can be combined to increase the depth and breadth of anti-PD-1/PD-L1 therapies. Local intratumoral delivery of messenger RNA (mRNA)-based immunotherapies provides an opportunity to stimulate innate and adaptive immune responses against tumors and modulate tumor microenvironment, while limiting the side-effects related to systemic administration of immuno-modulatory therapeutics. We examined the local immunotherapy of synthetic mRNAs encoding immunomodulatory cytokines (single chain interleukin-12 (IL-12), interferon alpha (IFN-α), granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-15 sushi(IL-15)) alone and in combination with anti-PD-1 antibodies across 12 syngeneic mouse tumor models representing a diverse range of murine tumor types. Single agent treatment with cytokine mRNAs resulted in a significant anti-tumor response in 8 out of 12 tumor models. Combining cytokine mRNA with systemic anti-PD-1 immunotherapy further improved the anti-tumor response and resulted in tumor growth inhibition in two additional models otherwise unresponsive to single agent treatments. Transcriptome and cytokine analyses have been performed to understand factors which determine sensitivity to single agent and combination treatments with cytokine mRNA and anti-PD-1 antibodies. In summary, the combination of local cytokine mRNA immunotherapy with immune checkpoint blockade demonstrated improvement in the anti-tumor activity in a range of preclinical cancer models representing different murine tumor types. Based on these and other data, clinical testing of cytokine encoding mRNA mixture has recently been initiated (NCT03871348).

Citation Format: Natalia V. Malkova, Tatiana Tolstykh, Mikhail Levit, Joachim Theilhaber, Andrew Hebert, Kevin Atchison, Adalis Maisonet, Christian Hotz, Ugur Sahin, Alexei Protopopov, Jack Pollard, Sukhvinder Sidhu, Dmitri Wiederschain, Timothy R. Wagenaar. Combination of local mRNA immunotherapy with systemic immune checkpoint blockade demonstrates anti-tumor activity across a diverse range of preclinical syngeneic tumor models [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 4451.
Abstract 4474: A quantitative flow cytometry method for the measurement of HLA-DR expression level on monocyte subsets
Authors: Huang Wei
Published: September 2020

There is growing evidence that solid tumor cancer is often associated with a systemic immunosuppressive environment which correlates with poor responses to immunotherapy. The frequency of CD14+HLA-DRlo/neg monocytes, also called monocytic myeloid derived suppressor cells (M-MDSCs), is often used as a flow cytometry based biomarker for the measurement of the level of immunosuppression in cancer immunotherapy research. While this approach has been demonstrated to work in clinical investigation studies with well-controlled cytometer settings and analysis methods, it is difficult to produce consistent results and compare measurements from different laboratories due to lack of standardization. The BD Horizon™ Dri Monoset panel is designed to measure the absolute counts and relative frequency of classical, intermediate and nonclassical monocyte subsets for research use. The assay uses whole blood samples analyzed by flow cytometry using a consensus reagent panel and gating strategy published by an international organization. When used in combination with BD Quantibrite™ beads, the level of HLA-DR expression on each subset of monocytes can be quantified in antibody bound per cell (ABC) units independent of the cytometer used to perform the assay. Evaluating 10 normal blood donor samples, our data demonstrates using the BD Horizon™ Dri Monoset panel in combination with BD Quantibrite beads, quantification of HLA-DR expression level on monocyte subsets provides consistent flow cytometry results.

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Citation Format: Wei Huang. A quantitative flow cytometry method for the measurement of HLA-DR expression level on monocyte subsets [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 4474.
Abstract 4475: Site-specific profiling of TCR signaling
Authors: Phyo Zaw , Verma Rohan , Ho Won J. , Jaffee Elizabeth M.
Published: September 2020

Background: T cell exhaustion is a hyporesponsive state commonly found in cancer and is characterized by overexpression of inhibitory receptors and secretion of immunosuppressive cytokines. Immune checkpoint inhibitors (ICIs) target inhibitory receptors such as PD-1 and CTLA-4 to reinvigorate exhausted T cells and promote anti-tumor responses. While ICIs have improved clinical outcomes, no biomarker to date reliably determines the extent of T cell exhaustion. Since robust T cell receptor (TCR) signaling is critical for effective antitumor immunity, we hypothesized that interrogating the phospho-signaling states within the T cells along with their functional states will enhance our understanding of T cell exhaustion and yield potential biomarkers.

Methods: In this study, we developed a validated mass cytometry panel of 24 markers to quantify phosphorylation states of 8 intracellular kinases involved in the TCR signaling within multiple CD8+ T cell subtypes. To identify potential differences between the local and peripheral immunological responses, we profiled CD8+ T cells derived from four sites (tumor, tumor draining lymph node, spleen and peripheral blood) in mice bearing MC38-induced flank tumors. We performed a clustering analysis of the dataset in aggregate using FlowSOM and visualized the results with UMAP, a dimensionality reduction algorithm, to compare the phospho-profiles of CD8+ T cell subtypes in all four sites.

Results: Bulk analysis of CD8+ T cells demonstrates site-specific concordance between phosphoprotein markers and T cell functional markers (i.e. Ki67 and Granzyme B) with the highest expression in tumor followed by tumor draining lymph node, spleen and peripheral blood. Based on the results from the clustering analysis, site-specific breakdown of CD8+ T cells revealed high prevalence of effector, memory, and exhausted memory T cells in tumors compared to other sites where naïve T cells predominated. Despite these variations in CD8+ T cell immunophenotypic distribution, TCR signaling profiles correlated strongly with specific T cell subtypes across all sites.

Conclusion: These data demonstrate that subtype-specific TCR signaling is preserved systemically and that phospho-immune subtyping of CD8+ T cells in the peripheral blood may be used to identify T cell exhaustion states that are found in the tumor microenvironment. Further studies will be conducted to investigate the changes in the TCR phospho-profiles in response to ICI treatment and their associated functions.

Citation Format: Zaw Phyo, Rohan Verma, Won J. Ho, Elizabeth M. Jaffee. Site-specific profiling of TCR signaling [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 4475.
Abstract 4491: Characterizing long non-coding RNA expression of tumor-infiltrating lymphocytes across solid cancers
Authors: Dinalankara Wikum , Imada Eddie-Luidy , Jackson Christopher M. , Nirschl Thomas R. , Lim Michael , Drake Charles G. , Marchionni Luigi
Published: September 2020

Usually recognized as transcripts of length more than 200 bp and devoid of open reading frames, long non-coding RNAs (lncRNAs) span a vast range of the human genome. Once thought to be of relatively little biological importance, they have been shown to be involved in many biological processes and diseases, highlighting their important regulatory function, which is now gradually starting to be understood. For instance, the recent discovery of immune gene priming lncRNAs (IPLs) – a subset of lncRNAs that facilitate epigenetic priming of immune gene promoters – has demonstrated the hitherto unappreciated role of lncRNAs in orchestrating inflammatory and immune responses.

In this study we generated and analyzed bulk RNA sequencing data from a collection of purified cell populations obtained from patients with prostate cancer, glioblastoma, bladder cancer, and renal cell carcinoma. Each cohort was comprised of tumor infiltrating lymphocytes (TILs) and paired circulating lymphocytes, derived from matched peripheral blood samples, obtained by fluorescence-activated cell sorting (FACS).

The high depth of coverage in our data allowed the examination of expression patterns of CD4 and CD8 cell types at a level not possible with single cell sequencing, across relevant tumor phenotypes including T-cell exhaustion. To this end, we used the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) annotation, quantifying expression levels for over 100,000 coding and non-coding genes, encompassing enhancers and promoters recently characterized by the FANTOM consortium and examined their behavior with respect to immune function. We compared the behavior of coding genes and various categories of lncRNAs against each other, and identified important candidate lncRNAs for further functional study. Overall, our comprehensive study of TILs gene expression provides novel insights into lncRNA-directed networks controlling immune response mechanisms in cancer.

Citation Format: Wikum Dinalankara, Eddie-Luidy Imada, Christopher M. Jackson, Thomas R. Nirschl, Michael Lim, Charles G. Drake, Luigi Marchionni. Characterizing long non-coding RNA expression of tumor-infiltrating lymphocytes across solid 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 4491.
Abstract 4493: Enhancer reprogramming contributes to anti-PD1 resistance in melanoma
Authors: Maitituoheti Mayinuer , Tang Ming , Terranova Christopher J. , Keung Emily , Tomczak Katarzyna J. , Wargo Jennifer , Rai Kunal
Published: September 2020

Immune checkpoint blockade therapy has improved clinical responses and long-term survival benefit for patients with advanced melanoma, however the response rate is modest and a large fraction of treated patients do not experience clinical benefits. Therefore, there is tremendous need to identify combination strategies to improve responses and to overcome resistance to therapy. Emerging data suggest that epigenetic drugs can improve the responses to immunotherapy. However, we have limited understanding of epigenetic mechanisms that characterize responses to Immune checkpoint blockade therapy. Therefore, we generated comprehensive epigenomic landscapes of 36 samples from anti PD-1 treated metastatic melanoma patients by profiling 6 histone markers. To determine correlation of epigenetic features with gene expression, we generated RNA-Access data for 12 matched samples. We determined chromatin states using ChromHMM and ChromHMM profiling consolidated using Epilogos. Analysis of chromatin state differences and associated individual mark profiles with response rate suggested that pre-treatment samples from anti PD-1 non-responsive patients contain higher active enhancer state (enriched for H3K27Ac) compared to responsive patients. Many of these enhancers targeted key regulators of pathways that are shown to mediate resistance to immune checkpoint blockade therapy. Importantly, aberrant expression of these genes correlated well with enhancer gains. Inhibition of enhancers with bromodomain inhibitor along with anti PD-1 significantly decreased the tumor volume by increased T cell infiltration. Together, these findings reveal that enhancer gains on key oncogenes associate with poor response to Immune checkpoint therapy which could be potentially used for stratifying responder and resistant lesions.

Citation Format: Mayinuer Maitituoheti, Ming Tang, Christopher J. Terranova, Emily Keung, Katarzyna J. Tomczak, Jennifer Wargo, Kunal Rai. Enhancer reprogramming contributes to anti-PD1 resistance in melanoma [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 4493.