bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2082: Deciphering the nucleosome acidic patch binding at amino acid resolution
Authors: Skrajna Aleksandra , Simmons Holly , Smith Charlotte , Mcpherson Jeanne-Marie E. , Goldfarb Dennis , McGinty Robert K.
Published: July 2021

In all eukaryotic cells, nucleosomes provide basic organization of genomic DNA and serve as signaling hubs for gene expression, DNA replication and DNA damage repair. These genome-templated processes are tuned by chromatin enzymes that introduce chemical modifications to nucleosomes and control their positioning and occupancy. Mutations in genes encoding chromatin enzymes are highly correlated with numerous cancer types. A thorough exploration of how these chromatin enzymes act on their physiologic target, the nucleosome, is critical to understanding abnormal DNA methylation, histone posttranslational modifications, and chromatin composition, leading to cancer. In our recent nucleosome interactome proteomic screen, we demonstrated that the vast majority of nuclear proteins require a group of acidic residues on the nucleosome disk surface to interact with nucleosomes. This acidic patch and an adjacent region were recognized by over 50% and 18% of nuclear proteins, respectively, while almost half of the nucleosome disk surface contributed only minimally to nucleosome recognition. Overall, we paired about 300 proteins representing diverse nuclear functions including DNA methylation (DNMT1 and 3, Tet1), histone modification (HAT complexes, kinases), nucleosome remodeling (SWI/SNF), DNA repair (MRN complex), DNA replication (ORC complex), RNA processing, and cell cycle progression (APC/C) with specific nucleosome surface requirements. We have now repeated our screen at amino acid resolution using a library of fifteen nucleosomes containing single point mutations in and around the acid patch, including potential histone oncomutations identified to be overrepresented in cancers. Using our nucleosome library, we preformed pulldowns from human embryonic kidney 293 cell nuclear lysates to comprehensively evaluate the role of single histone residues in nucleosome recognition. Overall, this study dissects the primary nucleosome binding hot-spot at high resolution and provide a robust resource for further exploration of the nucleosome interactome in normal and cancer cell biology.

Citation Format: Aleksandra Skrajna, Holly Simmons, Charlotte Smith, Jeanne-Marie E. Mcpherson, Dennis Goldfarb, Robert K. McGinty. Deciphering the nucleosome acidic patch binding at amino acid resolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2082.
Abstract 2086: Differential immune-cell landscape in tissue and liquid biopsy specimens is associated with recurrence risk across meningioma methylation-subtypes
Authors: Herrgott Grayson A.
Published: July 2021

Background. Tumor-infiltrating immune cells can favor or inhibit tumor growth, constituting promising and alternative targets for treatment of patients with meningiomas (MNG), a prevalent primary intracranial tumor with no known therapy beyond surgery and radiation. Immune-cell composition can predict therapy response in other diseases, therefore, profiling immune-cell infiltrates in these tumors is crucial, preferentially by non-invasive approaches. Genome-wide methylation arrays are powerful tools to classify and assess cell composition either in tumor tissue or with liquid biopsy.

Objective: We aim to apply methylation-based classifiers to estimate immune-cell composition of tumor tissue and serum specimens to predict recurrence-free survival in patients with MNG.

Methods: We conducted unsupervised and supervised analyses of the methylome of a multicenter MNG cohort composed of 326 tissue, 60 serum and 9 control specimens. Immune-cell composition (B-cells, CD4-T & CD8-T cells, neutrophils, natural killer cells, and monocytes) and recurrence risk were estimated using methylation-based classifiers. We used the point-biserial correlation method to analyze associations across categorical clinical and molecular features.

Results: We identified four distinct methylation subgroups of MNG (in serum or tissue) that presented a differential immune cell landscape composition. In the tissue, MNG methylation subgroups were mutually exclusive in enrichment or depletion of NK-, cytotoxic T- or monocyte-cell methylation signatures and in the serum, they were enriched of monocyte- and B-cell signatures. Distinct Immune-cell signatures (Monocytes, CD8T and Neutrophils) were correlated with risk of recurrence or grade in MNG tissue and/or liquid biopsy specimens.

Conclusion: DNA methylation-based deconvolution allowed for the detection of differential immune-cell composition across MNG methylation-subtypes in tissue that could be detected in liquid biopsy specimens. Distinct immune-cell signatures correlated with MNG recurrence risk/grade (e.g. T-cell) in our cohort were reported to improve anti-tumoral immune response in many tumors. These results suggest that profiling tumor immune-cell landscape can inform tumor behavior and provide insight in application of existing and novel therapeutic approaches in MNG.

Citation Format: Grayson A. Herrgott. Differential immune-cell landscape in tissue and liquid biopsy specimens is associated with recurrence risk across meningioma methylation-subtypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2086.
Abstract 2087: Breast tissue-specific DNA methylation levels predicted by genetic variants in association with breast cancer
Authors: He Chunyan , Castle James , Lin Nan , Liu Jinpeng , Wang Chi , Liu Yunlong
Published: July 2021

Aberrant DNA methylation (DNAm) contributes to the development of breast cancer. Both genetic and environmental factors influence DNAm levels in a tissue-specific fashion. Previously studies have reported that genetically predicted DNAm levels at CpGs were associated with breast cancer risk. However, the prediction models were built based on DNAm measured in blood, which may not be the most relevant tissue for breast cancer. In this study, we aim to build statistical models to predict breast tissue-specific DNAm levels using genetic data and DNAm sequencing data of normal breast tissue from healthy women (N=293). We applied these models to the GWAS data from the Breast Cancer Association Consortium that includes 46,785 breast cancer patients and 42,892 controls. We evaluated the association of genetically predicted breast tissue-specific DNAm levels at CpGs with breast cancer risk using MetaXcan. Due to our small sample size of normal breast tissue samples, we restricted our statistical models to those that were well-validated and highly correlated between predicted and measured DNAm levels (r≥0.6). We thus identified 45 CpGs that were significantly associated with breast cancer risk after correction for multiple testings, and many of these CpGs were also differentially methylation between breast tumor and normal tissue samples. Genes annotated to these CpG sites are enriched in Wnt signaling, cell cycle, and stem cell proliferation pathways, including known genes such as FGFR2, KLF4, CASC8, TERT, and EMBP1. We also identified novel putative DNAm markers for the development of breast cancer. Our study provides insight into tissue-specific genetic regulation of DNAm in normal breast tissue.

Citation Format: Chunyan He, James Castle, Nan Lin, Jinpeng Liu, Chi Wang, Yunlong Liu. Breast tissue-specific DNA methylation levels predicted by genetic variants in association with breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2087.
Abstract 2088: The effect of sorghum on epigenetic modifications in colon cancer
Authors: Kamagate Zeguela , Smolensky Dmitriy , Tsuji Petra
Published: July 2021

Colorectal cancer is a major public health issue, accounting for nearly 150,000 cases annually. Because colorectal cancer is correlated with inflammation and oxidative cellular stress, it would be highly beneficial to exploit bioactive components in our diet that could potentially inhibit cancer promotion. Certain varieties of the dietary grain sorghum (S. bicolor) contain high amounts bioactive polyphenols, which may contribute to the prevention of colon cancer due to their antioxidant properties, anti-inflammatory, and anti-carcinogenesis effects, some of which may be mediated by epigenetic mechanisms. Tumor suppressor genes are often hyper-methylated in tumors. Therefore, DNA methylation and histone acetylation patterns may affect the expression of genes that play a role in the promotion or prevention of colon cancer. Our objective is to investigate how high-polyphenol sorghum varietals impact epigenetic mechanisms in human colon cancer cells, including quantitating global DNA methylation and histone acetylation. We treated HCT116 human colon cancer cells with high-polyphenol sorghum extracts or solvent control, or 5 µM epigallocatechin gallate as a positive control, as it's known to decrease DNA methylation. Total RNA, protein, and DNA were harvested after 24 and 48 hours. mRNA expression of DNA methyltransferases (DNMT) were quantitated with qPCR. Our preliminary results suggest that high polyphenol sorghum may decrease the mRNA expression of DNMT1, the key enzyme that upholds methylation patterns after DNA synthesis. Furthermore, mRNA expression of DNMT 3A, which is the enzyme responsible for de novo DNA methylation, also indicated a decrease. We further plan to assess protein expression and catalytic activity of DNMTs and histone acetyltransferases in addition to global DNA methylation and histone acetylation to investigate the impact of these high polyphenol sorghum varietals on relevant epigenetic mechanisms in both HCT116 and CACO-2 cells. Consumption of high-polyphenol sorghum as part of the human diet may lead to global or gene-specific hypo-methylation or hyper-acetylation, and this may be of importance in the prevention of colon cancer. Research supported by USDA ARS Kansas.

Citation Format: Zeguela Kamagate, Dmitriy Smolensky, Petra Tsuji. The effect of sorghum on epigenetic modifications in colon cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2088.
Abstract 2116: Promoter enrichment of subnucleosomes using breast cancer cell-free DNA
Authors: Zukowski Alexis , Han Amy , Kabos Peter , Ramachandran Srinivas
Published: July 2021

Breast cancer is the leading cancer diagnosis and the second major cause of cancer-related deaths in women worldwide. The use of non-invasive cell-free DNA (cfDNA) to detect and assess cancer dynamics has recently gained traction with a focus on targeted mutation panels. However, mutation panels have to contend with non-tumor origin of mutations like clonal hematopoiesis and the emergence of novel mutations in the tumor. A potential alternative is to harness the epigenomic, or non-genetic, features of cfDNA. In a healthy individual, blood cell turnover is the major contributor to the cfDNA pool. In cancer, tumor DNA adds to the cfDNA pool, which represents the end product of endogenous nucleases acting on accessible genomic DNA. Since genomic DNA is protected by histone proteins, cfDNA maps the chromatin structure of individual cells that turn over. Subnucleosomes (partially formed structures of nucleosomes that are the building blocks of chromatin) are by-products of transcription and thus reflect small protections enriched in active genes. The enrichment of subnucleosomes at promoters correlate with gene expression profiles of cfDNA tissues-of-origin and based on this knowledge, we hypothesized that we could reconstruct the transcriptional profiles of cancer cells by selectively targeting promoter regions. We first extracted cfDNA from 9 healthy female donors and 8 patient donors with various stages of breast cancer (Stage I, n=1; Stage III, n=1; Stage IV, n=4). We used a single-stranded DNA library protocol that robustly captures highly nicked cfDNA, enabling the genome-wide mapping of both nucleosomes and subnucleosomes. We performed targeted capture of promoter-proximal, nucleosome-protected sequences in cfDNA using non-overlapping tiling probes from transcription start sites to 300 bp downstream. After whole-genome sequencing of pooled libraries, we show that 76.4% (n=13/17) of samples exhibited >10X enrichment compared to unenriched samples, and 64.7% (n=11/17) of samples exhibited >100X enrichment. The enriched samples allowed us to profile >10,000 genes, whereas unenriched samples enabled profiling between 100-10,000 genes at an average sequencing depth of 40 million reads. Overall, we obtain higher depth per sequencing read after enrichment resulting in a high-resolution snapshot of promoter-nucleosome dynamics derived by probing only ~0.18% of the genome. We believe that this significant advancement will allow us not only to identify presence of cancer but also detect distinct tumor states.

Citation Format: Alexis Zukowski, Amy Han, Peter Kabos, Srinivas Ramachandran. Promoter enrichment of subnucleosomes using breast cancer cell-free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2116.
Abstract 2119: Genome-wide epigenetic alterations in T-cell prolymphocytic leukemia
Authors: Tian Shulan , Zhang Henan , Klee Eric , Yan Huihuang , Ding Wei
Published: July 2021

T-cell prolymphocytic leukemia (T-PLL) is a rare disease showing a rapid clinical course, with a median survival of <1 year. Whole-genome and whole-exome sequencing have identified key genetic lesions in T-PLL, including structural alterations such as inversions, translocations, and large copy number variants, as well as recurrent somatic mutations of genes encoding chromatin regulators and of those in the JAK-STAT signaling pathway. Epigenetic alteration is implicated in the susceptibility and progression of both cancer and non-cancerous diseases. However, genome-wide epigenetic data has not been generated for T-PLL, which prohibits the mechanistic studies of transcriptional misregulation in T-PLL. This study used micrococcal nuclease digestion and sequencing (MNase-seq) to profile the chromatin accessible regions, i.e., gene regulatory regions such as promoters, enhancers and insulators, in both T-PLL patients and healthy individuals. Our analysis revealed the prevalence of lost open chromatin regions in T-PLL. We also generated histone H3 lysine 4 monomethylation (H3K4me1) and lysine 27 acetylation (H3K27ac) chromatin immunoprecipitation and sequencing (ChIP-seq) data from the same samples. We identified 5,462 and 2,833 active enhancers (>=2.5 kb away from transcription start sites) that are lost and gained in T-PLL, respectively, compared to normal. The differential H3K27ac peaks are preferentially associated with the nearest genes differentially expressed between T-PLL and normal (chi-square test p <2.2e-16), indicating a role of epigenetic alteration in transcriptional misregulation. In addition, we identified alterations of active enhancers that target oncogenes with key roles in T-PLL, such as TCL1Aand MYC. Together, our analysis has provided insights into the epigenetic mechanisms that drive oncogenic activation in T-PLL.

Citation Format: Shulan Tian, Henan Zhang, Eric Klee, Huihuang Yan, Wei Ding. Genome-wide epigenetic alterations in T-cell prolymphocytic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2119.
Abstract 2125: Roles of KAT6A and KAT6B in the biology of estrogen positive breast cancer
Authors: Meaux Isabelle , Gorge-Bernat Dimitri , Paz Angele , Geslin Catherine , Debussche Laurent , Moll Jürgen , Henry Christophe
Published: July 2021

KAT6A and KAT6B are histone acetyl transferase (HAT) that are controlling gene expression by transferring acetyl groups to histones. Yu et al (Oncogene, 2017 36, 2910-2918) have shown that KAT6A has a role in breast cancer development by activating the ERα promoter and was found frequently amplified in 11% and is overexpressed in 15% of breast cancers. Altogether, these data support KAT6A as an attractive target in estrogen receptor driven breast cancer. KAT6B is a close homolog that shares 91% identity in the acetyl coA binding site. While the prevalence of gene amplification for KAT6B in breast cancer is only 1-2%, it is often overexpressed. In this study, we are exploring how KAT6A and KAT6B are contributing to ERα expression and the growth of KAT6A amplified breast cancer cell lines. To decipher each protein's role, we have designed specific siRNA against KAT6A and KAT6B and we tested their action either individually or in combination in the KAT6A gene amplified breast cancer cell lines T-47D, CAM-1 and ZR-75. Following treatment of T-47D, CAMA-1 and ZR75 cell lines with KAT6A or B siRNA we observed a decrease of ERα gene and protein expression for all siRNAs. The effect was more pronounced when using KAT6A over KAT6B and the effect of both siRNA A/B were additive. Phenotypically, the impact on cell line proliferation by applying clonogenic and incucyte assays, mirrors what is observed on ERα gene and protein expression. The effect on cellular proliferation of KAT6A is more prominent than KAT6B silencing, while the combined KAT6A + KAT6B silencing being more impactful than KAT6A silencing alone. In conclusion, our data show that KAT6A and KAT6B share similar function in the control of ER gene and protein expression. This study suggests that KAT6A and KAT6B may be paralogs, one compensating for the loss of the other. This translates into a more pronounced antiproliferative effect when both genes are silenced concomitantly.

Citation Format: Isabelle Meaux, Dimitri Gorge-Bernat, Angele Paz, Catherine Geslin, Laurent Debussche, Jürgen Moll, Christophe Henry. Roles of KAT6A and KAT6B in the biology of estrogen positive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2125.
Abstract 2129: Usp22 controls multiple signaling pathways in development and disease
Authors: Koutelou Evangelia , Kuang Xianghong , Dent Sharon Y.
Published: July 2021

Our research is focused on defining the functions of histone-modifying enzymes in normal cells so that we can understand how alterations in these activities contribute to tumor development or progression. The highly conserved SAGA complex plays important roles at multiple steps of gene transcription in yeast, flies, and mammalian cells. This modular complex houses two enzymatic activities, the GCN5 histone acetyltransferase, and the USP22 deubiquitinase. USP22 is overexpressed in highly aggressive, therapy-resistant cancers, but the normal functions of this deubiquitinase are not well defined. Our detailed analysis of the embryonic lethality observed in the Usp22-/- mouse model we generated highlighted a critical role for Usp22 in the developing placenta. We found that Usp22 deletion in mice results in embryonic lethality due to defects in the formation and organization of extra-embryonic placental tissues, culminating in failure to establish proper vascular interactions with the maternal circulatory system. These phenotypes arise from abnormal gene expression patterns that reflect defective kinase signaling, including TGFß and several receptor tyrosine kinase (RTK) pathways. Interestingly, overexpression of USP22 in mice leads to an over branching phenotype of the mammary gland, which is linked to the deregulation of the signaling pathways described above. Our results provide insights to potential angiogenic functions of the SAGA complex, indicate that Usp22 is critical for the proper execution of multiple signaling pathways important for normal development, and provide new clues towards Usp22 contributions to cancer and other disease states.

Citation Format: Evangelia Koutelou, Xianghong Kuang, Sharon Y. Dent. Usp22 controls multiple signaling pathways in development and disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2129.
Abstract 213: BART cancer: A web resource for transcriptional regulators in cancer genomes
Authors: Thomas Zachary V. , Wang Zhenjia , Zang Chongzhi
Published: July 2021

The goal of this study is to develop a comprehensive data resource for transcriptional regulator activities in various cancers. Dysregulation of gene expression plays an important role in cancer development. Identifying transcriptional regulators (TRs), including transcription factors and chromatin regulators, that drive the oncogenic gene expression program is a critical task in cancer research. Genomic TR profiling data from primary cancer samples are limited in the public domain. Here, we present BART Cancer, an interactive web resource database to display putative TRs that are responsible for regulating differentially expressed genes across 15 different cancer types included in The Cancer Genome Atlas (TCGA). BART Cancer integrates over 10,000 gene expression profiling RNA-seq datasets from TCGA with over 7,000 ChIP-seq datasets from the Cistrome Data Browser database and the Gene Expression Omnibus (GEO). BART Cancer uses Binding Analysis for Regulation of Transcription (BART) for predicting TRs from differentially expressed genes comparing cancer samples with normal samples for each cancer type. BART Cancer also displays the activities of over 900 TRs across cancer types, by integrating computational prediction results from BART and from the Cistrome Cancer database. Focusing on transcriptiona regulatory activities in human cancers, BART Cancer provides unique insights into epigenetics and transcriptional regulation in cancer, and is a useful data resource for genomics and cancer research communities. BART Cancer web resource can be accessed at: http://bartcancer.org.

Citation Format: Zachary V. Thomas, Zhenjia Wang, Chongzhi Zang. BART cancer: A web resource for transcriptional regulators in cancer genomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 213.
Abstract 2138: Whole genome cfDNA profiles reveal common signatures of Immune checkpoint inhibition response in kidney, melanoma, and lung cancers
Authors: Donnella Hayley , Zhang Yue , Wang Irving , Vallania Francesco , Louie Maggie , Lin C. Jimmy
Published: July 2021

Immune checkpoint inhibition (ICI) via anti-PD-1/PD-L1 and anti-CTLA4, has improved clinical outcomes for multiple cancers, including non-small cell lung cancer (NSCLC), kidney cancer, and melanoma. Despite this success, response rates remain low, highlighting the need for more robust predictive biomarkers. In this study, we used cell-free DNA (cfDNA) profiles from patients undergoing ICI therapy to identify common signatures associated with responses shared among the three cancers. Whole-genome sequencing (mean coverage=18X) of cfDNA was performed on pre-treatment plasma samples from 126 patients across three cancers (NSCLC, n=91; kidney, n=21; melanoma, n=14). Transcriptional activation for protein-coding genes was then inferred by modeling fragment distribution around each transcription start site (TSS-GAP). Transcription factor binding activity (TFBA) was estimated by measuring binding site accessibility across the genome.

To delineate potential signatures of response, we performed a gene set enrichment analysis (GSEA) based on weighted average effect sizes of TSS-GAP levels between response groups across the three cancer types. GSEA results showed an enrichment of DNA repair and cell cycle genes in non-responders and of EMT processing genes in responders. To identify shared signatures of ICI response, we performed a meta-analysis by (1) computing the effect size between response groups for TFBA and TSS-GAP features in each cancer type; (2) calculating a weighted-average effect size across cancer types; (3) performing gene selection based on the degree of heterogeneity among cancer types, followed by false discovery rate correction and assessment of significance through Monte Carlo permutation testing. This analysis identified 13 transcription factors and 269 genes consistently enriched in response groups across these cancer types. Notably, this analysis revealed significantly higher accessibility in STAT5A (p=0.02), JUN (p=0.02) and JUNB (p=0.03) in non-responders, suggesting JAK/STAT-pathway dependency as a common feature in ICI resistance.

Using our platform that detects both tumor and non-tumor-derived signals, we identified common signatures of ICI response, revealing a potential pathway of resistance through JAK/STAT signaling and a possible EMT signature of response in kidney, melanoma, and NSCLC. These findings warrant further investigation into using cfDNA signatures for patient stratification and response monitoring.

Citation Format: Hayley Donnella, Yue Zhang, Irving Wang, Francesco Vallania, Maggie Louie, C. Jimmy Lin. Whole genome cfDNA profiles reveal common signatures of Immune checkpoint inhibition response in kidney, melanoma, and lung cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2138.
Abstract 2151: Neuroendocrine cancer cells have changed HOX code during trans-differentiation
Authors: Cheng Siyuan , Yang Shu , Shi Yingli , Shi Runhua , Yeh Yunshin , Yu Xiuping
Published: July 2021

Background: HOX genes encode Homeobox-containing proteins. There are 39 HOX genes organized into 4 clusters in human. The nested and partially overlapping expression of HOX genes in an anatomic region can determine its tissue specificity, which is termed as “HOX code”. In this study, we examined the expression of HOX genes in neuroendocrine prostate cancer (NEPCa), an aggressive subtype prostate cancer that arises from prostate adenocarcinoma (AdPCa) trough trans-differentiation.

Methods: The HOX genes expression data were extracted from Cancer Cell Line Encyclopedia (CCLE) dataset. All in silico analysis were performed by using R language. Immunohistochemistry (IHC), dual immunofluorescence staining, Western blot and RT-qPCR were conducted to access the expression of HOXs.

Results: Using the HOXs' mRNA expression data from CCLE, we generated HOX codes for 25 different types of tissues. These HOX codes were validated in TCGA pan cancer. By calculating the Pearson correlation, we were able to use 9 HOX codes including prostatic HOX code to identify the tissue origins of the cancer samples. Further, we found that in prostate cancer, the NEPCa samples have lost prostatic HOX code while majority of the AdPCa samples maintain the prostatic HOX code. The expression of HOXB13, the most prominent HOX expressed in prostatic tissues, was increased in AdPCa along with PCa progression but was decreased in NEPCa. Similarly, we found that in breast cancer, a sub-group of samples correlated well with the HOX code of mammary gland, but the rest did not. By comparing the differentially expressed genes in these two subgroups of samples, we found that the neuroendocrine markers including CHGA, CHGB and SYP were higher in HOX code-negative samples compared with HOX code-positive ones. Additionally, we observed a similar phenomenon in colorectal cancer samples: The expression of neurogenesis genes were enriched in HOX code-negative subgroup.

Conclusions: 1) The expression of HOXB13 is decreased in NEPCa. 2) NEPCa has changed HOX code, suggesting the loss of prostatic identity in these samples. 3) The association of neuroendocrine phenotype with the changes in HOX code is not limited to prostate cancer but also is observed in other types of cancer.

Significance: The HOX codes we established can be used in pan cancer research to identify the tissue origins of cancer samples and to study the trans-differentiation of cancer cells.

Funding: This study is supported by: The LSUHS Office of Research SEED awards, NIH R01 CA226285 and Feist-Weiller Cancer Center.

Citation Format: Siyuan Cheng, Shu Yang, Yingli Shi, Runhua Shi, Yunshin Yeh, Xiuping Yu. Neuroendocrine cancer cells have changed HOX code during trans-differentiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2151.
Abstract 2156: Genomics and molecular analysis of Aurora kinase B (AURKB) in response to antiretroviral (ARV) treatment in lung cancer
Authors: Marima Rahaba Makgotso , Hull Rodney , Dlamini Zodwa , Penny Clement
Published: July 2021

Aurora kinase B (AURKB) is essential for normal physiological processes. However, aberrant AURKB expression has been reported in various cancers, including lung cancer. Lung cancer is a leading non-AIDS defining cancer (NADCs) and the relationship between the use of antiretrovirals (ARVs) and lung cancer is poorly understood. The anti-proliferative effects of Efavirenz (EFV) and Lopinavir/ritonavir (LPV/r) have also been documented. This study aimed at determining the genomic and molecular roles of AURKB in lung cancer in response to ARV treatment. For this purpose, cellular (xCELLigence RTCA), molecular (RT-qPCR) and bioinformatics tools were used in normal fibroblasts (MRC-5) and adenocarcinoma (A549) lung cells. Real-Time Cell Analysis (RTCA) data confirmed the anti-proliferative effects of ARVs in a time-dependent manner. AURKB gene expression was elevated in A549 compared to MRC-5 in non-ARV treated. Interestingly, p53 and CASP3 gene expression was downregulated. Contrarily, ARV treatment resulted in the formation of a negative signaling loop due to AURKB being downregulated, while CASP3 and p53 were upregulated. KEGG analysis demonstrated AURKB, CASP3 and p53 as cell cycle related genes. STRING database searches showed a strong protein-protein interaction (PPI) between AURKB and p53, and CAP3 and p53, but a weak PPI between AURKB and CASP3. Gene Ontology (GO) analysis revealed a decline in serine/threonine kinase (AURKB) activity in cancer cells in response to ARV treatment. Although not yet confirmed, AURKB displays oncogene features, while its overexpression has been shown to deregulate p53. The association between the use of ARVs and lung carcinogenesis remains to be fully comprehended and targeting AURKB signaling may help shed light on this relationship.

Citation Format: Rahaba Makgotso Marima, Rodney Hull, Zodwa Dlamini, Clement Penny. Genomics and molecular analysis of Aurora kinase B (AURKB) in response to antiretroviral (ARV) treatment in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2156.
Abstract 2159: Oscillating p53 temporal dynamics enable proliferative recovery of cells following DNA damage
Authors: Lu Dan , Jimenez Alba , Jambhekar Ashwini , Lahav Galit
Published: July 2021

The transcription factor and tumor suppressor protein p53 regulates cellular outcomes (e.g. cell cycle arrest, senescence or apoptosis) following DNA damage. Cellular outcomes can be influenced by modulating the temporal expression dynamics of p53, which in turn alters target gene mRNA expressions patterns. However, it is not clear how changes in such mRNA dynamics would eventually results in differences in temporal protein expression dynamics, which ultimately determines the cell outcome. By quantifying mRNA and protein by RNA-Seq and mass-spectrometry, respectively over time, we systematically categorized the different dynamics which could arise of p53 target mRNAs and proteins. We show that while p53 target proteins plateaus under pulsatile dynamics, the majority of target proteins are enhanced and accumulates under sustained dynamics including many regulators of terminal cell fates such as apoptosis and senescence. Next we derived synthesis and degradation rates based on empirical measurements to model how different p53 dynamics could lead to the assortment of subsequent target protein dynamics. We show that target protein dynamics are highly governed by protein degradation rate, implying the temporal selection of target gene expression is not pre-determined by the initiating stress signal, but rather through differences in the inherent protein degradation rates. Furthermore, we identify multiple unique signaling network motifs which results in target protein accumulation only under sustained (persistent) but not pulsatile (oscillatory) p53 dynamics. Our results highlight the diversity of mechanisms cells evolved to decode transcription factor dynamics as well as the role of p53 in governing cellular outcome, important both in understanding cellular information processing as well as therapeutic implications for cancer treatments.

Citation Format: Dan Lu, Alba Jimenez, Ashwini Jambhekar, Galit Lahav. Oscillating p53 temporal dynamics enable proliferative recovery of cells following DNA damage [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2159.
Abstract 2164: Overexpression of the TERT binding proteins GABPA/B in Glioblastoma
Authors: Timmer Marco , Papazacharias Efthymios , Goldbrunner Roland
Published: July 2021

Enhanced expression of TERT in gliomas is a result of two hotspot mutations, C228T and C250T, at the promoter region. GA-binding proteins selectively bind at these positions, respectively causing an activation of the promoter and overexpression of TERT. GABP is a multimeric protein consisting of GABPA and GABPB with its isoforms GABPB1, GABPB1-L, GABPB1-S, GABPB2. In this study, we investigated the mRNA expression and association between TERT and GABPA/B isoforms in tumor samples of different glioma grades. The expression was determined by quantitative real-time PCR and the results were statistically analyzed. We present that TERT is mainly expressed in primary glioblastomas. All GA-binding proteins progress through the glioma grades and have the highest expression levels in secondary glioblastomas. In secondary glioblastomas after chemotherapy, GABPB1 and GABPB1-L are lower expressed than without treatment. In high grades, TERT and GABPA, GAPB1, GABPB1-L, GABPB1-S are upregulated compared to low grades. Between primary and secondary glioblastomas with and without chemotherapy, TERT is elevated in the former while GABPB1 is increased in the secondary glioblastomas. GABPA and GABPB1, GABPB1-L and GABPB1-S positive correlate in primary glioblastomas. The present study confirms the upregulation of TERT in primary glioblastomas while all GABP proteins rise with the malignancy of the gliomas. TERT and all GABP proteins seem to play a key role in the gliomagenesis.

Citation Format: Marco Timmer, Efthymios Papazacharias, Roland Goldbrunner. Overexpression of the TERT binding proteins GABPA/B in Glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2164.
Abstract 2178: Spectrum of pathogenic germline mutations in Chinese esophageal squamous cell carcinoma patients through next-generation sequencing
Authors: Cai Ruijun , Zheng Yating , Xie Wenzhuan , Huang Mengli
Published: July 2021

Background: Esophageal Squamous Cell Carcinoma (ESCC) is one of the leading cause of cancer death in China, while the nature of genetic factors related to ESCC has not been well-studied. The purpose of this study is to assess the inherited genetic factors regarding pathogenic germline mutations in Chinese ESCC population.

Methods: Tumor tissue samples from Chinese patients with ESCC were analyzed using next generation sequencing (NGS) (panel on 381/733-gene). MSI was evaluated by NGS of 500 known MSI loci. PD-L1 expression was evaluated using immunohistochemistry (Dako 22C3). TMB was defined as total number of somatic non-synonymous mutations in coding region.

Results: Genomic profiling of DNA of 271 ESCC patients were analyzed using NGS, of which 251 (92.6%) harbored 354 pathogenic or very likely pathogenic germline mutations in 94 genes. In ESCC patients with germline mutations, the most frequently germline mutated genes were CYP2C19 (54.18%), followed by UGT1A1 (41.04%), RAC1 (35.06%), VEGFA (34.66%), DPYD (33.47%), CD74 (31.47%), MGMT (31.08%), CYP2D6 (29.88%), BCL2L11 (12.35%), FANCA (7.97%), ALK (7.57%), APC (7.17%), and BARD1 (5.98%). Of all the 94 germline mutated genes, 26.6% (n=25) lay in the DNA damage repair (DDR) pathways. The most frequently germline mutated DDR genes were FANCA (7.97%), followed by BARD1 (5.98%), FANCG (5.98%), BLM (5.58%), BRCA2 (5.18%), BRCA1 (4.78%), FANCD2 (4.78%), POLD1 (3.98%), ATM (3.59%), and POLE (3.58%). MSI status analysis was performed in 246 of 251 ESCC patients with germline mutated genes, and the results showed that all the patients with germline mutated genes were determined to be MSS. In addition, among 251 ESCC patients with germline mutated genes, 163 of them were tested for PD-L1. The results showed that 45 (27.6%) of the ESCC patients were PD-L1 positive (CPS≥10) and 118 (72.4%) were PD-L1 negative. Of the 247 ESCC patients with germline mutations that could be evaluated for TMB, 60 (24.29%) patients had TMB≥10Muts/Mb.

Conclusions: As the first study to explore the pathogenic germline mutation profile of Chinese ESCC patients, our study provides valuable clues for the assessment and clinical management of genetic susceptibility to ESCC patients.

Citation Format: Ruijun Cai, Yating Zheng, Wenzhuan Xie, Mengli Huang. Spectrum of pathogenic germline mutations in Chinese esophageal squamous cell carcinoma patients through next-generation sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2178.
Abstract 2205: Molecular subtypes of head and neck cancer in patients with African ancestry
Authors: Mezghani Nadia , Yao Alexandria G. , Taylor Alison M. , Momen-Heravi Fatemeh
Published: July 2021

Epidemiological data identifies disparities in black patients for head and neck squamous carcinoma (HNSCC) screening, detection, treatment, and survival. Although socioeconomic and environmental factors play a role in the existing racial disparities, HNSCC incidence and survival rates in the black population cannot be attributed to these factors alone. To investigate the role race plays in the genomics of head and neck cancer, we examined HNSCC samples from 49 black and 446 white patients in the Cancer Genome Atlas (TCGA). We used computationally-derived ancestry identifications to correlate race with HNSCC molecular features. We then characterized the extent to which genomic alterations in black patients impact their clinical outcomes. We found that black patients lived significantly fewer disease-free months and had a poorer overall survival than white patients. Black patients showed a higher frequency of human papillomavirus (HPV)-negative than HPV-positive tumors compared to white patients. Black patients were found to suffer higher rates of metastasis and more aggressive lymph node involvement. Differences in patient primary tumor site were also identified, with black patients having a higher prevalence of tumors in the larynx and lower prevalence of tumors in the tongue compared to white patients. We also found higher frequencies of RUNX1T1, KMT2D, and UNC13C mutations and lower frequency of PIK3CA mutations in black patients. We found a significant enrichment of MYC signaling and amplifications in the tumors of black patients compared to white patients. Novel data uncovered by this project brings us closer to understanding the racial disparities in HNSCC, and advances research aimed at eliminating those disparities. Unique tumor mutations and molecular signatures show promising clinical utility in providing more targeted, individualized screening diagnostic, and treatment modalities to reduce outcome disparities in the black population.

Citation Format: Nadia Mezghani, Alexandria G. Yao, Alison M. Taylor, Fatemeh Momen-Heravi. Molecular subtypes of head and neck cancer in patients with African ancestry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2205.
Abstract 2215: Landscape of RET fusion identified by next-generation sequencing in a Chinese multi-cancer retrospective analysis
Authors: Lei Ting , Wang Weiran , Wang Danhua , Fu Junfeng , Wang Yu , Wang Ze , Fan Zhe , Lv Zhenyang , Ma Tonghui
Published: July 2021

Background: Fusion of RET with several partner genes has been detected in papillary thyroid, lung, colorectal, pancreatic and breast cancers. FDA has approved Retevmo (Selpercatinib) for lung and thyroid cancers with RET gene mutations or fusions. Here we focused on the prevalence of RET fusions in a Multi-cancer cohort (besides lung and thyroid cancers) for patients (pts) whom might benefit from RET inhibitors in clinical development.

Methods: Genomic profiling was performed on 12,888 lung cancer pts, 2,848 colorectal cancer pts, 1,785 liver cancer pts, 1,169 Gastric cancer pts and 232 thyroid cancer pts from Jan. 2017 to Dec. 2019 using next-generation sequencing (NGS), which covers all exons of RET and specific intron 7-11 containing the break points of fusions. The fusion patterns of RET were analyzed.

Results: A total of 165 RET fusions were identified in approximately 0.86% (163/18,922) of this Chinese multi-cancer cohort. The RET fusion-positive rates were 1.05% (135/12,888) in lung cancer pts, 0.39% (11/2,848) in the colorectal cancer pts, 0.06% (1/1,785) in liver cancer pts, 0.09% (1/1,169) in the 1169 Gastric cancer pts and 6.03% (15/232) in the 232 thyroid cancer pts tested. The most common partners were KIF5B (62.04%) and CCDC6 (21.17%) in lung cancer, NCOA4 (45.45%) and CCDC6 (27.27%) in colorectal cancer, and CCDC6 (93.33%) and NCOA4 (6.67%) in thyroid cancer. The most frequent regions of RET fusions were intron 11 (140/165) and intron 10 (15/165). The common fusion partners detected in different cancers are variable, indicating that the same oncogene has different carcinogenic mechanisms in cancers, and the sensitivity of these fusions to RET inhibitors in different cancers needs to be further studied.

Conclusions: This study revealed the molecular features of RET rearrangement in Chinese cancer pts, which might result in more effective personalized diagnoses and therapies.

Citation Format: Ting Lei, Weiran Wang, Danhua Wang, Junfeng Fu, Yu Wang, Ze Wang, Zhe Fan, Zhenyang Lv, Tonghui Ma. Landscape of RET fusion identified by next-generation sequencing in a Chinese multi-cancer retrospective analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2215.
Abstract 2216: Exploration of the genomic features of pan-neuroendocrine tumors in a Chinese retrospective analysis
Authors: Ye Jinyan , Wang Weiran , Wang Danhua , Ma Tonghui
Published: July 2021

Background: A neuroendocrine tumor (NET) begins in the specialized cells of the body's neuroendocrine system. Most NETs take years to develop and grow slowly. However, some NETs can be fast-growing. NETs can occur in any part of the body, including gastrointestinal (GI) tract (43%), lung (30%), pancreas (7%) and other organs. Here, we reported an analysis of genomic features in 16 GI tract, 45 lung and 13 pancreas NETs.

Methods: Patients (pts) with neuroendocrine tumors were enrolled, and surgical tumor tissues or plasma samples were collected. Mutation profiling was performed by next-generation sequencing (NGS).

Results: Compared with GI tract NETs patients (Age±SD, 52±11.2), lung NETs patients (Age±SD 62±8.4, P< 0.001) occurred in older patients, and the median age (±SD) of pancreas NETs patients was 58 (±10.8). Mutations were identified in 66 of NETs patients (89.19%), including 12 GI tract (75%), 43 lung (95.56%) and 11 pancreas (84.62%) NETs. Mutations of TP53 (43.85%, 7/16), APC (31.25%, 5/16) and KRAS (25%, 4/16) in GI tract NETs; TP53 (80%, 36/45), LRP1B (24.44%, 11/45) and EGFR (20%, 9/36) in lung NETs and MEN1 (30.77%4/13) in pancreas NETs were observed as the most commonly genetic variations in different type of NETs, which located in different signal pathways and suggested different pathogenesis. Meanwhile, there was no MEN1 mutations and only one LRP1B or EGFR mutation (6.25%, 1/16) occurring in GI tract NETs, one MEN1 mutation (2.22%, 1/44) occurring in lung NETs, and one TP53, KRAS or LRP1B mutation (7.69%, 1/12) and no APC or EGFR mutations occurring in pancreas NETs. In total, although gastrointestinal tract, lung and pancreas NETs all begin in the cells, which have traits of both hormone-producing endocrine cells and nerve cells, the mutation spectrums are very different. On the contrary, the mutations carried by NETs in different locations are related to the organ.

Conclusions: In summary, genomic characterization of NETs may offer insights into tumorigenesis and identify potential therapeutic targets in this disease.

Citation Format: Jinyan Ye, Weiran Wang, Danhua Wang, Tonghui Ma. Exploration of the genomic features of pan-neuroendocrine tumors in a Chinese retrospective analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2216.