Genome-wide host methylation profiling of anal and cervical carcinoma

HPV infection results in changes in host gene methylation which, in turn, are thought to contribute to the neoplastic progression of HPV-associated cancers. The objective of this study was to identify joint and disease-specific genome-wide methylation changes in anal and cervical cancer as well as changes in high-grade pre-neoplastic lesions. Formalin-fixed paraffin-embedded (FFPE) anal tissues (n = 143; 99% HPV+) and fresh frozen cervical tissues (n = 28; 100% HPV+) underwent microdissection, DNA extraction, HPV genotyping, bisulfite modification, DNA restoration (FFPE) and analysis by the Illumina HumanMethylation450 Array. Differentially methylated regions (DMR; t test q<0.01, 3 consecutive significant CpG probes and mean Δβ methylation value>0.3) were compared between normal and cancer specimens in partial least squares (PLS) models and then used to classify anal or cervical intraepithelial neoplasia-3 (AIN3/CIN3). In AC, an 84-gene PLS signature (355 significant probes) differentiated normal anal mucosa (NM; n = 9) from AC (n = 121) while a 36-gene PLS signature (173 significant probes) differentiated normal cervical epithelium (n = 10) from CC (n = 9). The CC progression signature was validated using three independent publicly available datasets (n = 424 cases). The AC and CC progression PLS signatures were interchangeable in segregating normal, AIN3/CIN3 and AC and CC and were found to include 17 common overlapping hypermethylated genes. Moreover, these signatures segregated AIN3/CIN3 lesions similarly into cancer-like and normal-like categories. Distinct methylation changes occur across the genome during the progression of AC and CC with overall similar profiles and add to the evidence suggesting that HPV-driven oncogenesis may result in similar non-random methylomic events. Our findings may lead to identification of potential epigenetic drivers of HPV-associated cancers and also, of potential markers to identify higher risk pre-cancerous lesions.

907 Modulation of tumor immunogenicity by DNA methylation of immune synapse genes in cancers

Background

Cancer immunotherapy represents a major paradigm shift in cancer care. Despite such breakthrough, majority of cancer patients remains refractory to existing immunotherapeutic modalities highlighting the inherent capacity of tumors to escape immunosurveillance mechanisms. Frequently, cancer cells utilize the epigenetic machinery to silence tumor suppressors or activate oncogenes for survival and proliferation. Likewise, tumor cells might employ the epigenetic reprogramming of immune-related pathways to evade the immune system. Methylation is one of the major epigenetic mechanisms modulating gene transcription. Thus, we investigated the methylation profile of both co-stimulatory and immune checkpoint genes in cancer.

Methods

Data from The Cancer Genome Atlas (TCGA) were used for methylation profiling and RNA-sequencing analysis. Twenty-six epithelial cancer cell lines with more than 3 mock and three 5-azacitidine–treated samples were selected for analysis from the GSE57342 dataset. t-distributed stochastic neighbor embedding (t-SNE) was calculated using 247 probes for the selected 20 genes across all TCGA samples. t-SNE analysis was performed on 8,186 solid tumors and 745 normal adjacent tissues for methylation levels for all probes. For principal component analysis, first and second principal components were used to represent the overall methylation status for 8,931 tumor and normal samples in the TCGA database. Survival analyses were retrieved from a prior publication.1

Results

We found that methylation profile of immune synapse genes is distinct in tumor versus normal adjacent tissue. Interestingly, our results demonstrate hypermethylation of co-stimulatory genes such as CD40 and hypo-methylation of immune checkpoint genes such as HHLA2 and PDL1 across multiple tumor types in comparison with the normal adjacent tissue. In addition, an inverse correlation between methylation and gene expression was manifest among tumor and normal adjacent tissue, confirming the epigenetic mechanism of gene suppression by gene methylation. Furthermore, we observed a reversal of hypermethylation of the co-stimulatory genes including CD40 by the demethylating agent 5-azacytidine in the data set of 26 epithelial cancer cell lines. Finally, we found that that hypomethylation of co-stimulatory genes within the immune synapse correlates with functional T cell recruitment to the tumor microenvironment and is followed by a favorable clinical outcome in melanoma patients.

Conclusions

Our finding unveils methylation of immune synapse genes as a crucial driver of the immune evasive phenotype of cancer cells. Notably, identification of actionable targets to restore tumor immunogenicity is an attractive strategy in combination with immune checkpoint blockade.

Acknowledgements

This work was supported by NIH grant K08 CA194273, the Immunology Innovation Fund, an NCI Cancer Center Support grant, (P30-CA076292), the Miriam and Sheldon G. Adelson Foundation, and the Moffitt Foundation.

Reference

Liu J, Lichtenberg T, Hoadley KA, Poisson LM, Lazar AJ, Cherniack AD, Kovatich AJ, Benz CC, Levine DA, Lee AV, Omberg L, Wolf DM, Shriver CD, Thorsson V, Cancer Genome Atlas Research N, Hu H. An integrated TCGA pan-cancer clinical data resource to drive high-quality survival outcome analytics. Cell 2018;173(2):400–16 e11.

760 In vivo demethylation-mediated reversal of tumor cell-intrinsic cGAS silencing improves the efficacy of STING agonist therapy

Background

While STING-activating agents have shown limited efficacy in early phase clinical trials, multiple lines of evidence suggest the importance of the so far unappreciated tumor cell-intrinsic STING function in antitumor immune responses. Accordingly, we have shown that although there is a widespread impairment of STING signaling among human melanomas, its restoration through epigenetic reprogramming can augment antigenicity and T cell recognition of melanoma cells.1 2 In this study, we determined if rescue of tumor cell-intrinsic STING signaling using a DNA methyltransferase inhibitor can improve the therapeutic efficacy of a STING agonist in mouse models of melanoma.

Methods

We subjected three distinct murine melanoma cell lines (B16-F10, B16-ISG and Yumm1.7) to treatment with 5-aza-2'-deoxycytidine (5AZADC) and evaluated their activation of STING following stimulation with the STING agonist ADU-S100. Using a B16-F10 subcutaneous model, we assessed the effect of 5AZADC treatment on the efficacy of intratumorally administered ADU-S100 in STINGgt/gt mice. Additionally, we performed mechanistic studies using T-cell depletion experiments as well as phenotypic and gene expression profiling.

Results

We observed reconstitution of cGAS in all three 5AZADC-pretreated cell lines as well as up to a 46-fold increase in induction of IFN-beta (p < 0.001) and a 4.5-fold increase in MHC class I surface expression (p < 0.01) compared to untreated controls following stimulation with ADU-S100. In B16-F10 tumor-bearing mice, while treatment with a combination of 5AZADC plus ADU-S100 resulted in a marked increase in Ifnb1 transcripts within tumors (p < 0.001), it significantly delayed tumor growth compared to treatment with ADU-S100 alone (p = 0.0244 on day 22). Antibody-mediated depletion studies in mice receiving the combination therapy further indicated that this antitumor activity depends on the generation of functional tumor antigen-specific CD8+ T cells (p = 0.0111 on day 22); however, tumor growth remained unaltered by the depletion of CD4+ T cells.

Conclusions

We show that reversal of methylation silencing of cGAS in murine melanoma cell lines using a clinically available DNA methylation inhibitor can improve agonist-induced STING activation and type I IFN induction, which in tumor-bearing mice is capable of inducing tumor regression through a CD8+ T cell-dependent immune response. These findings not only provide mechanistic insight into how STING signaling dysfunction in tumor cells can contribute to impaired responses to STING agonist therapy, but also suggest, depending on tumor cell-intrinsic STING signaling status, its pharmacologic restoration should be considered for improving therapeutic efficacy of STING agonists in future clinical studies.

Acknowledgements

Funding:

NCI P50 CA168536, Cindy and Jon Gruden Fund, Chris Sullivan Fund, V Foundation, Dr. Miriam and Sheldon G. Adelson Medical Research Foundation.

References

Falahat R, Perez-Villarroel P, Mailloux AW, Zhu G, Pilon-Thomas S, Barber GN, Mulé JJ. STING signaling in melanoma cells shapes antigenicity and can promote antitumor T-cell activity. Cancer Immunol Res 2019;7(11):1837–48.

Falahat R, Berglund A, Putney RM, Perez-Villarroel P, Aoyama S, Pilon-Thomas S, Barber GN, Mulé JJ. Epigenetic reprogramming of tumor cell–intrinsic STING function sculpts antigenicity and T cell recognition of melanoma. PNAS 2021;118(15).

Abstract 781: DNA methylation patterns between aggressive and indolent prostate tumors from Puerto Rican men

Background: In 2020, approximately 191,930 new prostate cancer (PCa) cases and 33,330 deaths are estimated in the US only. Hispanic/Latinos (H/L) are the second largest racial/ethnic group in the US. A previous study reported that prostate cancer-specific mortality rate among Puerto Rican men with prostate cancer is higher than ones of non-Hispanic Whites and non-Hispanic Blacks. The aims of this study are to: (1) assess the methylation patterns between aggressive and indolent PCa, (2) to study the methylation status of DNA repair genes between these groups, and (3) to assess the ancestry proportions of the study participants. Variations in methylation patterns will be detected between study groups.

Methods: Archived formalin fixed paraffin-embedded (FFPE) prostate tumors (n=24) were collected through the Puerto Rico Biobank. Tumor specimens were classified as aggressive (n=11) and indolent (n=13) cases based on the Gleason scores (6+7(3+4) vs. 7(4+3)+8+9). Tumor areas and adjacent normal tissue were annotated on the H&E slides by a pathologist and extracted by macro-dissection. The Illumina 850K DNA methylation platform was used to measure DNA methylation patterns. The raw data was processed using minfi and normalized. Amount of missing values, histogram of β-values, principal component analysis (PCA) was to assess quality and to detect outliers.

Results: A PCA model clearly separated the normal samples from the tumor samples. One of the most significantly differently methylated genes was AOX1. Further comparisons using TCGA PRAD data base revealed the predictable negative correlation between the gene expression and the average β-values. Regarding the PCa aggressiveness, 23 probes were identified as potential candidates using a p&lt;0.001 and a Δβ-value of 0.2 as cut-off. These probes where located in six hypermethylated genes; RREB1, FAM71F2, JMJD1C, COL5A3, RAE1, GABRQ, and eleven hypomethylated; COL9A2, FAM179A, SLC17A2, PDE10A, PLEKHS1, TNNI2, OR51A4, RNF169, SPNS2, ADAMTSL5, and CYP4F12. Of the 179 candidate DNA repair genes. We found two significant differentially methylated DNA repair genes: JMJD1C and RNF169 between groups. The results from the ancestry proportions for African, European, and Indigenous American were: 24.1%, 64.2%, and 9% respectively.

Conclusion: The identification of DNA methylation patterns related to PCa in Puerto Rican (PR) H/L men along with specific patterns related to aggressiveness and DNA repair constitutes a pivotal effort on the understanding of PCa disparities in this population. This constitutes a unique effort to provide an overview regarding methylation and ancestry patterns in PR H/L men. Acknowledgements; supported by U54 CA163071 and U54 CA163068-07

Citation Format: Jong Y. Park, Gilberto Ruiz-Deya, Jarline Encarnacion, Juile Dutil, Liang Wang, Carmen Ortiz Sanchez, Ryan Putney, Anders Berglund, Youngchul Kim, Jaime Matta. DNA methylation patterns between aggressive and indolent prostate tumors from Puerto Rican men [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 781.

The 12-CK Score: Global Measurement of Tertiary Lymphoid Structures

There is emerging evidence that the adaptive anti-tumor activity may be orchestrated by secondary lymphoid organ-like aggregates residing in the tumor microenvironment. Known as tertiary lymphoid structures, these lymphoid aggregates serve as key outposts for lymphocyte recruitment, priming and activation. They have been linked to favorable outcomes in many tumor types, and more recently, have been shown to be effective predictors of response to immune checkpoint blockade. We have previously described a 12-chemokine (12-CK) transcriptional score which recapitulates an overwhelming enrichment for immune-related and inflammation-related genes in colorectal carcinoma. Subsequently, the 12-CK score was found to prognosticate favorable survival in multiple tumors types including melanoma, breast cancer, and bladder cancer. In the current study, we summarize the discovery and validation of the 12-CK score in various tumor types, its relationship to TLSs found within the tumor microenvironment, and explore its potential role as both a prognostic and predictive marker in the treatment of various cancers.

Reduction of the risk of PML in natalizumab treated MS patients in Sweden: An effect of improved PML risk surveillance

BACKGROUND

Natalizumab (NTZ) treatment of multiple sclerosis (MS) has been associated with increased risk of progressive multifocal leukoencephalopathy (PML). The aim of the present study was to evaluate the impact of PML risk assessment on PML incidence in NTZ treated MS patients.

METHODS

By using information from the population-based Swedish MS registry a retrospective cohort was established of patients treated with NTZ between 2006-2018. The effect on PML incidence before and after utilizing a risk management plan, including JC virus (JCV) serology, was analyzed.

RESULTS

In December 2018, 804 PML cases associated with NTZ therapy of MS had been reported globally, including 9 cases from Sweden. The estimated PML incidence 2018 in Sweden and globally was 0.7 (0.3-1.4) and 4.15 (3.9-4.4) per 1,000 person years, respectively. In Sweden, JCV serology was introduced 2012 for PML risk assessment and the cumulative risk of PML was significantly lower 2012-2018 compared to the period 2006-2011 (p=0.042). The mean NTZ exposure time was 60.1 months (SD 37.2) in the first period (2006-2011) and 32.6 months (SD 22.0) in the second period (2012-2018). The number of patients treated with NTZ decreased, and the number of patients at increased risk of PML was 1.9 % at the end of the study period.

CONCLUSION

Since 2006 the incidence of PML associated with NTZ treatment of MS has decreased in Sweden. Our findings suggest that this reduction is due to an effective adoptation and adherence to the established risk management plan that implies switching patients at increased PML risk from NTZ to other highly efficacious therapies. A less pronounced decline in PML incidence has recently been observed in France, but not globally.

Molecular Determinants of Thyroid Nodules with Indeterminate Cytology and RAS Mutations

Background:RAS gene family mutations are the most prevalent in thyroid nodules with indeterminate cytology and are present in a wide spectrum of histological diagnoses. We evaluated differentially expressed genes and signaling pathways across the histological/clinical spectrum of RAS-mutant nodules to determine key molecular determinants associated with a high risk of malignancy. Methods: Sixty-one thyroid nodules with RAS mutations were identified. Based on the histological diagnosis and biological behavior, the nodules were grouped into five categories indicating their degree of malignancy: non-neoplastic appearance, benign neoplasm, indeterminate malignant potential, low-risk cancer, or high-risk cancer. Gene expression profiles of these nodules were determined using the NanoString PanCancer Pathways and IO 360 Panels, and Angiopoietin-2 level was determined by immunohistochemical staining. Results: The analysis of differentially expressed genes using the five categories as supervising parameters unearthed a significant correlation between the degree of malignancy and genes involved in cell cycle and apoptosis (BAX, CCNE2, CDKN2A, CDKN2B, CHEK1, E2F1, GSK3B, NFKB1, and PRKAR2A), PI3K pathway (CCNE2, CSF3, GSKB3, NFKB1, PPP2R2C, and SGK2), and stromal factors (ANGPT2 and DLL4). The expression of Angiopoietin-2 by immunohistochemistry also showed the same trend of increasing expression from non-neoplastic appearance to high-risk cancer (p < 0.0001). Conclusions: The gene expression analysis of RAS-mutant thyroid nodules suggests increasing upregulation of key oncogenic pathways depending on their degree of malignancy and supports the concept of a stepwise progression. The utility of ANGPT2 expression as a potential diagnostic biomarker warrants further evaluation.

Abstract PO-227: DNA methylation as a predictor of aggressive prostate cancer in Puerto Rican men

Background: Incidence and mortality rates among Hispanic/Latino (H/L) men with prostate cancer (PCa) are almost same as non-Hispanic whites (NHW) men. However, these data may be over-generalized because all H/L subgroups are aggregated into one broad group. Therefore, few studies focused on health disparity of PCa in H/L men. Data from the Puerto Rico (PR) Cancer Registry shows that in men, PCa is the #1 cancer, both in terms of incidence (39.9% of all cancer cases) and mortality (18.3% of all cancer deaths). Recent studies reported that PR men have a higher rate of poor outcomes than NHW regardless of treatment and also after surgical treatment.

Further, PR patients had significantly higher PCa specific mortality than non-Hispanic blacks. Although PCa is normally characterized by a slow progression, ~20-30% of cases are associated with an aggressive phenotype associated with metastasis and death. A key molecular feature of this aggressive phenotype is the dysregulation of DNA repair genes.The objective of this pilot study was to investigate epigenetic differences in tumor DNA methylation, between PR and NHW men to identify specific biomarkers for PCa in PR men. Methods: Archived paraffin-embedded (FFPE) blocks of 24 prostate tumor and 24 adjacent normal tissues were collected through the Puerto Rico Biobank. We selected 12 aggressive and 12 indolent cases based on aggressiveness, mainly based on the Gleason scores and clinical stage. Both 24 tumor and 24 normal tissues were measured methylation level using epigenome wide Illumina EPICDNA methylation platform. Results: DNA methylation analysis showed a clear distinction between tumor and normal tissues. In addition, twenty significant differentially methylated genes associated with aggressive disease were identified including: SLC5A8, FGF12, LCP1, TRH, PFKFB3, and LIN28B Six significantly differentially methylated genes associated with aggressive cases. We also identified 27 DNA repair genes, which were differentially methylated (log2 FC &gt; 0.1)) between aggressive and indolent PR cases. 7genes were hypermethylated and 20 genes were hypomethylated. Multiple DNA repair genes were differentially methylated including ATM, ERCC5, XRCC2, XRCC3, and BRCA1. The ancestry analysis for these men showed a distribution where the European ancestry is the more prevalent (64%) followed by West African ancestry (21%) and Indigenous American ancestry (15%). Although our results have to be validated with large independent samples, for the first time, a few potential DNA methylation biomarkers for PCa progression in PR men were identified. The outcomes of these studies could lead to development of better methods for clinicians to stratify PR men with PCa that have high risk of metatastic and lethal disease with an optimal treatment. The aggressive PCa we are studying may be a cancer disparity in the PR population that has not been identified.

Supported by grants #: U54 CA163071-07 and U54 CA163068-07.

Citation Format: Gilberto Ruiz-Deya, Jamie Matta, Jarline Encarnacion-Medina, Carmen Ortiz-Sanchez, Liang Wang, Anders Berglund, Youngchul Kim, Jong Park. DNA methylation as a predictor of aggressive prostate cancer in Puerto Rican men [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-227.

Medication adherence/persistence among patients with active multiple sclerosis in Finland

Objectives

To explore adherence, persistence, and treatment patterns in patients with multiple sclerosis (MS) in Finland treated with disease‐modifying therapies (DMTs) for active MS in 2005‐2018.

Materials and Methods

The study cohort was identified using the Drug Prescription Register of Social Insurance Institute, Finland. All patients had at least one prescription of glatiramer acetate (GA), beta‐interferons, teriflunomide, or delayed‐release dimethyl fumarate (DMF). Adherence was calculated using proportion of days covered (PDC) (cutoff ≥0.8). Time to non‐persistence was calculated by the number of days on index DMT treatment before the first treatment gap (≥90 days) or switch and analyzed with time‐to‐event methodology.

Results

The cohort included 7474 MS patients (72.2% female; mean age 38.9 years). Treatment switches were steady over 2005‐2012, peaked in 2015. PDC means (standard deviations) were GA, 0.87 (0.17); beta‐interferons, 0.88 (0.15); DMF, 0.89 (0.14); teriflunomide, 0.93 (0.10). Adherence frequencies were GA, 78.4%; beta‐interferons, 81.3%; DMF, 86.9%; teriflunomide, 91.7%. Logistic regression showed that age group, DMT and the starting year, sex, and hospital district independently affected adherence. Patients receiving teriflunomide and DMF, males, and older patients were more likely to persist on treatment. There was no difference in persistence between patients prescribed teriflunomide and DMF, or between GA and beta‐interferons.

Conclusions

Oral DMTs had greater adherence and persistence than injectable DMTs.

Multi-Omics and Informatics Analysis of FFPE Tissues Derived from Melanoma Patients with Long/Short Responses to Anti-PD1 Therapy Reveals Pathways of Response

Simple Summary

Immune based therapies have benefited many melanoma patients, but many patients still do not respond. This study analyzes biospecimens obtained from patients undergoing a type of immune based therapy called anti-PD-1 to understand mechanisms of response and resistance to this treatment. The operational definition of good response utilized in this investigation permitted us to examine the biochemical pathways that are facilitating anti-PD-1 responses independent of prior therapies received by patients. Currently, there are no clinically available tests to reliably test for the outcome of patients treated with anti-PD-1 therapy. The purpose of this study was to facilitate the development of prospective biomarker-directed trials to guide therapy, as even though the side effect profile is favorable for anti-PD-1 therapy, some patients do not respond to therapy with significant toxicity. Each patient may require testing for the pathways upregulated in the tumor to predict optimal benefit to anti-PD-1 treatment.

Abstract

Anti-PD-1 based immune therapies are thought to be dependent on antigen processing and presentation mechanisms. To characterize the immune-dependent mechanisms that predispose stage III/IV melanoma patients to respond to anti-PD-1 therapies, we performed a multi-omics study consisting of expression proteomics and targeted immune-oncology-based mRNA sequencing. Formalin-fixed paraffin-embedded tissue samples were obtained from stage III/IV patients with melanoma prior to anti-PD-1 therapy. The patients were first stratified into poor and good responders based on whether their tumors had or had not progressed while on anti-PD-1 therapy for 1 year. We identified 263 protein/gene candidates that displayed differential expression, of which 223 were identified via proteomics and 40 via targeted-mRNA analyses. The downstream analyses of expression profiles using MetaCore software demonstrated an enrichment of immune system pathways involved in antigen processing/presentation and cytokine production/signaling. Pathway analyses showed interferon (IFN)-γ-mediated signaling via NF-κB and JAK/STAT pathways to affect immune processes in a cell-specific manner and to interact with the inducible nitric oxide synthase. We review these findings within the context of available literature on the efficacy of anti-PD-1 therapy. The comparison of good and poor responders, using efficacy of PD-1-based therapy at 1 year, elucidated the role of antigen presentation in mediating response or resistance to anti-PD-1 blockade.

Comparative Genomics Reveals Distinct Immune-oncologic Pathways in African American Men with Prostate Cancer

PURPOSE

The role of immune-oncologic mechanisms of racial disparities in prostate cancer remains understudied. Limited research exists to evaluate the molecular underpinnings of immune differences in African American men (AAM) and European American men (EAM) prostate tumor microenvironment (TME).

EXPERIMENTAL DESIGN

A total of 1,173 radiation-naïve radical prostatectomy samples with whole transcriptome data from the Decipher GRID registry were used. Transcriptomic expressions of 1,260 immune-specific genes were selected to assess immune-oncologic differences between AAM and EAM prostate tumors. Race-specific differential expression of genes was assessed using a rank test, and intergene correlational matrix and gene set enrichment was used for pathway analysis.

RESULTS

AAM prostate tumors have significant enrichment of major immune-oncologic pathways, including proinflammatory cytokines, IFNα, IFNγ, TNFα signaling, ILs, and epithelial-mesenchymal transition. AAM TME has higher total immune content score (ICS^HIGH) compared with 0 (37.8% vs. 21.9%, P = 0.003). AAM tumors also have lower DNA damage repair and are genomically radiosensitive as compared with EAM. IFITM3 (IFN-inducible transmembrane protein 3) was one of the major proinflammatory genes overexpressed in AAM that predicted increased risk of biochemical recurrence selectively for AAM in both discovery [HR_AAM = 2.30; 95% confidence interval (CI), 1.21-4.34; P = 0.01] and validation (HR_AAM = 2.42; 95% CI, 1.52-3.86; P = 0.0001) but not in EAM.

CONCLUSIONS

Prostate tumors of AAM manifest a unique immune repertoire and have significant enrichment of proinflammatory immune pathways that are associated with poorer outcomes. Observed immune-oncologic differences can aid in a genomically adaptive approach to treating prostate cancer in AAM.

Influence of gene expression on survival of clear cell renal cell carcinoma

Approximately 10%‐20% of patients with clinically localized clear cell renal cell carcinoma (ccRCC) at time of surgery will subsequently experience metastatic progression. Although considerable progression was seen in the systemic treatment of metastatic ccRCC in last 20 years, once ccRCC spreads beyond the confines of the kidney, 5‐year survival is less than 10%. Therefore, significant clinical advances are urgently needed to improve overall survival and patient care to manage the growing number of patients with localized ccRCC. We comprehensively evaluated expression of 388 candidate genes related with survival of ccRCC by using TCGA RNAseq (n = 515), Total Cancer Care (TCC) expression array data (n = 298), and a well characterized Moffitt RCC cohort (n = 248). We initially evaluated all 388 genes for association with overall survival using TCGA and TCC data. Eighty‐one genes were selected for further analysis and tested on Moffitt RCC cohort using NanoString expression analysis. Expression of nine genes (AURKA, AURKB, BIRC5, CCNE1, MK167, MMP9, PLOD2, SAA1, and TOP2A) was validated as being associated with poor survival. Survival prognostic models showed that expression of the nine genes and clinical factors predicted the survival in ccRCC patients with AUC value: 0.776, 0.821 and 0.873 for TCGA, TCC and Moffitt data set, respectively. Some of these genes have not been previously implicated in ccRCC survival and thus potentially offer insight into novel therapeutic targets. Future studies are warranted to validate these identified genes, determine their biological mechanisms and evaluate their therapeutic potential in preclinical studies.

Methylation of immune synapse genes modulates tumor immunogenicity

Cancer immune evasion is achieved through multiple layers of immune tolerance mechanisms including immune editing, recruitment of tolerogenic immune cells, and secretion of immunosuppressive cytokines. Recent success with immune checkpoint inhibitors in cancer immunotherapy suggests a dysfunctional immune synapse as a pivotal tolerogenic mechanism. Tumor cells express immune synapse proteins to suppress the immune system, which is often modulated by epigenetic mechanisms. When the methylation status of key immune synapse genes was interrogated, we observed disproportionately hypermethylated costimulatory genes and hypomethylation of immune checkpoint genes, which were negatively associated with functional T cell recruitment to the tumor microenvironment. Therefore, the methylation status of immune synapse genes reflects tumor immunogenicity and correlates with survival.

Survival after primary breast cancer surgery following propofol or sevoflurane general anesthesia-A retrospective, multicenter, database analysis of 6305 Swedish patients

BACKGROUND

Retrospective studies indicate that the choice of anesthetic can affect long-term cancer survival. Propofol seems to have an advantage over sevoflurane. However, this is questioned for breast cancer. We gathered a large cohort of breast cancer surgery patients from seven Swedish hospitals and hypothesized that general anesthesia with propofol would be superior to sevoflurane anesthesia regarding long-term breast cancer survival.

METHODS

We identified all patients who were anaesthetized for breast cancer surgery between 2006 and 2012. The patients were matched to the Swedish Breast Cancer Quality Register, to retrieve tumor characteristics, prognostic factors, and adjuvant treatment as well as date of death. Overall survival between patients undergoing sevoflurane and propofol anesthesia was analyzed with different statistical approaches: (a) multiple Cox regression models adjusted for demographic, oncological, and multiple control variables, (b) propensity score matching on the same variables, but also including the participating centers as a cofactor in a separate analysis.

RESULTS

The database analysis identified 6305 patients. The 5-year survival rates were 91.0% and 81.8% for the propofol and sevoflurane group, respectively, in the final model (P = .126). Depending on the statistical adjustment method used, different results were obtained, from a non-significant to a "proposed" and even a "determined" difference in survival that favored propofol, with a maximum of 9.2 percentage points higher survival rate at 5 years (hazard ratio 1.46, 95% CI 1.10-1.95).

CONCLUSIONS

It seems that propofol may have a survival advantage compared with sevoflurane among breast cancer patients, but the inherent weaknesses of retrospective analyses were made apparent.

Abstract 1173: Disparity in pediatric B-cell acute lymphoblastic leukemia relapse between Hispanics and Non-Hispanic Whites: A potential role of miR-3158-3p

Background: Hispanics (HSP) have a higher risk of pediatric acute lymphoblastic leukemia (ALL) relapse compared to Non-Hispanic Whites (NHW). Although previous studies suggest a biological contribution to the ethnic disparity, the biological mechanism is not fully elucidated. In this study, we evaluated the potential role of miRNAs in the disparity of pediatric B-ALL early relapse in a two-stage pilot study.

Methods: We first performed a discovery phase on 14 HSP (7 relapse and 7 remission) and 14 NHW (7 relapse and 7 remission) preselected initial diagnostic B-ALL, minimal residual disease negative specimens without adverse cytogenetic features. Global miRNA expression profiles were compared between remission and relapse patients in the combined sample (14 relapse vs 14 remission) and between ethnic groups (14 HSP vs 14 NHW). We then selected candidate miRNAs that were differentially expressed between combined remission and relapse samples as well as between HSP and NHW for validation. Validation and expression of candidate miRNAs within each ethnic group were performed on a publicly available data from the Therapeutically Applicable Research To Generate Effective Treatments (TARGET) program using 22 HSP (12 relapse and 10 remission) and 71 NHW (39 relapse and 32 remission) that had miRNA-seq, ethnicity and relapse data available.

Results: In the discovery phase, miR-3158-3p, miR-378j and miR-4642 were differentially expressed between remission and relapse samples as well as between HSP and NHW. The expressions of miR-3158-3p (fold change (FC)=0.87, p=0.046), and miR-378j (FC=0.85, p=0.043) were decreased in relapse compared to remission patients, but the decrease was more prominent in NHW (miR-3158-3p: FC=0.83, p=0.047 and miR-378j: FC=0.81, p=0.077) than HSP (miR-3158-3p: FC=0.91, p=0.35 and miR-378j: FC=0.89, p=0.18). In contrast, the expression of miR-4642 was elevated (FC=1.29, p=0.011) in relapse compared to remission patients, but the elevation was more prominent in HSP (FC=1.58, p=0.005) than NHW (FC=1.04, p=0.51). In addition, miR-3158-3p (FC=0.87, p=0.040) and miR-4642 (FC=0.81, p=0.047) were under-expressed in NHW compared to HSP, while miR-378j (FC=1.23, p=0.013) was overexpressed in NHW compared to HSP. The under-expression of miR-3158-3p in relapse compared to remission samples (NHW: FC=0.75, p=0.007; overall: FC=0.86, p=0.07) was validated in the independent TARGET dataset. In silico analysis using DIANA microT predicted that miR-3158-3p targeted three genes, SMAD4, SHC and NFKB1, that are implicated in leukemia.

Conclusion: This study adds to the accumulating evidence that miRNAs have critical roles in pediatric B-ALL relapse and provides preliminary evidence, for the first time, that miRNA expression may contribute to the ethnic disparity in pediatric B-ALL relapse. However, these findings need to be validated in a larger cohort and the biological role of the miRNAs in the disparity of pediatric B-ALL relapse needs to be elucidated.

Citation Format: Ernest K. Amankwah, Anders Berglund, Karen Rabin, Patrick A. Brown, Jong Y. Park. Disparity in pediatric B-cell acute lymphoblastic leukemia relapse between Hispanics and Non-Hispanic Whites: A potential role of miR-3158-3p [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1173.

Abstract 274: Multifaceted function of microRNA-299-3p fosters an antitumor environment through modulation of androgen receptor and VEGFA signaling pathways in prostate cancer cells

MicroRNAs (miRNAs) play crucial roles in the regulation of prostate cancer (PCa) through modulation of signaling pathways. Androgen receptor (AR) signaling is central to PCa and PCa therapy. The therapeutic suitability of miRNAs that target AR has not been investigated thoroughly. Here, we illustrate the clinical relevance, functional significance and therapeutic benefit of miR-299-3p, an AR targeting microRNA, in PCa progression. We noted a loss of expression of miR-299-3p in prostate tumors compared to noncancerous prostate tissue in clinical specimens. Studies on the impact of miR-299-3p restoration on AR function, phenotypic changes associated with cancer progression and involvement of the downstream components of the AR signaling pathway were conducted using in vitro and in vivo model systems. Replenishment of miR-299-3p in C4-2B, 22Rv-1, and PC-3 cells contributed to cell cycle arrest, reduced cell proliferation, migration and increased expression of apoptotic markers. Additionally, expression of miR-299-3p reduced AR, PSA and VEGFA expression. AGO-RNA pulldown experiment showed enrichment of AR, VEGFA and miR-299-3p in the RISC in the extracts of C4-2B cells overexpressing miR-299-3p. Overexpression of miR-299-3p inhibited epithelial-mesenchymal transition signaling, through inhibition of expression of Slug, TGF-Β3, phospho-AKT, and phospho-PRAS40 and up-regulation of E-cadherin. Replenishment of miR-299-3p showed reduced tumor growth in xenograft mice models. Furthermore, we also tested the benefit of miR-299-3p restoration in combination treatment with enzalutamide and docetaxel which showed a synergistic effect on drug sensitivity. In conclusion, this study has identified novel mechanisms of antitumor and antimigration functions of miR-299-3p through modulation of AR and VEGFA signaling pathways which leads to improved drug sensitivity of PCa.

Citation Format: Kavya Ganapathy, Stephen Staklinski, Md Faqrul Hasan, Richard Ottman, Thomas Andl, Anders Berglund, Jong Park, Ratna Chakrabarti. Multifaceted function of microRNA-299-3p fosters an antitumor environment through modulation of androgen receptor and VEGFA signaling pathways in prostate cancer cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 274.

Modeling of Xerostomia After Radiotherapy for Head and Neck Cancer: A Registry Study

Aim

Data from a local quality registry are used to model the risk of late xerostomia after radiotherapy for head and neck cancer (HNC), based on dosimetric- and clinical variables. Strengths and weaknesses of using quality registry data are explored.

Methods

HNC patients treated with radiotherapy at the Karolinska University hospital are entered into a quality registry at routine follow up, recording morbidity according to a modified RTOG/LENT-SOMA scale. Other recorded parameters are performance status, age, gender, tumor location, tumor stage, smoking status, chemotherapy and radiotherapy data, including prescribed dose and organ-at-risk (OAR) dose. Most patients are entered at several time points, but at variable times after treatment. Xerostomia was modeled based on follow-up data from January 2014 to October 2018, resulting in 753 patients. Two endpoints were considered: maximum grade ≥2 (XER_G≥2) or grade ≥3 (XER_G≥3) late xerostomia. Univariate Cox regression was used to select variables for two multivariate models for each endpoint, one based on the mean dose to the total parotid volume (D_tot) and one based on the mean dose to the contralateral parotid (D_contra). Cox regression allows the estimation of the risk of xerostomia at different time points; models were presented visually as nomograms estimating the risk at 9, 12, and 24 months respectively.

Results

The toxicity rates were 366/753 (49%) for XER_G≥2 and 40/753 (5.3%) for XER_G≥3. The multivariate models included several variables for XER_G≥2, and dose, concomitant chemotherapy and age were included for XER_G≥3. Induction chemotherapy and an increased number of fractions per week were associated with a lower risk of XER_G≥2. However, since the causality of these relationships have limited support from previous studies, alternative models without these variables were also presented. The models based on the mean dose to the total parotid volume and the contralateral parotid alone were very similar.

Conclusion

Late xerostomia after radiotherapy can be modeled with reasonable predictive power based on registry data; models are presented for different endpoints highly relevant in clinical practice. However, the risk of modeling indirect relationships, given the unavoidably heterogeneous registry data, needs to be carefully considered in the interpretation of the results.

Overlapping volumes in re-irradiation for head and neck cancer - an important factor for patient selection

BACKGROUND

There is a lack of consensus concerning the definition of re-irradiation and re-irradiation volumes in head and neck cancer (HNC). The aim of the present study is to introduce a more strict definition of the re-irradiated volume that might better predict the risk of serious side-effects from treatment.

METHODS

Fifty-four consecutive patients re-irradiated for HNC cancer were retrospectively analysed. CT images were deformably registered and the dose distributions accumulated after conversion to EQD2. Patients with a cumulative dose of ≥100 Gy in the overlapping volume (V100) were included in the study. Survival data and radiation-related acute and late toxicities were recorded.

RESULTS

The overall survival of all included patients at 2 and 5 years was 42.6 and 27.3% respectively and the progression free survival at 2 and 5 years was 32.5 and 28.5% respectively. The overall rate of any event of severe (grade ≥ 3) acute and late toxicity was 26 and 51%, respectively. We found that severe acute toxicity was more common in patients who had a larger overlapping volume (V100 > mean) where 43% of the patients experienced grade ≥ 3 acute toxicity, compared to the patients with smaller overlapping volumes (V100 < mean) where only 11% had severe toxicity (p = 0.02). The seemingly high rates of late toxicity in the present study could be due to the use of a more strict definition of re-irradiation. In previous studies also patients with low dose overlap are included and our results imply that there is a risk that previous studies might have overestimated the risk-benefit ratio in re-irradiation of HNC.

CONCLUSIONS

Our study describes the outcome of a patient material where a more strict definition of the re-irradiated volume is used. With this definition, which could better describe the volume of highest risk for serious complications, we found that larger such overlapping volumes result in an increase in severe acute side-effects. A clear definition of re-irradiation and re-irradiation volumes is of utmost importance for future studies of HNC to make results from different studies comparable.

Innovations in research and clinical care using patient-generated health data

Patient-generated health data (PGHD), or health-related data gathered from patients to help address a health concern, are used increasingly in oncology to make regulatory decisions and evaluate quality of care. PGHD include self-reported health and treatment histories, patient-reported outcomes (PROs), and biometric sensor data. Advances in wireless technology, smartphones, and the Internet of Things have facilitated new ways to collect PGHD during clinic visits and in daily life. The goal of the current review was to provide an overview of the current clinical, regulatory, technological, and analytic landscape as it relates to PGHD in oncology research and care. The review begins with a rationale for PGHD as described by the US Food and Drug Administration, the Institute of Medicine, and other regulatory and scientific organizations. The evidence base for clinic-based and remote symptom monitoring using PGHD is described, with an emphasis on PROs. An overview is presented of current approaches to digital phenotyping or device-based, real-time assessment of biometric, behavioral, self-report, and performance data. Analytic opportunities regarding PGHD are envisioned in the context of big data and artificial intelligence in medicine. Finally, challenges and solutions for the integration of PGHD into clinical care are presented. The challenges include electronic medical record integration of PROs and biometric data, analysis of large and complex biometric data sets, and potential clinic workflow redesign. In addition, there is currently more limited evidence for the use of biometric data relative to PROs. Despite these challenges, the potential benefits of PGHD make them increasingly likely to be integrated into oncology research and clinical care.

Empirically-derived synthetic populations to mitigate small sample sizes

Limited sample sizes can lead to spurious modeling findings in biomedical research. The objective of this work is to present a new method to generate synthetic populations (SPs) from limited samples using matched case-control data (n = 180 pairs), considered as two separate limited samples. SPs were generated with multivariate kernel density estimations (KDEs) with unconstrained bandwidth matrices. We included four continuous variables and one categorical variable for each individual. Bandwidth matrices were determined with Differential Evolution (DE) optimization by covariance comparisons. Four synthetic samples (n = 180) were derived from their respective SPs. Similarity between observed samples with synthetic samples was compared assuming their empirical probability density functions (EPDFs) were similar. EPDFs were compared with the maximum mean discrepancy (MMD) test statistic based on the Kernel Two-Sample Test. To evaluate similarity within a modeling context, EPDFs derived from the Principal Component Analysis (PCA) scores and residuals were summarized with the distance to the model in X-space (DModX) as additional comparisons. Four SPs were generated from each sample. The probability of selecting a replicate when randomly constructing synthetic samples (n = 180) was infinitesimally small. MMD tests indicated that the observed sample EPDFs were similar to the respective synthetic EPDFs. For the samples, PCA scores and residuals did not deviate significantly when compared with their respective synthetic samples. The feasibility of this approach was demonstrated by producing synthetic data at the individual level, statistically similar to the observed samples. The methodology coupled KDE with DE optimization and deployed novel similarity metrics derived from PCA. This approach could be used to generate larger-sized synthetic samples. To develop this approach into a research tool for data exploration purposes, additional evaluation with increased dimensionality is required. Moreover, given a fully specified population, the degree to which individuals can be discarded while synthesizing the respective population accurately will be investigated. When these objectives are addressed, comparisons with other techniques such as bootstrapping will be required for a complete evaluation.

DNA methylation changes in infants between 6 and 52 weeks

Infants undergo extensive developments during their first year of life. Although the biological mechanisms involved are not yet fully understood, changes in the DNA methylation in mammals are believed to play a key role. This study was designed to investigate changes in infant DNA methylation that occurs between 6 and 52 weeks. A total of 214 infant saliva samples from 6 or 52 weeks were assessed using principal component analyses and t-distributed stochastic neighbor-embedding algorithms. Between the two time points, there were clear differences in DNA methylation. To further investigate these findings, paired two-sided student’s t-tests were performed. Differently methylated regions were defined as at least two consecutive probes that showed significant differences, with a q-value < 0.01 and a mean difference > 0.2. After correcting for false discovery rates, changes in the DNA methylation levels were found in 42 genes. Of these, 36 genes showed increased and six decreased DNA methylation. The overall DNA methylation changes indicated decreased gene expression. This was surprising because infants undergo such profound developments during their first year of life. The results were evaluated by taking into consideration the extensive development that occurs during pregnancy. During the first year of life, infants have an overall three-fold increase in weight, while the fetus develops from a single cell into a viable infant in 9 months, with an 875-million-fold increase in weight. It is possible that the findings represent a biological slowing mechanism in response to extensive fetal development. In conclusion, our study provides evidence of DNA methylation changes during the first year of life, representing a possible biological slowing mechanism. We encourage future studies of DNA methylation changes in infants to replicate the findings by using a repeated measures model and less stringent criteria to see if the same genes can be found, as well as investigating whether other genes are involved in development during this period.

GENE-46. XAF1 DRIVES DIFFERENTIAL PLASTICITY TOWARDS ADAPTIVE RESISTANCE BETWEEN MGMT-HYPERMETHYLATED AND MGMT-HYPOMETHYLATED GLIOBLASTOMA

Although, the epigenetic regulation of O6-alkylguanine DNA alkyltransferase (MGMT) in GBM is an established surrogate of intrinsic resistance to temozolomide (TMZ), the evolution of GBM habitats towards adaptive resistance to TMZ relative to MGMT promoter methylation status remains unclear. We report a novel epigenetic regulation of plasticity towards adaptive resistance in GBM. Using an adaptive TMZ resistance model of MGMT-hypermethylated and MGMT-hypomethylated GBM cellular habitats, a counter-intuitive inverse correlation was noted between intrinsic MGMT-dependent TMZ resistance versus plasticity towards adaptive TMZ resistance. Upon TMZ challenge, GBM cellular habitats with lower intrinsic resistance demonstrated significant genetic perturbations and aggressive phenotypic alterations compared to GBM habitats with higher intrinsic resistance. A resulting gene signature associated with plasticity for adaptive resistance from our model significantly correlated with GBM survival in the TCGA dataset. XAF-1 emerged as a key gene whose epigenetic regulation mediated differential plasticity towards adaptive resistance to TMZ in GBM habitats. Genetic silencing of XAF-1 significantly compromised plasticity towards adaptive resistance. XAF1 expression was found to highly correlate with promoter methylation status, and negatively correlate with long-term survival in GBM patient survival. Our studies have shed some light with respect to the plasticity of GBM habitats towards adaptive resistance evolution to TMZ relative to MGMT promoter methylation status. Particularly, a novel and translational role for XAF1 in GBM has been uncovered.

Reduced sexual size dimorphism in a pipefish population where males do not prefer larger females

Within a species' distribution, populations are often exposed to diverse environments and may thus experience different sources of both natural and sexual selection. These differences are likely to impact the balance between costs and benefits to individuals seeking reproduction, thus entailing evolutionary repercussions. Here, we look into an unusual population (Baltic Sea) of the broadnosed pipefish, Syngnathus typhle, where males do not seem to select females based on size and hypothesize that this pattern may derive from a reduction in direct benefits to the male. We further hypothesize that if larger females do not persistently secure a higher reproductive success, either through pre- or postcopulatory sexual selection, a decrease in sexual size dimorphism in the Baltic population should be apparent, especially when contrasted with a well-studied population, inhabiting similar latitudes (Swedish west coast), where males prefer larger females. We found that, in the Baltic population, variation in female quality is low. We were unable to find differences in abortion rates or protein concentration in oocytes produced by females of contrasting sizes. Direct benefits from mating with large partners seem, thus, reduced in the Baltic population. We also found no evidence of any postcopulatory mechanism that could favor larger mothers as embryo development was unrelated to female size. While female size can still be selected through intrasexual competition or fecundity selection, the pressure for large female body size seems to be lower in the Baltic. Accordingly, we found a noticeable decrease in sexual size dimorphism in the Baltic population. We conclude that, although far from negating the significance of other selective processes, sexual selection seems to have a decisive role in supporting pipefish sexual size asymmetries.

Rationale and Design of the CAN Study: an RCT of Survival after Propofol- or Sevoflurane-based Anesthesia for Cancer Surgery

Background:

Based on animal data only, some clinicians have adopted propofol-based anesthesia for cancer surgery with the aim of increased survival.

Objective:

Our objective is to verify or refute the hypothesis that survival increases after cancer surgery with propofol compared with sevoflurane for anesthesia maintenance. This aim deserves a large-scale randomized study. The primary hypothesis is an absolute increase of minimum 5%-units in 1- and 5-year survival with propofol- based anesthesia for breast or colorectal cancer after radical surgery, compared with sevoflurane-based anesthesia.

Method:

Ethics and medical agency approvals were received and pre-study registrations at clinicaltrial.gov and EudraCT were made for our now ongoing prospective, randomized, open-label, multicenter study. A power analysis based on a retrospective study, including a safety margin for drop outs, resulted in a total requirement of 8,000 patients. The initial inclusion period constituted a feasibility phase with an emphasis on the functionality of the infrastructure at the contributing centers and at the monitoring organization, as well as on protocol adherence.

Conclusion:

The infrastructure and organization work smoothly at the different contributing centers. Protocol adherence is good, and the monitors are satisfied. We expect this trial to be able to either verify or refute that propofol is better than sevoflurane for cancer surgery.

Acidity promotes tumour progression by altering macrophage phenotype in prostate cancer

BACKGROUND

Tumours rapidly ferment glucose to lactic acid even in the presence of oxygen, and coupling high glycolysis with poor perfusion leads to extracellular acidification. We hypothesise that acidity, independent from lactate, can augment the pro-tumour phenotype of macrophages.

METHODS

We analysed publicly available data of human prostate cancer for linear correlation between macrophage markers and glycolysis genes. We used zwitterionic buffers to adjust the pH in series of in vitro experiments. We then utilised subcutaneous and transgenic tumour models developed in C57BL/6 mice as well as computer simulations to correlate tumour progression with macrophage infiltration and to delineate role of acidity.

RESULTS

Activating macrophages at pH 6.8 in vitro enhanced an IL-4-driven phenotype as measured by gene expression, cytokine profiling, and functional assays. These results were recapitulated in vivo wherein neutralising intratumoural acidity reduced the pro-tumour phenotype of macrophages, while also decreasing tumour incidence and invasion in the TRAMP model of prostate cancer. These results were recapitulated using an in silico mathematical model that simulate macrophage responses to environmental signals. By turning off acid-induced cellular responses, our in silico mathematical modelling shows that acid-resistant macrophages can limit tumour progression.

CONCLUSIONS

This study suggests that tumour acidity contributes to prostate carcinogenesis by altering the state of macrophage activation.

Educational level and management and outcomes in non-small cell lung cancer. A nationwide population-based study

OBJECTIVES

We examined associations between educational level and clinical presentation, patterns of management and mortality in patients with non-small cell lung cancer (NSCLC) in Sweden, a country with a National Health Care System.

MATERIALS AND METHODS

We identified 39,671 patients with a NSCLC diagnosis 2002-2016 in Lung Cancer Data Base Sweden (LCBaSe), a population-based research database. In analyses adjusted for comorbidity and other prognostic factors, odds Ratios (OR) and hazard Ratios (HR) were estimated to examine associations between patients' educational level and aspects of management and mortality.

RESULTS

Stage at diagnosis and waiting times did not differ between educational groups. In multivariable analysis, the likelihood to undergo PET/CT and assessment in a multidisciplinary team setting were higher in patients with high compared to low education (aOR 1.14; CI 1.05-1.23 and aOR 1.22; CI 1.14-1.32, respectively). In patients with early stage IA-IIB disease, the likelihood to undergo stereotactic radiotherapy was elevated in patients with high education (aOR 1.40; CI 1.03-1.91). Both all-cause (aHR 0.86; CI 0.77-0.92) and cause-specific mortality (aHR 0.83; CI 0.74-0.92) was lower in patients with high compared to low education in early stage disease (IA-IIB). In higher stage NSCLC no differences were observed. Patterns were similar in separate assessments stratified by sex and histopathology.

CONCLUSIONS

While stage at diagnosis and waiting times did not differ between educational groups, we found socioeconomic differences in diagnostic intensity, multidisciplinary team assessment, stereotactic radiotherapy and mortality in patients with NSCLC. These findings may in part reflect social gradients in implementation and use of novel diagnostic and treatment modalities. Our findings underscore the need for improved adherence to national guidelines.

An immunoproteomic approach to characterize the CAR interactome and signalosome

Adoptive transfer of T cells that express a chimeric antigen receptor (CAR) is an approved immunotherapy that may be curative for some hematological cancers. To better understand the therapeutic mechanism of action, we systematically analyzed CAR signaling in human primary T cells by mass spectrometry. When we compared the interactomes and the signaling pathways activated by distinct CAR-T cells that shared the same antigen-binding domain but differed in their intracellular domains and their in vivo antitumor efficacy, we found that only second-generation CARs induced the expression of a constitutively phosphorylated form of CD3ζ that resembled the endogenous species. This phenomenon was independent of the choice of costimulatory domains, or the hinge/transmembrane region. Rather, it was dependent on the size of the intracellular domains. Moreover, the second-generation design was also associated with stronger phosphorylation of downstream secondary messengers, as evidenced by global phosphoproteome analysis. These results suggest that second-generation CARs can activate additional sources of CD3ζ signaling, and this may contribute to more intense signaling and superior antitumor efficacy that they display compared to third-generation CARs. Moreover, our results provide a deeper understanding of how CARs interact physically and/or functionally with endogenous T cell molecules, which will inform the development of novel optimized immune receptors.

21-hydroxylase autoantibodies are more prevalent in Turner syndrome but without an association to the autoimmune polyendocrine syndrome type I

Turner syndrome (TS) is associated with an increased frequency of autoimmunity. Frequently observed autoimmune diseases in TS are also seen in the autoimmune polyendocrine syndrome type I (APS I), of which Addison disease is a key component. An overlapping antibody profile between TS and APS I could be considered. The aim of this work was to study women with TS regarding 21-hydroxylase (21-OH) antibodies and interferon omega (IFN-ω) antibodies, a highly specific marker for APS I, to determine if there are immunological overlaps between TS and APS I. Blood samples from 141 TS were assayed for 21-OH antibodies and IFN-ω antibodies using in-vitro-transcribed and translated autoantigen. Indices with a cut-off point of 57 and 200 for 21-OH antibody and IFN-ω antibody were used as reference. The median age of TS was 31·6 years (range = 11·2-62·2). Positive indices of 21-OH antibodies were present in six TS (4%), with a mean of 144·8 (range = 60-535). None had apparent adrenal insufficiency. There was no age difference comparing 21-OH antibody-positive TS (median age = 33·9 years, range = 17·7-44·7) and 21-OH antibody-negative TS (median age = 31·6 years, range = 11·2-62·2) (P = 0·8). No TS was positive for IFN-ω antibodies (mean = 42·4, range = -435-191). No overlapping autoimmune profile between TS and APS I was found. Autoimmunity against 21-OH among TS patients was more prevalent than previously identified, suggesting an increased risk of adrenal failure in TS. However, whether adrenal impairment will develop remains unknown.

The 'Woman in Red' effect: pipefish males curb pregnancies at the sight of an attractive female

In an old Gene Wilder movie, an attractive woman dressed in red devastated a man's current relationship. We have found a similar 'Woman in Red' effect in pipefish, a group of fish where pregnancy occurs in males. We tested for the existence of pregnancy blocks in pregnant male black-striped pipefish (Syngnathus abaster). We allowed pregnant males to see females that were larger and even more attractive than their original high-quality mates and monitored the survival and growth of developing offspring. After exposure to these extremely attractive females, males produced smaller offspring in more heterogeneous broods and showed a higher rate of spontaneous offspring abortion. Although we did not observe a full pregnancy block, our results show that males are able to reduce investment in current broods when faced with prospects of a more successful future reproduction with a potentially better mate. This 'Woman in Red' life-history trade-off between present and future reproduction has similarities to the Bruce effect, and our study represents, to our knowledge, the first documentation of such a phenomenon outside mammals.

Decreased Suppression and Increased Phosphorylated STAT3 in Regulatory T Cells are Associated with Benefit from Adjuvant PD-1 Blockade in Resected Metastatic Melanoma

PURPOSE

PD-1 blockade induces durable responses in patients with metastatic melanoma and prolongs relapse-free survival in patients with resected melanoma; however, current biomarkers do not consistently associate with patient responses. In this study, we investigated the impact of nivolumab therapy on peripheral blood regulatory T cells (Treg) and its relation to patient outcomes.

EXPERIMENTAL DESIGN

Peripheral blood Tregs and conventional CD4⁺ T cells from patients with resected high-risk melanoma treated with adjuvant nivolumab were assessed for gene expression changes by RNA-seq. Percentages of circulating Tregs and phosphorylated-STAT3 (pSTAT3) expression levels were assessed by flow cytometry and validated in an independent cohort of active disease patients. Suppressive function of Tregs was assessed in allogeneic mixed lymphocyte reactions.

RESULTS

Tregs from non-relapse patients had increased expression of proliferation associated genes. An increase in the proportion of circulating Tregs and pSTAT3 expression and a reduction in Treg-suppressive capacity were observed in non-relapsing, but not relapsing patient samples 13 weeks after starting treatment. In vitro blockade of PD-1 increased Treg percentages and pSTAT3 expression, and reduced Treg-suppressive function. PD-1 blockade also led to IL10 production by T cells, resulting in higher Treg proliferation. The addition of a STAT3 inhibitor ameliorated the increase in Tregs, enhanced suppressive function, and decreased T-cell IL10 production in vitro.

CONCLUSIONS

These results demonstrate that induction of pSTAT3, reduced suppressive function, and a paradoxical increase in Treg proliferation are novel correlates of patient benefit from PD-1 blockade.

Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer

Tumor-associated macrophages (TAMs) are attractive targets for immunotherapy. Recently, studies in animal models showed that treatment with an anti-TAM antibody directed against the scavenger receptor MARCO resulted in suppression of tumor growth and metastatic dissemination. Here we investigated the expression of MARCO in relation to other macrophage markers and immune pathways in a non-small cell lung cancer (NSCLC) cohort (n = 352). MARCO, CD68, CD163, MSR1 and programmed death ligand-1 (PD-L1) were analyzed by immunohistochemistry and immunofluorescence, and associations to other immune cells and regulatory pathways were studied in a subset of cases (n = 199) with available RNA-seq data. We observed a large variation in macrophage density between cases and a strong correlation between CD68 and CD163, suggesting that the majority of TAMs present in NSCLC exhibit a protumor phenotype. Correlation to clinical data only showed a weak trend toward worse survival for patients with high macrophage infiltration. Interestingly, MARCO was expressed on a distinct subpopulation of TAMs, which tended to aggregate in close proximity to tumor cell nests. On the transcriptomic level, we found a positive association between MARCO gene expression and general immune response pathways including strong links to immunosuppressive TAMs, T-cell infiltration and immune checkpoint molecules. Indeed, a higher macrophage infiltration was seen in tumors expressing PD-L1, and macrophages residing within tumor cell nests co-expressed MARCO and PD-L1. Thus, MARCO is a potential new immune target for anti-TAM treatment in a subset of NSCLC patients, possibly in combination with available immune checkpoint inhibitors.

Clinical and prognostic significance of changes in haemoglobin concentration during 1 year of androgen-deprivation therapy for hormone-naïve bone-metastatic prostate cancer

OBJECTIVE

To estimate the strength of change in haemoglobin (Hb) concentrations during 1 year of androgen-deprivation therapy (ADT) as a predictor of survival in hormone-naïve patients with bone-metastatic (Stage M1b) prostate cancer.

PATIENTS AND METHODS

The patients included in this study were taken from the randomised trial (number 5) carried out by the Scandinavian Prostate Cancer Group (SPCG), comparing parenteral oestrogen with total androgen blockade (TAB) in hormone-naïve M1b prostate cancer. We identified 597 men where Hb measurements were made at enrolment, as well as at 3, 6 and 12 months of ADT. The time-dependent impact of Hb concentration changes on overall survival (OS) was analysed using multivariate Cox proportional hazards analysis. The 10-year OS according to increase/decrease in Hb concentration for the three treatment periods was demonstrated using Kaplan-Meier curves.

RESULTS

Multivariate analysis of changes in Hb concentration between baseline and 3 months showed better survival in patients with a decrease in Hb concentration (hazard ratio [HR] 1.42, 95% confidence interval [CI] 1.11-1.80) compared to those with an increase, whilst there was no difference in survival associated with a change in Hb concentration between 3 and 6 months (HR 0.93, 95% CI 0.76-1.12). Contrary to the first 3 months, poorer survival was seen in patients with a decrease in Hb concentration between 6 and 12 months (HR 0.76, 95% CI 0.62-0.92) compared to those with an increase.

CONCLUSIONS

In a large cohort of Scandinavian men with hormone-naïve M1b prostate cancer, an increase in Hb concentration between baseline and 3 months of ADT was associated with significantly poorer survival, whereas an increase between 6 and 12 months was associated with better survival. These findings provide new information about patterns of change in Hb concentrations during 12 months of ADT for M1b prostate cancer, and survival. Clinicians should be aware of the prognostic value of Hb concentration changes during ADT in M1b prostate cancer.

Point-of-care versus central laboratory testing of INR in acute stroke

OBJECTIVES

Effective anticoagulant therapy is a contraindication to thrombolysis, which is an effective treatment of ischemic stroke if given within 4.5 hours of symptom onset. INR above 1.7 is generally considered a contraindication for thrombolysis. Rapid measurement of INR in warfarin-treated patients is therefore of major importance in order to be able to decide on thrombolysis or not. We asked whether INR measured on a point-of-care instrument would be as good as a central laboratory instrument.

MATERIAL AND METHODS

A total of 529 consecutive patients who arrived at the emergency department at a large urban teaching hospital with stroke symptoms were enrolled in the study. INR was measured with a CoaguChek and a Sysmex instrument. Basic clinical information such as age, sex, and diagnosis (if available) was recorded. INR from the instruments was compared using linear regression and Bland-Altman plot.

RESULTS

Of 529 patients, 459 had INR results from both instruments. Among these, 3 patients were excluded as outliers. The rest (n = 456) showed good correlation between the methods (R²  = 0.97). In the current setting, CoaguChek was in median 63 minutes faster than Sysmex.

CONCLUSION

Our results indicate that point-of-care testing is a safe mean to rapidly acquire a patient's INR value in acute clinical situations.

Suppression of STING signaling through epigenetic silencing and missense mutation impedes DNA damage mediated cytokine production

The production of cytokines in response to DNA damage events may be an important host defense response to help prevent the escape of pre-cancerous cells. The innate immune pathways involved in these events are known to be regulated by cellular molecules such as STING (stimulator of interferon genes), which controls type I interferon and pro-inflammatory cytokine production in response to the presence of microbial DNA or cytosolic DNA that has escaped from the nucleus. STING signaling has been shown to be defective in a variety of cancers, such as colon cancer and melanoma, actions which may enable damaged cells to escape the immunosurveillance system. Here, we report through examination of databases that STING signaling may be commonly suppressed in a greater variety of tumors due to loss-of-function mutation or epigenetic silencing of the STING/cGAS promoter regions. In comparison, RNA activated innate immune pathways controlled by RIG-I/MDA5 were significantly less affected. Examination of reported missense STING variants confirmed that many exhibited a loss of function phenotype and could not activate cytokine production following exposure to cytosolic DNA or DNA-damage events. Our data implies that the STING signaling pathway may be recurrently suppressed by a number of mechanisms in a considerable variety of malignant disease and be a requirement for cellular transformation.

Tumour radiosensitivity is associated with immune activation in solid tumours

PURPOSE

Our goal was to determine whether tumour radiosensitivity is associated with activation of the immune system across all tumour types as measured by two gene expression signatures (GESs).

METHODS

We identified 10,240 genomically profiled distinct solid primary tumours with gene expression analysis available from an institutional de-identified database. Two separate GESs were included in the analysis, the radiosensitivity index (RSI) GES (a 10-gene GES as a measure of radiosensitivity) and the 12-chemokine (12-CK) signature (a 12-gene GES as a measure of immune activation). We tested whether the RSI and 12-CK were associated with each other across all tumour samples and, in an exploratory analysis, their prognostic significance in predicting distant metastasis-free survival (DMFS) among a well-characterised, independent cohort of 282 early-stage breast cancer cases treated with surgery and post-operative radiation alone without systemic therapy. The lower the RSI score, the higher the tumour radiosensitivity; whereas, the higher the 12-CK score the higher the immune activation.

RESULTS

Using an RSI cut-point of ≤0.3745, RSI-low tumours (n = 4,291, 41.9%) had a significantly higher median 12-CK GES value (0.54 [-0.136, 1.095]) compared with RSI-high tumours (-0.17 [-0.82, 0.42]; p < 0.001) across all tumour samples, indicating that radiosensitivity is associated with immune activation. In an exploratory analysis of early-stage breast cancer cases, a multivariable model with patient age, RSI and 12-CK provided a strong composite model for DMFS (p = 0.02), with RSI (hazard ratio [HR] 0.63 [95% confidence interval 0.36, 1.09]) and 12-CK (HR 0.66 [0.41, 1.04]) each providing comparable contributions.

CONCLUSIONS

Tumour radiosensitivity is associated with immune activation as measured by the two GESs.

Anxiety and depression symptoms among sub-fertile women, women pregnant after infertility treatment, and naturally pregnant women

BACKGROUND

Infertility has been associated with psychological distress, but whether these symptoms persist after achieving pregnancy via assisted reproductive technology (ART) remains unclear. We compared the prevalence of anxiety and depressive symptoms between women seeking for infertility treatment and women who conceived after ART or naturally.

METHODS

Four hundred and sixty-eight sub-fertile non-pregnant women, 2972 naturally pregnant women and 143 women pregnant after ART completed a questionnaire in this cross-sectional study. The Anxiety subscale of the Hospital Anxiety and Depression Scale (HADS-A≥8) and Edinburgh Postnatal Depression Scale (EPDS≥12) were used for assessing anxiety and depressive symptoms, respectively. Multivariate Poisson regression models with robust variance were applied to explore associations with anxiety and depressive symptoms.

RESULTS

The prevalence of anxiety and depressive symptoms among sub-fertile, non-pregnant women (57.6% and 15.7%, respectively) were significantly higher compared to women pregnant after ART (21.1% and 8.5%, respectively) and naturally pregnant women (18.8% and 10.3%, respectively). History of psychiatric diagnosis was identified as an independent risk factor for both anxiety and depressive symptoms. The presence of at least one unhealthy lifestyle behavior (daily tobacco smoking, weekly alcohol consumption, BMI≥25, and regular physical exercise<2h/week) was also associated with anxiety (Prevalence Ratio, PR: 1.24; 95%CI: 1.09-1.40) and depressive symptoms (PR: 1.25; 95%CI: 1.04-1.49).

CONCLUSIONS

Women pregnant after ART showed no difference in anxiety and depressive symptoms compared to naturally pregnant women. However, early psychological counseling and management of unhealthy lifestyle behaviors for sub-fertile women may be advisable, particularly for women with a previous history of psychiatric diagnosis.

The role of comorbidity in the management and prognosis in nonsmall cell lung cancer: a population-based study

BACKGROUND

Coexisting disease constitutes a challenge for the provision of optimal cancer care. The influence of comorbidity on lung cancer management and prognosis remains incompletely understood. We assessed the influence of comorbidity on treatment intensity and prognosis in a population-based setting in patients with nonsmall cell lung cancer.

MATERIAL AND METHODS

Our study was based on information available in Lung Cancer Data Base Sweden (LcBaSe), a database generated by record linkage between the National Lung Cancer Register (NLCR) and several other population-based registers in Sweden. The NLCR includes data on clinical characteristics on 95% of all patients with lung cancer in Sweden since 2002. Comorbidity was assessed using the Charlson Comorbidity Index. Logistic regression and time to event analysis was used to address the association between comorbidity and treatment and prognosis.

RESULTS

In adjusted analyses encompassing 19,587 patients with a NSCLC diagnosis and WHO Performance Status 0-2 between 2002 and 2011, those with stage-IA-IIB disease and severe comorbidity were less likely to be offered surgery (OR: 0.45; 95% CI: 0.36-0.57). In late-stage disease (IIIB-IV), severe comorbidity was also associated with lower chemotherapy treatment intensity (OR: 0.76; 95% CI: 0.65-0.89). In patients with early, but not late-stage disease, severe comorbidity in adjusted analyses was associated with an increased all-cause mortality, while lung cancer-specific mortality was largely unaffected by comorbidity burden.

CONCLUSIONS

Comorbidity contributes to the poor prognosis in NSCLC patients. Routinely published lung cancer survival statistics not considering coexisting disease conveys a too pessimistic picture of prognosis. Optimized management of comorbid conditions pre- and post-NSCLC-specific treatment is likely to improve outcomes.

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