bluuebunny/crossref_metadata_2025 huggingface dataset:
Path Planning and Setup Orientation for Automated Dimensional Inspection Using Coordinate Measuring Machines
Authors: Abdulhameed Osama , Al-Ahmari Abdulrahman , Mian Syed Hammad , Aboudaif Mohamed K.
Published: December 2020

Inspection planning is considered an essential practice in the manufacturing industries because it ensures enhanced product quality and productivity. A reasonable inspection plan, which can reduce inspection costs and achieve high customer satisfaction, is therefore very important in the production industry. Considerations such as preparations for part inspection, measuring machines, and their setups as well as the measurement path are described in an inspection plan which is subsequently translated into part inspection machine language. Therefore, the measurement of any component using a coordinate measuring machine (CMM) is the final step preceded by several other procedures, such as the preparation of the part setup and the generation of the probe path. Effective measurement of components using CMM can only be done if the preceding steps are properly optimized to automate the whole inspection process. This paper has proposed a method based on artificial intelligence techniques, namely, artificial neural network (ANN) and genetic algorithm (GA), for fine-tuning output from the different steps to achieve an efficient inspection plan. A case study to check and validate the suggested approach for producing effective inspection plans for CMMs is presented. A decrease of nearly 50% was observed in the travel path of the probe, whereas the CMM measurement time was reduced by almost 25% during the actual component measurement. The proposed method yielded the optimum part setup and the most appropriate measuring sequence for the part considered.
Patterns of Human Leukocyte Antigen Class I and Class II Associations and Cancer
Authors: Liu Zhiwei , Derkach Andriy , Yu Kelly J. , Yeager Meredith , Chang Yu-Sun , Chen Chien-Jen , Gyllensten Ulf , Lan Qing , Lee Mei-Hsuan , McKay James D. , Rothman Nathaniel , Yang Hwai-I , Hildesheim Allan , Pfeiffer Ruth M.
Published: December 2020

Human leukocyte antigen (HLA) gene variation is associated with risk of cancers, particularly those with infectious etiology or hematopoietic origin, given its role in immune presentation. Previous studies focused primarily on HLA allele/haplotype-specific associations. To answer whether associations are driven by HLA class I (essential for T-cell cytotoxicity) or class II (important for T-cell helper responses) genes, we analyzed GWAS from 24 case–control studies and consortia comprising 27 cancers (totaling >71,000 individuals). Associations for most cancers with infectious etiology or of hematopoietic origin were driven by multiple HLA regions, suggesting that both cytotoxic and helper T-cell responses are important. Notable exceptions were observed for nasopharyngeal carcinoma, an EBV-associated cancer, and CLL/SLL forms of non-Hodgkin lymphomas; these cancers were associated with HLA class I region only and HLA class II region only, implying the importance of cytotoxic T-cell responses for the former and CD4+ T-cell helper responses for the latter. Our findings suggest that increased understanding of the pattern of HLA associations for individual cancers could lead to better insights into specific mechanisms involved in cancer pathogenesis.

Significance:

GWAS of >71,000 individuals across 27 cancer types suggest that patterns of HLA Class I and Class II associations may provide etiologic insights for cancer.
Racial/Ethnic Disparities in All-Cause Mortality among Patients Diagnosed with Triple-Negative Breast Cancer
Authors: Wang Fei , Zheng Wei , Bailey Christina E. , Mayer Ingrid A. , Pietenpol Jennifer A. , Shu Xiao-Ou
Published: December 2020

It is unclear whether racial/ethnic disparities in triple-negative breast cancer (TNBC) mortality remain after accounting for clinical characteristics, treatment, and access-to-care–related factors. In this study, women with a primary diagnosis of TNBC during 2010–2014 were identified from the National Cancer Database. Hazard ratios (HR) and 95% confidence intervals (CI) for 3- and 5-year all-cause mortality associated with race/ethnicity were estimated using Cox proportional hazards models with stepwise adjustments for age, clinical characteristics, treatment, and access-to-care–related factors. Of 78,708 patients, non-Hispanic (NH) black women had the lowest 3-year overall survival rates (79.4%), followed by NH-whites (83.1%), Hispanics (86.0%), and Asians (87.1%). After adjustment for clinical characteristics, NH-blacks had a 12% higher risk of dying 3 years post-diagnosis (HR, 1.12; 95% CI, 1.07–1.17), whereas Hispanics and Asians had a 24% (HR, 0.76; 95% CI, 0.70–0.83) and 17% (HR, 0.83; 95% CI, 0.73–0.94) lower risk than their NH-white counterparts. The black–white disparity became non-significant after combined adjustment for treatment and access-to-care–related factors (HR, 1.04; 95% CI, 0.99–1.09), whereas the white-Hispanic and white-Asian differences remained. Stratified analyses revealed that among women aged less than or equal to 50 with stage III cancer, the elevated risk among NH-blacks persisted (HR, 1.20; 95% CI, 1.04–1.39) after full adjustments. Similar results were seen for 5-year mortality. Overall, clinical characteristics, treatment, and access-to-care–related factors accounted for most of the white–black differences in all-cause mortality of TNBC but explained little about Hispanic- and Asian-white differences.

Significance:

These findings highlight the need for equal healthcare to mitigate the black–white disparity and for investigations of contributors beyond healthcare for lower mortality among Asians and Hispanics.
Abstract IA12: Dynamic metabolic regulation of epigenetic remodeling in macrophages
Authors: Fan Jing
Published: December 2020

Over the course of an immune response, macrophages undergo a sequence of functional transitions. These transitions are coupled to dynamic rewiring of cellular metabolism. The impact of metabolic state on chromatin modifications allows the dynamic metabolic reprogramming to orchestrate immunity during immune responses. Specifically, we found that in response to the classic stimuli lipopolysaccharide and interferon-γ, pyruvate dehydrogenase complex is profoundly inhibited over time, mediating the metabolic transition from the early pro-inflammatory stage to the later more immunosuppressive stage. The regulation of PDHC activity dynamically controls cellular acetyl-coA availability. We will discuss how this affects histone acetylation in macrophages over a course of prolonged stimulation and upon repeated stimulation. Furthermore, our study revealed that several metabolites directly involved in the addition or removal of histone methylation, such as S-adenosyl-methionine and succinate, show highly dynamic changes during the immune response. We will discuss which specific epigenetic modifications are sensitive to fluctuations in metabolite levels. This work reveals important mechanisms connecting metabolism, epigenetic and changes in macrophage functions during immune response.

Citation Format: Jing Fan. Dynamic metabolic regulation of epigenetic remodeling in macrophages [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr IA12.
Abstract IA18: Clock Control of HIF Activity and Muscle Tissue Regeneration
Authors: Peek Clara Bien
Published: December 2020

Circadian clocks generate rhythmic pulses of glucose metabolism and respiration to divide energy-producing and energy-consuming processes into separate periods in the light-dark cycle. At the cellular level, clocks direct the expression of thousands of genes involved in metabolism, tissue growth, and repair, yet our understanding of how clocks detect signals in the environment to coordinate transcription and metabolic flux at precise stages during development and in post-mitotic cells remains poorly understood. A breakthrough in understanding circadian mechanisms in metabolic plasticity came from our discovery that molecular clock transcription factors respond to changes in environmental oxygen. We uncovered a link between circadian clocks and the control of the oxygen- and mitochondrial stress-responsive hypoxia-inducible factor (HIF) pathway, which controls adaptation to low oxygen environments, such as during tumorigenesis and ischemic injury. Here, we demonstrate a role for the circadian clock in post-muscle injury myogenesis and tissue regeneration. Indeed, loss of Bmal1 in adult muscle stem cell populations leads to impaired regeneration after ischemic muscle injury in mice. Furthermore, we observe time-of-day differences in muscle regeneration rates, with more rapid tissue repair following injury during the dark (active) phase. In addition, myogenesis is reduced in primary Bmal1-/- myoblasts compared to controls, a phenotype that is exaggerated in hypoxic conditions. Finally, we observe that loss of Bmal1 in myoblasts leads to chromatin remodeling that alters transcription of genes involved in metabolic flux and myogenic gene expression. Together, our studies demonstrate that circadian clocks in muscle stem cells control metabolic and genomic reprogramming under hypoxia to regulate in vitro myogenesis and in vivo skeletal muscle regeneration.

Citation Format: Clara Bien Peek. Clock Control of HIF Activity and Muscle Tissue Regeneration [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr IA18.
Abstract PO-037: Leveraging polyamine metabolic stress to enhance sensitivity to epigenetic therapy for prostate cancer
Authors: Rowsam Aryn M. , Affronti Hayley C. , Rosario Spencer R. , Long Mark D.
Published: December 2020

While polyamines are required for proliferation in all cells, the prostate synthesizes and secretes high levels into its lumen, resulting in depletion of intracellular polyamines. To meet polyamine biosynthetic demands, which is enhanced in Prostate Cancer (CaP), there is high flux through one carbon metabolism to provide S’-Adenosylmethionine (SAM), which donates its aminopropyl group to polyamine synthesis. This flux is driven by Spermidine/ Spermine N1-Acetyltransferase (SSAT) which adds acetyl groups to spermidine and spermine, leading to their secretion. To deal with the stress, the methionine salvage pathway (MSP) recycles one carbon units lost during polyamine synthesis back to the methionine cycle for SAM replenishment, by methylthioadenine phosphorylase (MTAP). We have shown increased polyamine catabolism by SSAT stabilization and MTAP inhibition results in cell death in in vitro, in vivo, and ex vivo CaP models. We expect the CaP epigenome to be impacted by stressed acetyl-CoA and SAM pools, which are used by chromatin modifying enzymes, and that this stress will alter CaP sensitivity to epigenetic based drugs. While epigenetic therapies are currently being investigated in the clinic for targeting CaP, their success has been limited due to toxicity and non-specificity. We hypothesize that increased flux through polyamine metabolism and one carbon metabolism disrupts SAM and acetyl-CoA pool maintenance, making CaP cells sensitized to therapy targeting their utilization. Our findings suggest that certain histone modifications are affected by treatment with BENSpm in vitro. Additionally, we have found treatment of CaP cells with BENSpm and MTDIA induces significant broad DNA methylation changes. Furthermore, our preliminary data shows that the addition of metabolic therapies, BENSpm and MTDIA, to an epigenetic targeting drug, JQ1, further suppresses CaP growth in vitro. We expect that future studies combining our metabolic therapies with epigenetic drugs targeting acetyl-CoA and SAM usage will maintain anti-tumor efficacy with reduced systemic toxicity.

Citation Format: Aryn M. Rowsam, Hayley C. Affronti, Spencer R. Rosario, Mark D. Long. Leveraging polyamine metabolic stress to enhance sensitivity to epigenetic therapy for prostate cancer [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PO-037.
Abstract PO-052: Combinatorial targeting of chromatin and metabolism for synergistic anti-cancer efficacy
Authors: Sheikh Tahir N. , Chen Xiao , Xu Xinjing , Patwardhan Parag P. , Schwartz Gary K. , Lu Chao
Published: December 2020

Altered cellular metabolic network and chromatin landscape represent two molecular hallmarks of cancer. Despite considerable interests, targeting metabolic or chromatin regulatory pathways as monotherapy was met with limited success in pre-clinical and clinical studies, in part due to the ability of cancer cells to rewire and adapt to the stress induced by therapeutic intervention. Therefore, there is a critical need to understand resistance programs and to identify strategies for more effective combinatorial therapies. We have previously uncovered that DNA and histone modifications are exquisitely sensitive to perturbations of the metabolic state. During tumor initiation, this metabolism-chromatin “crosstalk” is often hijacked by cancer cells to respond to fluctuations in signaling and nutrient abundance, but the role of such interplay in drug resistance has remained elusive. Here we demonstrated that cancer cells which developed resistance to inhibitor of glutamine catabolism (CB-839) displayed increased ratio of α-ketoglutarate to succinate that acts as a metabolic regulator of TET-family DNA hydroxylases and Jumonji-family histone demethylases. Accordingly, CB-839 resistant cancer cells showed global DNA hypomethylation and decreased levels of H3K9me3 and H3K27me3, which in turn resulted in increases in histone acetylation and a gene expression program that promoted metabolic adaptation to inhibition of glutaminolysis. Importantly, this altered chromatin landscape also represented a therapeutic vulnerability, as CB-839 resistant cells were selectively hyper-sensitive to small-molecule inhibitors of BET domain such as JQ1 and PLX51107. We are currently testing the possible synergistic effects of clinical stage glutaminase and BET inhibitors across various cancer types. Taken together, these results highlight the potential of exploring and therapeutically exploiting metabolic and chromatin interactions for developing rationally designed, precision combinatorial anti-cancer treatment strategies.

Citation Format: Tahir N. Sheikh, Xiao Chen, Xinjing Xu, Parag P. Patwardhan, Gary K. Schwartz, Chao Lu. Combinatorial targeting of chromatin and metabolism for synergistic anti-cancer efficacy [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PO-052.
Abstract PO-055: Pan-cancer metabolic profiling of the tumor microenvironment
Authors: Rohatgi Neha , Ghoshdastider Umesh , Baruah Probhonjon , Skanderup Anders Jacobsen
Published: December 2020

Tumors are heterogeneous cellular environments with entwined metabolic dependencies. However, it is challenging to differentially profile metabolism in cancer and infiltrating non-malignant cells inside patient tumors. Here, we used a tumor transcriptome deconvolution approach to profile the metabolic states of cancer and non-cancer (stromal) cells in bulk tumors of 20 solid tumor types. This analysis highlighted metabolic genes and processes recurrently upregulated in cancer cells across tumor types, including the mitochondrial dicarboxylate carrier SLC25A10. Intriguingly, the tryptophan-degrading dioxygenase, IDO1, was highly recurrently overexpressed in stroma compared to cancer cells and normal tissue, suggesting that tryptophan-mediated suppression of antitumor immune response is predominantly constrained by the stroma. Oxidative phosphorylation was unexpectedly the most upregulated metabolic process in cancer cells compared to both stromal cells and a large atlas of cancer cell lines, suggesting that the warburg effect may be less pronounced in cancer cells in vivo. Overall, our analysis highlights fundamental differences in metabolic states of cancer and stromal cells inside tumors and establishes a pan-cancer resource to interrogate tumor metabolism.

Citation Format: Neha Rohatgi, Umesh Ghoshdastider, Probhonjon Baruah, Anders Jacobsen Skanderup. Pan-cancer metabolic profiling of the tumor microenvironment [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PO-055.
Abstract PO-056: Role of the metabolite N-acetylaspartate in breast cancer progression
Authors: Balasubramanian Akhila , Zhang Weijie , Gu Franklin , Ambati Chandra , Putluri Nagireddy , Zhang Xiang , Namboodiri Aryan , Ambs Stefan , Sreekumar Arun
Published: December 2020

Breast cancer (BCa) is a disease that affects over a quarter million women in the US every year. Our laboratory studies reprogrammed energy metabolism in BCa, which is an essential hallmark of the disease. Specifically, we focus on the metabolic rewiring events that occur in BCa, intending to identify cancer-associated metabolic vulnerabilities to treat this aggressive disease. Using a global metabolic profiling approach, we have determined that the metabolite N-acetylaspartate (NAA) is highly accumulated in patients with BCa. Prior studies involving NAA in other cancer types have attributed its accumulation to the upregulation of the enzyme N-acetyl transferase (NAT8L), which synthesizes NAA. However, using matched gene expression data, we found that the accumulation of NAA in these BCa tumors rather coincides with the downregulation of aspartoacylase (ASPA), the enzyme that breaks down NAA. To determine the role of NAA in BCa progression, we generated multiple cell line models containing either NAT8L knockdown, ASPA overexpression, or a combination of the two in the cell line MDA-MB231 in a bid to deplete intracellular NAA. We used these models to test for metastasis by tail vein injection in immunocompromised mice. Consistent with our expectations and other reports, NAT8L knockdown resulted in reduced lung metastasis. Interestingly, however, NAA depletion via ASPA overexpression increased metastasis to the lung in vivo. Furthermore, the combination of ASPA overexpression with the knockdown of NAT8L led to a moderate phenotype between the two independent genetic modifications. Our findings of the metastasis-promoting effect of NAA depletion via ASPA overexpression leads to us believe that it is not just the accumulation of NAA but also its utilization that is important for breast cancer progression. Our future experiments are directed towards determining how NAA utilization causes a pro-tumorigenic phenotype. We would also like to study the current inconsistency between ASPA transcript levels in patient tumors and its observed tumor-promoting function in xenograft experiments. Completion of these studies will potentially define the importance of elevated NAA levels in the context of aggressive BCa. Since NAA is a metabolite that can be detected in serum, our study could also lead to the development of NAA as a non-invasive biomarker for early detection of aggressive BCa, thus providing a bigger window for therapeutic intervention.

Citation Format: Akhila Balasubramanian, Weijie Zhang, Franklin Gu, Chandra Ambati, Nagireddy Putluri, Xiang Zhang, Aryan Namboodiri, Stefan Ambs, Arun Sreekumar. Role of the metabolite N-acetylaspartate in breast cancer progression [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PO-056.
Abstract PO-059: SOX2-mediated 5hmC dysregulation in GBM Stem Cells
Authors: Lopez-Bertoni Hernando
Published: December 2020

Primary brain tumors are among the most devastating forms of cancer and glioblastoma (GBM) represents the most aggressive and lethal form of the disease. We now know that GBM contain small subsets of cells that display tumor-propagating stem-like phenotypes (i.e. glioma stem cells or GSCs) that act as critical determinants of GBM resistance to current treatments and tumor recurrence for which there is no proven therapy. Altered patterns of DNA methylation are widely reported in human GBM. However, substantial knowledge gaps remain in our understanding of the molecular mechanisms responsible for this epigenetic dysregulation, its downstream consequences and role in the GBM tumor propagating phenotype. Understanding and ultimately targeting the epigenetic mechanisms that induce and maintain these tumor-propagating cell subsets is critical to improving GBM therapy and patient outcomes. DNA methylation generally occurs in cytosine-guanine (CpG) sequences and is established by DNMTs, which catalyze the conversion of cytosine to 5-methylcytosine (5mC). DNA methylation is a reversible process and is partially mediated by the ten-eleven translocation (TET) family of enzymes which function as deoxygenases to catalyze the conversion of 5mC to 5-hydroxymethylcytosine (5hmC). Levels of 5hmC closely track with the differentiation state of cells with terminally differentiated cells containing high levels of 5hmC and less differentiated cells having very low levels. Multiple studies found negative correlations between 5hmC levels and glioma grade and loss of 5hmC correlates with poor prognosis of GBM patients, strongly suggesting that these enzymes activate tumor suppressing mechanisms. Our preliminary data shows that exogenous SOX2 represses the TET2 demethylase and decreases 5hmC, the enzymatic product catalyzed by TET proteins, in GSCs. TET2 repression using 2 independent shRNA hairpins efficiently decreases 5hmc levels and significantly enhanced self-renewal capacity and tumor growth capacity of low-passage GSC isolates. We also show that SOX2 induces expression of miR-10b-5p, a known onco-miR predicted to target TET2, and inhibiting this miRNA partially rescues the reduction in 5hmC expression observed in GSCs expressing transgenic SOX2, thus implicating miR-10b-5p as a critical mediator of SOX2-induced onco-methylation, GSC induction and glioma malignancy. Our preliminary results support a mechanism in which SOX2 represses TET2 leading to 5hmC loss by directly activating miR-10b-5p transcription and predicts that targeting this novel mechanism of epigenetic dysregulation by inhibiting miR-10b-5p in vivo will can lead to pre-clinical GBM therapeutics.

Citation Format: Hernando Lopez-Bertoni. SOX2-mediated 5hmC dysregulation in GBM Stem Cells [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PO-059.
Abstract B17: IKKα/STAT3 antagonistic signaling regulates fungi-bacteria endosymbiosis-associated carcinogenesis
Authors: Song Na-Young , Li Xin , Badger Jonathan H. , Brown Jami Willette , Sun Xhonghe , Shi Gongping , Zhu Feng , Jiang Chengfei , O'hUigin Colum , Wu Xiaolin , Trinchieri Giorgio , Hu Yinling
Published: December 2020

Clinically, oral fungating lesions frequently occur in cancer patients following radiation and chemotherapy. However, their role in carcinogenesis has not been fully understood. Our previous finding showed that defective IKKα-mediated autoreactive T cells promote fungal infection and esophageal malignancy, but whether IKKα-mediated altered epithelial properties regulate fungal colonization and carcinogenesis remains to be tested. To investigate whether IKKα-mediated altered epithelial properties regulate fungal colonization and carcinogenesis, we orally infected mice lacking Ikkα (IkkαΔSOE) or both Ikkα and Stat3 (IkkαΔSOEStat3ΔSOE) in the stem cells of the skin and mouth with fungi. We found that oral fungal infection enhanced Ikkα ablation-mediated skin and oral carcinogenesis in association with increased oral and skin bacteria counts and altered oral bacteria phylum from gram-positive to gram-negative. Enhanced oral fungal/bacterial infection increased inflammasome activities and systemic IL-17A/IL-1β signals. Surprisingly, Stat3 ablation rescued these phenotypes in IkkαΔSOEStat3ΔSOE mice. In addition, amoxicillin treatment inhibited skin carcinogenesis and oral/skin bacteria counts and reversed oral bacteria phyla in fungal-inoculated IkkαΔSOE mice. These findings highlight that cancer cell IKKα/STAT3 antagonizing pathways determine susceptibility to fungal and bacterial colonization, which impacts carcinogenesis. Human head and neck squamous cell carcinomas also share oncogenic pathways and bacteria sequences/counts with mice, suggesting that oral fungating/ulcerating lesions enhance local and distal tumorigenesis in humans.

Citation Format: Na-Young Song, Xin Li, Jonathan H. Badger, Jami Willette Brown, Xhonghe Sun, Gongping Shi, Feng Zhu, Chengfei Jiang, Colum O'hUigin, Xiaolin Wu, Giorgio Trinchieri, Yinling Hu. IKKα/STAT3 antagonistic signaling regulates fungi-bacteria endosymbiosis-associated carcinogenesis [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr B17.
Abstract B26: Comparative analysis of breast tumor microbiome in Black non-Hispanic (BNH) and White non-Hispanic (WNH) women
Authors: Thyagarajan Srikantha , Zhang Yan , Thapa Santosh , Allen Michael S. , Phillips Nicole , Vishwanatha Jamboor K.
Published: December 2020

African American women are approximately twice as likely to be diagnosed with highly aggressive estrogen receptor-negative (ER-) and TNBC subtypes of breast cancer than Caucasian women. Among biologic factors, microbiota has been implicated in the etiology of several kinds of cancer including breast cancer. Few recent studies have shown that the breast niche-specific microbiota may have a major influence on breast tumorigenesis as shown by a decreased abundance of bacterial species with known immunomodulatory and probiotic effect in paired tumor tissue as compared to normal tissue derived from healthy patients, including different microbiota profiles in different subtypes of breast cancer. To understand whether the breast tissue harbors microbiota profiles that are uniquely race-specific we have analyzed tumor and matched normal and tumor tissue using 16S rRNA targeted sequencing strategy. Two distinct breast tumor types derived from women were included in this study: triple-negative breast cancer (TNBC) and triple-positive breast cancer (TPBC) derived from BNH and WNH women. The data were analyzed for microbiota composition, abundance, and diversity parameters, alpha diversity and beta diversity. The preliminary microbiome analysis revealed specific differences in abundance both at the phylum and genus levels between WNH and BNH women breast tissues; the alpha diversity matric, Shannon index measuring both richness and evenness of microbiota diversity showed differences in microbial diversity between normal breast tumor tissue and the matched normal adjacent to tumor tissue. The microbiota richness was relatively lower in BNH TNBC tumor tissue as compared to its matched normal adjacent to tumor zone as defined by pathologic analysis. In contrast, the microbiota richness was higher in WNH TNBC tumor tissue as compared to its matched normal breast tissue. The multivariate analysis of beta diversity revealed a distinct clustering in BNH and WNH TNBC microbiota between both tumors as compared to normal tissue and BNH as compared to WNH racial groups. Research reported in this publication was supported by the National Institute on Minority Health and Health Disparities of the National Institutes of Health under Award Numbers S21MD012472 and U54MD006882.

Note: This abstract was not presented at the conference.

Citation Format: Srikantha Thyagarajan, Yan Zhang, Santosh Thapa, Michael S. Allen, Nicole Phillips, Jamboor K. Vishwanatha. Comparative analysis of breast tumor microbiome in Black non-Hispanic (BNH) and White non-Hispanic (WNH) women [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr B26.
Abstract B38: Virome assembly and annotation in brain tissue based on next-generation sequencing
Authors: Yuan Zihao , Ye Xiaohua , Zhang Ningyan , An Zhiqiang , Zheng Wenjin
Published: December 2020

Glioblastoma multiforme (GBM) is one of the most lethal brain tumors, and the virosphere in brain and its correlation with GBM triggering is controversy. The previous research in brain virosphere was mainly limited to the presence of human cytomegalovirus (HCMV); a comprehensive assessment of the brain virome based on the recently sequenced data and the understanding of the novel sequences that cannot be mapped to the known reference sequences are lacking. Here, we characterized the virome from 111 GBM samples and 57 normal brain samples from 8 projects in SRA database by known and novel viruses in a tested and comprehensive assembly approach. The annotation of those contigs showed most of the viral sequences belongs to the Retroviridae. A novel picornavirus, which was recently discovered from the invertebrate, can be detected in some GBM samples in full genome length. Furthermore, our analysis showed that the herpes virus fragments that are annotated as Epstein-Barr virus (EBV) only exist in the GBM with less than 1% of the EBV whole genome, supporting the absence of herpes virus in GBM. The further analysis showed that the contigs that have no annotations from the known databases may have the antibody properties and antibody epitopes to be the future drug targets. In this study, we characterized the virosphere in GBM and normal brain at a global level, to provide a basis for future GBM research and therapies.

Citation Format: Zihao Yuan, Xiaohua Ye, Ningyan Zhang, Zhiqiang An, Wenjin Zheng. Virome assembly and annotation in brain tissue based on next-generation sequencing [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr B38.
Abstract IA15: Role of human papillomaviruses in carcinogenesis
Authors: Tommasino Massimo
Published: December 2020

Infectious agents represent a major group of risk factors for cancer development and contribute to about 15% of human cancers worldwide. Six viruses and one bacterium, i.e., human papillomavirus (HPV), hepatitis C virus (HCV), hepatitis B virus, human T-lymphotropic virus type I (HTLV-1), Epstein-Barr virus (EBV), Kaposi sarcoma-associated virus (KSHV), and Helicobacter pylori, have been clearly associated with human carcinogenesis. The mucosal high-risk (HR) HPV types are the etiologic factors of cervical cancers and subset of oropharyngeal cancers. In addition, ongoing studies concerning a subgroup of HPV types that infect the skin suggest their involvement, together with ultraviolet radiation (or solar exposure), in the development of nonmelanoma skin cancer (NMSC). Biologic studies have demonstrated that the products of two early genes from the HR HPV types, E6 and E7, play a key role in cancer development. Both viral oncoproteins are able to target several cellular pathways leading to the evasion of the immune surveillance and cellular transformation. These studies also substantially contributed to our understanding of key mechanisms involved in the normal life of the cell. In the last few years, we have performed additional studies on cutaneous and mucosal HPV types and have characterized novel oncogenic viral mechanisms involved in the evasion of the immune response and/or in cellular transformation. A few examples will be presented.

Citation Format: Massimo Tommasino. Role of human papillomaviruses in carcinogenesis [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr IA15.
Abstract IA20: Gut microbiota dysbiosis and dietary fermentable fibers in a pickle: A brew for liver cancer
Authors: Vijay-Kumar Matam
Published: December 2020

Dietary soluble fibers are fermented by gut bacteria into short-chain fatty acids (SCFA), which are considered broadly health promoting. Accordingly, consumption of such fibers ameliorates metabolic syndrome in a subset (40%) of Toll-like receptor 5-deficient (TLR5KO) mice. However, incorporating fermentable fiber inulin, but not nonfermentable fiber cellulose, into a compositionally defined purified diet induced hyperbilirubinemia and cholemia as primary clinical symptoms and hallmarks of cholestasis. These cholestatic mice eventually developed robust, multinodular hepatocellular carcinoma (HCC; a type of liver cancer) within 6 months. Inulin-induced HCC progressed via early onset of cholestasis, hepatocyte death, followed by liver inflammation primarily driven by neutrophils. Such neutrophilic inflammation is characterized by elevated levels of neutrophil elastase and myeloperoxidase, and hepatic reactive oxygen species, malondialdehyde and 8-hydroxy-2’-deoxyguanosine, a marker of DNA damage. Pathogenesis of such HCC was microbiota dependent and observed in multiple strains of dysbiotic mice, but not in germ-free or antibiotics-treated TLR5KO mice. Furthermore, inulin-enriched diet induced both dysbiosis and HCC in wild-type (WT) mice co-housed or cross-fostered with TLR5KO mice. Pharmacologic inhibition of fermentation or depletion of fermenting bacteria markedly reduced intestinal SCFA and prevented HCC. Intervening with cholestyramine to prevent enterohepatic recirculation of bile acids also conferred protection against such HCC. Thus, notwithstanding the health benefits of inulin, enrichment of foods with fermentable fiber should be approached with great caution as it may increase risk of HCC and warrants that refined fibers need to be redefined.

Citation Format: Matam Vijay-Kumar. Gut microbiota dysbiosis and dietary fermentable fibers in a pickle: A brew for liver cancer [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr IA20.
Abstract IA22: The role of the intestinal microbiome in allogeneic hematopoietic cell transplantation
Authors: van den Brink Marcel
Published: December 2020

Relationships between microbiota composition and clinical outcomes of patients following allogeneic hematopoietic cell transplantation (allo-HCT) have been described in single-center studies. Geographic variations in the composition of human microbial communities and differences in clinical practices across institutions raise the question of whether these associations are generalizable. Therefore, we studied 8,767 fecal samples from 1,362 allo-HCT patients at four centers on three continents by 16S ribosomal sequencing. In an observational study, we examined associations between microbiota diversity and overall survival during two years of follow-up after allo-HCT with proportional-hazards analysis. We observed reproducible patterns of microbiota disruption characterized by loss of diversity and domination by single taxa. Low diversity in the peri-neutrophil engraftment period was reproducibly associated with increased risk of death (multivariate-adjusted HR 0.48, 95% CI 0.30-0.77, p = 0.002 in the largest cohort). Subset analysis suggested that these reductions in overall survival were in part due to an increased risk of transplant-related mortality and graft-versus-host disease. Baseline pre-HCT samples already bore evidence of microbiome disruption, and low diversity prior to transplantation was associated with poor survival. In addition, we found that Enterococcus faecium dominates the intestinal microbiota of up to 65% allo-HCT patients early after transplant at all four transplant centers. Enterococcus domination was associated with an increased incidence of acute graft-versus-host disease (GVHD), increased GVHD-related mortality, and reduced overall survival. Post-transplant expansion of Enterococci was also observed in mouse models of GVHD in the absence of antibiotic treatment. Spiking a minimal flora with Enterococci in gnotobiotic mice exacerbated lethal GVHD. Metagenomic sequencing of human and murine Enterococcus-dominated fecal samples revealed an enrichment of lactose and galactose degradation genes, a pathway necessary for Enterococcus growth in vitro. A lactose-free chow attenuated the intestinal outgrowth of Enterococcus and reduced the severity of lethal GVHD in mice. In patients, a lactose-nonabsorber genotype was associated with an increased Enterococcus abundance after cessation of antibiotic treatment after allo-HCT. In conclusion, the concordance of microbiota disruption patterns and their associations with clinical outcomes suggest that approaches to manipulate the intestinal microbiota with the aim of improving allo-HCT clinical outcomes may be generalizable.

Citation Format: Marcel van den Brink. The role of the intestinal microbiome in allogeneic hematopoietic cell transplantation [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr IA22.
Abstract IA25: Tumors alter gut microbiota to suppress immunity and foster progression
Authors: Hribe-Herranz Mireia , Bittinger Kyle , Tanes Ceylan , Rafail Stavros , Pierini Stefano , Ben-Joseph Edgar , Tanyi Janos , Facciabene Andrea
Published: December 2020

Immune dysfunction is commonly observed in patients with cancer contributing to tumor progression. While previous work established a connection between the gut microbiota and the immune system, the mechanisms by which microbiotas contribute to cancer-associated immune dysfunction are not well understood. Using multiple mouse cancer models, we demonstrated robust alterations of gut microbiota in tumor-bearing mice and a substantial change in antimicrobial peptides produced by the gut epithelium. We identified an overall reduction in IFN-γ T cells in tumor-bearing mice, which was rescued with antibiotics treatment or by co-housing tumor-bearing mice with healthy mice. Similar to mouse, we observed changes in gut microbiota and antimicrobial peptides levels of patients diagnosed with ovarian or lung cancer. We identify Firmicutes Ruminococcus members as key promoters of immune dysfunctions and tumor development. These findings identify a new mechanism of immune modulation utilized by tumors to undermine the immune responses and promote tumor progression.

Citation Format: Mireia Hribe-Herranz, Kyle Bittinger, Ceylan Tanes, Stavros Rafail, Stefano Pierini, Edgar Ben-Joseph, Janos Tanyi, Andrea Facciabene. Tumors alter gut microbiota to suppress immunity and foster progression [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr IA25.
Abstract IA28: Targeting the microbiome in cancer immunotherapy
Authors: Trinchieri Giorgio
Published: December 2020

Commensal microorganisms colonize barrier surfaces of all multicellular organisms, including those of humans. For more than 500 million years commensal microorganisms and their hosts have coevolved and adapted to each other. As a result, the commensal microbiota affects many immune and nonimmune functions of their hosts, and de facto the two together comprise one metaorganism. The commensal microbiota communicates with the host via biologically active molecules. Recently, it has been reported that microbial imbalance may play a critical role in the development of multiple diseases, such as cancer, autoimmune conditions, and increased susceptibility to infection. The commensal microbiota not only may affect the development, progression, and immune evasion of cancer but has also important effects on the response to cancer immune- and chemotherapy. In my presentation I will discuss some recent analysis of the role of the microbiome in anti-PD1 therapy in melanoma patients, the preliminary data of a fecal microbiota transfer clinical trial (performed at the University of Pittsburgh Cancer Center) in anti-PD1 refractory melanoma patients, as well as mouse data on the effect of dietary fibers on anti-PD1 cancer therapy.

Citation Format: Giorgio Trinchieri. Targeting the microbiome in cancer immunotherapy [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr IA28.
Abstract PR01: Right-sided colonic biofilms are associated with adenoma formation in patients with Lynch syndrome
Authors: Bruggeling Carlijn , Witjes Vera , Garza Daniel , Fransen Milou , Krekels Joyce , Bisseling Tanya , van Kouwen Mariëtte , Hoogerbrugge Nicoline , Lücker Sebastian , Dutilh Bas , Nagtegaal Iris , Boleij Annemarie
Published: December 2020

Colonic bacterial biofilms are an emerging manifestation in colorectal cancer (CRC); they exhibit carcinogenic properties and are frequently present on right-sided cancerous lesions. Whether bacterial biofilms propose a risk factor for early carcinogenesis in humans is yet unresolved. Therefore, we studied bacterial biofilms in tandem with adenoma formation in patients with Lynch syndrome (LS). LS patients carry a pathogenic germline variant in one of the DNA mismatch repair (MMR) genes, resulting in a variable predisposition to develop colonic cancerous lesions. A total of 100 LS patients were included in our study, consisting of 23 MLH1, 24 MSH2, 36 MSH6, and 17 PMS2 MMR variants. During regular screening colonoscopies, normal-appearing forceps biopsies were taken from colon ascendens (right colon) and descendens (left colon). Biopsies were screened for bacterial biofilms using fluorescent in situ hybridization by targeting bacterial 16s rRNA. The frequency of colorectal adenomas (tubular adenomas and [tubulo]villous adenomas) before and during colonoscopy was registered. Overall, 60% of patients presented with a biofilm, of which most were right-sided (right-sided: 25%, both sides: 21%, left-sided: 14%). Interestingly, adenomas were more frequently present in patients with a right-sided biofilm (right-sided: 64%, both sides: 58%) than in patients with a left-sided biofilm (29%) or no biofilm (38%). The occurrence of bacterial biofilms was not correlated with age, BMI, or MMR-variant. Statistical analysis revealed that right-sided bacterial biofilms correlated with right-sided adenomas (Pearson: 0.272, p=0.007) and left-sided adenomas (Pearson: 0.227, p=0.026), while left-sided biofilms were not correlated with left- or right-sided adenomas (Pearson: 0.037, p=0.718 and -.127, p=.213). To model the probability of right-sided adenoma formation, we performed a binary logistic regression analysis and found that age (odds ratio: 1.065 [CI: 1.024; 1.108, p=0.002]) and right-sided biofilms (odds ratio: 3.020 [CI: 1.151; 7.926, p=0.025]) significantly contributed. Our data suggest that right-sided bacterial biofilms are a hallmark for high-risk LS patients and may play a role in early carcinogenesis.

This abstract is also being presented as Poster A06.

Citation Format: Carlijn Bruggeling, Vera Witjes, Daniel Garza, Milou Fransen, Joyce Krekels, Tanya Bisseling, Mariëtte van Kouwen, Nicoline Hoogerbrugge, Sebastian Lücker, Bas Dutilh, Iris Nagtegaal, Annemarie Boleij. Right-sided colonic biofilms are associated with adenoma formation in patients with Lynch syndrome [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr PR01.
Abstract PR10: Candida albicans infection mediates gastrointestinal track malignancy independently of Il17a in an APECED mouse model
Authors: Zhu Feng , Willette-Brown Jami , Phan Trang , Zhao Yongmei , Tran Bao , Filler Scott G. , Lionakis Mihalis S. , Hu Yinling
Published: December 2020

The cytokine Il17a plays an important role in protection against fungal infection, yet it also serves as a pathogenic factor in several inflammation-related cancers. Previously we reported that fungal infection promotes the development of esophageal squamous cell carcinoma (ESCC) in the IKKalpha kinase-dead KA knock-in (KA) mice that mimic a human autoimmune disorder, autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). Our data showed that KA T cells failed to induce Il17a in response to fungal infection. However, the role of Il17a in fungal infection-mediated esophageal carcinogenesis remains to be further determined. In this study, we crossed KA mice with Il17a-/- mice to generate KA;Il17a-/- double mutant mice. We orally inoculated WT, Il17a-/-, KA, and KA;Il17a-/- mice with Candida albicans weekly for 3 months to investigate gastrointestinal (GI) track tumorigenesis, including the SCC development in the oral cavity, esophagus, and forestomach. We found that loss of Il17a leads to much earlier onset of GI track tumors in KA;Il17a-/- mice than that in KA mice. KA;Il17a-/- mice also died much earlier compared to KA mice, which is likely due to increased C. albicans burden in the absence of Il17a. The incidence of GI track tumors is comparable between KA and KA;Il17a-/- mice, suggesting that C. albicans infection-associated GI track tumorigenesis is independent of Il17a in KA mouse model. To further understand the underlying mechanism, we performed single-cell RNA sequencing analysis for CD45+ immune cells isolated from long-term C. alibicans-infected mouse esophagi of WT, Il17a-/-, KA, and KA;Il17a-/- mouse cohorts. Interestingly, the neutrophil population was significantly increased in the esophagi of KA and KA;Il17a-/- mice compared to WT and Il17a-/- mice. However, KA neutrophils exhibited reduced capacity in killing C. albicans with reduced NETs formation compared to WT neutrophils, suggesting that the defect in NETs formation may play a pivotal role in GI track tumorigenesis in the context of fungal infection. We are currently investigating how the interplay between C. albicans infection and host neutrophils regulates Candida infection-associated GI track tumorigenesis.

This abstract is also being presented as Poster B01.

Citation Format: Feng Zhu, Jami Willette-Brown, Trang Phan, Yongmei Zhao, Bao Tran, Scott G. Filler, Mihalis S. Lionakis, Yinling Hu. Candida albicans infection mediates gastrointestinal track malignancy independently of Il17a in an APECED mouse model [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr PR10.