bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3457: Plasma metabolomic changes in mice with time restricted feeding-attenuated pulmonary metastasis of Lewis lung carcinoma
Authors: Yan Lin , Rust Bret M. , Picklo Matthew J.
Published: September 2020

Erratic eating behavior disrupts diurnal rhythms of metabolism and may contribute to obesity. Time-restricted feeding (TRF), in which food is available in the active period of the day (the dark phase for nocturnal animals), restores metabolic homeostasis in mice. In a mouse model of Lewis lung carcinoma (LLC), we found that TRF (12 hours, dark phase) attenuates obesity-enhanced spontaneous metastasis to the lungs in a study that compared differences in the extent of metastasis among four dietary groups: non-LLC-bearing mice fed the standard AIN93G diet and LLC-bearing mice fed the AIN93G, an obesogenic high-fat diet (HFD) or TRF with the HFD. With the goal of determining potential plasma fingerprints underlying TRF efficacy, we performed untargeted metabolomic analysis upon the plasma samples from this study. Using gas chromatography time-of-flight mass spectrometry, we identified 152 compounds of which 24 differed among the four groups. Ten analytes that were the most influential in treatment separation were alpha-tocopherol, phenylalanine, isoleucine, leucine, pyruvic acid, dihydrocholestrol, arachidonic acid (ARA), docosahexaenoic acid (DHA), lactic acid, and cholesterol. In mice fed the AIN93G diet, compared to non-LLC-bearing mice LLC elevated alpha-tocopherol, ARA, isoleucine, phenylalanine, cholesterol, lauric acid, and 4-hydroxybenzoate and decreased lactic acid, lactamide, and pyruvic acid. In LLC-bearing mice, compared to the AIN93G diet the HFD elevated asparagine, leucine, phenylalanine, dehydrocholesterol, p-cresol sulfate, and hexuronic acid and decreased 1,5-anhydroglucitol, palmitoleic acid, myristic acid, lauric acid, and 4-hydrobenzoate. Compared to the HFD, TRF elevated linoleic acid and 2-hydroxyhexanoic acid and decreased alpha-tocopherol, asparagine, isoleucine, leucine, phenylalanine, dihydrocholesterol, p-cresol sulfate, hexuronic acid, and DHA. This study showed that LLC metastatic growth and an increase in dietary fat consumption disrupted metabolic homeostasis, as reflected in plasma analyte changes compared to their respective controls. TRF, through its temporal regulation of food intake, restored HFD-mediated metabolic disruption and may have contributed to its inhibition of obesity-enhanced LLC metastasis.

Citation Format: Lin Yan, Bret M. Rust, Matthew J. Picklo. Plasma metabolomic changes in mice with time restricted feeding-attenuated pulmonary metastasis of Lewis 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 3457.
Abstract 3462: Gender differences in dietary behavior and urinary gallic acid concentrations in racial minorities in New York City
Authors: Zambrano Cristina , Lu Wenyue , Johnson Cicely , Beeber Maayan , Panitz April , Ibrahim Safa , Fraser Marilyn , Ma Grace , Navder Khursheed , Yeh Ming-Chin , Ogunwobi Olorunseun
Published: September 2020

Nutrition is important for cancer prevention. Previous research has found that socioeconomic factors may affect access to a healthy diet, which may impact the risk of cancer. To investigate this association, we assessed dietary behavior and the urinary concentrations of gallic acid, an antioxidant found in various fruits and vegetables, in racial minorities in New York City. Ninety-one (91) participants were recruited from a senior center in East Harlem, New York City, a racially diverse and underserved community. A National Institute of Health (NIH) - validated diet survey questionnaire was used to collect dietary behavior data. Demographic and cancer information were also collected. All 91 participants completed the survey and forty-five (45) participants provided urine samples for gallic acid analysis. Associations between demographic factors and the intake of certain foods were assessed. Gender differences were significantly associated with dietary behavior and urinary gallic acid concentrations. Female participants had a higher daily intake of fruits compared to male participants (p<0.05). Additionally, female participants had significantly higher urinary gallic acid concentrations compared to male participants (p<0.05). Other associations were also observed. Age was negatively associated with the quantity of french fries/fried potatoes and white potatoes intake (p<0.05), while positively associated with frequency of fruit intake (p<0.05). Furthermore, Asian race was associated with a higher frequency of fruit intake (p<0.05), compared to other races. Among all recruited participants, we collected information on three cancer cases. Compared to non-cancer cases, participants with cancer reported a significantly lower fruit intake quantity (p<0.05). In a multivariate analysis, we observed a significant association between fruit intake quantity and urinary gallic acid concentration (p<0.05) after controlling for income. Our findings suggest that gender differences in dietary behavior and urinary gallic acid concentration may explain some of the gender differences in cancer incidence and prevalence observed in racial minority groups.

Citation Format: Cristina Zambrano, Wenyue Lu, Cicely Johnson, Maayan Beeber, April Panitz, Safa Ibrahim, Marilyn Fraser, Grace Ma, Khursheed Navder, Ming-Chin Yeh, Olorunseun Ogunwobi. Gender differences in dietary behavior and urinary gallic acid concentrations in racial minorities in New York City [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 3462.
Abstract 3475: CYP3A5 inhibitor bergamottin present in grape fruit extract blocks prostate cancer cell growth
Authors: Vetrichelvan Opalina , Gorjala Priyatham , Goodman Oscar , Mitra Ranjana
Published: September 2020

Background: Previous research has revealed that the androgen receptor (AR), which upon activation goes to the nucleus, is the driving force of prostate cancer growth. Once activated, AR promotes transcription of genes responsible for promoting cancer growth. Previous studies have shown that inhibition of CYP3A5 blocks the activation process of the AR. CYP3A5 is a liver enzyme and together with CYP3A4 processes 50% of all commonly prescribed drugs. CYP3A5 is the extrahepatic form expressed in both normal and malignant prostate. Bergamottin, a compound found in grapefruit juice, is a known CYP3A4/5 inhibitor. Based on CYP3A5's ability to regulate AR activation, we tested the effects of bergamottin on AR activation to see if the compound can be utilized as a dietary supplement to reduce prostate cancer growth.

Methods: Western blotting, cell fractionation, and immunofluorescence were used to observe the effects of bergamottin on AR, amount of AR in nucleus/cytoplasm, and cellular localization of AR, respectively. MTT based cell growth measurement was used to see how prostate cancer cell growth was affected by bergamottin.

Results: Cell growth assay revealed that bergamottin reduced prostate cancer cell growth. The IC50 for LNCaP cells was observed to be 2.4 μM. Growth of RWPE1 cells (non transformed prostate epithelium) was not effected at the same concentration of bergamottin. Western blot analysis showed that total AR protein expression was downregulated in the bergamottin treated LNCaP and MDAPCa2b cells. Cell fractionation assay revealed that bergamottin significantly reduced nuclear AR after DHT induction compared to non-treated cells. Immunofluorescence assay confirmed reduced nuclear AR in the bergamottin treated LNCaP and MDAPCa2b cells. Furthermore, bergamottin reduced PSA levels both inside the cells and in the growth media indicating that it inhibits AR downstream signaling.

Conclusion: Our results concluded that bergamottin successfully blocked AR activation and downstream signaling, and consequently slowed down prostate cancer cell growth. The implication of this experiment is the potential use of bergamottin as a food supplement alongside other prostate cancer treatments in order to aid in blocking prostate cancer growth.

Citation Format: Opalina Vetrichelvan, Priyatham Gorjala, Oscar Goodman Jr, Ranjana Mitra. CYP3A5 inhibitor bergamottin present in grape fruit extract blocks prostate cancer cell growth [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 3475.
Abstract 3491: COX-2 inhibitor use and risk of skin cancer: three prospective cohort studies
Authors: Yen Hsuan , Yen Hsi , Drucker Aaron , Han Jiali , Li Wen-Qing , Li Tricia , Qureshi Abrar , Cho Eunyoung
Published: September 2020

Skin cancer is the most commonly diagnosed type of cancer, with continually rising incidence rates. Cyclooxygenase-2 (COX-2) inhibitor use has been associated with lower risk of several cancers, though epidemiological studies on skin cancer risk have been limited and inconclusive. To evaluate whether COX-2 inhibitor use is associated with decreased risk of basal cell carcinoma (BCC), cutaneous squamous cell carcinoma (cSCC), and melanoma, we analyzed COX-2 inhibitor use and risk of skin cancer based on three prospective cohorts–the Nurses' Health Study (NHS, 2000-2012), NHS II (2001-2011), and the Health Professionals Follow-up Study (HPFS, 2002-2012). COX-2 inhibitor use and duration were assessed by biennial questionnaires, with cSCC and melanoma cases verified by pathological records. Over 1.54 million person-years of follow-up, 16,098 BCC, 1,973 cSCC, and 625 invasive melanoma cases were documented. Multivariable hazard ratios (HRs) and 95% confidence intervals (CIs) for the association of COX-2 inhibitor use with risk of BCC, cSCC, and melanoma were estimated using Cox proportional hazards models. We pooled the results between the three cohorts using a fixed effects model. For ever vs. never users, COX-2 inhibitor use was associated with a modestly increased risk of BCC (multivariable HR 1.10, 95% CI 1.06–1.15) and cSCC (multivariable HR 1.12, 95% CI 1.00–1.27). The effect estimate was similar for melanoma, but was non-significant (multivariable HR 1.10, 95% CI 0.89–1.38). In conclusion, COX-2 inhibitor use was not associated with decreased skin cancer risk and instead was associated with modestly increased risk of BCC and cSCC. Further investigation is necessary to replicate these results.

Citation Format: Hsuan Yen, Hsi Yen, Aaron Drucker, Jiali Han, Wen-Qing Li, Tricia Li, Abrar Qureshi, Eunyoung Cho. COX-2 inhibitor use and risk of skin cancer: three prospective cohort studies [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 3491.
Abstract 3497: The physical activity paradox in lung cancer: A systematic review and meta-analysis
Authors: Rana Benny , Hu Liang , Harper Andrew , Cao Chao , Peters Cheryl , Brenner Darren , Yang Lin
Published: September 2020

Objective: To deliver a systematic review of the literature synthesizing data on the association of occupational physical activity with lung cancer risk in observational studies.

Design: Systematic review with meta-analysis.

Data Source: A literature search was performed in electronic databases of PubMed/Medline and Embase.

Eligibility criteria for selecting studies: We screened for peer-reviewed articles from prospective cohort and case-control studies assessing the association of occupational physical activity with lung cancer risk. A sex-specific meta-analysis assessed the association of high (compared to low) level occupational physical activity with lung cancer risk, estimating the relative risk (RR) and odds ratio (OR) with a 95% confidence interval (CI).

Results: The systematic search identified 2065 articles, among which, 13 journal articles met the inclusion criteria. The meta-analysis adjusted for age, status and/or intensity of smoking, with a pooled sample size of 623,741 participants (men: 263,530; women: 358,589). A random-effect model of four prospective and four case-control studies indicated that men who engage in high-level occupational physical activity had a 16% higher risk (OR 1.16, 95% CI 1.00 to 1.35) of lung cancer than those engaging in low-level occupational physical activity. There was no association observed among women (RR=1.05, 95% CI 0.81 to 1.36) based on three available studies (prospective cohort: n=2; case-control: n=1).

Conclusions: Findings from the review suggest a higher risk of lung cancer among men reported high-level occupational physical activity. Further prospective studies incorporating rigorous measures of domain-specific physical activity and other occupational exposures are needed to elucidate this association.

Citation Format: Benny Rana, Liang Hu, Andrew Harper, Chao Cao, Cheryl Peters, Darren Brenner, Lin Yang. The physical activity paradox in lung cancer: A systematic review and meta-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 3497.
Abstract 3543: Facile genome-wide detection of genomic fusions and other somatic chromosomal abnormalities through Bionano Whole Genome Imaging
Authors: Hastie Alex , Pang Andy W. , Lee Joyce , Lam Ernest T. , Anantharaman Thomas , Sadowski Henry , Oldakowski Mark
Published: September 2020

Genome instability is a key hallmark of cancer. Instability is important because it allows the genome to acquire growth advantage by amplifying or creating oncogenes by fusing otherwise non-pathogenic genes and by deleting/inactivating tumor suppressor genes. Several gene fusions have been discovered and some have been exploited for therapies as they produce fusion proteins that can be targeted by chemotherapeutics such as tyrosine-kinase inhibitors targeting BCR-ABL used to treat CML. In addition, other genomic fusions serve as diagnostic or prognostic indicators important for cancer management. Clinically, fusions are generally detected through targeted assays like NGS panels, PCR and FISH, or through karyotyping. High resolution, whole genome approaches to detect fusions are needed as current approaches have innate limitations, such as karyotyping (low resolution) and whole genome sequencing (blind in the ~66% of the genome containing repeats). Bionano whole genome imaging is able fill in the gaps, providing high resolution (~2kbp breakpoint precision) and ability to span complicated genomic repeats.

Here we demonstrate an easy, fluid, largely automated workflow for whole genome detection of fusions and other somatic variants. The Bionano workflow involves a novel rapid isolation protocol for extremely high molecular weight DNA, labeling the DNA to create a barcode across the genome and automated data collection using the Bionano Saphyr system. The assay is inexpensive and the whole workflow can be accomplished from cells/tissue to variant calls within 4 days turnaround time. Because this approach is whole genome and not masked/hidden by repeat elements, we are able to detect novel fusions that have not previously been detected. In a standard assay, whole genome imaging can detect variants at 5% allele fraction and with increased coverage fusions down to 1% allele fraction can be efficiently detected. Whole genome imaging for novel fusion detection and genome instability studies will likely play an increasing role as a complementary genomics tool in cancer research going forward.

Citation Format: Alex Hastie, Andy W. Pang, Joyce Lee, Ernest T. Lam, Thomas Anantharaman, Henry Sadowski, Mark Oldakowski. Facile genome-wide detection of genomic fusions and other somatic chromosomal abnormalities through Bionano Whole Genome Imaging [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 3543.
Abstract 3559: Protein secretion rates of VEGF and CA9 in normoxia and hypoxia
Authors: Lee Sandy Che-Eun Serena , Levitin Fiana , Hulme Stephanie , Rumantir Ryan , Sykes Jenna , Koritzinsky Marianne
Published: September 2020

Tumor hypoxia results in poor patient outcome due to treatment resistance as well as biological changes that stimulate angiogenesis, vasculogenesis, migration, invasion and immune suppression. These hypoxia-induced adverse biological changes are often mediated by membrane bound or secreted proteins through transcriptional and translational upregulation. Thus, understanding the regulation of how secreted proteins in hypoxia can therefore reveal novel therapeutic targets. Proteins that traverse through the secretory pathway form disulfide bonds in the endoplasmic reticulum (ER). Recent data from our lab have demonstrated that disulfide bond formation remains incomplete in ER cargo proteins like LDLR and Flu-HA in the absence of oxygen. To address whether hypoxia-induced proteins were likewise impaired, radioactive pulse chase assays were performed to measure disulfide bond formation and secretion capacity under both normoxic and hypoxic conditions. Here, we demonstrate that both hypoxia induced proteins carbonic anhydrase 9 (CA9) and vascular endothelial growth factor (VEGF) complete disulfide bond formation and are secreted with equal kinetics under hypoxia and normoxia. These proteins hence have a superior ability to be expressed in the absence of oxygen. Additionally, in a global in silico analysis of all proteins that traverse through the ER, we discovered that hypoxia-induced proteins on average contain fewer free cysteines and shorter-range disulfide bonds in comparison to other proteins. These traits may contribute to their superior ability to form correct disulfide bonds in hypoxia. These data show that the ability of proteins to form native disulfide bonds in hypoxia varies widely which can ultimately contribute to their expression in the extracellular space.

Citation Format: Sandy Che-Eun Serena Lee, Fiana Levitin, Stephanie Hulme, Ryan Rumantir, Jenna Sykes, Marianne Koritzinsky. Protein secretion rates of VEGF and CA9 in normoxia and hypoxia [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 3559.
Abstract 3572: Merlin deficiency induces redox imbalance in breast cancer
Authors: Mota Mateus , Metge Brandon , Shevde-Samant Lalita
Published: September 2020

Merlin is encoded by the NF2 gene and, as a tumor suppressor, stalls cell proliferation by contact-dependent growth inhibition. Prior work from our laboratory has established that Merlin levels are significantly decreased in breast tumor tissues representing advanced grade. Moreover, Merlin expression is completely lost in cases representing metastatic breast cancer. Therefore, we mimicked Merlin deficiency by stably knocking down NF2 in non-metastatic breast cancer cells. Recognizing the role of metabolic reprogramming in tumor progression, we undertook untargeted metabolomics analysis - this effort identified low levels of reduced glutathione (GSH) in Merlin-deficient cells. Given the role of GSH as the most abundant antioxidant cofactor, we explored if a major reactive oxygen species (ROS) clearance mechanism is compromised in Merlin-deficient breast cancer cells. Indeed, accumulated levels of ROS were detected in Merlin-deficient cells, suggesting that Merlin deficiency causes redox imbalance. Quenching of elevated ROS levels attenuated migration and invasion capabilities indicating a role of ROS in intensifying malignant behaviors upon Merlin deficiency. Furthermore, dysregulated STAT3 activity upregulated the expression of NADPH oxidase (NOX) enzymes in Merlin-deficient breast cancer cells compared to their control counterparts. These findings were also recapitulated in non-tumorigenic Nf2 −/- mouse embryonic fibroblasts further supporting the key role of Merlin in these phenotypes. In conclusion, ROS accumulation and increased malignancy in Merlin-deficient cells may be the result of a dysregulated cellular redox management system.

Citation Format: Mateus Mota, Brandon Metge, Lalita Shevde-Samant. Merlin deficiency induces redox imbalance in breast 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 3572.
Abstract 3615: Profiling of BRCA1 & BRCA2 mutations in Egyptian colorectal cancer patients via next generation sequencing
Authors: El-Din Youssef Amira Salah , Touny Ahmed Osama , Hassan Zeinab K. , Eldin Mohammed Mohey , Lotfy Mai M. , Nassar Auhood , El-Hadidi Mohamed , Kishk Ali , sayed ola , Zekri Abdel-Rahman N.
Published: September 2020

Aim: This study aimed to sequence BRCA1 & BRCA2 genes to identify the frequency of the detected genetic mutations in the disease progression of colorectal cancer (CRC) and to estimate colorectal cancer risks in those BRCA mutation carriers.

Material and methods: 140 biopsy samples were collected from Egyptian patients categorized into inflammatory bowel disease (IBD) (n=20), colonic polyp (CP) (n=38) and CRC (n=62) patients as well as subjects with chronic colitis served as a control group (n=20). The libraries were performed using Qiaseq UMI-based targeted panel and sequenced via Ion proton sequencer. The detected genetic variants at 500x were annotated against Cosmic, dbSNP, exac all, Polyphen2, Sift and Clinvar databases.

Results: Analysis revealed that BRCA1 gene harbored 26, 19, 8 and 11 variants in the CRC, CP, IBD and control groups; respectively. Exon 10 was the most affected exon harbored 7 pathogenic variants in the CRC group. Two out of 7 were the most frequently detected common pathogenic variants associated with disease progression from colitis to CRC (c.1961delA (11%) & c.3214delC (16%). Moreover, 3 common begnin SNP variants were found to be related to ethnicity (c.3548A>G (58%), c.2612C>T (60%), c.4900A>G (69%).

Moreover, BRCA2 gene harbored 48, 29, 24 and 18 variants in the CRC, CP, IBD and control groups respectively. Exon 2, 11, 23 were the most affected exons harbored 12 pathogenic variants in the CRC group. Four out of 12 were the most frequently detected common pathogenic variants associated with disease progression from colitis to CRC (c.3860delA (8%), c.5351delA (18%), c.9097delA (24%) & c.36delT (34%).

Conclusion: Our data showed that BRCA1 & BRCA2 genes analyzed by Next-Generation Sequencing (NGS) identifies large number of pathogenic and begnin variants that are crucial for understanding CRC predisposition and early detection. Also, developing personalized therapies that efficiently target the individual CRC-specific mutations.

Key words: Egyptian Colorectal cancer, BRCA1, BRCA2, pathogenic, begnin, Next Generation Sequencing

Citation Format: Amira Salah El-Din Youssef, Ahmed Osama Touny, Zeinab K. Hassan, Mohammed Mohey Eldin, Mai M. Lotfy, Auhood Nassar, Mohamed El-Hadidi, Ali Kishk, ola sayed, Abdel-Rahman N. Zekri. Profiling of BRCA1 & BRCA2 mutations in Egyptian colorectal cancer patients via next generation sequencing [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 3615.
Abstract 3619: High quality library preparation and accurate sequencing from highly damaged matched patient sample sets
Authors: Heider Margaret R.
Published: September 2020

Preparation of high quality next-generation sequencing (NGS) libraries is critical for accurate identification of disease-causing mutations, but clinical scientists are often limited by the input DNA quality. In cancer genomics, a common source of DNA is formalin-fixed, paraffin-embedded (FFPE) tissue from patient biopsy, and in most cases high quality fresh or frozen tissue samples are not available. FFPE DNA poses many notable challenges for preparing NGS libraries, including low input amounts and extensive damage from fixation, storage, and extraction methods. Sequencing artifacts arising from damaged DNA bases raise the level of apparent mutations, making it more difficult to discern true, low frequency, disease-related variants from noise.

We developed a second-generation, multi-enzyme DNA repair mix (V2) that is designed to repair the most prevalent damage types found in FFPE DNA including cytosine deamination, oxidative damage, abasic sites, nicks, and gaps. We tested the application of the V2 enzymatic repair mix in Illumina library preparation for DNA samples extracted from a series of matched patient sample sets, which included: FFPE normal and tumor tissue, and frozen normal and tumor tissue for each patient. Following this, we performed target enrichment, deep sequencing, and variant calling analyses.

Our library preparation workflow integrates enzymatic repair upstream of Illumina library preparation without an additional bead purification step, maximizing library yield and complexity from precious FFPE samples. Rescue of damaged DNA molecules for library conversion and repair of damaged DNA bases improved on-target rate, coverage uniformity, and duplication rates. With a matched frozen sample for each FFPE specimen, we demonstrate that repair of damaged DNA bases improves sequencing accuracy by reducing the number of false-positive variant calls. We propose that enzymatic repair enables researchers to capture as much useable, accurate data from poor quality FFPE samples as possible.

Citation Format: Margaret R. Heider. High quality library preparation and accurate sequencing from highly damaged matched patient sample sets [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 3619.
Abstract 362: The regulation of SOX7 and its tumor suppressive role in oral squamous cell carcinoma
Authors: Ahn Chi-Hyun , Hong Kyoung Ok , Shin Ji-Ae , Hong Seong-Doo , Cho Sung-Dae
Published: September 2020

SRY-related HMG-box 7(SOX7), a transcription factor belonging to the SOX family, has been reported to be down-regulated in some types of cancers. However, its biologic role in oral squamous cell carcinoma (OSCC) remains unknown. We found expression of SOX7 protein was decreased in OSCC tissues compared with normal oral mucosa. SOX7 expression in patients with OSCC was inversely associated with positive lymph node metastasis, advanced TNM stage, and poor prognosis. These results were in accordance with data obtained from our in vitro experiments on the OSCC cell lines. Moreover, ectopic expression of SOX7 suppressed cell proliferation, migration, and invasion in HSC-4 and SCC-9 cells. Importantly, we discovered that SOX7 expression likely inhibited vasculogenic mimicry formation associated with clinically poor outcome and impaired expression of VE-cadherin in OSCC cell lines as well as lung cancer and breast cancer cells. Our findings suggest that SOX7 could be a potential marker for predicting the prognosis of patients with OSCC and plays an important role as a tumor suppressor in oral tumorigenesis and progression. This work was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT, and Future Planning [2017R1D1A1B03029317, 2018R1D1A1B07043080, and 2019R1A2C1085896].

Citation Format: Chi-Hyun Ahn, Kyoung Ok Hong, Ji-Ae Shin, Seong-Doo Hong, Sung-Dae Cho. The regulation of SOX7 and its tumor suppressive role in oral squamous cell 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 362.
Abstract 3641: Successful classification of hematological neoplasm by array profile
Authors: Grace Colin , Boneva Temenuzhka , Nacheva Elisabeth P.
Published: September 2020

In addition to structural chromosome aberrations resulting in fusion genes, the genome profile of haematological malignancies is characterized by copy number changes (gains and losses) relative to the ploidy level. Array comparative genome hybridization (aCGH)1 Combined with FISH and/or multiplex PCR array screening offers a reliable tool for assessment of genome complexity in haematological malignancies in diagnostic settings.

The aCGH assay in our diagnostic algorithm uses 8 × 60K SurePrint G3 (Agilent, USA). The slides are scanned to measure the fluorescence ratio (FR), software evaluates imbalances.

We recognize that the raw data in the form of log ratios, some 64,000 data points, contain sufficient information to identify the disease category without resorting to converting the log ratios to gains and losses and mapping them to individual chromosomes, a process open to operator interpretation.

As an alternative and bearing in mind the current interest in machine learning, we attempted to auto-classify the data for the modest collection of 2,300 patient samples in our archive, according to their WHO classification. We were able to collect 175 samples for each group classified as myelodisplasia (MDS), acute myeloid leukemia (AML), myeloma (MM) and chronic lymphocytic leukemia (CLL),

We used a Logistic Regression Classifier implemented in Mathematica 12. The classifier took only 2 minutes on average to complete the training. We took a total of 700 array sample files, each of 59,032 data points, of which 100 were randomly selected as a validation set. The balance of 600 files, distributed evenly and randomly over the 4 test diseases were used as a training set. We used a Confusion Matrix to evaluate and display the results as shown in the table.

Confusion MatrixAMLCLLMDSMMTotalAML1609025CLL0150116MDS0116017MM1021417Predicted17162715

In spite of the small training set we correctly classified the MDS (16/17), CLL (15/16) and MM (14/17), 9 AML were reported as MDS a due to sharing genome imbalances. There was also confusion between the B cell disorders, MM and CLL known to carry overlapping genome aberrations.

The auto classification offered by this method is a promising attempt to support a speedy and reliable assessment of genome complexity. There is no doubt that a better classifier would have been created with a larger training set.

1 Kallioniemi A et al., Kallioniemi OP, Sudar DA, Rutovitz D, Gray JW, Waldman F, Pinkel D (1992). “Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors”. Science. 258 (5083): 818-821).

Citation Format: Colin Grace, Temenuzhka Boneva, Elisabeth P. Nacheva. Successful classification of hematological neoplasm by array profile [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 3641.
Abstract 3650: A noncanonical histone target of NSD2 may contribute to oncogenesis
Authors: Weiss Nicole , Luo Minkui
Published: September 2020

The NSD family of protein lysine methyltransferases (PKMTs), containing members NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, cause epigenetic aberrations when dysregulated in cancer and are thus attractive therapeutic targets. These enzymes share a canonical activity catalyzing the dimethylation of histone 3 lysine 36 (H3K36me2), a mark associated with gene activation. In cancer, these enzymes are often overexpressed, amplified, or mutated, resulting in increased global H3K36me2 and transcriptional activation. In addition to transcriptional regulation, NSD2 has also been reported to be involved in pathways such as DNA replication and repair, which cannot be readily rationalized via its H3K36 methylation activity. This suggests that NSD2 has unidentified substrates that carry out its additional biological function(s), nonredundant with NSD1/3. Furthermore, NSD2 has a recurring glutamate to lysine mutation in the catalytic SET domain at 1099 (E1099K), which results in gain-of-function activity on H3K36. Our preliminary data has shown that NSD2 has noncanonical histone targets that are augmented by NSD2 E1099K to drive oncogenesis. We are using cell based approaches to dissect its downstream biology to reveal NSD2's oncogenic potential.

Citation Format: Nicole Weiss, Minkui Luo. A noncanonical histone target of NSD2 may contribute to oncogenesis [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 3650.
Abstract 3657: Analysis of the regulation of PD-L1 expression and methyl transferases levels following inhibition of histone deacetylases in cancer cells
Authors: Natarajan Umamaheswari , Venkatesan Thiagarajan , Mathuram Theodore L. , Das Jayanta K. , Rathinavelu Appu
Published: September 2020

Epigenetic alterations are known to play important roles in cancer initiation and progression. Therefore, deregulation of epigenetic modifications is considered as a hallmark of cancer; therefore many components of this process are being explored as therapeutic targets. PD-L1 is expressed in most cancer cells, which confers aggressive growth ability and allows the cancers to escape from the immune system of the body. The effects of PD-L1 are mediated through PD-1, also known as CD279, which is normally expressed on the surface of lymphoid and non-lymphoid derived cells. The binding of PD-L1 to the PD-1 receptor mediates immune checkpoint inhibition to regulate T-cell responses. When we analyzed the levels of PD-L1, the expression was high in HCC827 cells, followed by H460, H1975, H226, SJSA1, and U87MG cells. Treatment of HCC827 cells with SAHA, which is a broad-spectrum HDAC inhibitor, was able to reduce the PD-L1 levels in time and dose dependent manner in HCC827. Also, the PD-L1 levels were found to be negatively correlated to the p21 expression following HDAC inhibition. The qRT-PCR analysis revealed significant decreases in the levels of methyltransferase enzymes such as DNMT3A, DNMT3B, PRMT1, SUV39H1, KAT6B, NSD1, SETD1B, and WHSC1. Analysis of the protein levels also confirmed significant reductions following treatment with SAHA. While decreasing the levels of the methyltransferases, SAHA treatment was able to increase the levels of acetylated forms of H2B, H3, and H4. Since acetylation mediated unwinding of the DNA is generally responsible for the increased expression of various genes, it is interesting to see a concomitant reduction in the levels of some of the crucial methyltransferases that are known to produce inhibitory effects. It is suspected that the decrease in the PD-L1, PRMT1, SUV39H1, and DNMT3A levels following HDAC inhibition may be mainly due to reduced transcription. However, it is not clear whether p21 has any negative control on the transcription of the affected genes. Additional studies are required to fully understand the actual mechanisms that may be involved in the regulation of PD-L1 and methyltransferases expression by HDAC inhibitors. (This research was supported by the Royal Dames of Cancer Research Inc., Fort Lauderdale, Florida).

Citation Format: Umamaheswari Natarajan, Thiagarajan Venkatesan, Theodore L. Mathuram, Jayanta K. Das, Appu Rathinavelu. Analysis of the regulation of PD-L1 expression and methyl transferases levels following inhibition of histone deacetylases in cancer 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 3657.
Abstract 3658: Brd4-bound enhancers drive critical sex differences in glioblastoma
Authors: Kfoury-Beaumont Najla , Qi Zongtai , Wilkinson Michael , Broestl Lauren , Berrett Kristopher , Moudgil Arnav , Sankararaman Sumithra , Chen Xuhua , Gertz Jay , Mitra Robi , Rubin Joshua B.
Published: September 2020

Sex can be an important determinant of cancer phenotype and exploring sex-specific tumor biology holds promise for identifying novel therapeutic targets and new approaches to cancer treatment. In an established model of glioblastoma, we discovered transcriptome-wide sexual dimorphism in gene-expression that was concordant with sex differences in H3K27ac marks, large Brd4-bound enhancer usage, and Brd4 co-localization with Myc and p53. The sex-specific enhancer usage drove sex differences in stem cell function and tumorigenicity. Moreover, male and female GBM cells exhibited opposing responses to pharmacological or genetic inhibition of Brd4. Brd4 knockdown or inhibition decreased male GBM cell clonogenicity and in vivo tumorigenesis, while increasing both in female GBM cells. These results were validated in male and female patient-derived GBM cell lines. Thus, for the first time, Brd4 activity is revealed to drive a sexually dimorphic stem cell and tumorigenic phenotype, resulting in diametrically opposite responses to BET inhibition in male and female glioblastoma cells. This has critical implications for the clinical evaluation and use of BET inhibitors.

Citation Format: Najla Kfoury-Beaumont, Zongtai Qi, Michael Wilkinson, Lauren Broestl, Kristopher Berrett, Arnav Moudgil, Sumithra Sankararaman, Xuhua Chen, Jay Gertz, Robi Mitra, Joshua B. Rubin. Brd4-bound enhancers drive critical sex differences in glioblastoma [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 3658.
Abstract 3709: miR-21-3p: A potential oncomir in breast cancer
Authors: Amirfallah Arsalan , Arason Adalgeir , Agnarsson Bjarni A. , Johannsson Oskar Th , Hilmarsdottir Bylgja , Barkardottir Rosa Bjork , Reynisdottir Inga
Published: September 2020

MIR21 is a well known oncomir in many cancer types including breast cancer. Most studies that have described the oncogenic properties of MIR21 have focused on the leading strand miR-21-5p. Fewer studies have focused on the passenger strand miR-21-3p, but in a few types of cancer it has been shown to have oncogenic properties. A handful of studies suggest that miR-21-3p could be a biomarker in breast cancer. MIR21 is located at 17q23.1, a region which is often amplified in breast tumors. It overlaps the 3´ end of VMP1 but it has its own distinct promoter. The aim of this study was to analyze whether miR-21-3p associated with prognostic factors in breast cancer.

The levels of miR-21-5p and miR-21-3p were measured by qPCR in 144 breast tumors from a cohort of breast cancer patients (cohort 1). The association of expression levels with clinical and pathological factors was analyzed by Student´s t-test and Anova, and with survival by Kaplan-Meier, the log-rank test, and the Cox proportional hazards test. To confirm the results, available data were used from breast cancer cohorts from The Cancer Genome Atlas (TCGA) (n=256) and METABRIC (n=1286).

The mean expression levels of miR-21-5p were significantly higher than those of miR-21-3p in breast tumors from cohort 1 (p=2.2e−10). However, only miR-21-3p was more highly expressed in tumors than normal breast tissue (p=0.003), and in all three cohorts there was a strong positive correlation between MIR21 copy number and miR-21-3p expression levels. There was a significant higher expression of miR-21-3p in HER2 positive tumors compared to HER2 negative tumors in the two larger cohorts (p < 0.05), and high miR-21-3p levels associated with higher histograde in the largest cohort (9.2e−14). A shorter breast cancer specific survival was associated with higher miR-21-3p expression in the METABRIC cohort (HR 1.338, CI 1.104-1.622, p=0.003). HER2 was the largest confounding factor but even after adjustment for HER2 positivity the effect remained significant (HR 1.260, CI 1.036-1.532, p = 0.021).

Our data show that miR-21-3p is expressed in breast tissue and tumors. Furthermore, our preliminary data suggest that miR-21-3p may be an indicator of worse outcome for breast cancer patients. However, additional work is needed to elucidate the association of miR-21-3p expression with distinct prognostic factors in breast cancer.

Citation Format: Arsalan Amirfallah, Adalgeir Arason, Bjarni A. Agnarsson, Oskar Th Johannsson, Bylgja Hilmarsdottir, Rosa Bjork Barkardottir, Inga Reynisdottir. miR-21-3p: A potential oncomir in breast 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 3709.
Abstract 3717: LncRNA RNF157-AS1 inhibits autophagy in ovarian cancer cells by downregulating ARHI: The different role in proliferation and drug resistance
Authors: Xu Sujuan , Xu Pengfei
Published: September 2020

Ovarian cancer(OC) is the commonest cause of female cancer death. Long noncoding RNAs (lncRNAs) has been shown to have regulatory roles in the procession of many cancers, including OC. Here, in our previous study, we reported that lncRNA RNF157-AS1 was overexpression in OC tissues, which is confirmed by GSE144077 and TCGA matched GTEx normal data. Further experiments revealed that RNF157-AS1 knockdown significantly repressed the proliferation both in vitro and in vivo and overexpressed RNF157-AS1 promoted the proliferation of OC cells. However, the higher expression of RNF157-AS1 predicted a better prognosis for OC patients in TCGA database. RNA-seq analysis revealed that ARHI was significant overexpressed after RNF157-AS1 silencing and it is negative correlated with RNF157-AS1 in TCGA and matched GTEx normal data. ARHI, a autophagy-related gene, could induced autophagy in OC cells. Because of 70% of OC patients were diagnosed with advanced tumors and need to chemotherapy. Overexpression of RNF157-AS1 could inhibit autophagy-associated cell death and promote rapid proliferation of OC cells, while overexpressed RNF157-AS1 decrease autophagy and induced cells apoptosis under adverse environment. To test our hypothesis, CCK8 assay suggested overexpression of RNF157-AS1 significantly decreased the chemoresistance to cisplatin (DDP) and silencing of RNF157-AS1 increased the DDP-resistance of OC cells, which are confirmed by clone formation assay and apoptosis experiments. Western blot assay also suggested that RNF157-AS1 silencing promote ARHI, LC3II/I and beclin1 expression. To our knowledge, this is the first report revealed that the different roles of RNF157-AS1 in OC cells' proliferation and chemoresistance and our study also can provide guidance for clinical treatment of OC patients.

Citation Format: Sujuan Xu, Pengfei Xu. LncRNA RNF157-AS1 inhibits autophagy in ovarian cancer cells by downregulating ARHI: The different role in proliferation and drug resistance [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 3717.
Abstract 3731: Targeting the isocitrate dehydrogenase 1 (IDH1) metabolic enzyme in prostate cancer
Authors: Gonthier Kevin , Weidmann Cindy , Frégeau-Proulx Lilianne , Audet-Walsh Étienne
Published: September 2020

Prostate cancer cells (PCa) are dependent on the androgen receptor (AR) for their aberrant proliferation and survival. We have recently discovered that AR induces a reprogramming of PCa cell metabolism by controlling the cytoplasmic wild-type enzyme isocitrate dehydrogenase 1 (IDH1), which results in an enhanced proliferation of tumour cells. However, the specific metabolic functions of IDH1 in PCa or how to use the reliance of tumour cells on this enzyme as a therapeutic avenue, is elusive. In in vitro human PCa models, we showed that IDH1 protein levels and activity are increased in an AR-dependent manner. Using pharmacological and genetic tools, we showed that IDH1 is a major contributor to the replenishment of NADPH levels in PCa. This cofactor plays a key role in the synthesis of biomaterials required for cellular division, and our results indicate that IDH1 contribute to 30-40% of total cellular NADPH levels. In that context, blockade of IDH1 was shown to alter the mTOR signaling, a central regulator of cellular anabolism, which is linked to decreased cellular proliferation rates. FDA-approved pharmacological inhibitors of mutant IDH1 significantly inhibited IDH activity and proliferation in PCa cells, suggesting that such inhibitors could be used to treat PCa patients even in absence of IDH1 mutation. Globally, our results demonstrate that IDH1 is a key player in proliferative anabolic pathways in PCa. Importantly, they also support the hypothesis that inhibition of IDH1 using already-approved molecules represents one viable therapeutic solution.

Citation Format: Kevin Gonthier, Cindy Weidmann, Lilianne Frégeau-Proulx, Étienne Audet-Walsh. Targeting the isocitrate dehydrogenase 1 (IDH1) metabolic enzyme in prostate 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 3731.
Abstract 3734: Expression of serine synthetic enzymes alters the sensitivity of ER-positive breast cancer cells to tamoxifen
Authors: Metcalf Stephanie , Kruer Traci , Dougherty Susan , Wittliff James L. , Klinge Carolyn M. , Clem Brian F.
Published: September 2020

Estrogen receptor positive breast cancer (ER+BC) is the most common form of breast cancer accounting for 65-75% of all diagnoses, yet, due to the availability of targeted therapies, has the best overall survival outcomes. However, it is estimated that up to 30% of all patients develop resistance to these therapies, resulting in recurrence or disease progression. Phosphoserine aminotransferase 1 (PSAT1), which is an enzyme within the serine synthetic pathway (SSP), has previously been implicated in endocrine resistance. Therefore, we sought to determine if there was a functional correlation between expression of PSAT1 or other serine synthetic enzymes and sensitivity to 4-hydroxytamoxifen (4-OHT) treatment. To investigate the correlation between PSAT1, another SSP enzyme phosphoglycerate dehydrogenase (PHGDH), and endocrine resistance, we examined clinical data from ER+ patients who received tamoxifen as their sole endocrine therapy. Using two separate cohorts, we confirmed that higher PSAT1 and PHDGH expression negatively correlates with poorer outcomes in tamoxifen treated ER+ BC patients. Next, we found that SSP enzyme expression and serine synthesis are elevated in tamoxifen resistant compared to tamoxifen-sensitive ER+ BC cells in vitro. To determine relevance to endocrine sensitivity, we modified the expression of both PSAT1 or PHGDH in each cell type. While overexpression of PSAT1 in tamoxifen-sensitive MCF-7 cells diminished 4-OHT inhibition, conversely, silencing of PSAT or PHGDH resulted in decreased proliferation in tamoxifen-resistant LCC9 treated with 4-OHT. Taken together, we postulate that overexpression of SSP enzymes appear to contribute to tamoxifen resistance in ER+BC and indicate a potential combinatorial therapeutic option.

Citation Format: Stephanie Metcalf, Traci Kruer, Susan Dougherty, James L. Wittliff, Carolyn M. Klinge, Brian F. Clem. Expression of serine synthetic enzymes alters the sensitivity of ER-positive breast cancer cells to tamoxifen [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 3734.