Modeling phenotypic heterogeneity towards evolutionarily inspired osteosarcoma therapy

Osteosarcoma is the most common bone sarcoma in children and young adults. While universally delivered, chemotherapy only benefits roughly half of patients with localized disease. Increasingly, intratumoral heterogeneity is recognized as a source of therapeutic resistance. In this study, we develop and evaluate an in vitro model of osteosarcoma heterogeneity based on phenotype and genotype. Cancer cell populations vary in their environment-specific growth rates and in their sensitivity to chemotherapy. We present the genotypic and phenotypic characterization of an osteosarcoma cell line panel with a focus on co-cultures of the most phenotypically divergent cell lines, 143B and SAOS2. Modest environmental (pH, glutamine) or chemical perturbations dramatically shift the success and composition of cell lines. We demonstrate that in nutrient rich culture conditions 143B outcompetes SAOS2. But, under nutrient deprivation or conventional chemotherapy, SAOS2 growth can be favored in spheroids. Importantly, when the simplest heterogeneity state is evaluated, a two-cell line coculture, perturbations that affect the faster growing cell line have only a modest effect on final spheroid size. Thus the only evaluated therapies to eliminate the spheroids were by switching therapies from a first strike to a second strike. This extensively characterized, widely available system, can be modeled and scaled to allow for improved strategies to anticipate resistance in osteosarcoma due to heterogeneity.

Insights into the weathering behavior of pyrite in alkaline soil through electrochemical characterizations: Actual hazards or potentially benefits?

Pyrite is the most common metal sulfide mineral in the crust and readily weathers under natural circumstances to release H⁺ to acidify surrounding groundwater and soil, resulting in heavy metal ions in the surrounding environment (e.g., meadow and saline soils). Meadow and saline soils are two common, widely distributed alkaline soils and can affect pyrite weathering. Currently, the weathering behaviors of pyrite in saline and meadow soil solutions have not been systematically studied. Electrochemistry coupled with surface analysis methods were employed to study pyrite weathering behaviors in simulated saline and meadow soil solutions in this work. Experimental results suggest that saline soil and higher temperatures increase pyrite weathering rates due to the lower resistance and greater capacitance. Surface reactions and diffusion control the weathering kinetics, and the activation energies for the simulated meadow and saline soil solutions are 27.1 and 15.8 kJ mol^-1, respectively. In-depth investigations reveal that pyrite is initially oxidized to Fe(OH)₃ and S⁰, and Fe(OH)₃ further transforms into goethite γ-FeOOH and hematite α-Fe₂O₃, while S⁰ ultimately converts into sulfate. When these iron compounds enter alkaline soils, the alkalinity of soil changes, and iron (hydr)oxides effectively reduce the bioavailability of heavy metals and benefit alkaline soils. Meanwhile, weathering of natural pyrite ores containing toxic elements (such as Cr, As, and Cd) makes these elements bioavailable and potentially degrades the surrounding environment.

Biochar Promotes Arsenopyrite Weathering in Simulated Alkaline Soils: Electrochemical Mechanism and Environmental Implications

Oxidation dissolution of arsenopyrite (FeAsS) is one of the important sources of arsenic contamination in soil and groundwater. Biochar, a commonly used soil amendment and environmental remediation agent, is widespread in ecosystems, where it participates in and influences the redox-active geochemical processes of sulfide minerals associated with arsenic and iron. This study investigated the critical role of biochar on the oxidation process of arsenopyrite in simulated alkaline soil solutions by a combination of electrochemical techniques, immersion tests, and solid characterizations. Polarization curves indicated that the elevated temperature (5-45 °C) and biochar concentration (0-1.2 g·L^-1) accelerated arsenopyrite oxidation. This is further confirmed by electrochemical impedance spectroscopy, which showed that biochar substantially reduced the charge transfer resistance in the double layer, resulting in smaller activation energy (E_a = 37.38-29.56 kJ·mol^-1) and activation enthalpy (ΔH* = 34.91-27.09 kJ·mol^-1). These observations are likely attributed to the abundance of aromatic and quinoid groups in biochar, which could reduce Fe(III) and As(V) as well as adsorb or complex with Fe(III). This hinders the formation of passivation films consisting of iron arsenate and iron (oxyhydr)oxide. Further observation found that the presence of biochar exacerbates acidic drainage and arsenic contamination in areas containing arsenopyrite. This study highlighted the possible negative impact of biochar on soil and water, suggesting that the different physicochemical properties of biochar produced from different feedstock and under different pyrolysis conditions should be taken into account before large-scale applications to prevent potential risks to ecology and agriculture.

CX3CR1 deficiency-induced TIL tumor restriction as a novel addition for CAR-T design in solid malignancies

Advances in the understanding of the tumor microenvironment have led to development of immunotherapeutic strategies, such as chimeric antigen receptor T cells (CAR-Ts). However, despite success in blood malignancies, CAR-T therapies in solid tumors have been hampered by their restricted infiltration. Here, we used our understanding of early cytotoxic lymphocyte infiltration of human lymphocytes in solid tumors in vivo to investigate the receptors in normal, adjacent, and tumor tissues of primary non-small-cell lung cancer specimens. We found that CX3CL1-CX3CR1 reduction restricts cytotoxic cells from the solid-tumor bed, contributing to tumor escape. Based on this, we designed a CAR-T construct using the well-established natural killer group 2, member D (NKG2D) CAR-T expression together with overexpression of CX3CR1 to promote their infiltration. These CAR-Ts infiltrate tumors at higher rates than control-activated T cells or IL-15-overexpressing NKG2D CAR-Ts. This construct also had similar functionality in a liver-cancer model, demonstrating potential efficacy in other solid malignancies.

Arsenic release from arsenopyrite weathering in acid mine drainage: Kinetics, transformation, and effect of biochar

Arsenopyrite (FeAsS) oxidative dissolution provides an important source for the occurrence of high arsenic in acid mine drainage (AMD). Biochar is a potent material that can dramatically sequestrate an array of heavy metals in water. However, little is known about the role of biochar on the fate of As from arsenopyrite in AMD. This study investigates the effects of biochar concentrations, AMD acidities, and temperatures on the release of As from arsenopyrite in a simulated AMD over a range of environmentally relevant conditions. Results show that biochar inhibits As release and further acidification without changing the arsenopyrite weathering mechanism. Arsenopyrite is first oxidized to Fe(II), As(III) and S⁰ and ultimately oxidized to Fe(III), As(V) and SO₄^2-, respectively. Higher concentration, temperature or higher acidity promotes the arsenic release rate. Electrochemical studies showed that biochar inhibited As release and acidification for reduced the charge transfer resistance at the double layer and film resistance at the passivation layer, which was mainly attributed to Fe(III) ions in AMD being adsorbed, oxidized, and As complexed to biochar-Fe-As(V). This study reveals the release mechanism of As from arsenopyrite weathering in AMD and suggests the applicability of biochar in mitigating arsenic pollution and further acidification in sulfide mineral mine drainage.

Protocol for the isolation of CD8+ tumor-infiltrating lymphocytes from human tumors and their characterization by single-cell immune profiling and multiome

Understanding the heterogenicity of tumor-infiltraing lymphocyte (TIL) populations and the immunobiology in human cancer is a key to establish efficient immunotherapies. Here, we have established a protocol for the characterization of CD8⁺ TILs in tumors by single-cell RNA-seq paired to VDJ profiling and chromatin structure including dissociation of tumor biopsies. We have also provided guidance for subsequent fluorescence-activated cell sorting (FACS), single-cell encapsulation, bioinformatics analysis, and troubleshooting.

For complete details on the use and execution of this protocol, please refer to Anadon et al. (2022).

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Single-cell suspension preparation and TILs sorting from frozen human ovarian tumors

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Single-cell isolation, library preparation, and quality control for scRNA-seq + VDJ

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Single nucleus isolation, library preparation, and quality control for 10× Multiome

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scRNA-seq + VD and Multiome data integration and TIL trajectory identification

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Whole-genome sequencing reveals complex genomic features underlying anti-CD19 CAR T-cell treatment failures in lymphoma

CD19-directed chimeric antigen receptor (CAR-19) T cells are groundbreaking immunotherapies approved for use against large B-cell lymphomas. Although host inflammatory and tumor microenvironmental markers associate with efficacy and resistance, the tumor-intrinsic alterations underlying these phenomena remain undefined. CD19 mutations associate with resistance but are uncommon, and most patients with relapsed disease retain expression of the wild-type receptor, implicating other genomic mechanisms. We therefore leveraged the comprehensive resolution of whole-genome sequencing to assess 51 tumor samples from 49 patients with CAR-19-treated large B-cell lymphoma. We found that the pretreatment presence of complex structural variants, APOBEC mutational signatures, and genomic damage from reactive oxygen species predict CAR-19 resistance. In addition, the recurrent 3p21.31 chromosomal deletion containing the RHOA tumor suppressor was strongly enriched in patients for whom CAR T-cell therapy failed. Pretreatment reduced expression or monoallelic loss of CD19 did not affect responses, suggesting CAR-19 therapy success and resistance are related to multiple mechanisms. Our study showed that tumor-intrinsic genomic alterations are key among the complex interplay of factors that underlie CAR-19 efficacy and resistance for large B-cell lymphomas.

Tumor Expression Quantitative Trait Methylation Screening Reveals Distinct CpG Panels for Deconvolving Cancer Immune Signatures

DNA methylation signatures in tumors could serve as reliable biomarkers that are accessible in archival tissues for tracking the epigenetic dynamics shaped by both cancer cells and the tumor microenvironment. However, given the ultrahigh dimensionality and noncollapsible nature of the data, it remains challenging to screen all CpG sites to identify the most promising marker panels. In this article, we introduce the concept of tumor-based expression quantitative trait methylation (eQTM) for the prioritization and systematic mining of predictive biomarkers. In melanoma as a disease model, eQTM CpGs and genes represent new and efficient candidate targets to be investigated for both prognostic and immune status monitoring purposes. Three cis-eQTM CpGs (cg07786657, cg12446199, and cg00027570) were strongly associated with and can serve as surrogate biomarkers for the tumor immune cytolytic activity score (CYT). In addition, multiple eQTM genes could be further exploited for predicting immunoregulatory phenotypes. A targeted gene panel analysis identified one eQTM in TCF7 (cg25947408) as a novel candidate biomarker for uncoupling overall T-cell differentiation and exhaustion status in a tumor. The prognostic significance of this eQTM as an independent signature to CYT was validated by both The Cancer Genome Atlas and Moffitt melanoma cohort data. Overall, eQTMs represent a mechanistically distinct class of potential biomarkers that can be used to predict patient prognosis and immune status.

SIGNIFICANCE

This study provides a novel and promising approach to identify targeted epigenetic biomarkers in cancer and will spur further analysis in tumor immune phenotyping.

Coupling the immunomodulatory properties of the HDAC6 inhibitor ACY241 with Oxaliplatin promotes robust anti-tumor response in Non-small cell lung cancer

Although immunotherapy provides durable therapeutic response in a subset of Non-small cell lung cancer (NSCLC) patients, there is still a need for broadly applicable therapeutic strategies. HDAC inhibitors are a promising class of drugs whose immunomodulatory properties are now being appreciated. In the present study, we evaluated the immunomodulatory properties of the HDAC6 inhibitor, Citarinostat (ACY241) on lung tumor immune compartment and its therapeutic potential in combination with Oxaliplatin. Lung adenocarcinoma-bearing mice were treated with ACY241 or vehicle after which immune profiling and RNA-sequencing were conducted in tumor-associated T cells and macrophages. Ex vivo T cell functional studies, tumor growth assessment and survival of tumor-bearing mice treated with ACY241 and/or Oxaliplatin were also conducted. ACY241 treatment promoted increased presence of T and NK cells as well as activation, proliferation, and effector profile of T cells in the lung tumors of treated mice. Furthermore, tumor-associated macrophages exhibited increased expression of MHC and co-stimulatory molecules while expression of inhibitory ligands were reduced. RNA-sequencing of tumor-associated T cells and macrophages revealed significant genomic changes that is consistent with ACY241-mediated enhancement of immune priming. Finally, ACY241 treatment led to significantly enhanced tumor-associated T cell effector functionality in lung cancer-bearing mice and in patient-derived tumors when combined with the chemotherapy drug Oxaliplatin. Collectively, our studies support ACY241 as a promising HDAC6 inhibitor which coupled with Oxaliplatin promotes robust therapeutic outcomes in a pre-clinical model of NSCLC.

Tumor-associated Tregs obstruct antitumor immunity by promoting T cell dysfunction and restricting clonal diversity in tumor-infiltrating CD8+ T cells

BACKGROUND

Accumulation of regulatory T cells (Treg) has been described to often correlate with poor prognosis in many solid tumors. How Treg presence impinges on limited functionality and clonal composition of tumor-associated CD8 +T cells has important implications for their therapeutic targeting in the tumor microenvironment. In the present study, we investigated how accumulation of Tregs contributes to T cell dysfunction and clonal constriction of tumor-infiltrating CD8 +T cells.

METHODS

Resected melanoma and lung adenocarcinoma tissues from tumor-bearing mice or patients were analyzed. The proportions and phenotype as well as clonal diversity of tumor-associated CD8 +T cells were evaluated by flow cytometry and single-cell T-cell receptor (TCR) sequencing, respectively, at early or advanced tumor stages or under Treg depletion conditions. Furthermore, antigen-specific T cells were evaluated on adoptive transfer into tumor-bearing mice in the presence or absence of anti-CTLA-4 antibody or CTLA-4 Ig. Lastly, tumor-bearing mice were treated with anti-KLRG1 antibody and/or bromodomain inhibitor JQ1 with interleukin (IL)-2 immune complexes to determine therapeutic efficacy.

RESULTS

We demonstrate that the emergence of exhaustion-like phenotype and impaired effector functionality in tumor-associated CD8 +T cells is positively correlated with Treg accumulation in the tumor bed and this dysfunctional phenotype becomes reversed on Treg reduction in murine melanoma and lung cancer models. Heightened tumor-associated Treg-expressed CTLA-4 is key to emergence and sustenance of this phenotype. Furthermore, TCR sequencing revealed a clonal shrinkage of tumor-infiltrating CD8 +T cells as tumor progressed, which was associated with reduced survival profile concomitant to increasing Treg proportions. Limited IL-2 availability was a key mechanism contributing to this peripheral repertoire reshaping as Treg depletion improved IL-2 levels, rescued CD8 +T cell viability, and improved their clonal diversity. Finally, targeted reduction of tumor but not peripheral Tregs through JQ1 and/or anti-KLRG1 antibody significantly improved antitumor response in melanoma-bearing mice when supplemented with IL-2 immune complexes.

CONCLUSION

Collectively, our study reveals a bimodal program enacted by Tregs to support T cell dysfunction in the tumor bed and highlights a promising therapeutic regimen for localized reprogramming of the tumor microenvironment to curb Treg impairment of antitumor CD8 +T cell response in favor of improved antitumor immunity.

Coupling the immunomodulatory properties of the HDAC6 inhibitor ACY241 with Oxaliplatin promotes robust anti-tumor response in non-small cell lung cancer

While HDAC inhibitors have shown promise in hematologic cancers, their efficacy remains limited in solid cancers. In the present study, we evaluated the immunomodulatory properties of the HDAC6 inhibitor, Citarinostat (ACY241) on lung tumor immune compartment and its therapeutic potential in combination with Oxaliplatin. As a single agent, ACY241 treatment promoted increased infiltration, activation, proliferation, and effector function of T cells in the tumors of lung adenocarcinoma-bearing mice. Furthermore, tumor-associated macrophages exhibited downregulated expression of inhibitory ligands in favor of increased MHC and co-stimulatory molecules in addition to higher expression of CCL4 that favored increased T cell numbers in the tumors. RNA-sequencing of tumor-associated T cells and macrophages after ACY241 treatment revealed significant genomic changes that is consistent with improved T cell viability, reduced inhibitory molecular signature, and enhancement of macrophage capacity for improved T cell priming. Finally, coupling these ACY241-mediated effects with the chemotherapy drug Oxaliplatin led to significantly enhanced tumor-associated T cell effector functionality in lung cancer-bearing mice and in patient-derived tumors. Collectively, our studies highlight the molecular underpinnings of the expansive immunomodulatory activity of ACY241 and supports its suitability as a partner agent in combination with rationally selected chemotherapy agents for therapeutic intervention in NSCLC.

Evaluation of Tumor DNA Sequencing Results in Patients with Gastric and Gastroesophageal Junction Adenocarcinoma Stratified by TP53 Mutation Status

Background

Gastric cancer (GC) and gastroesophageal junction adenocarcinomas (GEJ) are molecularly diverse. TP53 is the most frequently altered gene with approximately 50% of patients harboring mutations. This qualitative study describes the distinct genomic alterations in GCs and GEJs stratified by TP53 mutation status.

Patients and Methods

Tumor DNA sequencing results of 324 genes from 3741 patients with GC and GEJ were obtained from Foundation Medicine. Association between gene mutation frequency and TP53 mutation status was examined using Fisher’s exact test. Functional gene groupings representing molecular pathways suggested to be differentially mutated in TP53 wild-type (TP53WT) and TP53 mutant (TP53MUT) tumors were identified. The association of the frequency of tumors containing a gene mutation in the molecular pathways of interest and TP53 mutation status was assessed using Fisher’s exact test with a P-value of <.01 deemed statistically significant for all analyses.

Results

TP53 mutations were noted in 61.6% of 2946 GCs and 81.4% of 795 GEJs (P < .001). Forty-nine genes had statistically different mutation frequencies in TP53WT vs. TP53MUT patients. TP53WT tumors more likely had mutations related to DNA mismatch repair, homologous recombination repair, DNA and histone methylation, Wnt/B-catenin, PI3K/Akt/mTOR, and chromatin remodeling complexes. TP53MUT tumors more likely had mutations related to fibroblast growth factor, epidermal growth factor receptor, other receptor tyrosine kinases, and cyclin and cyclin-dependent kinases.

Conclusion

The mutational profiles of GCs and GEJs varied according to TP53 mutation status. These mutational differences can be used when designing future studies assessing the predictive ability of TP53 mutation status when targeting differentially affected molecular pathways.

Transcriptomic analyses of esophageal cancer patients with brain metastases

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Background: Brain metastases from esophageal cancer are extremely rare with an estimated incidence of 1.7% but limited survival. Some reports highlight the rich microvascular density of such tumors and their distinctive degree of HER2, HIF1-a and EGFR expression, further emphasizing the potential role of angiogenesis in their neurotropic behavior. With this in mind, we aimed to illustrate the transcriptomic landscape of brain metastases from esophageal cancers and better understand the disease biology. Methods: Following IRB approval, we collected retrospective data on patients with a diagnosis of esophageal cancer with histology-proven brain metastases treated at our institution between 2008 and 2020. We identified 10 adequate, paired samples with available tissue for RNA extraction. Expression data was generated using NanoString TS 360 panels to characterize gene signatures of interest and analyzed using GSEA_4.1.0. Results: All 10 patients were Caucasian, 90% were male. Median age was 63 years. All had adenocarcinoma with G2-G3 histology. Median follow-up was 39.4 mos (95%CI, 27.4 to 51.4). At data cutoff, 6 patients had died. Median OS was 24.6 mos. Median time from curative surgery to CNS recurrence was 8.3 mos. Ninety percent of patients developed brain metastases within 24 mos of surgery. Median time from brain metastases to death was 4.7 mos. Almost a third of patients had HER2 positive disease. 48 gene signatures were analyzed; 5 being significantly enriched between metastatic and primary site accounting for cell cycle, DNA damage repair, MYC, mTOR signaling and immortality and stemness. Out of a pool of 760, significant overlap was seen between 12 genes across the 5 signatures of interest: POLE, LIG1, FEN1 (involved in DNA repair and replication); AURKA and PLK1 (cell proliferation and triggers for G2/M transition), BUB1 (establishment of the mitotic spindle checkpoint and chromosome congression), MCM2 and MCM4 (initiation of genome replication); BRIP1 and RAD51 (critical in homologous recombinational repair); CCNE1 (cell cycle G1/S transition) and WRAP53 (dual role as p53 regulator and protein involved in telomere elongation and DNA repair). ERBB2 was similarly enriched in primary and metastatic sites. Conclusions: These preliminary data demonstrate that the genomic basis of brain metastases in esophageal cancer goes beyond EGFR/ERBB2 signaling. A complex genomic interaction is present in brain metastases as compared to primary site that offers these cells the advantage for neurotropism. To our knowledge this is the first study attempting to illustrate genomic differences between primary and matched brain metastasis sites in esophageal cancer.

Arsenopyrite weathering in acid rain: Arsenic transfer and environmental implications

Arsenopyrite is widely distributed and weathers readily in the nature, releases As and pollutes the surrounding environment. Acid rain is acidic in nature as contains sulfur oxides (SO_x) and nitrogen oxides (NO_x), and is a typical hazardous material to human. When arsenopyrite encounters acid rain, their interaction effect may aggregate environmental degradation. In this work, the weathering behavior of arsenopyrite in simulated acid rain was studied using the electrochemical techniques and surface analysis. Cyclic voltammetry and Raman and XPS confirmed that FeAsS was oxidized to Fe²⁺, AsO₃^3- and S⁰ at the initial phase, then, Fe²⁺ was converted to Fe³⁺, S⁰ transformed to SO₃^2- and ultimately to SO₄^2-, and AsO₃^3- to AsO₄^3- with the accumulation of H⁺. Polarization curve revealed higher temperature or higher acidity of acid rain increased the weathering trend and rate of arsenopyrite, and electrochemical impedance spectroscopic measurements showed the causes behind this to be smaller resistance and greater capacitance at the double layer and passivation film. Arsenopyrite weathering rate and temperature has a relationship: lnk = -3824.8/T + 10.305, via a transition state with activation enthalpy 29.37 kJ mol^-1 and activation entropy - 167.40 J mol^-1 K^-1. This study provides a rapid and quantitative in-situ electrochemical method for arsenopyrite weathering and an improved understanding of arsenopyrite weathering in acid rain condition. The results have powerful implications for the remediation and management of As-bearing sites affected by mining activities in acid rain area.

Effects of long-term norepinephrine treatment on normal immortalized ovarian and fallopian tube cells

Sustained adrenergic stimulation by norepinephrine (NE) contributes to ovarian carcinoma metastasis and impairment of chemotherapy response. Although the effect of sustained NE stimulation in cancer progression is well established, less is known about its role in cancer initiation. To determine the extent to which stress hormones influence ovarian cancer initiation, we conducted a long-term (> 3 months; > 40 population doublings) experiment in which normal immortalized fallopian tube secretory (iFTSEC283) and ovarian surface epithelial (iOSE11) cell lines and their isogenic pairs containing a p53 mutation (iFTSEC283p53R175H; iOSE11p53R175H), were continuously exposed to NE (100 nM, 1 μM, 10 μM). Fallopian tube cells displayed a p53-independent increase in proliferation and colony-forming ability in response to NE, while ovarian surface epithelial cells displayed a p53-independent decrease in both assays. Fallopian tube cells with mutant p53 showed a mild loss of chromosomes and TP53 status was also a defining factor in transcriptional response of fallopian tube cells to long-term NE treatment.

Abstract 736: HOXA5 induction by norepinephrine in precursor cells of ovarian cancer

Chronic stress induced by repetitive activation of the sympathetic nervous system leads to rapid release of catecholamines like norepinephrine (NE). Several studies have shown that increased levels of NE can contribute to tumor progression by promoting tumor growth, migration and invasion of ovarian cancer cells. However, the role of NE in tumor initiation remains mostly unknown. The purpose of this study was to explore the acute and chronic effects of NE on immortalized normal fallopian tube and ovarian cell lines presumed to be the origin of epithelial ovarian cancers. Normal immortalized ovarian (iOSE11) and fallopian tube (iFTE283) surface epithelial cells were treated with 10µM NE for 15 min, 1h and 4h followed by whole-transcriptome RNA-Seq. 234 and 313 differentially expressed genes were identified at 1h and 4h time points in iFTE283 cells respectively; while 53 and 34 differentially expressed genes were identified at 1h and 4h time points in iOSE11 cells. Gene ontology analysis using Panther Statistical Overrepresentation Test was performed on these differentially expressed genes. Panther Protein Class analysis revealed ‘transcription factor' to be the most significantly overrepresented at both 1h and 4h time-points. Promoter enrichment analysis using oPOSSUM database identified transcription factor HOXA5 to be consistently enriched at both time points in both cell lines. Time course studies performed by qPCR and luciferase promoter assays for HOXA5 transcription factor in normal cells (iOSE11, iFTE283), partially transformed cells (iOSE11-p53R175H, iFTE283-p53R175H, iFTE282-p53R175H and iOSE4-cMyc) and cancer cells (OvCAR8, SkoV3) revealed that HOXA5 induction by NE occurred only in normal immortalized cells and partially transformed p53R175H overexpressing cells, but not in cancer cells. In contrast, chronic exposure to NE for 4 months followed by HOXA5 time course study by qPCR revealed attenuation of HOXA5 induction in normal as well as p53R175H overexpressing cells. Additionally, long term NE treatment lead to increased proliferation and colony forming capacity in iFTE283, iFTE283-p53R175H and iFTE282-p53R175H cells. p53R175H overexpressing iFTE283 cells also showed slight increase in chromosomal instability, as measured by karyotype, after 4 months of treatment with NE. These observations suggest that HOXA5 plays a central role in regulating the early response to NE in normal as well as p53R175H overexpressing ovarian epithelial and fallopian tube cells, but this induction is attenuated in cancer cells as well as in normal and partially transformed cells that are exposed to long term NE treatment. We will further assess the induction of HOXA5 by NE through promoter bashing experiments.

Citation Format: Sweta Dash, Ling Cen, Sean Yoder, Tania Mesa, Andrew Smith, Chaomei Zhang, Jamie Teer, Guillermo Armaiz-Pena, Alvaro Monteiro. HOXA5 induction by norepinephrine in precursor cells of ovarian 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 736.

TFEB links MYC signaling to epigenetic control of myeloid differentiation and acute myeloid leukemia

MYC oncoproteins regulate transcription of genes directing cell proliferation, metabolism and tumorigenesis. A variety of alterations drive MYC expression in acute myeloid leukemia (AML) and enforced MYC expression in hematopoietic progenitors is sufficient to induce AML. Here we report that AML and myeloid progenitor cell growth and survival rely on MYC-directed suppression of Transcription Factor EB (TFEB), a master regulator of the autophagy-lysosome pathway. Notably, although originally identified as an oncogene, TFEB functions as a tumor suppressor in AML, where it provokes AML cell differentiation and death. These responses reflect TFEB control of myeloid epigenetic programs, by inducing expression of isocitrate dehydrogenase-1 (IDH1) and IDH2, resulting in global hydroxylation of 5-methycytosine. Finally, activating the TFEB-IDH1/IDH2-TET2 axis is revealed as a targetable vulnerability in AML. Thus, epigenetic control by a MYC-TFEB circuit dictates myeloid cell fate and is essential for maintenance of AML.

Association of a novel endometrial cancer biomarker panel with prognostic risk, platinum insensitivity, and targetable therapeutic options

During the past decade, the age-adjusted mortality rate for endometrial cancer (EC) increased 1.9% annually with TP53 mutant (TP53-mu) EC disproportionally represented in advanced disease and deaths. Therefore, we aimed to assess pivotal molecular parameters that differentiate clinical outcomes in high- and low-risk EC. Using the Cancer Genome Atlas, we analyzed EC specimens with available DNA sequences and quantitative gene-specific RNA expression data. After polymerase ɛ (POLE)-mutant specimens were excluded, differential gene-specific mutations and mRNA expressions were annotated and integrated. Consequent to TP53-mu failure to induce p21, derepression of multiple oncogenes harboring promoter p21 repressive sites was observed, including CCNA2 and FOXM1 (P < .001 compared with TP53 wild type [TP53-wt]). TP53-wt EC with high CCNA2 expression (CCNA2-H) had a targeted transcriptomic profile similar to that of TP53-mu EC, suggesting CCNA2 is a seminal determinant for both TP53-wt and TP53-mu EC. CCNA2 enhances E2F1 function, upregulating FOXM1 and CIP2A, as observed in TP53-mu and CCNA2-H TP53-wt EC (P < .001). CIP2A inhibits protein phosphatase 2A, leading to AKT inactivation of GSK3β and restricted oncoprotein degradation; PPP2R1A and FBXW7 mutations yield similar results. Upregulation of FOXM1 and failed degradation of FOXM1 is evidenced by marked upregulation of multiple homologous recombination genes (P < .001). Integrating these molecular aberrations generated a molecular biomarker panel with significant prognostic discrimination (P = 5.8×10⁻⁷); adjusting for age, histology, grade, myometrial invasion, TP53 status, and stage, only CCNA2-H/E2F1-H (P = .0003), FBXW7-mu/PPP2R1A-mu (P = .0002), and stage (P = .017) were significant. The generated prognostic molecular classification system identifies dissimilar signaling aberrations potentially amenable to targetable therapeutic options.

Comprehensive evaluation of genomic alterations in patients with gastric and gastroesophageal adenocarcinoma stratified according to TP53 mutation status

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Background: Gastric (GC) and gastroesophageal adenocarcinomas (GEA) are molecularly diverse. Molecular biomarkers of clinical significance have been identified that impact treatment decision making. TP53 is the most frequently altered gene with approximately 50% of patients harboring mutations. However, TP53 mutations have not yet been confirmed as a target of therapeutic benefit. This study aimed to identify distinct genomic alterations that are dominant in TP53 mutated (MUT) versus wild-type (WT) GC and GEA in order to elucidate alternative therapeutic targets within these subsets. Methods: De-identified data for 3741 patients with GC and GEA was obtained from Foundation Medicine. The data obtained were age, gender, tumor mutational burden (TMB), and the distinct genomic alterations noted on DNA sequencing. The dataset was sorted by TP53 mutation status. Differences in mutation frequency were detected using the Fisher’s exact test of independence with a p-value of < 0.01 designated as the cutoff value for statistical significance. Results: The dataset consisted of 2946 GCs and 795 GEAs. TP53 mutations were present in 65.8% of specimens. 61.6% of GCs and 81.4% of GEAs were TP53 MUT positive (p = < .001). Median TMB score and the frequency of tumors with a TMB score > 10 was similar in both TP53 MUT and WT groups. 49 genes had statistically different mutation frequencies in TP53 MUT vs. WT patients. Top co-occurring genetic alterations in TP53 MUT patients included amplification and point mutations in MYC, CCNE1, MET, ERBB2, and EGFR. Amplification and point mutations in MDM2, CDK4, ARID1A, PIK3CA, and ERBB3 were the top co-occurring genetic alterations in TP53 WT patients. Conclusions: There was a high frequency of TP53 mutations in this group of GC and GEA patients, with a higher incidence of TP53 mutations identified in GEA samples. The mutational profiles of these tumors differed according to TP53 mutation status. These differences may be able to serve as the foundation for future clinical investigations.

The genomic landscape of undifferentiated embryonal sarcoma of the liver is typified by C19MC structural rearrangement and overexpression combined with TP53 mutation or loss

Undifferentiated embryonal sarcoma of the liver (UESL) is a rare and aggressive malignancy. Though the molecular underpinnings of this cancer have been largely unexplored, recurrent chromosomal breakpoints affecting a noncoding region on chr19q13, which includes the chromosome 19 microRNA cluster (C19MC), have been reported in several cases. We performed comprehensive molecular profiling on samples from 14 patients diagnosed with UESL. Congruent with prior reports, we identified structural variants in chr19q13 in 10 of 13 evaluable tumors. From whole transcriptome sequencing, we observed striking expressional activity of the entire C19MC region. Concordantly, in 7 of 7 samples undergoing miRNAseq, we observed hyperexpression of the miRNAs within this cluster to levels >100 fold compared to matched normal tissue or a non-C19MC amplified cancer cell line. Concurrent TP53 mutation or copy number loss was identified in all evaluable tumors with evidence of C19MC overexpression. We find that C19MC miRNAs exhibit significant negative correlation to TP53 regulatory miRNAs and K-Ras regulatory miRNAs. Using RNA-seq we identified that pathways relevant to cellular differentiation as well as mRNA translation machinery are transcriptionally enriched in UESL. In summary, utilizing a combination of next-generation sequencing and high-density arrays we identify the combination of C19MC hyperexpression via chromosomal structural event with TP53 mutation or loss as highly recurrent genomic features of UESL.

[Analysis of ASXL1 gene variant in patients with myelodysplastic syndrome]

OBJECTIVE

To detect ASXL1 gene variants among patients with myelodysplastic syndrome (MDS) and explore their correlation with variants of other genes and clinical features of patients.

METHODS

For 149 patients with MDS, genomic DNA was amplified by PCR and subject to direct sequencing to identify variants of ASXL1, U2AF1, SF3B1, DNMT3A, TET2, IDH1/2, NPM1, FLT3-ITD and C-KIT genes.

RESULTS

ASXL1 variants were found among 37 patients (24.8%). Other commonly mutated genes included U2AF1 (22.8%), TET2 (11.4%), DNMT3A (9.4%), NPM1 (8.1%) and SF3B1 (6.0%). The frequency of concurrent U2AF1 and TET2 variants among patients with ASXL1 variants was slightly higher than that of wild-type patients. No significant difference was found in median age, MDS subtype, karyotype, peripheral leukocytes, hemoglobin, platelet levels, and bone marrow blast counts between the ASXL1-variant and the wild-type groups (P> 0.05). Twenty-nine patients harboring ASXL1 variants were followed up, 37.9% progressed to acute myeloid leukemia (AML). The rate of transformation in ASXL1-variant group was significantly higher than the wild-type group (37.9% vs. 14.1%, P< 0.01).

CONCLUSION

ASXL1 showed a high frequency of variant among MDS patients, which was frequently accompanied with U2AF1 and TET2 variants. Compared with the wild type group, patients with ASXL1 variants were more likely to progress to AML.

Induction of zonal-specific cellular morphology and matrix synthesis for biomimetic cartilage regeneration using hybrid scaffolds

Cartilage is anisotropic in nature and organized into distinct zones. Our goal was to develop zonal-specific three-dimensional hybrid scaffolds which could induce the generation of zonal-specific cellular morphology and extracellular matrix (ECM) composition. The superficial and middle zones comprised two layers of hyaluronic acid (HA) hydrogel which enveloped specifically orientated or randomly arranged polylactic acid nanofibre meshes. The deep zone comprised a HA hydrogel with multiple vertical channels. Primary bovine chondrocytes were seeded into the individual zonal scaffolds, cultured for 14 days and then the ECM was analysed. The aligned nanofibre mesh used in the superficial zone induced an elongated cell morphology, lower glycosaminoglycan (GAG) and collagen II production, and higher cell proliferation and collagen I production than the cells in the middle zone scaffold. Within the middle zone scaffold, which comprised a randomly orientated nanofibre mesh, the cells were clustered and expressed more collagen II. The deep zone scaffold induced the highest GAG production, the lowest cell proliferation and the lowest collagen I expression of the three zones. Assembling the three zones and stabilizing the arrangement with a HA hydrogel generated aligned, randomly aggregated and columnar cells in the superficial, middle and deep zones. This study presents a method to induce zonal-specific chondrocyte morphology and ECM production.

Proteogenomic landscape of squamous cell lung cancer

How genomic and transcriptomic alterations affect the functional proteome in lung cancer is not fully understood. Here, we integrate DNA copy number, somatic mutations, RNA-sequencing, and expression proteomics in a cohort of 108 squamous cell lung cancer (SCC) patients. We identify three proteomic subtypes, two of which (Inflamed, Redox) comprise 87% of tumors. The Inflamed subtype is enriched with neutrophils, B-cells, and monocytes and expresses more PD-1. Redox tumours are enriched for oxidation-reduction and glutathione pathways and harbor more NFE2L2/KEAP1 alterations and copy gain in the 3q2 locus. Proteomic subtypes are not associated with patient survival. However, B-cell-rich tertiary lymph node structures, more common in Inflamed, are associated with better survival. We identify metabolic vulnerabilities (TP63, PSAT1, and TFRC) in Redox. Our work provides a powerful resource for lung SCC biology and suggests therapeutic opportunities based on redox metabolism and immune cell infiltrates.

Squamous cell lung cancer has dismal prognosis due to the dearth of effective treatments. Here, the authors perform an integrated proteogenomic analysis of the disease, revealing three proteomics-based subtypes and suggesting potential therapeutic opportunities.

Abstract 3010: Osteosarcoma cell lines display both shared and unique vulnerabilities to 140 targeted small molecules with RNA-seq revealing putative mechanisms

BACKGROUND: Osteosarcoma is the most common bone sarcoma in children, adolescents, and young adults. Osteosarcoma primarily arises through tumor suppressor inactivation, most typically due to TP53 attenuation mechanisms. Increasingly additional oncogenic and tumor suppressor pathways are being recognized in subsets of osteosarcoma. We hypothesized that novel insights into mechanisms of sensitivity and resistance for emerging targeted therapies could be elucidated by combining activity and genomic information across cell line models of osteosarcoma.

METHODS: In this study we evaluated 6 established osteosarcoma cell lines (U2-OS, MG-63, OS252, SAOS-2, 143B, MNNG) representing several TP53 and other tumor suppressor inactivation mechanisms with human osteoblasts as a control. We have obtained RNA-seq profiles detailing genomic variants, gene fusions, and expression of both protein-coding and miRNA genes for these cell lines. In addition to genomic changes, we evaluated 140 chemical probes and candidate drug molecules across these cell lines.

RESULTS: RNAseq identified TP53 changes in 5 of 6 cell lines with OS252, SAOS2 and MG-63 having intron 1 translocations and 143B and MNNG sharing a TP53 gain-of-function mutation. Variant calling from the whole exome sequencing data revealed additional putatively oncogenic mutations. Additionally, we observed differential gene expression patterns compared to control samples in genes associated with genomic stability, epigenetic regulation, and transcriptional activity. Differential sensitivities to several classes of small molecules were seen across the cell lines and were associated with genomic changes that warrant additional investigation such as: RAD51 pathway genomic findings associated with sensitivity to RS-1, disulfuram activity varying according to aldehyde dehydrogenase activity, and variable response to inhibitors of ATR and specific CDKs that are associated with the expression of their respective targets. Additional pathways of interest that demonstrate differential response to small molecules include histone/protein deacetylation, telomerase activity, protein translation, and others. Unique vulnerabilities associated with tumor suppressor or oncogenic changes specific to an individual cell line will be presented.

CONCLUSIONS: By characterizing response to small molecules in the context of gene expression, underlying pathway vulnerabilities may be determined for further testing suggesting potential biomarkers for basket trials. Other agents with shared sensitivities to agents across cell lines may be translated in a different manner.

Citation Format: Elliot J. Kahen, Darcy Welch, Jamie Teer, Andrew S. Brohl, Sean J. Yoder, Yonghong Zhang, Ling Cen, Damon Reed. Osteosarcoma cell lines display both shared and unique vulnerabilities to 140 targeted small molecules with RNA-seq revealing putative mechanisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3010.

[Characterizing the molecular cytogenetics in acute monocytic leukemia]

OBJECTIVE

To characterize the molecular genetics of 81 patients with acute monocytic leukemia (AML).

METHODS

Fluorescence in situ hybridization (FISH) was employed to detect MLL gene rearrangements. Combined mutations of 17 genes were detected by DNA-based PCR and Sanger sequencing.

RESULTS

Sixty seven patients were found to harbor at least one mutation. The most commonly mutated gene was NPM1 (n=18), which was followed by FLT3-ITD (n=16), NRAS (n=16), DNMT3A (n=15), TET2 (n=12), RUNX1 (n=11) and KRAS (n=9). Based on the functions of mutated genes, the most frequently involved genes were those involved in DNA methylation (38.27%), tyrosine kinase receptor signaling (32.1%), transcription regulation (28.4%), and RAS pathway (24.7%). Single gene mutation predominated in patient with cytogenetic abnormalities, while coexistence of 2 mutations have predominated in patient with normal cytogenetic findings. Stratified by cytogenetic findings, patients with single gene mutations (intermediate-risk group) had significantly higher complete remission (CR) rates than those with ≥2 gene mutations (unfavorable-risk group) (91.7% vs. 57.6% , 87.5% vs. 25.0%, P =0.0319, 0.0117, respectively).

CONCLUSION

Over 80% of AML patients were found to harbor at least one mutation. Their clinical phenotype and prognosis may be impacted by the synergy of MLL gene rearrangement and multiple mutations. For patients under the same risk stratification, the number of mutations is reversely correlated with the CR rate.

[Clinical feature and cytogenetic analysis of 28 patients with bone marrow invasion non-Hodgkin's lymphoma]

OBJECTIVE

To study the correlation of hematomorphology, bone marrow cytogenetics and clinical biochemical parameters with the prognosis of non-Hodgkin's lymphoma with bone marrow invasion.

METHODS

Morphological analysis of bone marrow cells was performed by routine bone marrow puncture.Chromosome samples were prepared by short-term bone marrow culture. Karyotype analysis was carried out by R-banding in 28 patients. P53 gene was detected by fluorescence in situ hybridization (FISH). Serum lactate dehydrogenase (LDH) of all patients was determined and compared.

RESULTS

In all patients, bone marrow morphology showed invasion of lymphoma. Chromosome analysis revealed abnormal karyotypes in 19 cases, which yielded an incidence of 67.85%. The proportion of lymphoma cells in bone marrow among those with an abnormal karyotype was much higher than those with a normal karyotype (60.2% vs. 33.5%, P<0.05). FISH assay showed that 9 (32.14%) patients had P53 gene deletion. And the deletion was much more common among those with an abnormal karyotype (42.11% vs. 11.11%, P<0.05). The serum LDH level in patients with an abnormal karyotype was significantly higher compared with whose with a normal karyotype (1464.37 U/L vs. 294.33 U/L, P<0.05).

CONCLUSION

Patients with abnormal karyotypes have a higher rate of P53 gene deletion, and their LDH level is significantly higher than those with a normal karyotype, which predicted a relatively poor prognosis.

S100A9-induced overexpression of PD-1/PD-L1 contributes to ineffective hematopoiesis in myelodysplastic syndromes

Myelodysplastic syndromes (MDS) are characterized by dysplastic and ineffective hematopoiesis that can result from aberrant expansion and activation of myeloid-derived suppressor cells (MDSCs) within the bone marrow (BM) niche. MDSCs produce S100A9, which mediates premature death of hematopoietic stem and progenitor cells (HSPCs). The PD-1/PD-L1 immune checkpoint impairs immune responses by inducing T-cell exhaustion and apoptosis, but its role in MDS is uncharacterized. Here we report an increased expression of PD-1 on HSPCs and PD-L1 on MDSCs in MDS versus healthy donors, and that this checkpoint is also activated in S100A9 transgenic (S100A9Tg) mice, and by treatment of BM mononuclear cells (BM-MNC) with S100A9. Further, MDS BM-MNC treated with recombinant PD-L1 underwent cell death, suggesting that the PD-1/PD-L1 interaction contributes to HSPC death in MDS. In accordance with this notion, PD-1/PD-L1 blockade restores effective hematopoiesis and improves colony-forming capacity in BM-MNC from MDS patients. Similar findings were observed in aged S100A9Tg mice. Finally, we demonstrate that c-Myc is required for S100A9-induced upregulation of PD-1/PD-L1, and that treatment of MDS HSPCs with anti-PD-1 antibody suppresses the expression of Myc target genes and increases the expression of hematopoietic pathway genes. We conclude anti-PD-1/anti-PD-L1 blocking strategies offer therapeutic promise in MDS in restoring effective hematopoiesis.

Bayesian Electromagnetic Spatio-Temporal Imaging of Extended Sources Based on Matrix Factorization

Accurate estimation of the locations and extents of neural sources from electroencephalography and magnetoencephalography (E/MEG) is challenging, especially for deep and highly correlated neural activities. In this study, we proposed a new fully data-driven source imaging method, source imaging based on spatio-temporal basis function (SI-STBF), which is built upon a Bayesian framework, to address this issue. The SI-STBF is based on the factorization of a source matrix as a product of a sparse coding matrix and a temporal basis function (TBF) matrix, which includes a few TBFs. The prior of the TBF is set in the empirical Bayesian manner. Similarly, for the spatial constraint, the SI-STBF assumes the prior covariance of the coding matrix as a weighted sum of several spatial covariance components. Both the TBFs and the coding matrix are learned from E/MEG simultaneously through variational Bayesian inference. To enable inference on high-resolution source space, we derived a scalable algorithm using convex analysis. The performance of the SI-STBF was assessed using both simulated and experimental E/MEG recordings. Compared with L₂-norm constrained methods, the SI-STBF is superior in reconstructing extended sources with less spatial diffusion and less localization error. By virtue of the spatio-temporal factorization of source matrix, the SI-STBF also produces more accurate estimations than spatial-only constraint method for high correlated and deep sources.

Automatic System for Obstructive Sleep Apnea Events Detection Using Convolutional Neural Network

Obstructive Sleep Apnea (OSA) is characterized by repetitive episodes of airflow reduction (hypopnea) or cessation (apnea), which, as a prevalent sleep disorder, can cause people to stop breathing for 10 to 30 seconds at a time and lead to serious problems such as daytime fatigue, impaired memory, and depression. This work intends to explore automatic detection of OSA events with 1-second annotation based on blood oxygen saturation, oronasal airflow, and ribcage and abdomen movements. Deep Learning (DL) technology, specifically, Convolutional Neural Network (CNN), is employed as a feature detector to learn the characteristics of the highorder correlation among visible data and corresponding labels. A fully-connected layer in the last stage of the CNN is connected to the output layer and constructs the desired number of outputs for sleep apnea events classification. A leave-one-out cross-validation has been conducted on the PhysioNet Sleep Database provided by St. Vincents University Hospital and University College Dublin, and an average accuracy of $79 .61$% across normal, hypopnea, and apnea, classes is achieved.

Human tRNA-Derived Small RNAs Modulate Host-Oral Microbial Interactions

Coevolution of the human host and its associated microbiota has led to sophisticated interactions to maintain a delicate homeostasis. Emerging evidence suggests that in addition to small molecules, peptides, and proteins, small regulatory noncoding RNAs (sRNAs) might play an important role in cross-domain interactions. In this study, we revealed the presence of diverse host transfer RNA-derived small RNAs (tsRNAs) among human salivary sRNAs. We selected 2 tsRNAs (tsRNA-000794 and tsRNA-020498) for further study based on their high sequence similarity to specific tRNAs from a group of Gram-negative oral bacteria, including Fusobacterium nucleatum, a key oral commensal and opportunistic pathogen. We showed that the presence of F. nucleatum triggers exosome-mediated release of tsRNA-000794 and tsRNA-020498 by human normal oral keratinocyte cells. Furthermore, both tsRNA candidates exerted a growth inhibition effect on F. nucleatum, likely through interference with bacterial protein biosynthesis, but did not affect the growth of Streptococcus mitis, a health-associated oral Gram-positive bacterium whose genome does not carry sequences bearing high similarity to either tsRNA. Our data provide the first line of evidence for the modulatory role of host-derived tsRNAs in the microbial-host interaction.

Microbiome Associated with Severe Caries in Canadian First Nations Children

Young Indigenous children in North America suffer from a higher degree of severe early childhood caries (S-ECC) than the general population, leading to speculation that the etiology and characteristics of the disease may be distinct in this population. To address this knowledge gap, we conducted the first microbiome analysis of an Indigenous population using modern molecular techniques. We investigated the caries-associated microbiome among Canadian First Nations children with S-ECC. Thirty First Nations children <72 mo of age with S-ECC and 20 caries-free children were recruited in Winnipeg, Canada. Parents or caregivers completed a questionnaire on general and dental health, diet, and demographics. The plaque microbiome was investigated by sequencing the 16S rRNA gene. Sequences were clustered into operational taxonomic units and taxonomy assigned via the Human Oral Microbiome Database, then analyzed at the community level with alpha and beta diversity measures. Compared with those who were caries free, children with S-ECC came from households with lower income; they were more likely to live in First Nations communities and were more likely to be bottle-fed; and they were weaned from the bottle at a later age. The microbial communities of the S-ECC and caries-free groups did not differ in terms of species richness or phylogenetic diversity. Beta diversity analysis showed that the samples significantly clustered into groups based on caries status. Twenty-eight species-level operational taxonomic units were significantly different between the groups, including Veillonella HOT 780 and Porphyromonas HOT 284, which were 4.6- and 9-fold higher, respectively, in the S-ECC group, and Streptococcus gordonii and Streptococcus sanguinis, which were 5- and 2-fold higher, respectively, in the caries-free group. Extremely high levels of Streptococcus mutans were detected in the S-ECC group. Overall, First Nations children with S-ECC have a significantly different plaque microbiome than their caries-free counterparts, with the S-ECC group containing higher levels of known cariogenic organisms.

Abstract 1565: OnPLS-based integrative proteogenomics analysis of lung squamous cell cancer

Introduction: Multivariate projection methods such as PCA and PLS has been widely applied for analysis of biological and chemical data. OnPLS is a recent extension to these methods suitable for integrative analysis of omics data. With OnPLS it is possible to compare multiple omics datasets to identify joint variation and variation locally unique for each of the studied datasets. OnPLS is a new approach for truly integrative analysis of omics data to be contrasted to commonly applied approaches limiting analysis to 1) comparing findings from individually analyzed blocks of data 2) pairwise comparison of individual probes.

Experimental: A Java based implementation of OnPLS was used for the statistical modeling. 116 lung squamous cell cancer samples were characterized using gene expression profiling and global proteomics. The OnPLS model was applied to jointly model variation between mRNA and protein expression. Enrichment analysis of factor loadings was performed using the Enrichr tools to identify biological mechanisms explained by the different joint and unique components of the OnPLS model.

Results: Using a cross-validation procedure the model with the highest predictive ability was calculated having two joint components and one locally unique component for each of the proteomics and gene expression datasets. The model explained 21.9% of the variation in the expression data and 26.1% of the variation in the proteomics data. The first joint component captures the highest degree of common variation between mRNA and protein activity. From the mRNA data, this component is related to immune infiltrates, especially monocytes and B-cells, whereas this component is related to extracellular matrix activity from the protein data. This suggests covariance of mRNA immune-related gene expression and extracellular matrix-related protein expression. As expected, local variation specific to the protein measurements involved regulation of protein activation and processing. mRNA-specific variation is related to keratinization, a key process in squamous cell cancer.

Conclusion: OnPLS offers an interesting approach for integrative analysis of omics data. Applying this approach to proteo-genomics data of lung squamous cell cancers suggest similar patterns of activity is represented in protein and gene expression data, however the biological processes associated with this activity may be distinct.

Citation Format: Fredrik Pettersson, Paul A. Stewart, Robbert J. Slebos, Eric A. Welsh, Ling Cen, Yonghong Zhang, Zhihua Chen, Chia-Ho Cheng, Guolin Zhang, Bin Fang, Victoria Izumi, Sean Yoder, Katherine Fellows, Y Ann Chen, Jamie K. Teer, Steven Eschrich, John M. Koomen, Anders Berglund, Eric B. Haura. OnPLS-based integrative proteogenomics analysis of lung squamous cell cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1565. doi:10.1158/1538-7445.AM2017-1565

Abstract 205: Underlying mechanisms of genome-proteome discordance in squamous cell lung cancer

Introduction: Genomic analyses have yielded a tremendous amount of data on the genetic changes in lung cancers, but translating these experiments into actionable information benefitting lung squamous cell carcinoma (SQLC) patients has proven more difficult. Studies by the NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC), our group, and others have demonstrated that gene and protein expression show only moderate correlation, demonstrating limitations in explaining phenotypic changes from genomics alone. These findings indicate a clear need for integrative proteogenomics to better understand tumor biology, especially in a complex disease like SQLC.

Experimental: We have assembled a comprehensive proteogenomic dataset including DNA copy number (Affymetrix CytoScan HD Assay), targeted exome sequencing (Agilent Comprehensive Cancer Panel), RNA-sequencing (Illumina NextSeq), and shotgun proteomics (Q Exactive LC-MS/MS) on 116 surgically resected SQLC tumor samples with extensive clinical and follow up data.

Results: We have identified 6584 high confidence proteins from preliminary proteomic analysis. After quality control filtering, we utilized 5562 gene-protein pairs for further analysis. Clustering of patient RNA expression in this patient cohort has been unable to fully reproduce the molecular classification previously published for SQLC. Furthermore, proteomic results indicate yet another potential classification strategy selecting patient subgroups that differ at protein level. We observed a 0.29 median Spearman’s correlation of 5562 gene-protein pairs. There were 2781 highly correlated gene-protein pairs (greater than median) and 2781 poorly correlated gene-protein pairs (less than median) including 773 anti-correlated gene-protein pairs (less than 0). We hypothesized that poorly correlated gene-protein pairs could be functionally related in a pathway-dependent manner. Enrichment analysis of poorly correlated proteins identified pathways related to mRNA processing, growth factor signaling (EGFR, FGFR), and nonsense-mediated decay (NMD). Interestingly, there were 9 frequently mutated SQLC genes in the low correlation gene-protein pairs but only 3 in the highly correlated pairs. We found three distinct patient subgroups by clustering poorly correlated proteins. Analysis of these subgroups showed differentially expressed pathways related to mRNA processing, ubiquitination, and NMD.

Conclusion: Differential modulation of the proteome outside of genomic regulation may suggest important regulatory mechanisms in cancer and give new insights into treating SQLC. Analysis of poorly correlated gene-protein pairs suggests certain pathways are dysregulated in cancer, and ongoing DNA analysis and future analyses involving miRNAs, RNA-binding proteins, and the ubiquitin proteome system will help elucidate our preliminary findings.

Citation Format: Paul A. Stewart, Robbert J. Slebos, Eric A. Welsh, Ling Cen, Yonghong Zhang, Zhihua Chen, Chia-Ho Cheng, Fredrik Pettersson, Anders Berglund, Guolin Zhang, Bin Fang, Victoria Izumi, Sean Yoder, Katherine Fellows, Ann Chen, Jamie K. Teer, Steven A. Eschrich, John M. Koomen, Eric B. Haura. Underlying mechanisms of genome-proteome discordance in squamous cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 205. doi:10.1158/1538-7445.AM2017-205

Abstract 206: Proteogenomic classifications and outcome in squamous cell carcinoma of the lung

Introduction: Genomic analyses have yielded a tremendous amount of knowledge on the genetic changes in lung cancers, but translating this information into actionable data benefitting patients has proven difficult. The integration of proteomic analyses with genomics and gene expression profiling allows a more detailed description of the biological processes, thus improving our understanding of cancer phenotypes. These insights can potentially be used for better classification and help to guide patient selection for targeted therapies.

Experimental: We analyzed 116 surgically resected squamous cell lung carcinoma samples for copy-number alterations, gene expression profiling, targeted exome-sequencing and global proteomic profiling. The cohort consisted of mostly early stage tumors (83% Stage I or II) with complete follow-up (median 58 months). Copy number status was analyzed using the Affymetrix CytoScan array, DNA mutation status was assessed using a customized version of the Agilent Comprehensive Cancer Panel for targeted sequencing, and gene expression profiling was carried out by RNA-sequencing. Proteomic analysis was performed using TMT labeling, 12- fraction bRPLC separation and LC-MS/MS analysis with a Thermo Q-Exactive mass spectrometer. Database searches were performed using multiple search engines against RefSeq version 78, and summarized using IDPicker 3.

Results: The non-redundant protein inventory consisted of more than 6,000 protein groups with a protein FDR &lt;5%. Tumors were classified according to well established gene expression criteria into 4 classes: Classical, Basal, Primitive and Secretory. At the protein level, the Classical subtype was associated with xenobiotic and energy metabolism; the Basal subtype with defense responses and extracellular matrix changes; the Primitive subtype with nucleic acid metabolism; and the Secretory subtype with p38 signaling. These findings confirm and expand on previous mRNA expression studies of squamous cell lung carcinoma. Proteomics-based classification identified two sub-categories within the Classical subtype, which were characterized by inflammatory and stress response signaling. Within this group, patients with high expression of inflammation-associated proteins had better cancer-specific survival than those with low expression (p=0.04, Log-rank test). Targeted exome sequencing of 154 cancer-associated genes revealed frequent mutations in TP53, CDKN2A, NFE2L2, and other genes. Proteomic expression of genes located in amplified chromosomal regions was used to identify driver genes in squamous cell lung carcinoma.

Conclusion: Our results provide new biological insights from the addition of protein measurements to genomic datasets that have the potential to improve classification. The data suggest that proteins involved in immune responses are important for the biological behavior and outcome of the Classical subtype in squamous cell lung carcinoma.

Citation Format: Robbert J.C. Slebos, Paul A. Stewart, Eric A. Welsh, Ling Cen, Yonghong Zhang, Zhihua Chen, Chia-Ho Cheng, Fredrik Pettersson, Anders E. Berglund, Guolin Zhang, Bin Fang, Victoria Izumi, Sean J. Yoder, Katherine M. Fellows, Y Ann Chen, Jamie Teer, Steven Eschrich, John Koomen, Eric Haura. Proteogenomic classifications and outcome in squamous cell carcinoma of the lung [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 206. doi:10.1158/1538-7445.AM2017-206

Arginine Improves pH Homeostasis via Metabolism and Microbiome Modulation

Dental caries can be described as a dysbiosis of the oral microbial community, in which acidogenic, aciduric, and acid-adapted bacterial species promote a pathogenic environment, leading to demineralization. Alkali generation by oral microbes, specifically via arginine catabolic pathways, is an essential factor in maintaining plaque pH homeostasis. There is evidence that the use of arginine in dentifrices helps protect against caries. The aim of the current study was to investigate the mechanistic and ecological effect of arginine treatment on the oral microbiome and its regulation of pH dynamics, using an in vitro multispecies oral biofilm model that was previously shown to be highly reflective of the in vivo oral microbiome. Pooled saliva from 6 healthy subjects was used to generate overnight biofilms, reflecting early stages of biofilm maturation. First, we investigated the uptake of arginine by the cells of the biofilm as well as the metabolites generated. We next explored the effect of arginine on pH dynamics by pretreating biofilms with 75 mM arginine, followed by the addition of sucrose (15 mM) after 0, 6, 20, or 48 h. pH was measured at each time point and biofilms were collected for 16S sequencing and targeted arginine quantification, and supernatants were prepared for metabolomic analysis. Treatment with only sucrose led to a sustained pH drop from 7 to 4.5, while biofilms treated with sucrose after 6, 20, or 48 h of preincubation with arginine exhibited a recovery to higher pH. Arginine was detected within the cells of the biofilms, indicating active uptake, and arginine catabolites citrulline, ornithine, and putrescine were detected in supernatants, indicating active metabolism. Sequencing analysis revealed a shift in the microbial community structure in arginine-treated biofilms as well as increased species diversity. Overall, we show that arginine improved pH homeostasis through a remodeling of the oral microbial community.

[Clinical and genetic features of a patient with myeloid neoplasm in association with PDGFRA and EVI1 gene rearrangements]

OBJECTIVE

Todelineate the clinical and genetic features of a patient with myeloproliferative neoplasm (MPN) in association with PDGFRA and EVI1 genes rearrangements.

METHODS

Clinical data of the patient was collected. Conventional cytogenetics, fluorescence in situ hybridization (FISH) and nested PCR were carried out for the patient.

RESULTS

The patient has featured recurrent rash, joint pain, and intermittent fever. Laboratory tests showed hyperleukocytosis and marked eosinophilia. Physical examination revealed splenomegaly. His karyotype was 46,XY,t(3;5)(q26;q15)[6]/46,XY[10]. FISH assay showed that both PDGFRA and EVI1 genes were rearranged. Molecular studies of the mRNA suggested that there was a in-frame fusion between exon 12 of the PDGFRA gene and exon 9 of the FIP1L1 gene. Imatinib was initiated at a dosage of 200 mg, and after 10 months, the signal of the FIP1L1-PDGFRA fusion gene was undetectable in bone marrow sample. However, the expression of EVI1 mRNA was stable, with no significant difference found between the patient and 10 healthy controls.

CONCLUSION

MPN in association with PDGFRA and EVI1 genes rearrangements have unique clinical and genetic features. Genetic testing is helpful for early diagnosis. Imatinib may be effective for the treatment.

[Correlation of cytogenetic changes with VEGF and TRacp-5b levels among 60 elderly patients with multiple myeloma]

OBJECTIVE

To assess the correlation of cytogenetic changes with serum vascular endothelial growth factor (VEGF) and serum tartrate resistant acid phosphatase (TRacp-5b) levels among elderly patients with multiple myeloma (MM).

METHODS

Chromosomal changes were analyzed with a modified culturing method in the presence of IL-6. Serum levels of VEGF and TRacp-5b were determined with enzyme-linked immunosorbent assays (ELISA).

RESULTS

Among the 60 MM patients, chromosomal abnormalities were found in 27 cases, including 22 with numerical abnormalities and 15 with structural abnormalities. Many patients had both numerical and structural abnormalities. For 33 patients with a normal karyotype, the levels of VEGF and TRacp-5b were 117.35 ± 55.26 pg/mL and 4.15 ± 2.15 U/L, respectively, while for 27 patients with an abnormal karyotype, the levels of VEGF and TRacp-5b were 190.26 ± 85.74 pg/ml and 5.96 ± 2.24 U/L, respectively. The difference between the two groups was significant (P<0.05).

CONCLUSION

Compared with MM patients with a normal karyotype, the levels of VEGF and TRacp-5b are higher in those with cytogenetic abnormalities.