The relationship between body-mass index and overall survival in non-small cell lung cancer by sex, smoking status, and race: A pooled analysis of 20,937 International lung Cancer consortium (ILCCO) patients

INTRODUCTION

The relationship between Body-Mass-Index (BMI) and lung cancer prognosis is heterogeneous. We evaluated the impact of sex, smoking and race on the relationship between BMI and overall survival (OS) in non-small-cell-lung-cancer (NSCLC).

METHODS

Data from 16 individual ILCCO studies were pooled to assess interactions between BMI and the following factors on OS: self-reported race, smoking status and sex, using Cox models (adjusted hazard ratios; aHR) with interaction terms and adjusted penalized smoothing spline plots in stratified analyses.

RESULTS

Among 20,937 NSCLC patients with BMI values, females = 47 %; never-smokers = 14 %; White-patients = 76 %. BMI showed differential survival according to race whereby compared to normal-BMI patients, being underweight was associated with poor survival among white patients (OS, aHR = 1.66) but not among black patients (aHR = 1.06; pinteraction = 0.02). Comparing overweight/obese to normal weight patients, Black NSCLC patients who were overweight/obese also had relatively better OS (pinteraction = 0.06) when compared to White-patients. BMI was least associated with survival in Asian-patients and never-smokers. The outcomes of female ever-smokers at the extremes of BMI were associated with worse outcomes in both the underweight (pinteraction<0.001) and obese categories (pinteraction = 0.004) relative to the normal-BMI category, when compared to male ever-smokers.

CONCLUSION

Underweight and obese female ever-smokers were associated with worse outcomes in White-patients. These BMI associations were not observed in Asian-patients and never-smokers. Black-patients had more favorable outcomes in the extremes of BMI when compared to White-patients. Body composition in Black-patients, and NSCLC subtypes more commonly seen in Asian-patients and never-smokers, may account for differences in these BMI-OS relationships.

Improved detection and precise relative quantification of the urinary cancer metabolite biomarkers - Creatine riboside, creatinine riboside, creatine and creatinine by UPLC-ESI-MS/MS: Application to the NCI-Maryland cohort population controls and lung cancer cases

Creatine riboside (CR) is a novel metabolite of cancer metabolism. It is a urinary diagnostic biomarker of lung and liver cancer risk and prognosis. The level of CR is highly positive correlated in tumor and urine indicating that it is derived from human lung and liver cancers. A precise and sensitive ultra-pressure liquid chromatography-tandem mass spectrometry (UPLC-ESI-MS/MS) method was developed and validated for simultaneous quantification of the noninvasive biomarker CR, along with creatinine riboside (CNR), and their precursors creatine and creatinine, utilizing the labeled internal standard creatine riboside-13C,15N2 (CR-13C,15N2). Chromatography was carried out on a hydrophilic interaction chromatography column under a gradient mobile phase condition. MRM transitions were monitored for CR (264.1 > 132.1, m/z), CNR (246.1 > 113.9, m/z), creatine (132.0 > 72.0, m/z), creatinine (114.0 > 85.8, m/z) and CR-13C,15N2 (267.1 > 134.9, m/z) with a 11.0 min run time in the positive mode ionization. The calibration plot of the method was linear over the concentration range of 4.50-10,000 nM. Method validation was performed according to regulatory guidelines established for sensitivity, selectivity, calibration curve, stability at different storage conditions, reinjection reproducibility, ruggedness with acceptable accuracy, and precision. This assay was applied for the quantification of CR along with CNR, creatine and creatinine in a subset of urine and serum samples from the National Cancer Institute - Maryland (NCI-MD) cohort population controls and lung cancer cases. It can be standardized and used in multiple laboratories for cancer diagnosis and determining the efficacy of cancer therapy and monitoring cancer recurrence.

Cytokine Storms in Cancer and COVID-19

During the COVID-19 pandemic, research on "cytokine storms" has been reinvigorated in the field of infectious disease, but it also has particular relevance to cancer research. Interleukin-6 (IL-6) has emerged as a key component of the immune response to SARS-CoV-2, such that the repurposing of anti-IL-6 therapeutics for COVID-19 is now a major line of investigation, with several ongoing clinical trials. We lay a framework for understanding the role of IL-6 in the context of cancer research and COVID-19 and suggest how lessons learned from cancer research may impact SARS-CoV-2 research and vice versa.

A small protein encoded by a putative lncRNA regulates apoptosis and tumorigenicity in human colorectal cancer cells

Long noncoding RNAs (lncRNAs) are often associated with polysomes, indicating coding potential. However, only a handful of endogenous proteins encoded by putative lncRNAs have been identified and assigned a function. Here, we report the discovery of a putative gastrointestinal-tract-specific lncRNA (LINC00675) that is regulated by the pioneer transcription factor FOXA1 and encodes a conserved small protein of 79 amino acids which we termed FORCP (FOXA1-Regulated Conserved Small Protein). FORCP transcript is undetectable in most cell types but is abundant in well-differentiated colorectal cancer (CRC) cells where it functions to inhibit proliferation, clonogenicity, and tumorigenesis. The epitope-tagged and endogenous FORCP protein predominantly localizes to the endoplasmic reticulum (ER). In response to ER stress, FORCP depletion results in decreased apoptosis. Our findings on the initial characterization of FORCP demonstrate that FORCP is a novel, conserved small protein encoded by a mis-annotated lncRNA that regulates apoptosis and tumorigenicity in well-differentiated CRC cells.

Cancer-Type-Specific Bacteria: Freeloaders or Partners?

A paper published in Science probes over 1500 tumor samples from multiple cancer types for markers of a tumor microbiome and viable bacteria. Unique intertumoral and intracellular signatures associated with clinical biomarkers and metabolic pathways provide clues to the roles bacteria play in carcinogenesis.

Abstract 19: Targeting Delta133p53 isoform with small-molecule compounds to modulate cellular senescence

Cellular senescence (CS) and senescence-associated secretory phenotype (SASP) contribute to aging and age-related diseases. Mechanistically, the stress sensor p53 plays a pivotal role in the initiation and maintenance of CS. In humans, TP53 is expressed as 12 isoforms that contribute to the fine-tuning of p53 activity. Delta133p53 is generated from an alternative promoter located in intron 4 and is therefore devoid of both the transactivation domain and part of the DNA binding domain. Delta133p53 is predominantly located in the nucleus and is largely regulated at the protein level through chaperone-assisted selective autophagic degradation. Delta133p53 counteracts p53-mediated replicative CS and reduces the secretion of SASP cytokines. Delta133p53 is expressed in most normal tissues, but its expression is deregulated in age-associated diseases such as cancer, neurodegenerative diseases, and premature aging disorders. Delta133p53 is downregulated in exhausted CD8+ T cells, nearly senescent fibroblasts from Hutchinson-Gilford progeria syndrome patients, and astrocytes from irradiated brains and Alzheimer’s disease and amyotrophic lateral sclerosis patients. Delta133p53 overexpression extends the replicative lifespan in normal cells but does not cause immortalization or malignant transformation. Hence, delta133p53 appears to be a safe, novel therapeutic target to regulate CS. The present study aims at identifying small-molecule compounds that stabilize or prevent the degradation of delta133p53 protein and inhibit CS. To screen for activators of delta133p53, we developed two cell-based high-throughput screening (HTS) assays using an inducible vector for the expression of an eGFP-tag recombinant protein, and a luminescent peptide tag (HiBiT) appended onto the endogenous gene. The biologic activity of the fusion proteins was confirmed by evaluating the i) nuclear localization, ii) autophagic degradation during CS, and iii) ability to delay replicative CS. In collaboration with the National Center for Advancing Translational Sciences (NCATS), we screened a collection of ~8,350 compounds that includes all drugs that have been approved for use by the US Food and Drug Administration. Selected compounds were then screened in a secondary assay to evaluate their efficacy at reducing SASP cytokines secretion. Several candidate compounds are currently being investigated to confirm their effect on endogenous delta133p53 expression and CS. We have established robust cell-based HTS assays to screen for activators of delta133p53 and identified candidate compounds that could potentially develop into novel therapeutic leads to treat major life-threatening diseases.

Citation Format: Delphine Lissa, Kyra Ungerleider, Izumi Horikawa, Patricia Dranchak, Erin Oliphan, Jessica Beck, Sebastien Jo, James Inglese, Curtis C. Harris. Targeting Delta133p53 isoform with small-molecule compounds to modulate cellular senescence [abstract]. In: Proceedings of the AACR Special Conference on Advancing Precision Medicine Drug Development: Incorporation of Real-World Data and Other Novel Strategies; Jan 9-12, 2020; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_1):Abstract nr 19.

Radiation-induced astrocyte senescence is rescued by Δ133p53

BACKGROUND

Cellular senescence and the senescence-associated secretory phenotype (SASP) may contribute to the development of radiation therapy-associated side effects in the lung and blood vessels by promoting chronic inflammation. In the brain, inflammation contributes to the development of neurologic disease, including Alzheimer's disease. In this study, we investigated the roles of cellular senescence and Δ133p53, an inhibitory isoform of p53, in radiation-induced brain injury.

METHODS

Senescent cell types in irradiated human brain were identified with immunohistochemical labeling of senescence-associated proteins p16INK4A and heterochromatin protein Hp1γ in 13 patient cases, including 7 irradiated samples. To investigate the impact of radiation on astrocytes specifically, primary human astrocytes were irradiated and examined for expression of Δ133p53 and induction of SASP. Lentiviral expression of ∆133p53 was performed to investigate its role in regulating radiation-induced cellular senescence and astrocyte-mediated neuroinflammation.

RESULTS

Astrocytes expressing p16INK4A and Hp1γ were identified in all irradiated tissues, were increased in number in irradiated compared with untreated cancer patient tissues, and had higher labeling intensity in irradiated tissues compared with age-matched controls. Human astrocytes irradiated in vitro also experience induction of cellular senescence, have diminished Δ133p53, and adopt a neurotoxic phenotype as demonstrated by increased senescence-associated beta-galactosidase activity, p16INK4A, and interleukin (IL)-6. In human astrocytes, Δ133p53 inhibits radiation-induced senescence, promotes DNA double-strand break repair, and prevents astrocyte-mediated neuroinflammation and neurotoxicity.

CONCLUSIONS

Restoring expression of the endogenous p53 isoform, ∆133p53, protects astrocytes from radiation-induced senescence, promotes DNA repair, and inhibits astrocyte-mediated neuroinflammation.

Radiation-induced brain injury: current concepts and therapeutic strategies targeting neuroinflammation

Continued improvements in cancer therapies have increased the number of long-term cancer survivors. Radiation therapy remains one of the primary treatment modalities with about 60% of newly diagnosed cancer patients receiving radiation during the course of their disease. While radiation therapy has dramatically improved patient survival in a number of cancer types, the late effects remain a significant factor affecting the quality of life particularly in pediatric patients. Radiation-induced brain injury can result in cognitive dysfunction, including hippocampal-related learning and memory dysfunction that can escalate to dementia. In this article, we review the current understanding of the mechanisms behind radiation-induced brain injury focusing on the role of neuroinflammation and reduced hippocampal neurogenesis. Approaches to prevent or ameliorate treatment-induced side effects are also discussed along with remaining challenges in the field.

Functional Genomic Complexity Defines Intratumor Heterogeneity and Tumor Aggressiveness in Liver Cancer

Chronic inflammation and chromosome aneuploidy are major traits of primary liver cancer (PLC), which represent the second most common cause of cancer-related death worldwide. Increased cancer fitness and aggressiveness of PLC may be achieved by enhancing tumoral genomic complexity that alters tumor biology. Here, we developed a scoring method, namely functional genomic complexity (FGC), to determine the degree of molecular heterogeneity among 580 liver tumors with diverse ethnicities and etiologies by assessing integrated genomic and transcriptomic data. We found that tumors with higher FGC scores are associated with chromosome instability and TP53 mutations, and a worse prognosis, while tumors with lower FGC scores have elevated infiltrating lymphocytes and a better prognosis. These results indicate that FGC scores may serve as a surrogate to define genomic heterogeneity of PLC linked to chromosomal instability and evasion of immune surveillance. Our findings demonstrate an ability to define genomic heterogeneity and corresponding tumor biology of liver cancer based only on bulk genomic and transcriptomic data. Our data also provide a rationale for applying this approach to survey liver tumor immunity and to stratify patients for immune-based therapy.

Body Mass Index (BMI), BMI Change, and Overall Survival in Patients With SCLC and NSCLC: A Pooled Analysis of the International Lung Cancer Consortium

INTRODUCTION

The relationships between morbid obesity, changes in body mass index (BMI) before cancer diagnosis, and lung cancer outcomes by histology (SCLC and NSCLC) have not been well studied.

METHODS

Individual level data analysis was performed on 25,430 patients with NSCLC and 2787 patients with SCLC from 16 studies of the International Lung Cancer Consortium evaluating the association between various BMI variables and lung cancer overall survival, reported as adjusted hazard ratios (aHRs) from Cox proportional hazards models and adjusted penalized smoothing spline plots.

RESULTS

Overall survival of NSCLC had putative U-shaped hazard ratio relationships with BMI based on spline plots: being underweight (BMI < 18.5 kg/m2; aHR = 1.56; 95% confidence interval [CI]:1.43-1.70) or morbidly overweight (BMI > 40 kg/m2; aHR = 1.09; 95% CI: 0.95-1.26) at the time of diagnosis was associated with worse stage-specific prognosis, whereas being overweight (25 kg/m2 ≤ BMI < 30 kg/m2; aHR = 0.89; 95% CI: 0.85-0.95) or obese (30 kg/m2 ≤ BMI ≤ 40 kg/m2; aHR = 0.86; 95% CI: 0.82-0.91) was associated with improved survival. Although not significant, a similar pattern was seen with SCLC. Compared with an increased or stable BMI from the period between young adulthood until date of diagnosis, a decreased BMI was associated with worse outcomes in NSCLC (aHR = 1.24; 95% CI: 1.2-1.3) and SCLC patients (aHR=1.26 (95% CI: 1.0-1.6). Decreased BMI was consistently associated with worse outcome, across clinicodemographic subsets.

CONCLUSIONS

Both being underweight or morbidly obese at time of diagnosis is associated with lower stage-specific survival in independent assessments of NSCLC and SCLC patients. In addition, a decrease in BMI at lung cancer diagnosis relative to early adulthood is a consistent marker of poor survival.

Lung Cancer Risk in Never-Smokers of European Descent is Associated With Genetic Variation in the 5p15.33 TERT-CLPTM1Ll Region

INTRODUCTION

Inherited susceptibility to lung cancer risk in never-smokers is poorly understood. The major reason for this gap in knowledge is that this disease is relatively uncommon (except in Asians), making it difficult to assemble an adequate study sample. In this study we conducted a genome-wide association study on the largest, to date, set of European-descent never-smokers with lung cancer.

METHODS

We conducted a two-phase (discovery and replication) genome-wide association study in never-smokers of European descent. We further augmented the sample by performing a meta-analysis with never-smokers from the recent OncoArray study, which resulted in a total of 3636 cases and 6295 controls. We also compare our findings with those in smokers with lung cancer.

RESULTS

We detected three genome-wide statistically significant single nucleotide polymorphisms rs31490 (odds ratio [OR]: 0.769, 95% confidence interval [CI]: 0.722-0.820; p value 5.31 × 10-16), rs380286 (OR: 0.770, 95% CI: 0.723-0.820; p value 4.32 × 10-16), and rs4975616 (OR: 0.778, 95% CI: 0.730-0.829; p value 1.04 × 10-14). All three mapped to Chromosome 5 CLPTM1L-TERT region, previously shown to be associated with lung cancer risk in smokers and in never-smoker Asian women, and risk of other cancers including breast, ovarian, colorectal, and prostate.

CONCLUSIONS

We found that genetic susceptibility to lung cancer in never-smokers is associated to genetic variants with pan-cancer risk effects. The comparison with smokers shows that top variants previously shown to be associated with lung cancer risk only confer risk in the presence of tobacco exposure, underscoring the importance of gene-environment interactions in the etiology of this disease.

Urinary Metabolites Diagnostic and Prognostic of Intrahepatic Cholangiocarcinoma

BACKGROUND

Liver cancer is the second leading cause of cancer-related deaths worldwide. With a predicted 2.4-fold rise in liver cancer incidence by 2020, there is an urgent need for early, inexpensive diagnostic biomarkers to deploy in the clinic.

METHODS

We employed ultraperformance liquid chromatography tandem mass-spectrometry (UPLC/MS-MS) for the quantitation of four metabolites, creatine riboside (CR), N-acetylneuraminic acid (NANA), cortisol sulfate, and a lipid molecule designated as 561+, in urine samples from the NCI-MD cohort comprising 98 hepatocellular carcinoma (HCC) cases, 101 high-risk subjects, and 95 controls. Validation was carried out in the TIGER-LC cohort [n = 370 HCC and intrahepatic cholangiocarcinoma (ICC) cases, 471 high-risk subjects, 251 controls], where ICC, the second most common primary hepatic malignancy, is highly prevalent. Metabolite quantitation was also conducted in TIGER-LC tissue samples (n = 48 ICC; n = 51 HCC).

RESULTS

All profiled metabolites were significantly increased in liver cancer when compared with high-risk subjects and controls in the NCI-MD study. In the TIGER-LC cohort, the four-metabolite profile was superior at classifying ICC than a clinically utilized marker, CA19-9, and their combination led to a significantly improved model (AUC = 0.88, P = 4E-8). Metabolites CR and NANA were significantly elevated in ICC when compared with HCC cases in both urine and tissue samples. High levels of CR were associated with poorer prognosis in ICC.

CONCLUSIONS

Four metabolites are significantly increased in HCC and ICC and are robust at classifying ICC in combination with the clinically utilized marker CA19-9.

IMPACT

Noninvasive urinary metabolite biomarkers hold promise for diagnostic and prognostic evaluation of ICC.

Cross-Cancer Pleiotropic Associations with Lung Cancer Risk in African Americans

BACKGROUND

Identifying genetic variants with pleiotropic associations across multiple cancers can reveal shared biologic pathways. Prior pleiotropic studies have primarily focused on European-descent individuals. Yet population-specific genetic variation can occur, and potential pleiotropic associations among diverse racial/ethnic populations could be missed. We examined cross-cancer pleiotropic associations with lung cancer risk in African Americans.

METHODS

We conducted a pleiotropic analysis among 1,410 African American lung cancer cases and 2,843 controls. We examined 36,958 variants previously associated (or in linkage disequilibrium) with cancer in prior genome-wide association studies. Logistic regression analyses were conducted, adjusting for age, sex, global ancestry, study site, and smoking status.

RESULTS

We identified three novel genomic regions significantly associated (FDR-corrected P <0.10) with lung cancer risk (rs336958 on 5q14.3, rs7186207 on 16q22.2, and rs11658063 on 17q12). On chromosome16q22.2, rs7186207 was significantly associated with reduced risk [OR = 0.43; 95% confidence interval (CI), 0.73-0.89], and functional annotation using GTEx showed rs7186207 modifies DHODH gene expression. The minor allele at rs336958 on 5q14.3 was associated with increased lung cancer risk (OR = 1.47; 95% CI, 1.22-1.78), whereas the minor allele at rs11658063 on 17q12 was associated with reduced risk (OR = 0.80; 95% CI, 0.72-0.90).

CONCLUSIONS

We identified novel associations on chromosomes 5q14.3, 16q22.2, and 17q12, which contain HNF1B, DHODH, and HAPLN1 genes, respectively. SNPs within these regions have been previously associated with multiple cancers. This is the first study to examine cross-cancer pleiotropic associations for lung cancer in African Americans.

IMPACT

Our findings demonstrate novel cross-cancer pleiotropic associations with lung cancer risk in African Americans.

The Gut-Brain Axis, Paving the Way to Brain Cancer

The gut-brain axis formed by blood and lymphatic vessels paves the way for microbiota to impact the brain. Bacterial populations in the gut are a good candidate for a nongenetic factor contributing substantively to brain tumor development and to the success of therapy. Specifically, suppression of the immune system and induction of inflammation by microbiota sustain proliferative signaling, limit cell death, and induce angiogenesis as well as invasiveness. In addition, altered microbial metabolites and their levels could stimulate cell proliferation. We propose here a novel gear model connecting these complex interdisciplinary fields. Our model may impact mechanistic studies of brain cancer and better treatment outcomes through precision oncology.

Alcohol consumption and lung cancer risk: A pooled analysis from the International Lung Cancer Consortium and the SYNERGY study

BACKGROUND

There is inadequate evidence to determine whether there is an effect of alcohol consumption on lung cancer risk. We conducted a pooled analysis of data from the International Lung Cancer Consortium and the SYNERGY study to investigate this possible association by type of beverage with adjustment for other potential confounders.

METHODS

Twenty one case-control studies and one cohort study with alcohol-intake data obtained from questionnaires were included in this pooled analysis (19,149 cases and 362,340 controls). Adjusted odds ratios (OR) or hazard ratios (HR) with corresponding 95% confidence intervals (CI) were estimated for each measure of alcohol consumption. Effect estimates were combined using random or fixed-effects models where appropriate. Associations were examined for overall lung cancer and by histological type.

RESULTS

We observed an inverse association between overall risk of lung cancer and consumption of alcoholic beverages compared to non-drinkers, but the association was not monotonic. The lowest risk was observed for persons who consumed 10-19.9 g/day ethanol (OR vs. non-drinkers = 0.78; 95% CI: 0.67, 0.91), where 1 drink is approximately 12-15 g. This J-shaped association was most prominent for squamous cell carcinoma (SCC). The association with all lung cancer varied little by type of alcoholic beverage, but there were notable differences for SCC. We observed an association with beer intake (OR for ≥20 g/day vs nondrinker = 1.42; 95% CI: 1.06, 1.90).

CONCLUSIONS

Whether the non-monotonic associations we observed or the positive association between beer drinking and squamous cell carcinoma reflect real effects await future analyses and insights about possible biological mechanisms.

Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017

The National Cancer Institute (NCI) sponsored a 2-day workshop, "Next Steps in Studying the Human Microbiome and Health in Prospective Studies," in Bethesda, Maryland, May 16-17, 2017. The workshop brought together researchers in the field to discuss the challenges of conducting microbiome studies, including study design, collection and processing of samples, bioinformatics and statistical methods, publishing results, and ensuring reproducibility of published results. The presenters emphasized the great potential of microbiome research in understanding the etiology of cancer. This report summarizes the workshop and presents practical suggestions for conducting microbiome studies, from workshop presenters, moderators, and participants.

Abstract PR07: Role of the microbiota in inflammation and lung cancer

We recently conducted the first comprehensive characterization of the lung cancer microbiome, utilizing 16S rRNA gene sequencing of lung tissue from controls and cancer cases, with validation by metagenomics analysis of RNA-seq unmapped reads from lung cancer samples in The Cancer Genome Atlas. Evidence from 16S rRNA and metagenomics analysis indicated that specific bacteria are associated with the development of lung cancer in humans. However, the functional role of bacteria in the inflammatory microenvironment of the lung and the incidence and progression of lung cancer is unknown. Cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infections. We hypothesized that lung colonization with selected bacterial strains will affect the immune microenvironment and accelerate the rate of tumor development in an autochthonous mouse model of lung cancer. Specifically, we focused on Acidovorax, a taxon we found to be enriched in lung squamous cell carcinoma (SCC) from smokers and with TP53 mutations. KrasLSL-G12D/+ and Trp53LSL-R172H/+ mice (KPC mouse model), conditionally expressing oncogenic Kras and a gain-of-function mutant p53 (a combination of mutations commonly found in human lung cancer), were exposed to Acidovorax temperans via intranasal delivery. Two weeks after exposure to 5 x 106 PFU Ad-Cre (specifically activating the conditional alleles in the lungs), mice were randomly assigned to treatment groups. A biweekly intranasal instillation of 109 CFU Acidovorax temperans (ATCC #49666) was administered in PBS and compared with a sham treatment (PBS alone) for a total of six instillations. One week after the last bacteria instillation (13 weeks after Ad-Cre treatment), mice were subjected to magnetic resonance imaging (MRI). We found a significant increase in tumor volume in animals inoculated with Acidovorax temperans as compared to sham-treated animals (p=0.03), and increased lung weight as a percent of total body weight.

To delineate the interactions between the bacteria and the immune system of the host, we co-cultured Acidovorax temperans with human primary macrophages. Our findings show that when Acidovorax temperans is engulfed by M2-like macrophages, the phagocytotic activity of the macrophages is attenuated. In addition, when T cells were co-cultured with M2 macrophages pre-exposed to Acidovorax temperans, their cytotoxicity was inhibited. This inhibition was governed by the CD47-SIRPα “Don’t eat me” signal. These preliminary data indicate that Acidovorax temperans contributes to lung tumorigenesis in the presence of activated Kras and mutant p53. We are conducting additional experiments to investigate the specificity of this observation with respect to Acidovorax temperans and to better understand the role of the microbiota in cancer initiation and progression.

This abstract is also being presented as Poster B19.

Citation Format: Ana I. Robles, Tomer Cooks, Eleazar Vega-Valle, Marie Vetizou, Uriel Rose, Akihiko Miyanaga, Akriti Trehan, Takahiro Oike, Brid M. Ryan, Shurjo Sen, Leigh Greathouse, Giorgio Trinchieri, Curtis C. Harris. Role of the microbiota in inflammation and lung cancer [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr PR07.

Abstract A32: Prognostic stratification of stage I lung adenocarcinoma patients by HOXA9 promoter methylation ddPCR and blood vessel invasion analysis in FFPE tissues

Surgery with curative intent is the standard of care for stage I lung adenocarcinoma. However, disease recurrence eventually occurs in about a third of the patients. Consequently, prognostic biomarkers are urgently needed to predict recurrence following surgery and potentially guide the decision to administer adjuvant chemotherapy for high-risk patients. The type of biospecimens and the choice of assay platform are key issues in the process of cancer biomarker clinical development. Here, we demonstrate the application of a droplet digital PCR (ddPCR)-based assay to analyze DNA methylation in formalin-fixed, paraffin-embedded (FFPE) biospecimens. In recent years, ddPCR has become increasingly used clinically due to its ability to reliably detect and quantitate rare alleles, as well as its technical simplicity, rapidity, and cost-effectiveness. In addition, FFPE tissues are generated during routine pathologic assessment of resected patients, and are generally available for testing molecular markers. We developed a ddPCR assay to quantify HOXA9 promoter methylation in FFPE samples, with high sensitivity, specificity, and reproducibility. High HOXA9 promoter methylation has been associated with worse outcome of resected stage I lung adenocarcinoma patients in multiple studies. Here, the prognostic value of HOXA9 promoter methylation alone or in combination with blood vessel invasion (BVI), another well-described prognostic biomarker for patients with early stage lung adenocarcinoma, was evaluated by Kaplan-Meier survival analyses and Cox regression modeling, using 188 FFPE biospecimens, in two independent sets. We replicated previous observations that HOXA9 promoter is methylated de novo in stage I tumors (P &lt;0.0001), and that high methylation is associated with worse prognosis (Hazard Ratio [HR], 3.37; P=0.0002). HOXA9 methylation was associated with a transcriptome signature enriched in genes marked by Polycomb in Embryonic Stem Cells, a signature previously associated with poor differentiation and worse overall patient survival. Addition of this molecular marker improved a risk model comprising clinical and pathologic parameters (age, sex, smoking status, and tumor stage and size; P=0.003, nested likelihood ratio test). As expected, BVI was independently associated with poor outcome (HR, 2.62; P=0.054). A score that combined BVI with HOXA9 promoter methylation further stratified high-risk patients (Trend P=0.0001 comparing 0, 1 or 2 positive markers). Collectively, our results support the use of ddPCR to quantify HOXA9 promoter methylation and the analysis of BVI from routine pathology FFPE specimens to identify patients at high risk of recurrence. Our findings pave the way for future clinical evaluation of these promising prognostic markers. If validated in a larger independent study, these biomarkers should be considered in prospective trials to evaluate the benefit of adjuvant chemotherapy in high-risk early-stage lung adenocarcinoma patients.

Citation Format: Delphine Lissa, Teruhide Ishigame, Rintaro Noro, Marguerite J. Tucker, Elise D. Bowman, Curtis C. Harris, Ana I. Robles. Prognostic stratification of stage I lung adenocarcinoma patients by HOXA9 promoter methylation ddPCR and blood vessel invasion analysis in FFPE tissues [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr A32.

Abstract A18: Diagnostic and prognostic utility of urinary creatine riboside for early stage non-small cell lung cancer

This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR02) of the Conference Proceedings.

Citation Format: Takahiro Oike, Yasuyuki Kanke, Amelia Parker, Majda Haznadar, Kristopher W. Krausz, Elise D. Bowman, Ana I. Robles, Frank J. Gonzalez, Curtis C. Harris. Diagnostic and prognostic utility of urinary creatine riboside for early stage non-small cell lung cancer [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr A18.

Interaction between the microbiome and TP53 in human lung cancer

Background

Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infections. Herein, we hypothesize that somatic mutations together with cigarette smoke generate a dysbiotic microbiota that is associated with lung carcinogenesis. Using lung tissue from 33 controls and 143 cancer cases, we conduct 16S ribosomal RNA (rRNA) bacterial gene sequencing, with RNA-sequencing data from lung cancer cases in The Cancer Genome Atlas serving as the validation cohort.

Results

Overall, we demonstrate a lower alpha diversity in normal lung as compared to non-tumor adjacent or tumor tissue. In squamous cell carcinoma specifically, a separate group of taxa are identified, in which Acidovorax is enriched in smokers. Acidovorax temporans is identified within tumor sections by fluorescent in situ hybridization and confirmed by two separate 16S rRNA strategies. Further, these taxa, including Acidovorax, exhibit higher abundance among the subset of squamous cell carcinoma cases with TP53 mutations, an association not seen in adenocarcinomas.

Conclusions

The results of this comprehensive study show both microbiome-gene and microbiome-exposure interactions in squamous cell carcinoma lung cancer tissue. Specifically, tumors harboring TP53 mutations, which can impair epithelial function, have a unique bacterial consortium that is higher in relative abundance in smoking-associated tumors of this type. Given the significant need for clinical diagnostic tools in lung cancer, this study may provide novel biomarkers for early detection.

Electronic supplementary material

The online version of this article (10.1186/s13059-018-1501-6) contains supplementary material, which is available to authorized users.

A Nucleolar Stress-Specific p53-miR-101 Molecular Circuit Functions as an Intrinsic Tumor-Suppressor Network

Background

Activation of intrinsic p53 tumor-suppressor (TS) pathways is an important principle underlying cancer chemotherapy. It is necessary to elucidate the precise regulatory mechanisms of these networks to create new treatment strategies.

Methods

Comprehensive analyses were carried out by microarray. Expression of miR-101 was analyzed by clinical samples of lung adenocarcinomas.

Findings

We discovered a functional link between p53 and miR-101, which form a molecular circuit in response to nucleolar stress. Inhibition of RNA polymerase I (Pol I) transcription resulted in the post-transcriptional activation of miR-101 in a p53-dependent manner. miR-101 induced G2 phase–specific feedback regulation of p53 through direct repression of its target, EG5, resulting in elevated phosphorylation of ATM. In lung cancer patients, low expression of miR-101 was associated with significantly poorer prognosis exclusively in p53 WT cases. miR-101 sensitized cancer cells to Pol I transcription inhibitors and strongly repressed xenograft growth in mice. Interestingly, the most downstream targets of this circuit included the inhibitor of apoptosis proteins (IAPs). Repression of cIAP1 by a selective inhibitor, birinapant, promoted activation of the apoptosis induced by Pol I transcription inhibitor in p53 WT cancer cells.

Interpretation

Our findings indicate that the p53–miR-101 circuit is a component of an intrinsic TS network formed by nucleolar stress, and that mimicking activation of this circuit represents a promising strategy for cancer therapy.

Fund

National Institute of Biomedical Innovation, Ministry of Education, Culture, Sports & Technology of Japan, Japan Agency for Medical Research and Development.